bluuebunny/crossref_metadata_2025 huggingface dataset:
A targeted search for strongly lensed supernovae with the Las Cumbres Observatory
Authors: Craig Peter , O’Connor Kyle , Chakrabarti Sukanya , Rodney Steven A , Pierel Justin R , McCully Curtis , Perez-Fournon Ismael
Published: September 2024

Gravitationally lensed supernovae (glSNe) are of interest for time delay cosmology and SN physics. However, glSNe detections are rare, owing to the intrinsic rarity of SN explosions, the necessity of alignment with a foreground lens, and the relatively short window of detectability. We present the Las Cumbres Observatory Lensed Supernova Search, LCOLSS, a targeted survey designed for detecting glSNe in known strong lensing systems. Using cadenced $r^\prime$-band imaging, LCOLSS targeted 114 galaxy–galaxy lensing systems with high expected SN rates, based on estimated star formation rates. No plausible glSN was detected by LCOLSS during our two year observing program. We carry out an analysis here to measure a detection efficiency for these observations. We then perform Monte Carlo simulations using the predicted supernova rates to determine the expected number of glSN detections. The results of the simulation suggest an expected number of detections and 68 per cent Poisson confidence intervals, $N_{\mathrm{ SN}} = 0.20, [0,2.1]$, $N_{\mathrm{ Ia}} = 0.08, [0,2.0]$, $N_{\mathrm{ CC}} = 0.12, [0,2.0]$, for all SNe, Type Ia SNe, and core-collapse (CC) SNe, respectively. These results are broadly consistent with the absence of a detection in our survey. Analysis of the survey strategy can provide insights for future efforts to develop targeted glSN discovery programs, especially considering the large anticipated yields of upcoming surveys.
Exploring the high-density reflection model for the soft excess in RBS 1124
Authors: Madathil-Pottayil A , Walton D J , García Javier , Miller Jon , Gallo Luigi C , Ricci C , Reynolds Mark T , Stern D , Dauser T , Jiang Jiachen , Alston William , Fabian A C , Hardcastle M J , Kosec Peter , Nardini Emanuele , Reynolds Christopher S
Published: September 2024

‘Bare’ active galactic nuclei (AGN) are a subclass of Type 1 AGN that show little or no intrinsic absorption. They offer an unobscured view of the central regions of the AGN and therefore serve as ideal targets to study the relativistic reflection features originating from the innermost regions of the accretion disc. We present a detailed broad-band spectral analysis (0.3–70 keV) of one of the most luminous bare AGN in the local Universe, RBS 1124 ($z= 0.208$) using a new, co-ordinated high signal-to-noise observation obtained by XMM–Newton and NuSTAR. The source exhibits a power-law continuum with $\Gamma \sim$ 1.8 along with a soft excess below 2 keV, a weak neutral iron line and curvature at high energies (${\sim} 30$ keV). The broad-band spectrum, including the soft excess and the high-energy continuum, is well fit by the relativistic reflection model when the accretion disc is allowed to have densities of log$(n_{\rm e}$/cm$^{-3}$) $\gtrsim 19.2$. Our analysis therefore suggests that when high-density effects are considered, relativistic reflection remains a viable explanation for the soft excess.
The MAGPI survey: orbital distributions, intrinsic shapes, and mass profiles for MAGPI-like eagle galaxies using Schwarzschild dynamical models
Authors: Santucci Giulia , Lagos Claudia Del P , Harborne Katherine E , Derkenne Caro , Poci Adriano , Thater Sabine , McDermid Richard M , Mendel J Trevor , Wisnioski Emily , Croom Scott M , Ferré-Mateu Anna , Muller Eric G M , van de Sande Jesse , Sharma Gauri , Sweet Sarah M , Tsukui Takafumi , Valenzuela Lucas M , van de Ven Glenn , Zafar Tayyaba
Published: September 2024

Schwarzschild dynamical models are now regularly employed in large surveys of galaxies in the local and distant Universe to derive information on galaxies’ intrinsic properties such as their orbital structure and their (dark matter and stellar) mass distribution. Comparing the internal orbital structures and mass distributions of galaxies in the distant Universe with simulations is key to understanding what physical processes are responsible for shaping galaxy properties. However, it is first crucial to understand whether observationally derived properties are directly comparable with intrinsic ones in simulations. To assess this, we build Schwarzschild dynamical models for MUSE-like IFS (integral field spectroscopy) cubes (constructed to be like those obtained by the Middle Ages Galaxy Properties with Integral Field Spectroscopy, MAGPI survey) of 75  galaxies at $z \sim$ 0.3 from the eagle simulations. We compare the true particle-derived properties with the galaxies’ model-derived properties. In general, we find that the models can recover the true galaxy properties qualitatively well, with the exception of the enclosed dark matter, where we find a median offset of 48 per cent, which is due to the assumed Navarro–Frenk–White profile not being able to reproduce the dark matter distribution in the inner region of the galaxies. We then compare our model-derived properties with Schwarzschild models-derived properties of observed MAGPI galaxies and find good agreement between MAGPI and eagle: the majority of our galaxies (57 per cent) have non-oblate shapes within 1 effective radius. More triaxial galaxies show higher fractions of hot orbits in their inner regions and tend to be more radially anisotropic.
The HYENAS project: a prediction for the X-ray undetected galaxy groups
Authors: Cui Weiguang , Jennings Fred , Dave Romeel , Babul Arif , Gozaliasl Ghassem
Published: September 2024

Galaxy groups contain the majority of bound mass with a significant portion of baryons due to the combination of halo mass and abundance (Cui 2024). Hence they serve as a crucial missing piece in the puzzle of galaxy formation and the evolution of large-scale structures in the Universe. In observations, mass-complete group catalogues are normally derived from galaxy redshift surveys detected through various three-dimensional group-finding algorithms. Confirming the reality of such groups, particularly in the X-rays, is critical for ensuring robust studies of galaxy evolution in these environments. Recent works have reported numerous optical groups that are X-ray undetected (see, e.g. Popesso et al. 2024), sparking debates regarding the reasons for the unexpectedly low hot gas fraction in galaxy groups. To address this issue, we utilize zoomed-in simulations of galaxy groups from the novel Hyenas project to explore the range of hot gas fractions within galaxy groups and investigate the intrinsic factors behind the observed variability in X-ray emission. We find that the halo formation time can play a critical role–we see that groups in haloes that formed earlier exhibit up to an order of magnitude brighter X-ray luminosities compared to those formed later. This suggests that undetected X-ray groups are preferentially late-formed haloes and highlights the connection between gas fraction and halo formation time in galaxy groups. Accounting for these biases in galaxy group identification is essential for advancing our understanding of galaxy formation and achieving precision in cosmological studies.
Adjusting methylation levels with nucleus proportions highlights functional significance of differentially methylated cytosines associated with pre-eclampsia
Authors: Zheng Xiaoguo , Wen Yanqin , Zhao Xinzhi
Published: September 2024

Studies on DNA methylation alterations associated with pre-eclampsia (PE) have improved our understanding of the mechanisms underlying this disorder. However, differentially methylated cytosines (DMCs) have not been adjusted for cell-type heterogeneity, hampering the identification of alterations that drive disease risk. Using a reference-based, cell-type deconvolution approach, we estimated the nuclear proportions of 335 placental samples based on DNA methylation data. We found that the nuclei of total trophoblast lineages accounted for more than 80% of the placental samples, with a significant increase in PE placentas. The nuclear proportions of stromal and Hofbauer cells decreased in PE placentas. Our nuclear proportion estimation reflected previous histological knowledge on the changes in cell type proportions in PE placentas. We corrected 2125 DMCs associated with early-onset PE for cell-type heterogeneity by adjusting for the nuclear proportions and observed a notable reduction in the association signals, with 145 probes not reaching epigenome-wide significance. After correction, the top 200 significant DMCs were strongly enriched in active enhancers in trophoblast lineages, whereas 145 non-significant probes were enriched in regions with a quiescent state of chromatin. Our results suggest that future epigenetic studies of PE should focus on functional regulatory sequences.
The microbiome and acute organ injury: focus on kidneys
Authors: Patel Shishir Kumar , Gooya Mahta , Guo Qisen , Noel Sanjeev , Rabb Hamid
Published: September 2024

The microbiome of critically ill patients is significantly altered by both effects of the illnesses and clinical interventions provided during intensive care. Studies have shown that manipulating the microbiome can prevent or modulate complications of critical illness in experimental models and preliminary clinical trials. This review aims to discuss general concepts about the microbiome, including mechanisms of modifying acute organ dysfunction. The focus will be on the effects of microbiome modulation during experimental acute kidney injury (excluding septic acute kidney injury) and comparison with other experimental acute organ injuries commonly seen in critically ill patients.
ECHO OEM virtual community of learning for primary care
Authors: Furlan A D , Severin C , Harbin S , Irvin E , Carnide Nancy , Nowrouzi-Kia Behdin , Macdonald Sara , Thompson Aaron , Liao Qing , Smith Peter , Adisesh Anil
Published: September 2024

Background

Health issues caused and/or exacerbated by work are common in patients seeking primary health care. Yet, primary care providers generally receive little or no training in the assessment and management of occupational injuries and illnesses.

Aims

To conduct a pilot project to develop, implement and evaluate a programme to teach occupational and environmental medicine to primary healthcare providers.

Methods

We followed the Extensions for Community Healthcare Outcomes (ECHO) model to connect primary healthcare providers with experts in Occupational and Environmental Medicine (OEM). We employed an observational pre–post study design to assess changes in self-efficacy, knowledge, attitudes and beliefs towards OEM.

Results

From September 2021 to June 2022, we offered two cycles of 12 sessions each. Participants came from medicine, nursing, psychology, occupational and physical therapy, chiropractic, kinesiology, social work, and pharmacy. Sixty-seven participants completed both pre- and post-ECHO questionnaires. Self-efficacy and knowledge ratings significantly increased after attendance at ECHO compared to the pre-ECHO responses. Attitudes and beliefs were unchanged in most of the items assessed. Participants rated their satisfaction with ECHO between 59% and 97%.

Conclusions

Our pilot study demonstrated the challenges in implementing the first ECHO OEM in Canada. Findings show acceptability and satisfaction, improved self-efficacy, and small increases in knowledge, but not overall attitudes and beliefs. There is a need to understand barriers to participation and to target participants with less knowledge and experience in occupational and environmental medicine.
Transcriptional corepressors in maize maintain meristem development
Authors: Gregory Jason , Liu Xue , Chen Zongliang , Gallardo Cecilia , Punskovsky Jason , Koslow Gabriel , Galli Mary , Gallavotti Andrea
Published: September 2024

The formation of the plant body proceeds in a sequential postembryonic manner through the action of meristems. Tightly coordinated meristem regulation is required for development and reproductive success, eventually determining yield in crop species. In maize (Zea mays), the RAMOSA1 ENHANCER LOCUS2 (REL2) family of transcriptional corepressors includes four members, REL2, RELK1 (REL2-LIKE1), RELK2, and RELK3. In a screen for rel2 enhancers, we identified shorter double mutants with enlarged ear inflorescence meristems (IMs) carrying mutations in RELK1. Expression and genetic analysis indicated that REL2 and RELK1 cooperatively regulate ear IM development by controlling genes involved in redox balance, hormone homeostasis, and differentiation, ultimately tipping the meristem toward an environment favorable to expanded expression of the ZmWUSCHEL1 gene, which encodes a key stem-cell promoting transcription factor. We further demonstrated that RELK genes have partially redundant yet diverse functions in the maintenance of various meristem types during development. By exploiting subtle increases in ear IM size in rel2 heterozygous plants, we also showed that extra rows of kernels are formed across a diverse set of F1 hybrids. Our findings reveal that the REL2 family maintains development from embryonic initiation to reproductive growth and can potentially be harnessed for increasing seed yield in a major crop species.
Feasibility of a Multidomain Resiliency Assessment in Patients With Advanced Heart Failure Requiring Surgery: A Pilot Study
Authors: Green Karlyn J , North Rebecca , DeVore Adam D , Green Samantha , Poole Ashley K
Published: September 2024

Objective

The resiliency of patients who have advanced heart failure (HF) and undergo a physical stressor such as heart transplantation or left ventricular assist device implantation has yet to be studied in the physical, cognitive, and psychosocial domains. The primary aim of this pilot study was to assess the feasibility of a multidomain resiliency assessment in patients who have advanced HF and require surgery.

Methods

A battery of assessments in each of the domains was completed at baseline before surgical intervention, after intensive care discharge, and 3 and 6 months after surgery. Feasibility was assessed through completion rates, time required to complete the assessments, and qualitative feedback from assessors.

Results

Although various completion rates were noted at different time points, high completion rates were seen for grip strength, the modified Fried frailty phenotype, and the Montreal Cognitive Assessment. Additionally, when controlled for patients who were medically restricted from physical function, the Short Physical Performance Battery, gait speed, and the 30-second chair stand test also had high completion rates. A trend toward return to baseline status or an improvement in baseline status was observed in all physical and cognitive assessments and most psychosocial assessments at 3 and 6 months. Minimal change was noted in the Brief Resilience Scale questionnaire.

Conclusion

This pilot study demonstrates that a multidomain assessment of resiliency is feasible in patients with advanced HF. Future studies are needed to help determine specific assessments or patient factors that would help predict positive postsurgical outcomes in this population.

Impact

This study has implications for clinical practice on the most feasible assessments in multiple domains for patients who have advanced HF and are being evaluated for heart transplantation or left ventricular assist device.
Unraveling the hemolytic toxicity tapestry of peptides using chemical space complex networks
Authors: Castillo-Mendieta Kevin , Agüero-Chapin Guillermin , Mora José R , Pérez Noel , Contreras-Torres Ernesto , Valdes-Martini José R , Martinez-Rios Felix , Marrero-Ponce Yovani
Published: September 2024

Peptides have emerged as promising therapeutic agents. However, their potential is hindered by hemotoxicity. Understanding the hemotoxicity of peptides is crucial for developing safe and effective peptide-based therapeutics. Here, we employed chemical space complex networks (CSNs) to unravel the hemotoxicity tapestry of peptides. CSNs are powerful tools for visualizing and analyzing the relationships between peptides based on their physicochemical properties and structural features. We constructed CSNs from the StarPepDB database, encompassing 2,004 hemolytic peptides, and explored the impact of seven different (dis)similarity measures on network topology and cluster (communities) distribution. Our findings revealed that each CSN extracts orthogonal information, enhancing the motif discovery and enrichment process. We identified 12 consensus hemolytic motifs, whose amino acid composition unveiled a high abundance of lysine, leucine, and valine residues, whereas aspartic acid, methionine, histidine, asparagine, and glutamine were depleted. Additionally, physicochemical properties were used to characterize clusters/communities of hemolytic peptides. To predict hemolytic activity directly from peptide sequences, we constructed multi-query similarity searching models, which outperformed cutting-edge machine learning-based models, demonstrating robust hemotoxicity prediction capabilities. Overall, this novel in silico approach uses complex network science as its central strategy to develop robust model classifiers, characterize the chemical space, and discover new motifs from hemolytic peptides. This will help to enhance the design/selection of peptides with potential therapeutic activity and low toxicity.
The Effect of a Cervical Brace on Postoperative Axial Symptoms Following Single-level Anterior Cervical Discectomy and Fusion
Authors: Yu Qunfei , Ren Ying , Wang Zhan , Xu Guoping , Ma Yaojing , Ye Feifei
Published: September 2024

Study Design:

Retrospective study.

Objective:

This study aims to investigate the effect of cervical brace utilization on postoperative axial symptoms in patients undergoing single-segment anterior cervical discectomy and fusion (ACDF).

Summary of Background Data:

Anterior cervical discectomy and fusion (ACDF) is the most commonly used surgical method in the treatment of cervical spondylosis. For patients with single-segment ACDF. The absence of a neck brace after surgery is safe and does not affect the outcome of surgery. However, the effect on the incidence of AS is unclear.

Methods:

Patients who underwent anterior cervical single-segment ACDF between May 2020 and August 2021 were retrospectively analyzed. Participants were divided into brace group and nonbraced groups. The incidence of axial symptoms, cervical mobility, and postoperative quality of life were then compared between the 2 groups.

Results:

A total of 121 patients were included in this study: 62 in the brace group and 59 in the nonbraced group. There were no statistically significant variations observed in the overall demographic characteristics, including age, sex, body mass index, smoking status, and disease duration. The study findings showed that there was a significant decrease in the occurrence of axial symptoms among patients in nonbraced group, in addition to a considerable increase in cervical mobility 1 month following the surgery.

Conclusions:

The omission of a cervical brace following surgery in patients undergoing single-segment ACDF reduced the incidence of early postoperative axial symptoms, improved their overall quality of life, and facilitated the recovery of postoperative cervical mobility.
Orbital Pigmented Epithelioid Melanocytoma Tumor Associated With Nevus of Ota (Oculodermal Melanocytosis)
Authors: Albano de Guimarães Juliana , Chahud Fernando , Cruz Antonio Augusto V.
Published: September 2024

The authors report a patient with nevus of Ota (oculodermal melanocytosis) who presented with pigmented epithelioid melanocytoma in the right orbit. A 36-year-old female patient attended with proptosis OD and diplopia for 3 months. MRI disclosed an expansive lesion adhered to the right inferior rectus muscle, enlargement of the superior orbital fissure, and filling of the right cavernous sinus. Excision of the orbital mass through a transconjunctival inferior fornix access disclosed a heavily pigmented lesion. Anatomopathological study revealed a diagnosis of pigmented epithelioid melanocytoma. A positron emission tomography scan did not show any metastasis. The patient was submitted to radiotherapy, had an improvement of the proptosis and diplopia, and showed no distant metastases for 3 years now. Pigmented epithelioid melanocytoma belongs to the group of heavily pigmented neoplasms, as do atypical blue nevus, which is characterized by prominent melanin production and a low degree of malignancy.
Secondary hypogammaglobulinemia: diagnosis and management of a pediatric condition of clinical importance
Authors: DiGiacomo Daniel , Barmettler Sara
Published: September 2024

Purpose of review

Secondary hypogammaglobulinemia, or low serum immunoglobulins, is associated with a variety of medications or medical conditions and may be symptomatic and lead to increased infectious risk. There is limited data regarding the study of acquired, or secondary, hypogammaglobulinemia (SHG) in pediatrics. The data to date has suffered from methodologic issues including retrospective study design, lack of baseline immunoglobulin measurements, and limited longitudinal follow-up.

Recent findings

There is emerging research on the impact of B-cell depleting therapies, specifically rituximab and chimeric antigen T-cells, along with other autoimmune and malignant disease states, in the development of SHG in pediatric patients. This review will also summarize other relevant pediatric conditions related to SHG.

The clinical relevance of SHG in pediatrics is increasingly appreciated. Improved understanding of the specific etiologies, risk factors, and natural history of SHG have informed screening and management recommendations.
Local Public Health Strategies for Addressing Social Determinants of Health—Analysis of Recent Community Health Improvement Plans
Authors: Johnson Karl , Oruganti Nidhi , Cilenti Dorothy , Wiesman John , Jensen Todd , Hassmiller Kristen
Published: September 2024

Context:

The Public Health 3.0 (PH3.0) framework encourages local health departments (LHDs) to address the social determinants of health (SDOHs) that impact health equity.

Objective:

This study sought to understand how often LHDs are working to address SDOH, which SDOHs are most often being addressed, as well as the mix of strategies that have been proposed to address this work.

Design:

We reviewed recent Community Health Improvement Plans (CHIPs) to analyze the current involvement of LHDs in addressing SDOH.

Setting:

CHIPs published from 2020.

Participants:

Accredited LHDs from across the United States (n = 80).

Main Outcome Measures:

We developed a qualitative guidebook to characterize CHIP strategies based on the SDOH domain they addressed and the strategic mechanism they proposed.

Results:

Across our entire sample, CHIPs were roughly 1.5 times more likely to address Health Care Access than Food Insecurity and Access to Healthy Food (65%), Neighborhood Infrastructure (61%), or Affordable Housing (65%), and they were 3 to 4 times more likely to address Health Care Access than Safe Housing (23%), Education Access and Quality (31%), or Economic Stability (24%). Across all major domains, a few concerned policy changes and a handful focused on improving systems or developing the built environment. Most strategies focused on service provision through events or the education of the public and professionals on health-related topics.

Conclusions:

The results of this study demonstrate that not all SDOHs are addressed equally by LHDs within their CHIPs. There is significant variation in how SDOHs are addressed along at 2 dimensions: first, in the likelihood that a CHIP addresses the domain and, second, in the mechanism by which each domain is addressed. Practically, the list of strategies we documented from the 80 CHIPs included in our sample may serve as the basis for strategies that other communities may wish to consider when addressing SDOH.
Macular Optical Coherence Tomography Findings in Patients With Syphilitic Optic Neuropathy—A Case Series and Systematic Review
Authors: Sverdlichenko Irina , McDonald Heather M. , Xie Jim Shen Chu , Margolin Edward A.
Published: September 2024

Background:

Syphilis is a sexually or congenitally acquired infectious disease that can affect multiple organs systems, including the eye. When left undiagnosed and untreated, it can lead to significant morbidity and mortality. Syphilitic optic neuropathy can be difficult to diagnose because it can mimic many other nonsyphilitic causes of optic nerve involvement, leading to delay in treatment. Diagnosing ocular syphilis may be facilitated by assessing for specific outer retina abnormalities on macular optical coherence tomography (OCT).

Methods:

This was a case series and case-based systematic review. For the case series, a retrospective chart review was conducted of all patients who presented to a tertiary university–affiliated neuro-ophthalmology practice over 6 months with undifferentiated optic neuropathy and were eventually diagnosed with syphilitic optic neuropathy. For the systematic review, OVID MEDLINE, EMBASE, and COCHRANE CENTRAL databases were searched to identify all cases of syphilitic optic neuropathy with macular OCT. The primary research outcome was the prevalence of cases with outer retinal abnormalities on OCT.

Results:

Four cases were identified that were eligible for inclusion. The ages ranged from 27 to 62 years old, and 2 of the patients were female. On examination, vision ranged from Snellen 20/50 to hand motion; all patients had optic neuropathy, and macular OCT revealed chorioretinitis characterized by retinal pigment epithelium (RPE) excrescences. The patients subsequently underwent uveitis workup and were diagnosed with syphilis. They were treated with intravenous penicillin and showed improvement in outer retina appearance on follow-up. The systematic review consisted of 24 cases and 35 eyes with syphilitic optic neuropathy and reported macular OCT findings. Eighty-three percent (20/24) were males, and the mean age was 47.7 years (SD: 49.2). The mean visual acuity at presentation was Snellen 20/57. On fundoscopy, 25.7% (9/35) of eyes had vitritis, whereas 22.8% (8/35) had placoid chorioretinal lesions. On OCT, 45.7% (16/35) of eyes had abnormal outer retina findings, most commonly disruption of the ellipsoid zone (EZ) and/or RPE excrescences. All patients were treated with penicillin or ceftriaxone, and final mean visual acuity was Snellen 20/29.

Conclusions:

All 4 patients identified in the case series, and nearly half of patients with syphilitic optic neuropathy described in the literature had concurrent-specific outer retina abnormalities (disruption of EZ and/or placoid chorioretinitis in the form of RPE excrescences) seen on macular OCT. We recommend that clinicians obtain macular OCT for all patients presenting with undifferentiated optic neuropathy.
Adaptation to soil type contributes little to local adaptation in an Italian and a Swedish ecotype of
Arabidopsis thaliana
on contrasting soils
Authors: Ellis Thomas James , Ågren Jon
Published: September 2024

Natural populations are subject to selection caused by a range of biotic and abiotic factors in their native habitats. Identifying these agents of selection and quantifying their effects is key to understanding how populations adapt to local conditions. We performed a factorial reciprocal-transplant experiment using locally adapted ecotypes of
Arabidopsis thaliana
at their native sites to distinguish the contributions of adaptation to soil type and climate. Overall adaptive differentiation was strong at both sites. However, we found only very small differences in the strength of selection on local and non-local soil, and adaptation to soil type at most constituted only a few per cent of overall adaptive differentiation. These results indicate that local climatic conditions rather than soil type are the primary driver of adaptive differentiation between these ecotypes.
Low temperature Cu–Cu direct bonding in air ambient by ultrafast surface grain growth
Authors: Lee Yun-Fong , Huang Yu-Chen , Chang Jui-Sheng , Cheng Ting-Yi , Chen Po-Yu , Huang Wei-Chieh , Lo Mei-Hsin , Fu Kuan-Lin , Lai Tse-Lin , Chang Po-Kai , Yu Zhong-Yen , Liu Cheng-Yi
Published: September 2024

Fine-grain copper (Cu) films (grain size: 100.36 nm) with a near-atomic-scale surface (0.39 nm) were electroplated. Without advanced post-surface treatment, Cu–Cu direct bonding can be achieved with present-day fine-grain Cu films at 130℃ in air ambient with a minimum pressure of 1 MPa. The instantaneous growth rate on the first day is 164.29 nm d
−1
. Also, the average growth rate (∆
R
/∆
t
) is evaluated by the present experimental results: (i) 218.185 nm d
−1
for the first-day period and (ii) 105.58 nm d
−1
during the first 14-day period. Ultrafast grain growth and near-atomic-scale surface facilitate grain boundary motion across the bonding interface, which is the key to achieve Cu–Cu direct bonding at 130℃ in air ambient.
A light in the dark: a mid-Cretaceous bioluminescent firefly with specialized antennal sensory organs
Authors: Cai Chenyang , Tihelka Erik , Ballantyne Lesley , Li Yan-Da , Huang Diying , Engel Michael S. , Kundrata Robin
Published: September 2024

The beetle superfamily Elateroidea comprises the most biodiverse bioluminescent insects among terrestrial light-producing animals. Recent exceptional fossils from the Mesozoic era and phylogenomic studies have provided valuable insights into the origin and evolution of bioluminescence in elateroids. However, due to the fragmentary nature of the fossil record, the early evolution of bioluminescence in fireflies (Lampyridae), one of the most charismatic lineages of insects, remains elusive. Here, we report the discovery of the second Mesozoic bioluminescent firefly,
Flammarionella hehaikuni
Cai, Ballantyne & Kundrata gen. et sp. nov., from the Albian/Cenomanian of northern Myanmar (
ca
99 Ma). Based on the available set of diagnostic characters, we interpret the specimen as a female of stem-group Luciolinae. The fossil possesses deeply impressed oval pits on the apices of antennomeres 3–11, representing specialized sensory organs likely involved in olfaction. The light organ near the abdominal apex of
Flammarionella
resembles that found in extant light-producing lucioline fireflies. The growing fossil record of lampyrids provides direct evidence that the stunning light displays of fireflies were already established by the late Mesozoic.
Endophytic pyrroloquinoline quinone enhances banana growth and immunity against Fusarium wilt for plant-microbe mutualisms
Authors: Hung Shih-Hsun Walter , Yu Man-Yun , Liu Chia-Ho , Huang Tsai-Ching , Peng Jian-Hau , Jang Nai-Yun , Kuo Chih-Horng , Yang Yu-Liang , Ho Ying-Ning , Chiang En-Pei Isabel , Hwang Hau-Hsuan , Huang Chieh-Chen
Published: September 2024

Fusarium wilt has a substantial impact on global banana production, posing a threat to food security worldwide. However, breeding new Fusarium-resistant cultivars is difficult and time-consuming. Alternatively, endophytic biostimulants that could combat such pervasive plant diseases provide possible novel solutions. Our prior research demonstrated that a pyrroloquinoline quinone (PQQ)-producing endophytic bacterium, Burkholderia seminalis 869T2, can enhance the growth of various plant species and protect bananas from Fusarium wilt in the field. PQQ is a peptide-derived redox cofactor known to stimulate mitochondrial biogenesis and metabolism in animals, but its molecular roles, especially in plants, remain to be elucidated. In this study, multi-omics approaches were employed to explore the potential mechanisms through which PQQ influences banana plants. The result of in situ imaging mass spectrometry revealed that the endophytic metabolite PQQ does not function through direct antagonism against Fusarium. The follow-up transcriptomic profiling shows it could regulate plant respiration, TCA cycle, oxidative phosphorylation, NAD/NADP-dependent dehydrogenases, MAPK signalling, and various phytohormone signalling pathways. Furthermore, PQQ appeared to trigger plant systemic immunity, thereby enhancing plant health and resistance to biotic stress. Beyond that, the complete genome of 869T2 was determined for follow-up comparative genomics analyses, revealing its genetic contexts, potential evolutionary events of PQQ operons among the Burkholderia species, and the absence of human virulence-facilitating genes within those PQQ-producing agricultural isolates. In summary, this study facilitates our understanding of PQQ in plant-microbe mutualisms and provides scientific evidence for its future application in agriculture.
Mast cells promote pathology and susceptibility in tuberculosis
Authors: Gupta Ananya , Taneja Vibha , Rangel Moreno Javier , Abhimanyu  , Ahmed Mushtaq , Naqvi Nilofer , Chauhan Kuldeep S. , de León Daniela Trejo-Ponce , Ramírez-Martínez Gustavo , Jiménez-Alvarez Luis , Luna-Rivero Cesar , Zuniga Joaquin , Kaushal Deepak , Khader Shabaana A.
Published: September 2024

Tuberculosis (TB), caused by the bacteriumMycobacterium tuberculosis(Mtb), infects approximately one-fourth of the world’s population. While most infected individuals are asymptomatic, latent TB infection (LTBI) can progress to cause pulmonary TB (PTB). We recently reported an increased accumulation of mast cells (MCs) in lungs of macaques with PTB, compared with LTBI in macaques. MCs respond in vitro toMtbexposure via degranulation and by inducing proinflammatory cytokines. In the current study, we show the dominant production of chymase by MCs in granulomas of humans and macaques with PTB. Using scRNA seq analysis, we show that MCs found in LTBI and healthy lungs in macaques are enriched in genes involved in tumor necrosis factor alpha, cholesterol and transforming growth factor beta signaling. In contrast, MCs clusters found in PTB express transcriptional signatures associated with interferon gamma, oxidative phosphorylation, and MYC signaling. Additionally, MC deficiency in the mouse model showed improved control ofMtbinfection that coincided with reduced accumulation of lung myeloid cells and diminished inflammation at chronic stages. Thus, these collective results provide novel evidence for the pathological contribution of MCs duringMtbinfection and may represent a novel target for host directive therapy for TB.
Lysyl Oxidases are Necessary for Myometrial Contractility and On-Time Parturition in Mice
Authors: Ouellette Alexis , Do Christina , Cohn-Guthrie Sydney , Lam Ying-Wai , Mahendroo Mala , Nallasamy Shanmugasundaram
Published: September 2024

The extracellular matrix (ECM) plays a pivotal role in the maintenance of tissue mechanical homeostasis. Collagens and elastic fibers are the most predominant fibrous ECM proteins providing tissue mechanical function through covalent cross-linking which is mediated by the lysyl oxidase family of enzymes. In this study, the function of lysyl oxidases in maintaining the integrity of the extracellular matrix in the myometrium and its impact on parturition-timing was investigated. Gene and protein expression analyses demonstrate that a sub-set of the lysyl oxidase family of enzymes are highly induced in pregnant myometrium. Inhibition of the activity of the lysyl oxidase family of enzymes through β-aminopropionitrile (BAPN) delays parturition in mice, in part, due to myometrial dysfunction. In BAPN treated mice, the expression of genes encoding contraction associated proteins such as connexin 43, oxytocin receptor and prostaglandin synthase 2 is significantly reduced in the myometrium compared to the untreated control mice. Proteomic analysis revealed that the composition of the ECM is altered in response to BAPN treatment which demonstrates that the inhibition of the activity of lysyl oxidases disrupted the integrity of the myometrial ECM. Our findings demonstrate that the lysyl oxidases-mediated ECM function is necessary for the myometrium to transition from a quiescent to a contractile phenotype at term for on-time parturition.
The personal space and the collective behavior of crowd disasters
Authors: Lugo Igor , Alatriste-Contreras Martha G.
Published: September 2024

The personal space in dense crowd situations is commonly underestimated. However, the self-awareness of it can prevent and handle risk situations. The aim of this study was to explore theoretically the use of the personal space as a key concept for designing simple computational models related to collective behaviors and crushing events. We used an agent-based model related to transitional rules associated with the Shelling’s spatial proximity model of segregation. Based on an explorative data analysis and model validation, we found that the dynamics of crowd events showed significant statistical regularities between dense situations and the individual perception of the personal space. These results suggests that crushing events in dense crowd situations are highly probable and that the density levels are the key for delaying the presence of such disasters.
Developing heterospecific Sterile Insect Technique for pest control: insights from the spotted wing flyDrosophila suzukii
Authors: Cerasti Flavia , Cristofaro Massimo , Mastrantonio Valentina , Scifo Jessica , Verna Adriano , Canestrelli Daniele , Porretta Daniele
Published: September 2024

BACKGROUND

Reproductive interference (i.e., sexual interaction between males of one species and females of another species that reduce the fitness of one or both the interacting individuals) is an important species interaction significantly affecting population dynamics and persistence. However, its exploitation in pest control remains overlooked. Here, we investigated the possible integration of reproductive interference into the Sterile Insect Technique (SIT) to develop a heterospecific SIT (h-SIT). Under this approach, contrary to the classic SIT, sterile heterospecific males from closely related, non-pest species are released to compete with the pest population for mates. At this aim, we focused on the invasive pest speciesDrosophila suzukiiand usedD. melanogasteras the control species. First, we investigated the effect of irradiation onD. melanogastersterility and longevity. Then, we tested the mating performance of irradiated males and their ability to reduce theD. suzukiifitness.

RESULTS

We found by microcosm experiments that: i) irradiation induced high levels ofD. melanogastermale sterility without reducing longevity; ii) irradiatedD. melanogastermales courtD. suzukiifemales as much asD. suzukiimales and they couple, mate and fecund heterospecific females; iii) irradiatedD. melanogastermales significantly reduce the offspring ofD. suzukiifemales under two different species ratios.

CONCLUSIONS

Our results provide the first foundation to develop a heterospecific Sterile Insect Technique againstD. suzukiiand fuel to test this approach against other groups of pest species.
Presence of distinct operant phenotypes and transient withdrawal-induced escalation of operant ethanol intake in female rats
Authors: Pitock Joseph R , Wheeler Shannon R , Ayala Arleen Perez , Hou Shikun , Soto Nathaly Arce , Glover Elizabeth J
Published: September 2024

Operant self-administration is frequently used to investigate the neurobiological mechanisms underlying alcohol seeking and drinking and to test the efficacy of drugs under development for the treatment of alcohol use disorder (AUD). Although widely used by the research community, there is a paucity of operant ethanol self-administration studies that include female subjects. The current study characterizes home cage drinking and operant ethanol self-administration in female Sprague Dawley, Long Evans, and Wistar rats. Rats underwent three weeks of intermittent-access two-bottle choice home cage drinking before being trained to lever press for ethanol in standard operant chambers equipped with contact lickometers. After capturing baseline operant performance, rats were chronically exposed to control or ethanol liquid diet using the Lieber-DeCarli method. Operant ethanol self-administration was re-evaluated after chronic liquid diet exposure to determine whether female rats exhibit similar withdrawal-induced escalation of ethanol intake as is regularly observed in male rats. Our findings reveal the presence of three distinct operant phenotypes (Drinker, Responder, Nonresponder), the prevalence of which within each strain is strikingly similar to our previous observations in males. Within a given phenotype, rats of each strain performed similarly during operant testing. Ethanol intake during home cage drinking was unable to predict future operant phenotype. Relative to controls, Drinkers chronically exposed to ethanol liquid diet exhibited a significant, but transient, escalation in consummatory, but not appetitive, responding during acute withdrawal. Collectively, these data closely parallel many of our previous observations in males while also highlighting potential sex differences in drinking strategies following dependence. The presence of the Responder phenotype reinforces the importance of using direct measures of ethanol consumption. Our findings provide new insight into similarities and differences in operant ethanol self-administration between males and females and emphasize the importance of including females in future studies of ethanol drinking and dependence.
Understanding Ecological Systems Using Knowledge Graphs: An Application to Highly Pathogenic Avian Influenza
Authors: Robertson Hailey , Han Barbara A. , Castellanos Adrian A. , Rosado David , Stott Guppy , Zimmerman Ryan , Drake John M. , Graeden Ellie
Published: September 2024

Ecological systems are complex. Representing heterogeneous knowledge about ecological systems is a pervasive challenge because data are generated from many subdisciplines, exist in disparate sources, and only capture a subset of important interactions underpinning system structure, resilience, and dynamics. Knowledge graphs have been successfully applied to organize heterogeneous data systematically and to predict new linkages representing unobserved relationships in complex systems. Though not previously applied broadly in ecology, knowledge graphs have much to offer in an era of global change when system dynamics are responding to rapid changes across multiple scales simultaneously. We developed a knowledge graph to demonstrate the method’s utility for ecological problems focused on highly pathogenic avian influenza (HPAI), a highly transmissible virus with a broad animal host range, wide geographic distribution, and rapid evolution with pandemic potential. We describe the development of a graph to include a wide range of data related to HPAI including pathogen-host associations, animal species distributions, and human population demographics, using a semantic ontology that defines relationships within the data and between datasets. We use the graph to perform a set of proof-of-concept analyses validating the method and identifying new relationships and features of HPAI ecology, underscoring the generalizable value of knowledge graphs to ecology including their utility in revealing previously known relationships between entities and generating testable hypotheses in support of a deeper mechanistic understanding of ecological systems.
The Importance of Nonsense Errors: Estimating the Rate and Implications of Drop-Off Errors during Protein Synthesis
Authors: Cope Alexander L. , Pak Denizhan , Gilchrist Michael A.
Published: September 2024

The process of mRNA translation is both energetically costly and relatively error-prone compared to transcription and replication. Nonsense errors during mRNA translation occur when a ribosome drops off a transcript before reaching a stop codon, resulting in energetic investment in an incomplete and likely non-functional protein. Nonsense errors impose a potentially significant energy burden on the cell, making it critical to quantify their frequency and energetic cost. Here, we present a model of ribosome movement for estimating protein production, elongation, and nonsense error rates from high-throughput ribosome profiling data. Applying this model to an exemplary ribosome profiling dataset inS. cerevisiae, we find that nonsense error rates vary between codons, in conflict with the general assumption of uniform rates across sense codons. Using our parameter estimates, we find multiple lines of evidence that selection against nonsense errors is a prominent force shaping coding-sequence evolution, including that nonsense errors place an energetic burden on cells comparable to ribosome pausing. Our results indicate greater consideration should be given to the impact of nonsense errors in shaping coding-sequence evolution.
DendroTweaks: An interactive approach for unraveling dendritic dynamics
Authors: Makarov Roman , Chavlis Spyridon , Poirazi Panayiota
Published: September 2024

Neurons rely on the interplay between dendritic morphology and ion channels to transform synaptic inputs into a sequence of somatic spikes. Detailed biophysical models with active dendrites have been instrumental in exploring this interaction. However, such models can be challenging to understand and validate due to the large number of parameters involved. In this work, we introduceDendroTweaks— a toolbox designed to illuminate how morpho-electric properties map to dendritic events and how these dendritic events shape neuronal output.DendroTweaksfeatures a web-based graphical interface, where users can explore single-cell neuronal models and adjust their morphological and biophysical parameters with real-time visual feedback. In particular,DendroTweaksis tailored to interactive fine-tuning of subcellular properties, such as kinetics and distributions of ion channels, as well as the dynamics and allocation of synaptic inputs. It offers an automated approach for standardization and refinement of voltage-gated ion channel models to make them more comprehensible and reusable. The toolbox allows users to run various experimental protocols and record data from multiple dendritic and somatic locations, thereby enhancing model validation. Finally, it aims to deepen our understanding of which dendritic properties are essential for neuronal input-output transformation. Using this knowledge, one can simplify models through a built-in morphology reduction algorithm and export them for further use in faster, more interpretable networks. WithDendroTweaks, users can gain better control and understanding of their models, advancing research on dendritic input-output transformations and their role in network computations.