bluuebunny/crossref_metadata_2025_split huggingface dataset:
Maternal breastfeeding and education impact infant growth and development more than in-utero HIV/antiretroviral therapy exposure in context of universal antiretroviral therapy
Authors: Cherkos Ashenafi S. , LaCourse Sylvia M. , Kinuthia John , Mecha Jerphason , Enquobahrie Daniel A. , Escudero Jaclyn N. , John-Stewart Grace 
Published: November 2023

Background:
Exposure to HIV and antiretroviral therapy (ART) in utero may influence infant growth and development. Most available evidence predates adoption of universal ART (Option B+ ART regimens). In a recent cohort, we compared growth and development in HIV-exposed uninfected (HEU) to HIV-unexposed (HUU) infants.

Design:
Prospective cohort study: data from Impact of Maternal HIV on Mycobacterium Tuberculosis Infection among Peripartum Women and their Infants (MiTIPS) in Western Kenya.

Methods:
Women were enrolled during pregnancy. Mother–infant pairs were followed until 24 months postpartum. We used multivariable linear mixed-effects models to compare growth rates [weight-for-age z score (WAZ) and height-for-age z score (HAZ)] and multivariable linear regression to compare overall development between HEU and HUU children.

Results:
About 51.8% (184/355) of the infants were HEU, 3.9% low birthweight (<2.5 kg), and 8.5% preterm (<37 gestational weeks). During pregnancy, all mothers of HEU received ART; 67.9% started ART prepregnancy, and 87.3% received 3TC/FTC, TDF, and EFV. In longitudinal analyses, HEU children did not differ significantly from HUU in growth or development (P > 0.05 for all). In the combined HEU/HUU cohort, higher maternal education was associated with significantly better growth and development: WAZ [β = 0.18 (95% CI 0.01–0.34)], HAZ [β = 0.26 (95% CI 0.04–0.48)], and development [β = 0.24 (95% CI 0.02–0.46)]. Breastfeeding was associated with significantly better HAZ [β=0.42 (95% CI 0.19–0.66)] and development [β =0.31 (95% CI 0.08–0.53)].

Conclusion:
HEU children in the setting of universal maternal ART had a similar growth trajectory and development to HUU children. Breastfeeding and maternal education improved children's weight, height, and overall development irrespective of maternal HIV status.
Tactile Sensitivity to the Frequency Spectrum of Complex Vibrotactile Signals
Authors: Le Thanh-loan Sarah , Bailly Gilles , Vezzoli Eric , auvray Malika , Gueorguiev David 
Published: November 2023

Haptic interactions with objects induce complex vibrotactile signals that are central to tactile perception. Despite the broad literature on vibrotactile perception, there is surprisingly little knowledge of the sensory processing of complex tactile signals made of multiple frequencies. To fill this gap, the study reported here investigated the impact of the constitutive pure tones of a complex vibrotactile signal on its perception. Participants completed a 3-AFC task, in which they were asked to identify an odd signal among two complex references. The odd signal was created by removing one pure tone from the reference, which varied in spectral composition, harmonicity, and inter-frequency intervals. Each reference signal was made of either two, three, or four pure tones. The results revealed that the removed pure tone’s value as well as the inter-frequency interval play a significant role on participants’ performance whereas changes in harmonicity, complexity have little impact. In addition, the results showed that the smaller the ratio between the removed frequency and the lowest one of the reference signals, the better the participants’ capacity to identify the one with a missing tone. Overall, the detection of a missing tone in a complex signal predominantly depends on the tone’s frequency value of the removed signal suggesting a tactile sensitivity to the frequency spectrum of complex vibrotactile signals.NEW & NOTEWORTHYThis research reports an investigation of the respective roles of frequency range, harmonicity, and complexity on human perception of vibrotactile signals. The results revealed that only pure tones that are close to the lower end of the frequency spectrum are noticed when they are missing. This finding sheds new light on the mechanisms of frequency selectivity in touch.
The prevalence of copy number increase at multiallelic CNVs associated with cave colonization in Mexican tetra (Astyanax mexicanus)
Authors: Pokrovac Ivan , Rohner Nicolas , Pezer Željka 
Published: November 2023

AbstractCopy number variation is a common contributor to phenotypic diversity, yet its involvement in ecological adaptation is not easily discerned. Instances of parallelly evolving populations of the same species in a similar environment marked by strong selective pressures present opportunities to study the role of copy number variants (CNVs) in adaptation. By identifying CNVs that repeatedly occur in multiple populations of the derived ecotype and are not (or are rarely) present in the populations of the ancestral ecotype, the association of such CNVs with adaptation to the novel environment can be inferred. We used this paradigm to identify CNVs associated with recurrent adaptation of the Mexican tetra (Astyanax mexicanus) to cave environment. Using a read-depth approach, we detected CNVs from previously re-sequenced genomes of 44 individuals belonging to two ancestral surface and three derived cave populations. We identified 102 genes and 292 genomic regions that repeatedly diverge in copy number between the two ecotypes and occupy 0.8% of the reference genome. Functional analysis revealed their association with processes previously recognized to be relevant for adaptation, such as vision, immunity, oxygen consumption, metabolism, and neural function and we propose that these variants have been selected for in the cave or surface waters. The majority of the ecotype-divergent CNVs are multiallelic and display copy-number increases in cave fish compared to surface fish. Our findings suggest that multiallelic CNVs - including gene duplications, and divergence in copy number provide a fast route to produce novel phenotypes associated with adaptation to subterranean life.Significance StatementDuplications and deletions of genomic sequences occur frequently within a population. Such inter-individual difference in the amount of genetic material is known as copy number variation and is associated with differences in phenotypic traits. Despite its pervasiveness, the evolutionary impact of copy number variation in complex organisms is difficult to discern, primarily due to the infeasibility of setting up evolutionary experiments in the laboratory. Instances of multiple populations that evolved the same traits in similar environments represent naturally occurring evolutionary experiments and valuable opportunities to study the molecular basis of adaptation. Mexican tetra represents such a system and we use the genomes of surface and cave-dwelling populations to study the role of copy number variation in the recurrent cave adaptation.
Modulation of Human Frontal Midline Theta by Neurofeedback: A Systematic Review and Quantitative Meta-Analysis
Authors: Pfeiffer Maria , Kübler Andrea , Hilger Kirsten 
Published: November 2023

AbstractHuman brain activity consists of different frequency bands associated with varying functions. Oscillatory activity of frontal brain regions in the theta range (4-8Hz) is linked to cognitive processing and can be modulated by neurofeedback - a technique where participants receive real-time feedback about their brain activity and learn to modulate it. However, criticism of this technique evolved, and high heterogeneity of study designs complicates a valid evaluation of its effectiveness. This meta-analysis provides the first systematic overview over studies attempting to modulate frontal midline theta with neurofeedback in healthy human participants. Out of 1431 articles screened, 14 studies were eligible for systematic review and 11 for quantitative meta-analyses. Studies were evaluated following the DIAD model and the PRISMA guidelines. A significant across-study effect of medium size (Hedges’g= .66; 95%-CI [−0.62, 1.73]) with substantial between-study heterogeneity (Q(16) = 167.43,p< .0001) was observed and subanalysis revealed effective frontal midline theta upregulation. We discuss moderators of effect sizes and provide guidelines for future research in this dynamic field.
Restoration of Cone Circuit Functionality in the Regenerating Adult Zebrafish Retina
Authors: Abraham Evelyn , Hartmann Hella , Yoshimatsu Takeshi , Baden Tom , Brand Michael 
Published: November 2023

SummaryUnlike humans, teleosts like zebrafish exhibit robust retinal regeneration after injury from endogenous stem cells. However, understanding the functional recovery of the regenerated retina remains a challenge. In particular, it is unclear if regenerating cone-photoreceptors can regain physiological function and integrate correctly into post-synaptic circuits. To bridge this gap, we employed two-photon calcium imaging of living retina, focusing on photoreceptor responses before and after an intense light-induced lesion in the adult zebrafish retina. To assess the functional recovery of cones and their downstream circuits, we exploited the colour opponency in adult zebrafish cones. We find that UV cones exhibit an intrinsic Off-response to short-wavelength blue light, but an On-response to longer-wavelength green light, which depends on feedback signals from outer retinal circuits. Accordingly, we examined the presence and quality of Off-versus On-responses, to assess the functional recovery of cones and their correct integration into outer retinal circuits. We find that regenerated UV cones regain both Off-responses to short-wavelength and On-responses to long-wavelength within 3 months after light lesion. Hence, physiological circuit functionality is restored in regenerated cone photoreceptors, suggesting that inducing endogenous regeneration is a promising strategy for human retinal repair.Graphical abstract
scLongTree: an accurate computational tool to infer the longitudinal tree for scDNAseq data
Authors: Khan Rituparna , Mallory Xian 
Published: November 2023

AbstractA subclonal tree that depicts the evolution of cancer cells is of interest in understanding how cancer grows, prognosis and treatment of cancer.Longitudinal single-cell DNA sequencing data (scDNA-seq) is the single-cell DNA sequencing data sequenced at different time points. It provides more knowledge of the order of the mutations than the scDNA-seq taken at only one time point, and thus facilitates the inference of the subclonal tree. There is only one existing tool LACE that can infer a subclonal tree based on the longitudinal scDNA-seq, and it is limited in accuracy and scale.We presented scLongTree, a computational tool that can accurately infer the longitudinal subclonal tree based on the longitudinal scDNA-seq. ScLongTree can be scalable to hundreds of mutations, and outper-formed state-of-the-art methods SCITE, SiCloneFit and LACE on a comprehensive simulated dataset. The test on a real dataset SA501 showed that scLongTree can more accurately interpret the progres-sive growth of the tumor than LACE. ScLongTree is freely available onhttps://github.com/compbio-mallory/sclongitudinal infer.
The Parkinson’s disease risk gene cathepsin B promotes fibrillar alpha-synuclein clearance, lysosomal function and glucocerebrosidase activity in dopaminergic neurons
Authors: Jones-Tabah Jace , He Kathy , Senkevich Konstantin , Karpilovsky Nathan , Deyab Ghislaine , Cousineau Yuting , Nikanorova Daria , Goldsmith Taylor , Pellitero Esther del Cid , Chen Carol X-Q. , Luo Wen , You Zhipeng , Abdian Narges , Pietrantonio Isabella , Goiran Thomas , Ahmad Jamil , Ruskey Jennifer A. , Asayesh Farnaz , Spiegelman Dan , Waters Cheryl , Monchi Oury , Dauvilliers Yves , Dupré Nicolas , Miliukhina Irina , Timofeeva Alla , Emelyanov Anton , Pchelina Sofya , Greenbaum Lior , Hassin-Baer Sharon , Alcalay Roy N. , Milnerwood Austen , Durcan Thomas M. , Gan-Or Ziv , Fon Edward A. 
Published: November 2023

AbstractVariants in theCTSBgene encoding the lysosomal hydrolase cathepsin B (catB) are associated with increased risk of Parkinson’s disease (PD). However, neither the specificCTSBvariants driving these associations nor the functional pathways that link catB to PD pathogenesis have been characterized. CatB activity contributes to lysosomal protein degradation and regulates signaling processes involved in autophagy and lysosome biogenesis. Previousin vitrostudies have found that catB can cleave monomeric and fibrillar alpha-synuclein, a key protein involved in the pathogenesis of PD that accumulates in the brains of PD patients. However, truncated synuclein isoforms generated by catB cleavage have an increased propensity to aggregate. Thus, catB activity could potentially contribute to lysosomal degradation and clearance of pathogenic alpha synuclein from the cell, but also has the potential of enhancing synuclein pathology by generating aggregation-prone truncations. Therefore, the mechanisms linking catB to PD pathophysiology remain to be clarified. Here, we conducted genetic analyses of the association between common and rareCTSBvariants and risk of PD. We then used genetic and pharmacological approaches to manipulate catB expression and function in cell lines and induced pluripotent stem cell-derived dopaminergic neurons and assessed lysosomal activity and the handling of aggregated synuclein fibrils. We find that catB inhibition impairs autophagy, reduces glucocerebrosidase (encoded byGBA1) activity, and leads to an accumulation of lysosomal content. In cell lines, reduction ofCTSBgene expression impairs the degradation of pre-formed alpha-synuclein fibrils, whereasCTSBgene activation enhances fibril clearance. In midbrain organoids and dopaminergic neurons treated with alpha-synuclein fibrils, catB inhibition potentiates the formation of inclusions which stain positively for phosphorylated alpha-synuclein. These results indicate that the reduction of catB function negatively impacts lysosomal pathways associated with PD pathogenesis, while conversely catB activation could promote the clearance of pathogenic alpha-synuclein.
Synthetic Echocardiograms Generation Using Diffusion Models
Authors: Pellicer Alexandre Olive , Singh Yadav Amit Kumar , Bhagtani Kratika , Xiang Ziyue , Pizlo Zygmunt , Gradus-Pizlo Irmina , Delp Edward J. 
Published: November 2023

AbstractAn echocardiogram is a video sequence of a human heart captured using ultrasound imaging. It shows heart structure and motion and helps in diagnosis of cardiovascular diseases. Deep learning methods, which require large amounts of training data have shown success in using echocardiograms to detect cardiovascular disorders such as valvular heart disease. Large datasets of echocardiograms that can be used for machine learning training are scarce. One way to address this problem is to use modern machine learning generative methods to generate synthetic echocardiograms that can be used for machine learning training. In this paper, we propose a video diffusion method for the generation of echocardiograms. Our method uses a 3D selfattention mechanism and a super-resolution model. We demonstrate that our proposed method generates echocardiograms with higher resolution and with lesser artifacts, compared to existing echocardiogram generation methods.
Conversational Chemistry: A Novel Approach to Chemical Search and Property Prediction
Authors: Ben-Joseph JJ , Oates Tim 
Published: November 2023

AbstractWe have developed an approach to train a chemical property prediction model using both English and the SELFIES chemical language describing the structure of small, drug-like molecules. This model generates chemical embedding vectors, which we then use to train classification models. Our straightforward softmax classification model surpasses the commonly-used message passing neural network architecture in certain chemical property prediction tasks. Moreover, these chemical embedding vectors can be employed in other applications, such as building a chemical search engine that enables users to find new drugs with natural language queries (e.g., “low toxicity blood brain barrier permeable drug that inhibits HIV replication”).
Identification of genes with oscillatory expression in glioblastoma – The paradigm ofSOX2
Authors: Fu R.Z , Cottrell O , Cutillo L , Rowntree A , Zador Z , Wurdak H , Papalopulu N , Marinopoulou E. 
Published: November 2023

AbstractQuiescence, a reversible state of cell-cycle arrest, is an important state during both normal development and cancer progression. For example, in glioblastoma (GBM) quiescent glioblastoma stem cells (GSCs) play an important role in re-establishing the tumour, leading to relapse. While most studies have focused on identifying differentially expressed genes between proliferative and quiescent cells as potential drivers of this transition, recent studies have shown the importance of protein oscillations in controlling the exit from quiescence of neural stem cells. Here, we have undertaken a genome-wide bioinformatic inference approach to identify genes whose expression oscillates and which may be good candidates for controlling the transition to and from the quiescent cell state in GBM. Our analysis identified, among others, a list of important transcription regulators as potential oscillators, including the stemness geneSOX2, which we verified to oscillate in quiescent GSCs. These findings expand on the way we think about gene regulation and introduce new candidate genes as key regulators of quiescence.
Functional brain networks are associated with both sex and gender in children
Authors: Dhamala Elvisha , Bassett Dani S. , Yeo B.T. Thomas , Homes Avram J. 
Published: November 2023

AbstractSex and gender are associated with human behavior throughout the lifespan and across health and disease, but whether they are associated with similar or distinct neural phenotypes is unknown. Here, we demonstrate that, in children, sex and gender are uniquely reflected in the intrinsic functional connectivity of the brain. Unimodal networks are more strongly associated with sex while heteromodal networks are more strongly associated with gender. These results suggest sex and gender are irreducible to one another not only in society but also in biology.
Emergence of the Novel Infectious bursal disease viruse Variant in Vaccinated Poultry Flocks in Egypt
Authors: Shahein Momtaz A. , Sultan Hesham A. , Zanaty Ali , Adel Amany , Mosaad Zienab , Said Dalia , Erfan Ahmed , Samy Mohamed , Selim Abdullah , Selim Karim , Naguib Mahmoud M. , Hassan Heba , Shazly Osama El , El-badiea Zeinab A. , Moawad Mahmoud K. , Samir Abdelhafez , Shahaby Mohamed El , Farghaly Eman , Eid Samah , Abdelaziz Mohamed N , Hamoud Mohamed M , Mehana Osama , Hagag Naglaa M. , Samy Ahmed 
Published: November 2023

AbstractInfectious bursal disease viruses (IBDVs) have a profound impact on poultry production worldwide, directly causing mortality rates of up to 100%, and indirectly through their immunosuppressive effects. Since the emergence of the antigenically modified very virulent IBDV (vvIBDV) in Egypt in late 1999, the country has experienced recurrent outbreaks with high mortality rates and typical vvIBDV gross lesions. However, a notable shift occurred in 2023, characterized by a substantial increase in reported subclinical IBDV cases exhibiting atrophied bursa and associated immunosuppression. To assess the field situation, we examined samples from 21 farms in 2023 and 18 farms from 2021 and 2022, all of which experienced IBD outbreaks based on clinical diagnosis. These samples were submitted to our laboratory for confirmatory testing and subsequently subjected to VP2-HVR sequencing. Phylogenetic analysis revealed that all samples collected in 2021 and 2022 clustered with classical virulent strains and very virulent IBDV. In 2023, one sample clustered with the Egyptian vvIBDV, while one sample clustered with classic virulent IBDV, and the remaining 2023 samples clustered with the Chinese novel variant IBDV (nVarIBDV). The alignment of deduced amino acid sequences for VP2 revealed that all Egyptian classic virulent strains were similar to the Winterfield or Leukert strains. In contrast, vvIBDV strains exhibited two out of the three typical residues found in Egyptian antigenically atypical vvIBDV, namely Y220F and G254S, but not A321T, and one sample was identical to the European vvIBDV (emerged in 1989). Meanwhile, all variant strains recognized in the present study exhibited typical residues found in variant IBDV, in addition to the three conserved amino acid residues found only in Chinese variant IBDVs. However, all Egyptian variant strains showed a mutation at position 321 (321V), which represents the most exposed part of the capsid and is known to have a massive impact on IBDV antigenicity, with the exception of one sample that had 318G instead. This report highlights the emergence of a new variant IBDV clustered with the Chinese new variant in Egypt, causing bursa atrophy and spreading subclinically in broiler farms over a wide geographic distance, resulting in massive economic losses due to immunosuppression.
SARS-CoV-2 and its ORF3a, E and M viroporins activate inflammasome in human macrophages and induce of IL-1αin pulmonary epithelial and endothelial cells
Authors: Ambrożek-Latecka Magdalena , Kozlowski Piotr , Hoser Grażyna , Bandyszewska Magdalena , Hanusek Karolina , Nowis Dominika , Gołąb Jakub , Grzanka Małgorzata , Piekiełko-Witkowska Agnieszka , Schulz Luise , Hornung Franziska , Deinhardt-Emmer Stefanie , Kozlowska Ewa , Skirecki Tomasz 
Published: November 2023

AbstractInflammasome assembly is a potent mechanism responsible for the host protection against pathogens, including viruses. When compromised, it can allow viral replication, while when disrupted, it can perpetuate pathological responses by IL-1 signaling and pyroptotic cell death. SARS-CoV-2 infection was shown to activate inflammasome in the lungs of COVID-19 patients, however, potential mechanisms responsible for this response are not fully elucidated. In this study, we investigated the effects of ORF3a, E and M SARS-CoV-2 viroporins in the inflammasome activation in major populations of alveolar sentinel cells: macrophages, epithelial and endothelial cells. We demonstrated that each viroporin is capable of activation of the inflammasome in macrophages to trigger cell death and IL-1αrelease from epithelial and endothelial cells. Small molecule NLRP3 inflammasome inhibitors reduced IL-1 release but weakly affected the pyroptosis. Importantly, we discovered that while SARS-CoV-2 could not infect the pulmonary microvascular endothelial cells it induced IL-1αand IL-33 release. Together, these findings highlight the essential role of macrophages as the major inflammasome-activating cell population in the lungs and point to endothelial cell expressed IL-1αas a potential novel component driving the pulmonary immunothromobosis in COVID-19.