bluuebunny/crossref_metadata_2025_split huggingface dataset:
Applying biostimulants boosts forage productivity without affecting soil biotic and abiotic parameters on a Central Coast California rangeland
Authors: Carey Chelsea J. , Strohm Hayley , Smith Ford , Biaggi Mark 
Published: January 2022

AbstractThere is increasing interest in using biostimulant products, such as microbial inoculants and humic substances, to help manage rangelands regeneratively. Understanding how plant and soil communities on rangelands respond to these products is therefore important. In this study, we examined the combined effects of a commercial inoculant and humic product that are currently on the market, and asked whether they influenced rangeland forage productivity and quality, soil microbial biomass and community composition, and abiotic soil parameters in Central Coastal California. We found that forage productivity and some metrics of forage quality responded positively to the foliar application of a commercial microbial inoculant and humic product, but that these benefits were not mirrored by changes belowground in the microbial community or abiotic parameters. Depending on the goals of using the products, this could be seen as a winning scenario and suggests microbial inoculants and humic products could warrant attention as a potential tool for regenerative stewardship of rangelands. While our study derives from one ranch and therefore requires confirmation of its ubiquity prior to broadscale adoption, our results provide new insights into the usefulness of this approach for managing rangeland productivity in California’s Central Coast.
Robust hydrogel-integrated microsystems enabled by enhanced interfacial bonding strength
Authors: Bae Sang Wook , Kim Yong-Woo , Sun Jeong-Yun , Kwon Sunghoon 
Published: January 2022

AbstractNoncovalent hydrogels, compared to covalent hydrogels, have distinctive advantages including biocompatibility and self-healing property but tend to have poor mechanical robustness, thus restricting their application spectrum. A clue to increase utility of such soft hydrogels without chemical bulk modification can be witnessed in biological organ walls where soft mucous epithelial layers are juxtaposed with tough connective tissues. Perhaps, similarly, bonding noncovalent hydrogels to stronger materials, such as tough hydrogels, might be a viable approach for increasing stability and scalability as well as creating novel functions for hydrogel-based systems. However when attempting to bond these two materials, each of the four existing hydrogel-hydrogel bonding method has practical shortcomings. In this work, we introduce a mucosa-inspired bonding method that realizes interfacial bonding of noncovalent hydrogels to tough, hybrid hydrogels without external glue or bulk modification of the noncovalent gel while preserving interfacial micropatterns. The procedure is simple and we confirmed broad applicability with various noncovalent hydrogels and tough hydrogels. We demonstrated the utility of our bonding method with novel applications regarding in vitro assay, soft robotics and biologically inspired systems.
Transcriptomic changes in the pituitary of female mice with androgen excess through dihydrotestosterone (DHT) treatment
Authors: Joseph Serene , Divall Sara , Wu Sheng 
Published: January 2022

AbstractAndrogen excess in women is associated with the development of PCOS and its abnormalities. The Hypothalamus Pituitary Ovarian axis signaling is altered with excessed androgens, leading to anovulation and infertility. Previous studies in the lab have shown that AR signaling in the pituitary alters gonadotrophin release. Hence, the present pioneering study was an approach to determine the transcriptomic changes responsible to the phenotype seen with DHT excess. RNA seq data showed that 583 genes were differentially regulated by DHT in pituitary, of which 344 were upregulated and 239 downregulated. Pathways involved for these genes included endoplasmic reticulum, Golgi apparatus, calcium signaling and vesicles. Meanwhile, Transcriptional factor analysis showed that majority of the genes changed had Androgen responsive elements.
Intestinal epithelial MHC class II regulation by HDAC3 instructs microbiota-specific CD4+ T cells
Authors: Eshleman Emily M. , Shao Tzu-Yu , Woo Vivienne , Rice Taylor , Whitt Jordan , Engleman Laura , Way Sing Sing , Alenghat Theresa 
Published: January 2022

AbstractAberrant immune responses to resident microbes promote inflammatory bowel disease and other chronic inflammatory conditions. However, how microbiota-specific immunity is controlled in mucosal tissues remains poorly understood. Here, we find that mice lacking epithelial expression of microbiota-sensitive histone deacetylase 3 (HDAC3) exhibit increased accumulation of commensal-specific CD4+ T cells in the intestine, provoking the hypothesis that epithelial HDAC3 may instruct local microbiota-specific immunity. Consistent with this, microbiota-specific CD4+ T cells and epithelial HDAC3 expression were concurrently induced following early-life microbiota colonization. Further, epithelial-intrinsic ablation of HDAC3 promoted T cell driven-colitis and primed development of pathogenic commensal-specific Th17 cells. Mechanistically, HDAC3 was essential for MHC class II (MHCII) expression by the intestinal epithelium, and epithelial-intrinsic MHCII actively limited commensal-specific Th17 cells and prevented microbiota-triggered inflammation. Remarkably, HDAC3 enabled the microbiota to induce MHCII on epithelial cells and limit the number of commensal-specific T cells in the intestine. Collectively, these data reveal a central role for an epithelial histone deacetylase in controlling development of tissue-intrinsic T cells that recognize commensal microbes and drive pathologic inflammation.
Cooperative phagocytosis underlies macrophage immunotherapy of solid tumours and initiates a broad anti-tumour IgG response
Authors: Andrechak Jason C. , Dooling Lawrence J. , Hayes Brandon H. , Kadu Siddhant , Zhang William , Pan Ruby , Vashisth Manasvita , Irianto Jerome , Alvey Cory M. , Discher Dennis E. 
Published: January 2022

AbstractMacrophages are abundant in solid tumours and typically associate with poor prognosis, but macrophage clusters in tumour nests have also been reported as beneficial even though dispersed macrophages would have more contacts with cancer cells. Here, by maximizing both phagocytic activity and macrophage numbers, we discover cooperative phagocytosis by low entropy clusters in rapidly growing engineered immuno-tumouroids. The results fit the calculus of proliferation-versus-engulfment, and rheological measurements and molecular perturbations provide a basis for understanding phagocytic disruption of a tumour’s cohesive forces in soft cellular phases. The perturbations underscore the utility of suppressing a macrophage checkpoint in combination with an otherwise ineffective tumour-opsonizing monoclonal antibody, and the approach translates in vivo to tumour elimination that durably protects mice from re-challenge and metastasis. Adoptive transfer of engineered macrophages increases the fraction of mice that eliminate tumours and potentially overcomes checkpoint blockade challenges in solid tumours like insufficient permeation of blocking antibodies and on-target, off-tumour binding. Finally, anti-cancer IgG induced in vivo are tumour-specific but multi-epitope and contribute to a phagocytic feedback that drives macrophage clustering in vitro. Given that solid tumours remain challenging for immunotherapies, durable anti-tumour responses here illustrate unexpected advantages in maximizing net phagocytic activity.
Novel Methods for Elucidating Modality Importance in Multimodal Electrophysiology Classifiers
Authors: Ellis Charles A. , Sendi Mohammad S.E. , Zhang Rongen , Carbajal Darwin A. , Wang May D. , Miller Robyn L. , Calhoun Vince D. 
Published: January 2022

AbstractMultimodal classification is increasingly common in biomedical informatics studies. Many such studies use deep learning classifiers with raw data, which makes explainability difficult. As such, only a few studies have applied explainability methods, and new methods are needed. In this study, we propose sleep stage classification as a testbed for method development and train a convolutional neural network with electroencephalogram (EEG), electrooculogram, and electromyogram data. We then present a global approach that is uniquely adapted for electrophysiology analysis. We further present two local approaches that can identify subject-level differences in explanations that would be obscured by global methods and that can provide insight into the effects of clinical and demographic variables upon the patterns learned by the classifier. We find that EEG is globally the most important modality for all sleep stages, except non-rapid eye movement stage 1 and that local subject-level differences in importance arise. We further show that sex, followed by medication and age had significant effects upon the patterns learned by the classifier. Our novel methods enhance explainability for the growing field of multimodal classification, provide avenues for the advancement of personalized medicine, and yield novel insights into the effects of demographic and clinical variables upon classifiers.
Maturation of prefrontal input to dorsal raphe nucleus increases behavioral persistence in mice
Authors: Gutierrez-Castellanos Nicolas , Sarra Dario , Godinho Beatriz S. , Mainen Zachary F. 
Published: January 2022

AbstractThe ability to persist towards a desired objective is a fundamental aspect of behavioral control whose impairment is implicated in several behavioral disorders. One of the prominent features of behavioral persistence is that its maturation occurs relatively late in development. This is presumed to echo the developmental time course of a corresponding circuit within late-maturing parts of the brain, such as the prefrontal cortex, but the specific identity of the responsible circuits is unknown. Here, we describe the maturation of the projection from layer 5 neurons of the prefrontal cortex to the dorsal raphe nucleus in mice. We show using pathway-specific optogenetic stimulation that this connection undergoes a dramatic increase in synaptic potency between postnatal weeks 3 and 8, corresponding to the transition from juvenile to adult. We then show that this period corresponds to an increase in the behavioral persistence that mice exhibit in a foraging task. Finally, we use genetic targeting to selectively ablate this pathway in adulthood and show that mice revert to a behavioral phenotype similar to juveniles. These results suggest that the prefrontal to dorsal raphe pathway is a critical anatomical and functional substrate of the development and manifestation of behavioral control.
GNNQQNY: Methodology for biophysical and structural understanding of aggregation
Authors: Burra Gunasekhar , Maina Mahmoud B. , Serpell Louise C. , Thakur Ashwani K. 
Published: January 2022

AbstractGNNQQNY sequence offers crucial information about the formation and structure of an amyloid fibril. In this study, we demonstrate a reproducible solubilisation protocol where the reduction of pH to 2.0 resulted in the generation of GNNQQNY monomers. The subsequent ultracentrifugation step removes the residual insoluble peptide from the homogeneous solution. This procedure ensures and allows the peptides to remain monomers till their aggregation is triggered by adjusting the pH to 7.2. The aggregation kinetics analysis showed a distinct lag-phase that is concentration-dependent, indicating nucleation-dependent aggregation kinetics. Nucleation kinetics analysis suggested a critical nucleus of size ∼7 monomers at physiological conditions. The formed nucleus acts as a template for further self-assembly leading to the formation of highly ordered amyloid fibrils. These findings suggest that the proposed solubilisation protocol provides the basis for understanding the kinetics and thermodynamics of amyloid nucleation and elongation in GNNQQNY sequences. This procedure can also be used for solubilising such small amyloidogenic sequences for their biophysical studies.
Efficient learning in children with rapid GABA boosting after training
Authors: Frank Sebastian M. , Becker Markus , Qi Andrea , Geiger Patricia , Frank Ulrike I. , Malloni Wilhelm M. , Sasaki Yuka , Greenlee Mark W. , Watanabe Takeo 
Published: January 2022

AbstractIt is unclear why and how children learn more efficiently than adults, although inhibitory systems, which play an important role in stabilizing learning, are immature in children. Here, we found that despite a lower baseline concentration of γ-aminobutyric acid (GABA) in early visual cortical areas in children (8 to 11 years old) than adults (18 to 35 years old), children exhibited a rapid boost of GABA immediately after visual training, whereas the concentration of GABA in adults remained unchanged after training. Moreover, behavioral experiments showed that children stabilized visual learning much faster than adults, showing rapid development of resilience to retrograde interference. These results together suggest that inhibitory systems in children’s brains are more dynamic and adapt more quickly to stabilize learning than in adults.One Sentence SummaryChildren learn more efficiently than adults due to faster stabilization of learning with rapid GABA boosting after training.
Local climate and vernalization requirements explain the latitudinal patterns of flowering initiation in the crop wild relativeLinum bienne
Authors: Landoni Beatrice , Suárez-Montes Pilar , Habeahan Rico H. F. , Brennan Adrian C. , Pérez-Barrales Rocío 
Published: January 2022

AbstractBackground and AimsDays to flowering initiation in species with large geographic distribution often correlate with latitude. Latitude reflects climatic gradients, but it is unclear if large-scale differentiation in flowering results from adaptation to local climate, and whether adaptation to local climate could constrain shifts in distribution and colonization of new environments.MethodsIn its Western range in Europe,L. biennepopulations were surveyed to describe latitudinal patterns of flowering initiation and determine its correlation with the local climate of populations. This was measured under standardized greenhouse conditions, with a vernalization experiment to learn if chilling advances flowering, and with a reciprocal transplant experiment at three sites along the latitudinal gradient, recording flowering at the central site and plant survival in all sites. Also, genetic differentiation of populations along the latitudinal range was studied using microsatellite markers.Key ResultsFlowering initiation varied with latitude, with southern populations flowering earlier than northern populations. Latitude also predicted population response to vernalization, with chilling inducing a greater advance of flowering initiation in northern than southern populations. In general, plant survival in the reciprocal transplant experiment decreased with the geographic distance of populations to the experimental site and, at the central site, flowering initiation varied with latitude of origin. However, across experiments, the local climate of populations better predicted the differentiation in flowering initiation and vernalization response than latitude of origin. Finally, the microsatellite data revealed genetic differentiation of populations forming two groups that agree with a Mediterranean and Atlantic lineage.ConclusionsThe consistent result across experiments of a latitudinal cline in flowering initiation and in the vernalization response suggests that flowering is under genetic regulation and yet dependent on particular environmental and climatic cues at local scale. However, the genetic differentiation suggests that past population history might influenced the flowering initiation patterns detected.
Multiplex labeling and manipulation of endogenous neuronal proteins using sequential CRISPR/Cas9 gene editing
Authors: Droogers Wouter J , Willems Jelmer , MacGillavry Harold D , de Jong Arthur PH 
Published: January 2022

AbstractRecent advances in CRISPR/Cas9-mediated knock-in methods enable labeling of individual endogenous proteins with fluorophores, to determine their spatiotemporal expression in intact biological preparations. However, multiplex knock-in methods remain limited, particularly in postmitotic cells, due to a high degree of crosstalk between genome editing events. We present Conditional Activation of Knock-in Expression (CAKE), which delivers efficient, flexible and accurate multiplex genome editing in neurons. CAKE is based on sequential gRNA expression operated by a Cre- or Flp-recombinase to control the time window for genomic integration of each donor sequence, which diminishes crosstalk between genome editing events. Importantly, CAKE is compatible with multiple CRISPR/Cas9 strategies, and we show the utilization of CAKE for co-localization of various endogenous proteins, including synaptic scaffolds, ion channels and neurotransmitter receptor subunits. Knock-in efficacy was highly sensitive to DNA vector amount, while knock-in crosstalk was dependent on the rate of donor DNA integration and timing of Cre activation. We applied CAKE to study the co-distribution of endogenous synaptic proteins using dual-color single-molecule localization microscopy, and we introduced dimerization modules to acutely control synaptic receptor dynamics in living neurons. Taken together, CAKE is a versatile method for multiplex protein labeling, enabling accurate detection, precise localization and acute manipulation of endogenous proteins in single cells.
Contribution of behavioural variability to representational drift
Authors: Sadeh Sadra , Clopath Claudia 
Published: January 2022

AbstractNeuronal responses to similar stimuli change dynamically over time, raising the question of how internal representations can provide a stable substrate for neural coding. Recent work has suggested a large degree of drift in neural representations even in sensory cortices, which are believed to store stable representations of the external world. While the drift of these representations is mostly characterized in relation to external stimuli, the behavioural state of the animal (for instance, the level of arousal) is also known to strongly modulate the neural activity. We therefore asked how the variability of such modulatory mechanisms can contribute to representational changes. We analysed large-scale recording of neural activity from the Allen Brain Observatory, which was used before to document representational drift in the mouse visual cortex. We found that, within these datasets, behavioural variability significantly contributes to representational changes. This effect was broadcasted across various cortical areas in the mouse, including the primary visual cortex, higher order visual areas, and even regions not primarily linked to vision like hippocampus. Our computational modelling suggests that these results are consistent with independent modulation of neural activity by behaviour over slower time scales. Importantly, our analysis suggests that reliable but variable modulation of neural representations by behaviour can be misinterpreted as representational drift, if neuronal representations are only characterized in the stimulus space and marginalised over behavioural parameters.
Counting fluorescently labeled proteins in tissues in the spinning disk microscope using single-molecule calibrations
Authors: Liao Maijia , Kuo Yin-Wei , Howard Jonathon 
Published: January 2022

AbstractQuantification of molecular numbers and concentrations in living cells is critical for testing models of complex biological phenomena. Counting molecules in cells requires estimation of the fluorescence intensity of single molecules, which is generally limited to imaging near cell surfaces, in isolated cells, or where motions are diffusive. To circumvent this difficulty, we have devised a calibration technique for spinning-disk confocal (SDC) microscopy, commonly used for imaging in tissues, that uses single-step bleaching kinetics to estimate the single-fluorophore intensity. To cross-check our calibrations, we compared the brightness of fluorophores in the SDC microscope to those in the total-internal-reflection (TIRF) and epifluorescence microscopes. We applied this calibration method to quantify the number of EB1-eGFP proteins in the comets of growing microtubule ends and to measure the cytoplasmic concentration of EB1-eGFP in sensory neurons in fly larvae. These measurements allowed us to estimate the dissociation constant of EB1-eGFP from the microtubules as wells as the GTP-tubulin cap size. Our results show the unexplored potential of single-molecule imaging using spinning disk confocal microscopy and provide a straight-forward method to count the absolute number of fluorophores in tissues which can be applied to a wide range of biological systems and imaging techniques.
Parent‐delivered contingency management for a treatment‐refusing young adult with gaming disorder: Case report
Authors: Riley Ben J. , Baigent Michael , Battersby Malcolm W. , King Daniel L. 
Published: January 2022

AbstractOnline video gaming is a popular activity among people of all ages. For some, however, gaming can become problematic. While evidence exists for the effectiveness of cognitive behavioural therapy for gaming disorder (GD), a major challenge is that adolescents and young adults, particularly males, are often reluctant to seek help and engage long term with a mental health practitioner. This report presents a case involving brief parent‐delivered contingency management for a 19‐year‐old male with GD who refused to engage with treatment services following a significant decline in functioning and a high‐lethality suicide attempt. This approach led to a substantial reduction in gaming time, as well as related gains in self‐care and independence. This case highlights the value and feasibility of developing a therapeutic alliance with a parent to manage excessive gaming behaviours among treatment‐refusing individuals with GD. Practical challenges and associated lessons from managing this case are discussed.
Practitioner points

Brief parent‐delivered contingency management was implemented for a 19‐year‐old treatment‐refusing male with GD.

This approach led to a substantial reduction in the young man's gaming time as well as related gains in areas of self‐care and independence at 6‐month follow‐up.

This case highlights the value and feasibility of developing a therapeutic alliance with a parent to manage excessive gaming behaviours among treatment‐refusing individuals with GD.
Soluble PD‐L1 and B7‐H4 serum levels during the course of physiological pregnancy
Authors: Mach Pawel , Köninger Angela , Reisch Beatrix , Kimmig Rainer , Gellhaus Alexandra 
Published: January 2022

AbstractProblemThe aim of this study was to evaluate the soluble programmed death‐ligand (sPD‐L1) and soluble B7‐H4 (sB7‐H4) serum concentration levels longitudinal throughout the three trimesters of uncomplicated pregnancies.Method of the studysPD‐L1 and sB7‐H4 levels were determined with enzyme‐linked immunosorbent assay (ELISA). The patients (n = 26) were divided into three groups according to the pregnancy trimester. Among 26 women involved in the study 14 had longitudinal sB7‐H4 and sPD‐L1 measurements in each trimester of pregnancy.ResultsDuring the course of pregnancy, the sB7‐H4 blood serum levels were significant higher in second trimester than in first and third trimester, whereas sPD‐L1 levels increased significantly over the course of pregnancy.ConclusionThe highest serum levels of sPD‐L1 in the third trimester suggest increasing suppression of maternal immunity throughout pregnancy, whereas elevated sB7‐H4 concentration levels in second trimester suggests different profile of T‐cell regulation in physiological pregnancy.