bluuebunny/crossref_metadata_2025 huggingface dataset:
Neighborhood Social Vulnerability and Interstage Weight Gain: Evaluating the Role of a Home Monitoring Program
Authors: Shustak Rachel J. , Huang Jing , Tam Vicky , Stagg Alyson , Giglia Therese M. , Ravishankar Chitra , Mercer-Rosa Laura , Guevara James P. , Gardner Monique M.
Published: March 2023

Introduction

Poor interstage (IS) weight gain is a risk factor for adverse outcomes in infants with hypoplastic left heart syndrome (HLHS). We sought to examine the association of neighborhood social vulnerability and IS weight gain and determine if this association is modified by enrollment in our institution’s Infant Single Ventricle Management and Monitoring Program (ISVMP).

Methods

We performed a retrospective single-center study of infants with HLHS before (2007-2010) and after (2011-2020) the introduction of the ISVMP. The primary outcome was IS weight gain, and the secondary outcome was IS growth failure. Multivariable linear and logistic regression models were used to examine the association between Social Vulnerability Index (SVI) and the outcomes. We introduced an interaction term into the models to test for effect modification by ISVMP.

Results

We evaluated 217 ISVMP infants and 111 pre-ISVMP historical controls. SVI was associated with IS growth failure (P = 0.001), however, enrollment in ISVMP strongly attenuated this association (P = 0.04). Pre-ISVMP, high and middle vulnerability infants gained 4 gm/day less and were significantly more likely to experience growth failure than low vulnerability infants (high vs. low: aOR 12.5; 95% CI 2.5-62.2; middle vs. low: aOR 7.8; 95% CI 2.0-31.2). After the introduction of the ISVMP, outcomes did not differ by SVI tertile. Middle and high SVI infants enrolled in ISVMP gained 4 gm/day and 2 gm/day more, respectively, than pre-ISVMP controls.

Conclusion

In infants with HLHS, high social vulnerability is a risk factor for poor IS weight gain. However, enrollment in ISVMP significantly reduces growth disparities.
An ultrasensitive method for detecting mutations from short and rare cell-free DNA
Authors: Wang Lin , Zhuang Yu , Yu Yue , Guo Zhiwei , Guo Qiaomei , Qiao Lihua , Wang Xueqing , Liang Xiaohui , Zhang Pengpeng , Li Qifan , Huang Chenjun , Cong Rong , Li Yinghui , Che Bin , Lin Guomin , Rao Mingming , Hu Rongjun , Lou Jiatao , Wang Wei , Yang Guohua
Published: March 2023

Background

Cell-free DNA (cfDNA) promises to serve as surrogate biomarkers for non-invasive molecular diagnostics. Disease-specific cfDNA, such as circulating tumor DNA (ctDNA), was short and rare, making the detection performance of the current targeted sequencing methods unsatisfying.

Methods

Through introducing a linear pre-amplification process and optimizing the adapter ligation with customized reagents, we developed the One-PrimER Amplification (OPERA) system. In this study, we examined its performance in detecting mutations of low variant allelic frequency (VAF) in various samples with short-sized DNA fragments.

Results

In cell line-derived samples containing sonication-sheared DNA fragments with 50-150 bp (peak at 70-80 bp), OPERA was capable of detecting mutations as low as 0.0025% VAF, while CAPP-Seq only detected mutations of >0.03% VAF. Both single nucleotide variant and insertion/deletion can be detected by OPERA. In synthetic fragments as short as 80 bp with low VAF (0.03%-0.1%), the detection sensitivity of OPERA was significantly higher compared to that of droplet digital polymerase chain reaction. The error rate was 5.9×10−5errors per base after de-duplication in plasma samples collected from healthy volunteers. By suppressing “single-strand errors”, the error rate can be further lowered by >5 folds inEGFRT790M hotspot. In plasma samples collected from lung cancer patients, OPERA detected mutations in 57.1% stage I patients with 100% specificity and achieved a sensitivity of 30.0% in patients with tumor volume of less than 1 cm3.

Conclusions

OPERA can effectively detect mutations in rare and highly-fragmented DNA.

Trial registration

This study has been registered on ChiCTR (ChiCTR1900024028) at 23rdJune 2019. Keywords: cell-free DNA; library preparation; liquid biopsy; mutation; next-generation sequencing.
Does one session of dry needling effect vital capacity in people with Parkinsons Disease?
Authors: Tahara Ariany Klein , Gastaldi Ada Clarice , Chinaglia Abel Gonçalves , Monteiro Rafael Luiz Martins , Tumas Vitor , Pereira Santiago Paulo Roberto
Published: March 2023

Respiratory function problems are caused by both motor and non-motor symptoms of Parkinson’s disease (PD). One major problem involving the changes in respiratory function in people with PD is a decrease in chest movement caused by musculoskeletal problems around the neck and upper trunk. The relationship between these respiratory changes and pulmonary volume in people with PD can lead to the main cause of mortality as the disease progresses. Dry needling technique (DNT) is a myofascial release technique that has been reported to provide an immediate effect on pain, decreased muscle spasm or tightness and lead to restoration of range of motion of upper trunk by using needles to stimulate hypersensitive and painful nodules in the musculature called trigger points (TP). However, to date, the use of this technique has not been reported to release muscle tightness or pain in people with PD. The present study aimed to explore the effects of a single session of bilateral DNT to the trapezius muscles trigger point on chest expansion and vital capacity which could lead to improvements in respiratory function in people with PD. Thirty-eight people with PD were randomly allocated to DN and Sham needling treatment groups. The maximum and mean volumes of vital capacity were assessed by using a ventilometer at pre-intervention, immediately after intervention, and one-week follow-up. Mixed Model Analysis of Variance (MM ANOVA) tests with post hoc pairwise comparisons were used to test the differences between groups and assessment time points. No interaction effects were found between groups and assessment time points for maximum and mean vital capacity volume. In addition, no statistically significant main effects of DNT were found for both groups and assessment time points for either maximum or mean vital capacity volume. These findings can provide evidence that a single session of dry needling does not help to improve respiratory function in people with PD. However, slight improvements in vital capacity were observed in the DN group, which may be clinically relevant when considering progressive neurodegenerative disease. More sessions of dry needling need to be explored over a greater time period to determine if longer term effect are possible with this treatment.
Identifying potential risk genes and pathways for neuropsychiatric and substance use disorders using intermediate molecular mediator information
Authors: Gedik Huseyin , Nguyen Tan Hoang , Peterson Roseann E. , Chatzinakos Christos , Riley Brien P. , Vladimirov Vladimir I. , Bacanu Silviu-Alin
Published: March 2023

Neuropsychiatric and substance use disorders (NPSUD) have a complex etiology that includes environmental and polygenic risk factors with significant cross-trait rG. Genome Wide Association Studies (GWAS) of NPSUD yield numerous association signals. However, for most of these regions, we do not yet have a firm understanding of either the specific risk variants or the effects of these variants. Post-GWAS methods allow researchers to use GWAS summary statistics and functional genomics data to infer the likely molecular mediators (transcript, protein and methylation abundances) for the effect of variants on disorders. One group of post-GWAS approaches is commonly referred to as transcriptome/proteome/methylome wide association studies, which are abbreviated as T/P/MWAS (or collectively as XWAS). Since these approaches use biological mediators, the multiple testing burden is reduced to the number of genes (∼20,000) instead of millions GWAS SNPs leading to increased signal detection. In this work, our aim is to uncover likely risk genes for NPSUD by performing XWAS analyses in two tissues – blood and brain. Firstly, XWAS using the Summary-data based Mendelian Randomization (SMR), which takes GWAS summary statistics, reference xQTL data and a reference LD panel as inputs, was conducted to identify putative causal risk genes. Second, given the large comorbidities among NPSUD and the shared cis-xQTLs between blood and brain, we improved XWAS signal detection in NPSUD for underpowered analyses by performing joint concordance analyses between XWAS results i) across the two tissues and ii) across NPSUD. All XWAS signals i) were adjusted for HEIDI (non-causality) p-values and ii) used to test for pathway enrichment. The results suggest that there were widely shared gene/protein signals within the Major Histocompatibility (MHC) region on chromosome 6 (BTN3A2andC4A)and elsewhere in the genome (RERE, FURIN, ZDHHC5andNEK4). The identification of putative molecular genes and pathways underlying risk may offer new targets for therapeutic development. Some of our analyses’ more immediate actionable signals might relate to vitamins, i.e., i) inKYAT3(a part of the kynurenine pathway with vitamin B6 as a cofactor) for post-traumatic stress disorder and ii) omega-3 and vitamin D pathways for bipolar disorder.
Effect of experimental hookworm infection on insulin resistance in people at risk of Type 2 Diabetes: a randomized, placebo-controlled trial
Authors: Pierce Doris R. , McDonald Malcolm , Merone Lea , Becker Luke , Thompson Fintan , Lewis Chris , Field Matthew A. , Rahman Tony , Croese John , Loukas Alex , McDermott Robyn , Giacomin Paul R.
Published: March 2023

The reduced prevalence of insulin resistance and type 2 diabetes (T2D) in countries with endemic parasitic worm infections suggests a protective role for worms against metabolic disorders, however clinical evidence has been non-existent. This 2-year randomized controlled trial of hookworm infection in 40 people at risk of T2D involved treatment with either 20 or 40Necator americanusthird-stage larvae (L3) or Placebo. Primary outcome was safety, with homeostatic model assessment of insulin resistance (HOMA-IR), fasting blood glucose (FBG), and body mass being the key metabolic outcomes. Adverse events were more frequent in hookworm-treated participants, where 44% experienced transient gastrointestinal symptoms. FBG and HOMA-IR were significantly lowered in both hookworm-treated groups at 1-year, and body mass was significantly lowered after L3-20 treatment at 2-years. Overall, hookworm infection was well tolerated in people at risk of T2D, and were associated with improved insulin resistance, warranting further exploration of the benefits of hookworms on metabolic health.
Serial passaging affects stromal cell mechanosensitivity on hyaluronic acid hydrogels
Authors: Sumey Jenna L. , Harrell Abigail M. , Johnston Peyton C. , Caliari Steven R.
Published: March 2023

There is tremendous interest in developing hydrogels as tunablein vitrocell culture platforms to study cell response to mechanical cues in a controlled manner. However, little is known about how common cell culture techniques, such as serial expansion on tissue culture plastic, affect subsequent cell behavior when cultured on hydrogels. In this work we leverage a methacrylated hyaluronic acid hydrogel platform to study stromal cell mechanotransduction. Hydrogels are first formed through thiol-Michael addition to model normal soft tissue (e.g., lung) stiffness (E~ 1 kPa). Secondary crosslinking via radical photopolymerization of unconsumed methacrylates allows matching of early- (E~ 6 kPa) and late-stage fibrotic tissue (E~ 50 kPa). Early passage (P1) primary human mesenchymal stromal cells (hMSCs) display increased spreading, myocardin-related transcription factor-A (MRTF-A) nuclear localization, and focal adhesion size with increasing hydrogel stiffness. However, late passage (P5) hMSCs show reduced sensitivity to substrate mechanics with lower MRTF-A nuclear translocation and smaller focal adhesions on stiffer hydrogels compared to early passage hMSCs. Similar trends are observed in an immortalized human lung fibroblast line. Overall, this work highlights the implications of standard cell culture practices on investigating cell response to mechanical signals usingin vitrohydrogel models.
Dual neutralization of influenza virus hemagglutinin and neuraminidase by a bispecific antibody leads to improved antiviral activity
Authors: Moirangthem Romila , Cordela Sapir , Khateeb Dina , Mandelboim Michal , Jönsson Friederike , Bruel Timothée , Bar-On Yotam
Published: March 2023

Targeting multiple viral proteins is pivotal for sustained viral suppression. In recent years, several broadly neutralizing antibodies that target the influenza virus hemagglutinin and neuraminidase glycoproteins have been developed. However, the impact of dual neutralization of these two glycoproteins on the course of infection has not been thoroughly tested. Here we demonstrate that a bispecific antibody that neutralizes both the hemagglutinin and the neuraminidase has a dual antiviral activity as it blocks infection and prevents the release of progeny viruses from the infected cells. We further show that dual neutralization of the hemagglutinin and the neuraminidase by a bispecific antibody is advantageous over antibody combination as it results in an improved neutralization capacity and augmented antibody effector functions. Notably, the bispecific antibody showed enhanced antiviral activity in influenza virus-infected mice. These findings suggest that dual neutralization of the hemagglutinin and neuraminidase could be effective in controlling influenza virus infection.
Long-read single-cell sequencing reveals expressions of hypermutation clusters of isoforms in human liver cancer cells
Authors: Liu Silvia , Yu Yan-Ping , Ren Bao-Guo , Ben-Yehezkel Tuval , Obert Caroline , Smith Mat , Wang Wenjia , Ostrowska Alina , Soto-Gutierrez Alejandro , Luo Jian-Hua
Published: March 2023

The protein diversity of mammalian cells is determined by arrays of isoforms from genes. Genetic mutation is essential in species evolution and cancer development. Accurate Long-read transcriptome sequencing at single-cell level is required to decipher the spectrum of protein expressions in mammalian organisms. In this report, we developed a synthetic long-read single-cell sequencing technology based on LOOPseq technique. We applied this technology to analyze 447 transcriptomes of hepatocellular carcinoma (HCC) and benign liver from an individual. Through Uniform Manifold Approximation and Projection (UMAP) analysis, we identified a panel of mutation mRNA isoforms highly specific to HCC cells. The evolution pathways that led to the hyper-mutation clusters in single human leukocyte antigen (HLA) molecules were identified. Novel fusion transcripts were detected. The combination of gene expressions, fusion gene transcripts, and mutation gene expressions significantly improved the classification of liver cancer cells versus benign hepatocytes. In conclusion, LOOPseq single-cell technology may hold promise to provide a new level of precision analysis on the mammalian transcriptome.
Prevalence of Cardiometabolic Disease Risk Factors in People living with HIV Initiating Anti-retroviral Therapy at a High-Volume HIV Clinic in Kampala, Uganda
Authors: Amutuhaire Willington , Mulindwa Frank , Castelnuovo Barbara , Brusselaers Nele , Schwarz Jean-Marc , Edrisa Mutebi , Dujanga Simon , Salata Robert A. , Yendewa George A.
Published: March 2023

Background

Cardiometabolic diseases are a leading cause of HIV-related morbidity and mortality, yet routine screening is not undertaken in high burden countries. We aimed to assess the prevalence and risk factors of the metabolic syndrome (MetS) and its components in adult Ugandan people living with HIV (PLHIV) initiating dolutegravir-based antiretroviral therapy (ART).

Methods

We analyzed baseline data of PLHIV aged ≥ 18 years enrolled in the GLUMED (Glucose metabolism changes in Ugandan HIV patients on Dolutegravir) Study from January to October 2021. MetS was defined as having 3 or more of the following: abdominal obesity, hypertension (HTN), elevated fasting glucose, elevated triglycerides and low high-density lipoprotein cholesterol. Multiple logistic regression was used to assess associations between potential risk factors and MetS and its components.

Results

309 PLHIV were analyzed (100% ART-naive, 59.2% female, median age 31 years and median CD4 count 318 cells/mm3). The prevalence of MetS was 13.9%. The most common cardiometabolic condition was dyslipidemia (93.6%), followed by abdominal obesity (34.0%), hyperglycemia (18.4%), and HTN (8.1%). In adjusted analysis, MetS was associated with age > 40 years (odds ratio 3.33, 95% confidence interval 1.45-7.67) and CD4 count > 200 cells/mm3(3.79, 1.23-11.63). HTN was associated with age > 40 years (2.96, 1.32-6.64), and dyslipidemia was associated with urban residence (4.99, 1.35-18.53).

Conclusion

Cardiometabolic risk factors were common in this young Ugandan cohort of PLHIV initiating dolutegravir-based ART, underscoring the need for programmatic implementation of surveillance and management of comorbidities in Uganda and similar settings.

Key points

In Ugandan HIV patients initiating antiretroviral treatment, the prevalence of cardiometabolic risk factors was substantial: metabolic syndrome 13.9%, dyslipidemia 93.6%, abdominal obesity 34.0%, hyperglycemia 18.4%, and hypertension 8.1%. This highlights the need for early screening and management of comorbidities.
Rapid evolution of pre-zygotic reproductive barriers in allopatric populations
Authors: Mahilkar Anjali , Nagendra Prachitha , Venkataraman Pavithra , Deshmukh Saniya , Saini Supreet
Published: March 2023

Adaptive divergence leading to speciation is the major evolutionary process generating diversity in life forms. The most commonly observed form of speciation is allopatric speciation which requires that gene flow be prevented between populations by physical or temporal barriers, as they adapt to their respective environments. Eventually, these adaptive responses drive the populations far apart in the genotypic space such that individuals from the two populations become reproductively isolated. A widely accepted theory is that speciation simply occurs as a by-product of adaptive response of the populations1,2. Several ecological and laboratory examples of allopatric speciation exist3–6. However, we know little about the nature (pre- or post-zygotic) of barriers that arise first in this process. Understanding the first barriers that arise between populations is key, as populations diverge towards becoming distinct species. In recent years, fungi been used as model organisms to answer questions related to evolution of reproductive isolation3,7–9. Here we show rapid evolution of pre-zygotic barriers between allopatric yeast populations. We further demonstrate that these pre-zygotic barriers arise due to altered mating kinetics of the evolved population. Moreover, our non-adaptive evolution experiments with yeast under limited selection pressure also show rapid emergence of reproductive isolation. Overall, our results show that evolution of pre-zygotic reproductive barriers can occur as result of natural selection or drift. These barriers result because of altered mating kinetics or mate preference.

One sentence summary

Pre-zygotic barriers to gene flow can arise due to adaptation or drift.
The genetic and physiological basis ofArabidopsis thalianatolerance toPseudomonas viridiflava
Authors: Duque-Jaramillo Alejandra , Ulmer Nina , Alseekh Saleh , Bezrukov Ilja , Fernie Alisdair R. , Skirycz Aleksandra , Karasov Talia L. , Weigel Detlef
Published: March 2023

The opportunistic pathogenPseudomonas viridiflavacolonizes more than fifty agricultural crop species and is the most commonPseudomonasin the phyllosphere of EuropeanArabidopsis thalianapopulations. Belonging to theP. syringaecomplex, it is genetically and phenotypically distinct from well-characterizedP. syringae sensu stricto. Despite its prevalence, we lack knowledge of howA. thalianaresponds to its native isolates at the molecular level. Here, we characterize the host response in anA. thaliana-P. viridiflavapathosystem.

We measured host and pathogen growth in axenic infections, and used immune mutants, transcriptomics, and metabolomics to determine defense pathways influencing susceptibility toP. viridiflavainfection.

Infection withP. viridiflavaincreased jasmonic acid (JA) levels and the expression of ethylene defense pathway marker genes. The immune response in a susceptible host accession was delayed compared to a tolerant one. Mechanical injury rescued susceptibility, consistent with an involvement of JA.

The JA/ethylene pathway is important for suppression ofP. viridiflava, yet suppression capacity varies between accessions. Our results shed light on howA. thalianacan suppress the ever-presentP. viridiflava, but further studies are needed to understand howP. viridiflavaevades this suppression to spread broadly acrossA. thalianapopulations.
Dual impact of PTEN mutation on CSF dynamics and cortical networks via the dysregulation of neural precursors and their interneuron descendants
Authors: DeSpenza Tyrone , Kiziltug Emre , Allington Garrett , Barson Daniel G. , O’Connor David , Robert Stephanie M. , Mekbib Kedous Y. , Nanda Pranav , Greenberg Ana , Singh Amrita , Duy Phan Q. , Mandino Francesca , Zhao Shujuan , Lynn Anna , Reeves Benjamin C. , Marlier Arnaud , Getz Stephanie A. , Nelson-Williams Carol , Shimelis Hermela , Walsh Lauren K. , Zhang Jinhui , Wang Wei , OuYang Annaliese , Smith Hannah , Butler William , Carter Bob S. , Deniz Engin , Lake Evelyn M. R. , Constable Todd , Gûnel Murat , Lifton Richard P. , Alper Seth L. , Chih Jin Sheng , Crair Michael C. , Moreno-De-Luca Andres , Luikart Bryan W. , Kahle Kristopher T.
Published: March 2023

Expansion of the cerebrospinal fluid (CSF)-filled cerebral ventricles (ventriculomegaly) is the quintessential feature of congenital hydrocephalus (CH) but also seen in autism spectrum disorder (ASD) and several neuropsychiatric diseases.PTENis frequently mutated in ASD; here, we showPTENis abona fiderisk gene for the development of ventriculomegaly, including neurosurgically-treated CH.Pten-mutant hydrocephalus is associated with aqueductal stenosis due to the hyperproliferation of periventricularNkx2.1+neural precursors (NPCs) and CSF hypersecretion from inflammation-dependent choroid plexus hyperplasia. The hydrocephalicPten-mutant cortex exhibits ASD-like network dysfunction due to impaired activity ofNkx2.1+NPC-derived inhibitory interneurons.Raptordeletion or post-natal Everolimus corrects ventriculomegaly, rescues cortical deficits, and increases survival by antagonizing mTORC1-dependentNkx2.1+cell pathology. These results implicate a dual impact of PTEN mutation on CSF dynamics and cortical networks via the dysregulation of NPCs and their interneuron descendants. These data identify a non-surgical treatment target for hydrocephalus and have implications for other developmental brain disorders.

HIGHLIGHTS

PTEN de novomutations are associated with cerebral ventriculomegaly in autism spectrum disorder (ASD) and congenital hydrocephalus (CH).

Pten-mutant hydrocephalus is associated with aqueductal stenosis due to the hyperproliferation of medial ganglionic eminenceNkx2.1+neural precursors and CSF hypersecretion from inflammation-induced choroid plexus hyperplasia.

The hydrocephalicPten-mutant cortex exhibits ASD-like network dysfunction due to impaired activity ofNkx2.1+NPC-derived inhibitory interneurons.

mTORC1 inhibition viaRaptordeletion or early post-natal treatment with rapamycin or everolimus increases survival and amelioratesPten-mutant ventriculomegaly and cortical pathology.
Generalizing biological surround suppression based on center surround similarity via deep neural network models
Authors: Pan Xu , DeForge Annie , Schwartz Odelia
Published: March 2023

Sensory perception is dramatically influenced by the context. Models of contextual neural surround effects in vision have mostly accounted for Primary Visual Cortex (V1) data, via nonlinear computations such as divisive normalization. However, surround effects are not well understood within a hierarchy, for neurons with more complex stimulus selectivity beyond V1. We utilized feedforward deep convolutional neural networks and developed a gradient-based technique to visualize the most suppressive and excitatory surround. We found that deep neural networks exhibited a key signature of surround effects in V1, highlighting center stimuli that visually stand out from the surround and suppressing responses when the surround stimulus is similar to the center. We found that in some neurons, especially in late layers, when the center stimulus was altered, the most suppressive surround surprisingly can follow the change. Through the visualization approach, we generalized previous understanding of surround effects to more complex stimuli, in ways that have not been revealed in visual cortices. In contrast, the suppression based on center surround similarity was not observed in an untrained network. We identified further successes and mismatches of the feedforward CNNs to the biology. Our results provide a testable hypothesis of surround effects in higher visual cortices, and the visualization approach could be adopted in future biological experimental designs.

Author summary

Neural responses and perception of a visual stimulus are influenced by the context, such as what spatially surrounds a given feature. Contextual surround effects have been extensively studied in the early visual cortex. But the brain processes visual inputs hierarchically, from simple features up to complex objects in higher visual areas. Contextual effects are not well understood for higher areas of cortex and for more complex stimuli. Utilizing artificial deep neural networks and a visualization technique we developed, we found that deep networks exhibited a key signature of surround effects in the early visual cortex, highlighting center stimuli that visually stand out from the surround and suppressing responses when the surround stimulus is similar to the center. We found in some neurons, especially in late layers, when the center stimulus was altered, the most suppressive surround could surprisingly follow. This is a generalization of known surround effects for more complex stimuli that has not been revealed in the visual cortex. Our findings relate to notions of efficient coding and salience perception, and emerged without incorporating specialized nonlinear computations typically used to explain contextual effects in the early cortex. Our visualization approach provides a new experimental paradigm and a testable hypothesis of surround effects for more complex stimuli in higher cortical areas; the visualization approach could be adopted in biological experimental designs.
Vessel Density Mapping of Cerebral Small Vessels on 3D High Resolution Black Blood MRI
Authors: Sarabi Mona Sharifi , Ma Samantha J. , Jann Kay , Ringman John M. , Wang Danny J.J. , Shi Yonggang
Published: March 2023

Cerebral small vessels are largely inaccessible to existing clinical in vivo imaging technologies. This study aims to present a novel analysis pipeline for vessel density mapping of cerebral small vessels from high-resolution 3D black-blood MRI at 3T. Twenty-eight subjects (10 under 35 years old, 18 over 60 years old) were imaged with the T1-weighted turbo spin-echo with variable flip angles (T1w TSE-VFA) sequence optimized for black-blood small vessel imaging with iso-0.5mm spatial resolution at 3T. Hessian-based vessel segmentation methods (Jerman, Frangi and Sato filter) were evaluated by vessel landmarks and manual annotation of lenticulostriate arteries (LSAs). Using optimized vessel segmentation, large vessel pruning and non-linear registration, a semiautomatic pipeline was proposed for quantification of small vessel density across brain regions and further for localized detection of small vessel changes across populations. Voxel-level statistics was performed to compare vessel density between two age groups. Additionally, local vessel density of aged subjects was correlated with their corresponding gross cognitive and executive function (EF) scores using Montreal Cognitive Assessment (MoCA) and EF composite scores compiled with Item Response Theory (IRT). Jerman filter showed better performance for vessel segmentation than Frangi and Sato filter which was employed in our pipeline. Cerebral small vessels on the order of a few hundred microns can be delineated using the proposed analysis pipeline on 3D black-blood MRI at 3T. The mean vessel density across brain regions was significantly higher in young subjects compared to aged subjects. In the aged subjects, localized vessel density was positively correlated with MoCA and IRT EF scores. The proposed pipeline is able to segment, quantify, and detect localized differences in vessel density of cerebral small vessels based on 3D high-resolution black-blood MRI. This framework may serve as a tool for localized detection of small vessel density changes in normal aging and cerebral small vessel disease.
Pyruvate dehydrogenase dependent metabolic program affects oligodendrocyte maturation and remyelination
Authors: Sajjad M , Zahoor Insha , Rashid Faraz , Rattan Ramandeep , Giri Shailendra
Published: March 2023

The metabolic need of the premature oligodendrocytes (Pre-OLs) and mature oligodendrocytes (OLs) are distinct. The metabolic control of oligodendrocyte maturation is not fully understood. Here we show that the terminal maturation and higher mitochondrial respiration in the oligodendrocyte is an integrated process controlled through pyruvate dehydrogenase (Pdh). Combined bioenergetics and metabolic studies show that mature oligodendrocytes show elevated TCA cycle activity than the premature oligodendrocytes. Our signaling studies show that the increased TCA cycle activity is mediated by the activation of Pdh due to inhibition of pyruvate dehydrogenases isoform-1 (Pdhk1) that phosphorylates and inhibits Pdh. Accordingly, when Pdhk1 is directly expressed in the premature oligodendrocytes, they fail to mature. While Pdh converts pyruvate into the acetyl-CoA by its oxidative decarboxylation, our study shows that Pdh also activates a unique molecular switch required for oligodendrocyte maturation by acetylating the bHLH family transcription factor Olig1. Pdh inhibition via Pdhk1 blocks the Olig1-acetylation and hence, oligodendrocyte maturation. Using the cuprizone model of demyelination, we show that Pdh is deactivated during the demyelination phase, which is reversed in the remyelination phase upon cuprizone withdrawal. In addition, Pdh activity status correlates with the Olig1-acetylation status. Hence, the Pdh metabolic node activation allows a robust mitochondrial respiration and activation of a molecular program necessary for the terminal maturation of oligodendrocytes. Our findings open a new dialogue in the developmental biology that links cellular development and metabolism. These findings have far-reaching implications for the development of therapies for a variety of demyelinating disorders including multiple sclerosis.
Astrocytes control cocaine-induced synaptic plasticity and reward through the matricellular protein hevin
Authors: Mongrédien Raphaële , Anesio Augusto , Fernandes Gustavo J. D. , Eagle Andrew L. , Maldera Steeve , Pham Cuong , Vilette Adèle , Bianchi Paula , Franco Clara , Louis Franck , Gruszczynski Carole , Betancur Catalina , Erdozain Amaia M. , Robison Alfred J. , Boucard Antony A. , Li Dongdong , Cruz Fabio C. , Gautron Sophie , Heck Nicolas , Vialou Vincent
Published: March 2023

Drug addiction involves profound modifications of neuronal plasticity in the nucleus accumbens, which may engage various cell types. Here, we report prominent effects of cocaine on calcium signals in astrocytes characterized byin vivofiber photometry. Astrocyte calcium signals in the nucleus accumbens are sufficient and necessary for the acquisition of cocaine seeking behavior. We identify the astrocyte-secreted matricellular protein hevin as an effector of the action of cocaine and calcium signals on reward and neuronal plasticity.
Seed Longevity is Controlled by Metacaspases
Authors: Liu Chen , Hatzianestis Ioannis H. , Pfirrmann Thorsten , Reza Salim H. , Minina Elena A. , Moazzami Ali , Stael Simon , Gutierrez-Beltran Emilio , Pitsili Evgenia , Dörmann Peter , D’ Andrea Sabine , Gevaert Kris , Romero-Campero Francisco , Ding Pingtao , Nowack Moritz K. , Van Breusegem Frank , Jones Jonathan D. G. , Bozhkov Peter V , Moschou Panagiotis N.
Published: March 2023

To survive extreme desiccation, seeds enter dormancy that can last millennia. This dormancy involves the accumulation of protective but structurally disordered storage proteins through unknown adjustments of proteolytic surveillance mechanisms. Mutation of all six types II metacaspases (MCAs)-II in the model plant Arabidopsis revealed their essential role in modulating these proteolytic mechanisms. MCA-II mutant seeds fail to properly target at the endoplasmic reticulum (ER) the AAA ATPase Cell Division Cycle 48 (CDC48) to dispose of misfolded proteins. MCA-IIs cleave a CDC48 adaptor, the ubiquitination regulatory X domain-containing (PUX) responsible for localizing CDC48 to the lipid droplets. When cleaved, CDC48-PUX is inactivated and allows a lipid droplet-to-ER shuttling of CDC48, an important step in the regulation of seeds’ lifespan. In sum, we uncover antagonism between proteolytic pathways bestowing longevity.

One-Sentence Summary

Metacaspase proteases confer seed longevity by antagonizing CDC48 activity.
EndogenousStaphylococcus aureusCRISPR-cassystem limits phage proliferation and efficiently excises from the genome as part of the SCCmeccassette
Authors: Mikkelsen Kasper , Bowring Janine Zara , Ng Yong Kai , Frisinger Frida Svanberg , Maglegaard Julie Kjærsgaard , Li Qiuchun , Sieber Raphael N. , Petersen Andreas , Andersen Paal Skytt , Rostøl Jakob T. , Høyland-Kroghsbo Nina Molin , Ingmer Hanne
Published: March 2023

CRISPR-Cas is an adaptive immune system that allows bacteria to inactivate mobile genetic elements. Approximately 50% of bacteria harbor CRISPR-cas, however in the human pathogenStaphylococcus aureus, CRISPR-casloci are less common and often studied in heterologous systems. We analyzed the prevalence of CRISPR-casin genomes of methicillin resistantStaphylococcus aureus(MRSA) isolated in Denmark. Only 2.9 % of the strains carried CRISPR-cassystems, but for strains of sequence type ST630 over half were positive. All CRISPR-casloci were type III-A and located within the staphylococcal chromosomal cassette (SCCmec) type V(5C2&5) conferring β-lactam resistance. Curiously, only 23 different CRISPR spacers were identified in 69 CRISPR-positive strains and almost identical SCCmeccassettes, CRISPR arrays andcasgenes, are present in staphylococcal species other thanaureus, suggesting that these were transferred horizontally. For the ST630 strain 110900, we demonstrate that the SCCmeccassette containing CRISPR-casexcises from the chromosome at high frequency. However, the cassette was not transferable under the conditions investigated. One of the CRISPR spacers targets a late gene in the lytic bacteriophage (phage) virus philPLA-RODI, and we show that the system protects against phage infection by reducing phage burst size. However, CRISPR-Cas can be overloaded or bypassed by CRISPR escape mutants. Our results imply that the endogenous type III-A CRISPR-Cas system inS. aureusis active against targeted phages, albeit with low efficacy. This suggests nativeS. aureusCRISPR-Cas offers only partial immunity, and in nature may work in tandem with other defense systems.

Importance

CRISPR-Cas is an adaptive immune system enabling bacteria and archaea to protect themselves against mobile genetic elements such as phages. In strains ofStaphylococcus aureus, CRISPR-casis rare, but when present, it is located within the SCCmecelement encoding resistance to methicillin and other β-lactam antibiotics. We show that the entire module is excisable, with almost identical versions found in different species ofnon-aureusstaphylococci suggesting that the system only rarely acquires new spacers inS. aureus. Additionally, we show that in its endogenous form, theS. aureusCRISPR-Cas is active but inefficient against lytic phages, with phages being able to form escape mutants or overload the system. This leads us to propose that CRISPR-Cas inS. aureusoffers only partial immunity in native systems, and so may work together with other defense systems to prevent phage-mediated killing.
Schlafen14 Regulates Gene Expression Depending on Codon Usage
Authors: Valenzuela Carlos , Saucedo Sergio , Llano Manuel
Published: March 2023

Schlafen (SLFN) is a family of proteins upregulated by type I interferons with a regulatory role in translation. Intriguingly, SLFN14 associates with the ribosome and can degrade rRNA, tRNA, and mRNAin vitro, but a role in translation is still unknown. Ribosomes are important regulatory hubs during translation elongation of mRNAs rich in rare codons. Therefore, we evaluated the potential role of SLFN14 in the expression of mRNAs enriched in rare codons, using HIV-1 genes as a model. We found that SLFN14 regulates in a variety of cell types, including primary immune cells, the expression of HIV-1 and non-viral genes based on their codon adaptation index, a measurement of the synonymous codon usage bias; consequently, SLFN14 inhibited the replication of HIV-1. The potent inhibitory effect of SLFN14 on the expression of the rare codon-rich transcript HIV-1 Gag was minimized by codon optimization. Mechanistically, we found that the endoribonuclease activity of SLFN14 is required, and that ribosomal, but not messenger, RNA degradation is associated with the transcript selectivity of SLFN14. Therefore, we propose that SLFN14 impairs the expression of transcripts rich in rare codons, in a catalytic-dependent manner.
Antibiotic prescribing in remote versus face-to-face consultations for acute respiratory infections in English primary care: An observational study using TMLE
Authors: Vestesson Emma , De Corte Kaat Lieve An , Chappell Paul , Crellin Elizabeth , Clarke Geraldine M
Published: March 2023

Background The COVID-19 pandemic has led to an ongoing increase in the use of remote consultations in general practice in England. Though the evidence is limited, there are concerns that the increase in remote consultations could lead to more antibiotic prescribing. Methods We used patient-level primary care data from the Clinical Practice Research Datalink to estimate the association between consultation mode (remote vs face-to-face) and antibiotic prescribing in England for acute respiratory infections (ARI) between April 2021 - March 2022. We used targeted maximum likelihood estimation, a causal machine learning method with adjustment for patient-, clinician- and practice-level factors. Findings There were 45,997 ARI consultations (34,555 unique patients), of which 28,127 were remote and 17,870 face-to-face. For children, 48% of consultations were remote whereas for adults 66% were remote. For children, 42% of remote and 43% face-to-face consultations led to an antibiotic prescription; the equivalent in adults was 52% of remote and 42% face-to-face. Adults with a remote consultation had 23% (Odds Ratio (OR) 1.23 95% Confidence Interval (CI): 1.18-1.29) higher chance of being prescribed antibiotics compared to if they had been seen face-to-face. We found no significant association between consultation mode and antibiotic prescribing in children (OR 1.04 95% CI 0.98-1.11). Interpretation This study uses rich patient-level data and robust statistical methods and represents an important contribution to the evidence base on antibiotic prescribing in post-COVID primary care. The higher rates of antibiotic prescribing in remote consultations for adults are cause for concern. We see no significant difference in antibiotic prescribing between consultation mode for children. These findings should inform antimicrobial stewardship activities for health care professionals and policy makers. Future research should examine differences in guideline-compliance between remote and face-to-face consultations to understand the factors driving antibiotic prescribing in different consultation modes. Funding No external funding. Keywords general practice; England; antibiotics; remote consultations; telehealth; telemedicine; TMLE; causal inference; machine learning; acute respiratory infections; antimicrobial resistance; covid; ARTI; ARI; antibiotic prescribing; primary care
Reverse cholesterol transport and lipid peroxidation biomarkers in major depression and bipolar disorder: a systematic review and meta-analysis
Authors: Almulla Abbas F. , Thipakorn Yanin , Abo Algon Ali Abbas , Tunvirachaisakul Chavit , Al-Hakeim Hussein K. , Maes Michael
Published: March 2023

Background

Major depression (MDD) and bipolar disorder (BD) are linked to immune activation, increased oxidative stress, and lower antioxidant defenses.

Objectives

To systematically review and meta-analyze all data concerning biomarkers of reverse cholesterol transport (RCT), lipid-associated antioxidants, lipid peroxidation products, and autoimmune responses to oxidatively modified lipid epitopes in MDD and BD.

Methods

Databases including PubMed, Google scholar and SciFinder were searched to identify eligible studies from inception to January 10th, 2023. Guidelines of Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines were followed.

Results

The current meta-analysis included 176 studies (60 BD and 116 MDD) and examined 34,051 participants, namely 17,094 with affective disorders and 16,957 healthy controls. Patients with MDD and BD showed a) significantly decreases in RCT (mainly lowered high-density lipoprotein cholesterol and paraoxonase 1); b) lowered lipid soluble vitamins (including vitamin A, D, and coenzyme Q10); c) increased lipid peroxidation and aldehyde formation, mainly increased malondialdehyde (MDA), 4-hydroxynonenal, peroxides, and 8-isoprostanes; and d) Immunoglobulin (Ig)G responses to oxidized low-density lipoprotein and IgM responses to MDA. The ratio of all lipid peroxidation biomarkers / all lipid-associated antioxidant defenses was significantly increased in MDD (standardized mean difference or SMD=0.433; 95% confidence intervals (CI): 0.312; 0.554) and BD (SMD=0.653; CI: 0.501-0.806). This ratio was significantly greater in BD than MDD (p=0.027).

Conclusion

In MDD/BD, lowered RCT, a key antioxidant and anti-inflammatory pathway, may drive increased lipid peroxidation, aldehyde formation, and autoimmune responses to oxidative specific epitopes, which all together cause increased immune-inflammatory responses and neurotoxicity.
Conformation-dependent ligand hot spots in the spliceosomal RNA helicase BRR2
Authors: Vester Karen , Metz Alexander , Huber Simon , Loll Bernhard , Wahl Markus C.
Published: March 2023

The conversion of hits to leads in drug discovery involves the elaboration of chemical core structures to increase their potency. In fragment-based drug discovery, low-molecular-weight compounds are tested for protein binding and are subsequently modified, with the tacit assumption that the binding mode of the original hit will be conserved among the derivatives. However, deviations from binding mode conservation are rather frequently observed, but potential causes of these alterations remain incompletely understood. Here, two crystal forms of the spliceosomal RNA helicase BRR2 were employed as a test case to explore the consequences of conformational changes in the target protein on the binding behaviour of fragment derivatives. The initial fragment, sulfaguanidine, bound at the interface between the two helicase cassettes of BRR2 in one crystal form. Second-generation compounds devised by structure-guided docking were probed for their binding to BRR2 in a second crystal form, in which the original fragment-binding site was altered due to a conformational change. While some of the second-generation compounds retained binding to parts of the original site, others changed to different binding pockets of the protein. A structural bioinformatics analysis revealed that the fragment-binding sites correspond to predicted binding hot spots, which strongly depend on the protein conformation. This case study offers an example of extensive binding-mode changes during hit derivatization, which are likely to occur as a consequence of multiple binding hot spots, some of which are sensitive to the flexibility of the protein.
Buccaneer model building with neural network fragment selection
Authors: Alharbi Emad , Calinescu Radu , Cowtan Kevin
Published: March 2023

Tracing the backbone is a critical step in protein model building, as incorrect tracing leads to poor protein models. Here, a neural network trained to identify unfavourable fragments and remove them from the model-building process in order to improve backbone tracing is presented. Moreover, a decision tree was trained to select an optimal threshold to eliminate unfavourable fragments. The neural network was tested on experimental phasing data sets from the Joint Center for Structural Genomics (JCSG), recently deposited experimental phasing data sets (from 2015 to 2021) and molecular-replacement data sets. The experimental results show that using the neural network in the Buccaneer protein-model-building software can produce significantly more complete protein models than those built using Buccaneer alone. In particular, Buccaneer with the neural network built protein models with a completeness that was at least 5% higher for 25% and 50% of the original and truncated resolution JCSG experimental phasing data sets, respectively, for 28% of the recently collected experimental phasing data sets and for 43% of the molecular-replacement data sets.
Earnings quality and firm valuation: evidence from several European countries
Authors: Fassas Athanasios , Nerantzidis Michail , Tsakalos Ioannis , Asimakopoulos Ioannis
Published: March 2023

Purpose

This study aims to investigate the association between firm valuation and earnings quality in several European countries. Also, it examines if country-level governance and market development are important determinants of firm valuation.

Design/methodology/approach

Using a sample of 5,002 non-financial firms in 37 European countries over the years 2004 to 2019, the authors evaluate the research question using regression models.

Findings

The authors find a significant positive relationship between firm valuation and a multi-factor earnings quality measure based on four components (accruals, cash flows, operating efficiency and exclusions). The authors further show that stock market development is also a driver of firm value, while country-level governance is significant only in the case of a firm fixed effect model with time effects. The results are robust to alternative model specifications that control for endogeneity, sample heterogeneity and alternative proxies for firm valuation.

Practical implications

Policy makers and market participants could benefit from the findings, by exploiting the advantages of earnings quality in terms of high-ranking stocks whose earnings are backed by cash flows and other sustainable sources.

Originality/value

To the best of the authors’ knowledge, this study is the first to empirically test the relationship between earnings quality and firm value in the European setting during a period that incorporates the adoption of IFRS. This is quite interesting as it permits cross-border comparability in terms of financial reporting and provides deeper and more representative evidence.