bluuebunny/crossref_metadata_2025_split huggingface dataset:
Common neural correlates of disgust processing in childhood maltreatment and peer victimisation
Authors: Lim Lena , Rubia Katya , Lukito Steve 
Published: October 2024

Background
Childhood maltreatment and peer victimisation are common sources of early-life interpersonal stress. Childhood maltreatment is associated with atypical frontolimbic emotion processing and regulation, and increased vulnerability for self-harm/suicide. However, few studies have compared the neurofunctional correlates between caregiver- versus peer-inflicted mistreatment.

Aims
We compared the alterations of neurofunctional correlates of facial emotion processing in youths exposed to childhood maltreatment or peer victimisation, and explored their associations with self-harm.

Method
Functional magnetic resonance imaging data were collected from 114 age- and gender-matched youths (39 childhood maltreatment, 37 peer victimisation and 38 controls) during an emotion discrimination task. Region-of-interest (amygdala, insula) and whole-brain analyses were conducted.

Results
Groups differed significantly during disgust processing only. Both groups had lower activation in the right amygdala and bilateral posterior insula than controls; left insular underactivation was furthermore related to increased self-harm in maltreated youths. Compared with controls, at the whole-brain level, both groups also had underactivation in a cluster of bilateral limbic-thalamic-striatal, precuneus/posterior cingulate, temporal, fusiform/lingual and cerebellar regions, which was negatively associated with emotional problems in controls, as well as a cluster of somatosensory regions associated with increased self-harm in maltreated youths.

Conclusions
Early-life interpersonal stress from caregivers or peers is associated with common underactivation of limbic-thalamic-striatal, precuneus/posterior cingulate and somatosensory regions during disgust processing. The hypoactivation of key emotion and sensory processing and self-referential brain regions could be a potential suppressive mechanism to cope with the aversive emotion; however, it may also entail increased risk of affective psychopathology in seemingly healthy youths.
Decomposition of nonlinear collision operator in quantum Lattice Boltzmann algorithm
Authors: Kumar E. Dinesh , Frankel Steven H. 
Published: October 2024

Abstract
We propose a quantum algorithm to tackle the quadratic nonlinearity in the Lattice Boltzmann (LB) collision operator. The key idea is to build the quantum gates based on the particle distribution functions (PDF) within the coherence time for qubits. Thus, both the operator and a state vector are linear functions of PDFs, and upon quantum state evolution, the resulting PDFs will have quadraticity. To this end, we decompose the collision operator for a DmQn lattice model into a product of

operators, where n is the number of lattice velocity directions. After decomposition, the

operators with constant entries remain unchanged throughout the simulation, whereas the remaining

will be built based on the statevector of the previous time step. Also, we show that such a decomposition is not unique. Compared to the second-order Carleman-linearized LB, the present approach reduces the circuit width by half and circuit depth by exponential order. The proposed algorithm has been verified through the one-dimensional flow discontinuity and two-dimensional Kolmogrov-like flow test cases.
LCoRL Regulates Growth and Metabolism
Authors: Wyler Steven C , Gahlot Surbhi , Bideyan Lara , Yip Cecilia , Dushime Jasmine , Chen Bandy , Lee Jenny J , Tinajero Arely , Limboy Chelsea , Bordash Staci , Heaselgrave Samuel R , Nguyen Tammy-Nhu , Lee Syann , Bookout Angie , Lantier Loise , Fowlkes John L , You Young-Jai , Fujikawa Teppei , Elmquist Joel K 
Published: October 2024

Abstract
Genome-wide association studies (GWAS) in humans and livestock have identified genes associated with metabolic traits. However, the causality of many of these genes on metabolic homeostasis is largely unclear due to a lack of detailed functional analyses. Here we report ligand-dependent corepressor-like (LCoRL) as a metabolic regulator for body weight and glucose homeostasis. Although GWAS data show that LCoRL is strongly associated with body size, glucose homeostasis, and other metabolic traits in humans and livestock, functional investigations had not been performed. We generated Lcorl knockout mice (Lcorl−/−) and characterized the metabolic traits. We found that Lcorl−/− pups are born smaller than the wild-type (WT) littermates before reaching normal weight by 7 to 9 weeks of age. While aging, Lcorl−/− mice remain lean compared to WT mice, which is associated with a decrease in daily food intake. Glucose tolerance and insulin sensitivity are improved in Lcorl−/− mice. Mechanistically, this stunted growth is linked to a reduction of circulating levels of IGF-1. The expression of the genes downstream of GH signaling and the genes involved in glucose and lipid metabolism are altered in the liver of Lcorl−/− mice. Furthermore, Lcorl−/− mice are protected against a high-fat diet challenge and show reduced exercise capacity in an exercise stress test. Collectively, our results are congruent with many of the metabolic parameters linked to the Lcorl locus as reported in GWAS in humans and livestock.
Common modes of ERK induction resolve into context-specific signalling via emergent networks and cell-type-specific transcriptional repression
Authors: Perera Marta , Brickman Joshua M. 
Published: October 2024

ABSTRACT
Fibroblast Growth Factor signalling via ERK exerts diverse roles in development and disease. In mammalian preimplantation embryos and naïve pluripotent stem cells ERK promotes differentiation, whereas in primed pluripotent states closer to somatic differentiation ERK sustains self-renewal. How can the same pathway produce different outcomes in two related cell types? To explore context-dependent ERK signalling we generated cell and mouse lines that allow for tissue- and time-specific ERK activation. Using these tools, we find that specificity in ERK response is mostly mediated by repression of transcriptional targets that occur in tandem with reductions in chromatin accessibility at regulatory regions. Furthermore, immediate early ERK responses are largely shared by different cell types but produce cell-specific programmes as these responses interface with emergent networks in the responding cells. Induction in naïve pluripotency is accompanied by chromatin changes, whereas in later stages it is not, suggesting that chromatin context does not shape signalling response. Altogether, our data suggest that cell-type-specific responses to ERK signalling exploit the same immediate early response, but then sculpt it to specific lineages via repression of distinct cellular programmes.
The protamines of the spider Steatoda sp. provide an example of liquid–liquid phase separation chromatin transitions during spermiogenesis
Authors: Leyden Melissa R. , Michalik Peter , Baruffaldi Luciana , Mahmood Susheen , Kalani Ladan , Hunt Donald F. , Eirin-Lopez Jose Maria , Andrade Maydianne C. B. , Shabanowitz Jeffrey , Ausió Juan 
Published: October 2024

ABSTRACT
Although there is extensive information about sperm nuclear basic proteins (SNBP) in vertebrates, there is, by comparison, very little information in Arthropoda. This study aims to contribute to filling this gap by analyzing these proteins in the sperm of the noble false widow spider Steatoda nobilis (order Araneae, family Theridiidae). To this end, we have developed a protein extraction method that allows the extraction of both cysteine-containing and non-cysteine-containing protamines that is suitable for the preparation and analysis of SNBPs from samples in which the amount of starting tissue material is limited. We carried out top-down mass spectrometry sequencing and molecular phylogenetic analyses to characterize the protamines of S. nobilis and other spiders. We also used electron microscopy to analyze the chromatin organization of the Steatoda sperm and we found it to exhibit liquid–liquid phase spinodal decomposition during the late stages of spermiogenesis. These experiments further our knowledge on the distribution of SNBPs within the animal kingdom and provide additional support for a proposed evolutionary origin of many protamines from a histone H1 (H5) replication-independent precursor.
Emerin preserves stem cell survival through maintenance of centrosome and nuclear lamina structure
Authors: Jones Samuel D. , Miller Jack E. B. , Amos Madilynn M. , Hernández Julianna M. , Piaszynski Katherine M. , Geyer Pamela K. 
Published: October 2024

ABSTRACT
Drosophila female germline stem cells (GSCs) complete asymmetric mitosis in the presence of an intact, but permeable, nuclear envelope and nuclear lamina (NL). This asymmetric division requires a modified centrosome cycle, wherein mitotic centrosomes with mature pericentriolar material (PCM) embed in the NL and interphase centrosomes with reduced PCM leave the NL. This centrosome cycle requires Emerin, an NL protein required for GSC survival and germ cell differentiation. In emerin mutants, interphase GSC centrosomes retain excess PCM, remain embedded in the NL and nucleate microtubule asters at positions of NL distortion. Here, we investigate the contributions of abnormal interphase centrosomes to GSC loss. Remarkably, reducing interphase PCM in emerin mutants rescues GSC survival and partially restores germ cell differentiation. Direct tests of the effects of abnormal centrosomes were achieved by expression of constitutively active Polo kinase to drive enlargement of interphase centrosomes in wild-type GSCs. Notably, these conditions failed to alter NL structure or decrease GSC survival. However, coupling enlarged interphase centrosomes with nuclear distortion promoted GSC loss. These studies establish that Emerin maintains centrosome structure to preserve stem cell survival.
Machine learning in microscopy – insights, opportunities and challenges
Authors: Cunha Inês , Latron Emma , Bauer Sebastian , Sage Daniel , Griffié Juliette 
Published: October 2024

ABSTRACT
Machine learning (ML) is transforming the field of image processing and analysis, from automation of laborious tasks to open-ended exploration of visual patterns. This has striking implications for image-driven life science research, particularly microscopy. In this Review, we focus on the opportunities and challenges associated with applying ML-based pipelines for microscopy datasets from a user point of view. We investigate the significance of different data characteristics – quantity, transferability and content – and how this determines which ML model(s) to use, as well as their output(s). Within the context of cell biological questions and applications, we further discuss ML utility range, namely data curation, exploration, prediction and explanation, and what they entail and translate to in the context of microscopy. Finally, we explore the challenges, common artefacts and risks associated with ML in microscopy. Building on insights from other fields, we propose how these pitfalls might be mitigated for in microscopy.
Valacyclovir induced neurotoxicity, with therapeutic drug monitoring, in a hospital-based setting in the Netherlands
Authors: Eijsink Job F.H. , Udo Joost N. , Touw Daan J. , Dekkers Bart J. 
Published: October 2024

Background: Valacyclovir-induced neurotoxicity is a rare side effect. The aim of this study was to perform a retrospective analysis of patients with valacyclovir-induced neurotoxicity and establish valacyclovir plasma concentrations in a tertiary hospital between January 2018 and November 2022. Case descriptions: In total 208 patients were identified with measured acyclovir concentrations, and the electronic health records of these patients were analysed. Based on the in- and exclusion criteria, 4 patents were identified in whom high plasma concentrations were linked to neurotoxicity. The first patient experienced balance and coordination problems, visual hallucinations, speaking difficulties and headaches. The second patient experienced a progressive decline of consciousness, resulting in coma. The third patient also experienced reduced consciousness and was found unconscious on the floor during the night. The fourth patient experienced vertigo after administration of acyclovir. Conclusion: Based on this study, neurotoxicity appears to be an underreported adverse effect of valacyclovir therapy in a hospital setting. This side effect may have a high impact on individuals as well as on the duration of hospitalization. In order to exclude valacyclovir as the cause, clinicians should consider requesting an acyclovir plasma concentration as standard hospital-based intervention whenever a patient experiences neurotoxic symptoms. Moreover, pharmacists and clinicians should be made better aware of the interaction between valacyclovir and cyclosporine and/or mycophenolic acid, in particular in elderly patients with impaired kidney function.
Topology-optimized terahertz real-time reconfigurable multifunctional liquid-crystal-coding metasurface
Authors: Chen Yu , Li Jiaqi , Zhang Yajie , Luan Jiaqi , Cao Yang , Gao Dingshan , Li Peili 
Published: October 2024

In this paper, a reflective terahertz reconfigurable multifunctional coding metasurface based on topology optimization using liquid crystal (LC) is presented. First, the LC metasurface unit is topologically optimized using the NSGA-II multi-objective optimization algorithm. By applying the bias voltage to dynamically adjust the dielectric constant of the LC, the metasurface unit is capable of 2-bit coding at the frequency of 0.67 THz. Then, based on the designed metasurface unit, the array arrangements of the coding metasurface are reversely designed, which makes the metasurface realize flexible control and dynamic switching between beam assignment and vortex beam generation. The results show that for the beam assignment, the single-beam and multi-beam control can be realized with the reflected electromagnetic waves at continuous arbitrary angles in the range of elevation angle of 40° and azimuth angle of 360°. Moreover, the elevation angle and azimuth angle of each beam in the multi-beam can be controlled independently. Using the Fourier convolution addition operation, the control range of the single-beam elevation angle can be expanded. For the vortex beam, the single vortex beam and the multi-vortex beam can be generated in the range of elevation angle of 40° and azimuth angle of 360° with topological charges l=±1, ±2, ±3 at arbitrary angles. This provides flexibility and diversity in the generation of vortex beams. Therefore, the proposed terahertz LC metasurface can realize flexible control of reconfigurable functions and has certain application prospects in terahertz communication, phased array radar, and vortex radar.
Influence of normalization in characterization of pulses with different peak powers in a fiber laser by using soliton distillation
Authors: Tong Yiming , Lan Hengwen , Buczynski Ryszard , Tang Xiahui , Tang Ming , Deng Lei , Zhao Luming 
Published: October 2024

Soliton distillation is applied to pulses with different peak powers from a fiber laser. A specific normalization strategy is adopted to check the influence on soliton purification. During soliton distillation, we used the same normalization parameter, instead of individual optimized normalization parameters, for pulses with different peak powers, even for pulses with peak power differences larger than 3 dB. Simulation results suggest that the nonlinear Fourier transform can be performed by using the same normalization parameter for pulses of different intensities. The discrete spectrum energy of the purified soliton can be used to quantify the degree of deviation from the original pulse.
Observation of the Goos-Hänchen shift in monolayer WSe2 for an arbitrary linearly polarized incident light beam using weak measurement
Authors: Mandal Soumen , Sett Anuradha , Dey Dinesh Chandra , Das Akash , Pradhan Manik 
Published: October 2024

We report, to our knowledge, the first experimental investigation of the spatial
Goos-Hänchen (GH) shift at an absorbing material interface comprised
of monolayer (ML) tungsten di-selenide (WSe2) on a SiO2/Si substrate under a total internal
reflection (TIR) condition. The critical angle for this design is
drastically shifted to 23.31°, compared to the glass-air interface,
which was at 41.3°. Utilizing the weak value amplification (WVA)
approach, the behavior of spatial GH shifts at this interface with
various regulating parameters such as angle of incidence, polarization
angle, and post-selection angle has systematically been studied. At
critical incidence, the greatest shift of approximately 116 µm
exceeds the maximum limit of beam shift w0/2, where w0 is the beam waist (180 µm). A
generic theoretical model compatible with polarization-dependent
studies is also established that has demonstrated excellent agreement
with experimental results. Moreover, this work established three
distinct features that allow us to readily tweak the value of spatial
GH shifts. The observation of a controllable spatial GH shift at the
ML WSe2-SiO2/Si configuration has potential
implications for optical sensors, optical differential operation, and
other photonic manipulations.
Systematic review of thyroid function in NKX2-1-related disorders: Treatment and follow-up
Authors: Carmona-Hidalgo Beatriz , Herrera-Ramos Estefanía , Rodríguez-López Rocío , Nou-Fontanet Laia , C. Moreno José , Blasco-Amaro Juan Antonio , Léger Juliane , Ortigoza-Escobar Juan Darío ,   NKX2-1-Related Disorders Guideline Working Group
Published: October 2024

BackgroundNKX2-1, a crucial transcription factor in thyroid, lung, and brain development, is associated with rare disorders featuring thyroid dysfunction, neurological abnormalities, and respiratory symptoms. The primary challenge in managingNKX2-1-related disorders (NKX2-1-RD) is early diagnosis of the genetic defect and treating specific endocrine disorders. Levothyroxine (LT4) serves as the standard hypothyroidism treatment, with required dosages influenced by the severity of the individual’s disorder, which varies widely among affected individuals.ObjectivesThis systematic review aims to assess the effectiveness of LT4 treatment inNKX2-1-RD and explore optimal dosing strategies. The primary focus is on the challenges associated with the prompt diagnosis of genetic defects, rather than the established treatment protocols for individual endocrine failures.MethodsAdhering to PRISMA guidelines, the review includes 42 studies involving 110 genetically confirmedNKX2-1-RD patients with hypothyroidism. The study investigates congenital hypothyroidism as the most prevalent endocrine alteration, along with gestational and overt hypothyroidism. The administration of LT4 treatment, dosages, and patient responses are analyzed.ResultsAmong the findings, congenital hypothyroidism emerges as the predominant endocrine alteration in 41% of patients. Notably, LT4 treatment is administered in only 10% of cases, with a mean dose of 52 μg/day. The variability in initiation and dosage is likely influenced by the age at diagnosis. Positive responses, characterized by TSH adjustments within normal ranges, are observed in 11 monitored patients.ConclusionsEarly detection of congenital hypothyroidism is emphasized for timely LT4 initiation. Challenges in standardization are highlighted due to the variability in clinical manifestations and diagnostic procedures acrossNKX2-1-RD cases. While this review provides valuable insights into thyroid and pituitary disease treatment, limited details on LT4 treatment represent a significant study limitation. Key reporting points for future case studies are proposed to enhance the understanding and management ofNKX2-1-RD hypothyroidism.
Transcriptomic analysis of cellular senescence induced by ectopic expression of ATF6α in human breast cancer cells
Authors: Kim Ju Won , Bae So-Hyun , Moon Yesol , Kim Eun Kyung , Kim Yongjin , Park Yun Gyu , Han Mi-Ryung , Sohn Jeongwon 
Published: October 2024

Background
The transcriptomic profile of cellular senescence is strongly associated with distinct cell types, the specific stressors triggering senescence, and temporal progression through senescence stages. This implies the potential necessity of conducting separate investigations for each cell type and a stressor inducing senescence. To elucidate the molecular mechanism that drives endoplasmic reticulum (ER) stress-induced cellular senescence in MCF-7 breast cancer cells, with a particular emphasis on the ATF6α branch of the unfolded protein response. We conducted transcriptomic analysis on MCF-7 cells by ectopic expression of ATF6α.

Methods
Transcriptomic sequencing was conducted on MCF-7 cells at 6 and 9 hours post senescence induction through ATF6α ectopic expression. Comprehensive analyses encompassing enriched functional annotation, canonical pathway analysis, gene network analysis, upstream regulator analysis and gene set enrichment analysis were performed on Differentially Expressed Genes (DEGs) at 6 and 9 hours as well as time-related DEGs. Regulators and their targets identified from the upstream regulator analysis were validated through RNA interference, and their impact on cellular senescence was assessed by senescence-associated β-galactosidase staining.

Results
ATF6α ectopic expression resulted in the identification of 12 and 79 DEGs at 6 and 9 hours, respectively, employing criteria of a false discovery rate < 0.05 and a lower fold change (FC) cutoff |log2FC| > 1. Various analyses highlighted the involvement of the UPR and/or ER Stress Pathway. Upstream regulator analysis of 9 hour-DEGs identified six regulators and eleven target genes associated with processes related to cytostasis and ‘cell viability and cell death of connective tissue cells.’ Validation confirmed the significance of MAP2K1/2, GPAT4, and PDGF-BB among the regulators and DDIT3, PPP1R15A, and IL6 among the targets.

Conclusion
Transcriptomic analyses and validation reveal the importance of the MAP2K1/2/GPAT4-DDIT3 pathway in driving cellular senescence following ATF6α ectopic expression in MCF-7 cells. This study contributes to our understanding of the initial molecular events underlying ER stress-induced cellular senescence in breast cancer cells, providing a foundation for exploring cell type- and stressor-specific responses in cellular senescence induction.