bluuebunny/crossref_metadata_2025 huggingface dataset:
Uncertainty quantification of the virial black hole mass with conformal prediction
Authors: Yong Suk Yee , Ong Cheng Soon
Published: July 2023

Precise measurements of the black hole mass are essential to gain insight on the black hole and host galaxy co-evolution. A direct measure of the black hole mass is often restricted to nearest galaxies and instead, an indirect method using the single-epoch virial black hole mass estimation is used for objects at high redshifts. However, this method is subjected to biases and uncertainties as it is reliant on the scaling relation from a small sample of local active galactic nuclei. In this study, we propose the application of conformalized quantile regression (CQR) to quantify the uncertainties of the black hole predictions in a machine learning setting. We compare CQR with various prediction interval techniques and demonstrated that CQR can provide a more useful prediction interval indicator. In contrast to baseline approaches for prediction interval estimation, we show that the CQR method provides prediction intervals that adjust to the black hole mass and its related properties. That is it yields a tighter constraint on the prediction interval (hence more certain) for a larger black hole mass, and accordingly, bright and broad spectral line width source. Using a combination of neural network model and CQR framework, the recovered virial black hole mass predictions and uncertainties are comparable to those measured from the Sloan Digital Sky Survey. The code is publicly available.
DMPP-4: candidate sub-Neptune mass planets orbiting a naked-eye star
Authors: Barnes J R , Standing M R , Haswell C A , Staab D , Doherty J P J , Waller-Bridge M , Fossati L , Soto M , Anglada-Escudé G , Llama J , McCune C , Lewis F W
Published: July 2023

We present radial velocity measurements of the very bright (V ∼ 5.7) nearby F star, DMPP-4 (HD 184960). The anomalously low Ca ii H&K emission suggests mass-loss from planets orbiting a low activity host star. Periodic radial velocity variability with ∼10 m s−1 amplitude is found to persist over a >4 yr time-scale. Although the non-simultaneous photometric variability in four TESS sectors supports the view of an inactive star, we identify periodic photometric signals and also find spectroscopic evidence for stellar activity. We used a posterior sampling algorithm that includes the number of Keplerian signals, Np, as a free parameter to test and compare (1) purely Keplerian models (2) a Keplerian model with linear activity correlation and (3) Keplerian models with Gaussian processes. A preferred model, with one Keplerian and quasi-periodic Gaussian process indicates a planet with a period of $P_\textrm {b} = 3.4982^{+0.0015}_{-0.0027}$ d and corresponding minimum mass of $m_\textrm {b}\, \textrm {sin}\, i = 12.2^{+1.8}_{-1.9}$ M⊕. Without further high-time resolution observations over a longer time-scale, we cannot definitively rule out the purely Keplerian model with two candidates planets with $P_\textrm {b} = 2.4570^{+0.0026}_{-0.0462}$ d, minimum mass $m_\textrm {b}\, \textrm {sin}\, i = 8.0^{+1.1}_{-1.5}$ M⊕ and $P_\textrm {c} = 5.4196^{+0.6766}_{-0.0030}$ d and corresponding minimum mass of $m_\textrm {b}\, \textrm {sin}\, i = 12.2^{+1.4}_{-1.6}$ M⊕. The candidate planets lie in the region below the lower-envelope of the Neptune Desert. Continued mass-loss may originate from the highly irradiated planets or from an as yet undetected body in the system.
Borderline hyperbolic comet C/2021 O3 (PANSTARRS) was fading as it approached the Sun
Authors: Evangelista-Santana M , De Prá M , Carvano J M , de la Fuente Marcos C , de la Fuente Marcos R , Alarcon M R , Licandro J , Lazzaro D , Michimani J , Pereira W , Rondón E , Monteiro F , Arcoverde P , Corrêa T , Rodrigues T , Paganini-Martins C
Published: July 2023

We present an observational and numerical study of the borderline hyperbolic comet C/2021 O3 (PANSTARRS) performed during its recent passage through the inner Solar system. Our observations were carried out at OASI and SOAR between 2021 October and 2022 January, and reveal a low level of activity relative to which was measured for other long-period comets. In addition, we observed a decrease in brightness as the comet got closer to the Sun. Our photometric data, obtained as C/2021 O3 approached perihelion on 2022 April 21, show that the comet was much less active than what is usually expected in the cases of long-period comets, with Afρ values more in line with those of short-period comets (specifically, the Jupiter-family comets). On the other hand, the observed increase in the value of the spectral slope as the amount of dust in the coma decreased could indicate that the smaller dust particles were being dispersed from the coma by radiation pressure faster than they were injected by possible sublimation jets. The analysis of its orbital evolution suggests that C/2021 O3 could be a dynamically old comet, or perhaps a new one masquerading as a dynamically old comet, with a likely origin in the Solar system.
Shh–Gli2–Runx2 inhibits vascular calcification
Authors: Huang Aoran , Xu Tianhua , Lu Xiaomei , Ma Ling , Ma Haiying , Yu Yanqiu , Yao Li
Published: July 2023

Background

In patients with chronic kidney disease (CKD), vascular calcification (VC) is common and is associated with a higher risk of all-cause mortality. Shh, one ligand for Hedgehog (Hh) signaling, participates in osteogenesis and several cardiovascular diseases. However, it remains unclear whether Shh is implicated in the development of VC.

Methods

Inorganic phosphorus 2.6 mM was used to induce vascular smooth muscle cells (VSMCs) calcification. Mice were fed with adenine diet supplement with 1.2% phosphorus to induce VC.

Results

Shh was decreased in VSMCs exposed to inorganic phosphorus, calcified arteries in mice fed with an adenine diet, as well as radial arteries from patients with CKD presenting VC. Overexpression of Shh inhibited VSMCs ostosteoblastic differentiation and calcification, whereas its silencing accelerated these processes. Likewise, mice treated with smoothened agonist (SAG; Hh signaling agonist) showed alleviated VC, and mice treated with cyclopamine (CPN; Hh signaling antagonist) exhibited severe VC. Additionally, overexpression of Gli2 significantly reversed the pro-calcification effect of Shh silencing on VSMCs, suggesting that Shh inhibited VC via Gli2. Mechanistically, Gli2 interacted with Runx2 and promoted its ubiquitin proteasomal degradation, therefore protecting against VC. Of interest, the pro-degradation effect of Gli2 on Runx2 was independent of Smurf1 and Cullin4B.

Conclusions

Our study provided deeper insight to the pathogenesis of VC, and Shh might be a novel potential target for VC treatment.
The Effect of State and Local Flavored Cigar Sales Restrictions, on Retail Sales of Large Cigars, Cigarillos, and Little Cigars in Massachusetts, California, Illinois, and New York
Authors: Diaz Megan C , Yoon Stephanie N , Donovan Emily , Akbar Maham , Schillo Barbara A
Published: July 2023

Introduction

In 2009, the Family Smoking Prevention and Tobacco Control Act prohibited flavored cigarettes but allowed for flavored cigars. Since, there has been a 34% increase in youth cigar use and widened racial disparities. State and local jurisdictions have increasingly enacted flavored tobacco product sales restrictions. As more jurisdictions consider implementing flavor restrictions, it is important to understand their effect on tobacco markets that have high flavor proliferation, including the cigar market.

Aims and Methods

This study uses data from Truth Initiative’s flavor policy database and NielsenIQ retailer scanners for California, Illinois, Massachusetts, and New York. We use a three-way fixed-effect model to assess the impact of the percentage of the population covered by a flavored cigar sales restriction on per capita unit sales of cigars.

Results

We find that population coverage by cigar sales restrictions was significantly associated with decreases in per capita cigar sales. More specifically, a 25% increase in the percentage of the population covered by a flavored cigar sales restriction was associated with a decrease in per capita all cigar sales of 15%–19%, 4%–10% for large cigars, 17%–21% for cigarillos, and 2%–41% for little cigars.

Conclusion

Flavored cigar sales restrictions are an effective policy to reduce per capita cigar sales. The Food and Drug Administration (FDA)’s proposed product standards would increase population covered by a flavored cigar sales restriction to 100%, leading to potential significant reductions in cigar sales, especially little cigar, and cigarillo sales. This may also substantially reduce youth cigar use and racial disparities in cigar use.

Implications

In April 2022, the U.S. FDA published a proposed rule to prohibit characterizing flavors in all cigars and menthol cigarettes. Besides this proposed rule, there has been little federal action to date to reduce sales of flavored cigars. However, as of March 31, 2022, Massachusetts and 333 localities across 10 states have enacted policies that restrict the sale of flavored cigars and other tobacco products. We find that population coverage by cigar sales restrictions is significantly associated with decreases in per capita cigar sales.
Perspectives on the Use of Outpatient Parenteral Antibiotic Therapy for People who Inject Drugs: Results From an Online Survey of Infectious Diseases Clinicians
Authors: Solomon Daniel A , Beieler Alison M , Levy Sera , Eaton Ellen F , Sikka Monica K , Thornton Alice , Dhanireddy Shireesha
Published: July 2023

Injection-related infections require prolonged antibiotic therapy. Outpatient parenteral antimicrobial therapy (OPAT) has been shown to be feasible for people who inject drugs (PWID) in some settings. We report a national survey on practice patterns and attitudes of infectious diseases clinicians in the United States regarding use of OPAT for PWID.
Against the Spirit of the Age: The Rationale of Relational Contracts
Authors: Goodrich Peter
Published: July 2023

In his long-awaited treatise on the relational theory of contracting, David Campbell provides a rigorous, systematic and consistently lucid account of mutual recognition as the basis of all volitional obligations. Fiercely negotiated economic transactions find their social expression in legally enforceable agreements that are to be followed scrupulously to the letter both by the parties and by the courts. This is because, in his view, mutual recognition, the co-operative economic enterprise, is memorialised in the legal instrument. Using the example of the emergent doctrine of good faith, this article argues that while such literalism proffers an admirably bright line for enforcement of agreements, it reduces the import and value of the relational theory of contract as an ethical and political accounting of market transactions. Literalism here is problematic not simply because of the inherent historicity and social diversity of language, but because in concepts such as good faith or reasonable interpretation, the purpose of the inscribed transaction has to be evaluated not only in terms of the plurality of the contract’s clauses, but also with a view to the overall shared intent of the exchange. For the relational theory of contract to have the impact that it merits, it needs to strengthen its account of how mutual recognition and the ethical and political dimensions of relationship best gain expression in the good-faith interpretation of the proximities manifest in agreement.
DNA-dependent RNA polymerases in plants
Authors: Yang Dong-Lei , Huang Kun , Deng Deyin , Zeng Yuan , Wang Zhenxing , Zhang Yu
Published: July 2023

DNA-dependent RNA polymerases (Pols) transfer the genetic information stored in genomic DNA to RNA in all organisms. In eukaryotes, the typical products of nuclear Pol I, Pol II, and Pol III are ribosomal RNAs, mRNAs, and transfer RNAs, respectively. Intriguingly, plants possess two additional Pols, Pol IV and Pol V, which produce small RNAs and long noncoding RNAs, respectively, mainly for silencing transposable elements. The five plant Pols share some subunits, but their distinct functions stem from unique subunits that interact with specific regulatory factors in their transcription cycles. Here, we summarize recent advances in our understanding of plant nucleus-localized Pols, including their evolution, function, structures, and transcription cycles.
PYRIDOX(AM)INE 5′-PHOSPHATE OXIDASE3 ofArabidopsis thalianamaintains carbon/nitrogen balance in distinct environmental conditions
Authors: Steensma Priscille , Eisenhut Marion , Colinas Maite , Rosado-Souza Laise , Fernie Alisdair R , Weber Andreas P M , Fitzpatrick Teresa B
Published: July 2023

The identification of factors that regulate C/N utilization in plants can make a substantial contribution to optimization of plant health. Here, we explored the contribution of pyridox(am)ine 5′-phosphate oxidase3 (PDX3), which regulates vitamin B6 homeostasis, in Arabidopsis (Arabidopsis thaliana). Firstly, N fertilization regimes showed that ammonium application rescues the leaf morphological phenotype of pdx3 mutant lines but masks the metabolite perturbance resulting from impairment in utilizing soil nitrate as a source of N. Without fertilization, pdx3 lines suffered a C/N imbalance and accumulated nitrogenous compounds. Surprisingly, exploration of photorespiration as a source of endogenous N driving this metabolic imbalance, by incubation under high CO2, further exacerbated the pdx3 growth phenotype. Interestingly, the amino acid serine, critical for growth and N management, alleviated the growth phenotype of pdx3 plants under high CO2, likely due to the requirement of pyridoxal 5′-phosphate for the phosphorylated pathway of serine biosynthesis under this condition. Triggering of thermomorphogenesis by growth of plants at 28 °C (instead of 22 °C) did not appear to require PDX3 function, and we observed that the consequent drive toward C metabolism counters the C/N imbalance in pdx3. Further, pdx3 lines suffered a salicylic acid-induced defense response, probing of which unraveled that it is a protective strategy mediated by nonexpressor of pathogenesis related1 (NPR1) and improves fitness. Overall, the study demonstrates the importance of vitamin B6 homeostasis as managed by the salvage pathway enzyme PDX3 to growth in diverse environments with varying nutrient availability and insight into how plants reprogram their metabolism under such conditions.
Standardized 3D-CT lung volumes for patients with acute exacerbation of rheumatoid arthritis-associated interstitial lung disease
Authors: Tanaka Yuko , Suzuki Yuzo , Saku Aiko , Kono Masato , Hashimoto Dai , Hasegawa Hirotsugu , Yokomura Koshi , Inoue Yusuke , Hozumi Hironao , Karayama Masato , Furuhashi Kazuki , Enomoto Noriyuki , Fujisawa Tomoyuki , Inui Naoki , Suda Takafumi
Published: July 2023

Objectives

Fibrotic interstitial lung disease (ILD) is a progressive lung disease characterized by loss of lung volume, resulting in a leading cause of death in patients with RA. Crucially, acute exacerbation (AE) of ILD shows higher morbidity and mortality with rapid deterioration of the lungs. However, a quantitative assessment for physiological changes at AE has yet to be performed. This study hypothesized that quantitative assessments of lung volume (LV) accurately indicate disease severity and mortality risk in patients with AE-RA-ILD.

Methods

This multicentre cohorts study quantitatively assessed physiological changes of RA-ILD at diagnosis (n = 54), at AE (discovery-cohorts; n = 20, and validation-cohort; n = 33), and controls (n = 35) using 3D CT (3D-CT) images. LV was quantitatively measured using 3D-CT and standardized by predicted forced vital capacity.

Results

Patients with RA-ILD at diagnosis showed decreased LV, predominantly in lower lobes, compared with controls. Further substantial volume loss was found in upper- and lower lobes at AE compared with those at diagnosis. During AE, decreased standardized 3D-CT LV was associated with a worse prognosis in both cohorts. Subsequently, standardized 3D-CT LV was identified as a significant prognostic factor independent of age, sex and the presence of UIP pattern on CT by multivariate analyses. Notably, a composite model of age and standardized 3D-CT LV successfully classified mortality risk in patients with AE-RA-ILD.

Conclusion

Volume loss at AE in patients with RA-ILD was associated with increased mortality. Assessing physiological change using standardized 3D-CT might help evaluate disease severity and mortality risk in patients with AE-RA-ILD.
Unveiling Hidden Connections in Omics DataviapyPARAGON: an Integrative Hybrid Approach for Disease Network Construction
Authors: Arici M. Kaan , Tuncbag Nurcan
Published: July 2023

Omics technologies are powerful tools for detecting dysregulated and altered signaling components in various contexts, encompassing disease states, patients, and drug-perturbations. Network inference or reconstruction algorithms play an integral role in the successful analysis and identification of causal relationships between omics hits. However, accurate representation of signaling networks and identification of context-specific interactions within sparse omics datasets in complex interactomes pose significant challenges in integrative approaches. To address these challenges, we present pyPARAGON (PAgeRAnk-flux on Graphlet-guided network for multi-Omic data integratioN), a novel tool that combines network propagation with graphlets. By leveraging network motifs instead of pairwise connections among proteins, pyPARAGON offers improved accuracy and reduces the inclusion of nonspecific interactions in signaling networks. Through comprehensive evaluations on benchmark cancer signaling pathways, we demonstrate that pyPARAGON outperforms state-of-the-art approaches in node propagation and edge inference. Furthermore, pyPARAGON exhibits promising performance in discovering cancer driver networks. Notably, we demonstrate its utility in network-based stratification of patient tumors by integrating phosphoproteomic data from 105 breast cancer tumors with the interactome, leading to the discovery of tumor-specific signaling pathways. Overall, the development and evaluation of pyPARAGON significantly contributes to the field as an effective tool for the analysis and integration of multi-omic data in the context of signaling networks. pyPARAGON is available athttps://github.com/metunetlab/pyPARAGON.
Sustaining wakefulness: Brainstem connectivity in human consciousness
Authors: Edlow Brian L. , Olchanyi Mark , Freeman Holly J. , Li Jian , Maffei Chiara , Snider Samuel B. , Zöllei Lilla , Iglesias J. Eugenio , Augustinack Jean , Bodien Yelena G. , Haynes Robin L. , Greve Douglas N. , Diamond Bram R. , Stevens Allison , Giacino Joseph T. , Destrieux Christophe , van der Kouwe Andre , Brown Emery N. , Folkerth Rebecca D. , Fischl Bruce , Kinney Hannah C.
Published: July 2023

Consciousness is comprised of arousal (i.e., wakefulness) and awareness. Substantial progress has been made in mapping the cortical networks that modulate awareness in the human brain, but knowledge about the subcortical networks that sustain arousal is lacking. We integrated data fromex vivodiffusion MRI, immunohistochemistry, andin vivo7 Tesla functional MRI to map the connectivity of a subcortical arousal network that we postulate sustains wakefulness in the resting, conscious human brain, analogous to the cortical default mode network (DMN) that is believed to sustain self-awareness. We identified nodes of the proposed default ascending arousal network (dAAN) in the brainstem, hypothalamus, thalamus, and basal forebrain by correlatingex vivodiffusion MRI with immunohistochemistry in three human brain specimens from neurologically normal individuals scanned at 600-750 µm resolution. We performed deterministic and probabilistic tractography analyses of the diffusion MRI data to map dAAN intra-network connections and dAAN-DMN internetwork connections. Using a newly developed network-based autopsy of the human brain that integratesex vivoMRI and histopathology, we identified projection, association, and commissural pathways linking dAAN nodes with one another and with cortical DMN nodes, providing a structural architecture for the integration of arousal and awareness in human consciousness. We release theex vivodiffusion MRI data, corresponding immunohistochemistry data, network-based autopsy methods, and a new brainstem dAAN atlas to support efforts to map the connectivity of human consciousness.

One sentence summary

We performedex vivodiffusion MRI, immunohistochemistry, andin vivo7 Tesla functional MRI to map brainstem connections that sustain wakefulness in human consciousness.
Theranostic Bottle-Brush Polymers Tailored for Universal Solid-Tumour Targeting
Authors: Zhang Wei , Xu Yanwen , Guo Rongjun , Zhuang Peiling , Hong Huixia , Tan Hui , Wang Mingfeng
Published: July 2023

Nanomedicines involving nanotechnologies and engineering of nanomaterials for medicines have shown great promise in diagnosis and treatment of diseases including cancers. A major hurdle that limits the successful clinical translation of nanomedicines, however, is how to overcome the cascaded biological barriers and improve the delivery efficacy towards the disease sites and minimize the toxicity against healthy tissues and cells. Here, we report a type of bottle-brush-like polymers systematically optimized in their chemical structures, sizes, and surface charges that lead to their outstanding pharmacokinetics and tumour-targeting performances in a variety of both subcutaneous and orthotopic tumour models. The potential mechanism has been studied by revealing the structure-activity relationship of these polymers in overcoming the biological barriers, including their avoidance by the immune system and deep tumour infiltration. Our study may offer insight for a rational design of highly efficient delivery platform of polymeric nanomedicines that could effectively overcome the cascaded biological barriers and thus lead to high tumour-targeting efficacy and low toxicity.
Beam search decoder for enhancing sequence decoding speed in single-molecule peptide sequencing data
Authors: Kipen Javier , Jaldén Joakim
Published: July 2023

Next-generation single-molecule protein sequencing technologies have the potential to accelerate biomedical research significantly. These technologies offer sensitivity and scalability for proteomic analysis. One auspicious method is fluorosequencing, which involves: cutting naturalized proteins into peptides, attaching fluorophores to specific amino acids, and observing variations in light intensity as one amino acid is removed at a time. The original peptide is classified from the sequence of light-intensity reads, and proteins can subsequently be recognized with this information. The amino acid step removal is achieved by attaching the peptides to a wall on the C-terminal and using a process called Edman Degradation to remove an amino acid from the N-Terminal. Even though a framework (Whatprot) has been proposed for the peptide classification task, processing times remain restrictive due to the massively parallel data acquisicion system. In this paper, we propose a new beam search decoder with a novel state formulation that obtains much lower processing times with slightly higher accuracies than Whatprot. Furthermore, we explore how our novel state formulation may lead to even faster decoders in the future.

Author summary

Proteomic analyses are often carried on with mass spectrometry, but this method cannot identify low-abundance proteins. Single-molecule protein sequencing methods can overcome this issue, and fluorosequencing is one of these technologies. Fluorosequencing has attracted interest from investors, as evidenced by the recent funding of Erisyon, a company developing this technology. This technique contains a challenging classification task: determining the original peptide sequence from light-intensity observations obtained after several Edman cycles. A classifier based on a combination ofkNearest Neighbors (kNN) with Hidden Markov Models (HMM) had been shown to have close-to-optimal accuracy with tractable complexity. We propose in this paper a new algorithm that not only improves accuracy compared to state-of-the-art methods but also reduces computation time.
Applying Hierarchical Generalized Additive Models to Non-Compartmental Analysis of Pharmacokinetic Data
Authors: Woodward Andrew P.
Published: July 2023

Non-compartmental analysis (NCA) is a popular strategy for obtaining estimates of pharmacokinetic parameters, while requiring both minimal structural assumptions, and limited input by the analyst. As typically applied, its scope and depth are constrained by its statistical simplicity. Embedding the NCA within a hierarchical generalized additive model (HGAM) may facilitate the simultaneous analysis of data from multiple subjects, estimation of covariate effects in one stage, and implementation of censored responses, similarly to the capabilities of nonlinear multilevel models as widely applied in pharmacometrics. HGAM is an interesting extension to multilevel linear models that allows the effects of predictors to be implemented as smooth functions, which has been widely implemented in various disciplines to nonlinear trends, including for longitudinal data.

This approach extends the capability of previous implementations of spline-based methods applied to NCA, within an accessible workflow in open software. Application of HGAM to two example datasets, one describing oral drug administration, and one describing IV and oral drug administration with categorical covariates and censoring, illustrates the overall approach, including parameter estimation, visualization and model checking, and uncertainty quantification. A Bayesian approach to estimation facilitates interpretable expressions of the uncertainty in individual parameters, population parameters, and functions of parameters such as contrasts.
Impact of angiotensin-receptor blockers on intrarenal renin-angiotensin system activity in hypertension: A PK/PD modelling study
Authors: Smith Delaney , Layton Anita
Published: July 2023

The renin-angiotensin system (RAS) is a primary regulator of volume homeostasis and blood pressure, whose over-activation is commonly associated with hypertension. Indeed, medications that target the RAS are generally effective in reducing blood pressure. However, more can be learned about how these medications influence the intrarenal RAS. Angiotensin-receptor blockers (ARBs) in particular have been shown to exert different effects on the intrarenal and systemic RASs in various experimental models of hypertension. In rats chronically infused with angiotensin II (Ang II), ARBs consistently prevent intrarenal, but not systemic Ang II levels from rising. The former effect is sufficient in preventing the development of hypertension. The regulation of intrarenal RAS, independently of the systemic RAS, by ARBs has been hypothesized to be mediated by the inhibition of all positive feedback loops inherent to the intrarenal RAS, also known as the “key point breakdown effect.” To investigate the validity of this hypothesis, we developed a PK/PD model of the ARB Losartan that considers the kidney, and applied the model to study how this class of medication influences intrarenal RAS activity and consequently blood pressure regulation in male rats. Simulations indicate that ARBs more effectively inhibit the activation of the intrarenal RAS because, unlike in the plasma, this process relies on the accumulation of cell-associated Ang II. We hypothesize that it is by blocking this intracellular uptake pathway, and restricting Ang II to extracellular regions of the kidney where the peptide cannot initiate downstream signalling, that Losartan normalizes blood pressure. While the key point break down effect assists in this response, it alone is not sufficient. Our results highlight the intrarenal RAS as the key pharmacological target of ARB treatment and emphasize the importance of this local tissue RAS in the development of hypertension.
Multidrug Efflux in Gram-Negative Bacteria: Rationally Modifying Compounds to Avoid Efflux Pumps
Authors: Gurvic Dominik , Zachariae Ulrich
Published: July 2023

Gram-negative bacteria cause the majority of critically drug-resistant infections, necessitating the rapid development of new drugs with Gram-negative activity. However, drug design is hampered by the low permeability of the Gram-negative cell envelope and the function of drug efflux pumps, which extrude foreign molecules from the cell. A better understanding of the molecular determinants of compound recognition by efflux pumps is, therefore, essential. Here, we quantitatively analyse the activity of over 73,000 compounds across three strains ofE. coli– the wild-type, an efflux-deficient variant, and a hyper-permeable variant – to elucidate the molecular principles of evading efflux pumps. Our results show that, alongside a range of physicochemical features, the presence or absence of specific chemical groups in the compounds substantially increases the probability of avoiding efflux. Furthermore, comparison of our findings with inward permeability data highlights the primary role of efflux in determining drug bioactivity in Gram-negative bacteria.
HATCHet2: clone- and haplotype-specific copy number inference from bulk tumor sequencing data
Authors: Myers Matthew A. , Arnold Brian J. , Bansal Vineet , Mullen Katelyn M. , Zaccaria Simone , Raphael Benjamin J.
Published: July 2023

Multi-region DNA sequencing of primary tumors and metastases from individual patients helps identify somatic aberrations driving cancer development. However, most methods to infer copy-number aberrations (CNAs) analyze individual samples. We introduce HATCHet2 to identify haplotype- and clone-specific CNAs simultaneously from multiple bulk samples. HATCHet2 introduces a novel statistic, the mirrored haplotype B-allele frequency (mhBAF), to identify mirrored-subclonal CNAs having different numbers of copies of parental haplotypes in different tumor clones. HATCHet2 also has high accuracy in identifying focal CNAs and extends the earlier HATCHet method in several directions. We demonstrate HATCHet2’s improved accuracy using simulations and a single-cell sequencing dataset. HATCHet2 analysis of 50 prostate cancer samples from 10 patients reveals previously-unreported mirrored-subclonal CNAs affecting cancer genes.
Enigmas no longer: using Ultraconserved Elements to place several unusual hawk taxa and address the non-monophyly of the genusAccipiter(Accipitriformes: Accipitridae)
Authors: Catanach Therese A. , Halley Matthew R. , Pirro Stacy
Published: July 2023

Hawks, eagles, and their relatives (Accipitriformes: Accipitridae) are a diverse and charismatic clade of modern birds, with many members that are instantly recognized by the general public. However, surprisingly little is known about the relationships among genera within Accipitridae, and several studies have suggested that some genera (in particular, the megadiverse genusAccipiter) are not monophyletic. Here, we combine a new large dataset obtained from Ultraconserved Elements (UCEs), generated from whole genome sequencing (WGS) of 120 species, with publicly available legacy markers (i.e., a suite of commonly sequenced mitochondrial and nuclear genes) to infer a well-supported, time-calibrated phylogeny of 236 extant or recently extinct species. Our densely-sampled phylogeny, which includes 90% of recognized species, confirms the non-monophyly ofAccipiterand provides a sufficient basis to revise the genus-level taxonomy, such that all genera in Accipitridae represent monophyletic groups.
Bimodal distribution ofCandida albicansin children with Autism linked with ASD symptoms
Authors: Nirmalkar Khemlal , Patel Jigar , Kang Dae-Wook , Bellinghiere Andrew , Bowes Devin A. , Adams James B. , Krajmalnik-Brown Rosa
Published: July 2023

The gastrointestinal (GI) tract harbors an intricate and remarkably diverse microbial ecosystem that profoundly impacts various aspects of health and pathophysiology. While bacteria overwhelmingly represent most of the GI microbiota, it is imperative to consider the presence and function of fungal constituents (i.e., mycobiota) within the GI ecosystem. The substantial incidence of GI disorders and associated manifestations in children diagnosed with autism spectrum disorder (ASD) suggests a plausible contributory role of the gut mycobiota. Our investigation aimed to elucidate the gut mycobiota in a cohort comprising 38 typically developing children (TD) and 40 children with ASD. Fecal samples were collected from all participants and autism severity and GI symptoms were assessed to unravel the potential implications of mycobiota alterations in the gut. We employed fungal internal transcribed spacer (ITS) gene amplicon sequencing to analyze the fungal composition and investigate their relationship with GI and autism symptoms. Among gut mycobiota,Saccharomyces cerevisiaewas significantly lower (relative abundance) in ASD compared to TD children. TotalCandidaandC. albicansdemonstrated a bimodal distribution among children with ASD. Children with ASD with elevated Autism Treatment Evaluation Checklist (ATEC) scores (a more severe diagnosis) displayed an increased abundance ofC. albicansand a decreased abundance ofS. cerevisiae. A significant positive correlation was observed between ATEC scores and GI symptoms and between ATEC scores andC. albicans. Our findings propose that a deficit of beneficial fungi, specificallyS. cerevisiae,and an overgrowth ofC. albicansmay worsen autism severity in children with ASD. Future work employing more advanced techniques (i.e., shotgun metagenomics) is encouraged to advance understanding of the functional role of fungi/yeast, and their interplay between GI symptoms and autism severity in children with ASD.
Nanoscale clustering by O-antigen-Secretory Immunoglobulin-A binding limits outer membrane diffusion by encaging individualSalmonellacells
Authors: Hockenberry Alyson , Radiom Milad , Arnoldini Markus , Turgay Yagmur , Dunne Matthew , Adamcik Jozef , Stadtmueller Beth , Mezzenga Raffaele , Ackermann Martin , Slack Emma
Published: July 2023

Secreted immunoglobulins, predominantly SIgA, influence the colonization and pathogenicity of mucosal bacteria. While part of this effect can be explained by SIgA-mediated bacterial aggregation, we have an incomplete picture of how SIgA binding influences cells independently of aggregation. Here we show that akin to microscale crosslinking of cells, SIgA targeting theSalmonellaTyphimurium O-antigen extensively crosslinks the O-antigens on the surface of individual bacterial cells at the nanoscale. This crosslinking results in an essentially immobilized bacterial outer membrane. Membrane immobilization, combined with Bam-complex mediated outer membrane protein insertion results in biased inheritance of IgA-bound O-antigen, concentrating SIgA-bound O-antigen at the oldest poles during cell growth. By combining empirical measurements and simulations, we show that this SIgA-driven biased inheritance increases the rate at which phase-varied daughter cells become IgA-free: a process that can accelerate IgA escape via phase-variation of O-antigen structure. Our results show that O-antigen-crosslinking by SIgA impacts workings of the bacterial outer membrane, helping to mechanistically explain how SIgA may exert aggregation-independent effects on individual microbes colonizing the mucosae.
Visualization and estimation of stroke infarct volumes in rodents
Authors: Weber Rebecca Z. , Bernardoni Davide , Rentsch Nora H. , Achón Buil Beatriz , Halliday Stefanie , Augath Mark-Aurel , Razansky Daniel , Tackenberg Christian , Rust Ruslan
Published: July 2023

Stroke volume is a key determinant of infarct severity and an important metric treatments evaluation. However, accurate estimation of stroke volume can be challenging, due to the often confined 2-dimensional nature of available data. Here, we introduce a comprehensive semi-automated toolkit to reliably estimate stroke volumes based on (1) whole brainsex-vivomagnetic resonance imaging (MRI) and (2) brain sections that underwent immunofluorescence staining. We located and quantified infarct areas from MRI three days (acute) and 28 days (chronic) after photothrombotic stroke induction in whole mouse brains. MRI Results were compared with measures obtained from immunofluorescent histologic sections of the same brains. Using our toolkit, we found that infarct volume determined by post-mortem MRI was highly correlated with a deviation of only 6.6% (acute) and 4.9% (chronic) to the measurements as determined in the histological brain sections indicating that both methods are capable of accurately assessing brain tissue damage.
Role of transporters and enzymes in metabolism and distribution of 4 chlorokynurenine and metabolites
Authors: Patel Waseema , Shankar Ravi G. , Smith Mark A. , Snodgrass H. Ralph , Pirmohamed Munir , Jorgensen Andrea , Alfirevic Ana , Dickens David
Published: July 2023

4-chlorokynurenine (4-Cl-KYN) is in clinical development for potential CNS indications. We have sought to further understand the distribution and metabolism of 4-Cl-KYN as this information might provide a strategy to enhance the clinical development of this drug. We used excretion studies in rats,in vitrotransporter assays and pharmacogenetic analysis of clinical trial data to determine how 4-Cl-KYN and metabolites are distributed. Our data indicated that a novel acetylated metabolite (N-acetyl-4-Cl-KYN) did not affect the uptake of 4-Cl-KYN across the blood-brain barrier via LAT1. 4-Cl-KYN and metabolites were found to be renally excreted in rodents. In addition, we found that N-acetyl-4-Cl-KYN inhibited renal and hepatic transporters involved in excretion. Thus, this metabolite had the potential to limit the excretion of a range of compounds. Our pharmacogenetic analysis found that a SNP in N-acetyltransferase 8 (NAT8, rs13538) was linked to levels of N-acetyl-4-Cl-KYN relative to 4-Cl-KYN found in the plasma and that a SNP in SLC7A5 (rs28582913) was associated with the plasma levels of the active metabolite, 7-Cl-KYNA. Thus, we have a pharmacogenetics-based association for plasma drug level that could aid in the drug development of 4-Cl-KYN and have investigated the interaction of a novel metabolite with drug transporters.
Glycan-specific IgM is critical for human immunity toStaphylococcus aureus
Authors: Hendriks Astrid , Kerkman Priscilla F. , Varkila Meri R.J. , Haitsma-Mulier Jelle L.G. , Ali Sara , ten Doesschate Thijs , van der Vaart Thomas W. , de Haas Carla J.C. , Aerts Piet C. , Cremer Olaf L. , Bonten Marc J.M. , Nizet Victor , Liu George Y. , Codée Jeroen D.C. , Rooijakkers Suzan H.M. , van Strijp Jos A.G. , van Sorge Nina M.
Published: July 2023

Staphylococcus aureusis a major human pathogen but the immune factors that protect against it remain elusive. In particular, high opsonic IgG titers achieved in preclinicalS. aureusanimal immunization studies have consistently failed to translate to protection in human clinical trials. Here, we investigated the antibody responses to a conserved surface glycan, Wall Teichoic Acid (WTA). IgM and IgG antibodies specific to WTA were universally present in plasma from healthy individuals. Functionally, WTA-specific IgM outperformed IgG in opsonophagocytic killing ofS. aureusand conferred passive protection againstS. aureusinfectionin vivo. In the clinical setting, WTA-specific IgM responses, but not IgG responses, were significantly lower inS. aureusbacteremia patients compared to healthy individuals, correlated with mortality risk and showed impaired bacterial opsonization. Our findings can guide risk stratification of hospitalized patients and inform future design of antibody-based therapies and vaccines against seriousS. aureusinfection.
Putative staphylococcal enterotoxin possesses two common structural motifs for MHC-II binding
Authors: Rahman Shakilur , Saha Saradindu , Dasgupta Somdeb Bose , Das Amit Kumar
Published: July 2023

Staphylococcus aureushas become a significant cause of health risks in humankind. Staphylococcal superantigens (SAgs) or enterotoxins are the key virulent factors that can exhibit acute diseases to severe life-threatening conditions. Recent literature reportsS. aureushas steadily gained new enterotoxin genes over the past few decades. In spite of current knowledge of the established SAgs, several questions on these putative enterotoxins are still remaining unanswered. Keeping that in mind, this study sheds light on a putative enterotoxin SEl26 to characterize its structural and functional properties.In-silicoanalyses indicate its close relation with the conventional SAgs, especially the zinc-binding SAgs. Additionally, important residues have been predicted that are vital for T-Cell receptor (TcR) and major histocompatibility complex class II (MHC-II) interaction and compared them with established SAgs. Besides, our biochemical analyses exhibited the binding of this putative enterotoxin with MHC-II, followed by regulating pro-inflammatory and anti-inflammatory cytokines.
Spatial predictive context speeds up visual search by biasing local attentional competition
Authors: Bouwkamp Floortje G. , de Lange Floris P. , Spaak Eelke
Published: July 2023

The human visual system is equipped to rapidly and implicitly learn and exploit the statistical regularities in our environment. Within visual search, contextual cueing demonstrates how implicit knowledge of scenes can improve search performance. This is commonly interpreted as spatial context in the scenes becoming predictive of the target location, which leads to a more efficient guidance of attention during search. However, what drives this enhanced guidance is unknown. First, it is under debate whether the entire scene (global context) or more local context drives this phenomenon. Second, it is unclear how exactly improved attentional guidance is enabled by target enhancement and distractor suppression. In the present MEG experiment, we leveraged Rapid Invisible Frequency Tagging (RIFT) to answer these two outstanding questions. We found that the improved performance when searching implicitly familiar scenes was accompanied by a stronger neural representation of the target stimulus, at the cost specifically of those distractors directly surrounding the target. Crucially, this biasing of local attentional competition was behaviorally relevant when searching familiar scenes. Taken together, we conclude that implicitly learned spatial predictive context improves how we search our environment by sharpening the attentional field.
Disentangling the Innate Immune Responses of Intestinal Epithelial Cells and Lamina Propria Cells toSalmonellaTyphimurium Infection in Chickens
Authors: Sutton Kate , Nash Tessa , Sives Samantha , Borowska Dominika , Mitchell Jordan , Vohra Prerna , Stevens Mark P. , Vervelde Lonneke
Published: July 2023

Salmonella entericaserovar Typhimurium (STm) is a major foodborne pathogen and poultry are a key reservoir of human infections. To understand the host responses to early stages ofSalmonellainfection in poultry, we infected 2D and 3D enteroids, the latter of which contains leukocytes, neurons, and mesenchymal cells that are characteristic of the lamina propria. We infected these enteroids with wild-type (WT STm), a non-invasive mutant lacking theprgHgene (ΔprgHSTm), or treated them with STm lipopolysaccharide (LPS) and analysed the expression of innate immune related genes by qPCR at 4 and 8 h. The localisation of ZO-1 expression was disrupted in WT STm infected enteroids but notΔprgHSTm or LPS treated enteroids, suggesting a loss of barrier integrity. The innate immune response to LPS was more pronounced in 2D enteroids compared to 3D enteroids and by 8 hpi, the response in 3D enteroids was almost negligible. However, when STm adhered to or invaded the enteroids, both 2D and 3D enteroids exhibited an upregulation of inflammatory responses. The presence of lamina propria cells in 3D enteroids resulted in the unique expression of genes associated with immune functions involved in regulating inflammation. Moreover, 2D and 3D enteroids showed temporal differences in response to bacterial invasion or adherence. At 8 hpi, innate responses in 3D but not 2D enteroids continued to increase after infection with WT STm, whereas the responses to the non-invasive strain decreased at 8 hpi in both 2D and 3D enteroids. In conclusion, STm infection of chicken enteroids recapitulated several observations fromin vivostudies ofSalmonella-infected chickens, including altered epithelial barrier integrity based on ZO-1 expression and inflammatory responses. Our findings provide evidence thatSalmonella-infected enteroids serve as effective models for investigating host-pathogen interactions and exploring the molecular mechanisms of microbial virulence although the 3D model mimics the host more accurately due to the presence of a lamina propria.
Genetic barriers more than ecological adaptations shapedSerratia marcescensdiversity
Authors: Sterzi Lodovico , Nodari Riccardo , Di Marco Federico , Ferrando Maria Laura , Saluzzo Francesca , Spitaleri Andrea , Allahverdi Hamed , Papaleo Stella , Panelli Simona , Rimoldi Sara Giordana , Batisti Biffignandi Gherard , Corbella Marta , Cavallero Annalisa , Prati Paola , Farina Claudio , Cirillo Daniela Maria , Zuccotti Gianvincenzo , Bandi Claudio , Comandatore Francesco
Published: July 2023

Bacterial species often comprise well-separated lineages, likely emerged and maintained by genetic isolation and/or ecological divergence. How these two evolutionary actors interact in the shaping of bacterial population structure is currently not fully understood. In this study, we investigated the genetic and ecological drivers underlying the evolution ofSerratia marcescens, an opportunistic pathogen with high genomic flexibility and able to colonise diverse environments. Comparative genomic analyses revealed a population structure composed of five deeply-demarcated genetic clusters with open pan-genome but limited inter-cluster gene flow, partially explained by Restriction-Modification (R-M) systems incompatibility. Furthermore, a large-scale research on hundred-thousands metagenomic datasets revealed only a partial ecological separation of the clusters. Globally, two clusters only showed a peculiar gene composition and evident ecological adaptations. These results suggest that genetic isolation preceded ecological adaptations in the shaping of the species diversity, suggesting an evolutionary scenario for several bacterial species.
Nanobody repertoire generated against the spike protein of ancestral SARS-CoV-2 remains efficacious against the rapidly evolving virus
Authors: Ketaren Natalia E. , Mast Fred D. , Fridy Peter C. , Olivier Jean Paul , Sanyal Tanmoy , Sali Andrej , Chait Brian T. , Rout Michael P. , Aitchison John D.
Published: July 2023

To date, all major modes of monoclonal antibody therapy targeting SARS-CoV-2 have lost significant efficacy against the latest circulating variants. As SARS-CoV-2 omicron sublineages account for over 90% of COVID-19 infections, evasion of immune responses generated by vaccination or exposure to previous variants poses a significant challenge. A compelling new therapeutic strategy against SARS-CoV-2 is that of single domain antibodies, termed nanobodies, which address certain limitations of monoclonal antibodies. Here we demonstrate that our high-affinity nanobody repertoire, generated against wild-type SARS-CoV-2 spike protein (Mast, Fridy et al. 2021), remains effective against variants of concern, including omicron BA.4/BA.5; a subset is predicted to counter resistance in emerging XBB and BQ.1.1 sublineages. Furthermore, we reveal the synergistic potential of nanobody cocktails in neutralizing emerging variants. Our study highlights the power of nanobody technology as a versatile therapeutic and diagnostic tool to combat rapidly evolving infectious diseases such as SARS-CoV-2.