bluuebunny/crossref_metadata_2025 huggingface dataset:
Influence of Maternal Adverse Childhood Experiences on Birth Outcomes in American Indian and non-Hispanic White Women
Authors: Goldstein Ellen , Brown Roger L.
Published: June 2023

Purpose:

Maternal adverse childhood experiences (ACEs) are an antecedent risk during prenatal and postpartum periods. We examined race-based differences of the mediating influences of antepartum health risks (prenatal depression, high blood pressure, gestational diabetes) on associations between ACEs and maternal and birth outcomes (postpartum depression, preterm birth, low birthweight) among American Indian and non-Hispanic White women.

Methods:

Public use data from the South Dakota Pregnancy Risk Assessment Monitoring System PRAMS (2017-2019) were used for this secondary analysis of postpartum women. ACEs and depression were measured based on self-report survey results. Antepartum risks and birth outcomes were extracted from birth certificate data. A moderated mediation logit model estimated direct, indirect, and moderating effects by race, controlling for maternal characteristics and perinatal risks to understand ACEs' impact on pregnancy and birth outcomes between groups.

Results:

The sample included 2,343 postpartum women. American Indian versus non-Hispanic White women had a higher mean ACE score (3.37 vs. 1.64) and substantial disparities. Race-based differences were attributed to social, economic, and health-related factors. Adjusting for proportional differences, members of both groups with ACEs demonstrated significantly increased odds of prenatal and postpartum depression. ACEs influenced postpartum depression and preterm birth through the indirect effect of prenatal depression in both races. Prenatal depression indirectly influenced the relationship between ACEs and low birthweight in non-Hispanic White women.

Clinical Implications:

ACEs were associated with higher levels of prenatal depression, which may negatively influence maternal and birth outcomes in American Indian and non-Hispanic White women. Improving perinatal outcomes must emphasize psychosocial care along with medical care to address the high burden of maternal ACEs in the United States.
Apoptosis, Crypt Dropout, and Equivocal Immunohistochemical Staining May Indicate Cytomegalovirus Infection in Inflammatory Bowel Disease Patients
Authors: Ono Yuho , Gonzalez Raul S.
Published: June 2023

Cytomegalovirus (CMV) colitis superimposed on inflammatory bowel disease (IBD) can be challenging to diagnose. This study aimed to determine what histologic clues and immunohistochemistry (IHC) utilization practices, if any, can help diagnose CMV superinfection in IBD. Colon biopsies were reviewed from all patients with CMV colitis with and without IBD between 2010 and 2021 at one institution, along with a separate cohort of IBD patients with negative CMV IHC. Biopsies were assessed for histologic features of activity and chronicity, phlebitis, fibrin thrombi, basal crypt apoptosis, CMV viral cytopathic effect (VCE), and CMV IHC positivity. Features between groups were compared, with statistical significance set at P-value <0.05. The study included 251 biopsies from 143 cases (21 CMV-only, 44 CMV+IBD, 78 IBD-only). Compared with the IBD-only group, the CMV+IBD group was more likely to show apoptotic bodies (83% vs. 64%, P=0.035) and crypt dropout (75% vs. 55%, P=0.045). CMV was detected by IHC in 18 CMV+IBD cases without VCE on hematoxylin and eosin (41%). In the 23 CMV+IBD cases where IHC was performed on all concurrent biopsies, IHC was positive in at least 1 biopsy in 22 cases. Six individual CMV+IBD biopsies with no VCE on hematoxylin and eosin demonstrated equivocal IHC staining. Of these, 5 had evidence of CMV infection. IBD patients with superimposed CMV infection are more likely to demonstrate apoptotic bodies and crypt dropout compared with their noninfected counterparts. Equivocal IHC staining for CMV may indicate true infection in IBD patients, and staining multiple biopsies from the same accession can improve CMV detection.
Either High or low Risk
Authors: Perri Giampaolo , Marchegiani Giovanni , Partelli Stefano , Andreasi Valentina , Luchini Claudio , Bariani Elena , Bannone Elisa , Fermi Francesca , Mattiolo Paola , Falconi Massimo , Salvia Roberto , Bassi Claudio
Published: June 2023

Background:

Pancreatic acinar content has been associated with pancreas-specific complications after pancreatoduodenectomy (PD). The aim of this study was to improve the prediction ability of intraoperative risk stratification by integrating the pancreatic acinar score.

Methods:

A training and a validation cohort underwent PD with subsequent histologic assessment of pancreatic section margins for acinar content (Ac), fibrosis (Fc), and fat. Intraoperative risk stratification (pancreatic texture, duct diameter) and pancreas-specific complications (postoperative hyperamylasemia [POH], post pancreatectomy acute pancreatitis [PPAP], pancreatic fistula [POPF]) were classified according to ISGPS definitions.

Results:

In the validation cohort (n= 373), the association of pancreas-specific complications with higher Ac and lower Fc was replicated (all P<0.001). In the entire cohort (n= 761), the ISGPS classification allocated 275 (36%) patients into intermediate-risk classes B (POH 32%/PPAP 3%/POPF 17%) and C (POH 36%/PPAP 9%/POPF 33%). Using the acinar score (Ac ≥60% and/or Fc ≤10%), intermediate-risk patients could be dichotomized into a low- (POH 5%/PPAP 1%/POPF 6%) and a high- (POH 51%/PPAP 9%/POPF 38%) risk group (all P<0.001). The acinar score AUC for POPF prediction was 0.70 in the ISGPS intermediate-risk classes. Overall, 239 (31%) patients were relocated into the high-risk group from lower ISGPS risk classes using the acinar score.

Conclusions:

The risk of pancreas-specific complications appears to be dichotomous - either high or low - according to the acinar score, a tool to better target the application of mitigation strategies in cases of intermediate macroscopic features.
Clinical Practice Guideline Recommendations For Pediatric Multisystem Trauma Care
Authors: Freire Gabrielle C. , Beno Suzanne , Yanchar Nathalie , Weiss Matthew , Stang Antonia , Stelfox Thomas , Bérubé Melanie , Beaulieu Emilie , Gagnon Isabelle J , Zemek Roger , Berthelot Simon , Tardif Pier-Alexandre , Moore Lynne
Published: June 2023

Objective:

To systematically review clinical practice guidelines (CPG) for pediatric multisystem trauma, appraise their quality, synthesize the strength of recommendations and quality of evidence, and identify knowledge gaps.

Summary Background Data:

Traumatic injuries are the leading cause of death and disability in children, who require a specific approach to injury care. Difficulties integrating CPG recommendations may cause the observed practice and outcome variation in pediatric trauma care.

Methods:

We conducted a systematic review using Medline, Embase, Cochrane library, Web of Science, ClinicalTrials and grey literature, from January 2007 to November 2022. We included CPGs targeting pediatric multisystem trauma with recommendations on any acute care diagnostic or therapeutic interventions. Pairs of reviewers independently screened articles, extracted data, and evaluated the quality of CPGs using AGREE II.

Results:

We reviewed 19 CPGs, and 11 were considered high quality. Lack of stakeholder engagement and implementation strategies were weaknesses in guideline development. We extracted 64 recommendations: 6 (9%) on trauma readiness and patient transfer, 24 (38%) on resuscitation, 22 (34%) on diagnostic imaging, 3 (5%) on pain management, 6 (9%) on ongoing inpatient care and 3 (5%) on patient and family support. Forty-two (66%) recommendations were strong or moderate, but only 5 (8%) were based on high quality evidence. We did not identify recommendations on trauma survey assessment, spinal motion restriction, inpatient rehabilitation, mental health management, or discharge planning.

Conclusions:

We identified 5 recommendations for pediatric multisystem trauma with high quality evidence. Organizations could improve CPGs by engaging all relevant stakeholders and considering barriers to implementation. There is a need for robust pediatric trauma research, to support recommendations.
Efficacy of Pelvic Floor Ultrasound for Assessing Transobturator Tape Sling Procedure
Authors: Hu Yang , Zhu Shuxu , Lou Yelin , Zhang Heng , Huang Ting , Xie Liping
Published: June 2023

Importance

Complications after midurethral sling, which require a high degree of clinical suspicion for timely diagnosis, accurate evaluation, and proper intervention, are closely associated with surgical success or failure.

Objectives

This study aimed to evaluate the efficacy and complications of tension-free midurethral sling for stress urinary incontinence (SUI) using pelvic floor ultrasound.

Study Design

This retrospective study included 152 female patients with SUI admitted to the Jinhua Central Hospital between January 2020 and December 2021 who were selected. All patients underwent midurethral transobturator tape sling procedures and were divided into success, voiding dysfunction, overactive bladder, and failure groups according to postoperative efficacy and complications. The pelvic floor ultrasound examination was performed before and after the surgery.

Results

The posterior vesicourethral angle difference (P < 0.01) was significantly lower after the surgery than before the surgery. The rate of bladder neck funneling (P < 0.01) and the area of bladder neck funneling (P < 0.01) were smaller after the surgery than before the surgery. The tape–longitudinal smooth muscle distance, the tape–symphysis pubis distance, the sling angle, and the tape–bladder neck/urethra increased successively in the voiding dysfunction, overactive bladder, success, and failure groups.

Conclusions

Pelvic floor ultrasound can accurately evaluate the postoperative efficacy and complications of transobturator tape sling procedures for SUI and can reasonably guide the management of complications. Therefore, it is an effective imaging method for postoperative follow-up after tension-free midurethral tape suspension.
The bacteriology of diabetic foot ulcers and infections and incidence of Staphylococcus aureus Small Colony Variants
Authors: Lee James , Mashayamombe Matipaishe , Walsh Tom P. , Kuang Beatrice K. P. , Pena Guilherme N. , Vreugde Sarah , Cooksley Clare , Carda-Diéguez Miguel , Mira Alex , Jesudason David , Fitridge Robert , Zilm Peter S. , Dawson Joseph , Kidd Stephen P.
Published: June 2023

Introduction. Uninfected diabetes-related foot ulcer (DFU) progression to diabetes-related foot infection (DFI) is a prevalent complication for patients with diabetes. DFI often progresses to osteomyelitis (DFI-OM). Active (growing)

Staphylococcus aureus

is the most common pathogen in these infections. There is relapse in 40–60 % of cases even when the initial treatment at the DFI stage apparently clears infection.

Hypothesis.

S. aureus

adopts the quasi-dormant Small Colony Variant (SCV) state during DFU and consequently infection, and when present in DFI cases also permits survival in non-diseased tissues as a reservoir to cause relapse.

Aim. The aim of this study was to investigate the bacterial factors that facilitate persistent infections.

Methodology. People with diabetes were recruited from two tertiary hospitals. Clinical and bacterial data was taken from 153 patients with diabetes (51 from a control group with no ulcer or infection) and samples taken from 102 patients with foot complications to identify bacterial species and their variant colony types, and then compare the bacterial composition in those with uninfected DFU, DFI and those with DFI-OM, of whom samples were taken both from wounds (DFI-OM/W) and bone (DFI-OM/B). Intracellular, extracellular and proximal ‘healthy’ bone were examined.

Results.

S. aureus

was identified as the most prevalent pathogen in diabetes-related foot pathologies (25 % of all samples). For patients where disease progressed from DFU to DFI-OM,

S. aureus

was isolated as a diversity of colony types, with increasing numbers of SCVs present. Intracellular (bone) SCVs were found, and even within uninfected bone SCVs were present. Wounds of 24 % of patients with uninfected DFU contained active

S. aureus

. All patients with a DFI with a wound but not bone infection had previously had

S. aureus

isolated from an infection (including amputation), representing a relapse.

Conclusion. The presence of

S. aureus

SCVs in recalcitrant pathologies highlights their importance in persistent infections through the colonization of reservoirs, such as bone. The survival of these cells in intracellular bone is an important clinical finding supporting in vitro data. Also, there seems to be a link between the genetics of

S. aureus

found in deeper infections compared to those only found in DFU.
Characterizing common and rare variations in non-traditional glycemic biomarkers using multivariate approaches on multi-ancestry ARIC study
Authors: Ray Debashree , Loomis Stephanie J. , Venkataraghavan Sowmya , Tin Adrienne , Yu Bing , Chatterjee Nilanjan , Selvin Elizabeth , Duggal Priya
Published: June 2023

Glycated hemoglobin, fasting glucose, glycated albumin, and fructosamine are biomarkers that reflect different aspects of the glycemic process. Genetic studies of these glycemic biomarkers can shed light on unknown aspects of type 2 diabetes genetics and biology. While there exists several GWAS of glycated hemoglobin and fasting glucose, very few GWAS have focused on glycated albumin or fructosamine. We performed a multi-phenotype GWAS of glycated albumin and fructosamine from 7,395 White and 2,016 Black participants in the Atherosclerosis Risk in Communities (ARIC) study on the common variants from genotyped/imputed data. We found 2 genome-wide significant loci, one mapping to known type 2 diabetes gene (ARAP1/STARD10,p= 2.8 × 10−8) and another mapping to a novel gene (UGT1A,p= 1.4 × 10−8) using multi-omics gene mapping strategies in diabetes-relevant tissues. We identified additional loci that were ancestry-specific (e.g.,PRKCAfrom African ancestry individuals,p= 1.7 × 10−8) and sex-specific (TEX29locus in males only,p= 3.0 × 10−8). Further, we implemented multi-phenotype gene-burden tests on whole-exome sequence data from 6,590 White and 2,309 Black ARIC participants. Eleven genes across different rare variant aggregation strategies were exome-wide significant only in multi-ancestry analysis. Four out of 11 genes had notable enrichment of rare predicted loss of function variants in African ancestry participants despite smaller sample size. Overall, 8 out of 15 loci/genes were implicated to influence these biomarkers via glycemic pathways. This study illustrates improved locus discovery and potential effector gene discovery by leveraging joint patterns of related biomarkers across entire allele frequency spectrum in multi-ancestry analyses. Most of the loci/genes we identified have not been previously implicated in studies of type 2 diabetes, and future investigation of the loci/genes potentially acting through glycemic pathways may help us better understand risk of developing type 2 diabetes.
COGNITIVE REJUVENATION IN OLD RATS BY HIPPOCAMPAL OSKM GENE THERAPY
Authors: Horvath Steve , Lacunza Ezequiel , Mallat Martina Canatelli , Portiansky Enrique L. , Gallardo Maria D. , Brooke Robert T. , Chiavellini Priscila , Pasquini Diana C. , Girard Mauricio , Lehmann Marianne , Yan Qi , Lu Ake T. , Haghani Amin , Gordevicius Juozas , Abba Martin , Goya Rodolfo G.
Published: June 2023

Impaired performance in spatial learning and memory during aging in rats is associated with morphological and molecular changes in the brain, particularly in the hippocampus. Here, we assessed the cognitive performance of young (3.5 mo.) untreated rats and old (25.3 mo.) treated and control rats. Treatment was carried out by intrahippocampal injection of an adenovector that carries the GFP reporter gene as well as the 4 Yamanaka genes.

Learning and spatial memory performance were assessed by means of the Barnes maze test. The learning performance of the OSKM-treated old rats was significantly improved compared to that of the control old counterparts. A marginal (P=0.06) improvement in the spatial memory was recorded in the treated versus control old rats. OSKM gene expression induced no pathological changes in the brain. The morphology and number of hippocampal cell populations like astrocytes and mature neurons did not show any changes with the treatment in the old rats as compared with the control old counterparts. The rat pan tissue DNAm age marker revealed that old OSKM gene-treated rats show a trend towards a decrease in epigenetic age. The Limma package was used to assess differential methylation by fitting linear models to the methylation data for specific group comparisons. Comparison of differential methylation between old treated and old control hippocampal DNA samples identified 671 differentially methylated CpGs probes (DPMs) in the DNA of OSKM-treated hippocampi (p<0.05). Assessment of the DPMs in old versus young controls revealed the presence of 1,279 hypomethylated CpGs near the promoter regions in young hippocampi (versus old controls) and 914 hypermethylated CpGs near the promoter in young hippocampi compared to old control hippocampi. We found a subset of 174 hypomethylated CpGs in the hippocampal DNA from old OSKM rats and young controls both compared with old control hippocampi. This means that in the hippocampal DNA there is a common set of CpGs which are hypermethylated during aging and are demethylated by the OSKM genes. This observation suggested that in these 174 CpGs the hypermethylation induced by aging is reversed by the demethylation effect of the OSKM genes on the same 174 CpGs. This observation can be interpreted as a rejuvenation effect of the OSKM genes of the old hippocampal methylome. Our results extend to the rat the evidence that viral vector-mediated delivery of the Yamanaka genes in the brain has strong regenerative effects without adverse side effects.
Evaluation of 3-D printed swabs for respiratory sampling and testing for SARS-CoV-2 during the early pandemic period
Authors: Hasan Zahra , Iqbal Angila , Ahmed Imran , Khan Moiz , Jabeen Kauser , Islam Nazneen , Khan Erum , Sayani Saleem
Published: June 2023

Appropriate collection of respiratory samples is essential for accurate diagnostic testing of respiratory pathogens such as, SARS-CoV-2. Early in the pandemic, there was a shortage of nasopharyngeal (NP) swabs and difficulty in sampling suspected cases. Therefore, we developed a 3D printed nasal swab for anterior nares, paired with in-house viral transport medium (VTM). The utility of this 3D swab kit was investigated in comparison with the standard NP commercial swab and VTM, in 200 individuals between August and September 2021. Subjects were those presenting for diagnostic testing for SARS-CoV-2 using the RT-PCR (cobas Roche assay) assay. NP samples were taken from each subject using the standard NP and 3D swabs followed by RT-PCR on paired specimens. CT values for amplification of gene targets were evaluated to determine assay parameters based on viral load cut offs of ≤ CT 35 or, ≤ CT 37. For high to medium viral loads, 3D swab based PCR testing had a sensitivity of 93%, specificity of 99%, positive predictive value (PPV) of 98.5% and negative predictive value (NPV) of 96.2% respectively. For low viral loads, 3D swab testing had a sensitivity of 88%, specificity of 99%, with a PPV of 98.5% and NPV of 93.2%.%. 3D swab sampling of anterior nares was comparable with NP sampling using standard swabs for SARS-CoV-2 specimens with a medium to high viral load. Therefore, 3D swab based sampling is a reliable and convenient local solution for collecting respiratory samples for SARS-CoV-2 diagnostic testing.
AI Segmentation of Vestibular Schwannomas with Radiomic Analysis and Clinical Correlates
Authors: Milchenko Mikhail , Cross Kevin , Smith Harrison , LaMontagne Pamela , Chakrabarty Satrajit , Varagur Kaamya , Chatterjee Rano , Bhuvic Patel , Kim Albert , Marcus Daniel
Published: June 2023

Vestibular schwannoma (VS) is a benign, slow growing tumor that may affect hearing and balance. It accounts for 7-8% of all primary brain tumors. Gamma knife radiosurgery (GKRS) is a common treatment option for VS. Magnetic resonance imaging (MRI) is employed for diagnosis, surgery planning, and follow-up of VS. Long-term follow-up determines efficacy of VS treatment. Identifying MRI-derived markers to improve management of VS is challenging. This study describes MRI processing pipeline that automatically segments VS and investigates stability and outcome predictive power of radiomic MRI features.

We first preprocessed and segmented available pre-GKRS T1-weighted post-contrast MRI images in VS patients, using a Convolutional Neural Network (CNN) developed on DeepMedic framework. Then, we compared CNN and manual segmentations, extracted radiomic features from both manual and CNN segmentations of VS, and, finally, evaluated robustness of extracted features and clinical outcome analyses based thereof.

We found that homogeneity, robust maximum intensity and sphericity were the most robust across segmentations. We also found that maximum and minimum intensities were most predictive of tumor growth across all segmentation methods and subject cohorts. We used retrospective post-GK SRS data collected in our institution to build the processing pipeline for unsupervised segmenting of VS. This pipeline is released as a Docker image integrated with XNAT (extensible neuroimaging archive toolkit), an established open research imaging database platform15. Generated segmentations can be viewed and edited in the XNAT-based online OHIF (Open Health Imaging Foundation) viewer16in real time.
WFIKKN2 is a bifunctional axon guidance cue that signals through divergent DCC family receptors
Authors: Nickerson Kelsey R. , Tom Irene , Cortés Elena , Abolafia Jane R. , Özkan Engin , Gonzalez Lino C. , Jaworski Alexander
Published: June 2023

Axon pathfinding is controlled by attractive and repulsive molecular cues that activate receptors on the axonal growth cone, but the full repertoire of axon guidance molecules remains unknown. The vertebrate DCC receptor family contains the two closely related members DCC and Neogenin with prominent roles in axon guidance and three additional, divergent members – Punc, Nope, and Protogenin – for which functions in neural circuit formation have remained elusive. We identified a secreted Punc/Nope/Protogenin ligand, WFIKKN2, which guides mouse peripheral sensory axons through Nope-mediated repulsion. In contrast, WFIKKN2 attracts motor axons, but not via Nope. These findings identify WFIKKN2 as a bifunctional axon guidance cue that acts through divergent DCC family members, revealing a remarkable diversity of ligand interactions for this receptor family in nervous system wiring.

One-Sentence Summary

WFIKKN2 is a ligand for the DCC family receptors Punc, Nope, and Prtg that repels sensory axons and attracts motor axons.
CRISPR/Cas9-mediated Generation ofCOL7A1-deficient Keratinocyte Model of Recessive Dystrophic Epidermolysis Bullosa
Authors: Alipour Farzad , Ahmadraji Mana , Yektadoust Elham , Mohammadi Parvaneh , Baharvand Hossein , Basiri Mohsen
Published: June 2023

Objective

Recessive dystrophic epidermolysis bullosa (RDEB) is a genetic skin fragility and ultimately lethal blistering disease caused by mutations in theCOL7A1gene which is responsible for coding type VII collagen. Investigating the pathological mechanisms and novel candidate therapies for RDEB could be fostered by new cellular models. Here, we developed multiple immortalizedCOL7A1-deficient keratinocyte cell lines using CRISPR/Cas9 technology as RDEB cellular model.

Materials and Methods

In this experimental study, we used transient transfection to expressCOL7A1-targeting gRNA and Cas9 in HEK001 immortalized keratinocyte cell line followed by enrichment with fluorescent-activated cell sorting (FACS) via GFP expressing cells (GFP+HEK001). Homogenous single-cell clones were then isolated, genotyped, and evaluated for type VII collagen expression. We performed a scratch assay to confirm the functional effect ofCOL7A1knockout.

Results

We achieved 46.1% (p < 0.001) efficiency of indel induction in the enriched transfected cell population. Except for 4% of single nucleotide insertions, the remaining indels were deletions of different sizes. Out of nine single clones expanded, two homozygous and two heterozygousCOL7A1-deficient cell lines were obtained with defined mutation sequences. No off-target effect was detected in the knockout cell lines. Immunostaining and western blot analysis showed the lack of type VII collagen (COL7A1) protein expression in these cell lines. We also showed thatCOL7A1-deficient cells had higher motility compared with their wild-type counterparts.

Conclusion

We reported the first isogenic immortalizedCOL7A1-deficient keratinocyte lines that provide a useful cell culture model to investigate aspects of RDEB biology and potential therapeutic options.
Gastruloid-derived Primordial Germ Cell-like Cells (Gld-PGCLCs) develop dynamically within integrated tissues
Authors: Cooke Christopher B. , Barrington Christopher , Baillie-Benson Peter , Nichols Jennifer , Moris Naomi
Published: June 2023

Primordial Germ Cells (PGCs) are the early embryonic precursors of gametes - sperm and egg cells. PGC-like cells (PGCLCs) can currently be derivedin vitrofrom pluripotent cells exposed to signalling cocktails and aggregated into large embryonic bodies, but these do not recapitulate the native embryonic environment during PGC formation. Here we show that mouse gastruloids, a three-dimensionalin vitromodel of gastrulation, contain a population of Gastruloid-derived PGC-like cells (Gld-PGCLCs) that resemble early PGCsin vivo. Importantly, the conserved organisation of mouse gastruloids leads to coordinated spatial and temporal localisation of Gld-PGCLCs relative to surrounding somatic cells, even in the absence of specific exogenous PGC-specific signalling or extraembryonic tissues. In gastruloids, self-organised interactions between cells and tissues, including the endodermal epithelium, enables the specification and subsequent maturation of a pool of Gld-PGCLCs. As such, mouse gastruloids represent a new source of PGCLCsin vitroand, due to their inherent co-development, serve as a novel model to study the dynamics of PGC development within integrated tissue environments.
Revealing Chloroquine’s Antimalarial Mechanism: The Suppression of Nucleation Events during Heme to Hemozoin Transformation
Authors: Singh Rahul , Singh Rashmi , Srihari Velaga , Makde Ravindra D.
Published: June 2023

Malaria parasites generate toxic heme during hemoglobin digestion, which is neutralized by crystallizing into inert hemozoin (β-hematin). Chloroquine blocks this detoxification process, resulting in heme-mediated toxicity in malaria parasites. However, the exact mechanism of chloroquine’s action remains unknown. This study investigates the impact of chloroquine on the transformation of heme into β-hematin. The results show that chloroquine does not completely halt the transformation process but rather slows it down. Additionally, chloroquine complexation with free heme does not affect substrate availability or inhibit β-hematin formation. SEM and XRD studies indicate that the size of β-hematin crystal particles and crystallite increases in the presence of chloroquine, suggesting that chloroquine does not impede crystal growth. These findings suggest that chloroquine delays hemozoin production by perturbing the nucleation events of crystals and/or the stability of crystal nuclei. Thus, contrary to prevailing beliefs, this study provides a new perspective on the working mechanism of chloroquine.
Prolonged exposure to hypergravity increases number and size of cells and enhances lignin deposition in the stem ofArabidopsis thaliana(L.) Heynh
Authors: Shinohara Hironori , Muramoto Masaki , Tamaoki Daisuke , Kamachi Hiroyuki , Inoue Hiroshi , Kume Atsushi , Karahara Ichirou
Published: June 2023

We have performed a lab-based hypergravity cultivation experiment using a centrifuge equipped with a lighting system and examined long-term effects of hypergravity on the development of the main axis (stem) of the Arabidopsis (Arabidopsis thaliana(L.) Heynh.) primary inflorescence. Plants grown under 1 ×g(gravitational acceleration on Earth) conditions for 20-23 days and having the first visible flower bud were exposed to hypergravity at 8 ×gfor 10 days. We analyzed the effect of prolonged hypergravity conditions on growth, lignin deposition, and tissue anatomy of the main axis. As a result, the length of the main axis decreased and cross-sectional area, dry mass per unit length, cell number, lignin content of the main axis significantly increased under hypergravity. Lignin content in the rosette leaves also increased when they were exposed to hypergravity during their development. Except for interfascicular fibers, cross-sectional areas of the tissues composing the internode significantly increased under hypergravity in most type of the tissues in the basal part than the apical part of the main axis, indicating that the effect of hypergravity is more pronounced in the basal part than the apical part. The number of cells in fascicular cambium and xylem significantly increased under hypergravity both in the apical and basal internodes of the main axis, indicating a possibility that hypergravity stimulates procambium activity to produce xylem element more than phloem element. The main axis was suggested to be strengthened through changes in its morphological characteristics as well as lignin deposition under prolonged hypergravity conditions.
Spindle Chirp and other Sleep Oscillatory Features in Young Children with Autism
Authors: Cumming D , Kozhemiako N , Thurm AE , Farmer CA , Purcell SW , Buckley AW
Published: June 2023

Objectives

To determine whether spindle chirp and other sleep oscillatory features differ in young children with and without autism.

Methods

Automated processing software was used to re-assess an extant set of polysomnograms representing 121 children (91 with autism [ASD], 30 typically-developing [TD]), with an age range of 1.35-8.23 years. Spindle metrics, including chirp, and slow oscillation (SO) characteristics were compared between groups. SO and fast and slow spindle (FS, SS) interactions were also investigated. Secondary analyses were performed assessing behavioural data associations, as well as exploratory cohort comparisons to children with non-autism developmental delay (DD).

Results

Posterior FS and SS chirp was significantly more negative in ASD than TD. Both groups had comparable intra-spindle frequency range and variance. Frontal and central SO amplitude were decreased in ASD. In contrast to previous manual findings, no differences were detected in other spindle or SO metrics. The ASD group displayed a higher parietal coupling angle. No differences were observed in phase-frequency coupling. The DD group demonstrated lower FS chirp and higher coupling angle than TD. Parietal SS chirp was positively associated with full developmental quotient.

Conclusions

For the first time spindle chirp was investigated in autism and was found to be significantly more negative than in TD in this large cohort of young children. This finding strengthens previous reports of spindle and SO abnormalities in ASD. Further investigation of spindle chirp in healthy and clinical populations across development will help elucidate the significance of this difference and better understand this novel metric.
The critical role of spatio-temporal control in combinatorial chemo- and magnetic hyperthermia thermo-therapy: ‘the where’, ‘the how’ and ‘the when’
Authors: García-Hevia Lorena , Magalhães Andreia Patrícia , Genicio Nuria , Casafont Íñigo , Costa da Silva Milene , Fanarraga Mónica López , Bañobre-López Manuel , Gallo Juan
Published: June 2023

Combinatorial treatments hold the key to the future of cancer treatment as they enhance therapeutic indexes by inducing synergistic effects and reducing resistance processes, while often providing a safer option for patients with fewer off-target effects. However, combinatorial treatments bring extra problems to cancer management not only derived from the actual compatibility of the treatments, but also from their hands-on administration. Operational parameters such as administration order and dosing (dose, spacing) have to be optimized in order to positively impact patient prognosis. Here we present a systematic study on the optimization and the importance of these parameters within the framework of a combinatorial chemo-/thermo-therapy. Parameters like ‘where’, ‘how’ and ‘when’ are investigated in detail. Furthermore, we delve into the underlying biochemical mechanisms driving the observed effects through transcriptome analysis.
Machine learning and phylogenetic models identify predictors of genetic variation in Neotropical amphibians
Authors: Amador Luis , Arroyo-Torres Irvin , Barrow Lisa N.
Published: June 2023

Aim

Intraspecific genetic variation is key for adaptation and survival in changing environments and is known to be influenced by many factors, including population size, migration, and life history traits. We investigated genetic variation within Neotropical amphibian species to provide insights into how natural history traits, phylogeny, climatic, and geographic characteristics influence intraspecific diversity.

Location

Neotropics.

Taxon

Amphibians.

Methods

We assembled datasets using open-access databases for natural history traits, genetic sequences, phylogenetic trees, climatic, and geographic data. For each species, we calculated overall nucleotide diversity (π) and tested for isolation by distance (IBD) and isolation by environment (IBE). We then identified predictors of π, IBD, and IBE using Random Forest (RF) regression or RF classification. To incorporate phylogenetic relationships, we fitted phylogenetic generalized linear mixed models (PGLMMs) to predict π, IBD, and IBE.

Results

We compiled 4,052 mitochondrial DNA sequences from 256 amphibian species (230 frogs and 26 salamanders), georeferencing 2,477 sequences from 176 species that were not linked to occurrence data. RF regressions and PGLMMs were congruent in identifying range size and precipitation (σ) as the most important predictors of π. RF classification and PGLMMs identified minimum elevation as an important predictor of IBD, and maximum latitude and precipitation (σ) as the best predictors of IBE.

Main conclusions

This study unified machine learning and phylogenetic methods and identified predictors of genetic variation in Neotropical amphibians. This approach was valuable to determine which predictors were congruent between methods. We found that species with small ranges or living in zones with less variable precipitation tended to have low genetic diversity. We also showed that Western Mesoamerica, Andes, and Atlantic Forest biogeographic units harbor high diversity across many species that should be prioritized for protection. These results could play a key role in the development of conservation strategies for Neotropical amphibians.
SoyDNGP: A Web-Accessible Deep Learning Framework for Genomic Prediction in Soybean Breeding
Authors: Gao Pengfei , Zhao Haonan , Luo Zheng , Lin Yifan , Li Yaling , Kong Fanjiang , Fang Chao , Wang Xutong
Published: June 2023

Soybean is a globally significant crop, playing a vital role in human nutrition and agriculture. Its complex genetic structure and wide trait variation, however, pose challenges for breeders and researchers aiming to optimize its yield and quality. Addressing this biological complexity requires innovative and accurate tools for trait prediction. In response to this challenge, we have developed SoyDNGP, a Convolutional Neural Networks (CNN)-based model that offers significant advancements in the field of soybean trait prediction. Compared to existing methods, such as DeepGS and DNNGP, SoyDNGP boasts a distinct advantage due to its lower parameter volume and superior predictive accuracy. Through rigorous performance comparison, including prediction accuracy and model complexity, SoyDNGP consistently outperformed its counterparts. Furthermore, it effectively predicted complex traits with remarkable precision, demonstrating robust performance across different sample sizes and trait complexities. We also tested the versatility of SoyDNGP across multiple crop species, including Cotton, Maize, Rice, and Tomato. Our results showed its consistent and comparable performance, emphasizing SoyDNGP’s potential as a versatile tool for genomic prediction across a broad range of crops. To enhance its accessibility to users without extensive programming experience, we have designed a user-friendly web server, available athttp://xtlab.hzau.edu.cn/SoyDNGP. The server provides two primary features: ‘Trait Lookup’, offering users the ability to access pre-existing trait predictions for over 500 soybean accessions, and ‘Trait Prediction’, allowing for the upload of VCF files for trait estimation. By providing a high-performing, accessible tool for trait prediction and genomic analysis, SoyDNGP opens up new possibilities in the quest for efficient and optimized soybean breeding.
Herpes-like viral elements and universal subtelomeric ribosomal RNA genes in a chromosome-scale thraustochytrid genome assembly
Authors: Collier Jackie L. , Rest Joshua S. , Gallot-Lavallée Lucie , Lavington Erik , Kuo Alan , Jenkins Jerry , Plott Chris , Pangilinan Jasmyn , Daum Chris , Grigoriev Igor V. , Filloramo Gina V. , Novák Vanclová Anna M. G. , Archibald John M.
Published: June 2023

We used long-read sequencing to produce a telomere-to-telomere genome assembly for the heterotrophic stramenopile protistAurantiochytrium limacinumMYA-1381. Its ∼62 Mbp nuclear genome comprises 26 linear chromosomes with a novel configuration: subtelomeric rDNAs are interspersed with long repeated sequence elements denoted as LOng REpeated - TElomere And Rdna Spacers (LORE-TEARS). These repeats may play a role in chromosome end maintenance. A ∼300 Kbp circular herpesvirus-like genomic element is present at a high copy number. A 269 Kbp related virus-like element was found to reside between two complete sets of rRNA and LORE-TEAR sequences on one end of chromosome 15, indicating recent recombination between the viral and nuclear genome. Our data reveal new types of giant endogenous viral elements originating from herpes-like viruses and existing as either ‘stand-alone’ or integrated elements.
Modelling Human Post-Implantation Development via Extra-Embryonic Niche Engineering
Authors: Hislop Joshua , Alavi Amir , Song Qi , Schoenberger Rayna , Keshavarz F. Kamyar , LeGraw Ryan , Velazquez Jeremy , Mokhtari Tahere , Taheri Mohammad Nasser , Rytel Matthew , de Sousa Lopes Susana M Chuva , Watkins Simon , Stolz Donna , Kiani Samira , Sozen Berna , Bar-Joseph Ziv , Ebrahimkhani Mo R.
Published: June 2023

Implantation of the human embryo commences a critical developmental stage that comprises profound morphogenetic alteration of embryonic and extra-embryonic tissues, axis formation, and gastrulation events. Our mechanistic knowledge of this window of human life remains limited due to restricted access toin vivosamples for both technical and ethical reasons. Additionally, human stem cell models of early post-implantation development with both embryonic and extra-embryonic tissue morphogenesis are lacking. Here, we present iDiscoid, produced from human induced pluripotent stem cells via an engineered a synthetic gene circuit. iDiscoids exhibit reciprocal co-development of human embryonic tissue and engineered extra-embryonic niche in a model of human post-implantation. They exhibit unanticipated self-organization and tissue boundary formation that recapitulates yolk sac-like tissue specification with extra-embryonic mesoderm and hematopoietic characteristics, the formation of bilaminar disc-like embryonic morphology, the development of an amniotic-like cavity, and acquisition of an anterior-like hypoblast pole and posterior-like axis. iDiscoids offer an easy-to-use, high-throughput, reproducible, and scalable platform to probe multifaceted aspects of human early post-implantation development. Thus, they have the potential to provide a tractable human model for drug testing, developmental toxicology, and disease modeling.
Local, Quantitative Morphometry of Fibroproliferative Lung Injury using Laminin
Authors: Cox Brendan P. , Hannan Riley T. , Batrash Noora , Sturek Jeffrey M.
Published: June 2023

Investigations into the mechanisms of injury and repair in pulmonary fibrosis require consideration of the spatial heterogeneity inherent in the disease. Most scoring of fibrotic remodeling in preclinical animal models rely on the modified Ashcroft score, which is a semi-quantitative scoring rubric of macroscopic resolution. The obvious limitations inherent in manual pathohistological grading have generated an unmet need for unbiased, repeatable scoring of fibroproliferative burden in tissue. Using computer vision approaches on immunofluorescent imaging of the extracellular matrix (ECM) component laminin, we generate a robust and repeatable quantitative remodeling scorer (QRS). In the bleomycin lung injury model, QRS shows significant agreement with modified Ashcroft scoring with a significant Spearman coefficient r=0.768. This antibody-based approach is easily integrated into larger multiplex immunofluorescent experiments, which we demonstrate by testing the spatial apposition of tertiary lymphoid structures (TLS) to fibroproliferative tissue. The tool reported in this manuscript is available as a standalone application which is usable without programming knowledge.
MEK1/2-Targeting PROTACs Promote the Collateral Degradation of CRAF in KRAS Mutant Cells
Authors: Herrera-Montávez Carlos , Kurimchak Alison M. , Hu Xiaoping , Hu Jianping , Jin Jian , Duncan James S.
Published: June 2023

Activation of the RAS/MAPK pathway is one of the most frequent alterations in cancer; yet therapies targeting this pathway have shown limited benefit due to drug resistance. For example, resistance to MEK inhibitors in KRAS mutant cancer cells occurs due to relief of a negative feedback that promotes CRAF activation and CRAF-MEK protein interactions, bypassing MEK inhibition. Consequently, combining CRAF and MEK inhibitors for KRAS mutant cancer is an area of intense research. Here, we discovered that the MEK1/2 PROTAC (Proteolysis-Targeting Chimeras) degrader, MS934, caused collateral degradation of CRAF in KRAS mutant cells via a PROTAC-mechanism, offering a new strategy to simultaneously degrade both CRAF and MEK1/2. Importantly, CRAF has been shown to have essential kinase-independent growth and survival functions outside the MEK-ERK pathway in KRAS mutant cells, making CRAF degradation an attractive therapeutic avenue. Despite this, to the best of our knowledge, no CRAF PROTACs have been published. Importantly, our discovery of MS934 as a first-in-class dual CRAF/MEK degrader provides a newfound approach to overcome MEK inhibitor resistance due to relief of negative feedback, as well as block CRAF kinase-independent functions in KRAS mutant cells.
Expanding the list of sequence-agnostic enzymes for chromatin conformation capture assays with S1 nuclease
Authors: Gridina Maria , Popov Andrey , Shadskiy Artem , Torgunakov Nikita , Kechin Andrey , Khrapov Evgeny , Ryzhkova Oxana , Filipenko Maxim , Fishman Veniamin
Published: June 2023

This study presents a novel approach for mapping global chromatin interactions using S1 nuclease, a sequence-agnostic enzyme. We develop and outline a protocol that leverages S1 nuclease’s ability to effectively introduce breaks into both open and closed chromatin regions, allowing for comprehensive profiling of chromatin properties. Our S1 Hi-C method enables the preparation of high-quality Hi-C libraries, marking a significant advancement over previously established DNase I Hi-C protocols. Moreover, S1 nuclease’s capability to fragment chromatin to mono-nucleosomes suggests the potential for mapping the three-dimensional organization of the genome at high resolution. This methodology holds promise for an improved understanding of chromatin state-dependent activities and may facilitate the development of new genomic methods.
Disentangling the cascading effects of Grapevine Red Blotch Virus infection on vine physiology
Authors: Copp Cody R. , DeShields Joseph B. , Kar Suraj , Kirk Claire , Clark Ricky , Stowasser Marianna , KC Achala N. , Levin Alexander D.
Published: June 2023

Grapevine Red Blotch Virus is a major grapevine pathogen and is associated with reduced carbon assimilation and delayed berry ripening inVitis viniferaL. Recent work suggests that the virus alters leaf carbon metabolism prior to emergence of visible symptoms. Therefore, diurnal and seasonal measurements were conducted to quantify changes in leaf carbon balance and to elucidate the chronology of symptom progression in leaves and fruit. Healthy and infected vines were assayed in a commercial vineyard during which leaf water relations, photosynthesis, and nonstructural carbohydrates were measured. Additionally, sugar and anthocyanin accumulation in the fruit were monitored at the end of the season to characterize the impact of the virus on ripening. Virus infection significantly reduced carbon assimilation pre- and postveraison, but the impact was more pronounced postveraison and during the afternoon when vine water status was the lowest. Similarly, virus infection significantly increased leaf starch concentration pre- and postveraison, but increased leaf starch in infected vines was detected two weeks prior to veraison. Virus infection had the greatest impact on obstructing leaf carbon export postveraison, especially during the afternoon. The virus had no impact on chlorophyll fluorescence, indicating there was no sustained photosystem impairment and suggesting that changes in chlorophyll fluorescence were a transient response to reduced carbon assimilation and export. This study provides evidence that reduced carbon export constitutes a feedback inhibition response to accumulation of leaf starch prior to the appearance of visible symptoms or impacts to ripening, which may aid earlier detection of the virus.
Characterization of genetic and molecular tools for studying the endogenous expression ofLactate dehydrogenaseinDrosophila melanogaster
Authors: Rai Madhulika , Carter Sarah M. , Shefali Shefali A. , Chawla Geetanjali , Tennessen Jason M.
Published: June 2023

Drosophila melanogasterlarval development relies on a specialized metabolic state that utilizes carbohydrates and other dietary nutrients to promote rapid growth. One unique feature of the larval metabolic program is that Lactate Dehydrogenase (Ldh) activity is highly elevated during this growth phase when compared to other stages of the fly life cycle, indicating that Ldh serves a key role in promoting juvenile development. Previous studies of larval Ldh activity have largely focused on the function of this enzyme at the whole animal level, however,Ldhexpression varies significantly among larval tissues, raising the question of how this enzyme promotes tissue-specific growth programs. Here we characterize two transgene reporters and an antibody that can be used to studyLdhexpressionin vivo. We find that all three tools produce similarLdhexpression patterns. Moreover, these reagents demonstrate that the larvalLdhexpression pattern is complex, suggesting the purpose of this enzyme varies across cell types. Overall, our studies validate a series of genetic and molecular reagents that can be used to study glycolytic metabolism in the fly.