bluuebunny/crossref_metadata_2025 huggingface dataset:
On absolutely profinitely solitary lattices in higher rank Lie groups
Authors: Kammeyer Holger
Published: January 2023

We establish conditions under which lattices in certain simple Lie groups are profinitely solitary in the absolute sense, so that the commensurability class of the profinite completion determines the commensurability class of the group among finitely generated residually finite groups. While cocompact lattices are typically not absolutely solitary, we show that noncocompact lattices in

Sp
⁡
(
n
,

R

)

\operatorname {Sp}(n,\mathbb {R})

,

G

2
(
2
)

G_{2(2)}

,

E
8

(

C

)

E_8(\mathbb {C})

,

F
4

(

C

)

F_4(\mathbb {C})

, and

G
2

(

C

)

G_2(\mathbb {C})

are absolutely solitary if a well-known conjecture on Grothendieck rigidity is true.
Establishment of Safety of Hemostatic Net Application Utilizing Laser-Assisted Fluorescence Angiography With SPY-Q Software Analysis
Authors: Kachare Milind D , Moore Alec C , Little Jarrod , O’Daniel Thomas Gerald
Published: January 2023

Background

The hemostatic net, which was initially described as a method to decrease hematoma rates in facelift and necklift procedures, has since increased in practice and applicability. However, despite its demonstrated safety and efficacy, there exists significant skepticism with regard to its necessity; in particular, there is concern that the transcutaneous sutures may restrict dermal perfusion.

Objectives

The goal of this study was to assess flap perfusion, both before and after application of the hemostatic net, to determine if there was an objective decrease in tissue perfusion in relation to application of the hemostatic net, as measured by laser-assisted angiography (LAA).

Methods

Eight patients underwent cervicofacial flap reconstruction of cutaneous malignancy defects, after which a hemostatic net was applied. All patients underwent evaluation with LAA both before and after application of the net. The average relative and absolute perfusion of different zones of the flap were calculated.

Results

The average absolute change in relative perfusion was +6.41%, +0.31%, and +3.28% for zones 1, 2, and 3, respectively, after application of the hemostatic net. There was no statistical difference in relative tissue perfusion after application of the net. There were no instances of delayed healing, infections, ischemia, necrosis, or hematoma. One patient developed a seroma after the net was removed. No patients had scarring or residual track marks from the transcutaneous sutures.

Conclusions

With LAA, we were able to objectively demonstrate no significant decrease in tissue perfusion after the application of the hemostatic net.

Level of Evidence: 4
Predicting executive functioning from functional brain connectivity: network specificity and age effects
Authors: Heckner Marisa K , Cieslik Edna C , Patil Kaustubh R , Gell Martin , Eickhoff Simon B , Hoffstädter Felix , Langner Robert
Published: January 2023

Healthy aging is associated with altered executive functioning (EF). Earlier studies found age-related differences in EF performance to be partially accounted for by changes in resting-state functional connectivity (RSFC) within brain networks associated with EF. However, it remains unclear which role RSFC in EF-associated networks plays as a marker for individual differences in EF performance. Here, we investigated to what degree individual abilities across 3 different EF tasks can be predicted from RSFC within EF-related, perceptuo-motor, whole-brain, and random networks separately in young and old adults. Specifically, we were interested if (i) young and old adults differ in predictability depending on network or EF demand level (high vs. low), (ii) an EF-related network outperforms EF-unspecific networks when predicting EF abilities, and (iii) this pattern changes with demand level. Both our uni- and multivariate analysis frameworks analyzing interactions between age × demand level × networks revealed overall low prediction accuracies and a general lack of specificity regarding neurobiological networks for predicting EF abilities. This questions the idea of finding markers for individual EF performance in RSFC patterns and calls for future research replicating the current approach in different task states, brain modalities, different, larger samples, and with more comprehensive behavioral measures.
STRA6 is essential for induction of vascular smooth muscle lineages in human embryonic cardiac outflow tract development
Authors: Zhou Chikai , Häneke Timm , Rohner Eduarde , Sohlmér Jesper , Kameneva Polina , Artemov Artem , Adameyko Igor , Sahara Makoto
Published: January 2023

Aims

Retinoic acid (RA) signalling is essential for heart development, and dysregulation of the RA signalling can cause several types of cardiac outflow tract (OFT) defects, the most frequent congenital heart disease (CHD) in humans. Matthew-Wood syndrome is caused by inactivating mutations of a transmembrane protein gene STRA6 that transports vitamin A (retinol) from extracellular into intracellular spaces. This syndrome shows a broad spectrum of malformations including CHD, although murine Stra6-null neonates did not exhibit overt heart defects. Thus, the detailed mechanisms by which STRA6 mutations could lead to cardiac malformations in humans remain unclear. Here, we investigated the role of STRA6 in the context of human cardiogenesis and CHD.

Methods and results

To gain molecular signatures in species-specific cardiac development, we first compared single-cell RNA sequencing (RNA-seq) datasets, uniquely obtained from human and murine embryonic hearts. We found that while STRA6 mRNA was much less frequently expressed in murine embryonic heart cells derived from the Mesp1+ lineage tracing mice (Mesp1Cre/+; Rosa26tdTomato), it was expressed predominantly in the OFT region-specific heart progenitors in human developing hearts. Next, we revealed that STRA6-knockout human embryonic stem cells (hESCs) could differentiate into cardiomyocytes similarly to wild-type hESCs, but could not differentiate properly into mesodermal nor neural crest cell-derived smooth muscle cells (SMCs) in vitro. This is supported by the population RNA-seq data showing down-regulation of the SMC-related genes in the STRA6-knockout hESC-derived cells. Further, through machinery assays, we identified the previously unrecognized interaction between RA nuclear receptors RARα/RXRα and TBX1, an OFT-specific cardiogenic transcription factor, which would likely act downstream to STRA6-mediated RA signalling in human cardiogenesis.

Conclusion

Our study highlights the critical role of human-specific STRA6 progenitors for proper induction of vascular SMCs that is essential for normal OFT formation. Thus, these results shed light on novel and human-specific CHD mechanisms, driven by STRA6 mutations.
Electrocardiographic findings in patients with arrhythmogenic cardiomyopathy and right bundle branch block ventricular tachycardia
Authors: Laredo Mikael , Tovia-Brodie Oholi , Milman Anat , Michowitz Yoav , Roudijk Rob W , Peretto Giovanni , Badenco Nicolas , te Riele Anneline S J M , Sala Simone , Duthoit Guillaume , Arbelo Elena , Ninni Sandro , Gasperetti Alessio , van Tintelen J Peter , Paglino Gabriele , Waintraub Xavier , Andorin Antoine , Peichl Petr , Bosman Laurens P , Calo Leonardo , Giustetto Carla , Radinovic Andrea , Jorda Paloma , Casado-Arroyo Ruben , Zorio Esther , Bermúdez-Jiménez Francisco J , Behr Elijah R , Havranek Stepan , Tfelt-Hansen Jacob , Sacher Frederic , Hermida Jean-Sylvain , Nof Eyal , Casella Michela , Kautzner Josef , Lacroix Dominique , Brugada Josep , Duru Firat , Bella Paolo Della , Gandjbakhch Estelle , Hauer Richard , Belhassen Bernard
Published: January 2023

Aims

Little is known about patients with right bundle branch block (RBBB)-ventricular tachycardia (VT) and arrhythmogenic cardiomyopathy (ACM). Our aims were: (i) to describe electrocardiogram (ECG) characteristics of sinus rhythm (SR) and VT; (ii) to correlate SR with RBBB-VT ECGs; and (iii) to compare VT ECGs with electro-anatomic mapping (EAM) data.

Methods and results

From the European Survey on ACM, 70 patients with spontaneous RBBB-VT were included. Putative left ventricular (LV) sites of origin (SOOs) were estimated with a VT-axis-derived methodology and confirmed by EAM data when available. Overall, 49 (70%) patients met definite Task Force Criteria. Low QRS voltage predominated in lateral leads (n = 37, 55%), but QRS fragmentation was more frequent in inferior leads (n = 15, 23%). T-wave inversion (TWI) was equally frequent in inferior (n = 28, 42%) and lateral (n = 27, 40%) leads. TWI in inferior leads was associated with reduced LV ejection fraction (LVEF; 46 ± 10 vs. 53 ± 8, P = 0.02). Regarding SOOs, the inferior wall harboured 31 (46%) SOOs, followed by the lateral wall (n = 17, 25%), the anterior wall (n = 15, 22%), and the septum (n = 4, 6%). EAM data were available for 16 patients and showed good concordance with the putative SOOs. In all patients with superior-axis RBBB-VT who underwent endo-epicardial VT activation mapping, VT originated from the LV.

Conclusions

In patients with ACM and RBBB-VT, RBBB-VTs originated mainly from the inferior and lateral LV walls. SR depolarization and repolarization abnormalities were frequent and associated with underlying variants.
Outcome and safety of intraoperative defibrillation testing during device replacement: the Simpler trial
Authors: Milman Anat , Nof Eyal , Rav Acha Moshe , Beinart Roy , Kutyifa Valentina , Merkely Béla , Regev Ehud , Biffi Mauro , Cha Yong-Mei , Ovdat Tal , Klempfner Robert , Glikson Michael
Published: January 2023

Aims

Intraoperative defibrillation testing (DT) during implant or replacement of implantable cardioverter-defibrillators (ICDs) has been a matter of debate for many years. This debate was put to rest by the Simple and Nordic ICD trials, and the practice of testing during new implantations has essentially been almost abandoned. Old registries demonstrated an increased incidence of significant findings in DT during replacements. The aim of the present study was to evaluate frequency of significant findings and safety of DT in subjects undergoing device replacement.

Methods and results

A prospective observational multi-centre study included consecutive patients undergoing ICD generator replacement. The primary outcome was a failure to terminate induced ventricular fibrillation (VF) with a single shock 10 J below the maximal capacity of the device. Secondary outcomes included complications of DT. Patients were followed-up at 1- and 6-months post-procedure. A total of 92 patients were eligible, and consented to the study, of which 84 underwent DT during battery replacement. The median age was 68 years and 79.8% were males. Induction of VF was successful in 84 patients as was a successful conversion on the first attempt in all. There were no procedure-related complications. During follow up one patient had two appropriate ICD shock events. In four patients, ICD programming was changed. None suffered inappropriate shock. There was no evidence of lead malfunction. Two deaths occurred, none of which was related to arrhythmia.

Conclusion

The present study found DT was not associated with complications in patients undergoing ICD generator replacement but produced no clinically important information.
A convergent SAV scheme for Cahn–Hilliard equations with dynamic boundary conditions
Authors: Metzger Stefan
Published: January 2023

The Cahn–Hilliard equation is one of the most common models to describe phase separation processes in mixtures of two materials. For a better description of short-range interactions between the material and the boundary, various dynamic boundary conditions for this equation have been proposed. Recently, a family of models using Cahn–Hilliard-type equations on the boundary of the domain to describe adsorption processes was analysed (cf. Knopf, P., Lam, K. F., Liu, C. & Metzger, S. (2021) Phase-field dynamics with transfer of materials: the Cahn–Hilliard equation with reaction rate dependent dynamic boundary conditions. ESAIM: Math. Model. Numer. Anal., 55, 229–282). This family of models includes the case of instantaneous adsorption processes studied by Goldstein, Miranville and Schimperna (2011, A Cahn–Hilliard model in a domain with non-permeable walls. Phys. D, 240, 754–766) as well as the case of vanishing adsorption rates, which was investigated by Liu and Wu (2019, An energetic variational approach for the Cahn–Hilliard equation with dynamic boundary condition: model derivation and mathematical analysis. Arch. Ration. Mech. Anal., 233, 167–247). In this paper, we are interested in the numerical treatment of these models and propose an unconditionally stable, linear, fully discrete finite element scheme based on the scalar auxiliary variable approach. Furthermore, we establish the convergence of discrete solutions towards suitable weak solutions of the original model. Thereby, when passing to the limit, we are able to remove the auxiliary variables introduced in the discrete setting completely. Finally, we present simulations based on the proposed linear scheme and compare them to results obtained using a stable, nonlinear scheme to underline the practicality of our scheme.
Atypical Presentations of Extraparenchymal Neurocysticercosis
Authors: Fan Jason , Tang Rui , Zhang Lily , Hoang Phuong T. , Ayoade Folusakin , Diaz-Perez Julio A. , Moss Heather E. , Jiang Hong
Published: January 2023

Background:

Neurocysticercosis (NCC) is the most common parasitic infection of the central nervous system and is typically diagnosed through visualization of the cysts in the cerebral parenchyma by neuro-imaging. However, neuro-imaging may not detect extraparenchymal neurocysticercosis (EPNCC), which is a rare manifestation of the disease involving the subarachnoid, meningeal, and intraventricular spaces. We report 2 cases of extraparenchymal neurocysticercosis, and discuss the diagnostic challenges and management of this entity.

Methods:

Two cases were identified through clinical records.

Results:

Both patients had an insidious onset with slow progression of disease, and presented with papilledema and cerebrospinal fluid (CSF) eosinophilia. One case was diagnosed with spinal cord biopsy. The other was diagnosed with CSF serology and next-generation sequencing–based pathogen analysis. Both patients were treated with ventriculoperitoneal shunt, systemic antiparasitic agents, and immunosuppression.

Conclusions:

EPNCC is less common than parenchymal NCC. A high level of clinical suspicion is required given its rarity, long incubation period, and slow progression. Diagnosis and treatment can be challenging and requires a multidisciplinary approach.
Novel CAF-identifiers via transcriptomic analysis in oral cancer patients
Authors: Dwivedi Nehanjali , Shukla Nidhi , Das Manjula , Dhar Sujan K
Published: January 2023

Background

Cancer-associated fibroblasts (CAFs), a prominent component of the tumor microenvironment, plays an important role in tumor development, invasion, and drug resistance. The expression of distinct “CAF markers,” which separates CAFs from normal fibroblasts and epithelial cells, have traditionally been used to identify them. These commonly used CAF markers have been reported to differ greatly across microenvironmental subpopulations even within a cancer site.

Methods

Using an unbiased data analysis approach utilizing publicly available and in-house gene expression data from patient derived novel CAF cells, we identified a collection of markers in oral cancer to distinguish CAF populations from tumor epithelia and normal oral fibroblasts.

Results

COL1A1, SPARC, COL1A2, COL3A1 and TIMP-1 were identified as potential markers which can be utilized to differentiate cancer associated fibroblast from all other cell types including normal fibroblasts in oral cancer.
APOE3Christchurch modulates tau phosphorylation and β-catenin/Wnt/Cadherin signaling in induced pluripotent stem cell-derived cerebral organoids from Alzheimer’s cases
Authors: Mazzarino RC , Perez-Corredor P , Vanderleest TE , Vacano GN , Sanchez JS , Villalba-Moreno ND , Krausemann S , Mendivil-Perez MA , Aguillón D , Jimenez-Del-Río M , Baena A , Sepulveda-Falla D , Lopera FJ , Quiroz YT , Arboleda-Velasquez JF
Published: January 2023

Alzheimer’s disease (AD) is the most common cause of dementia among older adults.APOE3Christchurch (R136S,APOE3Ch) variant homozygosity was reported in an individual with extreme resistance to autosomal dominant AD due to thePSEN1E280A mutation. This subject had a delayed clinical age at onset and resistance to tauopathy and neurodegeneration despite extremely high amyloid plaque burden. We established induced pluripotent stem (iPS) cell-derived cerebral organoids from this resistant case and from a non-protected kindred control (withPSEN1E280A andAPOE3/3). We used CRISPR/Cas9 gene editing to successfully remove theAPOE3Chto wild type in iPS cells from the protected case and to introduce theAPOE3Chas homozygote in iPS cells from the non-protected case to examine causality. We found significant reduction of tau phosphorylation (pTau 202/205 and pTau396) in cerebral organoids with theAPOE3Chvariant, consistent with the strikingly reduced tau pathology found in the resistant case. We identified Cadherin and Wnt pathways as signaling mechanisms regulated by theAPOE3Chvariant through single cell RNA sequencing in cerebral organoids. We also identified elevated β-catenin protein, a regulator of tau phosphorylation, as a candidate mediator ofAPOE3Chresistance to tauopathy. Our findings show thatAPOE3Chis necessary and sufficient to confer resistance to tauopathy in an experimentalex-vivomodel establishing a foundation for the development of novel, protected case-inspired therapeutics for tauopathies, including Alzheimer’s.
Deep-learning based bioactive peptides generation and screening against Xanthine oxidase
Authors: Zhang Haiping , Saravanan Konda Mani , Zhang John Z.H. , Wu Xuli
Published: January 2023

In our previous work, we have developed LSTM_Pep to generatede novopotential active peptides by finetuning with known active peptides and developed DeepPep to effectively identify protein-peptide interaction. Here, we have combined LSTM_Pep and DeepPep to successfully obtained an activede novopeptide (ARG-ALA-PRO-GLU) of Xanthine oxidase (XOD) with IC50 value of 3.76mg/mL, and XOD inhibitory activity of 64.32%. Consistent with the experiment result, the peptide ARG-ALA-PRO-GLU has the highest DeepPep score, this strongly supports that we can generatede novopotential active peptides by finetune training LSTM_Pep over some known active peptides and identify those active peptides by DeepPep effectively. Our work sheds light on the development of deep learning-based methods and pipelines to effectively generate and obtain bioactive peptides with a specific therapeutic effect and showcases how artificial intelligence can help discoverde novobioactive peptides that can bind to a particular target.
Activation Dynamics of Ubiquitin Specific Protease 7
Authors: Valles Gabrielle J. , Jaiswal Nancy , Korzhnev Dmitry M. , Bezsonova Irina
Published: January 2023

Ubiquitin-specific protease 7 (USP7) is a deubiquitinating enzyme responsible for the regulation of key human oncoproteins and tumor suppressors including Mdm2 and p53, respectively. Unlike other members of the USP family of proteases, the isolated catalytic domain of USP7 adopts an enzymatically inactive conformation that has been well characterized using X-ray crystallography. The catalytic domain also samples an active conformation, which has only been captured upon USP7 substrate-binding. Here, we utilized CPMG NMR relaxation dispersion studies to observe the dynamic motions of USP7 in solution. Our results reveal that the catalytic domain of USP7 exchanges between two distinct conformations, the inactive conformation populated at 95% and the active conformation at 5%. The largest structural changes are localized within functionally important regions of the enzyme including the active site, the ubiquitin-binding fingers, and the allosteric helix of the enzyme, suggesting that USP7 can adopt its active conformation in the absence of a substrate. Furthermore, we show that the allosteric L299A activating mutation disturbs this equilibrium, slows down the exchange, and increases the residence time of USP7 in its active conformation, thus, explaining the elevated activity of the mutant. Overall, this work shows that the isolated USP7 catalytic domain pre-samples its “invisible” active conformation in solution, which may contribute to its activation mechanism.
Notch signaling regulates immunosuppressive tumor-associated macrophage function in pancreatic cancer
Authors: Yan Wei , Steele Nina G. , Kemp Samantha B. , Menjivar Rosa E. , Du Wenting , Carpenter Eileen S. , Donahue Katelyn L. , Brown Kristee L. , Irizarry-Negron Valerie , Yang Sion , Burns William R. , Zhang Yaqing , di Magliano Marina Pasca , Bednar Filip
Published: January 2023

Pancreatic ductal adenocarcinoma (PDA) continues to have a dismal prognosis. The poor survival of patients with PDA has been attributed to a high rate of early metastasis and low efficacy of current therapies, which partly result from its complex immunosuppressive tumor microenvironment. Previous studies from our group and others have shown that tumor-associated macrophages (TAMs) are instrumental in maintaining immunosuppression in PDA. Here, we explored the role of Notch signaling, a key regulator of immune response, within the PDA microenvironment. We identified Notch pathway components in multiple immune cell types within human and mouse pancreatic cancer. TAMs, the most abundant immune cell population in the tumor microenvironment, express high levels of Notch receptors with cognate ligands such asJAG1expressed on tumor epithelial cells, endothelial cells and fibroblasts. TAMs with activated Notch signaling expressed higher levels of immunosuppressive mediators including arginase 1 (Arg1) suggesting that Notch signaling plays a role in macrophage polarization within the PDA microenvironment. Combination of Notch inhibition with PD-1 blockade resulted in increased cytotoxic T cell infiltration, tumor cell apoptosis, and smaller tumor size. Our work implicates macrophage Notch signaling in the establishment of immunosuppression and indicates that targeting the Notch pathway may improve the efficacy of immune-based therapies in PDA patients.
Analysis of the molecular determinants for furin cleavage of the spike protein S1/S2 site in defined strains of the prototype coronavirus murine hepatitis virus (MHV)
Authors: Choi Annette , Kots Ekaterina D. , Singleton Deanndria T. , Weinstein Harel A. , Whittaker Gary R.
Published: January 2023

We have analyzed the spike protein S1/S2 cleavage site of selected strains of MHV by the cellular protease furin, in order to understand the structural requirements underlying the sequence selectivity of the scissile segment. The probability of cleavage of the various MHV strains was first evaluated from furin cleavage scores predicted by the ProP computer software, and then cleavage was measured experimentally with a fluorogenic peptide cleavage assay consisting of S1/S2 peptide mimics and purified furin. We found thatin vitrocleavability varied across MHV strains in line with predicted results—but with the notable exception of MHV-A59, which was not cleaved despite a high score predicted for its sequence. Using the known X-Ray structure of furin in complex with a substrate-like inhibitor as an initial structural reference, we carried out molecular dynamics (MD) simulations to learn the modes of binding of the peptides in the furin active site, and the suitability of the complex for initiation of the enzymatic cleavage. We thus identified the 3D structural requirements of the furin active site configuration that enable bound peptides to undergo cleavage, and the way in which the various strains tested experimentally are fulfilling these requirements. We find that despite some flexibility in the organization of the peptide bound to the active site of the enzyme, the presence of a histidine at P2 of MHV-A59 fails to properly orient the sidechain of His194 of the furin catalytic triad and therefore produces a distortion that renders the peptide/complex structural configuration in the active site incompatible with requirements for cleavage initiation. The Ser/Thr in P1 of MHV-2 and MHV-S has a similar effect of distorting the conformation of the furin active site residues produced by the elimination of the canonical salt-bridge formed by arginine in P1 position. This work informs a study of coronavirus infection and pathogenesis with respect to the function of the viral spike protein, and suggests an important process of viral adaptation and evolution within the spike S1/S2 structural loop.
Longitudinal changes in Alzheimer’s-related plasma biomarkers and brain amyloid
Authors: Bilgel Murat , An Yang , Walker Keenan A. , Moghekar Abhay R. , Ashton Nicholas J. , Kac Przemysław R. , Karikari Thomas K. , Blennow Kaj , Zetterberg Henrik , Jedynak Bruno M. , Thambisetty Madhav , Ferrucci Luigi , Resnick Susan M.
Published: January 2023

Introduction

Understanding longitudinal plasma biomarker trajectories relative to brain amyloid changes can help devise Alzheimer’s progression assessment strategies.

Methods

We examined the temporal order of changes in plasma amyloid-β ratio (Aβ42/Aβ40), glial fibrillary acidic protein (GFAP), neurofilament light chain (NfL), and phosphorylated tau ratios (p-tau181/Aβ42, p-tau231/Aβ42) relative to11C-Pittsburgh compound B (PiB) positron emission tomography (PET) cortical amyloid burden (PiB−/+). Participants (n = 199) were cognitively normal at index visit with a median 6.1-year follow-up.

Results

PiB groups exhibited different rates of longitudinal change in Aβ42/Aβ40(β= 5.41 × 10-4, SE = 1.95 × 10-4,p= 0.0073). Change in brain amyloid correlated with change in GFAP (r= 0.5, 95% CI = [0.26, 0.68]). Greatest relative decline in Aβ42/Aβ40(-1%/year) preceded brain amyloid positivity by 41 years (95% CI = [32, 53]).

Discussion

Plasma Aβ42/Aβ40may begin declining decades prior to brain amyloid accumulation, whereas p-tau ratios, GFAP, and NfL increase closer in time.
Poison exon annotations improve the yield of clinically relevant variants in genomic diagnostic testing
Authors: Felker Stephanie A , Lawlor James MJ , Hiatt Susan M , Thompson Michelle L , Latner Donald R , Finnila Candice R , Bowling Kevin M , Bonnstetter Zachary T , Bonini Katherine E , Kelly Nicole R , Kelley Whitley V , Hurst Anna CE , Kelly Melissa A , Nakouzi Ghunwa , Hendon Laura G , Bebin E Martina , Kenny Eimear E , Cooper Gregory M
Published: January 2023

Purpose

Neurodevelopmental disorders (NDDs) often result from rare genetic variation, but genomic testing yield for NDDs remains around 50%, suggesting some clinically relevant rare variants may be missed by standard analyses. Here we analyze “poison exons” (PEs) which, while often absent from standard gene annotations, are alternative exons whose inclusion results in a premature termination codon. Variants that alter PE inclusion can lead to loss-of-function and may be highly penetrant contributors to disease.

Methods

We curated published RNA-seq data from developing mouse cortex to define 1,937 PE regions conserved between humans and mice and potentially relevant to NDDs. We then analyzed variants found by genome sequencing in multiple NDD cohorts.

Results

Across 2,999 probands, we found six clinically relevant variants in PE regions that were previously overlooked. Five of these variants are in genes that are part of the sodium voltage-gated channel alpha subunit family (SCN1A, SCN2A, andSCN8A), associated with epilepsies. One variant is inSNRPB, associated with Cerebrocostomandibular Syndrome. These variants have moderate to high computational impact assessments, are absent from population variant databases, and were observed in probands with features consistent with those reported for the associated gene.

Conclusion

With only a minimal increase in variant analysis burden (most probands had zero or one candidate PE variants in a known NDD gene, with an average of 0.77 per proband), annotation of PEs can improve diagnostic yield for NDDs and likely other congenital conditions.
Identifying the suite of genes central to swimming in the biocontrol bacteriaPseudomonas protegensPf-5
Authors: Fabian BK , Foster C , Asher A , Hassan KA , Paulsen IT , Tetu SG
Published: January 2023

Swimming motility is a key bacterial trait, important to success in many niches, including assisting in colonization of host surfaces. Biocontrol bacteria, such asPseudomonas protegensPf-5 are increasingly being used as an agricultural tool to control crop diseases, where motility is a factor in successful colonization of the plant rhizosphere. Swimming motility has been studied in a range of bacteria and typically involves a suite of flagella and chemotaxis genes, however the specific gene set employed for both regulation and biogenesis can differ substantially between organisms. Here we used transposon directed insertion site sequencing (TraDIS), a genome-wide approach, to identify 249 genes involved inP. protegensPf-5 swimming motility. As expected, flagella and chemotaxis genes comprised a large proportion of these genes. However we also identified a suite of additional genes important for swimming, including genes related to peptidoglycan turnover, O-antigen biosynthesis, cell division, signal transduction, c-di-GMP turnover and phosphate transport, along with 27 conserved hypothetical proteins. Experimental gene knockout mutants and TraDIS data together suggest that defects in the Pst phosphate transporter lead to enhanced swimming motility. Overall, this study expands our knowledge of pseudomonad motility and highlights the utility of a TraDIS-based approach for systematically analyzing the functions of thousands of genes. This work sets a foundation for understanding how swimming motility may be related to the inconsistency in biocontrol bacteria effectiveness and reliability in the field.

Importance

Biocontrol bacteria, such asPseudomonas protegensPf-5 are increasingly being used as an agricultural tool to control crop diseases, and motility is a key factor in their successful colonization of plant surfaces. Here we use a high-throughput approach to identify the suite of genes important for swimming motility inP. protegensPf-5. These included flagella and chemotaxis genes, as well as a variety of cell surface, cell division and signalling genes. We also show that defects in the Pst phosphate transporter lead to enhanced swimming motility, a hitherto unreported link between phosphate transport and swimming motility. Understanding the genetic basis of swimming motility enhances our knowledge of key processes in biocontrol bacteria that are needed to ensure their competitive success. This will contribute to developing strategies to increase the utility of biocontrol bacteria in agricultural settings to prevent crop losses.
Lytic bacteriophage vB_KmiS-Kmi2C disrupts biofilms formed by members of theKlebsiella oxytocacomplex, and represents a novel virus family and genus
Authors: Newberry Fiona , Shibu Preetha , Smith-Zaitlik Thomas , Eladawy Mohamed , McCartney Anne L. , Hoyles Lesley , Negus David
Published: January 2023

AIMS

This study aimed to characterise the lytic phage vB_KmiS-Kmi2C, isolated from sewage water on a GES-positive strain ofKlebsiella michiganensis.

METHODS AND RESULTS

Comparative phylogenetic and network-based analyses were used to characterise the genome of phage vB_KmiS-Kmi2C (circular genome of 42,234 bp predicted to encode 55 genes), demonstrating it shared little similarity with other known phages. The phage was lytic on clinical strains ofK. oxytoca(n=2) andK. michiganensis(n=4), and was found to both prevent biofilm formation and disrupt established biofilms produced by these strains.

CONCLUSIONS

We have identified a phage capable of killing clinically relevant members of theKlebsiella oxytocacomplex (KoC). The phage represents a novel virus family (proposed nameDilsviridae) and genus (proposed nameDilsvirus).

SIGNIFICANCE AND IMPACT OF THE STUDY

Identification a novel lytic phage active against clinically relevant strains of the KoC provides an alternative to antibiotics to treat these increasingly antimicrobial-resistant opportunistic pathogens. The unusual way in which the phage can disrupt established biofilms may allow us to identify novel phage-based approaches for biofilm remediation in the future.
Mechanism of ribosome-associated mRNA degradation during tubulin autoregulation
Authors: Höpfler Markus , Absmeier Eva , Peak-Chew Sew-Yeu , Vartholomaiou Evangelia , Passmore Lori A. , Gasic Ivana , Hegde Ramanujan S.
Published: January 2023

Microtubules play crucial roles in cellular architecture, intracellular transport, and mitosis. The availability of free tubulin subunits impacts polymerization dynamics and microtubule function. When cells sense excess free tubulin, they trigger degradation of the encoding mRNAs, which requires recognition of the nascent polypeptide by the tubulin-specific ribosome-binding factor TTC5. How TTC5 initiates decay of tubulin mRNAs is unknown. Here, our biochemical and structural analysis reveals that TTC5 recruits the poorly studied protein SCAPER to the ribosome. SCAPER in turn engages the CCR4-NOT deadenylase complex through its CNOT11 subunit to trigger tubulin mRNA decay. SCAPER mutants that cause intellectual disability and retinitis pigmentosa in humans are impaired in CCR4-NOT recruitment, tubulin mRNA degradation, and microtubule-dependent chromosome segregation. Our findings demonstrate how recognition of a nascent polypeptide on the ribosome is physically linked to mRNA decay factors via a relay of protein-protein interactions, providing a paradigm for specificity in cytoplasmic gene regulation.
Membrane-binding properties of NS1 proteins from Zika and Dengue viruses: Comparative simulations in explicit bilayers reveal significant differences
Authors: Muthukumaran Rajagopalan , Sankararamakrishnan Ramasubbu
Published: January 2023

NS1 in flaviviruses is the only non-structural protein that is secretory and interacts with different cellular components. NS1 is localized in endoplasmic reticulum as a dimer to facilitate the viral replication. The crystal structures of NS1 homologs from zika (ZIKV) and dengue (DENV) viruses have revealed the organization of different domains in NS1 dimers. The β-roll and the connector and intertwined loop regions of wing domains of NS1 have been shown to interact with the membranes. The membrane-binding properties and the differences between ZIKV and DENV NS1 homologs in interacting with the membranes have not been investigated. In this study, we have performed molecular dynamics (MD) simulations of ZIKV and DENV NS1 systems in apo and in POPE bilayers with different cholesterol concentrations (0, 20 and 40%). In the simulations with bilayers, the NS1 protein was placed just above the membrane surface. At the end of 600 ns production runs, ZIKV NS1 inserts deeper inside the membrane compared to the DENV counterpart. The conformational landscape sampled by NS1 in the presence of membrane was analyzed. Unlike ZIKV NS1, the orientation of DENV NS1 is asymmetric in which one of the chains in dimer interacts with the membrane while the other is exposed to the solvent. The β-roll region in ZIKV NS1 penetrates beyond the headgroup region and some residues interact with the lipid acyl chains while the C-terminal region barely interacts with the headgroup. Specific residues in the intertwined region deeply penetrate inside the membrane with less interactions with water molecules. Our analysis showed that more charged residues of ZIKV NS1 are involved in stronger interactions with the headgroups than that found for DENV NS1. The role of hydrophobic and aromatic residues in interactions with acyl chain region is also evident. Presence of cholesterol affects the extent of insertion in the membrane and interaction of individual residues. This study clearly shows that the binding, insertion and interaction of ZIKV NS1 with the lipid bilayer significantly differs from its counterpart in DENV.
Adsorption of RNA to interfaces of biomolecular condensates enables wetting transitions
Authors: Erkamp Nadia A. , Farag Mina , Qian Daoyuan , Sneideris Tomas , Welsh Timothy J. , Ausserwöger Hannes , Weitz David A. , Pappu Rohit V. , Knowles Tuomas P. J.
Published: January 2023

Biomolecular condensates form via spontaneous and driven phase transitions of multivalent proteins and nucleic acids. These macromolecules can be organized in spatially inhomogeneous ways that lead to multiple coexisting dense phases with distinct macromolecular interfaces. While considerable attention has focused on the physical driving forces that give rise to phase separation from bulk solutions, the interactions that underlie adsorption driven wetting transitions remain unclear. Here, we report that pyrimidine-rich RNAs function as adsorbents that enable cascades of wetting transitions that include partial and complete wetting of condensates formed by purine-rich RNAs. Computations show that macromolecules that are scaffolds of condensates are oriented perpendicular to condensate interfaces whereas adsorbents are oriented parallel to interfaces. Our results yield heuristics for the design of synthetic materials that can be based on RNA-rich condensates featuring bespoke interfaces and distinct local microenvironments created by the interplay between scaffolds versus adsorbents.
High frequency soil polarization can phenotype crop roots noninvasively
Authors: Gu Huijie , Cseresnyés Imre , Butnor John R. , Li Baoru , Mary Benjamin , Sun Hongyong , Zhang Xiying , Lu Yang , Liu Xiuwei
Published: January 2023

Noninvasive and nondestructive root phenotyping techniques under field conditions are sorely needed to advance plant root science. Soil polarization measured by electrical capacitance (ECsoil) has the potential to meet this requirement, but whether it specifically detects root properties remains unexplored. We carried out manipulative experiments where wheat (Triticum aestivumL.) and maize (Zea maysL.) roots were buried in soil or immersed in hydroponic solution combined with pot trials to reveal the mechanism of root trait detection by ECsoil, while a field experiment was conducted to test its feasibility to determine root depth distribution. We found that ECsoilmeasured at low current frequency (< 1 kHz) was not significantly affected by the addition of roots to the system either by burying roots in soil or immersing them in solution. At frequency greater than10 kHz a shift occurred, and root polarization contributed more to ECsoilwhich was positively correlated with root volume. When ECsoilwas measured at high frequency (30 kHz −100 kHz) it was well correlated with root volume vertical distribution in the field. The measurement error after soil moisture calibration at depths of 10 cm, 20 cm, 30 cm and 40 cm was 0.4%, 12.0%, 1% and 34%, respectively. Our results demonstrate that ECsoilis a robust method to measurein situroot distribution and we believe the newly available high frequency measurement equipment combined with novel root prediction models will enable ECsoilto be widely used for root phenotyping in the future.
Pathogenesis of Breakthrough Infections with SARS-CoV-2 Variants in Syrian Hamsters
Authors: Plunkard Jessica , Mulka Kathleen , Zhou Ruifeng , Tarwater Patrick , Zhong William , Lowman Margaret , Wong Amanda , Pekosz Andrew , Villano Jason
Published: January 2023

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19, has evolved into multiple variants. Animal models are important to understand variant pathogenesis, particularly for those with mutations that have significant phenotypic or epidemiological effects. Here, cohorts of naïve or previously infected Syrian hamsters (Mesocricetus auratus) were infected with variants to investigate viral pathogenesis and disease protection. Naïve hamsters infected with SARS-CoV-2 variants had consistent clinical outcomes, tissue viral titers, and pathology, while hamsters that recovered from initial infection and were reinfected demonstrated less severe clinical disease and lung pathology than their naïve counterparts. Males had more frequent clinical signs than females in most variant groups, but few sex variations in tissue viral titers and lung pathology were observed. These findings support the use of Syrian hamsters as a SARS-CoV-2 model and highlight the importance of considering sex differences when using this species.

Importance

With the continued circulation and emergence of new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants, understanding differences between the initial and a subsequent reinfection on disease pathogenesis is critical and highly relevant. This study characterizes Syrian hamsters as an animal model to study reinfection with SARS-CoV-2. Previous infection reduced the disease severity of reinfection with different SARS-CoV-2 variants.
Effectiveness of Paxlovid - a review
Authors: Paltra Sydney , Conrad Tim
Published: January 2023

Paxlovid is an oral treatment for mild to moderate COVID-19 cases with a high risk for severe course of the disease. For this review, we have performed a comprehensive literature review. We present a summary of currently available data on Paxlovid’s ability to reduce the risk of progressing to a severe disease state. Our findings can be concluded as follows: data from the time when the Delta-variant was dominant shows that Paxlovid reduced the risk of hospitalization or death by 87.8% for unvaccinated, non-hospitalized high-risk individuals. Data from the time when the Omicron variant was dominant found decreased risk reductions, varying between 41% and 46%, combining various vaccination statuses. However, one study, which differentiated by age, found that the administration of Paxlovid reduced the risk of hospitalization by 67% for individuals aged 65 and older, but only by 27% for individuals aged 40-64. From the available data, one can conclude that Paxlovid cannot substitute vaccination, but its low manufacturing cost as well as its easy administration make it a valuable tool in fighting COVID-19, especially for countries with a low vaccination rate.
TGFB1 Induces Fetal Reprogramming and Enhances Intestinal Regeneration
Authors: Chen Lei , Dupre Abigail , Qiu Xia , Pellon-Cardenas Oscar , Walton Katherine D. , Wang Jianming , Perekatt Ansu O. , Hu Wenwei , Spence Jason R. , Verzi Michael P.
Published: January 2023

The adult gut epithelium has a remarkable ability to recover from damage. To achieve cellular therapies aimed at restoring and/or replacing defective gastrointestinal tissue, it is important to understand the natural mechanisms of tissue regeneration. We employed a combination of high throughput sequencing approaches, mouse genetic models, and murine and human organoid models, and identified a role for TGFB signaling during intestinal regeneration following injury. At 2 days following irradiation (IR)-induced damage of intestinal crypts, a surge in TGFB1 expression is mediated by monocyte/macrophage cells at the location of damage. Depletion of macrophages or genetic disruption of TGFB-signaling significantly impaired the regenerative response following irradiation. Murine intestinal regeneration is also characterized by a process where a fetal transcriptional signature is induced during repair. In organoid culture, TGFB1-treatment was necessary and sufficient to induce a transcriptomic shift to the fetal-like/regenerative state. The regenerative response was enhanced by the function of mesenchymal cells, which are also primed for regeneration by TGFB1. Mechanistically, integration of ATAC-seq, scRNA-seq, and ChIP-seq suggest that a regenerative YAP-SOX9 transcriptional circuit is activated in epithelium exposed to TGFB1. Finally, pre-treatment with TGFB1 enhanced the ability of primary epithelial cultures to engraft into damaged murine colon, suggesting promise for the application of the TGFB-induced regenerative circuit in cellular therapy.

GRAPHIC ABSTRACT
IL-17 undermines longevity and stress tolerance by inhibiting a protective transcriptional network
Authors: Lu Qiongxuan , Vladareanu Ioana , Zhao Lina , Nilsson Lars , Henriksson Johan , Chen Changchun
Published: January 2023

Aberrant cytokine secretion contributes to the pathogenesis of autoimmune diseases and age-related disorders, but the molecular mechanism underlying this is not entirely clear. Here, we elucidate how interleukin-17 (IL-17) overactivation shortens lifespan and damages defense mechanisms against stress inC. elegans. Our analysis reveals that NHR-49, theC. elegansortholog of human PPARα and HNF4, is the central component in the transcriptional network undermined by increased IL-17 signaling. Both NHR-49 and its coactivator MDT-15 physically interact with the downstream components of IL-17 pathway, and their expression is significantly decreased when IL-17 signaling is enhanced. IL-17 overactivation also induces the expression and nucleus entry of theC. elegansortholog of NF-κB inhibitor NFKI-1/IκBζ to repress the activity of transcriptional coactivator MDT-15 and CBP-1. IL-17 signaling acts on neurons to modulate the activity of NFKI-1/IκBζ and NHR-49. In addition, persistent IL-17 activation decreases the expression of HLH-30/TFEB, leading to the reduced transcription of lysosomal lipase genes in the distal tissues. All these jointly contribute to the increased sensitivity to oxidative stress of animals with enhanced IL-17 signaling. Collectively, our work illustrates a transcription system undermined by IL-17 overactivation in the animals without NF-κB, and provides mechanistic insight into the pathogenesis of abnormal IL-17 secretion.
Investigating the influence of total productive maintenance key success factors on the social sustainability dimension of manufacturing SMEs
Authors: Samadhiya Ashutosh , Agrawal Rajat , Garza-Reyes Jose Arturo
Published: January 2023

Purpose

Key success factors (KSFs) of total productive maintenance (TPM) have historically played a vital role in attaining economic and ecological sustainability but have overlooked social sustainability. Hence, this study analyses and ranks the most significant TPM KSFs for attaining social sustainability in manufacturing small and medium enterprises (SMEs).

Design/methodology/approach

The research employs a deductive methodology to identify the relevant TPM KSFs and social sustainability indicators and then uses Fuzzy Technique for Order of Preference by Similarity to Ideal Solution (TOPSIS) to rank the TPM KSFs in order to achieve social sustainability, followed by a sensitivity analysis to assess the methodological robustness.

Findings

The findings indicate that the top five TPM KSFs influencing social sustainability are employee health and safety, organizational culture, top management commitment, employee engagement and effective communication and effective workplace management. In addition, the results indicate that effective equipment utilization is the least significant TPM key factor affecting social sustainability.

Research limitations/implications

SME manufacturing managers do not need to worry about all of the TPM KSFs if they only concentrate on the ones that will have the most impact. If managers use the top 5 TPM KSFs as a starting point, they may create customized TPM training programs for their companies. As a result, this will facilitate the efforts of their personnel toward social sustainability.

Originality/value

In the existing literature, little emphasis has been paid to social sustainability and how SMEs may implement these practices. This research adds to the current theory of TPM and social sustainability and sheds light on how SMEs might use TPM to advance toward more socially sustainable operations.