bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractThiosulfate-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 ImportanceTCBS 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

AbstractMicroenvironment 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

AbstractRNA-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

AbstractAntiseizure 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

AbstractProtein 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

AbstractThe 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

AbstractBackgroundShared 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.MethodsWe 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.ResultsThe 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).ConclusionsMany 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

ABSTRACTBackgroundPenile 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.MethodsThis 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.ResultsEighty 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.ConclusionsTumor 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

AbstractBackgroundLittle data exists on collaborative care (CC) sustainability.ObjectiveDescribe 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 MeasuresClinic (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.ResultsOf 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.ConclusionDespite 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 SourceAgency 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

AbstractAnimals 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

AbstractBACKGROUNDAlicyclobacillus 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.RESULTSBovicin 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.CONCLUSIONSThe 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

SummaryDishevelled (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.