bluuebunny/crossref_metadata_2025 huggingface dataset:
Genes responsible for the formation of asymmetrical mandibular teeth in the giant mealworm beetle,Zophobas atratus
Authors: Toga Kouhei , Yokoi Kakeru , Togawa Toru
Published: January 2025

ABSTRUCT

The mandibles of coleopteran insects are typical examples of external morphological asymmetry in animals. The developmental molecular mechanisms underlying the external morphological asymmetry remain to be elucidated compared to those of the internal asymmetric organ. In the tenebrionid beetle,Zophobas atratus, the inner teeth of adult mandibles are asymmetric, while the pupal mandibles are nearly symmetric. The asymmetric morphogenesis is assumed to be caused by the left-right regulatory differences of inner teeth formation, but even the developmental mechanisms involved in the inner teethper seremains unknown. In this study, we investigated the morphogenetic process involved in the formation of inner teeth and searched for genes responsible for this process. Morphological observation showed that the inner teeth of adults formed during 0-5 days after pupal molting. Left mandibles possessed the characteristic second inner teeth, whereas the right mandibles exhibited invaginations between apical and second inner teeth. We performed RNAi for candidate genes and successfully identified four genes (paired, alistaless, Lim1, andmlpt) involved in the formation of inner teeth. Among them,mlptRNAi had a strong effect on the morphology of the right mandibles, suggesting its involvement in the asymmetrical formation of mandibles.
Association between theta-band resting-state functional connectivity and declarative memory abilities in children
Authors: Gander Soléane , Rouge Coralie , Peiffer Anna , Wens Vincent , Tiège Xavier De , Urbain Charline
Published: January 2025

Declarative memory formation critically relies on the synchronization of brain oscillations in the theta (4–8 Hz) frequency band within specific brain networks. The development of this capacity is closely linked to the functional organization of these networks already at rest. However, the relationship between theta-band resting-state functional connectivity and declarative memory abilities remains unexplored in children. Here, using magnetoencephalography, we examined the association between declarative memory performance and pre-learning resting-state functional connectivity across frequency bands in 32 school-aged children. Declarative memory was assessed as the percentage of correct retrieval of 50 new associations between non-objects and magical functions, while resting-state functional connectivity was measured through power envelope correlation of the theta, alpha, low and high beta frequency bands. We found that stronger theta-band resting-state functional connectivity within occipito-temporo-frontal networks correlated with better declarative memory retrieval, while no correlation was observed in the alpha and beta frequency bands. These findings suggest that the functional brain architecture at rest, specifically involving theta-band oscillations, supports declarative memory in children. This mechanism may facilitate the subsequent rapid transformation of sensory input into visuo-semantic representations, highlighting the critical role of theta-band connectivity in early cognitive development.
Secreted Frizzled-Related Protein 1a regulates hematopoietic development in a dose-dependent manner
Authors: Ide Amber D. , Carpenter Kelsey A. , Elaswad Mohamed , Opria Katherine , Marcellin Kendersley , Gilliland Carla , Grainger Stephanie
Published: January 2025

Hematopoietic stem and progenitor cells (HSPCs) arise only during embryonic development, and their identity specification, emergence from the floor of the dorsal aorta, and proliferation are all tightly regulated by molecular mechanisms such as signaling cues. Among these, Wnt signaling plays an important role in HSPC specification, differentiation, and self-renewal, requiring precise modulation for proper development and homeostasis. Wnt signaling is initiated when a Wnt ligand binds to cell surface receptors such as those encoded by thefrizzledgene family, activating intracellular signaling pathways that regulate gene expression. Secreted frizzled-related proteins (Sfrps) are known modulators of Wnt signaling, acting as both agonists and antagonists of this pathway. Yet,in vivofunctions of Sfrps in HSPC development remain incompletely understood. Here, we demonstrate that Sfrp1a regulates zebrafish HSPC development and differentiation in a dose-dependent manner. In Sfrp1a loss of function animals, we observe an increase in HSPCs, an upregulation of canonical Wnt signaling, and a decrease in differentiation into both lymphoid and myeloid lineages. Conversely, at low-dosesfrp1aoverexpression, there is a decrease in HSPCs and an increase in lymphoid differentiation. High-dosesfrp1aoverexpression phenocopies the loss of function animals, with an increase in HSPCs, increased canonical Wnt signaling, and decreased lymphoid and myeloid differentiation. These findings highlight the importance of dose-dependent modulation of Sfrps, paralleling what is observed in hematopoietic cancers where SFRP1 loss-of-function and gain-of-function variants can drive tumorigenesis.

One sentence summary

Sfrp1a is required for hematopoietic stem cell development.
Seeking rhythmic patterns in microglial cells within the circadian pineal gland from male rats
Authors: Freites Carlos L. , Avila Martin , Amiotti Juan B. , Muñoz Estela M.
Published: January 2025

Microglia, the innate immune cells of the brain, constitute a highly dynamic cell population that displays several functions influenced by the light:dark (L:D) cycle. Within the pineal gland (PG), a key organ of the circadian timing system, microglia actively participate in its development and homeostasis. However, little is known about their rhythmic features in this circadian organ. This study aimed to elucidate morphological and functional phenotypes of pineal microglial cells at two time points of the L:D cycle. We performed immunofluorescence staining and confocal microscopy on paraffin-embedded pineal sections from 3– and 18-month-old Wistar rats, analyzing samples collected at midday (ZT6) and midnight (ZT18). Our results showed that the density and spatial distribution of IBA1+microglial cells did not vary between ZT6 and ZT18 in the 3-month-old PG. However, these cells exhibited reduced size and amoeboid-like shapes, along with a reduction in the expression of the phagocytosis inhibitor SIRP alpha, at ZT18 compared to ZT6. Moreover, IBA1+cells were immunoreactive for the lysosomal marker CD68 and the autophagic marker LC3B at both ZTs. Additionally, contacts with PAX6+cells were detected in the two ZTs analyzed. Interestingly, IBA1+cells showed attenuated or abolished rhythmicity in morphological parameters and SIRP alpha expression levels in the 18-month-old PG. Our findings suggest that microglia undergo transitions into alerted states at night, characterized by small, rounded shapes and enhanced phagocytic capacity. This adaptation likely prepares them to respond to potential invading agents and other insults in the PG, which could impact the nocturnal melatonin production.

Key points

Microglia within the rat pineal gland exhibit daily morphological and functional adaptations, enhancing their effectivity to respond against potential challenges in a time-dependent manner.

Oscillatory features of pineal microglia diminish with aging, suggesting an attenuation of their functions.

Nocturnal reactivity of microglia within the pineal organ may influence its physiology, potentially affecting melatonin synthesis.
iAPEX: Improved APEX-based proximity labeling for subcellular proteomics using an enzymatic reaction cascade
Authors: Sroka Tommy J. , Sanwald Lea K. , Prasai Avishek , Hoeren Josefine , von der Malsburg Karina , Chaumet Valerie , Haberkant Per , Feistel Kerstin , Mick David U.
Published: January 2025

Ascorbate peroxidase (APEX) is a versatile labeling enzyme used for live-cell proteomics at high spatial and temporal resolution. However, toxicity of its substrate hydrogen peroxide and background labeling by endogenous peroxidases limit its use toin vitrostudies of specific cell types. By combining APEX2 with a D-amino acid oxidase to locally produce hydrogen peroxide, we establish a more versatile, improved APEX (iAPEX) workflow that minimizes hydrogen peroxide toxicity and reduces non-specific background labeling. We employ iAPEX to perform live-cell proteomics of a cellular microdomain, the primary cilium, in previously inaccessible cell lines, leading to the identification of new ciliary proteins. Our study robustly validates common ciliary proteins across two distinct cell lines, while observed differences may reflect heterogeneity in primary cilia proteomes. iAPEX proximity labeling inXenopus laevisprovides a proof-of-concept for futurein vivoapplications.
Epigenome-wide analysis reveals novel DNA methylation signatures significantly associated with the infant pupillary light reflex, a candidate intermediate phenotype for autism
Authors: Fish Laurel A. , Gliga Teodora , Gui Anna , Ali Jannath Begum , Mason Luke , Johnson Mark H. , Charman Tony , Falck-Ytter Terje , Jones Emily J. H. , Kandaswamy Radhika , Happé Francesca , Wong Chloe C. Y.
Published: January 2025

Autism is a highly heterogeneous neurodevelopmental condition, currently diagnosed based on behavioural characteristics. Candidate early intermediate phenotypes, such as the Pupillary Light Reflex (PLR), a reflexive constriction of the pupil in response to increased optical luminance, may provide insights into etiological factors and potential biomarkers, such as DNA methylation (DNAm), involved in the emergence of autism. We conducted epigenome-wide DNAm association analyses of 9-, 14-, 24-month PLR onset latency and constriction amplitude in a sample of 51 infants enriched for autism family history, using buccal DNA collected at 9-months.

Our epigenome-wide analysis (EWAS) identified four stringently significant differentially methylated probes (p< 2.4 × 10−7) associated with cross-section PLR latency measurements at 14– and 24-months, and with 14-to 24-month PLR latency developmental change. Differentially methylated probes associated with PLR amplitude were identified, but at a less stringent discovery threshold (p< 5 × 10−5). Our region analyses identified several significant differentially methylated regions associated with both PLR latency and amplitude Downstream exploratory pathway analysis identified enrichment for multiple developmental biological processes, as well as several susceptibility genes to autism and related neurodevelopmental conditions includingNR4A2, HNRNPU and NAV2. Our findings provide novel insight into the role of DNAm in PLR development and illuminate biological mechanisms underpinning altered PLR in infancy in emerging autism.
Non-mutated human tau stimulates Alzheimer’s disease-relevant neurodegeneration in a microglia-dependent manner
Authors: Roy Ethan R. , Wang Qiang , Huang Kexin , Li Sanming , Fan Yuanyuan , Escobar Estrella , Huang Shuning , Herrera Juan J. , Li Wenbo , Pridans Clare , Zhou Xiaobo , Ju Cynthia , Cao Wei
Published: January 2025

The accumulation of abnormal, non-mutated tau protein is a key pathological hallmark of Alzheimer’s disease (AD). Despite its strong association with disease progression, the mechanisms by which tau drives neurodegeneration in the brain remain poorly understood. Here, we selectively expressed non-mutated or mutated human microtubule-associated protein tau (hMAPT) in neurons across the brain and observed neurodegeneration in the hippocampus, especially associated with non-mutated human tau. Single-nuclei RNA sequencing confirmed a selective loss of hippocampal excitatory neurons by the wild-type tau and revealed the upregulation of neurodegeneration-related pathways in the affected populations. The accumulation of phosphorylated tau was accompanied by cellular stress in neurons and reactive gliosis in multiple brain regions. Notably, the lifelong absence of microglia significantly and differentially influenced the extent of neurodegeneration in the hippocampus and thalamus. Therefore, our study established an AD-relevant tauopathy mouse model, elucidated both neuron-intrinsic and neuron-extrinsic responses, and highlighted critical and complex roles of microglia in modulating tau-driven neurodegeneration.
High Performance protocol for ultra-short DNA sequencing using Oxford Nanopore Technology (ONT)
Authors: Žemaitis Lukas , Palepšienė Rūta , Juzėnas Simonas , Alzbutas Gediminas , Burgi Pierre-Yves , Heinis Thomas , Charmet Jérôme , Angeloni Suter Silvia , Jost Martin , Raišutis Renaldas , Simmel Friedrich , Galminas Ignas
Published: January 2025

In recent years, Oxford Nanopore Technologies (ONT) has gained substantial attention across various domains of nucleic acids’ research, owing to its unique advantages over other sequencing platforms. Originally developed for long-read sequencing, ONT technology has evolved, with recent advancements enhancing its applicability beyond long reads to include short, synthetic DNA-based applications. However, sequencing short DNA fragments with nanopore technology often results in lower data quality, likely due to a lack of protocols optimised for these fragment sizes. To address this challenge, we refined the standard ONT library preparation protocol to improve its performance for ultra-short DNA targets. Utilising the same core reagents required for conventional ONT workflows, we introduced targeted alterations to enhance compatibility with shorter fragment lengths. We then benchmarked these adjustments against libraries prepared using the standard ONT protocol. Here, we present a comprehensive, step-by-step protocol that is accessible to researchers of varied technical expertise, facilitating high-quality sequencing of ultra-short DNA fragments. This protocol represents a significant improvement in sequencing quality for short DNA fragments using ONT technology, broadening the range of possible applications.

Graphical abstract
Characterization of the Gastrointestinal Tract Holstein x Angus Cross Cattle Microbiome During Harvest after Feed Withdrawal
Authors: Costello M.K. , McClure J.C. , Brown J.A. , Mantovani H.C. , Ricke S.C.
Published: January 2025

Stress during the beef pre-harvest period can induce an inflammatory response and acidotic conditions in the gastrointestinal tract (GIT), which affects the gastrointestinal tract microbiome. The objective of this study was to characterize the status of the GIT microbiome at harvest in beef cattle entering a small USDA processing facility. Nine beef cattle were shipped from a producer in Columbia County, WI to the USDA processing facility at University of Wisconsin-Madison and were harvested across four dates. Digesta samples were collected from eight GIT locations: rumen solids, rumen liquids, abomasum, duodenum, jejunum, ileum, cecum, and large intestines. After DNA extraction with the DNeasy Blood & Tissue Kit, the V4 region of the 16S rRNA gene was amplified and sequenced on the Illumina MiSeq platform. Sequences were analyzed for alpha and beta diversity metrics (ANOVA and ADONOS), core microbiome, ANCOM, and co-occurrence network analyses. Harvest date and GIT location had a significant impact on microbial diversity and community composition (P<0.05), and there was an interaction between GIT location and harvest date (P<0.05). Taxonomic composition shifted throughout the GIT, thoughPrevotellaandTreponemawere core members in several different GIT locations. The co-occurrence analysis revealed microorganisms potentially associated with clinical infections, such asMoryellain the rumen andAcinetobacterin the hindgut, were considered keystone species. These results suggest that the pre-harvest period may negatively impact the beef cattle GIT microbiome. Modulating the GIT microbiome during the pre-harvest period may offer an opportunity to improve food safety.
Attentional enhancement and suppression of stimulus-synchronized BOLD oscillations
Authors: Rafeh Reebal W. , Ngo Geoffrey N. , Muller Lyle E. , Khan Ali R. , Menon Ravi S. , Mur Marieke , Schmitz Taylor W.
Published: January 2025

Visual cortical neurons synchronize their firing rates to periodic visual stimuli. EEG is commonly used to study directed attention by frequency-tagging brain responses to multiple stimuli oscillating at different frequencies, but is limited by its coarse spatial resolution. Here we leverage frequency-tagging fMRI (ft-fMRI) to study the influence of directed attention on the fine-grained spatiotemporal dynamics of competing stimulus-driven visual cortical oscillations. Our analysis reveals that distinct populations of visual cortical neurons exhibit in-phase (enhancing) or anti-phase (suppressive) synchronization with the oscillating stimuli. Directed attention homogeneously increases the amplitude of anti-phase BOLD oscillations across the visual hierarchy, consistent with a distributed suppressive field. In contrast, attentional modulation of in-phase BOLD oscillations increases hierarchically from V1 to hV4. The strength of anti-phase, but not in-phase, modulation predicted psychophysical correlates of attentional performance. Our results strongly corroborate the biased competition model of attention and unveil a novel BOLD correlate of attentional suppression.
DNA repair is essential forVibrio choleraegrowth on Thiosulfate-Citrate-Bile Salts-Sucrose (TCBS) Medium
Authors: Wessel Alex J. , Johnson Drew T.T. , Waters Christopher M.
Published: January 2025

Thiosulfate-citrate-bile salts-sucrose (TCBS) agar is a selective and differential media for the enrichment of pathogenicVibrios. We observed that an exonuclease VII (exoVII) mutant ofVibrio choleraefailed to grow on TCBS agar, suggesting that DNA repair mutant strains may be hampered for growth in this selective media. Examination of the selective components of TCBS revealed that bile acids were primarily responsible for toxicity of theexoVIImutant. Suppressor mutations in DNA gyrase restored growth of theexoVIImutants on TCBS, suggesting that TCBS inhibits DNA gyrase similar to the antibiotic ciprofloxacin. To better understand what factors are important forV. choleraeto grow on TCBS, we generated a randomly-barcoded TnSeq (RB-TnSeq) library inV. choleraeand have used it to uncover a range of DNA repair mutants that also fail to grow on TCBS agar. The results of this study suggest that TCBS agar causes DNA damage toV. choleraesimilarly to the mechanism of action of fluoroquinolones, and overcoming this DNA damage is critical forVibriogrowth on this selective medium.

Abstract Importance

TCBS is often used to diagnose cholera infection. We found that many mutantV. choleraestrains are attenuated for growth on TCBS agar, meaning they could remain undetected using this culture-dependent method. Hypermutator strains with defects in DNA repair pathways might be especially inhibited by TCBS. In addition,V. choleraegrown successively on TCBS agar develops resistance to ciprofloxacin.
Intracellular tension relaxation engineered through D-enantiomeric hydrogel maneuvers neurogenesis and immunomodulation to facilitate spinal cord repair
Authors: Li Ya , Wang Yulin , Fang Xinyu , Zhang Hengtong , Li Ruicheng , Cai Rupeng , Li Xiaohui , Yang Zhaopu , Li Xiaoyun , Huang Zhongbing , Yin Guangfu , Ao Qiang
Published: January 2025

Microenvironment mechanics plays a vital role in regulating morphogenesis and immune response after injury, but their exploration has been hindered by the fragile mechanical strength and oxidative physiological environment in spinal cord injury (SCI). Here, we engineered self-assembly hydrogels of enantiomeric peptides with neural tissue-matching mechanical properties to persistently manipulate cellular membrane tension and mechanotransduction through stereo conformational recognition and consequent protein affinity difference. The D-enantiomeric hydrogel-induced intracellular tension relaxation activates neurogenesis and ECM remolding in astrocytes, suppresses pro-inflammation and promotes pro- regeneration in microglia, which significantly facilitates neuroprotection and functional recovery in a rat severe SCI model. The intracellular tension relaxation-induced morphogenesis may be neural characteristics, contrary to non-neural cells, as the downstream mechanical signaling is activated by the resulted neurogenic morphology change. Overall, inducing intracellular tension relaxation is a potential effective strategy for promoting nerve regeneration.
Identification and classification of abundant RNA-binding proteins in the mouse lens and interactions of Carhsp1, Igf2bp1/ZBP1, and Ybx1 with crystallin and β-actin mRNAs
Authors: Rayêe Danielle , Hwang Dong-Woo , Chang William K. , Karp Ilana N. , Zhao Yilin , Bowman Teresa , Lachke Salil A. , Singer Robert H. , Eliscovich Carolina , Cvekl Ales
Published: January 2025

RNA-binding proteins (RBPs) are critical regulators of mRNAs controlling all processes such as RNA transcription, transport, localization, translation, mRNA:ncRNA interactions, and decay. Cellular differentiation is driven by tissue-specific and/or tissue-preferred expression of proteins needed for the optimal function of mature cells, tissues and organs. Lens fiber cell differentiation is marked by high levels of expression of crystallin genes encoding critical proteins for lens transparency and light refraction. Herein we performed proteomic and transcriptomic analyses of RBPs in differentiating mouse lenses to identify the most abundant RBPs and establish dynamic changes of their expression in differentiating lens. Expression analyses include highly abundant RBPs, including Carhsp1, Igf2bp1/ZBP1, Ybx1, Pabpc1, Ddx39, and Rbm38. Binding sites of Carhsp1, Ybx1, and Igf2bp1/ZBP1 were predicted in various crystallin and β-actin mRNAs. Immunoprecipitations using antibodies against Carhsp1, Igf2bp1/ZBP1, and Ybx1 confirmed their interactions with αA-, αB-, and γA-crystallin mRNAs. A combination of single molecule RNA FISH (smFISH) and immunofluorescence was used to probein vivointeractions of these RBPs with αA-, αB-crystallin, and β-actin mRNAs in cytoplasm and nucleoplasm of cultured mouse lens epithelial cells. Together, these results open new avenues to perform comprehensive genetic, cell, and molecular biology studies of individual RBPs in the lens.
Acute Dose-Related Effect of Antiseizure Medicines on Open Field Exploration of Male Rats with Established Epilepsy
Authors: Wu Qian , Zierath Dannielle , Knox Kevin M. , White H. Steve , Barker-Haliski Melissa
Published: January 2025

Antiseizure medicines (ASMs) cause both acute and chronic behavioral side effects in individuals with epilepsy. While clinical and preclinical studies often focus on chronic effects, the acute dose-related impact of ASMs on behavior is underreported, especially in rodent temporal lobe epilepsy (TLE) models. Investigating the acute effects of both therapeutic and behaviorally impairing doses may inform clinically relevant adverse effects, such as sedation, hyperactivity, and impaired coordination, which are essential for evaluating drug safety and tolerability. This study investigated the acute effects of anticonvulsant doses of carbamazepine (CBZ), valproic acid (VPA), levetiracetam (LEV), and cenobamate (CNB) on locomotor activity and exploratory behavior in rats 8-13 weeks after kainic acid-induced status epilepticus to elicit confirmed spontaneous recurrent seizures consistent (SRS) with TLE. Behavioral outcomes were quantified using an automated open field task (OFT) in both epileptic and non-epileptic (naïve) rats. Our findings revealed that anticonvulsant doses of CNB affected locomotor behavior while other ASMs did not alter exploratory behavior. However, the motor impairing doses of CBZ and CNB equally suppressed exploratory behavior, likely due to sedative effects, in both epileptic and non-epileptic rats. LEV was unique, showing no sedative effects even at high doses, while VPA exhibited an anxiolytic effect in SRS rats and a sedative effect in naïve rats at high dose. This study provides essential insight into the efficacy and tolerability profiles of a diversity of FDA-approved ASMs in a clinically relevant TLE model. Thus, SRS may influence ASM tolerability in preclinical TLE models that may inform clinical translation.
PKD3 localizes to late endosomes to maintain Rab7-dependent endolysosomal homeostasis
Authors: Gutiérrez-Galindo Elena , Jursik Katharina , Frey Yannick , Meyer Florian , Hausser Angelika
Published: January 2025

Protein kinase D3 (PKD3) is an important regulator of triple-negative breast cancer (TNBC) progression by promoting invasion, proliferation, and stem cell maintenance. However, the mechanism underlying these cellular functions has remained unclear. Here, we report that endogenous PKD3 localizes to Rab7/Lamp1-positive vesicles in MDA-MB-231 cells cultured on stiff matrices. Notably, upon PKD3 depletion the size of Rab7-positive vesicles is smaller. This correlates with impaired endosomal acidification, which is associated with dysregulated Wnt signaling and a decline in stemness. Our data thus unveil a previously unrecognized role of PKD3 in regulating endolysosomal dynamics that contributes to the maintenance of the cancer stem cell population.
Monoclonal nanobodies alter the activity and assembly of the yeast vacuolar H+-ATPase
Authors: Knight Kassidy , Park Jun Bae , Oot Rebecca A. , Khan Md. Murad , Roh Soung-Hun , Wilkens Stephan
Published: January 2025

The vacuolar ATPase (V-ATPase; V1Vo) is a multi-subunit rotary nanomotor proton pump that acidifies organelles in virtually all eukaryotic cells, and extracellular spaces in some specialized tissues of higher organisms. Evidence suggests that metastatic breast cancers mislocalize V-ATPase to the plasma membrane to promote cell survival and facilitate metastasis, making the V-ATPase a potential drug target. We have generated a library of camelid single-domain antibodies (Nanobodies; Nbs) against lipid-nanodisc reconstituted yeast V-ATPase Voproton channel subcomplex. Here, we present an in-depth characterization of three anti-VoNbs using biochemical and biophysicalin vitroexperiments. We find that the Nbs bind Vowith high affinity, with one Nb inhibiting holoenzyme activity and another one preventing enzyme assembly. Using cryoEM, we find that two of the Nbs bind thecsubunit ring of the Voon the lumen side of the complex. Additionally, we show that one of the Nbs raised against yeast Vocan pull down human V-ATPase (HsV1Vo). Our research demonstrates Nb versatility to target and modulate the activity of the V-ATPase, and highlights the potential for future therapeutic Nb development.
Shared Decision-Making in Renal Replacement Therapy Selection: Patient Perceptions, Preferences, and Influencing Factors in a Nationwide Cross-Sectional Study in Japan
Authors: Shibagaki Yugo , Sofue Tadashi , Kawarazaki Hiroo , Toida Tatsunori , Suzuki Tomo , Nishiwaki Hiroki , Asano Kenichiro , Terawaki Hiroyuki , Ito Takafumi , Oka Hideaki , Nagai Kei , Murakami Minoru , Nagai Kojiro , Komukai Daisuke , Adachi Takayuki , Furukata Satoshi , Tsutsui Takaaki , Fujisaki Kiichiro , Sugitani Seita , Shimizu Hideaki , Nishino Tomoya , Asada Hiroaki , Shimizu Hideki , Tsukamoto Tatsuo , Nakaya Izaya , Yamada Yosuke , Inanaga Ryohei , Yamada Shohei , Nakanishi Shohei , Maeda Atsuhiro , Yamamoto Mari , Hirashio Shuma , Okamoto Takeshi , Nakamura Takayuki , Miyoshi Ken-ichi , Kado Hiroshi , Toda Susumu , Shibata Shigeru , Nishi Keiko , Yamamoto Makoto , Naganuma Tsukasa , Zamami Ryo , Furusho Masahide , Miyasato Hitoshi , Tamura Yukihiro , Raita Yoshihiko , Fukuhara Chisato , Uehara Keita , Inoue Kosuke , Taki Yasuhiro , Nakano Nobuyuki , Kurita Noriaki ,   the PREPARES Study Group
Published: January 2025

Background

Shared decision-making (SDM) is a key process in selecting renal replacement therapy (RRT). This study analyzed SDM perceptions, preferences, and patient- and facility-level factors influencing SDM among Japanese patients with chronic kidney disease (CKD) who selected RRT.

Methods

We analyzed 475 adult patients with CKD from 49 medical facilities. SDM awareness and recognition, preferences for SDM timing and frequency, discussion content, and desired professional involvement were assessed. Patient- and facility-level factors associated with SDM perceptions were evaluated using Poisson regression with cluster-robust variance estimation.

Results

The mean age of participants was 67.4 years. Overall, 71%, 24.4%, and 4.4% chose hemodialysis, peritoneal dialysis, and kidney transplantation, respectively. While 81.2% perceived that SDM was performed during RRT selection, only 4.7% were explicitly aware of the concept. Patients prioritized discussions about effects on daily life, financial burden, and family-related concerns. Most preferred SDM initiation when RRT was imminent, conducted over multiple sessions. Many patients valued the involvement of medical social workers and their usual non-nephrologist physicians in addition to nephrologists. Multiple outpatient visits for RRT selection, involving nurse participation and extended consultation times, were significantly associated with SDM perceptions (prevalence ratio: 1.59, 95% confidence interval: 1.05–2.42).

Conclusions

Many Japanese patients with CKD perceived SDM during RRT selection; however, they had limited awareness of the concept. The findings underscore the importance of establishing a system that facilitates repeated SDM discussions at critical moments for patients. These discussions should emphasize the impact of RRT on patients’ lives and involve a multidisciplinary team.
Analysis of CD8 and FOXP3 Expression Ratios in Tumor and Stromal Compartments of Penile Squamous Cell Carcinoma Across Different Subtypes and Grades
Authors: Canete-Portillo Sofia , Cubilla Antonio L. , Netto George J. , Chaux Alcides
Published: January 2025

Background

Penile squamous cell carcinoma (PSCC) remains a relatively rare but formidable malignancy, especially in regions with limited access to preventive measures. The tumor microenvironment (TME) –specifically, the balance between CD8+ cytotoxic T cells (CTLs) and FOXP3+ regulatory T cells (Tregs)– has emerged as a pivotal determinant of tumor progression and immune evasion. This study aimed to evaluate CD8+/FOXP3+ ratios in both tumor and stromal compartments across different PSCC subtypes and grades.

Methods

This retrospective study analyzed tissue microarray (TMA) samples from 108 patients with invasive PSCC. Immunohistochemical staining for CD8+ and FOXP3+ was performed. Tumor and stromal compartments were assessed separately. Ratios of CD8+/FOXP3+ were categorized as CD8 > FOXP3 or CD8 ≤ FOXP3. Associations with histologic subtype and grade were examined using Chi-Square or Fisher’s Exact tests, with Cramér’s V indicating effect size.

Results

Eighty TMA spots (15.2% of the total) had quantifiable data for both markers. We observed a significant association between CD8+/FOXP3+ ratio and histologic grade in both tumor (P=0.03) and stromal compartments (P=0.02), with moderate effect sizes (Cramér’s V ~ 0.3). Although no statistically significant associations emerged for histologic subtype, effect size measures suggested potential immune-infiltration differences across subtypes. Descriptive analyses indicated that tumor compartments often contained fewer T cells overall, while stromal areas demonstrated robust infiltration patterns.

Conclusions

Tumor grade appears to influence the relative infiltration of cytotoxic and regulatory T cells in PSCC, underscoring the need for compartment-specific immune profiling. These observations highlight the potential utility of CD8+/FOXP3+ ratios as prognostic markers and in guiding future immunotherapeutic strategies. Prospective studies incorporating larger cohorts and HPV stratification could further clarify the immunobiology of PSCC and inform personalized treatment approaches.
Evaluating sustained reach and effectiveness of collaborative care models: A Cross-sectional study of the New York State Collaborative Care Medicaid Program
Authors: Kim Kain , Feng Baoyi , Luan Mengxiao , Zou Jungang , Jones Amy , Gadbois Danielle , Schwartz Joseph E. , Chen Qixuan , Moise Nathalie
Published: January 2025

Background

Little data exists on collaborative care (CC) sustainability.

Objective

Describe and determine predictors of long-term CC reach and effectiveness Design: Cross-sectional observational study of the NY State CC Medicaid Program (CCMP), involving technical assistance (TA), quality monitoring, and fee-for-quality Medicaid reimbursement codes for implementing CC. We included clinics participating in CCMP from 2012-2019 with ≥0.5 full time equivalent (FTE) care manager and available 2021 and/or 2021 data.

Main Measures

Clinic (size, type, region, enrollment year); and CC program (care manager FTE, caseload/care manager FTE [target 100-150], screening [proportion of clinic screened for depression], engagement [proportion of CC patients contacted/engaged monthly], and psychiatrist consultations in unremitted patients) characteristics. Outcomes were reach (proportion of screen-detected depressed patients enrolled in CC) and effectiveness (proportion of CC enrolled patients achieving remission or 50% reduction in depressive symptoms [Target 50-60%]). We used multilevel negative binomial regression models, adjusting for clustering by healthcare system and county.

Results

Of eligible 160 clinics, 71.2% were Federally Qualified Health Centers (FQHCs); the median caseload/care manager FTE was 55.1, reach 13.0% and effectiveness 42.0%. In multivariable analyses, key CC factors associated with reach included engagement (adjusted Rate Ratio [aRR]=3.99 [1.82, 8.76]), care manager FTE (aRR=1.06 [1.02, 1.10]), and caseload/care manager FTE (aRR=1.23 [1.17, 1.29]); smaller clinic size (aRR=0.60 [0.53, 0.69]), earlier adoption (aRR=0.40 [0.23,0.69] in 2017-2019 vs. 2012-2014), and academic/private clinics (vs. FHQC) (aRR=0.66 [0.45, 0.96]) were also predictive. Caseload/care manager FTE (aRR=1.04 [1.01, 1.07]), psychiatry consultations (aRR=1.55 [1.19, 2.00]), and FQHCs (aRR=1.19 [1.02, 1.40]) were associated with greater CC effectiveness.

Conclusion

Despite ongoing fiscal and TA, CC clinics particularly struggle to achieve long-term reach. While majority FQHCs limit generalizability, we provide several targets for selecting ideal settings for CC, optimizing the pace of sustainability and considering de-implementation efforts when futile.

Primary Funding Source

Agency for Healthcare Research
Neural signatures of model-based and model-free reinforcement learning across prefrontal cortex and striatum
Authors: Miranda Bruno , Butler James L. , Malalasekera W. M. Nishantha , Behrens Timothy E. J. , Dayan Peter , Kennerley Steven W.
Published: January 2025

Animals integrate knowledge about how the state of the environment evolves to choose actions that maximise reward. Such goal-directed behaviour - or model-based (MB) reinforcement learning (RL) - can flexibly adapt choice to changes, being thus distinct from simpler habitual - or model-free (MF) RL - strategies. Previous inactivation and neuroimaging work implicates prefrontal cortex (PFC) and the caudate striatal region in MB-RL; however, details are scarce about its implementation at the single-neuron level. Here, we recorded from two PFC regions – the dorsal anterior cingulate cortex (ACC) and dorsolateral PFC (DLPFC), and two striatal regions, caudate and putamen – while two rhesus macaques performed a sequential decision-making (two-step) task in which MB-RL involves knowledge about the statistics of reward and state transitions. All four regions, but particularly the ACC, encoded the rewards received and tracked the probabilistic state transitions that occurred. However, ACC (and to a lesser extent caudate) encoded the key variables of the task - namely the interaction between reward, transition and choice – which underlies MB decision-making. ACC and caudate neurons also encoded MB-derived estimates of choice values. Moreover, caudate value estimates of the choice options flipped when a rare transition occurred, demonstrating value update based on structural knowledge of the task. The striatal regions were unique (relative to PFC) in encoding the current and previous rewards with opposing polarities, reminiscent of dopaminergic neurons, and indicative of a MF prediction error. Our findings provide a deeper understanding of selective and temporally dissociable neural mechanisms underlying goal-directed behaviour.
Combinatorial effects of bovicin HC5 and epsilon-polylysine againstAlicyclobacillus acidoterrestrisin orange juice
Authors: Iduu Nneka V
Published: January 2025

BACKGROUND

Alicyclobacillus acidoterrestris, a spoilage-causing bacterium in fruit juices remains a concern post-pasteurization, making antimicrobial peptides (AMPs) a promising alternative for its control. Bovicin HC5 and epsilon-polylysine were tested for their antimicrobial efficacy againstA. acidoterrestrisDSMZ 2498 in both AAM broth and orange juice. This study determined the minimum inhibitory concentrations (MICs) and minimum bactericidal concentration (MBC) for epsilon-polylysine and bovicin HC5 against 106CFU/mL vegetative cells and activated endospores ofA. acidoterrestrisDSMZ 2498. Their combined effect was also assessed using the checkerboard method. Viable cell counts were measured after 48 hours at 45 °C, and thermal resistance of endospores was examined after exposure to both AMPs as well as their combinations, by determining the exposure time (in minutes) required to kill 90 % of the initial population at 95 °C. Finally, atomic force microscopy (AFM) was employed to investigate their impact on the cell structure and morphology ofA. acidoterrestris.

RESULTS

Bovicin HC5 and epsilon-polylysine demonstrated antibacterial effects againstA. acidoterrestrisDSMZ 2498 inoculated in orange juice. The combination of both AMPs exhibited an additive effect, significantly reducing the number of viable cells after a 48-hour incubation at 45 °C and a 90 % reduction in thermal resistance at 95 °C. Atomic force microscopy (AFM) revealed structural and morphological changes inA. acidoterrestriscells treated by these AMPs.

CONCLUSIONS

The findings in this study revealed the potential application of bovicin HC5 and epsilon-polylysineas natural preservatives in hurdle technologies to controlA. acidoterrestrisand improve the microbiological stability and safety of fruit juices.
Image-based screens identify regulators of endogenous Dvl2 biomolecular condensates
Authors: Schubert Antonia , Heigwer Florian , Scheeder Christian , Voloshanenko Oksana , Kranz Dominique , Ragaller Franziska , Winkler Nadine , Miersch Thilo , Schmitt Barbara , Kuhse Melanie , Gimenes Daniel , Ordoñez-Rueda Diana , Schwarz Jennifer , Stein Frank , Jäger Dirk , Engel Ulrike , Boutros Michael
Published: January 2025

Dishevelled (Dvl) proteins are essential transducers in Wnt signaling pathways, which have been implicated in development, stem cell maintenance, and human diseases such as cancer. Several studies have shown that Dvl proteins form dynamic biomolecular condensates. However, how cellular signals and cell states influence the formation of biomolecular condensates remains poorly understood. Here, we analyzed cells with endogenous Dvl2 condensates using image-based cell sorting in combination with phosphoproteomics and identified protein enrichment for Wnt/PCP signaling and the G2/M cell cycle transition. We then performed an image-based high-throughput screen to identify small molecule kinase inhibitors that affect Dvl2 liquid-liquid phase separation. Strikingly, CK1δ/ε inhibition blocked Dvl2 condensate formation. Its effect on Wnt signaling was modulated in genetic epistasis experiments with loss-of-function alleles of APC, Axin1, and MCC. Our study highlights the interplay between post-translational modifications and condensate dynamics, opening new avenues for research on their role in cellular signaling and disease intervention.
Activation of cGAS-STING signaling pathway during HCV infection
Authors: Anwar Saleem , Islam Khursheed Ul , Azmi Iqbal , Iqbal Jawed
Published: January 2025

Hepatitis C virus (HCV) is a major global health issue, infecting over 170 million people worldwide and leading to severe liver diseases, including cirrhosis and hepatocellular carcinoma. The ability of HCV to persist and cause chronic infection is partly due to its evasion of the host’s innate immune responses, particularly those mediated by the RIG-I-MAVS pathway, which is critical for antiviral defense. Studies have shown the crucial role genome sensing of DNA viruses by cyclic GMP-AMP synthase (cGAS) followed cGAMP production and activation of downstream effector STING (stimulator of interferon genes) to induce IFN-β, however it is not understood in RNA viruses specially in HCV infection. In this study, we explored first time the mechanism of the cGAS-STING pathway in the context of HCV infection, specifically using the JFH-1 strain of HCV (genotype 2a). We observed that cGAS expression is significantly upregulated during the early HCV infection, leading to the production of the second messenger cyclic GMP-AMP (cGAMP), which in turn activates STING. This activation results in the significant induction of type I interferon responses, particularly interferon-β (IFN-β), which is essential for mounting an effective antiviral response. Moreover, our results demonstrated the translocation of cGAS and STING with cellular organelles such as the endoplasmic reticulum (ER) and mitochondria. This suggests that the cGAS-STING pathway is intricately linked with other cellular signaling networks in detecting and responding to HCV infection. Furthermore, knockdown experiments targeting cGAS, STING and RIG-I revealed that these proteins play a crucial role in suppressing HCV replication, underscoring their potential as therapeutic targets. These findings provide valuable insights into the molecular mechanisms of the cGAS-STING pathway in mediating the innate immune response against HCV. Understanding this pathway’s role in the immune defense against HCV opens up new possibilities for therapeutic strategies aimed at enhancing the host’s antiviral immunity and potentially developing new treatments for chronic HCV infection.
Understanding the high-order network plasticity mechanisms of ultrasound neuromodulation
Authors: Gatica Marilyn , Atkinson-Clement Cyril , Coronel-Oliveros Carlos , Alkhawashki Mohammad , Mediano Pedro A. M. , Tagliazucchi Enzo , Rosas Fernando E. , Kaiser Marcus , Petri Giovanni
Published: January 2025

Transcranial ultrasound stimulation (TUS) is an emerging non-invasive neuromodulation technique, offering a potential alternative to pharmacological treatments for psychiatric and neurological disorders. While functional analysis has been instrumental in characterizing TUS effects, understanding the underlying mechanisms remains a challenge. Here, we developed a whole-brain model to represent functional changes as measured by fMRI, enabling us to investigate how TUS-induced effects propagate throughout the brain with increasing stimulus intensity. We implemented two mechanisms: one based on anatomical distance and another on broadcasting dynamics, to explore plasticity-driven changes in specific brain regions. Finally, we highlighted the role of higher-order functional interactions in localizing spatial effects of off-line TUS at two target areas—the right thalamus and inferior frontal cortex—revealing distinct patterns of functional reorganization. This work lays the foundation for mechanistic insights and predictive models of TUS, advancing its potential clinical applications.

Significance Statement

Transcranial ultrasound stimulation (TUS) offers a non-invasive approach to modulating brain activity, holding promise for treating psychiatric and neurological disorders. Despite its potential, the mechanisms underlying its effects remain poorly understood. By integrating human fMRI data with whole-brain computational models, we identified how high-order functional interactions localize and propagate TUS-induced effects from local to global brain scales. This work introduces two mechanisms—distance-based propagation and diffusion-like broadcasting—that predict functional plasticity changes, providing a foundation for understanding and optimizing the biological and cognitive outcomes of TUS. Our findings offer critical insights into the dynamics of neuromodulation, bridging experimental results and clinical applications.
A novel broad-spectrum antibiotic targets multiple-drug-resistant bacteria with dual binding targets and no detectable resistance
Authors: He Wenyan , Huan Xueting , Li Yinchuan , Deng Qisen , Chen Tao , Xiao Wen , Chen Yijun , Ma Lingman , Liu Nan , Shang Zhuo , Wang Zongqiang
Published: January 2025

The rapid emergence of difficult-to-treat multidrug-resistant pathogens, combined with the scarcity of antibiotics possessing novel mechanisms, poses a significant threat to global public health. Here, we integrated the synthetic-bioinformatic natural product approach with peptide optimization to unveil the antibiotic-producing potential ofPaenibacillaceaebacteria. Our culture-independent approach led to the discovery of paenimycin, a novel 11-merdepsi-lipopeptide featuring an unprecedented dual-binding mechanism. By sequestering the phosphate and hydroxyl groups of lipid A in Gram-negative bacteria, as well as the phosphate groups of teichoic acids in Gram-positive bacteria, paenimycin exhibited potent and broad-spectrum efficacy against MDR pathogensin vitroandin vivomodels. Remarkably, paenimycin demonstrates no detectable resistance, favorable pharmacokinetics and low nephrotoxicity, positioning it as a promising candidate for treating serve and urgent MDR infections.
Deciphering the role of age and gender in perceiving organizational politics in construction
Authors: Dhanasekar Yuvaraj , Anandh K.S.
Published: January 2025

Purpose

The study investigates the impact of gender and age on the perception of organizational politics among construction professionals in Tamil Nadu, India, a region with unique sociocultural characteristics, which highlights the significance of a diverse, inclusive and equitable workplace.

Design/methodology/approach

A self-administered questionnaire was used to collect data from 251 construction professionals. The study focused on three key aspects of organizational politics perception: general political behavior, go along to get ahead and pay and promotion policies. Data were examined using descriptive statistics, the Mann-Whitney U test and regression analysis with the help of SPSS V23.

Findings

The study reveals that female professionals in the sample may be more sensitive to go along to get ahead and pay and promotion policies than their male counterparts, particularly those aged 29–38. The study also found significant gender-age interactions in organizational politics perception, with females experiencing a greater impact of age on general political behavior, go along to get ahead and pay and promotion policies.

Practical implications

The findings can help managers and practitioners design better interventions and policies to mitigate the negative effects of organizational politics, improve employee satisfaction and performance and foster a more diverse and fair work culture.

Originality/value

This is one of the first studies to explore the influence of gender and age on organizational politics perception in the construction sector, which is characterized by complexity and diversity. The study contributes to the literature on organizational politics and diversity in the construction industry.