bluuebunny/crossref_metadata_2025_split huggingface dataset:
Retrospective analysis of enhancer activity and transcriptome history
Authors: Boers Ruben , Boers Joachim , Tan Beatrice , van Leeuwen Marieke E. , Wassenaar Evelyne , Sanchez Erlantz Gonzalez , Sleddens Esther , Tenhagen Yasha , Mulugeta Eskeatnaf , Laven Joop , Creyghton Menno , Baarends Willy , van IJcken Wilfred F. J. , Gribnau Joost 
Published: February 2023

AbstractCell state changes in development and disease are controlled by gene regulatory networks, the dynamics of which are difficult to track in real time. In this study, we used an inducible DCM–RNA polymerase subunit b fusion protein which labels active genes and enhancers with a bacterial methylation mark that does not affect gene transcription and is propagated in S-phase. This DCM–RNA polymerase fusion protein enables transcribed genes and active enhancers to be tagged and then examined at later stages of development or differentiation. We apply this DCM-time machine (DCM-TM) technology to study intestinal homeostasis, revealing rapid and coordinated activation of enhancers and nearby genes during enterocyte differentiation. We provide new insights in absorptive–secretory lineage decision-making in intestinal stem cell (ISC) differentiation and show that ISCs retain a unique chromatin landscape required to maintain ISC identity and delineate future expression of differentiation-associated genes. DCM-TM has wide applicability in tracking cell states, providing new insights in the regulatory networks underlying cell state changes.
The amniotic fluid proteome changes with term labor and informs biomarker discovery in maternal plasma
Authors: Bhatti Gaurav , Romero Roberto , Gomez-Lopez Nardhy , Chaiworapongsa Tinnakorn , Than Nandor Gabor , Theis Kevin R. , Galaz Jose , Gotsch Francesca , Pique-Regi Roger , Berry Stanley M. , Kavdia Mahendra , Tarca Adi L. 
Published: February 2023

AbstractThe intra-uterine components of labor, namely, myometrial contractility, cervical ripening, and decidua/membrane activation, have been extensively characterized and involve a local pro-inflammatory milieu of cellular and soluble immune mediators. Targeted profiling has demonstrated that such processes extend to the intra-amniotic space, yet unbiased analyses of the proteome of human amniotic fluid during labor are lacking. Herein, we utilized an aptamer-based platform to characterize 1,310 amniotic fluid proteins and found that the proteome undergoes substantial changes with term labor (251 proteins with differential abundance, q < 0.1, and fold change > 1.25). Proteins with increased abundance in labor are enriched for immune and inflammatory processes, consistent with prior reports of labor-associated changes in the intra-uterine space. By integrating the amniotic fluid proteome with previously generated placental-derived single-cell RNA-seq data, we demonstrated the labor-driven upregulation of signatures corresponding to stromal-3 and decidual cells. We also determined that changes in amniotic fluid protein abundance are reflected in the maternal plasma proteome. Collectively, these findings provide novel insights into the amniotic fluid proteome in term labor and support its potential use as a source of biomarkers to distinguish between true and false labor by using maternal blood samples.
Evaluation of polyhydroxyalkanoate (PHA) synthesis by Pichia sp. TSLS24 yeast isolated in Vietnam
Authors: Thu Nguyen Thi Tam , Hoang Le Huy , Cuong Pham Kien , Viet-Linh Nguyen , Nga Tran Thi Huyen , Kim Dang Dinh , Leong Yoong Kit , Nhi-Cong Le Thi 
Published: February 2023

AbstractFollowing the rising concern on environmental issues caused by conventional fossil-based plastics and depleting crude oil resources, polyhydroxyalkanoates (PHAs) are of great interest by scientists and biodegradable polymer market due to their outstanding properties which include high biodegradability in various conditions and processing flexibility. Many polyhydroxyalkanoate-synthesizing microorganisms, including normal and halophilic bacteria, as well as algae, have been investigated for their performance in polyhydroxyalkanoate production. However, to the best of our knowledge, there is still limited studies on PHAs-producing marine yeast. In the present study, a halophilic yeast strain isolated from Spratly Island in Vietnam were investigated for its potential in polyhydroxyalkanoate biosynthesis by growing the yeast in Zobell marine agar medium (ZMA) containing Nile red dye. The strain was identified by 26S rDNA analysis as Pichia kudriavzevii TSLS24 and registered at Genbank database under code OL757724. The amount of polyhydroxyalkanoates synthesized was quantified by measuring the intracellular materials (predicted as poly(3-hydroxybutyrate) -PHB) by gravimetric method and subsequently confirmed by Fourier transform infrared (FTIR) spectroscopic and nuclear magnetic resonance (NMR) spectroscopic analyses. Under optimal growth conditions of 35 °C and pH 7 with supplementation of glucose and yeast extract at 20 and 10 gL−1, the isolated strain achieved poly(3-hydroxybutyrate) content and concentration of 43.4% and 1.8 gL−1 after 7 days of cultivation. The poly(3-hydroxybutyrate) produced demonstrated excellent biodegradability with degradation rate of 28% after 28 days of incubation in sea water.
A CRISPR-Cas9-mediated F0 screen to identify pro-regenerative genes in the zebrafish retinal pigment epithelium
Authors: Lu Fangfang , Leach Lyndsay L. , Gross Jeffrey M. 
Published: February 2023

AbstractOcular diseases resulting in death of the retinal pigment epithelium (RPE) lead to vision loss and blindness. There are currently no FDA-approved strategies to restore damaged RPE cells. Stimulating intrinsic regenerative responses within damaged tissues has gained traction as a possible mechanism for tissue repair. Zebrafish possess remarkable regenerative abilities, including within the RPE; however, our understanding of the underlying mechanisms remains limited. Here, we conducted an F0 in vivo CRISPR-Cas9-mediated screen of 27 candidate RPE regeneration genes. The screen involved injection of a ribonucleoprotein complex containing three highly mutagenic guide RNAs per target gene followed by PCR-based genotyping to identify large intragenic deletions and MATLAB-based automated quantification of RPE regeneration. Through this F0 screening pipeline, eight positive and seven negative regulators of RPE regeneration were identified. Further characterization of one candidate, cldn7b, revealed novel roles in regulating macrophage/microglia infiltration after RPE injury and in clearing RPE/pigment debris during late-phase RPE regeneration. Taken together, these data support the utility of targeted F0 screens for validating pro-regenerative factors and reveal novel factors that could regulate regenerative responses within the zebrafish RPE.
Novel insights into plant defensin ingestion induced metabolic responses in the polyphagous insect pest Helicoverpa armigera
Authors: Mulla Javed A. , Tamhane Vaijayanti A. 
Published: February 2023

AbstractLepidopteran insect pest Helicoverpa armigera is one of the most destructive pests of crop plants and several biotechnological approaches are being developed for its control. Plant defensins are small cationic and cysteine-rich peptides that play a role in plant defense. Ingestion of a defensin from Capsicum annuum (CanDef-20) induced a dose-dependent reduction in larval and pupal mass, delayed metamorphosis and also severely reduced fecundity and fertility in H. armigera. To understand the molecular mechanisms of CanDef-20 ingestion-mediated antibiosis in H. armigera larvae, a comparative transcriptomics analysis was carried out. Predominant downregulation of GOs represents serine-type endopeptidases, structural constituents of ribosomes and integral membrane components and differential upregulation of ATP binding, nucleus and translation, while up-regulation of nucleic acid binding represented by transposable elements, were detected. Different isoforms of lipase, serine endopeptidase, glutathione S-transferase, cadherin, alkaline phosphatase and aminopeptidases were found to be upregulated as a compensatory response to CanDef-20 ingestion. In vitro enzyme assays and qPCR analysis of some representative genes associated with vital cellular processes like metamorphosis, food digestion and gut membrane indicated adaptive differential regulations in CanDef-20 fed H. armigera larvae. We conclude that CanDef-20 ingestion affects insect metabolism in a number of ways through its interaction with cell membrane, enzymes, cytoplasmic proteins and triggering transposon mobilization which are linked to growth retardation and adaptive strategies in H. armigera.
Brown bear skin-borne secretions display evidence of individuality and age-sex variation
Authors: Clapham Melanie , Wilson Abbey E. , Williams Candace L. , Sergiel Agnieszka 
Published: February 2023

AbstractScent originates from excretions and secretions, and its chemical complexity in mammals translates into a diverse mode of signalling. Identifying how information is encoded can help to establish the mechanisms of olfactory communication and the use of odours as chemical signals. Building upon existing behavioural and histological literature, we examined the chemical profile of secretions used for scent marking by a solitary, non-territorial carnivore, the brown bear (Ursus arctos). We investigated the incidence, abundance, and uniqueness of volatile organic compounds (VOCs) from cutaneous glandular secretions of 12 wild brown bears collected during late and post-breeding season, and assessed whether age-sex class, body site, and individual identity explained profile variation. VOC profiles varied in the average number of compounds, compound incidence, and compound abundance by age-sex class and individual identity (when individuals were grouped by sex), but not by body site. Mature males differed from other age-sex classes, secreting fewer compounds on average with the least variance between individuals. Compound uniqueness varied by body site and age for both males and females and across individuals. Our results indicate that brown bear skin-borne secretions may facilitate age-sex class and individual recognition, which can contribute towards further understanding of mating systems and social behaviour.
The role of tracheal wall injury in the development of benign airway stenosis in rabbits
Authors: Zhang Jie , Liu Yue hong , Yang Zhen yu , Liu Zi yi , Wang Chang guo , Zeng Da xiong , Jiang Jun hong 
Published: February 2023

AbstractTo investigate the role of tracheal wall injury in the development of benign airway stenosis in rabbits. Prospective study. We injured the tracheal walls of 28 New Zealand white rabbits using four different methods. Experimental group: Group A (n = 7, mild injury of tracheal mucosa by ordinary brush under bronchoscopy); Group B (n = 7, severe injury of tracheal mucosa by nylon brush under tracheotomy); Group C (n = 7, tracheal cartilage was injured by vascular clamp after tracheotomy); Group D (n = 7, the tracheal cartilage was injured with vascular forceps and the tracheal mucosa was injured with a nylon brush after tracheotomy). Bronchoscopy was performed on each experimental rabbit at 1, 2, 3 and 4 weeks after operation. High-resolution computed tomography (HRCT) and endobronchial optical coherence tomography (EB-OCT) were performed at 4 weeks, and the rabbits were sacrificed after the examination. Their gross and histological findings were comparatively determined whether the experimental rabbit stenosis was established. No airway stenosis was observed in group A. In group B, 28.57% of experimental rabbits developed tracheal stenosis (granulation tissue proliferation was observed in rabbits No. 2 and No. 6 at 1, 2 and 3 weeks after operation, and the tracheal scar contracture was observed in No.6 rabbit at 4 weeks after operation). Fourteen rabbits in group C and group D had tracheal stenosis caused by granulation tissue proliferation at 1, 2 and 3 weeks after operation. At the fourth week after operation, 71.43% of experimental rabbits had tracheal stenosis due to granulation tissue hyperplasia, 7.14% of experimental rabbits had tracheal stenosis due to scar contracture and granulation hyperplasia, and 21.43% of experimental rabbits had tracheal stenosis due to scar contracture. EB-OCT scan showed that the cartilage layer with low signal reflection band was discontinuous. The injury of cartilage is the key factor of benign airway stenosis. Acute injury of airway mucosa alone is unlikely to cause airway stenosis, but combined with cartilage injury may aggravate airway stenosis. EB-OCT can clearly identify the airway layers of rabbits, which is helpful to evaluate the damage of tracheal cartilage and mucosa. The diagnostic potential of this technique makes EB-OCT a promising approach for the study and monitoring of airway diseases.
ERP and attachment dimensions as predictors of seeking care or food comfort in stressful situations
Authors: Uccula Arcangelo , Mercante Beniamina , Pozzati Caterina , Deriu Franca , Enrico Paolo 
Published: February 2023

AbstractIn this study, we aimed to test the association of the Late Positive Potential (LPP) response and attachment dimensions in the choice of care/food pictures and its reaction time (RT) in threatening versus neutral conditions. Fifty-two participants (38 females, Mage22.62) responded to the ECR questionnaire and were exposed to adequate visual stimuli, during EEG recording. Results showed that threatening stimuli increase the choice of care, decrease RT, and increase LPP magnitude in centro-parietal areas (Cpz, Pz, P3 and P4). Food choice was lower, with increased RT. Furthermore, larger LPP magnitude in centro-parietal cluster was associated with increased RT in the choice of care. Considering the dimensions of attachment, in threatening conditions, while anxiety was not associated with RT and care/food choice, avoidance was associated with an increase in care choice and RT. In conclusion, the specific association of increased RT in care choice with high LPP magnitude centro-parietal cluster may be explained in terms of a functional interference of these areas in the choice of care, but not of food. Further, we postulate that the increased RT of avoidant individuals may reflect a more articulated choice process.
Modeling present and future distribution of plankton populations in a coastal upwelling zone: the copepod Calanus chilensis as a study case
Authors: Rivera Reinaldo , Escribano Rubén , González Carolina E. , Pérez-Aragón Manuela 
Published: February 2023

AbstractPredicting species distribution in the ocean has become a crucial task to assess marine ecosystem responses to ongoing climate change. In the Humboldt Current System (HCS), the endemic copepodCalanus chilensisis one of the key species bioindicator of productivity and water masses. Here we modeled the geographic distribution ofCalanus chilensisfor two bathymetric ranges, 0–200 and 200–400 m. For the 0–200 m layer, we used the Bayesian Additive Regression Trees (BART) method, whereas, for the 200–400 m layer, we used the Ensembles of Small Models (ESMs) method and then projected the models into two future scenarios to assess changes in geographic distribution patterns. The models were evaluated using the multi-metric approach. We identified that chlorophyll-a (0.34), Mixed Layer Depth (0.302) and salinity (0.36) explained the distribution ofC. chilensis. The geographic prediction of the BART model revealed a continuous distribution from Ecuador to the southernmost area of South America for the 0–200 m depth range, whereas the ESM model indicated a discontinuous distribution with greater suitability for the coast of Chile for the 200–400 m depth range. A reduction of the distribution range ofC. chilensisis projected in the future. Our study suggests that the distribution ofC. chilensisis conditioned by productivity and mesoscale processes, with both processes closely related to upwelling intensity. These models serve as a tool for proposing indicators of changes in the ocean. We further propose that the speciesC. chilensisis a high productivity and low salinity indicator at the HCS. We recommend further examining multiple spatial and temporal scales for stronger inference.
Feasibility of an inertial measurement unit sensor-based guiding system for benign paroxysmal positional vertigo treatment: A pilot study
Authors: Pastor Cecilia A. Callejas , Kwon Chiheon , Joo Jung Sook , Kim Hee Chan , Shim Dae Bo , Ku Yunseo , Suh Myung-Whan 
Published: February 2023

AbstractPerforming an accurate canalith repositioning procedure (CRP) is important for treating benign paroxysmal positional vertigo, because inadequate rotational head angles can result in ineffective otolith mobilization and consequent treatment failure. Specialists-guided Epley maneuver reportedly had mean errors of 13.7°–24.4° while they were significantly larger (40.0°–51.5°) when self-administered. Similar results were obtained for the Barbeque maneuver: mean errors were 9.2°–13.0° by the specialists while they were significantly larger (22.9°–28.6°) when self-administered. Our study aimed to validate the feasibility of an inertial measurement unit sensor-based CRP (IMU-CRP) by analyzing the differences in accuracy in the rotational angles, comparing them with education-based conventional CRP (EDU-CRP). A pilot validation was also performed by analyzing the treatment success rate of IMU-CRP in patients with BPPV. This single-institution prospective, comparative effectiveness study examined 19 participants without active vertigo or prior knowledge of benign paroxysmal positional vertigo and CRP. Participants conducted the Epley and Barbeque roll maneuvers without and with auditory guidance (EDU-CRP vs. IMU-CRP, respectively) twice, and head rotation accuracies were compared. Differences in target angles based on the American Academy of Otolaryngology-Head and Neck Surgery guidelines were considered errors. For BPPV participants, treatment success was assessed based on the presence or absence of nystagmus, vertigo, and dizziness. For all the Epley and Barbeque roll maneuvers steps, the absolute errors were smaller for IMU- than for EDU-CRPs, with significant differences in steps 2–4 and 3–6 of the Epley and Barbeque roll maneuvers, respectively. A learning effect was found in steps 4 and 5 of the Barbeque roll maneuver but not in the Epley maneuver. The treatment success rates after 1 h were 71.4% and 100% for the Epley and Barbeque roll maneuvers, respectively. Real-time feedback on head rotation angles induced more appropriate movements in the Epley and Barbeque roll maneuvers. A guiding device based on head monitoring providing real-time auditory feedback may increase the self-administered CRP success rates in treating benign paroxysmal positional vertigo.
Scaling-up strategies for controllable biosynthetic ZnO NPs using cell free-extract of endophytic Streptomyces albus: characterization, statistical optimization, and biomedical activities evaluation
Authors: EL-Moslamy Shahira H. , Elnouby Mohamed S. , Rezk Ahmed H. , El-Fakharany Esmail M. 
Published: February 2023

AbstractIn this study, we identified a suitable precursor and good cellular compartmentalization for enhancing bioactive metabolites to produce biosynthetic zinc oxide nanoparticles (ZnO NPs). An effective medium for cultivating endophyticStreptomycesalbusstrain E56 was selected using several optimized approaches in order to maximize the yield of biosynthetic ZnO NPs. The highest biosynthetic ZnO NPs yield (4.63 g/L) was obtained when pipetting the mixed cell-free fractions with 100 mM of zinc sulfate as a precursor. The generation of biosynthetic ZnO NPs was quickly verified using a colored solution (white color) and UV–Visible spectroscopy (maximum peak, at 320 nm). On a small scale, the Taguchi method was applied to improve the culture medium for culturing the strain E56. As a result, its cell-dry weight was 3.85 times that of the control condition. And then the biosynthesis of ZnO NPs (7.59 g/L) was increased by 1.6 times. Furthermore, by using the Plackett–Burman design to improve the utilized biogenesis pathway, the biosynthesis of ZnO NPs (18.76 g/L) was increased by 4.3 times. To find the best growth production line, we used batch and fed batch fermentation modes to gradually scale up biomass output. All kinetics of studied cell growth were evaluated during fed-batch fermentation as follows: biomass yield was 271.45 g/L, yield coefficient was 94.25 g/g, and ZnO NPs yield was 345.32 g/L. In vitro, the effects of various dosages of the controllable biosynthetic ZnO NPs as antimicrobial and anticancer agents were also investigated. The treatments with controllable biosynthetic ZnO NPs had a significant impact on all the examined multidrug-resistant human pathogens as well as cancer cells.
A novel computational approach to pain perception modelling within a Bayesian framework using quantitative sensory testing
Authors: Drusko Armin , Baumeister David , McPhee Christensen Megan , Kold Sebastian , Fisher Victoria Lynn , Treede Rolf-Detlef , Powers Albert , Graven-Nielsen Thomas , Tesarz Jonas 
Published: February 2023

AbstractPain perception can be studied as an inferential process in which prior information influences the perception of nociceptive input. To date, there are no suitable psychophysical paradigms to measure this at an individual level. We developed a quantitative sensory testing paradigm allowing for quantification of the influence of prior expectations versus current nociceptive input during perception. Using a Pavlovian-learning task, we investigated the influence of prior expectations on the belief about the varying strength of association between a painful electrical cutaneous stimulus and a visual cue in healthy subjects (N = 70). The belief in cue-pain associations was examined with computational modelling using a Hierarchical Gaussian Filter (HGF). Prior weighting estimates in the HGF model were compared with the established measures of conditioned pain modulation (CPM) and temporal summation of pain (TSP) assessed by cuff algometry. Subsequent HGF-modelling and estimation of the influence of prior beliefs on perception showed that 70% of subjects had a higher reliance on nociceptive input during perception of acute pain stimuli, whereas 30% showed a stronger weighting of prior expectations over sensory evidence. There was no association between prior weighting estimates and CPM or TSP. The data demonstrates relevant individual differences in prior weighting and suggests an importance of top-down cognitive processes on pain perception. Our new psychophysical testing paradigm provides a method to identify individuals with traits suggesting greater reliance on prior expectations in pain perception, which may be a risk factor for developing chronic pain and may be differentially responsive to learning-based interventions.