bluuebunny/crossref_metadata_2025_split huggingface dataset:
LIM domain proteins Pinch1/2 regulate chondrogenesis and bone mass in mice
Authors: Lei Yiming , Fu Xuekun , Li Pengyu , Lin Sixiong , Yan Qinnan , Lai Yumei , Liu Xin , Wang Yishu , Bai Xiaochun , Liu Chuanju , Chen Di , Zou Xuenong , Cao Xu , Cao Huiling , Xiao Guozhi 
Published: October 2020

AbstractThe LIM domain-containing proteins Pinch1/2 regulate integrin activation and cell–extracellular matrix interaction and adhesion. Here, we report that deleting Pinch1 in limb mesenchymal stem cells (MSCs) and Pinch2 globally (double knockout; dKO) in mice causes severe chondrodysplasia, while single mutant mice do not display marked defects. Pinch deletion decreases chondrocyte proliferation, accelerates cell differentiation and disrupts column formation. Pinch loss drastically reduces Smad2/3 protein expression in proliferative zone (PZ) chondrocytes and increases Runx2 and Col10a1 expression in both PZ and hypertrophic zone (HZ) chondrocytes. Pinch loss increases sclerostin and Rankl expression in HZ chondrocytes, reduces bone formation, and increases bone resorption, leading to low bone mass. In vitro studies revealed that Pinch1 and Smad2/3 colocalize in the nuclei of chondrocytes. Through its C-terminal region, Pinch1 interacts with Smad2/3 proteins. Pinch loss increases Smad2/3 ubiquitination and degradation in primary bone marrow stromal cells (BMSCs). Pinch loss reduces TGF-β-induced Smad2/3 phosphorylation and nuclear localization in primary BMSCs. Interestingly, compared to those from single mutant mice, BMSCs from dKO mice express dramatically lower protein levels of β-catenin and Yap1/Taz and display reduced osteogenic but increased adipogenic differentiation capacity. Finally, ablating Pinch1 in chondrocytes and Pinch2 globally causes severe osteopenia with subtle limb shortening. Collectively, our findings demonstrate critical roles for Pinch1/2 and a functional redundancy of both factors in the control of chondrogenesis and bone mass through distinct mechanisms.
Microbial electroactive biofilms dominated by Geoalkalibacter spp. from a highly saline–alkaline environment
Authors: Yadav Sukrampal , Patil Sunil A. 
Published: October 2020

AbstractUnderstanding of the extreme microorganisms that possess extracellular electron transfer (EET) capabilities is pivotal to advance electromicrobiology discipline and to develop niche-specific microbial electrochemistry-driven biotechnologies. Here, we report on the microbial electroactive biofilms (EABs) possessing the outward EET capabilities from a haloalkaline environment of the Lonar lake. We used the electrochemical cultivation approach to enrich haloalkaliphilic EABs under 9.5 pH and 20 g/L salinity conditions. The electrodes controlled at 0.2 V vs. Ag/AgCl yielded the best-performing biofilms in terms of maximum bioelectrocatalytic current densities of 548 ± 23 and 437 ± 17 µA/cm2 with acetate and lactate substrates, respectively. Electrochemical characterization of biofilms revealed the presence of two putative redox-active moieties with the mean formal potentials of 0.183 and 0.333 V vs. Ag/AgCl, which represent the highest values reported to date for the EABs. 16S-rRNA amplicon sequencing of EABs revealed the dominance of unknown Geoalkalibacter sp. at ~80% abundance. Further investigations on the haloalkaliphilic EABs possessing EET components with high formal potentials might offer interesting research prospects in electromicrobiology.
Transcriptome sequencing of cochleae from constant-frequency and frequency-modulated echolocating bats
Authors: Ma Lu , Sun Haijian , Mao Xiuguang 
Published: October 2020

AbstractEcholocating bats are fascinating for their ability to ‘see’ the world in the darkness. Ultrahigh frequency hearing is essential for echolocation. In this study we collected cochlear tissues from constant-frequency (CF) bats (two subspecies of Rhinolophus affinis, Rhinolophidae) and frequency-modulated (FM) bats (Myotis ricketti, Vespertilionidae) and applied PacBio single-molecule real-time isoform sequencing (Iso-seq) technology to generate the full-length (FL) transcriptomes for the three taxa. In total of 10103, 9676 and 10504 non-redundant FL transcripts for R. a. hainanus, R. a. himalayanus and Myotis ricketti were obtained respectively. These data present a comprehensive list of transcripts involved in ultrahigh frequency hearing of echolocating bats including 26342 FL transcripts, 24833 of which are annotated by public databases. No further comparative analyses were performed on the current data in this study. This data can be reused to quantify gene or transcript expression, assess the level of alternative splicing, identify novel transcripts and improve genome annotation of bat species.
Perception of saccadic reaction time
Authors: Vencato Valentina , Madelain Laurent 
Published: October 2020

AbstractThat saccadic reaction times (SRTs) may depend on reinforcement contingencies has been repeatedly demonstrated. It follows that one must be able to discriminate one’s latencies to adequately assign credit to one’s actions, which is to connect behaviour to its consequence. To quantify the ability to perceive one’s SRT, we used an adaptive procedure to train sixteen participants in a stepping visual target saccade paradigm. Subsequently, we measured their RTs perceptual threshold at 75% in a conventional constant stimuli procedure. For each trial, observers had to saccade to a stepping target. Then, in a 2-AFC task, they had to choose one value representing the actual SRT, while the other value proportionally differed from the actual SRT. The relative difference between the two alternatives was computed by either adding or subtracting from the actual SRT a percent-difference value randomly chosen among a fixed set. Feedback signalling the correct choice was provided after each response. Overall, our results showed that the 75% SRT perceptual threshold averaged 23% (about 40 ms). The ability to discriminate small SRT differences provides support for the possibility that the credit assignment problem may be solved even for short reaction times.
Perceptual inference is impaired in individuals with ASD and intact in individuals who have lost the autism diagnosis
Authors: Jaffe-Dax Sagi , Eigsti Inge-Marie 
Published: October 2020

AbstractBeyond the symptoms which characterize their diagnoses, individuals with autism spectrum disorder (ASD) show enhanced performance in simple perceptual discrimination tasks. Often attributed to superior sensory sensitivities, enhanced performance may also reflect a weaker bias towards previously perceived stimuli. This study probes perceptual inference in a group of individuals who have lost the autism diagnosis (LAD); that is, they were diagnosed with ASD in early childhood but have no current ASD symptoms. Groups of LAD, current ASD, and typically developing (TD) participants completed an auditory discrimination task. Individuals with TD showed a bias towards previously perceived stimuli—a perceptual process called “contraction bias”; that is, their representation of a given tone was contracted towards the preceding trial stimulus in a manner that is Bayesian optimal. Similarly, individuals in the LAD group showed a contraction bias. In contrast, individuals with current ASD showed a weaker contraction bias, suggesting reduced perceptual inferencing. These findings suggest that changes that characterize LAD extend beyond the social and communicative symptoms of ASD, impacting perceptual domains. Measuring perceptual processing earlier in development in ASD will tap the causality between changes in perceptual and symptomatological domains. Further, the characterization of perceptual inference could reveal meaningful individual differences in complex high-level behaviors.
Absorption, translocation, and effects of Bt Cry1Ac peptides from transgenic cotton to the intercrops and soil functional bacteria
Authors: Zhang Wei , Cao Zhen , Wang Mian , Chen Xiaojiao , Wang Baomin 
Published: October 2020

AbstractInsecticidal proteins encoded by the truncated genes from Bacillus thuringiensis (Bt) in transgenic crops are released into soil mainly through root exudate and crop residues. In the present study, Bt Cry1Ac protein was hydrolyzed by pronase that was secreted by the soil bacterium Streptomyces griseus. Six peptides were identified as the products of enzymatic hydrolysis by nano liquid chromatography tandem mass spectrometry (LC–MS/MS). One of the six peptides was labeled with radioactive isotope iodine-125 and then purified. The 125I-peptide solution was irrigated to the rhizosphere soil of watermelon seedlings (Citrullus lanatus L.) and wheat seedlings (Triticum aestivum L.), which the two crops usually intercrop with cotton in China. Detection of radioactivity in both plant tissues within one hour proved adsorption, uptake and translocation of the peptide into watermelon and wheat seedlings. Three of the identified peptides were sprayed onto the seedling leaves of watermelon, wheat and maize (Zea mays L.) in the field or the growth chamber. No significant effects on plant growth were observed. These peptides also did not affect growth of organic phosphate-dissolving, nitrogen-fixing, and potassium-dissolving bacteria in the culture. This study provides a new view of GMO risk assessment methodology.
Effects of charge fluctuation and charge regulation on the phase transitions in stoichiometric VO2
Authors: Joshi Siddharth , Smieszek Nicholas , Chakrapani Vidhya 
Published: October 2020

AbstractDetailed electrical and photoemission studies were carried out to probe the chemical nature of the insulating ground state of VO2, whose properties have been an issue for accurate prediction by common theoretical probes. The effects of a systematic modulation of oxygen over-stoichiometry of VO2 from 1.86 to 2.44 on the band structure and insulator–metal transitions are presented for the first time. Results offer a different perspective on the temperature- and doping-induced IMT process. They suggest that charge fluctuation in the metallic phase of intrinsic VO2 results in the formation of e− and h+ pairs that lead to delocalized polaronic V3+ and V5+ cation states. The metal-to-insulator transition is linked to the cooperative effects of changes in the V–O bond length, localization of V3+ electrons at V5+ sites, which results in the formation of V4+–V4+ dimers, and removal of $$\pi^{*}$$

π

∗

screening electrons. It is shown that the nature of phase transitions is linked to the lattice V3+/V5+ concentrations of stoichiometric VO2 and that electronic transitions are regulated by the interplay between charge fluctuation, charge redistribution, and structural transition.
Brain structural correlates of functional capacity in first-episode psychosis
Authors: Alkan Erkan , Davies Geoff , Greenwood Kathy , L. Evans Simon 
Published: October 2020

AbstractImpaired functional capacity is a core feature of schizophrenia and presents even in first-episode psychosis (FEP) patients. Impairments in daily functioning tend to persist despite antipsychotic therapy but their neural basis is less clear. Previous studies suggest that volume loss in frontal cortex might be an important contributor, but findings are inconsistent. We aimed to comprehensively investigate the brain structural correlates of functional capacity in FEP using MRI and a reliable objective measure of functioning [University of California, San Diego Performance-Based Skills Assessment (UPSA)]. In a sample of FEP (n = 39) and a well-matched control group (n = 21), we measured cortical thickness, gray matter volume, and white matter tract integrity (fractional anisotropy, FA) within brain regions implicated by previous work. The FEP group had thinner cortex in various frontal regions and fusiform, and reduced FA in inferior longitudinal fasciculus (ILF). In FEP, poorer functional capacity correlated with reduced superior frontal volume and lower FA in left ILF. Importantly, frontal brain volumes and integrity of the ILF were identified as the structural correlates of functional capacity in FEP, controlling for other relevant factors. These findings enhance mechanistic understanding of functional capacity deficits in schizophrenia by specifying the underlying neural correlates. In future, this could help inform intervention strategies.
Synthetic Biology-derived triterpenes as efficacious immunomodulating adjuvants
Authors: Tateno Mizuki , Stone Barbara J. , Srodulski Sarah J. , Reedy Stephanie , Gawriluk Thomas R. , Chambers Thomas M. , Woodward Jerold , Chappell Joe , Kempinski Chase F. 
Published: October 2020

AbstractThe triterpene oil squalene is an essential component of nanoemulsion vaccine adjuvants. It is most notably in the MF59 adjuvant, a component in some seasonal influenza vaccines, in stockpiled, emulsion-based adjuvanted pandemic influenza vaccines, and with demonstrated efficacy for vaccines to other pandemic viruses, such as SARS-CoV-2. Squalene has historically been harvested from shark liver oil, which is undesirable for a variety of reasons. In this study, we have demonstrated the use of a Synthetic Biology (yeast) production platform to generate squalene and novel triterpene oils, all of which are equally as efficacious as vaccine adjuvants based on physiochemical properties and immunomodulating activities in a mouse model. These Synthetic Biology adjuvants also elicited similar IgG1, IgG2a, and total IgG levels compared to marine and commercial controls when formulated with common quadrivalent influenza antigens. Injection site morphology and serum cytokine levels did not suggest any reactogenic effects of the yeast-derived squalene or novel triterpenes, suggesting their safety in adjuvant formulations. These results support the advantages of yeast produced triterpene oils to include completely controlled growth conditions, just-in-time and scalable production, and the capacity to produce novel triterpenes beyond squalene.
Interleukin-26 activates macrophages and facilitates killing of Mycobacterium tuberculosis
Authors: Hawerkamp Heike C. , van Geelen Lasse , Korte Jan , Di Domizio Jeremy , Swidergall Marc , Momin Afaque A. , Guzmán-Vega Francisco J. , Arold Stefan T. , Ernst Joachim , Gilliet Michel , Kalscheuer Rainer , Homey Bernhard , Meller Stephan 
Published: October 2020

AbstractTuberculosis-causingMycobacterium tuberculosis(Mtb) is transmitted via airborne droplets followed by a primary infection of macrophages and dendritic cells. During the activation of host defence mechanisms also neutrophils and T helper 1 (TH1) and TH17 cells are recruited to the site of infection. The TH17 cell-derived interleukin (IL)-17 in turn induces the cathelicidin LL37 which shows direct antimycobacterial effects. Here, we investigated the role of IL-26, a TH1- and TH17-associated cytokine that exhibits antimicrobial activity. We found that both IL-26 mRNA and protein are strongly increased in tuberculous lymph nodes. Furthermore, IL-26 is able to directly kill Mtb and decrease the infection rate in macrophages. Binding of IL-26 to lipoarabinomannan might be one important mechanism in extracellular killing of Mtb. Macrophages and dendritic cells respond to IL-26 with secretion of tumor necrosis factor (TNF)-α and chemokines such as CCL20, CXCL2 and CXCL8. In dendritic cells but not in macrophages cytokine induction by IL-26 is partly mediated via Toll like receptor (TLR) 2. Taken together, IL-26 strengthens the defense against Mtb in two ways: firstly, directly due to its antimycobacterial properties and secondly indirectly by activating innate immune mechanisms.
Integrative transcriptomic analysis for linking acute stress responses to squamous cell carcinoma development
Authors: Nguyen Tran N. , Rajapakshe Kimal , Nicholas Courtney , Tordesillas Leticia , Ehli Erik A. , Davis Christel M. , Coarfa Cristian , Flores Elsa R. , Dickinson Sally E. , Curiel-Lewandrowski Clara , Tsai Kenneth Y. 
Published: October 2020

AbstractCutaneous squamous cell carcinoma (cuSCC) is the second most common skin cancer and commonly arises in chronically UV-exposed skin or chronic wounds. Since UV exposure and chronic wounds are the two most prominent environmental factors that lead to cuSCC initiation, we undertook this study to test whether more acute molecular responses to UV and wounding overlapped with molecular signatures of cuSCC. We reasoned that transcriptional signatures in common between acutely UV-exposed skin, wounded skin, and cuSCC tumors, might enable us to identify important pathways contributing to cuSCC. We performed transcriptomic analysis on acutely UV-exposed human skin and integrated those findings with datasets from wounded skin and our transcriptomic data on cuSCC using functional pair analysis, GSEA, and pathway analysis. Integrated analyses revealed significant overlap between these three datasets, thus highlighting deep molecular similarities these biological processes, and we identified Oncostatin M (OSM) as a potential common upstream driver. Expression of OSM and its downstream targets correlated with poorer overall survival in head and neck SCC patients. In vitro, OSM promoted invasiveness of keratinocytes and cuSCC cells and suppressed apoptosis of irradiated keratinocytes. Together, these results support the concept of using an integrated, biologically-informed approach to identify potential promoters of tumorigenesis.
Bundle analytics, a computational framework for investigating the shapes and profiles of brain pathways across populations
Authors: Chandio Bramsh Qamar , Risacher Shannon Leigh , Pestilli Franco , Bullock Daniel , Yeh Fang-Cheng , Koudoro Serge , Rokem Ariel , Harezlak Jaroslaw , Garyfallidis Eleftherios 
Published: October 2020

AbstractTractography has created new horizons for researchers to study brain connectivity in vivo. However, tractography is an advanced and challenging method that has not been used so far for medical data analysis at a large scale in comparison to other traditional brain imaging methods. This work allows tractography to be used for large scale and high-quality medical analytics. BUndle ANalytics (BUAN) is a fast, robust, and flexible computational framework for real-world tractometric studies. BUAN combines tractography and anatomical information to analyze the challenging datasets and identifies significant group differences in specific locations of the white matter bundles. Additionally, BUAN takes the shape of the bundles into consideration for the analysis. BUAN compares the shapes of the bundles using a metric called bundle adjacency which calculates shape similarity between two given bundles. BUAN builds networks of bundle shape similarities that can be paramount for automating quality control. BUAN is freely available in DIPY. Results are presented using publicly available Parkinson’s Progression Markers Initiative data.
5,7,3ʹ,4ʹ-Tetrahydroxyflav-2-en-3-ol 3-O-glucoside, a new biosynthetic precursor of cyanidin 3-O-glucoside in the seed coat of black soybean, Glycine max
Authors: Yoshida Kumi , Teppabut Yada , Sawaguchi Reo , Nakane Yuhsuke , Hayashi Emi , Oyama Kin-ichi , Nishizaki Yuzo , Goda Yukihiro , Kondo Tadao 
Published: October 2020

AbstractThe seed coat of mature black soybean, Glycine max, accumulates a high amount of cyanidin 3-O-glucoside (Cy3G), which is the most abundant anthocyanin in nature. In the pod, it takes two months for the seed coat color change from green to black. However, immature green beans rapidly adopt a black color within one day when the shell is removed. We analyzed the components involved in the color change of the seed coat and detected a new precursor of Cy3G, namely 5,7,3ʹ,4ʹ-tetrahydroxyflav-2-en-3-ol 3-O-glucoside (2F3G). Through quantitative analysis using purified and synthetic standard compounds, it was clarified that during this rapid color change, an increase in the Cy3G content was observed along with the corresponding decrease in the 2F3G content. Chemical conversion from 2F3G to Cy3G at pH 5 with air and ferrous ion was observed. Our findings allowed us to propose a new biosynthetic pathway of Cy3G via a colorless glucosylated compound, 2F3G, which was oxidized to give Cy3G.
Self-limiting electrospray deposition on polymer templates
Authors: Lei Lin , Gamboa Arielle R. , Kuznetsova Christianna , Littlecreek Sunshine , Wang Jingren , Zou Qingze , Zahn Jeffrey D. , Singer Jonathan P. 
Published: October 2020

AbstractElectrospray deposition (ESD) applies a high voltage to liquids flowing through narrow capillaries to produce monodisperse generations of droplets down to hundreds of nanometers in diameter, each carrying a small amount of the delivered solute. This deposition method has been combined with insulated stencil masks for fabricating micropatterns by spraying solutions containing nanoparticles, polymers, or biomaterials. To optimize the fabrication process for micro-coatings, a self-limiting electrospray deposition (SLED) method has recently been developed. Here, we combine SLED with a pre-existing patterned polymer film to study SLED’s fundamental behavior in a bilayer geometry. SLED has been observed when glassy insulating materials are sprayed onto conductive substrates, where a thickness-limited film forms as charge accumulates and repels the arrival of additional charged droplets. In this study, polystyrene (PS), Parylene C, and SU-8 thin films of varying thickness on silicon are utilized as insulated spraying substrates. Polyvinylpyrrolidone (PVP), a thermoplastic polymer is sprayed below its glass transition temperature (Tg) to investigate the SLED behavior on the pre-deposited insulating films. Furthermore, to examine the effects of in-plane confinement on the spray, a microhole array patterned onto the PS thin film by laser dewetting was sprayed with dyed PVP in the SLED mode. This was then extended to an unmasked electrode array showing that masked SLED and laser dewetting could be used to target microscale regions of conventionally-patterned electronics.
Prostate cancer risk prediction using a polygenic risk score
Authors: Sipeky Csilla , Talala Kirsi M. , Tammela Teuvo L. J. , Taari Kimmo , Auvinen Anssi , Schleutker Johanna 
Published: October 2020

AbstractHereditary factors have a strong influence on prostate cancer (PC) risk and poorer outcomes, thus stratification by genetic factors addresses a critical need for targeted PC screening and risk-adapted follow-up. In this Finnish population-based retrospective study 2283 clinically diagnosed and 455 screen-detected patients from the Finnish Randomised Study of Screening for Prostate Cancer (FinRSPC), 2400 healthy individuals have been involved. Individual genetic risk through establishment of a polygenic risk score based on 55 PC risk SNPs identified through the Finnish subset of the Collaborative Oncological Gene-Environment Study was assessed. Men with PC had significantly higher median polygenic risk score compared to the controls (6.59 vs. 3.83, P < 0.0001). The polygenic risk score above the control median was a significant predictor of PC (OR 2.13, 95% CI 1.90–2.39). The polygenic risk score predicted the risk of PC with an AUC of 0.618 (95% CI 0.60–0.63). Men in the highest polygenic risk score quartile were 2.8—fold (95% CI 2.4–3.30) more likely to develop PC compared with men in the lowest quartile. In the FinRSPC cohort, a significantly higher percentage of men had a PSA level of ≥ 4 ng/mL in polygenic risk score quartile four compared to quartile one (18.7% vs 8.3%, P < 0.00001). Adding the PRS to a PSA-only model contributed additional information in predicting PC in the FinRSPC model. Results strongly suggest that use of the polygenic risk score would facilitate the identification of men at increased risk for PC.