bluuebunny/crossref_metadata_2025 huggingface dataset:
A Propensity Score–Matched Comparison of Perioperative Outcomes in Prepectoral Smooth Versus Textured Tissue Expander Breast Reconstruction
Authors: Perez Kevin , Rodnoi Pope , Teotia Sumeet S. , Haddock Nicholas T.
Published: May 2023

Introduction

Textured tissue expanders (TEs) had previously gained popularity due to minimizing expander migration, rotation, and capsule migration. Recent studies, though, have revealed increased risk of anaplastic large-cell lymphoma associated with certain macrotextured implants, prompting surgeons at our institution to switch to smooth TEs; evaluation is thus required for specific viability and similarity of outcomes of smooth TEs. Our study aims to evaluate perioperative complications in prepectoral placement of smooth versus textured TEs.

Methods

Our retrospective study evaluated perioperative outcomes of patients who underwent bilateral prepectoral TE placement, with either smooth or textured TE, at an academic institution between 2017 and 2021 performed by 2 reconstructive surgeons. The perioperative period was defined as the interval between expander placement until conversion to flap/implant or removal of TE due to complications. Our primary outcomes included hematoma, seroma, wounds, infection, unspecified redness, total number of complications, and returns to operating room secondary to complications. Secondary outcomes included time to drain removal, total number of expansions, hospital length of stay, length of time until the next breast reconstruction procedure, next breast reconstruction procedure, and number of expansions.

Results

Two hundred twenty-two patients were evaluated in our study (141 textured, 81 smooth). After propensity matching (71 textured, 71 smooth), our univariate logistic regression showed no significant difference in perioperative complications between smooth and textured expanders (17.1% vs 21.1%;P= 0.396) or complications that required a return to the operating room (10.0% vs 9.2%;P= 0.809). No significant differences were noted for hematoma, seroma, infections, unspecified redness, or wounds between both groups. A significant difference was noted in days to drain out (18.57 ± 8.17 vs 20.13 ± 0.07,P= 0.001) and type of the next breast reconstruction procedure (P< 0.001). Our multivariate regression showed that breast surgeon, hypertension, smoking status, and mastectomy weight were significant for increased risk for complications.

Conclusion

Our study demonstrates similar rates and effectiveness of smooth versus textured TE when used for prepectoral placement, making smooth TEs a safe and valuable alternative for breast reconstruction because of their decreased risk of anaplastic large-cell lymphoma compared with textured TEs.
Postoperative Dysnatremia in Pediatric Patients Undergoing Palatoplasty
Authors: Lonfat Ewyanna , La Scala Giorgio C.
Published: May 2023

Objective:

Identifying predisposing factors to dysnatremia to improve perioperative care after cleft surgery.

Design:

Retrospective case series. Patient data were obtained through the electronic medical records of the hospital.

Setting:

Tertiary care university hospital.

Patients:

The inclusion criterion was the measurement of an abnormal natremia value, defined as Na >150 or <130 mmol/l after a cleft lip or cleft palate repair procedure. The exclusion criterion was natremia between 131 and 149 mmol/l.

Results:

Natremia measurements were available for 215 patients born between 1995 and 2018. Five patients presented with postoperative dysnatremia. Several predisposing factors to dysnatremia have been identified: drugs, infection, administration of intravenous fluids, and postoperative syndrome of inappropriate antidiuretic hormone secretion. Although the hospital environment contributes to dysnatremia development, the fact that only patients undergoing cleft palate repair develop natremia anomalies suggests that this surgery may be itself a risk factor.

Conclusion:

Children undergoing palatoplasty may be at higher risk to develop postoperative dysnatremia. Early recognition of symptoms and risk factors, postoperative monitoring, and prompt treatment of dysnatremia diminish the risk of neurological complications.
Diagnosis and Treatment of Rare Adult Embryonal Rhabdomyosarcoma in Maxillary Sinus
Authors: Liu Yue , Liu Yan , Wen Lian Ji , Yu Dan
Published: May 2023

Objective:

To investigate the clinicopathological features, imaging features, diagnosis, and prognosis of embryonal rhabdomyosarcoma (ERMS) in the maxillary sinus.

Methods:

The detailed clinical data of rare patients with embryonal ERMS of maxillary sinus admitted to our hospital were retrospectively analyzed, and the embryonal ERMS was confirmed by pathological examination and immunohistochemistry, and the relevant literature was reviewed.

Results:

A 58-year-old man was admitted to the hospital with the chief complaint of “numbness and swelling of the left cheek for 1 and a half months”. Blood routine, biochemistry, paranasal sinus computed tomography, and magnetic resonance imaging were performed after admission, and the pathology showed ERMS. At present, it is generally in good condition. Pathological examination showed that the cells were all small and round. Immunohistochemistry showed Desmin (+) and Ki-67 (+70%).

Conclusion:

The early symptoms of ERMS of the maxillary sinus are atypical and diverse, with a high degree of malignancy, rapid progression, strong invasiveness, and poor prognosis. Early diagnosis and treatment should be based on clinical characteristics, imaging examination, and immunohistochemical results.
Slit Ventricle Syndrome
Authors: Yan Xuelei , Zheng Junfei , Tao Xiaowei , Ma Yongqian , Qin Shiqiang
Published: May 2023

Slit ventricle syndrome (SVS) is a complication after ventriculoperitoneal shunt (VPS) or cystoperitoneal shunt(CPS), mostly due to excessive drainage of cerebrospinal. The disease is most often seen in children and has a complex pathogenesis. Clinical manifestations are mainly intermittent headache, slow refilling of the shunt reservoir, and slit-like ventricles on imaging. Surgery is the main treatment. We present a 22-year-old female patient with a previous 14-year history of CPS. The patient recently presented with typical symptoms but her ventricular morphology was normal. We performed VPS after diagnosis of SVS. After the surgery, the patient's symptoms improved and her condition was stable.
Paramedian Lateral-angled Mandibulotomy for Resection of Squamous Cell Carcinoma in the Oral Cavity
Authors: Han Xiaodong , Shao Xiaojun , Lin Xiaozhen
Published: May 2023

Mandibulotomy provides good access for monobloc compartmental resection of squamous cell carcinoma in the proper oral cavity. Various designs of osteotomy have been reported, but few of them have considered the local anatomical conditions, and thus related complications occasionally happen. We devised a paramedian lateral-angled mandibulotomy to reduce the side injuries.
Testing of Different Scanning Protocols Used for Precise 3D-printing of Mandibular Models
Authors: Micic Milutin , Jadzic Jelena , Milenkovic Petar , Antic Svetlana , Antonijevic Djordje , Djuric Marija
Published: May 2023

Multidetector computed tomography (MDCT) is often necessary to manufacture 3D-printed medical models (MMs) required for mandibular restoration due to trauma or malignant tumor. Although cone-beam computed tomography (CBCT) is a preferable method of mandibular imaging, additional scanning is often unjustified. To test whether a single radiologic protocol could be used for mandibular reconstructions, the human mandible was scanned with 6 MDCT and 2 CBCT protocols and later 3D-printed using a fused-deposition modelling technique. Then, we assessed linear measures on the mandible and compared them with MDCT/CBCT digital scans and 3D-printed MMs. Our data revealed that CBCT0.25 was the most precise protocol for manufacturing 3D-printed mandibular MMs, which is expected considering its voxel size. However, we noted that CBCT0.35 and Dental2.0H60s MDCT protocols were of comparable accuracy, indicating that this MDCT protocol could be a single radiologic protocol used to scan both donor and recipient regions required for mandibular reconstruction.
Development and Validation of Prediction Models and Risk Calculators for Post-Hepatectomy Liver Failure and Postoperative Complications using a Diverse International Cohort of Major Hepatectomies
Authors: Wang Jaeyun Jane , Feng Jean , Gomes Camilla , Calthorpe Lucia , Ashraf Ganjouei Amir , Romero-Hernandez Fernanda , Benedetti Cacciaguerra Andrea , Hibi Taizo , Abdelgadir Adam Mohamed , Alseidi Adnan , Abu Hilal Mohammad , Rashidian Nikdokht ,   International Post-Hepatectomy Liver Failure Study Group
Published: May 2023

Objective:

The study aim was to develop and validate models to predict clinically significant post-hepatectomy liver failure (PHLF) and serious complications (a Comprehensive Complication Index® [CCI®]>40) using preoperative and intraoperative variables.

Summary Background Data:

PHLF is a serious complication after major hepatectomy but does not comprehensively capture a patient’s postoperative course. Adding the CCI® as an additional metric can account for complications unrelated to liver function.

Methods:

The cohort included adult patients who underwent major hepatectomies at twelve international centers (2010–2020). After splitting the data into training and validation sets (70:30), models for PHLF and a CCI®>40 were fit using logistic regression with a lasso penalty on the training cohort. The models were then evaluated on the validation dataset.

Results:

Among 2,192 patients, 185 (8.4%) had clinically significant PHLF and 160 (7.3%) had a CCI®>40. The PHLF model had an area under the curve (AUC) of 0.80, calibration slope of 0.95, and calibration-in-the-large of −0.09, while the CCI® model had an AUC of 0.76, calibration slope of 0.88, and calibration-in-the-large of 0.02. When the models were provided only preoperative variables to predict PHLF and a CCI®>40, this resulted in similar AUCs of 0.78 and 0.71, respectively. Both models were used to build two risk calculators with the option to include or exclude intraoperative variables (PHLF Risk Calculator; CCI®>40 Risk Calculator).

Conclusions:

Using an international cohort of major hepatectomy patients, we used preoperative and intraoperative variables to develop and internally validate multivariable models to predict clinically significant PHLF and a CCI®>40 with good discrimination and calibration.
Comparative analysis of clinical breakpoints (CB), normalised resistance interpretation (NRI), and epidemiological cut-offs (ECOFFS), in interpreting antimicrobial resistance of E. coli isolates originating from poultry in different farm types in Tanzania.
Authors: Maganga Ruth , Sindiyo Emmanuel , Musyoki Victor Moses , Shirima Gabriel , Mmbaga Blandina T.
Published: May 2023

Existing breakpoint guidelines are not optimal for interpreting antimicrobial resistance data from animal studies and low-income countries, and therefore their utility for analysing such data is limited. There is need to integrate diverse data sets, such as those from low-income populations and animals, to improve data interpretation. There is very limited research on the relative merits of clinical breakpoints, epidemiological cut-offs, and normalised resistance interpretation breakpoints in interpreting microbiological data, particularly in animal studies and studies from low-income countries. The aim of this study was to compare antimicrobial resistance in E. coli isolates using ECOFFS, CLSI, and NRI breakpoints. A total of 69 non-repetitive poultry isolates were selected for investigation based on lactose fermentation on MacConkey agar and subsequent identification and confirmation as E. coli using chromogenic agar and uidA Polymerase Chain Reaction. Kirby Bauer disc diffusion technique was used for susceptibility testing. For each antimicrobial agent, inhibition zone diameters were measured, and ECOFFs, CLSI, and NRI bespoke breakpoints used for resistance interpretation. According to the interpretation of all breakpoints except ECOFFs, tetracycline resistance was significantly higher (TET) (67.8% – 69.5%), than ciprofloxacin (CIPRO) (18.6%– 32.2%), imipenem (IMI) (3.4% – 35%), and ceftazidime (CEF) (1.7% – 45.8%). Prevalence estimates of antimicrobial resistance (AMR) using CLSI and NRI bespoke breakpoints did not differ for CEF (1.7% CB and 1.7% COWT), IMI (3.4% CB and 4.0% COWT) and TET (67.8% CB and 69.5% COWT). However, with ECOFFs, antimicrobial resistance estimates for CEF, IMI, and CIP were significantly higher (45.8%, 35.6%, and 64.4%, respectively; P < 0.01). Across all the three breakpoints, resistance to ciprofloxacin varied significantly (32.2% CB, 64.4% ECOFFs, and 18.6% COWT). Antimicrobial resistance interpretation is influenced by the breakpoint used, necesscitating further standardisation, especially for microbiological breakpoints, in order to harmonise outputs. The AMR ECOFFs estimates in the present study were significantly higher compared to CLSI and NRI.
Case Report: A missed case of chronic Q fever Infective Endocarditis demonstrating the ongoing diagnostic challenges
Authors: Grey Victoria , Simos Peter , Runnegar Naomi , Eisemann Jared
Published: May 2023

The diagnosis of chronic Q fever is often difficult to for clinicians to make, particularly in the presence of a second pathology. In addition to the chronic constitutional symptoms the most common manifestations of chronic Q fever include infective endocarditis and endovascular infection. We describe a case of prosthetic valve infective endocarditis caused by both Streptococcus sanguinis and Coxiella burnetti on a background of a previous aortic graft and bioprosthetic aortic valve replacement two years earlier. The diagnosis of chronic Q fever infective endocarditis was delayed because the significance of the abnormal valve histology from the patient’s previous surgery was initially overlooked. It was only after the patient had relapsed on appropriate therapy for the S. sanguinis prosthetic valve endocarditis that a subsequent review of the operative valve histology, along with the patient’s epidemiological risk factors led to consideration of other causes of culture negative infective endocarditis. Histological examination of the valve tissue had shown exophytic fibrin vegetations and acute inflammation. Further clinical assessment revealed previous exposure to Q fever and Coxiella burnetti DNA was detected via Polymerase Chain Reaction on the valve tissue. Q fever infective endocarditis must be considered if valves are inflamed or have vegetations with a subsequent negative culture. It should also still be considered in the presence of an alternative bacteraemia if the patient has risk factors for exposure.
Effects of short-term restriction of animal products on blood biomarkers and cardiovascular disease risk
Authors: Loizidou Eleni M. , Simistiras Alexandros , Barmpounakis Petros , Glentis Stavros , Dimopoulos Alexandros , Anezaki Maria , Kontoyiannis Ioannis , Demiris Nikolaos , Rouskas Pavlos , Scarmeas Nikolaos , Yannakoulia Mary , Rouskas Konstantinos , Dimas Antigone S.
Published: May 2023

Dietary interventions constitute a means of untapped potential for the prevention and management of diseases including cardiovascular disease (CVD) and inflammatory disorders. The extent to which dietary modification can contribute to disease prevention and treatment however remains unclear. Here, we addressed the effects of a dietary pattern, involving periodic animal product restriction (APR), on markers of human health. We compared blood biomarkers, complete blood counts, anthropometric traits and blood pressure between two dietary states for a unique group of 200 individuals from Greece, who alternate between omnivory and APR, for religious reasons. We used linear mixed effects models to report changes in measured traits between dietary states. Short-term APR was linked to a reduction in levels of total and LDL cholesterol [both β=-0.3, p<0.0001], to a 72% decrease in CRP concentration [β=-1.3, p=0.001], to reduced platelet counts [β=-9.8, p<0.0001] and to a concurrent reduction in CVD risk (5.3% to 4.9%, p=0.02), shifting APR-practicing individuals from a high to a low-to-moderate risk group. Beneficial changes were recorded for markers of renal and liver function, with the exception of ALP [β=2.5, p<0.0001]. These changes were not detected in a control group of 211 continuously omnivorous individuals. Overall, short-term APR was linked to a biomarker profile associated with positive effects on health, suggesting that even modest dietary modifications can be harnessed towards disease prevention.
Automated multi-scale computational pathotyping (AMSCP) of inflamed synovial tissue
Authors: Bell Richard D. , Brendel Matthew , Konnaris Maxwell , Xiang Justin , Otero Miguel , Fontana Mark A. ,   Accelerating Medicines Partnership Rheumatoid Arthritis and Systemic Lupus Erythematosus (AMP RA/SLE) Consortium, DiCarlo Edward , Anolik Jennifer , Donlin Laura , Orange Dana , Mark Kenney H. , Schwarz Edward M. , Ivashkiv Lionel B , Wang Fei
Published: May 2023

Rheumatoid arthritis (RA) is a complex immune-mediated inflammatory disorder in which patients suffer from inflammatory-erosive arthritis. Recent advances on histopathology heterogeneity of RA pannus tissue revealed three distinct phenotypes based on cellular composition (pauci-immune, diffuse and lymphoid), suggesting distinct etiologies that warrant specific targeted therapy. Thus, cost-effective alternatives to clinical pathology phenotyping are needed for research and disparate healthcare. To this end, we developed an automated multi-scale computational pathotyping (AMSCP) pipeline with two distinct components that can be leveraged together or independently: 1) segmentation of different tissue types to characterize tissue-level changes, and 2) cell type classification within each tissue compartment that assesses change across disease states. Initial training and validation were completed on 264 knee histology sections from mice with TNF-transgenic (n=233) and injected zymosan induced (n=32) inflammatory arthritis. Peak tissue segmentation performance with a frequency weighted mean intersection over union was 0.94 ± 0.01 and peak cell classification F1 was 0.83 ± 0.12.

We then leveraged these models and adapted them to analyze RA pannus tissue clinically phenotyped as pauci-immune (n=5), diffuse (n=28) and lymphoid (n=27), achieving peak cell classification performance with F1 score of 0.81 ± 0.06. Regression analysis demonstrated a highly significant correlation between AMSCP of lymphocyte counts and average Krenn Inflammation Score (rho = 0.88; p<0.0001). While a simple threshold of 1.1% of plasma cells demonstrated the phenotyping potential of our automated approach vs. a clinical pathologist with a sensitivity and specificity of 0.81 and 0.73. Taken together, we find AMSCP to be a valuable cost-effective method for research. Follow-up studies to assess its clinical utility are warranted.
Mesenchymal stem cells ameliorate inflammation in an experimental model of Crohn’s disease via the mesentery
Authors: Dave Maneesh , Dev Atul , Somoza Rodrigo A , Zhao Nan , Viswanath Satish , Mina Pooja Rani , Chirra Prathyush , Obmann Verena Carola , Mahabeleshwar Ganapati H , Menghini Paola , Johnson Blythe Durbin , Nolta Jan , Soto Christopher , Osme Abdullah , Khuat Lam T , Murphy William , Caplan Arnold I , Cominelli Fabio
Published: May 2023

Objective

Mesenchymal stem cells (MSCs) are novel therapeutics for treatment of Crohn’s disease. However, their mechanism of action is unclear, especially in disease-relevant chronic models of inflammation. Thus, we used SAMP-1/YitFc, a chronic and spontaneous murine model of small intestinal inflammation, to study the therapeutic effect and mechanism of human bone marrow-derived MSCs (hMSC).

Design

hMSC immunosuppressive potential was evaluated through in vitro mixed lymphocyte reaction, ELISA, macrophage co-culture, and RT-qPCR. Therapeutic efficacy and mechanism in SAMP were studied by stereomicroscopy, histopathology, MRI radiomics, flow cytometry, RT-qPCR, small animal imaging, and single-cell RNA sequencing (Sc-RNAseq).

Results

hMSC dose-dependently inhibited naïve T lymphocyte proliferation in MLR via PGE2secretion and reprogrammed macrophages to an anti-inflammatory phenotype. hMSC promoted mucosal healing and immunologic response early after administration in SAMP model of chronic small intestinal inflammation when live hMSCs are present (until day 9) and resulted in complete response characterized by mucosal, histological, immunologic, and radiological healing by day 28 when no live hMSCs are present. hMSC mediate their effect via modulation of T cells and macrophages in the mesentery and mesenteric lymph nodes (mLN). Sc-RNAseq confirmed the anti-inflammatory phenotype of macrophages and identified macrophage efferocytosis of apoptotic hMSCs as a mechanism of action that explains their long-term efficacy.

Conclusion

hMSCs result in healing and tissue regeneration in a chronic model of small intestinal inflammation. Despite being short-lived, exert long-term effects via macrophage reprogramming to an anti-inflammatory phenotype.

Data Transparency Statement

Single-cell RNA transcriptome datasets are deposited in an online open access repository ‘Figshare’ (DOI:https://doi.org/10.6084/m9.figshare.21453936.v1)
Correspondence between Signaling and Developmental Patterns by Competing Cells: A Computational Perspective
Authors: Eidi Zahra , Khorasani Najme , Sadeghi Mehdi
Published: May 2023

Arrangement of variant phenotypes in ordered spatial assemblies during division of stem cells is essential for the self-organization of cell tissues. The cellular patterns of phenotypes competing for space and resources against one another are mostly driven by secreted diffusible chemical signaling clues. This complex process is carried out within a chronological framework of interplaying intracellular and intercellular events. This includes receiving external stimulants-whether secreted by other individuals or provided by the environment-interpreting these environmental signals and incorporating the information to designate cell fate. An enhanced understanding of the building blocks of this framework would be of help to set the scene for promising regenerative therapies. In this study, by proposing a designative computational map, we show that there is a correspondence between signaling and developmental patterns that are produced by competing cells. That is, the model provides an appropriate prediction for the final structure of the differentiated cells in a competitive environment. Besides, given that the final state of the cellular organization is known, the corresponding regressive signaling patterns are partly predictable following the proposed map.

Author Summary

Multicellular organisms are made of repeated divisions of single cells and aggregation of their offspring together. However, the aggregated formations are not colony-like accumulations of piled-up cells. Instead, they are “emergent” spatiotemporal structures of developmentally differentiated cell types. The functionally integrated structures remain relatively constant throughout the life of the organisms, despite the death and production of new cells. The question is: How differentiated cells are capable of making variant patterns without any predefined templates? It is shown that with a variety of differentiated cell types, emergence of complex patterns is feasible through the interplay of intercellular interactions and intracellular decision-making switches. Such conceptual understanding has the potential to generate a multitude of novel and precisely controlled cellular behaviors.
New semi-automated tool for the quantitation of MR imaging to estimate in vivo muscle disease severity in mice
Authors: Waters Emily A. , Haney Chad R. , Vaught Lauren. A , McNally Elizabeth M. , Demonbreun Alexis R.
Published: May 2023

The pathology in Duchenne muscular dystrophy (DMD) is characterized by degenerating muscle fibers, inflammation, fibro-fatty infiltrate, and edema, and these pathological processes replace normal healthy muscle tissue. Themdxmouse model is one of the most commonly used preclinical models to study DMD. Mounting evidence has emerged illustrating that muscle disease progression varies considerably inmdxmice, with inter-animal differences as well as intra-muscular differences in pathology in individualmdxmice. This variation is important to consider when conducting assessments of drug efficacy and in longitudinal studies. Magnetic resonance imaging (MRI) is a non-invasive method that can be used qualitatively or quantitatively to measure muscle disease progression in the clinic and in preclinical models. Although MR imaging is highly sensitive, image acquisition and analysis can be time intensive. The purpose of this study was to develop a semi-automated muscle segmentation and quantitation pipeline that can quickly and accurately estimate muscle disease severity in mice. Herein, we show that the newly developed segmentation tool accurately divides muscle. We show that measures of skew and interdecile range based on segmentation sufficiently estimate muscle disease severity in healthy wildtype and diseasedmdxmice. Moreover, the semi-automated pipeline reduced analysis time by nearly 10-fold. Use of this rapid, non-invasive, semi-automated MR imaging and analysis pipeline has the potential to transform preclinical studies, allowing for pre-screening of dystrophic mice prior to study enrollment to ensure more uniform muscle disease pathology across treatment groups, improving study outcomes.
PfAP2-MRP DNA-binding protein is a master regulator of parasite pathogenesis during malaria parasite blood stages
Authors: Subudhi Amit Kumar , Green Judith L. , Satyam Rohit , Lenz Todd , Salunke Rahul P. , Shuaib Muhammad , Isaioglou Ioannis , Abel Steven , Gupta Mohit , Esau Luke , Mourier Tobias , Nugmanova Raushan , Mfarrej Sara , Sivapurkar Rupali , Stead Zenaida , Rached Fathia Ben , Otswal Yogesh , Sougrat Rachid , Dada Ashraf , Kadamany Abdullah Fuaad , Fischle Wolfgang , Merzaban Jasmeen , Knuepfer Ellen , Ferguson David J.P. , Gupta Ishaan , Le Roch Karine G. , Holder Anthony A. , Pain Arnab
Published: May 2023

Malaria pathogenicity results from the parasite’s ability to invade, multiply within and then egress from the host red blood cell (RBC). Infected RBCs are remodeled, expressing antigenic variant proteins (such as PfEMP1, coded by thevargene family) for immune evasion and survival. These processes require the concerted actions of many proteins, but the molecular regulation is poorly understood. We have characterized an essentialPlasmodiumspecific Apicomplexan AP2 (ApiAP2) transcription factor inPlasmodium falciparum(PfAP2-MRP; Master Regulator of Pathogenesis) during the intraerythrocytic developmental cycle (IDC). An inducible gene knockout approach showed that PfAP2-MRP is essential for development during the trophozoite stage, and critical forvargene regulation, merozoite development and parasite egress. ChIP-seq experiments performed at 16 hour post invasion (h.p.i.) and 40 h.p.i. matching the two peaks of PfAP2-MRP expression, demonstrate binding of PfAP2-MRP to the promoters of genes controlling trophozoite development and host cell remodeling at 16 h.p.i. and antigenic variation and pathogenicity at 40 h.p.i. Using single-cell RNA-seq and fluorescence-activated cell sorting, we show de-repression of mostvargenes inΔpfap2-mrpparasites that express multiple PfEMP1 proteins on the surface of infected RBCs. In addition, theΔpfap2-mrpparasites overexpress several early gametocyte marker genes at both 16 and 40 h.p.i., indicating a regulatory role in the sexual stage conversion. Using the Chromosomes Conformation Capture experiment (Hi-C), we demonstrate that deletion of PfAP2-MRP results in significant reduction of both intra-chromosomal and inter-chromosomal interactions in heterochromatin clusters. We conclude that PfAP2-MRP is a vital upstream transcriptional regulator controlling essential processes in two distinct developmental stages during the IDC that include parasite growth, chromatin structure andvargene expression.
Host community structure can shape pathogen outbreak dynamics through a phylogenetic dilution effect
Authors: Toorians Marjolein E.M. , Smallegange Isabel M. , Davies T. Jonathan
Published: May 2023

Biodiversity loss and anthropogenic modifications to species communities are impacting the frequency and magnitude of disease emergence events. These changes may be related through mechanisms in which biodiversity either increases (amplifies) or decreases (dilutes) disease prevalence. Biodiversity effects can be direct, when contacts among competent hosts are substituted by contacts with sink hosts, or indirect through regulation of host abundances. Whether a disease is diluted or amplified depends on the competence of the host species in the community. Here, we introduce a multi-host compartmental disease model in which we assume that host competence is determined by evolutionary relatedness. By simulating communities of varying phylogenetic structure, and estimating community disease outbreak potential (R0), we show how differences in host phylogenetic relatedness can switch host communities from diluting to amplifying a disease, even when species richness is unchanged. We additionally show that phylogenetic dilution can occur simultaneously with amplification through species richness, highlighting the multidimensionality of the disease-diversity relationship. We illustrate our model using empirical data describing the relationship between phylogenetic distances separating hosts and their likelihood of disease sharing. Our study demonstrates how a phylogenetic dilution effect can emerge when we allow transmission to depend on host evolutionary histories.
Extensive Loss and Gain of Conserved Non-Coding Elements during Early Teleost Evolution
Authors: Iliopoulou Elisavet , Papadogiannis Vasileios , Tsigenopoulos Costas S. , Manousaki Tereza
Published: May 2023

Conserved Non-coding Elements (CNE) in vertebrates are enriched around transcription factor loci associated with development. However, loss and rapid divergence of CNEs has been reported in teleost fish, albeit taking only few genomes into consideration. Taking advantage of the recent increase in high-quality teleost genomes, we focus on studying the evolution of teleost CNEs, carrying out targeted genomic alignments and comparisons within the teleost phylogeny to detect CNEs and reconstruct the ancestral teleost CNE repertoire. This teleost-centric approach confirms previous observations of extensive vertebrate CNE loss early in teleost evolution, but also reveals massive CNE gain in the teleost stem-group over 300 million years ago. Using synteny-based association to link CNEs to their putatively regulated target genes, we show the most teleost gained CNEs are found in the vicinity of orthologous loci involved in transcriptional regulation and embryonic development that are also associated with CNEs in other vertebrates. Moreover, teleost and vertebrate CNEs share a highly similar motif and transcription factor binding site vocabulary. We suggest that early teleost CNE gains reflect a restructuring of the ancestral CNE repertoire through both extreme divergence andde novoemergence. Finally, we support newly identified pan-teleost CNEs have potential for accurate resolution of teleost phylogenetic placements in par with coding sequences, unlike ancestral only elements shared with spotted gar. This work provides new insight into CNE evolution with great value for follow-up work on phylogenomics, comparative genomics and the study of gene regulation evolution in teleosts.
Relative energetic economy of cleistogamous selfing in three populations of the perennialRuellia humilis
Authors: Soto Tatyana Y. , Ryan Nicholas A. , Oakley Christopher G.
Published: May 2023

Premise of research

What maintains mixed selfing and outcrossing is an enduring mystery in evolutionary biology. Cleistogamy, where individuals produce both potentially outcrossing chasmogamous and obligately selfing cleistogamous flowers, provides an ideal framework in which to study the evolutionary forces maintaining mixed-mating. Despite their promise for providing insight into mating system evolution, few studies of cleistogamous species have comprehensively investigated the relative costs and benefits of cleistogamous selfing.

Methodology

We quantified the necessary components to calculate the relative energetic cost of reproduction of the different flower types in three natural populations of the perennialRuellia humilisNutt (Acanthaceae). These components include flower dry mass, fertility (fruit set), and seed mass and number per fruit. We also measured pollen-ovule ratios for both flower types as another measure of relative energetic investment. We additionally tracked phenology of the two flower types and used the proportion of chasmogamous flowers to estimate maximum potential outcrossing rates.

Pivotal Results

We found that the energetic cost of reproduction via cleistogamous flowers was about 4-10 times less than that of reproduction via chasmogamous flowers, and this energetic economy was from both reduced mass and increased fertility of cleistogamous flowers. Pollen ovule ratios in cleistogamous flowers were one third to one half those of chasmogamous flowers, providing additional support for their energetic economy. Maximum potential outcrossing rates in these populations based on chasmogamous flower production were between 43-61%, but chasmogamous flowers can autogamously self at rates of 33-75%.

Conclusions

The relative energetic economy of cleistogamous flowers suggest that progeny from chasmogamous flowers would have to have 4-10 times greater relative fitness to explain their evolutionary maintenance. These values are likely even greater considering the reduced investment in pollen production in cleistogamous flowers. Ongoing work will quantify potential advantages of chasmogamous flowers due to inbreeding depression and heterosis.
Phylogenetic and spatial determinants of leaf endophyte microbiomes in the flowering plant genusHeuchera(Saxifragaceae)
Authors: Pantinople Dexcem J. , Conner Reagan , Sutton-Dauber Stephanie , Broussard Kelli , Siniscalchi Carolina M. , Engle-Wrye Nicholas J. , Jordan Heather R. , Folk Ryan A.
Published: May 2023

Premise: Endophytic plant-microbe interactions range from mutualistic relationships that confer important ecological and agricultural traits to neutral or quasi-parasitic relationships. In contrast to root-associated endophytes, the role of environmental and host-related factors for acquiring leaf endophyte communities remains relatively unexplored. Here we assess leaf endophyte diversity to test the hypothesis that membership of these microbial communities is driven primarily by abiotic environment and host phylogeny.

Methods:We used a broad geographic coverage of North America in the genus,Heuchera(Saxifragaceae). Bacterial and fungal communities were characterized with 16S and ITS amplicon sequencing, using QIIME2 to call operational taxonomic units and calculate species richness, Shannon diversity, and phylogenetic diversity. We assembled environmental predictors for microbial diversity at collection sites including latitude, elevation, temperature, precipitation, and soil parameters.

Results:We find differing assembly patterns for bacterial and fungal endophytes; we found that only host phylogeny is significantly associated with bacteria, while geographic distance alone was the best predictor of fungal community composition. Species richness and phylogenetic diversity are very similar across sites and species, with only fungi showing a response to aridity and precipitation for some metrics. Unlike what has been observed with root-associated microbial communities, in this system microbes show no relationship with pH or other soil factors.

Conclusions:Host phylogeny and geographic distance independently influence different microbial communities, while aridity and precipitation determine fungal diversity within leaves ofHeuchera. Our results indicate the importance of detailed clade-based investigation of microbiomes and the complexity of microbiome assembly within specific plant organs.
Mapping QTL for vernalization requirement identified adaptive divergence of the candidate geneFlowering Locus Cin polyploidCamelina sativa
Authors: Chaudhary Raju , Higgins Erin E. , Eynck Christina , Sharpe Andrew G. , Parkin Isobel A. P.
Published: May 2023

Vernalization requirement is an integral component of flowering in winter-type plants. The availability of winter ecotypes amongCamelinaspecies facilitated the mapping of QTL for vernalization requirement inC. sativa. An inter- and intraspecific crossing scheme between relatedCamelinaspecies, where two different sources of the winter-type habit were used, resulted in the development of two segregating populations. Linkage maps generated with sequence-based markers identified three QTL associated with vernalization requirement inC. sativa; two from the inter-specific (chromosomes 13 and 20) and one from the intra-specific cross (chromosome 8). Notably, the three loci were mapped to different homologous regions of the hexaploidC. sativagenome. All three QTL were found in proximity toFLOWERING LOCUS C(FLC), variants of which have been reported to affect the vernalization requirement in plants. Temporal transcriptome analysis for winter-typeCamelina alyssumdemonstrated reduction in expression ofFLCon chromosomes 13 and 20 during cold treatment, which would trigger flowering, sinceFLCwould be expected to suppress floral initiation.FLCon chromosome 8 also showed reduced expression in theC. sativassp.pilosawinter parent upon cold treatment, but was expressed at very high levels across all time points in the spring-typeC. sativa. The chromosome 8 copy carried a deletion in the spring-type line, which could impact its functionality. Contrary to previous reports, all threeFLCloci can contribute to controlling the vernalization response inC. sativaand provide opportunities for manipulating this requirement in the crop.

Significance Statement

Developing winterC. sativagermplasm is an important breeding goal for this alternative oilseed, with application in the food, fuel and bioproduct industries. Studying the genetic architecture of the vernalization response has shown that contrary to previous reports all threeFLCloci inCamelinaspecies could be exploited to manipulate this important trait.
Vocal-visual combinations in wild chimpanzees
Authors: Mine Joseph G. , Wilke Claudia , Zulberti Chiara , Bejhati Melika , Stoll Sabine , Machanda Zarin , Manser Andri , Slocombe Katie. E , Townsend Simon W.
Published: May 2023

Human communication is strikingly multi-modal, relying on vocal utterances combined with visual gestures, facial expressions and more. Recent efforts to describe multi-modal signal production in our ape relatives have shed important light on the evolutionary trajectory of this core hallmark of human language. However, whilst promising, a systematic quantification of primate signal production which filters out random combinations produced across modalities is currently lacking. Here, through recording the communicative behaviour of wild chimpanzees from the Kibale forest, Uganda we address this issue and generate the first repertoire of non-random combined vocal and visual components. Using collocation analysis, we identify more than 100 vocal-visual combinations which occur more frequently than expected by chance. We also probe how multi-modal production varies in the population, finding no differences between individuals as a function of age, sex or rank. The number of visual components exhibited alongside vocalizations was, however, associated with vocalization type and duration. We demonstrate that chimpanzees produce a vast array of combined vocal and visual components, exhibiting a hitherto underappreciated level of combinatorial complexity. We conclude that a multi-modal approach is crucial to accurately representing the communicative abilities of non-human primates.
REGENERATIVE GENE THERAPY IN THE HYPOTHALAMUS PROLONGS FERTILITY IN FEMALE RATS
Authors: Gallardo Maria D. , Girard Mauricio , Bigres Araceli , Lehmann Marianne , Rodriguez Silvia S. , Goya Rodolfo G.
Published: May 2023

There is substantial evidence that age-related ovarian failure in rats is preceded by abnormal responsiveness of the neuroendocrine axis to estrogen positive feedback. In middle-aged (M-A) female rats, we have demonstrated that intrahypothalamic gene therapy for insulin-like growth factor-I (IGF-I) started at 6 months of age extends the regular cyclicity of the animals beyond 10 month (the age at which MA rats stop ovulating) and preserves the integrity of the ovarian structure. Here, we implemented long-term regenerative gene therapy in the hypothalamus of young females. The goal was to extend fertility in the treated animals. We constructed a helper-dependent adenovector that harbors the green fluorescent protein (GFP) reporter gene as well as a gene tandem, termed STEMCCA, which harbors the 4 Yamanaka genes (oct4, sox2, klf4, and c-myc, OSKM), both under the control of a Tet-Off bidirectional promoter. An adenovector that only carries the gene for GFP was used as control. At 4 months of age 12 female rats received an intrahypothalamic injection of our OSKM-GFP vector (treated rats); 12 control rats a vector expressing GFP only (control rats). At 9.3 months of age control and treated rats were mated with young males. A group of 12 young intact female rats was also mated. The rate of pregnancy recorded was 83%, 8.3% and 25% for young, M-A control and M-A treated animals, respectively. Average litter size was 9, 3 and 3 for the corresponding groups. Mean pup BW was slightly higher in the M-A rats. In a preliminary study we confirmed that ovulation in our M-A females ceases at 10 months of age. Our results are in line with the evidence that viral vector-mediated delivery of the Yamanaka genes in the brain has strong regenerative effects without adverse side effects. The particular significance of the present results is that, for the first time, they show that long-term OSKM gene therapy in the hypothalamus is able to extend the functionality of such a complex system as the hypothalamo-pituitary-ovarian axis.
Integration of HLA-DR linkage disequilibrium to MHC class II predictions
Authors: Pedersen Mette Bøge , Asmussen Sarah Rosenberg , Sarfelt Freja Malou , Saksager Astrid Brix , Sackett Peter Wad , Nielsen Morten , Barra Carolina
Published: May 2023

Insights into peptide binding to HLA class II molecules is essential when studying the biological mechanisms behind cellular immunity, autoimmune diseases, and the development of immunotherapies and peptide vaccines. Currently, most of the publicly available data used to train state-of-the-art binding prediction methods for HLA-DR only includes DRB1 information. The role of the paralogue alleles, HLA-DRB3/4/5, and their strong linkage disequilibrium to DRB1 is often omitted when typing HLA-II alleles. This leads to ambiguities when making disease associations and interpreting HLA-restricted immune data. To resolve this issue, we present HLAAssoc-1.0, a method to infer HLA-DRB3/4/5 alleles by linkage disequilibrium to HLA-DRB1. We illustrate the usage of the tool and the importance of the integration of HLA-DRB3/4/5 alleles in the data analysis in different case studies including the interpretation of immunopetidomics data. Additionally, we infer allele information for the data used for training of NetMHCIIpan lacking HLA-DRB3/4/5 allele information and demonstrate that the retrained method achieved improved performance. In all cases, inferring HLA-DRB3/4/5 allele presence in non-fully typed HLA-II assays resulted in improved allele and motif deconvolutions. HLAAssoc-1.0 is available athttps://services.healthtech.dtu.dk/service.php?HLAAssoc-1.0.
The impact of RSV/SARS-CoV-2 co-infection on clinical disease and viral replication: insights from a BALB/c mouse model
Authors: Morris Dorothea R. , Qu Yue , Thomason Kerrie S. , Haas de Mello Aline , Preble Richard , Menachery Vineet D. , Casola Antonella , Garofalo Roberto P.
Published: May 2023

RSV and SARS-CoV-2 are prone to co-infection with other respiratory viruses. In this study, we use RSV/SARS-CoV-2 co-infection to evaluate changes to clinical disease and viral replication in vivo. To consider the severity of RSV infection, effect of sequential infection, and the impact of infection timing, mice were co-infected with varying doses and timing. Compared with a single infection of RSV or SARS-CoV-2, the co-infection of RSV/SARS-CoV-2 and the primary infection of RSV followed by SARS-CoV-2 results in protection from SARS-CoV-2-induced clinical disease and reduces SARS-CoV-2 replication. Co-infection also augmented RSV replication at early timepoints with only the low dose. Additionally, the sequential infection of RSV followed by SARS-CoV-2 led to improved RSV clearance regardless of viral load. However, SARS-CoV-2 infection followed by RSV results in enhanced SARS-CoV-2-induced disease while protecting from RSV-induced disease. SARS-CoV-2/RSV sequential infection also reduced RSV replication in the lung tissue, regardless of viral load. Collectively, these data suggest that RSV and SARS-CoV-2 co-infection may afford protection from or enhancement of disease based on variation in infection timing, viral infection order, and/or viral dose. In the pediatric population, understanding these infection dynamics will be critical to treat patients and mitigate disease outcomes.

Author Summary

Infants and young children are commonly affected by respiratory viral co-infections. While RSV and SARS-CoV-2 are two of the most prevalent respiratory viruses, their co-infection rate in children remains surprisingly low. In this study, we investigate the impact of RSV/SARS-CoV-2 co-infection on clinical disease and viral replication using an animal model. The findings indicate that RSV infection either simultaneously or prior to SARS-CoV-2 infection in mice protect against SARS-CoV-2-induced clinical disease and viral replication. On the other hand, infection with SARS-CoV-2 followed by RSV results in worsening of SARS-CoV-2-induced clinical disease, but also protection from RSV-induced clinical disease. These results highlight a protective role for RSV exposure, given this occurs before infection with SARS-CoV-2. This knowledge could help guide vaccine recommendations in children and sets a basis for future mechanistic studies.

Graphical Abstract