bluuebunny/crossref_metadata_2025 huggingface dataset:
The Fifth Residue of the Coat Protein of Turnip Mosaic Virus Is Responsible for Long-Distance Movement in a Local-Lesion Host and Aphid Transmissibility in a Systemic Host
Authors: Hu Wen-Chi , Tsai Jui-Chi , Cheng Hao-Wen , Huang Chung-Hao , Raja Joseph A. J. , Chang Fang-Yu , Chen Chin-Chih , Chiang Chu-Hui , Yeh Shyi-Dong
Published: March 2024

HC-Pro and coat protein (CP) genes of a potyvirus facilitate cell-to-cell movement and are involved in the systemic movement of the viruses. The interaction between HC-Pro and CP is mandatory for aphid transmission. Two turnip mosaic virus (TuMV) isolates, RC4 and YC5, were collected from calla lily plants in Taiwan. The virus derived from the infectious clone pYC5 cannot move systemically in Chenopodium quinoa plants and loses aphid transmissibility in Nicotiana benthamiana plants, like the initially isolated virus. Sequence analysis revealed that two amino acids, P5 and A206, of YC5 CP uniquely differ from RC4 and other TuMV strains. Recombination assay and site-directed mutagenesis revealed that the fifth residue of leucine (L) at the N-terminal region of the CP (TuMV-RC4), rather than proline (P) (TuMV-YC5), is critical to permit the systemic spread in C. quinoa plants. Moreover, the single substitution mutant YC5-CPP5L became aphid transmissible, similar to RC4. Fluorescence microscopy revealed that YC5-GFP was restricted in the petioles of inoculated leaves, whereas YC5-CPP5L-GFP translocated through the petioles of inoculated leaves, the main stem, and the petioles of the upper uninoculated leaves of C. quinoa plants. In addition, YC5-GUS was blocked at the basal part of the petiole connecting to the main stem of the inoculated C. quinoa plants, whereas YC5-CPP5L-GFP translocated to the upper leaves. Thus, a single amino acid, the residue L5 at the N-terminal region right before the 6DAG8 motif, is critical for the systemic translocation ability of TuMV in a local lesion host and for aphid transmissibility in a systemic host.
Functional Characterization of Core and Unique Calcite-Dissolving Bacteria Communities from Peanut Fields
Authors: Peper Alan , Newton Carter J. , Lim Sheena , Zheng Wendy , Brenneman Timothy , Yang Li
Published: March 2024

Calcium deficiency is a leading cause of reduced peanut ( Arachis hypogaea) seed quality and has been linked to increased disease susceptibility, specifically to soilborne fungal pathogens. Sufficient calcium at flowering time is critical to ensure proper pod development. Calcite-dissolving bacteria (CDB) isolated from farming fields can dissolve calcite (CaCO3) on plates and increase soluble calcium levels in soil. However, the phylogenetic diversity and geographic distribution of CDB is unclear. Here, we surveyed soil samples from 15 peanut-producing fields in three regions in southern Georgia, representing distinct soil compositions. We isolated CDB through differentiating media and identified 52 CDB strains. CDB abundance was not associated with any of the soil characteristics we evaluated. Three core genera, represented by 43 strains, were found in all three regions. Paenibacillus was the most common CDB found in all regions, making up 30 of the 52 identified strains. Six genera, represented by eight strains, are unique to one region. Members of the core and unique communities showed comparable solubilization indexes on plates. We conclude that a diversified phylogenetic population of CDB is present in Georgia peanut fields. Despite the phylogenetic diversity, as a population, they exhibit comparable functions in solubilizing calcite on plates.
Temporal Transcriptome Profiling of Pinus densiflora Infected with Pine Wood Nematode Reveals Genetically Programmed Changes upon Pine Wilt Disease
Authors: Lee Il Hwan , Choi Bae Young , Kim Dong Soo , Han Hyelim , Kim Yun-Hee , Shim Donghwan
Published: March 2024

Pine, an evergreen conifer, is widely distributed worldwide. It is economically, scientifically, and ecologically important. However, pine wilt disease (PWD) induced by the pine wood nematode (PWN) adversely affects pine trees. Many studies have been conducted on the PWN and its beetle vectors to prevent the spread of PWD. However, studies providing a comprehensive understanding of the pine tree transcriptome in response to PWN infection are lacking. Here, we performed temporal profiling of the pine tree transcriptome using PWD-infected red pine trees, Pinus densiflora, inoculated with the PWN by RNA sequencing. Our analysis revealed that defense-responsive genes involved in cell wall modification, jasmonic acid signaling, and phenylpropanoid-related processes were significantly enriched 2 weeks after PWD infection. Furthermore, some WRKY-type and MYB-type transcription factors were upregulated 2 weeks after PWD infection, suggesting that these transcription factors might be responsible for the genome-wide reprogramming of defense-responsive genes in the early PWD stage. Our comprehensive transcriptome analysis will assist in developing PWD-resistant pine trees and identifying genes to diagnose PWD at the early stage of infection, during which large-scale phenotypic changes are absent in PWD-infected pine trees.
Quality of life in adult patients with developmental dysplasia of the hip who were treated for hip dislocation during childhood
Authors: Sawamura Kenta , Kitoh Hiroshi , Matsushita Masaki , Mishima Kenichi , Kamiya Yasunari , Imagama Shiro
Published: March 2024

Developmental dysplasia of the hip (DDH) can lead to premature loss of hip function if not properly treated; however, few studies have focused on the long-term outcomes of DDH. We conducted a survey of health-related quality of life in adult patients with DDH who were treated for hip dislocation during childhood. We sent a questionnaire to 287 adult patients with DDH who were treated for hip dislocation during childhood in our institutions. We examined patient demographics, disease-specific medical history, and health-related quality of life using the short form-36. Physical component summary (PCS), mental component summary (MCS) and role/social component summary (RCS) were compared between the patients and Japanese standard values. Sixty-eight patients were evaluated after exclusion. The overall mean PCS, MCS and RCS scores of the patients were comparable to the standard values. The PCS was maintained until the age of 50, but it was significantly decreased in 10 patients over 50 years old. In addition, PCS was significantly lower in patients who underwent open reduction than in those who were conservatively reduced. The MCS and RCS of the patients did not differ from the standard values in each age and treatment group. Additionally, the PCS, MCS and RCS did not differ according to bilaterality, age at diagnosis, or requirement for additional surgeries. Physical quality of life was maintained until the age of 50 but rapidly declined thereafter in patients with DDH, especially in those who required open reduction during childhood.
Social Connectedness as a Determinant of Health in African-American Low-Income Families with Young Children: A Cross-Sectional Cohort Study
Authors: Clore Lauren , Agrawal Rajeev Mohan , Kolm Paul , Rethy Janine A.
Published: March 2024

Objective:

This cross-sectional study aimed to assess the level of social connectedness (SC) in African-American low-income families with young children attending a pediatric primary care clinic and examine its relationships with food insecurity and parental well-being.

Methods:

This cross-sectional analysis used data from the Healthy Children and Families program, a cohort intervention study addressing food insecurity, conducted by an urban pediatric clinic serving low-income predominantly African-American families. Twenty-seven families completed baseline screening tools, including the Social Provisions Scale five-question short form (SPS-5) to measure SC, a modified version of the United States Department of Agriculture (USDA) Household Food Security Survey Module six-item short form to assess food insecurity, and the Parental Stress Index Short Form to measure parental stress. Descriptive statistics, correlations, and partial correlations were conducted to analyze the data.

Results:

The average SPS-5 composite score was 14.5 on a scale of 5 to 20. Moderate negative correlations were identified between SC and food insecurity, weaker when controlled for parental stress. Strong negative correlations were identified between SC and parental stress that held when controlled for food insecurity.

Conclusion:

In this study, we propose a conceptual framework highlighting the complex interplay of social connectedness with other social determinants of child health. The findings align with the 2023 Surgeon General's Advisory on the epidemic on the healing effects of social connection and provide insight into the value of incorporating SC assessments into routine screenings in pediatric primary care settings. Further research is needed to explore causal relationships and evaluate the effectiveness of interventions designed to enhance SC in diverse populations.
Complete Retinal Pigment Epithelial and Outer Retinal Atrophy in Age-Related Macular Degeneration: A Longitudinal Evaluation
Authors: Wu Zhichao , Hodgson Lauren A.B. , Goh Kai Lyn , Guymer Robyn H.
Published: March 2024

Purpose:

There is a need for robust earlier biomarkers of atrophic age-related macular degeneration (AMD) that could act as surrogate endpoints for the geographic atrophy (GA) in early interventional trials. This study sought to examine the risk of progression of complete retinal pigment epithelium and outer retinal atrophy (cRORA) to the traditional atrophic endpoint of GA on color fundus photography (CFP). This study also compared the risk of progression for cRORA to that associated with the specific OCT features that define nascent GA (nGA), a strong predictor for GA development.

Methods:

One-hundred and forty participants with bilateral large drusen at baseline underwent OCT imaging and CFP at 6-monthly intervals for up to 36 months. OCT volume scans were graded for the presence of cRORA and nGA, and CFPs were graded for the presence of GA. The association and rate of progression to GA for cRORA and nGA were examined.

Results:

Both cRORA and nGA were significantly associated with GA development (adjusted hazard ratio [HR], 65.7 and 76.8 respectively; both P<0.001). The probability of progression of cRORA to GA over 24-months (26%) was significantly lower than the probability for progression of nGA (38%; P=0.039).

Conclusions:

This study confirmed that cRORA was a significant risk factor for developing GA, although its rate of progression was slightly lower compared to nGA. Whilst requiring replication in future studies, these findings suggest that the specific features of photoreceptor degeneration used to define nGA appear important when assessing risk of progression.
FUNCTIONAL AND ANATOMICAL OUTCOMES AFTER SHORT-TERM HEAVY SILICONE OIL ENDOTAMPONADE FOR INFERIOR RHEGMATOGENOUS RETINAL REDETACHMENT, A PILOT STUDY
Authors: Sborgia Luigi , Albano Valeria , Sborgia Alessandra , Viggiano Pasquale , Boscia Giacomo , Zerbinati Marta , Pozharitskiy Nikolai , Binetti Roberta , Dimiccoli Roberta , Fracchiolla Antonio , Boscia Francesco , Alessio Giovanni
Published: March 2024

Purpose:

To assess the success of the short-term location of the heavy silicone oil (Densiron 68, HSO) as endotamponade after pars plana vitrectomy (PPV) for rhegmatogenous complex retinal re-detachment (RRD).

Methods:

Consecutive, retrospective, nonrandomized, pilot study was conducted. Twenty-two eyes of 22 patients with complex inferior RRD previously tamponade with gas (SF6 or C3F8) or 1000cSt silicon oil (SSO) were selected. All were treated with heavy silicone oil HSO endotamponade, and its removal was performed after 1-month. The main outcomes were best corrected visual acuity (BCVA) and postoperative complications after the heavy silicone oil removal.

Results:

Of the 22 eyes, 10 were SSO endotamponade, 3 with fluorinated gas 14% C3F8, and 9 with 20% SF6 at first surgery. In all cases, a complex inferior RRD was observed after the first surgery, in 1-3 months after silicone oil removal or gas endotamponade introduction.

In ten cases the proliferative vitreoretinopathy PVR (grade B or C 1-3) was found. The main BCVA before HSO removal was 0.55± 0.20 logMAR (range 0.4-0.7) and after the HSO removal, it was 0.32± 0.29 logMAR (0.1-0.4).

Among the postoperative complications, only in 4 eyes the macular edema was found (medically resolved), in 4 eyes an increase of intraocular pressure (IOP), and none of these developed the epiretinal membrane (ERM).

Conclusion:

The main purpose of this study is to establish a short-term heavy silicone oil endotamponade in eyes with complex retinal detachment recurrences, reducing the possible postoperative complications and having a better prognosis for visual acuity outcomes.
A rare presentation of Nocardia Choroidal Abscess after Glioblastoma surgery
Authors: Visioli Giacomo , Beccia Alessandro , Lucchino Luca , Mastromarino Davide , Pirraglia Maria Pia
Published: March 2024

Purpose:

to report the natural history of a rare ocular manifestation of endogenous Nocardia farcinica infection in an immunocompromised patient, with involvement observed in both the anterior and posterior segments of the eye.

Methods and results:

Given the patient's limited mobility, a handheld fundus camera was utilized for bedside anterior segment and ocular fundus examinations. The findings included visual acuity of hand motion, posterior synechiae, vitreal opacity, and a large choroidal abscess. We monitored the lesion's progression through a series of follow-ups. Despite not employing intravitreal drug therapy, we noted a significant reduction in the lesion's size until the patient's overall health deteriorated.

Conclusions:

This case contributes valuable information to our understanding of the natural history of a rare condition like Nocardia endophthalmitis. We highlighted the usefulness of a handheld fundus camera in aiding infectious disease specialists in assessing the immediate response to systemic treatment.
Peripheral and central neurobiological effects of botulinum toxin A (BoNT/A) in neuropathic pain: a systematic review
Authors: Moreau Nathan , Korai Sohaib Ali , Sepe Giovanna , Panetsos Fivos , Papa Michele , Cirillo Giovanni
Published: March 2024

Botulinum toxin (BoNT), a presynaptic inhibitor of acetylcholine (Ach) release at the neuromuscular junction (NMJ), is a successful and safe drug for the treatment of several neurological disorders. However, a wide and recent literature review has demonstrated that BoNT exerts its effects not only at the “periphery” but also within the central nervous system (CNS). Studies from animal models, in fact, have shown a retrograde transport to the CNS, thus modulating synaptic function. The increasing number of articles reporting efficacy of BoNT on chronic neuropathic pain (CNP), a complex disease of the CNS, demonstrates that the central mechanisms of BoNT are far from being completely elucidated. In this new light, BoNT might interfere with the activity of spinal, brain stem, and cortical circuitry, modulating excitability and the functional organization of CNS in healthy conditions. Botulinum toxins efficacy on CNP is the result of a wide and complex action on many and diverse mechanisms at the basis of the maladaptive plasticity, the core of the pathogenesis of CNP. This systematic review aims to discuss in detail the BoNT's mechanisms and effects on peripheral and central neuroplasticity, at the basis for the clinical efficacy in CNP syndromes.
Ki-67 Testing in Breast Cancer: Assessing Variability With Scoring Methods and Specimen Types and the Potential Subsequent Impact on Therapy Eligibility
Authors: Bocklage Therese , Cornea Virgilius , Hickey Caylin , Miller Justin , Moss Jessica , Chambers Mara , Bachert S. Emily
Published: March 2024

Abemaciclib was originally FDA approved for patients with ER-positive/HER2-negative breast cancer with Ki-67 expression ≥20%. However, there were no guidelines provided on which specimen to test or which scoring method to use. We performed a comprehensive study evaluating the variation in Ki-67 expression in breast specimens from 50 consecutive patients who could have been eligible for abemaciclib therapy. Three pathologists with breast expertise each performed a blinded review with 3 different manual scoring methods [estimated (EST), unweighted (UNW), and weighted (WT) (WT recommended by the International Ki-67 in Breast Cancer Working Group)]. Quantitative image analysis (QIA) using the HALO platform was also performed. Three different specimen types [core needle biopsy (CNB) (n=63), resection (RES) (n=52), and axillary lymph node metastasis (ALN) (n=50)] were evaluated for each patient. The average Ki-67 for all specimens was 14.68% for EST, 14.46% for UNW, 14.15% for WT, and 11.15% for QIA. For the manual methods, the range between the lowest and highest Ki-67 for each specimen between the 3 pathologists was 8.44 for EST, 5.94 for WT, and 5.93 for UNW. The WT method limited interobserver variability with ICC1=0.959 (EST ICC1=0.922 and UNW=0.949). Using the aforementioned cutoff of Ki-67 ≥20% versus <20% to determine treatment eligibility, the averaged EST method yields 20 of 50 patients (40%) who would have been treatment-eligible, versus 15 (30%) for the UNW, 17 (34%) for the WT, and 12 (24%) for the QIA. There was no statistically significant difference in Ki-67 among the 3 specimen types. The average Ki-67 difference was 4.36 for CNB vs RES, 6.95 for CNB versus ALN, and RES versus ALN (P=0.93, 0.99, and 0.94, respectively). Our study concludes that further refinement in Ki-67 scoring is advisable to reduce clinically significant variation.
Outcomes for Pediatric Oncology and Hematopoietic Stem Cell Transplantation Patients Who Undergo Tracheostomy Placement: A Pediatric Health Information System Database Cohort Study, 2009–2020
Authors: Murphy Salem Sinead L. , Perez Jennifer M. , Staffa Steven J. , Duncan Christine N. , Graham Robert J.
Published: March 2024

OBJECTIVES:

To describe the epidemiology, surgical complications, and long-term outcomes after tracheostomy in pediatric oncology and/or hematopoietic stem cell transplantation (HSCT) patients in U.S. Children’s Hospitals.

DESIGN:

Retrospective cohort from the Pediatric Health information System (PHIS) database, 2009–2020.

SETTING:

The PHIS dataset incorporates data from 48 pediatric hospitals in the Children’s Hospital Association.

PATIENTS:

Patients 0–21 years old with an oncologic diagnosis and/or underwent HSCT, received a tracheostomy, and were discharged from hospital between January 1, 2009, and December 31, 2020.

INTERVENTIONS:

None.

MEASUREMENTS AND MAIN RESULTS:

There were 1061 patients included in the dataset, and 217 (20.5%) had undergone HSCT. The annual prevalence in tracheostomy usage did not change over the study period. The majority of patients (62.2%) underwent tracheostomy early (< 30 d) in the admission and those who underwent the procedure later (> 90 d) had a significant increase in mortality (52.6% vs. 17.6%;p< 0.001) and mechanical ventilation (MV) at discharge (51.9% vs. 24.5%;p< 0.001) compared with the early tracheostomy patients. Complications reported included tracheostomy site bleeding (< 1%) and infection (24%). The overall rate of MV at discharge was 32.6% and significantly associated with chronic lung (adjusted odds ratio [OR], 1.54; 95% CI, 1.03–2.32) and acute lung disease (OR, 2.18; 95% CI, 1.19–3.98). The overall rate of mortality was 19.6% within the cohort and significantly associated with HSCT (OR, 5.45; 95% CI, 3.88–7.70), diagnosis of sepsis (OR, 2.09; 95% CI, 1.28–3.41), and requirement for renal replacement therapy (OR, 2.76; 95% CI, 1.58–4,83).

CONCLUSIONS:

This study demonstrated a static prevalence of tracheostomy placement in the cohort population relative to the increasing trends in other reported groups. Regardless of underlying diagnosis, the study patients incurred substantial morbidity and mortality. However, tracheostomy specific complication rates were comparable with that of the general pediatric population and were not associated with increased odds of mortality within this population.
Patches in Congenital Diaphragmatic Hernia
Authors: Saxena Amulya K. , Hayward Romilly K.
Published: March 2024

Objective:

This systematic review aims to evaluate current choices in practice and outcomes of biomaterials used in patch repair of congenital diaphragmatic hernia (CDH).

Background:

Multiple biomaterials, both novel and combinations of pre-existing materials are employed in patch repair of large size CDHs.

Methods:

A literature search was performed across Embase, Medline, Scopus, and Web of Science. Publications that explicitly reported patch repair, material used, and recurrences following CDH repair were selected.

Results:

Sixty-three papers were included, presenting data on 4595 patients, of which 1803 (39.2%) were managed using 19 types of patches. Goretex® (GTX) (n=1106) was the most frequently employed patch followed by Dualmesh® (n=267), Surgisis® (n=156), Marlex®/GTX® (n=56), Tutoplast dura® (n=40), Dacron® (n=34), Dacron®/GTX® (n=32), Permacol® (n=24), Teflon® (n=24), Surgisis®/GTX® (n=15), Sauvage® Filamentous Fabric (n=13), Marlex® (n=9), Alloderm® (n=8), Silastic® (n=4), Collagen coated Vicryl® mesh (CCVM) (n=1), Mersilene® (n=1), and MatriStem® (n=1) Biomaterials were further subgrouped as: synthetic nonresorbable (SNOR) (n=1458), natural resorbable (NR) (n=241), combined natural and synthetic nonresorbable (NSNOR) (n=103), and combined natural and synthetic resorbable (NSR) (n=1). The overall recurrence rate for patch repair was 16.6% (n=299). For patch types with n>20, recurrence rate was lowest in GTX/Marlex (3.6%), followed by Teflon (4.2%), Dacron (5.6%), Dualmesh (12.4%), GTX (14.8%), Permacol (16.0%), Tutoplast Dura (17.5%), SIS/GTX (26.7%), SIS (34.6%), and Dacron/GTX (37.5%).When analyzed by biomaterial groups, recurrence was highest in NSR (100%), followed by NR (31.5%), NSNOR (17.5%), and SNOR the least (14.0%)

Conclusion:

In this cohort, over one-third of CDH were closed using patches. To date, 19 patch types/variations have been employed for CDH closure. GTX is the most popular, employed in over 60% of patients; however, excluding smaller cohorts (n<20), GTX/Marlex is associated with the lowest recurrence rate (3.6%). SNOR was the material type least associated with recurrence, while NSR experienced recurrence in every instance.
Development of an Experimental Protocol to Study the Neural Control of Force and Impedance in Wrist Movements with Robotics and fMRI
Authors: Schmidt Kristin , Berret Bastien , Sergi Fabrizio
Published: March 2024

Robotic exoskeletons have emerged as beneficial tools in the field of rehabilitation, yet their full potential is impeded by our limited knowledge of the neural control of movements during human-robot interaction. To personalize exoskeleton protocols and improve individuals' motor recovery, we must advance our understanding of how the brain commands movements in physical interaction tasks. However, interpreting the neural function associated with these movements is complex due to the simultaneous expression of at least two control policies: force and impedance control. This hinders our ability to isolate these control mechanisms and pinpoint their neural origins. In this study, we evaluate the capacity of external force fields to decouple the expression of force and impedance in a wrist-pointing task, a necessary step in isolating their neural substrates via neuroimaging. We first conducted simulations using a neuromuscular model to examine how both force and impedance commands are updated when participants are asked to perform reaching movements in the presence of an external force field. Then, we recruited seven participants to perform a wrist-pointing task with the MR-SoftWrist, an MRI-compatible wrist robot. The task included four different force field conditions -- no force, positive constant force, negative constant force, and divergent force, each carefully selected to decouple expression of force and impedance control. Furthermore, we evaluated the efficacy of our proposed conditions for a neuroimaging experiment through simulations of neural activity. We show that these force fields elicit distinct and predictable torque and stiffness expression, laying the groundwork for reliably identifying their associated neural activity in a future neuroimaging study.
PathEX: Make Good Choice for Whole Slide Image Extraction
Authors: Yang Xinda , Zhang Ranze , Yang Yuan , Zhang Yu , Chen Kai
Published: March 2024

Background

The tile-based approach has been widely used for slide-level predictions in whole slide image (WSI) analysis. However, the irregular shapes and variable dimensions of tumor regions pose challenges for the process. To address this issue, we proposed PathEX, a framework that integrates intersection over tile (IoT) and background over tile (BoT) algorithms to extract tile images around boundaries of annotated regions while excluding the blank tile images within these regions.

Methods

We developed PathEX, which incorporated IoT and BoT into tile extraction, for training a classification model in CAM (239 WSIs) and PAIP (40 WSIs) datasets. By adjusting the IoT and BoT parameters, we generated eight training sets and corresponding models for each dataset. The performance of PathEX was assessed on the testing set comprising 13,076 tile images from 48 WSIs of CAM dataset and 6,391 tile images from 10 WSIs of PAIP dataset.

Results

PathEX could extract tile images around boundaries of annotated region differently by adjusting the IoT parameter, while exclusion of blank tile images within annotated regions achieved by setting the BoT parameter. As adjusting IoT from 0.1 to 1.0, and 1 - BoT from 0.0 to 0.5, we got 8 train sets. Experimentation revealed that set C demonstrates potential as the most optimal candidate. Nevertheless, a combination of IoT values ranging from 0.2 to 0.5 and 1-BoT values ranging from 0.2 to 0.5 also yielded favorable outcomes.

Conclusions

In this study, we proposed PathEX, a framework that integrates IoT and BoT algorithms for tile image extraction at the boundaries of annotated regions while excluding blank tiles within these regions. Researchers can conveniently set the thresholds for IoT and BoT to facilitate tile image extraction in their own studies. The insights gained from this research provide valuable guidance for tile image extraction in digital pathology applications.
Strain intrinsic properties and environmental constraints together shape Escherichia coli dynamics and diversity over a twenty-year human gut time series
Authors: Condamine Benedicte , Morel-Journel Thibaut , Tesson Florian , Royer Guilhem , Magnan Melanie , Bernheim Aude , Denamur Erick , Blanquart Francois , Clermont Olivier
Published: March 2024

Escherichia coli is an increasingly antibiotic-resistant opportunistic pathogen. Few data are available on its ecological and evolutionary dynamics in its primary commensal niche, the vertebrate gut. Using Illumina and/or Nanopore technologies, we sequenced whole genomes of 210 E. coli isolates from 22 stools sampled during a 20-year period from a healthy man (ED) living in Paris, France. All phylogroups, except C, were represented, with a predominance of B2 (34.3%), followed by A and F (19% each) phylogroups. Thirty-five clones were identified based on their haplogroup and pairwise genomic single nucleotide polymorphism distance and classified in three phenotypes according to their abundance and residence time: 25 sub-dominant/transient (52 isolates), five dominant/transient (48 isolates) and five dominant/resident (110 isolates). Four over five dominant/resident clones belonged to B2 and closely related F phylogroups, whereas sub-dominant/transient clones belonged mainly to B1, A and D phylogroups. The long residence times of B2 clones seemed to be counterbalanced by lower colonization abilities. Clones with larger within-host frequency persisted for longer in the host. By comparing ED strain genomes to a collection of commensal E. coli genomes from 359 French individuals, we identified ED-specific genomic properties including a set of genes involved in a metabolic pathway (mhp cluster) and a very rare antiviral defense island. The E. coli colonization within the gut microbiota was shaped by both the intrinsic properties of the strain lineages, in particular longer residence of phylogroup B2, and the environmental constraints such as diet or phages.
The Architecture of Sponge Choanocyte Chambers Maximizes Mechanical Pumping Efficiency
Authors: Ogawa Takumi , Koyama Shuji , Omori Toshihiro , Kikuchi Kenji , de Maleprade Hélène , Goldstein Raymond E. , Ishikawa Takuji
Published: March 2024

Sponges, the basalmost members of the animal kingdom, exhibit a range of complex architectures in which microfluidic channels connect multitudes of spherical chambers lined with choanocytes, flagellated filter-feeding cells. Choanocyte chambers can possess scores or even hundreds of such cells, which drive complex flows entering through porous walls and exiting into the sponge channels. One of the mysteries of the choanocyte chamber is its spherical shape, as it seems inappropriate for inducing directional transport since many choanocyte flagella beat in opposition to such a flow. Here we combine direct imaging of choanocyte chambers in living sponges with computational studies of many-flagella models to understand the connection between chamber architecture and directional flow. We find that those flagella that beat against the flow play a key role in raising the pressure inside the choanocyte chamber, with the result that the mechanical pumping efficiency, calculated from the pressure rise and flow rate, reaches a maximum at a small outlet opening angle. Comparison between experimental observations and the results of numerical simulations reveal that the chamber diameter, flagellar wave number and the outlet opening angle of the freshwater spongeE. muelleri, as well as several other species, are related in a manner that maximizes the mechanical pumping efficiency. These results indicate the subtle balances at play during morphogenesis of choanocyte chambers, and give insights into the physiology and body design of sponges.
Admixture with cultivated sunflower likely facilitated establishment and spread of wild sunflower (H. annuus) in Argentina
Authors: Hernández Fernando , Vercellino Román B. , Todesco Marco , Bercovich Natalia , Alvarez Daniel , Brunet Johanne , Presotto Alejandro , Rieseberg Loren H.
Published: March 2024

A better understanding of the genetic and ecological factors underlying successful invasions is critical to mitigate the negative impacts of invasive species. Here, we study the invasion history ofHelianthus annuuspopulations from Argentina, with particular emphasis on the role of post-introduction admixture with cultivated sunflower (alsoH. annuus) and climate adaptation driven by large haploblocks. We conducted genotyping-by-sequencing of samples of wild populations as well as Argentinian cultivars and compared them with wild (including related annualHelianthusspecies) and cultivated samples from the native range. We also characterized samples for 11 known haploblocks associated with environmental variation in native populations to test whether haploblocks contributed to invasion success. Population genomics analyses supported two independent geographic sources for Argentinian populations, the central United States and Texas, but no significant contribution of related annualHelianthusspecies. We found pervasive admixture with cultivated sunflower, likely as result of post-introduction hybridization. Genomic scans between invasive populations and their native sources identified multiple genomic regions with evidence of selection in the invaded range. These regions significantly overlapped between the two native-invasive comparisons and showed disproportionally high crop ancestry, suggesting that crop alleles contributed to invasion success. We did not find evidence of climate adaptation mediated by haploblocks, yet outliers of genome scans were enriched in haploblock regions and, for at least two haploblocks, the cultivar haplotype was favored in the invaded range. Our results show that admixture with cultivated sunflower played a major role in the establishment and spread ofH. annuuspopulations in Argentina.
Application of Cancer Cell Line Encyclopedia for Measuring Correlation Between Transcriptomics and Proteomics as a Guide for System-level Insights
Authors: Williams Blake , Perry Darryl , Aspesi Peter , Parker Jefferson , Johnson Ted , Su Wendy , Tabacman Eduardo , Delisle Kirk , Avishan Kayvon , Myer Vic , Mapa Felipa , Hinterberg Michael , Williams Alan , Jennings Lori , Janjic Nebojsa , Loureiro Joseph
Published: March 2024

Robust and reliable proteome measurements provide mechanistic insights in biomedical research. SOMAmer (Slow Off-rate Modified Aptamer) reagents are modified, DNA-based, affinity reagents that measure defined target proteins with reproducibility and accuracy similar to monoclonal antibodies. Applying SOMAmer reagent technology, we developed SomaScan, a clinical proteome profiling platform with capability to measure 7,523 proteoforms for 6,594 human proteins by UniprotID in small sample volumes (e.g., 55μl plasma or serum). We evaluated the platform by profiling the proteome of a panel of well characterized Cell Line Encyclopedia (CCLE) cancer models. Unsupervised machine learning analyses demonstrate the SomaScan assay distinguishing cell lines on the basis of their proteome signatures, and identifying both tissue-specific and oncogenic pathways. The proteome measured by SomaScan correlates with published CCLE transcriptome at a level comparable to other published transcript to proteome studies. Taken together, we demonstrate that the SomaScan platform is a technically reproducible system suitable for biomedical and clinical applications that reliably illuminates underlying biomolecular mechanisms.
Targeting students of nonhealth academic fields for basic life support: they need to know why, what and how to do CPR
Authors: Sugimoto PN , Gouvêa GB , Salles IC , Carvalho HB , Aikawa P , Azi LMTA , Silva LFF , Macchione M , Semeraro F , Lockey A , Greif RT , Carmona MJC , Böttiger BW , Nakagawa NK
Published: March 2024

Education in basic life support is widely proposed to increase survival and quality-of-life in out-of-hospital sudden cardiac arrest. We aimed to assess knowledge, skills and attitudes regarding acute myocardial infarction and sudden cardiac arrest among university students of all fields of knowledge.

Methods

The local Ethical Research Committee approved this cross-sectional study. An electronic survey “KIDS SAVE LIVES BRAZIL” was sent to 58,862 students of 82 disciplines in three universities, aged ≥ 18 years. The survey covered three categories: knowledge, skills, and attitude. Each category was graded between 0 and 10 points (the highest).

Results

Among university students, 4,803 undergraduates (8.2 %) answered the survey, and were divided in three groups of disciplines: medicine (219, ∼21.7 years, 38% male), other-health-care (n=1,058; ∼22.9 years; 36% male), and nonhealth-care (n=3,526; ∼22.9 years; 35% male). All three groups showed significant differences between them (p<0.001). The nonhealth-care compared with medicine and other-health-care group showed, respectively, the lowest (p<0.001) median scores (25-75%) in knowledge [4.0 (0.0-9.3), 4.0 (4.0-8.0), and 4.0 (4.0-4.7)], skills [2.4 (1.2-3.3), 6.4 (4.0-8.3), 4.0 (2.4-6.2], and attitude [5.9 (5.9-6.8), 7.3 (5.9-7.3), and 7.3 (5.9-7.3)].

Conclusion

University students have the willingness to help victims suffering from acute myocardial infarction or sustaining sudden cardiac arrest. However, nonhealth-care students markedly lack knowledge and skills to perform cardiopulmonary resuscitation and automated external defibrillation. Our findings reveal a stark difference in basic life support competencies between students in health-care related fields and those in nonhealthy-care fields, emphasizing the need for universal basic life support training.

KEY MESSAGES

1. Our findings reveal a stark difference in basic life support competencies between students in health-care related fields and those in nonhealth fields, emphasizing the need for universal basic life support training.

2. An action for curriculum modification to include basic life support training for all students is timely and practical, given the global burden of heart disease and the proven benefits of early intervention in sudden cardiac arrest cases.

3. Our study contributes significantly to the ongoing discussion about public health education and the role of nonhealth professionals in emergency medical response. It may serve as a catalyst for policy changes within educational institutions and among healthcare policymakers, aiming to create a more resilient and responsive community in the face of out-of-hospital medical emergencies.
Factors that affect enrollment into a community-based health insurance scheme among households in Arba Minch Zuria District, Gamo Zone, Southern Ethiopia, 2023: A community-based unmatched case-control Study
Authors: Bujitie Silas Bukuno , daud Yusuf Haji
Published: March 2024

Background

Many low-and middle-income countries are affected by catastrophic health expenditures as out-of-pocket payments exceed the World Health Organization’s (WHO) 10% threshold level. The government of Ethiopia has been working to reduce out-of-pocket payments from 37% to less than 15% in its health sector transformation plan II; however, the scheme was marked by a low membership and dropout rate. The aim of the study was to identify determinants of enrolment into a community-based health insurance scheme (CBHIS) in Arba Minch Zuria District of Gamo Zone, Southern Ethiopia.

Methods

Unmatched case-control study was employed from February 8, 2023, to March 9, 2023, among 327 participants (109 cases and 218 controls to community-based health insurance (CBHI) scheme) in a 1:2 proportions. Multi-stage sampling technique was used to draw the study participants. Data were collected by using structured interviewer administered questionnaire and then entered into Epi-data and exported to SPSS for analysis. Bivariable and multivariable analysis was carried out using binary logistic regression. Significance was declared by using an adjusted odds ratio (AOR) with 95% confidence interval (CIs) and a p value of <0.05.

Results

A total of 327 participants (109 enrolled and 218 non-enrolled) were interviewed, resulting in a response rate of 100%. Family size (AOR=1.66; 95% CI: 1.00–2.73), wealth index (AOR=2.29; 95% CI: 1.25–4.19), awareness level of the community based health insurance scheme (AOR=3.78; 95% CI: 1.09–13.18), and perceived quality of health care (AOR=1.67; 95% CI: 1.02-2.75) were found to be determinant factors of enrollment in the scheme.

Conclusion

Strengthening community awareness activities, focusing on families of poor households, and improving the quality of health service delivery are highly recommended to improve enrollment in the scheme.
The transition from a non-westernized to westernized gut microbiome in Indian-Immigrants and Indo-Canadians is associated with dietary acculturation
Authors: D’Aloisio Leah D. , Ballal Mamatha , Ghosh Sanjoy , Haskey Natasha , Abulizi Nijiati , Karimianghadim Ramin , Liu Chuyi , Sruthi Pacha , Nagarajan Lakshmipriya , Vasudevan Sudha , Shetty Vignesh , Purandare Mrudgandha , Bhaumik Ushasi , Howlader Debaki Ranjan , Pakpour Sepideh , Barnett Jacqueline , Gibson Deanna L.
Published: March 2024

Background

Indian immigration to westernized countries has surged in recent years, with this demographic facing a higher risk of Inflammatory Bowel Disease (IBD) after migration. Studying the gut microbiome is crucial to understanding the factors contributing to IBD, yet Indians remain underrepresented in microbiome research,

Objective

This study investigates the gut microbiome of Indians residing in India, Indian immigrants in Canada, and Canadians of Indian ancestry to understand the impact of westernization on their gut. Given the higher risk of IBD among Indo-Canadians, these results provide insight into how westernization of the gut microbiome may influence incidence of IBD. Stool samples were collected from healthy Indians in India, Indian Immigrants in Canada, Indo-Canadians, plus Canadian-borne individuals with European descent and Euro-Immigrants as non-Indian/westernized controls (N= 174). 16S rRNA gene and shotgun sequencing compared microbial taxa and functional profiles across groups. Dietary and demographic data were collected to assess lifestyle patterns.

Results

Indians and Indo-Immigrants had distinct gut microbiotas from westernized groups, with high abundances ofPrevotellaspp. and a CAZyme profile reflecting their traditional high complex carbohydrate diet. The Indian microbiome also showed characteristics of high bacterial cell turnover, pathogenic potential, and stress tolerance, indicating their gut may be better primed to handle stressors on the gut. Indo-Canadians displayed a transitional microbiome towards westernization, which followed a pattern of increasing dietary acculturation.

Conclusions

The shift from a non-westernized to westernized microbiome in Indo-Canadians highlights the significant influence that westernization and dietary acculturation has on the gut microbiome. Given that 44% of the Canadian population is made up of first- and second-generation immigrants and westernized practices are being adopted worldwide, future research should investigate the health implications that such microbiome transitions have on immigrant populations and newly industrialized nations.
Liebenberg syndrome severity arises from variations inPitx1locus topology and ectopically transcribing cells
Authors: Bompadre Olimpia , Rouco Raquel , Darbellay Fabrice , Rauseo Antonella , Guerard-Millet Fanny , Gentile Claudia , Kmita Marie , Andrey Guillaume
Published: March 2024

Enhancer hijacking, a common cause of gene misregulation linked to disease, occurs when non-matching enhancers and promoters interact ectopically. This interaction is made possible by genetic changes that alter the arrangement or insulation of gene regulatory landscapes. While the concept of enhancer hijacking is well understood, the specific reasons behind the variation in phenotypic severity or the point at which those phenotypes become evident remain unexplored. In this work, we expand on the ectopic activation of the hindlimb-specific transcription factorPitx1by one of its own enhancers,Pen, in forelimb tissues that causes the Liebenberg syndrome. We combine a previously developedin-embryocell-tracing approach to a series of inversions and relocations to show that reduction inPitx1-Penrelative genomic positioning leads to increased proportions ofPitx1forelimb-expressing cells and more severe phenotypical outcomes. We demonstrate that thePitx1locus assumes an active topology when enhancer-promoter contacts are required for transcription and that its promoter generates consistent transcription levels across different alleles. Finally, we show that changes in 3D chromatin structure and enhancer-promoter contacts are not the result ofPitx1transcriptional activity. In summary, our work shows that variation in enhancer-promoter interactions can lead to pathogenic locus activation in variable proportions of cells which, in turn, define phenotypic severity.
Preference-Independent Encoding of Visual Saliency Within but Not Cross Features in the Mouse Superior Colliculus
Authors: Wu Ruixiang , Xu Jinhuai , Li Chunpeng , Zhang Zhaoji , Li Ling-yun , Li Ya-tang
Published: March 2024

Detecting conspicuous stimuli in a visual scene is crucial for animal survival, yet it remains debated how the brain encodes visual saliency. Here we investigate how visual saliency is represented in the superficial superior colliculus (sSC) of awake mice using two-photon calcium imaging. We report on a preference-independent saliency map in the sSC. Specifically, salient stimuli evoke stronger responses in both excitatory and inhibitory neurons compared to uniform stimuli, with similar encoding patterns observed in both neuron types. The largest response occurs when a salient stimulus is positioned at the receptive field center, with contextual effects extending ∼40° away from the center. The response amplitude correlates well with the saliency strength of stimuli and is not influenced by the orientation or motion direction preferences of neurons. However, saliency encoding does depend on specific visual features. Furthermore, neurons involved in saliency encoding exhibit weak orientation or direction selectivity, suggesting a complementary relationship between the saliency map and the feature map.
RGS10 deficiency facilitates distant metastasis by inducing epithelial-mesenchymal transition in breast cancer
Authors: Liu Yang , Jiang Yi , Qiu Peng , Ma Tie , Bai Yang , Bu Jiawen , Hu Yueting , Jin Ming , Zhu Tong , Gu Xi
Published: March 2024

Abstract

Distant metastasis is the major cause of death in patients with breast cancer. Epithelial–mesenchymal transition (EMT) contributes to breast cancer metastasis. Regulator of G protein-signaling (RGS) proteins modulate metastasis in various cancers. This study identified a novel role for RGS10 in EMT and metastasis in breast cancer. RGS10 protein levels were significantly lower in breast cancer tissues compared to normal breast tissues, and deficiency in RGS10 protein predicted a worse prognosis in patients with breast cancer. RGS10 protein levels were lower in the highly aggressive cell line MDA-MB-231 than in the poorly aggressive, less invasive cell lines MCF7 and SKBR3. Silencing RGS10 in SKBR3 cells enhanced EMT and caused SKBR3 cell migration and invasion. The ability of RGS10 to suppress EMT and metastasis in breast cancer was dependent on lipocalin-2 and miR-539-5p. These findings identify RGS10 as a tumor suppressor, prognostic biomarker, and potential therapeutic target for breast cancer.
Past, present, and future spatial distributions of deep-sea coral and sponge microbiomes revealed by predictive models
Authors: Busch Kathrin , Murillo Francisco Javier , Lirette Camille , Wang Zeliang , Kenchington Ellen
Published: March 2024

Knowledge of the spatial distribution patterns of biodiversity in the ocean is key to evaluate and ensure ocean integrity and resilience. Especially for the deep ocean, wherein situmonitoring requires sophisticated instruments and considerable ﬁnancial investments, modelling approaches are crucial to move from scattered data points to predictive continuous maps. Those modelling approaches are commonly run on the macrobial level, but spatio-temporal predictions of host-associated microbiomes are not being targeted. This is especially problematic as previous research has highlighted that host-associated microbes (microbiomes) may display distribution patterns that are not perfectly correlated with host animal biogeographies, but also with other factors such as prevailing environmental conditions. We here establish a new simulation approach and present predicted spatio-temporal distribution patterns of deep-sea sponge and coral microbiomes, making use of a combination of environmental data, host data and microbiome data to advance our understanding of deep-sea microbiomes. This approach allows predictions of microbiome spatio-temporal distribution patterns on scales that are currently not covered by classical sampling approaches at sea. This includes both predictions in space within regional oceanic provinces off eastern North America, and also in time, with predictions into the past and future, covering a time span of 214 years. In summary, our presented predictions allow (i) identiﬁcation of microbial biodiversity hotspots in the past, present, and future, (ii) evaluation of microbial-macrobial connections at case-study sites through trait-based predictions, and (iii) identiﬁcation of shifts in microbial community composition (key taxa) across environmental gradients and shifting environmental conditions.