bluuebunny/crossref_metadata_2025 huggingface dataset:
Population genetic structure of tropical bed bug (Hemiptera: Cimicidae) populations and their breeding pattern in Iraq
Authors: Baqir Hussein Ali , Ab Majid Abdul Hafiz
Published: February 2024

A study was conducted to investigate the population genetic structure and breeding pattern of 140 tropical bed bugs, Cimex hemipterus (F.) (Hemiptera: Cimicidae), collected from 14 infested sites in major cities in Iraq. The samples were genotyped using a set of 7 polymorphic microsatellite markers. High genetic variety was seen among populations, with an average of 2–9 alleles per locus. The number of alleles across 7 microsatellite loci was between 6 and 18. There was a notable disparity in the alleles per loci when comparing the overall population to those within it. The overall population exhibited an average observed heterozygosity of 0.175 and an average expected heterozygosity of 0.730. Among the population, the average observed heterozygosity was 0.173, while the average expected heterozygosity was 0.673. Analysis of molecular variance (AMOVA) revealed that 93% of the genetic variability was within the populations, and 7% was among them. The genetic differentiation coefficient (FST = 0.045), indicates a low degree of genetic differentiation and a high degree of inbreeding (FIS = 0.761), as indicated by notably significant positive inbreeding coefficients. Admixed individuals were revealed using STRUCTURE and neighbor-joining phylogenetic trees, demonstrating moderate gene flow between populations and a lack of genetic structure in the regional groups. Thus, both active dispersion and human-mediated dispersion possess the potential to influence the low population genetic structure of tropical bed bug C. hemipterus populations in Iraq, which can have implications toward tropical bed bug and management strategies.
Length–mass allometries of the larvae of aquatic dipterans: differences between taxa, morphological traits, and methods
Authors: Mocq Julien , Dekanová Vladimíra , Boukal David S
Published: February 2024

Body mass underpins many ecological processes at the level of individuals, populations, and communities. Often estimated in arthropods from linear morphological traits such as body length or head width, these relationships can vary even between closely related taxa. Length–mass relationships of mosquito (Diptera: Culicidae) larvae are poorly known despite the importance of this family to disease and aquatic ecology. To fill this gap, we measured ontogenetic changes in linear traits (body length, head width, and thorax width) and dry and wet masses and estimated length- and width–mass relationships in larvae of 3 culicid species inhabiting different niches: the tropical Aedes albopictus (Skuse, 1894), the temperate Culex pipiens (Linnaeus, 1758), and the snowmelt Ochlerotatus punctor (Kirby, 1837). We compared our results with published length–mass allometries of other aquatic dipteran larvae. We showed that thorax width and body length, but not head width, reliably predicted body mass for our 3 species. The length–mass allometry slopes in aquatic dipterans varied considerably between and within families but were independent of phylogeny, specimen handling, preservation techniques, and data fitting methods. Slope estimates became less precise with decreasing sample size and size range. To obtain reliable estimates of the allometric slopes, we have thus recommended using data on all larval stages for intraspecific allometries and a wide range of species for interspecific allometries. We also cautioned against the indiscriminate use of length–mass allometries obtained for other taxa or collected at lower taxonomic resolutions, e.g., when using length–mass relationships to estimate biomass production at a given site.
Quantification of eosinophilic area and its potential molecular feature in clear cell renal cell carcinoma
Authors: Wen Nengqiao , Li Xiaomin , Lu Jiangli , Pan Lu , Yang Ping , Zhang Yijun , Chen Keming , Cao Yun
Published: February 2024

Objective

Previous studies have acknowledged the presence of eosinophilic cytoplasm in clear cell renal cell carcinoma, yet the precise quantification method and potential molecular attributes in clear cell renal cell carcinoma remain elusive. This study endeavours to precisely quantify the eosinophilic attribute and probe into the molecular mechanisms governing its presence in clear cell renal cell carcinoma.

Methods

Data from cohorts of clear cell renal cell carcinoma patients who underwent nephrectomy, comprising The Cancer Genome Atlas cohort (n = 475) and Sun Yat-sen University Cancer Center cohort (n = 480), were aggregated to assess the eosinophilic attribute. Additionally, Omics data from Clinical Proteomic Tumor Analysis Consortium (CPTAC) (n = 58) were leveraged to explore the potential molecular features associated with eosinophilic clear cell renal cell carcinoma. Employing receiver operating characteristic curve analysis, the proportion of tumour cells with eosinophilic cytoplasm was determined, leading to the classification of each cohort into distinct groups: a clear group (<5%) and an eosinophilic group (≥5%).

Results

In both cohorts, the eosinophilic feature consistently correlated with higher International Society of Urological Pathology (ISUP) grade, elevated tumor stage, and the presence of necrosis. Furthermore, the Kaplan–Meier method demonstrated that patients in the eosinophilic group exhibited shorter overall survival or disease-free survival compared with those in the clear group, a pattern reaffirmed in various stratified survival analyses. Intriguingly, within The Cancer Genome Atlas cohort, the pathological characterization of cell cytoplasm (eosinophilic vs. clear) emerged as an independent risk factor for overall survival (hazard ratio = 2.507 [95% confidence interval: 1.328–4.733], P = 0.005) or disease-free survival (hazard ratio = 1.730 [95% confidence interval: 1.062–2.818], P = 0.028) via Cox regression analysis. Moreover, multi-Omics data unveiled frequent BAP1 mutations and down-regulation of Erythroblast Transformation-Specific-Related Gene associated with the eosinophilic feature in clear cell renal cell carcinoma. Additionally, patients with low expression of Erythroblast Transformation-Specific-Related Gene showed worse overall survival (P < 0.001).

Conclusions

The quantification of the eosinophilic feature serves as a robust predictor of clinical prognosis in clear cell renal cell carcinoma. Furthermore, the manifestation of this feature may be linked to BAP1 mutations and the down-regulation of Erythroblast Transformation-Specific-Related Gene in clear cell renal cell carcinoma. Significantly, the expression levels of Erythroblast Transformation-Specific-Related Gene manifest as an exemplary prognostic marker, providing exceptional predictive accuracy for the clinical prognosis in clear cell renal cell carcinoma.
Along with PaO2/FiO2 ratio and lymphopenia, low HLA-DR monocytes are the only additional parameter that independently predicts the clinical course of undifferentiated SARS-CoV-2 patients in emergency departments
Authors: Lafon Thomas , Chapuis Nicolas , Guerin Estelle , Daix Thomas , Otranto Marcela , Boumediene Ahmed , Jeannet Robin , Fontenay Michaela , Henri Hani Karam , Vignon Philippe , Monneret Guillaume , François Bruno , Jean-Philippe Jais , Feuillard Jean
Published: February 2024

Because one-third of patients deteriorate after their admission to the emergency department, assessing the prognosis of COVID-19 patients is of great importance. However, to date, only lymphopenia and the partial pressure of oxygen/fraction of inspired oxygen (PaO2/FiO2) ratio have been reported as partly predictive of COVID-19–related further deterioration, and their association has not been evaluated. We asked whether other key biomarkers of SARS-CoV-2 immunologic defects—increase in circulating immature granulocytes, loss of monocyte HLA-DR (mHLA-DR) expression, and monocyte differentiation blockade—could also predict further COVID-19 deterioration. A series of 284 consecutive COVID-19 patients, with the sole inclusion criterion of being an adult, were prospectively enrolled at emergency department admission (day 0) of 2 different hospitals: 1 for the exploratory cohort (180 patients) and 1 for the confirmatory cohort (104 patients). Deterioration was assessed over the next 7 days. Neither increased immature granulocyte levels nor monocyte differentiation blockade predicted patient worsening. Among more than 30 clinical, biological, and radiological parameters, the value of decreased P/F ratio and lymphopenia for prediction of further COVID-19 deterioration was strongly confirmed, and the loss of mHLA-DR was the only additional independent marker. Combined together in a simple OxyLymphoMono score, the 3 variables perfectly predicted patients who did not worsen and correctly predicted worsening in 59% of cases. By highlighting lymphocyte and monocyte defects as preceding COVID-19 deterioration, these results point on early immunosuppression in COVID-19 deterioration. Combining P/F ratio, lymphopenia, and loss of mHLA-DR together in a simple and robust score could offer a pragmatic method for COVID-19 patient stratification.
Factors Influencing Music Therapists’ Retention of Clinical Hours with Autistic Clients over Telehealth During the COVID-19 Pandemic
Authors: Richard Williams Nicole , Hurt-Thaut Corene , Thaut Michael H
Published: February 2024

The 2019 coronavirus disease pandemic influenced music therapists to migrate services to online platforms, though some lost clinical hours during the pandemic when telehealth was not a viable option. This survey study aimed to ascertain factors that helped music-based therapists to continue serving autistic clients over telehealth during the pandemic. We surveyed 193 accredited music therapists located mainly in Canada and the US. In addition to gathering data on general perceptions of telehealth music therapy and Neurologic Music Therapy (NMT), one-way ANOVAs were applied to determine differences in percent-change loss of clinical hours for music therapists: (1) working in different employment settings; (2) serving children, youth, adults, or a mixture of ages; and (3) practicing NMT or not. The general perception of telehealth music therapy was positive, and NMTs believed that the clear protocols and transformation design model were helpful to them in adapting services to telehealth. There were no significant differences in percent-change of clinical hours among music therapists in different employment settings or serving different client age groups. Music therapists who said they practiced within the NMT treatment model lost a significantly lower percentage of clinical hours with autistic clients than those who did not practice NMT. Possible reasons for this result and the need for further research are discussed.
Palliative prognostic scores for survival prediction of cancer patients: a systematic review and meta-analysis
Authors: Yoong Si Qi , Bhowmik Priyanka , Kapparath Sreerag , Porock Davina
Published: February 2024

Background

The palliative prognostic score is the most widely validated prognostic tool for cancer survival prediction, with modified versions available. A systematic evaluation of palliative prognostic score tools is lacking. This systematic review and meta-analysis aimed to evaluate the performance and prognostic utility of palliative prognostic score, delirium–palliative prognostic score, and palliative prognostic score without clinician prediction in predicting 30-day survival of cancer patients and to compare their performance.

Methods

Six databases were searched for peer-reviewed studies and grey literature published from inception to June 2, 2023. English studies must assess palliative prognostic score, delirium–palliative prognostic score, or palliative prognostic score without clinician-predicted survival for 30-day survival in adults aged 18 years and older with any stage or type of cancer. Outcomes were pooled using the random effects model or summarized narratively when meta-analysis was not possible.

Results

A total of 39 studies (n = 10 617 patients) were included. Palliative prognostic score is an accurate prognostic tool (pooled area under the curve [AUC] = 0.82, 95% confidence interval [CI] = 0.79 to 0.84) and outperforms palliative prognostic score without clinician-predicted survival (pooled AUC = 0.74, 95% CI = 0.71 to 0.78), suggesting that the original palliative prognostic score should be preferred. The meta-analysis found palliative prognostic score and delirium–palliative prognostic score performance to be comparable. Most studies reported survival probabilities corresponding to the palliative prognostic score risk groups, and higher risk groups were statistically significantly associated with shorter survival.

Conclusions

Palliative prognostic score is a validated prognostic tool for cancer patients that can enhance clinicians’ confidence and accuracy in predicting survival. Future studies should investigate if accuracy differs depending on clinician characteristics. Reporting of validation studies must be improved, as most studies were at high risk of bias, primarily because calibration was not assessed.
Medical financial hardship between young adult cancer survivors and matched individuals without cancer in the United States
Authors: Li Lihua , Zhang Donglan , Li Yan , Jain Mayuri , Lin Xingyu , Hu Rebecca , Liu Junxiu , Thapa Janani , Mu Lan , Chen Zhuo , Liu Bian , Pagán José A
Published: February 2024

Background

Young adult cancer survivors face medical financial hardships that may lead to delaying or forgoing medical care. This study describes the medical financial difficulties young adult cancer survivors in the United States experience in the post–Patient Protection and Affordable Care Act period.

Method

We identified 1009 cancer survivors aged 18 to 39 years from the National Health Interview Survey (2015-2022) and matched 963 (95%) cancer survivors to 2733 control individuals using nearest-neighbor matching. We used conditional logistic regression to examine the association between cancer history and medical financial hardship and to assess whether this association varied by age, sex, race and ethnicity, and region of residence.

Results

Compared with those who did not have a history of cancer, young adult cancer survivors were more likely to report material financial hardship (22.8% vs 15.2%; odds ratio = 1.65, 95% confidence interval = 1.50 to 1.81) and behavior-related financial hardship (34.3% vs 24.4%; odds ratio = 1.62, 95% confidence interval = 1.49 to 1.76) but not psychological financial hardship (52.6% vs 50.9%; odds ratio = 1.07, 95% confidence interval = 0.99 to 1.16). Young adult cancer survivors who were Hispanic or lived in the Midwest and South were more likely to report psychological financial hardship than their counterparts.

Conclusions

We found that young adult cancer survivors were more likely to experience material and behavior-related financial hardship than young adults without a history of cancer. We also identified specific subgroups of young adult cancer survivors that may benefit from targeted policies and interventions to alleviate medical financial hardship.
Hierarchical clustering analysis of musculoskeletal stress factors and their risk level in cardboard manufacturing: research from PLIBEL
Authors: Contreras-Valenzuela Martha Roselia , Martínez-Ibanez Carlos Alejandro
Published: February 2024

Objective: A hierarchical cluster analysis for the cardboard manufacturing industry was developed with the aim of identifying similarities between workstations in terms of musculoskeletal stress factors (MSFs) and their impact on workers’ bodies.

Methods: The hierarchical clustering analysis was conducted using data from 44 workstations, which included 6 body part divisions and 51 stress factors as variables with 36 answer options. Firstly, the content of the dataset was defined. Secondly, the data were agglomerated and classified into 3 clusters using Ward’s method based on the presence or absence of stress factors. Finally, the multivariable matrix was reduced to 2 factors: the x-axis representing the risk level of the workstation, and the y-axis representing the impact on the workers’ health.

Results: The study found that workers’ knees were the most affected body parts, with 47 cases. The resulting work-related musculoskeletal disorders included tendinitis, arthralgia, chondromalacia, and gonarthrosis. The MSF with the most significant impact on the body’s health was fatiguing work that involves repeated jumps, prolonged squatting, or kneeling, present in cluster 1 and cluster 3. Moreover, two of the most common MSFs associated with repeated work positions were identified: a mild forward flexion of the back (63 cases) in combination with one leg being used more often to support the body (56 cases).

Conclusions: It was possible to identify the main work-related musculoskeletal disorders and the associated stress factors for the cardboard manufacturing industry by using hierarchical cluster classification and analysis, enabling the classification of risk levels and the impact on body health for each workstation.
The association between work interval regularity and sleep regularity: a 2-week observational study in daytime employees
Authors: Ikeda Hiroki , Kubo Tomohide
Published: February 2024

Objectives: Several health issues are associated with irregular sleep patterns. However, it is unclear what causes workers to sleep irregularly. The work interval (WI) between the end of one day’s working hours and the start of the next day’s working hours contains sleep opportunities, and an irregular WI may result in irregular sleep. This study investigated this association among Japanese daytime workers.

Methods: This study recruited 141 daytime workers without shiftwork for a 14-day observational study. Participants reported the WI duration, WI timing, time in bed (TIB: difference between bedtime and wake-up time), and bedtime timing every day before bedtime. The SD over 14 days was used to calculate the regularity scores. Logistic regression analysis was performed. The dependent variables were ≥60 minutes of TIB SD and bedtime timing SD, whereas the independent variables were WI duration and timing SD.

Results: The odds ratios (ORs) (95% CIs) for ≥60 minutes of TIB SD across categories of WI duration SD were 1.000 (reference) for <30 minutes, 1.344 (0.337-5.360) for 30-60 minutes, and 4.743 (1.441-15.607) for ≥60 minutes. The ORs (95% CIs) for ≥60 min of bedtime timing SD across categories of WI timing SD were 1.000 for <30 minutes, 4.154 (1.574-10.965) for 30-60 minutes, and 7.714 (2.124-28.015) for ≥60 minutes.

Conclusions: Regularity of WI was associated with regularity of sleep. To ensure worker health, workers should have regular WI, and if they are exposed to irregular WI, they should make every effort to maintain regular sleep.
Langer and the claim for the social value of art
Authors: Barchana-Lorand Dorit
Published: February 2024

Susanne Langer sees the ‘the public importance of art’ as one of ‘the ultimate questions in a philosophy of art’. Indeed, Langer is often referred to as an authority on the justification of art education and is cited as providing good reasons for incorporating the arts in the curriculum. It is therefore surprising to note, as Elliot Eisner does, that Langer’s theory has had little influence on actual art education. For while many theoreticians in the social sciences and education have found Langer’s contribution to the understanding of the arts highly significant, Eisner laments that ‘alas, the lesson Susanne Langer was trying to teach … in her remarkable book, never took hold in … American public schools’. It seems that policy-makers outside of art education circles remain sceptical regarding the need for art education. The substantiation of art education requires firm ground against scepticism. It is therefore important to understand the ways in which Langer’s project fails to fulfil its promise. In examining Langer’s aesthetic theory, I will show that despite its philosophical acuity, Langer’s argument fails to persuade the art education sceptic who believes that art occupies a minor role in education and should therefore remain marginal in the school curriculum.
Bayesian smoothing for time-varying extremal dependence
Authors: Lee Junho , de Carvalho Miguel , Rua António , Avila Julio
Published: February 2024

We propose a Bayesian time-varying model that learns about the dynamics governing joint extreme values over time. Our model relies on dual measures of time-varying extremal dependence, that are modelled via a suitable class of generalized linear models conditional on a large threshold. The simulation study indicates that the proposed methods perform well in a variety of scenarios. The application of the proposed methods to some of the world’s most important stock markets reveals complex patterns of extremal dependence over the last 30 years, including passages from asymptotic dependence to asymptotic independence.
Unusual visual impairment after enhancement refractive surgery
Authors: Li Xia , Gu Yong
Published: February 2024

We reported a case of rapidly developed corneal epithelial in-growth (EI) deteriorating visual acuity (VA) within the initial postoperative day. A 37-year-old male presented with decreased VA for 2 years. He underwent LASIK surgery 13 years ago. After enhancement surgery, postoperative VA was much worse than preoperative best corrected visual acuity (BCVA) 20/20 and decreased rapidly. VA of OD was 20/40 on Day 1, and 20/70 on Day 5, OS 20/20 on Day 1, 20/25 on Day 10, and 20/50 on Day 13 postoperatively. Corneal topography and optical coherence tomography (OCT) showed distinctive features. The patient was diagnosed with corneal EI postoperatively. After scraping ectopic corneal epithelial cells, the cornea became transparent and VA improved. Despite its rarity, early postoperative EI can occur within 1 day after enhancement surgery and can progress rapidly. OCT and corneal topography provide distinctive manifestations aiding diagnosis.
HOMEOBOX2, the paralog of SIX-ROWED SPIKE1/HOMEOBOX1, is dispensable for barley spikelet development
Authors: Thirulogachandar Venkatasubbu , Govind Geetha , Hensel Götz , Kale Sandip M , Kuhlmann Markus , Eschen-Lippold Lennart , Rutten Twan , Koppolu Ravi , Rajaraman Jeyaraman , Palakolanu Sudhakar Reddy , Seiler Christiane , Sakuma Shun , Jayakodi Murukarthick , Lee Justin , Kumlehn Jochen , Komatsuda Takao , Schnurbusch Thorsten , Sreenivasulu Nese
Published: February 2024

The HD-ZIP class I transcription factor Homeobox 1 (HvHOX1), also known as Vulgare Row-type Spike 1 (VRS1) or Six-rowed Spike 1, regulates lateral spikelet fertility in barley (Hordeum vulgare L.). It was shown that HvHOX1 has a high expression only in lateral spikelets, while its paralog HvHOX2 was found to be expressed in different plant organs. Yet, the mechanistic functions of HvHOX1 and HvHOX2 during spikelet development are still fragmentary. Here, we show that compared with HvHOX1, HvHOX2 is more highly conserved across different barley genotypes and Hordeum species, hinting at a possibly vital but still unclarified biological role. Using bimolecular fluorescence complementation, DNA-binding, and transactivation assays, we validate that HvHOX1 and HvHOX2 are bona fide transcriptional activators that may potentially heterodimerize. Accordingly, both genes exhibit similar spatiotemporal expression patterns during spike development and growth, albeit their mRNA levels differ quantitatively. We show that HvHOX1 delays the lateral spikelet meristem differentiation and affects fertility by aborting the reproductive organs. Interestingly, the ancestral relationship of the two genes inferred from their co-expressed gene networks suggested that HvHOX1 and HvHOX2 might play a similar role during barley spikelet development. However, CRISPR-derived mutants of HvHOX1 and HvHOX2 demonstrated the suppressive role of HvHOX1 on lateral spikelets, while the loss of HvHOX2 does not influence spikelet development. Collectively, our study shows that through the suppression of reproductive organs, lateral spikelet fertility is regulated by HvHOX1, whereas HvHOX2 is dispensable for spikelet development in barley.
Gene regulatory networks underlying sulfate deficiency responses in plants
Authors: Fernández José David , Miño Ignacio , Canales Javier , Vidal Elena A
Published: February 2024

Sulfur (S) is an essential macronutrient for plants and its availability in soils is an important determinant for growth and development. Current regulatory policies aimed at reducing industrial S emissions together with changes in agronomical practices have led to a decline in S contents in soils worldwide. Deficiency of sulfate—the primary form of S accessible to plants in soil—has adverse effects on both crop yield and nutritional quality. Hence, recent research has increasingly focused on unraveling the molecular mechanisms through which plants detect and adapt to a limiting supply of sulfate. A significant part of these studies involves the use of omics technologies and has generated comprehensive catalogs of sulfate deficiency-responsive genes and processes, principally in Arabidopsis together with a few studies centering on crop species such as wheat, rice, or members of the Brassica genus. Although we know that sulfate deficiency elicits an important reprogramming of the transcriptome, the transcriptional regulators orchestrating this response are not yet well understood. In this review, we summarize our current knowledge of gene expression responses to sulfate deficiency and recent efforts towards the identification of the transcription factors that are involved in controlling these responses. We further compare the transcriptional response and putative regulators between Arabidopsis and two important crop species, rice and tomato, to gain insights into common mechanisms of the response to sulfate deficiency.
Prime editing in plants: prospects and challenges
Authors: Vats Sanskriti , Kumar Jitesh , Sonah Humira , Zhang Feng , Deshmukh Rupesh
Published: February 2024

Prime editors are reverse transcriptase (RT)-based genome-editing tools that utilize double-strand break (DSB)-free mechanisms to decrease off-target editing in genomes and enhance the efficiency of targeted insertions. The multiple prime editors that have been developed within a short span of time are a testament to the potential of this technique for targeted insertions. This is mainly because of the possibility of generation of all types of mutations including deletions, insertions, transitions, and transversions. Prime editing reverses several bottlenecks of gene editing technologies that limit the biotechnological applicability to produce designer crops. This review evaluates the status and evolution of the prime editing technique in terms of the types of editors available up to prime editor 5 and twin prime editors, and considers the developments in plants in a systematic manner. The various factors affecting prime editing efficiency in plants are discussed in detail, including the effects of temperature, the prime editing guide (peg)RNA, and RT template amongst others. We discuss the current obstructions, key challenges, and available resolutions associated with the technique, and consider future directions and further improvements that are feasible to elevate the efficiency in plants.
BOSS quasar outflows traced by C iv
Authors: Gillette Jarred , Hamann Fred
Published: February 2024

We investigate possible factors that drive fast quasar outflows using a sample of 39 249 quasars at median redshift 〈z〉 ≈ 2.17. Unique to this study, the quasar redshifts are re-measured based on the Mg ii emission line, and explore unprecedented outflow velocities (>6000 km s−1), while maintaining statistical significance. We measure reliable C iv blueshifts for 1178 quasars with velocities >2500 km s−1. From those, 255(13) quasars have blueshifts above 4000(6000) km s−1, with the highest C iv velocity ≈7000 km s−1. Several correlations are observed, where higher C iv blueshifts in general are in quasars with broader, weaker C iv emission profiles, weak He ii emission, larger Eddington ratios, and bluer ultraviolet (UV) continuum slope across the rest-frame UV to near-infrared. Analysis reveals two primary factors contributing to faster outflows: higher Eddington ratios, and softer far-UV continuum (hν >24.6 eV). We find supporting evidence that radiative line driving may generate extreme outflow velocities, influenced by multiple factors as suggested by the aforementioned correlations. This evidence highlights the importance of considering a multidimensional parameter space in future studies when analyzing large C iv blueshifts to determine the fundamental causes of outflows.
Spatially resolved microlensing time-scale distributions across the Galactic bulge with the VVV survey
Authors: Kaczmarek Zofia , McGill Peter , Evans N Wyn , Smith Leigh C , Golovich Nathan , Kerins Eamonn , Specht David , Dawson William A
Published: February 2024

We analyse 1602 microlensing events found in the VISTA Variables in the Via Lactea (VVV) near-infrared (NIR) survey data. We obtain spatially resolved, efficiency-corrected time-scale distributions across the Galactic bulge (|ℓ| < 10°, |b| < 5°), using a Bayesian hierarchical model. Spatially resolved peaks and means of the time-scale distributions, along with their marginal distributions in strips of longitude and latitude, are in agreement at a 1σ level with predictions based on the Besançon model of the Galaxy. We find that the event time-scales in the central bulge fields (|ℓ| < 5°) are on average shorter than the non-central (|ℓ| > 5°) fields, with the average peak of the lognormal time-scale distribution at 23.6 ± 1.9 d for the central fields and 29.0 ± 3.0 d for the non-central fields. Our ability to probe the structure of the bulge with this sample of NIR microlensing events is limited by the VVV survey’s sparse cadence and relatively small number of detected microlensing events compared to dedicated optical surveys. Looking forward to future surveys, we investigate the capability of the Roman telescope to detect spatially resolved asymmetries in the time-scale distributions. We propose two pairs of Roman fields, centred on (ℓ = ±9, 5°, b = −0.125°) and (ℓ = −5°, b = ±1.375°) as good targets to measure the asymmetry in longitude and latitude, respectively.
JWST spectroscopy of z ∼ 5–8 UV-selected galaxies: new constraints on the evolution of the Ly α escape fraction in the reionization era
Authors: Chen Zuyi , Stark Daniel P , Mason Charlotte , Topping Michael W , Whitler Lily , Tang Mengtao , Endsley Ryan , Charlot Stéphane
Published: February 2024

We describe JWST/NIRSpec prism measurements of Ly α emission in z ≳ 5 galaxies. We identify Ly α detections in 10 out of 69 galaxies with robust rest-optical emission-line redshift measurements at 5 ≤ z < 7 in the Cosmic Evolution Early Release Science (CEERS) and DDT-2750 observations of the Extended Groth Strip field. Galaxies at z ≃ 6 with faint continuum (F150W=27–29 mag) are found with extremely large rest-frame Ly α equivalent widths (EWs; ranging up to 286 Å). Likely Ly α detections are also seen in two new z > 7 galaxies (z = 7.49 and 7.17) from the second epoch of CEERS observations, both showing large Ly α EWs that likely indicate significant transmission through the intergalactic medium (IGM). We measure high Ly α escape fractions in the 12 Ly α emitters in our sample (median 0.28), two of which show $f_{\rm esc}^{ {\rm Ly}\alpha }$ near unity (>0.80). We find that $50_{-11}^{+11}$ per cent of z ≃ 6 galaxies with [O iii] + H β EW>1000 Å have $f_{\rm esc}^{ {\rm Ly}\alpha }$ >0.2, consistent with the fractions found in lower redshift samples with matched [O iii] + H β EWs. While uncertainties are still significant, we find that only $10_{-5}^{+9}$ per cent of z > 7 galaxies with similarly strong rest optical emission lines show such large $f_{\rm esc}^{ {\rm Ly}\alpha }$, as may be expected if IGM attenuation of Ly α increases towards higher redshifts. We identify photometric galaxy overdensities near the z ≳ 7 Ly α emitters, potentially providing the ionizing flux necessary to create large ionized sightlines that facilitate Ly α transmission. Finally, we investigate the absence of Ly α emission in a comparable (and spectroscopically confirmed) galaxy overdensity at z = 7.88 in the Abell 2744 field, discussing new prism spectra of the field obtained with the UNCOVER program.
Neutron star mergers as the dominant contributor to the production of heavy r-process elements
Authors: Chen Meng-Hua , Li Li-Xin , Chen Qiu-Hong , Hu Rui-Chong , Liang En-Wei
Published: February 2024

The discovery of the radioactively powered kilonova AT2017gfo, associated with the short-duration gamma-ray burst GRB 170817A and the gravitational wave source GW170817, has provided the first direct evidence supporting binary neutron star mergers as crucial astrophysical sites for the synthesis of heavy elements beyond iron through r-process nucleosysthesis in the universe. However, recent identification of kilonovae following long-duration gamma-ray bursts, such as GRB 211211A and GRB 230307A, has sparked discussions about the potential of neutron star–white dwarf mergers to also produce neutron-rich ejecta and contribute to the production of heavy r-process elements. In this work, we estimate the contribution of binary neutron star mergers to the total mass of r-process elements in the Milky Way and investigate the possibility of neutron star–white dwarf mergers as alternative astrophysical sites for r-process nucleosynthesis through an analysis of the total mass of the r-process elements in the Milky Way. Our results reveal that binary neutron star mergers can sufficiently account for the Galactic heavy r-process elements, suggesting that these events are the dominant contributor to the production of heavy r-process elements in the Milky Way. Considering the total mass of r-process elements in the Milky Way and the higher occurrence rate of neutron star–white dwarf mergers, it is unlikely that such mergers can produce a significant amount of neutron-rich ejecta, with the generated mass of r-process elements being lower than $0.005\, {\rm M}_{\odot }$.
Understanding the phenomenological and intrinsic blazar sequence using a simple scaling model
Authors: Wan Zhu-Jian , Xue Rui , Wang Ze-Rui , Xiao Hu-Bing , Fan Jun-Hui
Published: February 2024

The blazar sequence, including negative correlations between radiative luminosity Lrad and synchrotron peak frequency ν, and between Compton dominance Y and ν, is widely adopted as a phenomenological description of spectral energy distributions (SEDs) of blazars, although its underlying cause is hotly debated. In particular, these correlations turn positive after correcting Doppler boosting effect. In this work, we revisit the phenomenological and intrinsic blazar sequence with three samples, which are historical sample (SEDs are built with historical data), quasi-simultaneous sample (SEDs are built with quasi-simultaneous data) and Doppler factor corrected sample (a sample with available Doppler factors), selected from literature. We find that phenomenological blazar sequence holds in historical sample, but does not exist in quasi-simultaneous sample, and intrinsic correlation between Lrad and ν becomes positive in Doppler factor corrected sample. We also analyse if the blazar sequence still exists in subclasses of blazars, i.e. flat-spectrum radio quasars and BL Lacertae objects, with different values of Y. To interpret these correlations, we apply a simple scaling model, in which physical parameters of the dissipation region are connected to the location of the dissipation region. We find that the model generated results are highly sensitive to the chosen ranges and distributions of physical parameters. Therefore, we suggest that even though the simple scaling model can reproduce the blazar sequence under specific conditions that have been fine-tuned, such results may not have universal applicability. Further consideration of a more realistic emission model is expected.
Shining light on the hosts of the nano-Hertz gravitational wave sources: a theoretical perspective
Authors: Saeedzadeh Vida , Mukherjee Suvodip , Babul Arif , Tremmel Michael , Quinn Thomas R
Published: February 2024

The formation of supermassive black holes (SMBHs) in the Universe and its role in the properties of the galaxies is one of the open questions in astrophysics and cosmology. Though, traditionally, electromagnetic waves have been instrumental in direct measurements of SMBHs, significantly influencing our comprehension of galaxy formation, gravitational waves (GW) bring an independent avenue to detect numerous binary SMBHs in the observable Universe in the nano-Hertz range using the pulsar timing array observation. This brings a new way to understand the connection between the formation of binary SMBHs and galaxy formation if we can connect theoretical models with multimessenger observations namely GW data and galaxy surveys. Along these lines, we present here the first paper on this series based on romulus25 cosmological simulation on the properties of the host galaxies of SMBHs and propose on how this can be used to connect with observations of nano-Hertz GW signal and galaxy surveys. We show that the most dominant contribution to the background will arise from sources with high chirp masses which are likely to reside in low-redshift early-type galaxies with high stellar mass, largely old stellar population, and low star formation rate, and that reside at centres of galaxy groups and manifest evidence of recent mergers. The masses of the sources show a correlation with the halo mass and stellar mass of the host galaxies. This theoretical study will help in understanding the host properties of the GW sources and can help in establishing a connection with observations.
A Critical Appraisal of DNA Transfer from Plants to Parasitic Cyst Nematodes
Authors: Ko Itsuhiro , Kranse Olaf Prosper , Senatori Beatrice , Eves-van den Akker Sebastian
Published: February 2024

Plant-parasitic nematodes are one of the most economically important pests of crops. It is widely accepted that horizontal gene transfer—the natural acquisition of foreign genes in parasitic nematodes—contributes to parasitism. However, an apparent paradox has emerged from horizontal gene transfer analyses: On the one hand, distantly related organisms with very dissimilar genetic structures (i.e. bacteria), and only transient interactions with nematodes as far as we know, dominate the list of putative donors, while on the other hand, considerably more closely related organisms (i.e. the host plant), with similar genetic structure (i.e. introns) and documented long-term associations with nematodes, are rare among the list of putative donors. Given that these nematodes ingest cytoplasm from a living plant cell for several weeks, there seems to be a conspicuous absence of plant-derived cases. Here, we used comparative genomic approaches to evaluate possible plant-derived horizontal gene transfer events in plant parasitic nematodes. Our evidence supports a cautionary message for plant-derived horizontal gene transfer cases in the sugar beet cyst nematode, Heterodera schachtii. We propose a 4-step model for horizontal gene transfer from plant to parasite in order to evaluate why the absence of plant-derived horizontal gene transfer cases is observed. We find that the plant genome is mobilized by the nematode during infection, but that uptake of the said “mobilome” is the first major barrier to horizontal gene transfer from host to nematode. These results provide new insight into our understanding of the prevalence/role of nucleic acid exchange in the arms race between plants and plant parasites.
Secondary Contact, Introgressive Hybridization, and Genome Stabilization in Sticklebacks
Authors: Feng Xueyun , Merilä Juha , Löytynoja Ari
Published: February 2024

Advances in genomic studies have revealed that hybridization in nature is pervasive and raised questions about the dynamics of different genetic and evolutionary factors following the initial hybridization event. While recent research has proposed that the genomic outcomes of hybridization might be predictable to some extent, many uncertainties remain. With comprehensive whole-genome sequence data, we investigated the genetic introgression between 2 divergent lineages of 9-spined sticklebacks (Pungitius pungitius) in the Baltic Sea. We found that the intensity and direction of selection on the introgressed variation has varied across different genomic elements: while functionally important regions displayed reduced rates of introgression, promoter regions showed enrichment. Despite the general trend of negative selection, we identified specific genomic regions that were enriched for introgressed variants, and within these regions, we detected footprints of selection, indicating adaptive introgression. Geographically, we found the selection against the functional changes to be strongest in the vicinity of the secondary contact zone and weaken as a function of distance from the initial contact. Altogether, the results suggest that the stabilization of introgressed variation in the genomes is a complex, multistage process involving both negative and positive selection. In spite of the predominance of negative selection against introgressed variants, we also found evidence for adaptive introgression variants likely associated with adaptation to Baltic Sea environmental conditions.
The Effects of De Novo Mutation on Gene Expression and the Consequences for Fitness in Chlamydomonas reinhardtii
Authors: Balogun Eniolaye J , Ness Rob W
Published: February 2024

Mutation is the ultimate source of genetic variation, the bedrock of evolution. Yet, predicting the consequences of new mutations remains a challenge in biology. Gene expression provides a potential link between a genotype and its phenotype. But the variation in gene expression created by de novo mutation and the fitness consequences of mutational changes to expression remain relatively unexplored. Here, we investigate the effects of >2,600 de novo mutations on gene expression across the transcriptome of 28 mutation accumulation lines derived from 2 independent wild-type genotypes of the green algae Chlamydomonas reinhardtii. We observed that the amount of genetic variance in gene expression created by mutation (Vm) was similar to the variance that mutation generates in typical polygenic phenotypic traits and approximately 15-fold the variance seen in the limited species where Vm in gene expression has been estimated. Despite the clear effect of mutation on expression, we did not observe a simple additive effect of mutation on expression change, with no linear correlation between the total expression change and mutation count of individual MA lines. We therefore inferred the distribution of expression effects of new mutations to connect the number of mutations to the number of differentially expressed genes (DEGs). Our inferred DEE is highly L-shaped with 95% of mutations causing 0-1 DEG while the remaining 5% are spread over a long tail of large effect mutations that cause multiple genes to change expression. The distribution is consistent with many cis-acting mutation targets that affect the expression of only 1 gene and a large target of trans-acting targets that have the potential to affect tens or hundreds of genes. Further evidence for cis-acting mutations can be seen in the overabundance of mutations in or near differentially expressed genes. Supporting evidence for trans-acting mutations comes from a 15:1 ratio of DEGs to mutations and the clusters of DEGs in the co-expression network, indicative of shared regulatory architecture. Lastly, we show that there is a negative correlation with the extent of expression divergence from the ancestor and fitness, providing direct evidence of the deleterious effects of perturbing gene expression.
Human pangenome analysis of sequences missing from the reference genome reveals their widespread evolutionary, phenotypic, and functional roles
Authors: Wu Zhikun , Li Tong , Jiang Zehang , Zheng Jingjing , Gu Yizhou , Liu Yizhi , Liu Yun , Xie Zhi
Published: February 2024

Nonreference sequences (NRSs) are DNA sequences present in global populations but absent in the current human reference genome. However, the extent and functional significance of NRSs in the human genomes and populations remains unclear. Here, we de novo assembled 539 genomes from five genetically divergent human populations using long-read sequencing technology, resulting in the identification of 5.1 million NRSs. These were merged into 45284 unique NRSs, with 29.7% being novel discoveries. Among these NRSs, 38.7% were common across the five populations, and 35.6% were population specific. The use of a graph-based pangenome approach allowed for the detection of 565 transcript expression quantitative trait loci on NRSs, with 426 of these being novel findings. Moreover, 26 NRS candidates displayed evidence of adaptive selection within human populations. Genes situated in close proximity to or intersecting with these candidates may be associated with metabolism and type 2 diabetes. Genome-wide association studies revealed 14 NRSs to be significantly associated with eight phenotypes. Additionally, 154 NRSs were found to be in strong linkage disequilibrium with 258 phenotype-associated SNPs in the GWAS catalogue. Our work expands the understanding of human NRSs and provides novel insights into their functions, facilitating evolutionary and biomedical researches.
Zebrafish Mbd5 binds to RNA m5C and regulates histone deubiquitylation and gene expression in development metabolism and behavior
Authors: Guo Jianhua , Zou Zhongyu , Dou Xiaoyang , Zhao Xiang , Wang Yimin , Wei Liqiang , Pi Yan , Wang Yi , He Chuan , Guo Su
Published: February 2024

Complex biological processes are regulated by both genetic and epigenetic programs. One class of epigenetic modifications is methylation. Evolutionarily conserved methyl-CpG-binding domain (MBD)-containing proteins are known as readers of DNA methylation. MBD5 is linked to multiple human diseases but its mechanism of action remains unclear. Here we report that the zebrafish Mbd5 does not bind to methylated DNA; but rather, it directly binds to 5-methylcytosine (m5C)-modified mRNAs and regulates embryonic development, erythrocyte differentiation, iron metabolism, and behavior. We further show that Mbd5 facilitates removal of the monoubiquitin mark at histone H2A-K119 through an interaction with the Polycomb repressive deubiquitinase (PR-DUB) complex in vivo. The direct target genes of Mbd5 are enriched with both RNA m5C and H2A-K119 ubiquitylation signals. Together, we propose that zebrafish MBD5 is an RNA m5C reader that potentially links RNA methylation to histone modification and in turn transcription regulation in vivo.