bluuebunny/crossref_metadata_2025 huggingface dataset:
Speech Outcomes and Velopharyngeal Function in Children Undergoing Submucous Cleft Palate Repair
Authors: Álvarez Carvajal Drina C. , Inostroza-Allende Felipe , Geldres Meneses María B. , Giugliano Villarroel Carlos
Published: August 2023

Objective:

Describe and compare the results of speech and velopharyngeal function in children with classic and occult submucous cleft palate undergoing interdisciplinary treatment at the Gantz Foundation.

Methods:

The clinical history of all patients born between 2012 and 2017 with a diagnosis of classic or occult submucous cleft palate was retrospectively reviewed. Preoperative and postoperative medical, surgical, and speech and language history were collected.

Results:

Twenty-eight cases diagnosed at the age of 44.8±23.9 months were included. Of these, 71.4% presented classic submucous cleft, and 28.6% occult. Before primary surgery, 7.1% had a diagnosis of the syndrome, and 21.4% were under study. A total of 39.3% had hearing difficulties and 21.4% used tympanic ventilation tubes. A total of 60.7% had language problems, 39.3% had compensatory articulation, 17.9% had absent hypernasality, and 21.4% had absent nasal emission. The team indicated primary palate surgery in 71.4%, of which 85% performed the surgery at the mean age of 61.7±24.7 months. The surgical technique was Furlow in 88.2% of the cases and intravelar veloplasty in the remaining 11.8%. Then, 3 cases underwent velopharyngeal insufficiency surgery; 2 of them eliminated hypernasality and reduced nasal emission. The age of diagnosis (P=0.021) and the performance of velopharyngeal insufficiency surgery (P=0029) of the occult submucous cleft palate group was significatively later than the classic cleft palate group.

Conclusions:

Language, hearing, compensatory articulation, hypernasality, and nasal emission problems were recorded. A high percentage required primary surgery. Of these, a low proportion also required a velopharyngeal insufficiency surgery, which improved the velopharyngeal function of the children but did not completely adapt it. In this regard, early diagnosis is essential, as well as an analysis of each center primary closure protocol.
A Head-to-head Comparison of De Novo Sirolimus or Everolimus Plus Reduced-dose Tacrolimus in Kidney Transplant Recipients: A Prospective and Randomized Trial
Authors: Toniato de Rezende Freschi Juliana , Cristelli Marina Pontello , Viana Laila Almeida , Ficher Klaus Nunes , Nakamura Monica Rika , Proença Henrique , Dreige Yasmim Cardoso , de Marco Renato , de Lima Maria Gerbase , Foresto Renato Demarchi , Aguiar Wilson Ferreira , Medina-Pestana Jose , Tedesco-Silva Helio
Published: August 2023

Background.

Mammalian target of rapamycin inhibitors (mTORi), sirolimus (SRL) and everolimus (EVR), have distinct pharmacokinetic/pharmacodynamics properties. There are no studies comparing the efficacy and safety of de novo use of SRL versus EVR in combination with reduced-dose calcineurin inhibitor.

Methods.

This single-center prospective, randomized study included first kidney transplant recipients receiving a single 3 mg/kg antithymocyte globulin dose, tacrolimus, and prednisone, without cytomegalovirus (CMV) pharmacological prophylaxis. Patients were randomized into 3 groups: SRL, EVR, or mycophenolate sodium (MPS). Doses of SRL and EVR were adjusted to maintain whole blood concentrations between 4 and 8 ng/mL. The primary endpoint was the 12-mo incidence of the first CMV infection/disease.

Results.

There were 266 patients (SRL, n = 86; EVR, n = 90; MPS, n = 90). The incidence of the first CMV event was lower in the mTORi versus MPS groups (10.5% versus 7.8% versus 43.3%, P < 0.0001). There were no differences in the incidence of BK polyomavirus viremia (8.2% versus 10.1% versus 15.1%, P = 0.360). There were no differences in survival-free from treatment failure (87.8% versus 88.8% versus 93.3%, P = 0.421) and incidence of donor-specific antibodies. At 12 mo, there were no differences in kidney function (75 ± 23 versus 78 ± 24 versus 77 ± 24 mL/min/1.73 m2, P = 0.736), proteinuria, and histology in protocol biopsies. Treatment discontinuation was higher among patients receiving SRL or EVR (18.6% versus 15.6% versus 6.7%, P = 0.054).

Conclusions.

De novo use of SRL or EVR, targeting similar therapeutic blood concentrations, shows comparable efficacy and safety. The reduced incidence of CMV infection/disease and distinct safety profile of mTORi versus mycophenolate were confirmed in this study.
DeepMap: A deep learning-based model with a four-line code for prediction-based breeding in crops
Authors: Kumar Ajay , Sundaram Krishna T. , Gnanapragasam Niranjani , Singh Uma Maheshwar , Pranesh K. J. , Venkateshwarlu Challa , Paul Pronob J. , Hussain Waseem , Bhosale Sankalp , Kohli Ajay , Miro Berta , Singh Vikas Kumar , Sinha Pallavi
Published: July 2023

Prediction of phenotype through genotyping data using the emerging machine or deep learning technology has been proven successful in genomic prediction. We present here a graphical processing unit (GPU) enabled DeepMap configurable deep learning-based python package for the genomic prediction of quantitative phenotype traits. We found that deep learning captures non-linear patterns more efficiently than conventional statistical methods. Furthermore, we suggest an additional module inclusion of epistasis interactions and training of the model on Graphical Processing Units (GPUs) in addition to Central Processing Unit (CPU) to enhance efficiency and increase the model’s performance. We developed and demonstrated the application of DeepMap using a 3K rice genome panel and 1K-Rice Custom Amplicon (1kRiCA) data for several phenotypic traits including days to 50% flowering (DTF), number of productive tillers (NPT), panicle length (PL), plant height (PH), and plot yield (PY). We have found that DeepMap outperformed the best existing state-of-the-art models by giving higher predictive correlation and low mean squared error for the datasets studied. This prediction performance was higher than other compared models in the range of 13-31%. Similarly for Dataset-2, significantly higher predictions were observed than the compared models (16-20% higher prediction ability). On Dataset-3, we have also shown the better and versatile performance of our model across crops (wheat, maize, and soybean) for yield and yield-related traits. This demonstrates the potentiality of the framework and ease of use for future research in crop improvement. The DeepMap is accessible athttps://test.pypi.org/project/DeepMap-1.0/.

Short Summary

DeepMap is a deep learning-based breeder-friendly python package to perform genomic prediction. It utilizes epistatic interactions for data augmentation and outperforms the existing state-of-the-art machine/deep learning models such as Bayesian LASSO, GBLUP, DeepGS, and dualCNN. DeepMap developed for rice and tested across crops such as maize, wheat, soybean etc.
getphylo: rapid and automatic generation of multi-locus phylogenetic trees
Authors: Booth T. J. , Shaw Simon , Weber T.
Published: July 2023

Motivation

Phylogenetic trees are the primary tool for visualising evolutionary relationships. Traditionally, phylogenies are inferred from manually curated sets of marker genes. As available genomic data increases, there is increasing demand for tools to automatically build phylogenies from assembled genomes. Existing tools rely on reference databases of preselected marker genes, limiting their taxonomic scope. We sought to develop a tool that could quickly build phylogeny from input genomes alone.

Results

We developedgetphylo, a tool to automatically generate multi-locus phylogenetic trees from GenBank files. It has a low barrier to entry with minimal dependencies.getphylouses a parallelised, heuristic workflow to keep runtime and system requirements as low as possible.getphyloconsistently produces trees with topologies comparable to other tools in less time. Furthermore, asgetphylodoes not rely on reference databases, it has a virtually unlimited scope in terms of taxonomy (e.g., not limited to bacteria) and genetic scale (e.g., can analyse plasmids, prophage, and gene clusters). This combination of speed and flexibility makesgetphyloa valuable addition to the phylogenetics toolkit.

Availability

getphylois freely available and is downloadable through the Python Package Index (pip install getphylo;https://pypi.org/project/getphylo/) and GitHub (https://github.com/drboothtj/getphylo).
Salmonella-driven Intestinal Edema in Mice is Characterized by Tensed Fibronectin Fibers
Authors: Rappold Ronja , Kalogeropoulos Konstantinos , auf dem Keller Ulrich , Vogel Viola , Slack Emma
Published: July 2023

Intestinal edema is a common manifestation of numerous gastrointestinal diseases and is characterized by the accumulation of fluid in the interstitial space of the intestinal wall. Technical advances in laser capture microdissection and low-biomass proteomics now allow us to specifically characterize the intestinal edema proteome. Our data identifies a high abundance of antimicrobial factors, but also highlights major contributions from the blood clotting system, extracellular matrix (ECM) and protease – protease inhibitor networks. The ECM is a complex fibrillar network of macromolecules that provides structural and mechanical support to the intestinal tissue. One abundant component of the ECM observed in the Salmonella-driven intestinal edema is the mechanosensitive glycoprotein fibronectin. Using mechanosensitive staining of fibronectin reveals a solely tensed molecular conformation of fibronectin fibers present in the edema, opposed to other cecal tissue areas, despite the high abundance of proteases able to cleave fibronectin. Co-staining for fibrin(ogen) indicates the formation of a provisional matrix, similar to what is observed in response to skin injury. The absence of low tensional fibronectin fibers and the additional finding of a high number of protease inhibitors in the edema proteome could indicate a critical role of stretched fibronectin fibers in maintaining tissue integrity in the severely inflamed cecum. Understanding these processes may provide valuable functional diagnostic markers of intestinal disease progression.
Exploring congruent diversification histories with flexibility and parsimony
Authors: Andréoletti Jérémy , Morlon Hélène
Published: July 2023

Abstract

Using phylogenies of present-day species to estimate diversification rate trajectories – speciation and extinction rates over time – is a challenging task due to non-identifiability issues. Given a phylogeny, there exists an infinite set of trajectories that result in the same likelihood; this set has been coined a congruence class. Previous work has developed approaches for sampling trajectories within a given congruence class, with the aim to assess the extent to which congruent scenarios can vary from one another. Based on this sampling approach, it has been suggested that rapid changes in speciation or extinction rates are conserved across the class. Reaching such conclusions requires to sample the broadest possible set of distinct trajectories.

We introduce a new method for exploring congruence classes, that we implement in the R package CRABS. Whereas existing methods constrain either the speciation rate or the extinction rate trajectory, ours provides more flexibility by sampling congruent speciation and extinction rate trajectories simultaneously. This allows covering a more representative set of distinct diversification rate trajectories. We also implement a filtering step that allows selecting the most parsimonious trajectories within a class.

We demonstrate the utility of our new sampling strategy using a simulated scenario. Next, we apply our approach to the study of mammalian diversification history. We show that rapid changes in speciation and extinction rates need not be conserved across a congruence class, but that selecting the most parsimonious trajectories shrinks the class to concordant scenarios.

Our approach opens new avenues both to truly explore the myriad of potential diversification histories consistent with a given phylogeny, embracing the uncertainty inherent to phylogenetic diversification models, and to select among these different histories. This should help refining our inference of diversification trajectories from extant data.
More than just density: the role of egg number, food volume and container dimensions in mediating larval competition inDrosophila melanogaster
Authors: Venkitachalam Srikant , Sajith V. S. , Joshi Amitabh
Published: July 2023

Flies of the genusDrosophilahave been extensively used as model systems to study competition. Experiments using larval crowding in these species have furthered our understanding of competition ecology, stress-adaptation, density-dependent selection and population dynamics. Historically, larval competition has been induced by crowding the larvae in high density cultures, compared to low-density controls. However, recent studies have shown that two larval cultures having the same total eggs per mL food density, with different absolute quantities of eggs and food, can differ greatly in their density-specific fitness functions. Similarly, populations adapted to two types of cultures achieving the same density through different means, can also evolve different traits. Thus, it is clear that there is more to larval crowding than just eggs/food density, which has until now been the benchmark variable for quantifying larval crowding inDrosophilastudies. In the current study, we explore the consequences of implementing crowding in different ways, using a three-way factorial experiment with egg number and food volume, cast into different food column heights or cylindrical vials with different diameters. We find that not just the same density, but cultures having the same egg number and food volume combination but experienced in food columns of varying height and diameter can have very different pre-adult survivorship and development times. We further propose a new variable for quantifying larval crowding – effective density, which is the density within the larval feeding band, a volume of food close to the surface, with access to air, wherein a majority of the larvae feed. We show that effective density is a much better predictor of the outcomes of competition than the popularly used total eggs/food density.
Deep Batch Active Learning for Drug Discovery
Authors: Bailey Michael , Moayedpour Saeed , Li Ruijiang , Corrochano-Navarro Alejandro , Kötter Alexander , Kogler-Anele Lorenzo , Riahi Saleh , Grebner Christoph , Hessler Gerhard , Matter Hans , Bianciotto Marc , Mas Pablo , Bar-Joseph Ziv , Jager Sven
Published: July 2023

A key challenge in drug discovery is to optimize, in silico, various absorption and affinity properties of small molecules. One strategy that was proposed for such optimization process is active learning. In active learning molecules are selected for testing based on their likelihood of improving model performance. To enable the use of active learning with advanced neural network models we developed two novel active learning batch selection methods. These methods were tested on several public datasets for different optimization goals and with different sizes. We have also curated new affinity datasets that provide chronological information on state-of-the-art experimental strategy. As we show, for all datasets the new active learning methods greatly improved on existing and current batch selection methods leading to significant potential saving in the number of experiments needed to reach the same model performance. Our methods are general and can be used with any package including the popularDeepChemlibrary.
In vivoexpansion of gene-targeted hepatocytes through transient inhibition of an essential gene
Authors: De Giorgi Marco , Park So Hyun , Castoreno Adam , Cao Mingming , Hurley Ayrea , Saxena Lavanya , Chuecos Marcel A. , Walkey Christopher J. , Doerfler Alexandria M. , Furgurson Mia N. , Ljungberg M. Cecilia , Patel Kalyani R. , Hyde Sarah , Chickering Tyler , Lefebvre Stephanie , Wassarman Kelly , Miller Patrick , Qin June , Schlegel Mark K. , Zlatev Ivan , Li Rich Gang , Kim Jong , Martin James F. , Bissig Karl-Dimiter , Jadhav Vasant , Bao Gang , Lagor William R.
Published: July 2023

Homology Directed Repair (HDR)-based genome editing is an approach that could permanently correct a broad range of genetic diseases. However, its utility is limited by inefficient and imprecise DNA repair mechanisms in terminally differentiated tissues. Here, we tested “Repair Drive”, a novel method for improving targeted gene insertion in the liver by selectively expanding correctly repaired hepatocytesin vivo. Our system consists of transient conditioning of the liver by knocking down an essential gene, and delivery of an untargetable version of the essential genein ciswith a therapeutic transgene. We show that Repair Drive dramatically increases the percentage of correctly targeted hepatocytes, up to 25%. This resulted in a five-fold increased expression of a therapeutic transgene. Repair Drive was well-tolerated and did not induce toxicity or tumorigenesis in long term follow up. This approach will broaden the range of liver diseases that can be treated with somatic genome editing.
TEMPTED: time-informed dimensionality reduction for longitudinal microbiome studies
Authors: Shi Pixu , Martino Cameron , Han Rungang , Janssen Stefan , Buck Gregory , Serrano Myrna , Owzar Kouros , Knight Rob , Shenhav Liat , Zhang Anru R.
Published: July 2023

Longitudinal studies are crucial for understanding complex microbiome dynamics and their link to health. We introduce TEMPoral TEnsor Decomposition (TEMPTED), a time-informed dimensionality reduction method for high-dimensional longitudinal data that treats time as a continuous variable, effectively characterizing temporal information and handling varying temporal sampling. TEMPTED captures key microbial dynamics, facilitates beta-diversity analysis, and enhances reproducibility by transferring learned representations to new data. In simulations, it achieves 90% accuracy in phenotype classification, significantly outperforming existing methods. In real data, TEMPTED identifies vaginal microbial markers linked to term and preterm births, demonstrating robust performance across datasets and sequencing platforms.
Diabetes Detection from Diabetic Retinopathy-Absent Images Using Deep Learning Methodology
Authors: Rom Yovel , Aviv Rachelle , Cohen Gal Yaakov , Friedman Yehudit Eden , Dvey-Aharon Zack
Published: August 2023

Aims

Diabetes is one of the leading causes of morbidity and mortality in the United States and worldwide. This research aimed to develop an artificial intelligence (AI) machine learning model which can detect the presence of diabetes from fundus imagery of eyes without diabetic eye disease.

Methods

Our researchers trained a machine learning algorithm on the EyePACS dataset, consisting of 47,076 images. Patients were also divided into cohorts based on disease duration, each cohort consisting of patients diagnosed within the timeframe in question (e.g., 15 years) and healthy patients.

Results

The algorithm achieved 0.83 area under receiver operating curve (AUC) in detecting diabetes per image, and AUC 0.86 on the task of detecting diabetes per patient.

Conclusion

Our results suggest that diabetes may be diagnosed non-invasively using fundus imagery alone. This may enable diabetes diagnosis at point of care, as well as other, accessible venues, facilitating the diagnosis of many undiagnosed people with diabetes.
The circulating proteome and brain health: Mendelian randomisation and cross-sectional analyses
Authors: Walker Rosie May , Chong Michael , Perrot Nicolas , Pigeyre Marie , Gadd Danni A , Stolicyn Aleks , Shi Liu , Campbell Archie , Shen Xueyi , Whalley Heather C , Nevado Holgado Alejo , McIntosh Andrew M , Heitmeier Stefan , Rangarajan Sumathy , O'Donnell Martin , Smith Eric E , Yusuf Salim , Whiteley William N , Pare Guillaume
Published: August 2023

Decline in cognitive function is the most feared aspect of ageing. Poorer midlife cognitive function is associated with increased dementia and stroke risk. The mechanisms underlying variation in cognitive function are uncertain. Here, we assessed associations between 1160 proteins' plasma levels and two measures of cognitive function, the digit symbol substitution test (DSST) and the Montreal Cognitive Assessment in 1198 PURE-MIND participants. We identified five DSST performance-associated proteins (NCAN, BCAN, CA14, MOG, CDCP1), with NCAN and CDCP1 showing replicated association in an independent cohort, GS (N=1053). MRI-assessed structural brain phenotypes partially mediated (8-19%) associations between NCAN, BCAN, and MOG, and DSST performance. Mendelian randomisation analyses suggested higher CA14 levels might cause larger hippocampal volume and increased stroke risk, whilst higher CDCP1 levels might increase intracranial aneurysm risk. Our findings highlight candidates for further study and the potential for drug repurposing to reduce risk of stroke and cognitive decline.
KoNA: Korean Nucleotide Archive as a New Data Repository for Nucleotide Sequence Data
Authors: Ko Gunhwan , Lee Jae Ho , Sim Young Mi , Song Wangho , Yoon Byung-Ha , Byeon Iksu , Lee Bang Hyuck , Kim Sang-Ok , Choi Jinhyuk , Jang Insoo , Kim Hyerin , Yang Jin Ok , Jang Kiwon , Kim Sora , Kim Jong-Hwan , Jeon Jongbum , Jung Jaeeun , Hwang Seungwoo , Park Ji-Hwan , Kim Pan-Gyu , Kim Seon-Young , Lee Byungwook
Published: July 2023

During the last decade, generation and accumulation of petabase-scale high-throughput sequencing data have resulted in ethical and technical challenges, including access to human data, and transfer, storage, and sharing of enormous amount of data. To promote data-driven research in biology, the Korean government announced that all the biological data generated from government-funded research projects should be deposited in the Korea BioData Station (K-BDS), which consists of multiple databases for individual data types. We introduce the Korean Nucleotide Archive (KoNA), a repository for nucleotide sequence data. As of July 2022, the Korean Read Archive in KoNA has collected over 477 TB of raw next generation sequencing data from several national genome projects. To ensure data quality and prepare for international alignment, a standard operating procedure (SOP) was adopted, which is similar to the International Nucleotide Sequence Database Collaboration. The SOP includes quality control processes for submitted data and metadata using an automated pipeline followed by manual examination. To ensure fast and stable data transfer, a high-speed transmission system called GBox is used in KoNA. Furthermore, the data uploaded to or downloaded from KoNA through GBox can be readily processed in a cloud-computing service for genomic data analysis called Bio-Express. This seamless coupling of KoNA, GBox, and Bio-Express enhances data experience including submission, access, and analysis of raw nucleotide sequences. KoNA not only satisfies the unmet needs for a national sequence repository in Korea, but also provides datasets to researchers globally and contribute to advances in genomics. KoNA is available athttps://www.kobic.re.kr/kona/.
Urine-HILIC: Automated sample preparation for bottom-up urinary proteome profiling in clinical proteomics
Authors: Govender Ireshyn , Mokoena Rethabile , Stoychev Stoyan , Naicker Previn
Published: July 2023

Urine provides a diverse source of information related to a patient’s health status and is ideal for clinical proteomics because of its ease of collection. To date, there is no standard operating procedure for reproducible and robust urine sample preparation for mass spectrometry-based clinical proteomics. To this end, a novel workflow was developed based on an on-bead protein capture, clean up, and digestion without the requirement for processing steps such as precipitation or centrifugation. The workflow was applied to an acute kidney injury (AKI) pilot study. Urine from clinical samples and a pooled sample were subjected to automated sample preparation in a KingFisher™ Flex magnetic handling station using a novel urine-HILIC (uHLC) approach based on MagReSyn® HILIC microspheres. For benchmarking, the pooled sample was also prepared using a published protocol based on an on-membrane (OM) protein capture and digestion workflow. Peptides were analysed by LCMS in data independent acquisition (DIA) mode using a Dionex Ultimate 3000 UPLC coupled to a Sciex 5600 mass spectrometer. Data was searched in Spectronaut™ 17. Both workflows showed similar peptide and protein identifications in the pooled sample. The uHLC workflow was easier to set up and complete, having less hands-on time than the OM method, with fewer manual processing steps. Lower peptide and protein CV was observed in the uHLC technical replicates. Following statistical analysis, candidate protein markers were filtered, at ≥ 2-fold change in abundance, ≥ 2 unique peptides and ≤ 1% false discovery rate, and revealed many significant, differentially abundant kidney injury-associated urinary proteins. The pilot data derived using this novel workflow provides information on the urinary proteome of patients with AKI. Further exploration in a larger cohort using this novel high-throughput method is warranted.
Analyzing interaction of rhodacyanine inhibitor ‘MKT-077’ withPlasmodium falciparumHSP70 nucleotide binding domains
Authors: Nainani Chanchal , Upadhyay Vipul , Singh Bikramjit , Sandhu Komalpreet Kaur , Kaur Satinder , Hora Rachna , Mishra Prakash Chandra
Published: July 2023

MKT-077 and its derivatives are rhodacyanine inhibitors that hold potential in treatment of cancer, neurodegenerative diseases and malaria. These allosteric drugs act by inhibiting the ATPase action of heat shock proteins of 70kDa (HSP70). MKT-077 accumulates in the mitochondria and displays differential activity against HSP70 homologs. The fourPlasmodium falciparumHSP70s (PfHSP70) are present at various subcellular locations to perform distinct functions. In the present study, we have used bioinformatics tools to understand interactions between MKT-077 and PfHSP70s. Nature of the identified interactions is primarily hydrophobic with different PfHSP70 homologs showing variable propensity to bind MKT-077. Our molecular docking approach has helped us to predict the binding pocket and specific residues on PfHSP70s that are involved in interacting with MKT-077. Information derived from this article may form the foundation for design and development of MKT-077 based drugs against malaria.
Mapping immunological and host receptor binding determinants of SARS-CoV spike protein utilizing the Qubevirus platform
Authors: Sanders Carrie , Dzelamonyuy Aristide , Ntemafack Augustin , Alatoom Nadia , Nchinda Godwin , Georgiadis Millie , Waffo Alain Bopda
Published: July 2023

The motifs involved in tropism and immunological interactions of SARS-CoV spike (S) protein were investigated utilizing the Qubevirus platform. We showed that separately, 14 overlapping peptide fragments representing the S protein (F1-14 of 100 residues each) could be inserted into the C-terminus of A1 on recombinant Qubevirus without affecting its viability. Additionally, recombinant phage expression resulted in the surface exposure of different engineered fragments in an accessible manner. The F6 from S425-525, was found to contain the binding determinant of the recombinant human angiotensin converting enzyme 2 (rhACE2), with the shortest active binding motif situated between residues S437-492. Upstream, another fragment, F7, containing an overlapping portion of F6 would not bind to rhACE2, confirming not just only that residues were linear but equally also the appropriate structural orientation of F6 upon the Qubevirus. The F6 (S441-460) and other inserts, including F7/F8 (S601-620) and F10 (S781-800), were demonstrated to contain important immunological determinants through recognition and binding of S protein specific (anti-S) antibodies. An engineered chimeric insert bearing the fusion of all three anti-S reactive epitopes, improved substantially the recognition and binding to their cognate antibodies. These results provide insights into humoral immune relevant epitopes and tropism characteristics of the S protein with implications for the development of subunit vaccines or other biologics against SARS-CoV.

Significance

Mapping epitopes within the receptor binding domains of viruses which are essential for viral tropism is critical for developing antiviral agents and subunit vaccines. In this study we have engineered the surface of Qubevirus to display a peptide library derived from the SARS-CoV S protein. In biopanning with S protein antibodies, we have identified three peptide fragments (EP1, EP2 and EP3) which reacted selectively with antibodies specific to the S protein. We demonstrated that all recombinant phage displayed peptide fragments both individually and as chimera exposed important immunological epitopes to their cognate antibodies. A peptide fragment F6 situated at S425-525, was found containing the binding determinant of the recombinant human angiotensin converting enzyme 2 (rhACE2), with the shortest active binding motif situated between residues S437-492. The platform is rapidly to identify epitopes and receptor binding sites within viral receptors found in target host cell. Thus, this platform holds great significance.
Functional and anatomical connectivity predict brain stimulation’s mnemonic effects
Authors: Ezzyat Youssef , Kragel James E. , Solomon Ethan A. , Lega Bradley C. , Aronson Joshua P. , Jobst Barbara C. , Gross Robert E. , Sperling Michael R. , Worrell Gregory A. , Sheth Sameer A. , Wanda Paul A. , Rizzuto Daniel S. , Kahana Michael J.
Published: July 2023

Closed-loop direct brain stimulation is a promising tool for modulating neural activity and behavior. However, it remains unclear how to optimally target stimulation to modulate brain activity in particular brain networks that underlie particular cognitive functions. Here, we test the hypothesis that stimulation’s behavioral and physiological effects depend on the stimulation target’s anatomical and functional network properties. We delivered closed-loop stimulation as 47 neurosurgical patients studied and recalled word lists. Multivariate classifiers, trained to predict momentary lapses in memory function, triggered stimulation of the lateral temporal cortex (LTC) during the study phase of the task. We found that LTC stimulation specifically improved memory when delivered to targets near white matter pathways. Memory improvement was largest for targets near white matter that also showed high functional connectivity to the brain’s memory network. These targets also reduced low-frequency activity in this network, an established marker of successful memory encoding. These data reveal how anatomical and functional networks mediate stimulation’s behavioral and physiological effects, provide further evidence that closed-loop LTC stimulation can improve episodic memory, and suggest a method for optimizing neuromodulation through improved stimulation targeting.
HIV-1 Mediated Cortical Actin Disruption Mirrors ARP2/3 Defects Found in Primary T Cell Immunodeficiencies
Authors: Crater Jacqueline M. , Dunn Daniel , Nixon Douglas F. , O’Brien Robert L. Furler
Published: July 2023

During cell movement, cortical actin balances mechanical and osmotic forces to maintain cell function while providing the scaffold for cell shape. Migrating CD4+T cells have a polarized structure with a leading edge containing dynamic branched and linear F-actin structures that bridge intracellular components to surface adhesion molecules. These actin structures are complemented with a microtubular network beaded with membrane bound organelles in the trailing uropod. Disruption of actin structures leads to dysregulated migration and changes in morphology of affected cells. In HIV-1 infection, CD4+T cells have dysregulated movement. However, the precise mechanisms by which HIV-1 affects CD4+T cell movement are unknown. Here, we show that HIV-1 infection of primary CD4+T cells causes at least four progressive morphological differences as a result of virally induced cortical cytoskeleton disruption, shown by ultrastructural and time lapse imaging. Infection with a ΔNef virus partially abrogated the dysfunctional phenotype in infected cells and partially restored a wild-type shape. The pathological morphologies after HIV-1 infection phenocopy leukocytes which contain genetic determinants of specific T cell Inborn Errors of Immunity (IEI) or Primary Immunodeficiencies (PID) that affect the actin cytoskeleton. To identify potential actin regulatory pathways that may be linked to the morphological deformities, uninfected CD4+T cell morphology was characterized following addition of small molecule chemical inhibitors. The ARP2/3 inhibitor CK-666 recapitulated three of the four abnormal morphologies we observed in HIV-1 infected cells. Restoring ARP2/3 function and cortical actin integrity in people living with HIV-1 infection is a new avenue of investigation to eradicate HIV-1 infected cells from the body.
Perceptions on the genetic biocontrol of invasive carp
Authors: Erickson Sam E , Lhewa Pema , Rundquist Kasey , Schultz Sayard , Levers Lucy , Smanski Michael J
Published: July 2023

Common carp (Cyprinus carpio) is an invasive species that damages native aquatic ecosystems. Advances in genetic engineering have led to novel genetic biocontrol methods that have the potential to aid in the control of carp and other invasive species. Research and development of these technologies is proceeding in parallel with outreach activities which aim to inform and engage the public. Public perceptions on the ethics, economics, and policy decisions surrounding the possible application of genetic control technologies are important in decision-making processes. Here we report results from a survey of more than 1,300 adults that measures the perceptions of risks, benefits, and overall comfort with a panel of existing and proposed carp control methods. Our population sample largely agrees that carp control is an important issue that demands action. We observe trends suggesting that comfort levels with the possible future implementation of genetic biocontrol for common carp are strongly influenced by the perception of benefits compared to other methods, in particular effectiveness and environmental safety. No statistically significant correlations between comfort levels and river/lake use habits nor demographics are observed. There is a need for further research to identify how respondents from similar backgrounds come to different knowledge and attitudes on the matter.
Targeting BMI-1 to deplete antibody-secreting cells in autoimmunity
Authors: Polmear Jack , Hailes Lauren , Olshansky Moshe , Rischmueller Maureen , L’Estrange-Stranieri Elan , Fletcher Anne L , Hibbs Margaret L , Bryant Vanessa L , Good-Jacobson Kim L
Published: July 2023

Objectives

B cells drive the production of autoreactive antibody-secreting cells (ASCs) in autoimmune diseases such as Systemic Lupus Erythematosus (SLE) and Sjögren’s syndrome, causing long-term organ damage. Current treatments for antibody-mediated autoimmune diseases target B cells or broadly suppress the immune system. However, pre-existing long-lived ASCs are often refractory to treatment, leaving a reservoir of autoreactive cells that continue to produce antibody. Therefore, the development of novel treatment methods targeting ASCs is vital to improve patient outcomes. Our objective was to test whether targeting the epigenetic regulator BMI-1 could deplete ASCs in autoimmune conditionsin vivoandin vitro.

Methods

Use of a BMI-1 inhibitor in both mouse and human autoimmune settings was investigated.Lyn-/-mice, a model of SLE, were treated with the BMI-1 small molecule inhibitor PTC-028, before assessment of ASCs, serum antibody and immune complexes. To examine human ASC survival, a novel human fibroblast-based assay was established, and the impact of PTC-028 on ASCs derived from Sjögren’s syndrome patients evaluated.

Results

BMI-1 inhibition significantly decreased splenic and bone marrow ASCs inLyn-/-mice. The decline in ASCs was linked to aberrant cell cycle gene expression and led to a significant decrease in serum IgG3, immune complexes and anti-DNA IgG. PTC-028 was also efficacious in reducingex vivoplasma cell survival from both Sjögren’s syndrome patients and age-matched healthy donors.

Conclusion

These data provide evidence that inhibiting BMI-1 can deplete ASC in a variety of contexts and thus BMI-1 is a viable therapeutic target for antibody-mediated autoimmune diseases.
The fate of bacterial secondary metabolites in the rhizosphere:Streptomycesdegrades and feeds on cyclic lipopeptides produced by competitors
Authors: Rigolet Augustin , Argüelles Arias Anthony , Anckaert Adrien , Quinton Loïc , Rigali Sébastien , Tellatin Deborah , Burguet Pierre , Ongena Marc
Published: July 2023

Cyclic lipopeptides are key bioactive secondary metabolites produced by some plant beneficial rhizobacteria such asPseudomonasandBacillus. They exhibit antimicrobial properties, promote induced systemic resistance in plants and support key developmental traits including motility, biofilm formation and root colonization. However, our knowledge about the fate of lipopeptides once released in the environment and especially upon contact with neighboring rhizobacteria remains limited. Here, we investigated the enzymatic degradation ofBacillusandPseudomonascyclic lipopeptides byStreptomyces venezuelae. We observed thatStreptomycesis able to degrade the three lipopeptides surfactin, iturin and fengycin upon confrontation with ofB. velezensis in vitroandin plantaaccording to specific mechanisms.S. venezuelaewas also able to degrade the structurally diverse sessilin, tolaasin, orfamide, xantholisin and putisolvin-type lipopeptides produced byPseudomonas, indicating that this trait is likely engage in the interaction with various competitors.Furthermore, the degradation of CLPs is associated with the release of free amino and fatty acids and was found to enhanceStreptomycesgrowth, indicating a possible nutritional utilization. Thereby, this work stresses on how the enzymatic arsenal ofS. venezuelaemay contribute to its adaptation to BSMs-driven interactions with microbial competitors. The ability ofStreptomycesto degrade exogenous lipopeptides and feed on them adds a new facet to the implications of the degradation of those compounds byStreptomyces, where linearization of surfactin was previously reported as a detoxification mechanism. Additionally, we hypothesize that lipopeptide-producing rhizobacteria and their biocontrol potential are impacted by the degradation of their lipopeptides as observed with the polarized motility ofB. velezensis, avoiding the confrontation zone withStreptomycesand the loss of antifungal properties of degraded iturin. This work illustrates how CLPs, once released in the environment, may rapidly be remodeled or degraded by members of the bacterial community, with potential impacts on CLP-producing rhizobacteria and the biocontrol products derived from them.
Measurable ResidualIDH1before Allogeneic Transplant for Acute Myeloid Leukemia
Authors: Gui Gege , Dillon Laura W. , Ravindra Niveditha , Hegde Pranay S. , Andrew Georgia , Mukherjee Devdeep , Wong Zoë , Auletta Jeffery , Chaer Firas El , Chen Evan , Chen Yi-Bin , Corner Adam , Devine Steven M. , Iyer Sunil , Jimenez Jimenez Antonio Martin , De Lima Marcos J.G. , Litzow Mark R. , Kebriaei Partow , Spellman Stephen R , Zeger Scott L. , Page Kristin M. , Hourigan Christopher S.
Published: August 2023

Measurable residual disease (MRD) in adults with acute myeloid leukemia (AML) in complete remission is an important prognostic marker, but detection methodology requires optimization. The persistence of mutatedNPM1orFLT3-ITD in the blood of adult patients with AML in first complete remission (CR1) prior to allogeneic hematopoetic cell transplant (alloHCT) has been established as associated with increased relapse and death after transplant. The prognostic implications of persistence of other common AML-associated mutations, such asIDH1, at this treatment landmark however remains incompletely defined. We performed testing for residualIDH1variants (IDH1m) in pre-transplant CR1 blood of 148 adult patients undergoing alloHCT forIDH1-mutated AML at a CIBMTR site between 2013-2019. No post-transplant differences were observed between those testingIDH1m positive (n=53, 36%) and negative pre-transplant (overall survival: p = 0.4; relapse: p = 0.5). For patients withIDH1mutated AML co-mutated withNPM1and/orFLT3-ITD, only detection of persistent mutatedNPM1and/orFLT3-ITD was associated with significantly higher rates of relapse (p = 0.01). These data, from the largest study to date, do not support the detection ofIDH1mutation in CR1 blood prior to alloHCT as evidence of AML MRD or increased post-transplant relapse risk.
Enhancing gene transfer to renal tubules and podocytes by context-dependent selection of AAV capsids
Authors: Furusho Taisuke , Adachi Kei , Galbraith-Liss Mia , Sairavi Anusha , Das Ranjan , Nakai Hiroyuki
Published: July 2023

Despite recent remarkable advancements in adeno-associated virus (AAV) vector technologies, effective gene delivery to the kidney remains a significant challenge. Here we show that AAV vector transduction in proximal tubules and podocytes, the crucial targets for renal gene therapy, can be enhanced remarkably through a meticulous selection of both AAV capsids and route of administration, tailored to the condition of the kidney. In this study, we performed a side-by-side comparison of 47 AAV capsids using AAV Barcode-Seq and identified six AAV capsids, including AAV-KP1, that exhibit remarkable enhancement of renal transduction in mice when delivered locally via the renal vein or the renal pelvis. Individual capsid validation analyses revealed that local delivery of AAV-KP1, but not AAV9, enables remarkably enhanced proximal tubule transduction while minimizing off-target liver transduction. In a mouse model of chronic kidney disease, intravenous administration of AAV9, not AAV-KP1, showed efficient renal tubule and podocyte transduction, which was not observed in the control wild-type mice. We also provide evidence that these contrasting observations between AAV-KP1 and AAV9 are attributed to their distinct pharmacokinetic profiles. Thus, this study highlights the importance of context-dependent capsid selection and engineering for successful renal gene therapy.
Nepicastat, a dopamine-beta-hydroxylase inhibitor decreases blood pressure and induces the infiltration of macrophages and B cells in the heart of spontaneous hypertensive rats
Authors: Chandan Shivanshu , Kosher Ganesh
Published: July 2023

Nepicastat is a potent dopamine-beta-hydroxylase inhibitor that modulates the sympathetic nervous system by inhibiting the synthesis of norepinephrine. Nepicastat is a potential drug for the treatment of congestive heart failure. We sought to investigate the mechanistic role of Nepicastsat in the heart of Spontaneous Hypertensive Rats (SHR) rats. Here, we investigated if Nepicastat at both acute (7 days) and chronic administration (14 days) decrease blood pressure and echocardiography parameters in SHR rats. SHR 3-4 months male rats were administered either Nepicastsat (30mg/kg, orally), Enalapril (10 mg/kg, orally), or vehicle for 7 days or 14 days. Blood pressure and echocardiography parameters were recorded on day 0, day 3, day 7, and day 14 of drug administration. The animals were sacrificed, and tissues are collected for histology, qRTPCR, and flow cytometry analysis. At both acute and chronic administration, Nepicastat decreased systolic blood pressure and intraventricular septal thickness of SHR rats compared to vehicle groups. The decrease in blood pressure was comparable to Enalapril treated rats. Interestingly, Nepicastat also decreased the infiltrating macrophages and B cells in the hearts of SHR rats. In conclusion, Nepicastsat consistently decreased the systolic blood pressure but increased the macrophages and B cell infiltration in the heart of SHR rats.
Adapting antibacterial display to identify serum active macrocyclic peptide antibiotics
Authors: Randall Justin R. , Groover Kyra E. , O’Donnell Angela C. , Garza Joseph M. , Cole T. Jeffrey , Davies Bryan W.
Published: July 2023

The lack of available treatments for many antimicrobial resistant infections highlights the critical need for antibiotic discovery innovation. Peptides are an underappreciated antibiotic scaffold because they often suffer from proteolytic instability and toxicity towards human cells, makingin vivouse challenging. To investigate sequence factors related to serum activity, we adapt an antibacterial display technology to screen a library of peptide macrocycles for antibacterial potential directly in human serum. We identify dozens of new macrocyclic peptide antibiotic sequences and find that serum activity within our library is influenced by peptide length, cationic charge, and the number of disulfide bonds present. Interestingly, an optimized version of our most active lead peptide permeates the outer membrane of gram-negative bacteria without strong inner membrane disruption and kills bacteria slowly while causing cell elongation. This contrasts with traditional cationic antimicrobial peptides, which kill rapidly via lysis of both bacterial membranes. Notably, this optimized variant is not toxic to mammalian cells and retains its functionin vivo, suggesting therapeutic promise. Our results support the use of more physiologically relevant conditions when screening peptides for antimicrobial activity which retainin vivofunctionality.

Significance

Traditional methods of natural antibiotic discovery are low throughput and cannot keep pace with the development of antimicrobial resistance. Synthetic peptide display technologies offer a high-throughput means of screening drug candidates, but rarely consider functionality beyond simple target binding and do not consider retention of functionin vivo. Here, we adapt a function-based, antibacterial display technology to screen a large library of peptide macrocycles directly for bacterial growth inhibition in human serum. This screen identifies an optimized non-toxic macrocyclic peptide antibiotic retainingin vivofunction, suggesting this advancement could increase clinical antibiotic discovery efficiency.
Changes in coding and efficiency through modular modifications to a One Pot PURE system for in vitro transcription & translation
Authors: Ngo Phuoc H. T. , Ishida Satoshi , Busogi Bianca B. , Do Hannah , Ledesma Maximiliano A. , Kar Shaunak , Ellington Andrew
Published: July 2023

The incorporation of unnatural amino acids are attractive methods for improving or bringing new and novel functions in peptides and proteins. Cell-free protein synthesis using the Protein Synthesis Using Recombinant Elements (PURE) system is an attractive platform for efficient unnatural amino acid incorporation. In this work, we further adapted and modified the One Pot PURE for a robust and modular system of enzymatic single site-specific of unnatural amino acid. We demonstrated the flexibility of this system through the introduction of two orthogonal aminoacyl tRNA synthetases and the suppression of two distinctive stop codons.