bluuebunny/crossref_metadata_2025_split huggingface dataset:
A homozygous nonsense variant in the alternatively spliced VLDLR exon 4 causes a neurodevelopmental disorder without features of VLDLR cerebellar hypoplasia
Authors: Holling Tess , Abdelrazek Ibrahim M. , Elhady Ghada M. , Abd Elmaksoud Marwa , Ryu Seung Woo , Abdalla Ebtesam , Kutsche Kerstin 
Published: July 2024

AbstractVLDLR cerebellar hypoplasia is characterized by intellectual disability, non-progressive cerebellar ataxia, and seizures. The characteristic MRI findings include hypoplasia of the inferior portion of the cerebellar vermis and hemispheres, simplified cortical gyration, and a small brain stem. Biallelic VLDLR pathogenic variants cause loss-of-function of the encoded very low-density lipoprotein receptor. VLDLR exons 4 and 16 are alternatively spliced, resulting in the expression of four transcript variants, including two exon 4-lacking mRNAs expressed in the human brain. Previously reported VLDLR pathogenic variants affect all four transcript variants. Here we report on two sisters with facial dysmorphism, microcephaly, intellectual disability, and normal brain imaging. Exome sequencing in one patient identified the homozygous VLDLR nonsense variant c.376C>T; p.(Gln126*) in exon 4; her similarly affected sister also carried the homozygous variant and parents were heterozygous carriers. VLDLR transcript analysis identified mRNAs with and without exon 4 in patient fibroblasts, while exon 4-containing VLDLR mRNAs were predominantly detected in control fibroblasts. We found significantly reduced VLDLR mRNA levels in patient compared to control cells, likely caused by nonsense-mediated mRNA decay of exon 4-containing VLDLR transcripts. Expression of neuronal VLDLR isoforms produced from exon 4-lacking transcripts may have protected both patients from developing the cerebellar hypoplasia phenotype.
BRCA1 orchestrates the response to BI-2536 and its combination with alisertib in MYC-driven small cell lung cancer
Authors: Zhang Jiahui , Liu Xiaoli , Hou Peng , Lv Yang , Li Gongfeng , Cao Guozhen , Wang Huogang , Lin Wenchu 
Published: July 2024

AbstractPLK1 is currently at the forefront of mitotic research and has emerged as a potential target for small cell lung cancer (SCLC) therapy. However, the factors influencing the efficacy of PLK1 inhibitors remain unclear. Herein, BRCA1 was identified as a key factor affecting the response of SCLC cells to BI-2536. Targeting AURKA with alisertib, at a non-toxic concentration, reduced the BI-2536-induced accumulation of BRCA1 and RAD51, leading to DNA repair defects and mitotic cell death in SCLC cells. In vivo experiments confirmed that combining BI-2536 with alisertib impaired DNA repair capacity and significantly delayed tumor growth. Additionally, GSEA analysis and loss- and gain-of-function assays demonstrated that MYC/MYCN signaling is crucial for determining the sensitivity of SCLC cells to BI-2536 and its combination with alisertib. The study further revealed a positive correlation between RAD51 expression and PLK1/AURKA expression, and a negative correlation with the IC50 values of BI-2536. Manipulating RAD51 expression significantly influenced the efficacy of BI-2536 and restored the MYC/MYCN-induced enhancement of BI-2536 sensitivity in SCLC cells. Our findings indicate that the BRCA1 and MYC/MYCN-RAD51 axes govern the response of small cell lung cancer to BI-2536 and its combination with alisertib. This study propose the combined use of BI-2536 and alisertib as a novel therapeutic strategy for the treatment of SCLC patients with MYC/MYCN activation.
The parasitic lifestyle of an archaeal symbiont
Authors: Hamm Joshua N. , Liao Yan , von Kügelgen Andriko , Dombrowski Nina , Landers Evan , Brownlee Christopher , Johansson Emma M. V. , Whan Renee M. , Baker Matthew A. B. , Baum Buzz , Bharat Tanmay A. M. , Duggin Iain G. , Spang Anja , Cavicchioli Ricardo 
Published: July 2024

AbstractDPANN archaea are a diverse group of microorganisms characterised by small cells and reduced genomes. To date, all cultivated DPANN archaea are ectosymbionts that require direct cell contact with an archaeal host species for growth and survival. However, these interactions and their impact on the host species are poorly understood. Here, we show that a DPANN archaeon (Candidatus Nanohaloarchaeum antarcticus) engages in parasitic interactions with its host (Halorubrum lacusprofundi) that result in host cell lysis. During these interactions, the nanohaloarchaeon appears to enter, or be engulfed by, the host cell. Our results provide experimental evidence for a predatory-like lifestyle of an archaeon, suggesting that at least some DPANN archaea may have roles in controlling host populations and their ecology.
Asgard archaea defense systems and their roles in the origin of eukaryotic immunity
Authors: Leão Pedro , Little Mary E. , Appler Kathryn E. , Sahaya Daphne , Aguilar-Pine Emily , Currie Kathryn , Finkelstein Ilya J. , De Anda Valerie , Baker Brett J. 
Published: July 2024

AbstractDozens of new antiviral systems have been recently characterized in bacteria. Some of these systems are present in eukaryotes and appear to have originated in prokaryotes, but little is known about these defense mechanisms in archaea. Here, we explore the diversity and distribution of defense systems in archaea and identify 2610 complete systems in Asgardarchaeota, a group of archaea related to eukaryotes. The Asgard defense systems comprise 89 unique systems, including argonaute, NLR, Mokosh, viperin, Lassamu, and CBASS. Asgard viperin and argonaute proteins have structural homology to eukaryotic proteins, and phylogenetic analyses suggest that eukaryotic viperin proteins were derived from Asgard viperins. We show that Asgard viperins display anti-phage activity when heterologously expressed in bacteria. Eukaryotic and bacterial argonaute proteins appear to have originated in Asgardarchaeota, and Asgard argonaute proteins have argonaute-PIWI domains, key components of eukaryotic RNA interference systems. Our results support that Asgardarchaeota played important roles in the origin of antiviral defense systems in eukaryotes.
A topological mechanism for robust and efficient global oscillations in biological networks
Authors: Zheng Chongbin , Tang Evelyn 
Published: July 2024

AbstractLong and stable timescales are often observed in complex biochemical networks, such as in emergent oscillations. How these robust dynamics persist remains unclear, given the many stochastic reactions and shorter time scales demonstrated by underlying components. We propose a topological model that produces long oscillations around the network boundary, reducing the system dynamics to a lower-dimensional current in a robust manner. Using this to model KaiC, which regulates the circadian rhythm in cyanobacteria, we compare the coherence of oscillations to that in other KaiC models. Our topological model localizes currents on the system edge, with an efficient regime of simultaneously increased precision and decreased cost. Further, we introduce a new predictor of coherence from the analysis of spectral gaps, and show that our model saturates a global thermodynamic bound. Our work presents a new mechanism and parsimonious description for robust emergent oscillations in complex biological networks.
The influence of HLA genetic variation on plasma protein expression
Authors: Krishna Chirag , Chiou Joshua , Sakaue Saori , Kang Joyce B. , Christensen Stephen M. , Lee Isac , Aksit Melis Atalar , Kim Hye In , von Schack David , Raychaudhuri Soumya , Ziemek Daniel , Hu Xinli 
Published: July 2024

AbstractGenetic variation in the human leukocyte antigen (HLA) loci is associated with risk of immune-mediated diseases, but the molecular effects of HLA polymorphism are unclear. Here we examined the effects of HLA genetic variation on the expression of 2940 plasma proteins across 45,330 Europeans in the UK Biobank, with replication analyses across multiple ancestry groups. We detected 504 proteins affected by HLA variants (HLA-pQTL), including widespread trans effects by autoimmune disease risk alleles. More than 80% of the HLA-pQTL fine-mapped to amino acid positions in the peptide binding groove. HLA-I and II affected proteins expressed in similar cell types but in different pathways of both adaptive and innate immunity. Finally, we investigated potential HLA-pQTL effects on disease by integrating HLA-pQTL with fine-mapped HLA-disease signals in the UK Biobank. Our data reveal the diverse effects of HLA genetic variation and aid the interpretation of associations between HLA alleles and immune-mediated diseases.
Adaptative survival of Aspergillus fumigatus to echinocandins arises from cell wall remodeling beyond β−1,3-glucan synthesis inhibition
Authors: Dickwella Widanage Malitha C. , Gautam Isha , Sarkar Daipayan , Mentink-Vigier Frederic , Vermaas Josh V. , Ding Shi-You , Lipton Andrew S. , Fontaine Thierry , Latgé Jean-Paul , Wang Ping , Wang Tuo 
Published: July 2024

AbstractAntifungal echinocandins inhibit the biosynthesis of β−1,3-glucan, a major and essential polysaccharide component of the fungal cell wall. However, the efficacy of echinocandins against the pathogen Aspergillus fumigatus is limited. Here, we use solid-state nuclear magnetic resonance (ssNMR) and other techniques to show that echinocandins induce dynamic changes in the assembly of mobile and rigid polymers within the A. fumigatus cell wall. The reduction of β−1,3-glucan induced by echinocandins is accompanied by a concurrent increase in levels of chitin, chitosan, and highly polymorphic α−1,3-glucans, whose physical association with chitin maintains cell wall integrity and modulates water permeability. The rearrangement of the macromolecular network is dynamic and controls the permeability and circulation of the drug throughout the cell wall. Thus, our results indicate that echinocandin treatment triggers compensatory rearrangements in the cell wall that may help A. fumigatus to tolerate the drugs’ antifungal effects.
The highly differentiated gut of Pachnoda marginata hosts sequential microbiomes: microbial ecology and potential applications
Authors: Vidal-Verdú Àngela , Torrent Daniel , Iglesias Alba , Latorre-Pérez Adriel , Abendroth Christian , Corbín-Agustí Paola , Peretó Juli , Porcar Manuel 
Published: July 2024

AbstractInsect gut microbiomes play a crucial role in the insect development and are shaped, among other factors, by the specialized insect diet habits as well as the morphological structure of the gut. Rose chafers (Pachnoda spp.; Coleoptera: Scarabaeidae) have a highly differentiated gut characterized by a pronounced hindgut dilation which resembles a miniaturized rumen. Specifically, the species Pachnoda marginata has not been previously studied in detail in terms of microbial ecology. Here, we show a fine scale study of the highly compartmentalized gut of P. marginata by using amplicon and metagenomic sequencing to shed light on the bacterial, archaeal and fungal communities thriving in each section of the gut. We found a microbial gradient along the gut from aerobic (foregut) to strictly anaerobic communities (hindgut). In addition, we have characterized interesting biological activities and metabolic pathways of gut microbial communities related to cellulose degradation, methane production and sulfate reduction. Taken together, our results reveal the highly diverse microbial community and the potential of P. marginata gut as a source of industrially relevant microbial diversity.
Magnetic nanocomposite for lead (II) removal from water
Authors: Shahzad Asif , Aslibeiki Bagher , Slimani Sawssen , Ghosh Sagnik , Vocciante Marco , Grotti Marco , Comite Antonio , Peddis Davide , Sarkar Tapati 
Published: July 2024

AbstractA magnetic perovskite-spinel oxide nanocomposite synthesized through a sol–gel self-combustion process is used for the first time as an adsorbent to remove toxic heavy metals (i.e., Pb2+). The synthesized LaFeO3:CoFe2O4 ((LFO)1:(CFO)x) (x = 0.11–0.87) nanocomposites possess good stability, abundant oxygenated active binding sites, and unique structural features, making them suitable for removing divalent Pb2+ ions. Scanning electron microscopy, X-ray diffraction, BET surface area, magnetization measurements, zeta-potential analyses, and X-ray photoelectron spectroscopy were used to analyze the nanocomposites, and their structural changes after Pb2+ ions adsorption. Batch tests confirmed that (LFO)1:(CFO)x efficiently removes Pb2+ from water with a maximum adsorption capacity of 105.96 mg/g. The detailed quantitative study indicates that the interaction of hydroxyl groups with Pb2+ ions occurs through electrostatic interactions and complex formation. We also demonstrate a new ring-magnetic separator system that allows magnetic separation of the toxic ions at a higher speed compared to traditional block magnets. The unique structure, high porosity, large specific surface area, and oxygenated functional groups of (LFO)1:(CFO)x nanocomposites make them promising materials for removal of heavy metal ions and possibly other environmental pollutants. This study provides a new approach to preparing nanocomposites of magnetic spinel ferrites with perovskite oxides for environmental applications.
Nonparametric inference of higher order interaction patterns in networks
Authors: Wegner Anatol E. , Olhede Sofia C. 
Published: July 2024

AbstractLocal interaction patterns play an important role in the structural and functional organization of complex networks. Here we propose a method for obtaining parsimonious decompositions of networks into higher order interactions which can take the form of arbitrary motifs. The method is based on a class of analytically solvable generative models which in combination with non-parametric priors allow us to infer higher order interactions from dyadic graph data without any prior knowledge on the types or frequencies of such interactions. We test the presented approach on simulated data for which we recover the set of underlying higher order interactions to a high degree of accuracy. For empirical networks the method identifies concise sets of atomic subgraphs from within thousands of candidates that cover a large fraction of edges and include higher order interactions of known structural and functional significance. Being based on statistical inference the method also produces a fit of the network to analytically tractable higher order models opening new avenues for the systematic study of higher order interactions.
Self-adaptive rotational electromagnetic energy generation as an alternative to triboelectric and piezoelectric transductions
Authors: Rolo Pedro , Vidal João V. , Kholkin Andrei L. , Soares dos Santos Marco P. 
Published: July 2024

AbstractTriboelectric and piezoelectric energy harvesters can hardly power most microelectronic systems. Rotational electromagnetic harvesters are very promising alternatives, but their performance is highly dependent on the varying mechanical sources. This study presents an innovative approach to significantly increase the performance of rotational harvesters, based on dynamic coil switching strategies for optimization of the coil connection architecture during energy generation. Both analytical and experimental validations of the concept of self-adaptive rotational harvester were carried out. The adaptive harvester was able to provide an average power increase of 63.3% and 79.5% when compared to a non-adaptive 16-coil harvester for harmonic translation and harmonic swaying excitations, respectively, and 83.5% and 87.2% when compared to a non-adaptive 8-coil harvester. The estimated energy conversion efficiency was also enhanced from ~80% to 90%. This study unravels an emerging technological approach to power a wide range of applications that cannot be powered by other vibrationally driven harvesters.
Language or rating scales based classifications of emotions: computational analysis of language and alexithymia
Authors: Sikström Sverker , Nicolai Miriam , Ahrendt Josephine , Nevanlinna Suvi , Stille Lotta 
Published: July 2024

AbstractRating scales are the dominating tool for the quantitative assessment of mental health. They are often believed to have a higher validity than language-based responses, which are the natural way of communicating mental states. Furthermore, it is unclear how difficulties articulating emotions—alexithymia—affect the accuracy of language-based communication of emotions. We investigated whether narratives describing emotional states are more accurately classified by questions-based computational analysis of language (QCLA) compared to commonly used rating scales. Additionally, we examined how this is affected by alexithymia. In Phase 1, participants (N = 348) generated narratives describing events related to depression, anxiety, satisfaction, and harmony. In Phase 2, another set of participants summarized the emotions described in the narratives of Phase 1 in five descriptive words and rating scales (PHQ-9, GAD-7, SWLS, and HILS). The words were quantified with a natural language processing model (i.e., LSA) and classified with machine learning (i.e., multinomial regression). The results showed that the language-based responses can be more accurate in classifying the emotional states compared to the rating scales. The degree of alexithymia did not influence the correctness of classification based on words or rating scales, suggesting that QCLA is not sensitive to alexithymia. However, narratives generated by people with high alexithymia were more difficult to classify than those generated by people with low alexithymia. These results suggest that the assessment of mental health may be improved by language-based responses analyzed by computational methods compared to currently used rating scales.
Characteristics of Speech Auditory Brainstem Response in Preschool Children With Attention-Deficit/Hyperactivity Disorder
Authors: Sun Yuying , Zhou Jia , Zhu Huiqin , Liu Panting , Lin Huanxi , Xiao Zhenglu , Yu Xinyue , Qian Jun , Tong Meiling , Chi Xia , Hong Qin 
Published: July 2024

Objective:
This study aimed to investigate the characteristics of auditory processing (AP) in preschool children with attention-deficit/hyperactivity disorder (ADHD) using the speech auditory brainstem response (speech-ABR), which provides insights into the AP of speech signals in the central auditory nervous system (CANS).

Method:
A total of 84 preschool children diagnosed with ADHD, aged 4–6 years, were matched with 84 typically developing (TD) children based on gender and age. All children underwent speech-ABR testing, cognitive assessment using the Wechsler Preschool and Primary Scale of Intelligence–Fourth Edition or the Wechsler Intelligence Scale for Children–Fourth Edition, and a continuous performance test.

Results:
Children with ADHD exhibited significantly longer latencies of speech-ABR waveforms V, A, and D compared to TD children. Multiple linear regression analysis showed that the latencies of speech-ABR waves V, A, and D were affected by the presence of ADHD, but not by the full-scale intelligence quotient.

Conclusions:
This study revealed that preschool children with ADHD exhibited abnormal AP of speech signals in their CANS. The findings suggest that speech-ABR can be utilized as a reliable measure to evaluate AP ability in this population, as it remains unaffected by cognitive or attentional factors. The transient response (V, A) of speech-ABR was found to be a significant predictor of ADHD in a clinical setting. Early assessment of AP abnormalities via speech-ABR is recommended in preschool-age children to develop targeted interventions for ADHD.

Supplemental Material:

https://doi.org/10.23641/asha.26376502
Packet reception algorithm for redundant data links in transport drones
Authors: Lim Sung‐Ho , Lee Jong‐Hun , Seong Kilyoung , Kim Jae‐Kyung 
Published: July 2024

AbstractIn a drone system with dual data links, this article presents a redundant data processing algorithm that can minimize flight control instability without increasing the weight and price of the aircraft by software processing of duplicate received messages.
Compact wide single‐/dual‐band bandpass filter with equal inductance configuration in thin film IPD technology
Authors: Liu Zhi‐Hao , Liu Bao‐Guang , Cheng Chong‐Hu , Cheng Yong 
Published: July 2024

AbstractHere, based on thin film integrated passive device (TF‐IPD) technology, compact ultra‐wideband (UWB) bandpass filter (BPF) and dual‐band bandpass filter (DBBPF) with equal inductance configuration are proposed. The configuration of equal inductance in a circuit contributes to reducing variables, simplifying the physical structure, and shortening the debugging time in the TF‐IPD design process. Despite all the inductors being equal in value, a wide passband can still be achieved. The measured results show that the centre frequency of UBW BPF is 11.43 GHz, and the 3‐dB fractional bandwidth (FBW) is 133% (3.87–18.99 GHz). And the 3‐dB FBWs of DBBPF centred at 6.5 GHz and 16.2 GHz are 92% (3.51–9.49 GHz) and 35% (13.33–18.98 GHz), respectively. The stopband of UBW BPF and DBBPF can be extended to 47.7 GHz and 44.8 GHz in sizes of 321 µm × 856 µm and 235 µm × 846 µm, respectively (excluding measuring pads).
AC ripple on DC voltage: Experimental and theoretical investigation of the impact on accelerated ageing in electrical insulation
Authors: Gardan Giovanni , Montanari Gian Carlo 
Published: July 2024

AbstractWith the increasing penetration of DC systems into the high voltage and medium voltage power industry, DC voltage is becoming common for distribution/transmission and to supply different typologies of loads. The allowable extent of AC ripple superimposed to DC, and its effect on insulation ageing, is a long‐term discussed topic. The most harmful phenomenon causing extrinsic ageing acceleration and insulation system premature failure is partial discharges (PD); thus, the risk of incepting PD due to AC ripple could become a primary issue for electrical asset equipment reliability. In this work, the impact of AC sinusoidal ripple on insulation system life and reliability is dealt with, considering both intrinsic and extrinsic ageing but focusing on the latter, that is, the PD aspect. Experiments are performed to assess how the jump voltage (due to AC ripple) and the DC component impact on PD activity in terms of amplitude and repetition rate. For the first time, the correlation between the magnitude of jump voltage associated with ripple and PD inception is established, shedding a light on the allowable ripple extent which does not impact significantly on ageing and premature insulation failure. This approach can provide straightforward tools for design specification and ageing inference of insulation systems.