Miracle-dz/UniFAR-FTUs huggingface dataset:
Deacetylation of NAT10 by Sirt1 promotes the transition from rRNA biogenesis to autophagy upon energy stress

Abstract Anabolism and catabolism are tightly regulated according to the cellular energy supply. Upon energy stress, ribosomal RNA (rRNA) biogenesis is inhibited, and autophagy is induced. However, the mechanism linking rRNA biogenesis and autophagy is unclear. Here, we demonstrate that the nucleolar protein NAT10 plays a role in the transition between rRNA biogenesis and autophagy. Under normal conditions, NAT10 is acetylated to activate rRNA biogenesis and inhibit autophagy induction. Mechanistic studies demonstrate that NAT10 binds to and acetylates the autophagy regulator Che-1 at K228 to suppress the Che-1-mediated transcriptional activation of downstream genes Redd1 and Deptor under adequate energy supply conditions. Upon energy stress, NAT10 is deacetylated by Sirt1, leading to suppression of NAT10-activated rRNA biogenesis. In addition, deacetylation of NAT10 abolishes the NAT10-mediated transcriptional repression of Che-1, leading to the release of autophagy inhibition. Collectively, we demonstrate that the acetylation status of NAT10 is important for the anabolism-catabolism transition in response to energy stress, providing a novel mechanism by which nucleolar proteins control rRNA synthesis and autophagy in response to the cellular energy supply.
A reassessment of the vitamin D requirements of modern broiler genotypes

&NA; We hypothesized that performance and bone mineralization of 2 broiler lines will benefit from increasing vitamin D (vitD) supplementation above current commercial levels and by partial substitution of D3 by 25‐OH‐D3. Male Ross 308 and 708 chicks (n = 576), were offered diets with low (LD; 1,000), medium (MD; 4,000) or high levels of D3 (HD; 7,000 IU/kg), and medium levels of vitD where the majority of D3 was substituted by 25‐OH‐D3 (25MD; 1,000 D3+3,000 25‐OH‐D3 IU/kg). Performance was measured at the end of starter (day 10), grower (day 24), and finisher periods (day 38). Three birds per pen were dissected at the end of each period to assess tibia and femur ash percentage (%), ash weight, bone breaking strength (BBS), and serum levels of 25‐OH‐D3. Remaining birds were gait scored (GS) at day 37 of age. Genotype and diet did not interact for any trait, whilst performance was not affected by diet. Ross 708 had lower body weight (P < 0.005), higher feed conversion ratio over the grower period (P < 0.05), similar levels of 25‐OH‐D3, but higher GS (P < 0.05) than Ross 308. Serum 25‐OH‐D3 levels were affected by diet at the end of the starter and grower periods (P < 0.05), being lowest for LD and highest for 25MD. Diet affected GS (P < 0.01), being higher in LD than 25MD. Femur ash % was higher at the end of the starter and grower periods for 25MD than LD and for both HD and 25MD than LD (P < 0.05). Femur and tibia ash weight were higher for 25MD in comparison to LD birds (P < 0.05) at the end of the grower period. Femur and tibia BBS were higher (P < 0.05) for 25MD in comparison to LD at the end of the grower and finisher periods, respectively. Overall, effects of vitD supply were more pronounced for femur than for tibia mineralization. Results do not suggest supplementation of vitD above current maximum levels and support partial substitution by 25‐OH‐D3.
Contribution of Glottal Waveform in Speech Emotion: A Comparative Pairwise Investigation

In this work, we investigated the contribution of the glottal waveform in human vocal emotion expressing. Seven emotional states including moderate and intense versions of three emotional families as anger, joy, and sadness, plus a neutral state are considered, with speech samples in Mandarin Chinese. The glottal waveform extracted from speech samples of different emotion states are first analyzed in both time domain and frequency domain to discover their differences. Comparative emotion classifications are then taken out based on features extracted from two sources: original whole speech signal, or only glottal wave signal. Two sets of experiments are performed, as the generation of a performance-driven hierarchical classifier architecture, and pairwise classification on individual emotional states. The low difference between accuracies obtained from the two sources proved that a majority of emotional cues in speech could be conveyed through glottal waveform. The best distinguishable emotional pair by glottal waveform is intense anger against moderate sadness, with the accuracy up to 92.45%. It is also concluded in this work that glottal waveform represent better valence cues than arousal cues of emotion.
Glucose Controls the Expression of Polypyrimidine Tract-Binding Protein 1 via the Insulin Receptor Signaling Pathway in Pancreatic β Cells

In pancreatic β cells, glucose stimulates the biosynthesis of insulin at transcriptional and post-transcriptional levels. The RNA-binding protein, polypyrimidine tract-binding protein 1 (PTBP1), also named hnRNP I, acts as a critical mediator of insulin biosynthesis through binding to the pyrimidine-rich region in the 3’-untranslated region (UTR) of insulin mRNA. However, the underlying mechanism that regulates its expression in β cells is unclear. Here, we report that glucose induces the expression of PTBP1 via the insulin receptor (IR) signaling pathway in β cells. PTBP1 is present in β cells of both mouse and monkey, where its levels are increased by glucose and insulin, but not by insulin-like growth factor 1. PTBP1 levels in immortalized β cells established from wild-type (βIRWT) mice are higher than levels in β cells established from IR-null (βIRKO) mice, and ectopic re-expression of IR-WT in βIRKO cells restored PTBP1 levels. However, PTBP1 levels were not altered in βIRKO cells transfected with IR-3YA, in which the Tyr1158/1162/1163 residues are substituted with Ala. Consistently, treatment with glucose or insulin elevated PTBP1 levels in βIRWT cells, but not in βIRKO cells. In addition, silencing Akt significantly lowered PTBP1 levels. Thus, our results identify insulin as a pivotal mediator of glucose-induced PTBP1 expression in pancreatic β cells.
Children Prenatally Believed to have Isolated Mild Ventriculomegaly Short title: Isolated mild ventriculomegaly

Citation for pulished version (APA): Thorup, E. , Jensen, L. N. , Bak, G. S. , Ekelund, C. K. , Greisen, G. , Jørgensen, D. S. , Hellmuth, S. G. , Wulff, C. , Petersen, O. B. , Pedersen, L. H. , & Tabor, A. (2019). Neurodevelopmental disorder in children believed to have isolated mild ventriculomegaly prenatally. Ultrasound in obstetrics & gynecology : the official journal of the International Society of Ultrasound in Obstetrics and Gynecology, 54(2), 182-189. https://doi.org/10.1002/uog.20111
Competitive Data Trading in Wireless-Powered Internet of Things (IoT) Crowdsensing Systems with Blockchain

With the explosive growth of smart IoT devices at the edge of the Internet, embedding sensors on mobile devices for massive data collection and collective environment sensing has been envisioned as a cost-effective solution for IoT applications. However, existing IoT platforms and framework rely on dedicated middleware for (semi-) centralized task dispatching, data storage and incentive provision. Consequently, they are usually expensive to deploy, have limited adaptability to diverse requirements, and face a series of data security and privacy issues. In this paper, we employ permissionless blockchains to construct a purely decentralized platform for data storage and trading in a wireless-powered IoT crowdsensing system. In the system, IoT sensors use the power wirelessly transferred from RF-energy beacons for data sensing and transmission to an access point. The data is then forwarded to the blockchain for distributed ledger services, i.e., data/transaction verification, recording, and maintenance. Due to the coupled interference of wireless transmission and the transaction fee incurred by the blockchain’s distributed ledger services, rational sensors have to decide on their transmission rates to maximize their individual payoff. Thus, we formulate a noncooperative game model to analyze this competitive situation among the sensors. We provide the analytical condition for the existence of the Nash equilibria as well as a series of insightful numerical results about the equilibrium strategies in the game.
Phylogenomics Reveal the Dynamic Evolution of Fungal Nitric Oxide Reductases and Their Relationship to Secondary Metabolism

Abstract Fungi expressing P450nor, an unconventional nitric oxide (NO) reducing cytochrome P450, are considered significant contributors to environmental nitrous oxide (N2O) emissions. Despite extensive efforts, fungal contributions to N2O emissions remain uncertain. For example, the majority of N2O emitted from antibiotic-amended soil microcosms is attributed to fungal activity, yet axenic fungal cultures do not couple N-oxyanion respiration to growth and these fungi produce only minor quantities of N2O. To assist in reconciling these conflicting observations and produce a benchmark genomic analysis of fungal denitrifiers, genes underlying denitrification were examined in >700 fungal genomes. Of 167 p450nor—containing genomes identified, 0, 30, and 48 also harbored the denitrification genes narG, napA, or nirK, respectively. Compared with napA and nirK, p450nor was twice as abundant and exhibited 2–5-fold more gene duplications, losses, and transfers, indicating a disconnect between p450nor presence and denitrification potential. Furthermore, cooccurrence of p450nor with genes encoding NO-detoxifying flavohemoglobins (Spearman r = 0.87, p = 1.6e−10) confounds hypotheses regarding P450nor’s primary role in NO detoxification. Instead, ancestral state reconstruction united P450nor with actinobacterial cytochrome P450s (CYP105) involved in secondary metabolism (SM) and 19 (11%) p450nor-containing genomic regions were predicted to be SM clusters. Another 40 (24%) genomes harbored genes nearby p450nor predicted to encode hallmark SM functions, providing additional contextual evidence linking p450nor to SM. These findings underscore the potential physiological implications of widespread p450nor gene transfer, support the undiscovered affiliation of p450nor with fungal SM, and challenge the hypothesis of p450nor’s primary role in denitrification.
The Distance Precision Matrix: computing networks from non-linear relationships

Motivation Full‐order partial correlation, a fundamental approach for network reconstruction, e.g. in the context of gene regulation, relies on the precision matrix (the inverse of the covariance matrix) as an indicator of which variables are directly associated. The precision matrix assumes Gaussian linear data and its entries are zero for pairs of variables that are independent given all other variables. However, there is still very little theory on network reconstruction under the assumption of non‐linear interactions among variables. Results We propose Distance Precision Matrix, a network reconstruction method aimed at both linear and non‐linear data. Like partial distance correlation, it builds on distance covariance, a measure of possibly non‐linear association, and on the idea of full‐order partial correlation, which allows to discard indirect associations. We provide evidence that the Distance Precision Matrix method can successfully compute networks from linear and non‐linear data, and consistently so across different datasets, even if sample size is low. The method is fast enough to compute networks on hundreds of nodes. Availability and implementation An R package DPM is available at https://github.molgen. mpg.de/ghanbari/DPM. Supplementary information Supplementary data are available at Bioinformatics online.
Leptin levels in obese women with and without type 2 diabetes mellitus.

INTRODUCTION: The role of leptin has been more clear in the endocrinology area after the discovery of its secretion from the adipose tissue. The aim of the study is to investigate the leptin levels in obese women in whom type 2 diabetes mellitus were present or absent. MATERIALS AND METHODS: Thirty-five obese women with type 2 diabetes mellitus (group 1) and 34 obese women without type 2 diabetes mellitus (group 2) were enrolled in the study. In both groups the body mass index (BMI), waist circumference, and waist-to-hip ratio were measured. Leptin, HbA1c, creatinine and the lipid profile were assessed. RESULTS: Leptin was found to be statistically significantly lower in group 1 than in group 2 (40.22 +/- 17.77 ng/ml versus 50.12 +/- 15.51 ng/ml, respectively; p = 0.019). It was well correlated with BMI in group 1 (r = 0.60, p = 0.0001). In group 1 also, correlation of leptin was moderate with creatinine and high-density lipoprotein-cholesterol (r = 0.36, p = 0.037 versus r = 0.37, p = 0.027, respectively), whereas triglyceride had a negative correlation (r = -0.34, p = 0.046). In group 2, the only significant correlation with leptin was BMI (r = 0.41, p = 0.02). Leptin was also significantly lower in 17 subjects with poorly controlled diabetes mellitus than in 18 well-controlled diabetics (33.54 +/- 15.82 ng/ml versus 44.61 +/- 17.54 ng/ml, respectively; p = 0.038). CONCLUSION: Since leptin is lower in obese women with diabetes than without diabetes and additionally it is even lower in the poorly controlled diabetes subgroup, we think that further studies a rerequired to make clear the issue for lower leptin levels, whether it is a reason or an outcome.
Alcohol Use and Risk Factors for Sexual Aggression: Differences According to Relationship Status

The present study examined the ways alcohol use and risk factors for sexual assault perpetration vary by relationship status. Participants included 242 college men (age = 18-22 years) from a northeastern university who identified as being single or in a casual or committed dating relationship with a female partner. ANCOVAs and paired t tests compared individuals who were single, casually dating, and in committed relationships on self-reported alcohol use during sexual situations, beliefs about sexual communication, behavior associated with sexual aggression, and peer approval of sexual aggression. Differences in alcohol use during sexual situations and behavior associated with sexual aggression according to relationship status emerged. Post hoc analyses examining whether alcohol use during sexual situations moderated significant associations between relationship status and behavior associated with sexual aggression suggested that men in committed relationships who endorsed more frequent alcohol use during sexual situations also endorsed more behavior associated with sexual aggression. Findings suggest that individuals in committed relationships who often use alcohol during sexual situations may be at increased risk of sexually aggressive behavior.
Shared Transcriptional Control and Disparate Gain and Loss of Aphid Parasitism Genes

Abstract Aphids are a diverse group of taxa that contain agronomically important species, which vary in their host range and ability to infest crop plants. The genome evolution underlying agriculturally important aphid traits is not well understood. We generated draft genome assemblies for two aphid species: Myzus cerasi (black cherry aphid) and the cereal specialist Rhopalosiphum padi. Using a de novo gene prediction pipeline on both these, and three additional aphid genome assemblies (Acyrthosiphon pisum, Diuraphis noxia, and Myzus persicae), we show that aphid genomes consistently encode similar gene numbers. We compare gene content, gene duplication, synteny, and putative effector repertoires between these five species to understand the genome evolution of globally important plant parasites. Aphid genomes show signs of relatively distant gene duplication, and substantial, relatively recent, gene birth. Putative effector repertoires, originating from duplicated and other loci, have an unusual genomic organization and evolutionary history. We identify a highly conserved effector pair that is tightly physically linked in the genomes of all aphid species tested. In R. padi, this effector pair is tightly transcriptionally linked and shares an unknown transcriptional control mechanism with a subset of ∼50 other putative effectors and secretory proteins. This study extends our current knowledge on the evolution of aphid genomes and reveals evidence for an as-of-yet unknown shared control mechanism, which underlies effector expression, and ultimately plant parasitism.
Tunable DNA Hybridization Enables Spatially and Temporally Controlled Surface-Anchoring of Biomolecular Cargo

The controlled immobilization of biomolecules onto surfaces is relevant in biosensing and cell biological research. Spatial control is achieved by surface-tethering molecules in micro- or nanoscale patterns. Yet, there is an increasing demand for temporal control over how long biomolecular cargo stays immobilized until released into the medium. Here, we present a DNA hybridization-based approach to reversibly anchor biomolecular cargo onto micropatterned surfaces. Cargo is linked to a DNA oligonucleotide that hybridizes to a sequence-complementary, surface-tethered strand. The cargo is released from the substrate by the addition of an oligonucleotide that disrupts the duplex interaction via toehold-mediated strand displacement. The unbound tether strand can be reloaded. The generic strategy is implemented with small-molecule or protein cargo, varying DNA sequences, and multiple surface patterning routes. The approach may be used as a tool in biological research to switch membrane proteins from a locally fixed to a free state, or in biosensing to shed biomolecular receptors to regenerate the sensor surface.
Reasonable two‐stage adaptive designs for single‐arm phase II clinical trials

In cancer phase II trials, determining the sample size of a single‐arm two‐stage design remains a challenge. To overcome this problem, Simon's two‐stage design was extended to an adaptive design: at the interim analysis, the total sample size can be set to either of the two preplanned values. However, without any restriction on design construction, an optimal or suboptimal design derived may have counter‐intuitive or unreasonable design features, which make the chosen design less persuasive and inefficient. Thus, we thoroughly examined how the expected, total, and maximum sample sizes of the optimal or suboptimal designs are affected by excluding the counter‐intuitive or unreasonable designs. We adopted the four optimality criteria: minimizing the expected sample size at the null hypothesis (O1), minimizing the maximum expected sample size over the hypotheses (O2), and minimizing the maximum sample sizes with additional adaption of either of the former two (O3 or O4, respectively). We found that focusing on reasonable design may drastically reduce the maximum sample size when the first optimality criterion is applied. Under the other optimality criteria, although the impact on optimality brought by our proposed strategy may be slight, exclusion of unreasonable design is still useful to reduce the candidate designs, which will considerably reduce the computational time for design search and can facilitate the design choice among optimal and suboptimal designs. We further discuss the utility of our proposal in an example of a real clinical trial and conclude the paper with general recommendations.
[Pattern electroretinogram and macular perfusion in glaucoma].

PURPOSE To study microcirculatory and functional changes in macula in patients with Primary Open-Angle Glaucoma (POAG). MATERIAL AND METHODS The study included 95 POAG patients and 42 healthy control subjects. Whole en face image vessel density (wiVDRetina) was measured both in fovea and in parafovea using OCT-angiography (OCT-A) by means of SD-OCT AngioVue on Avanti RtVue xR (Optovue Inc., U.S.A.). Macular thickness and parameters of macular ganglion cell complex (GCC) were measured on the same day. Blood flow in the retrobulbar vessels was evaluated by means of Color Doppler Imaging (CDI). Pattern electroretinogram (PERG) was also taken from the study eyes. Correlations between PERG, SD-OCT GCC, macular thickness, and the parameters of OCT-A and CDI were studied. RESULTS The amplitude of t-PERG P50 decreased from 6.1±1.3 µV in normal eyes to 2.8±1.6 µV (p<0.0001) in early glaucoma and to 2.3±1.5 µV (p=0.93) in advanced stages. Relative vessel density of the capillary bed decreased from 51.3±3.0% in normal eyes to 45.9±5.0% (p<0.001) and to 41.8±5.0% (p=0.023) in early and advanced glaucoma respectively. The parameters of OCT-A and CDI correlated with morphological and functional parameters in normal and early glaucomatous eyes. CONCLUSION The study revealed reduction of macular microcirculation and decrease of PERG in early glaucoma. Correlations between the circulatory parameters and functional changes were found in early stages of the disease.
CRL4AMBRA1 targets Elongin C for ubiquitination and degradation to modulate CRL5 signaling

Multi‐subunit cullin‐RING ligases (CRLs) are the largest family of ubiquitin E3 ligases in humans. CRL activity is tightly regulated to prevent unintended substrate degradation or autocatalytic degradation of CRL subunits. Using a proteomics strategy, we discovered that CRL4AMBRA1 (CRL substrate receptor denoted in superscript) targets Elongin C (ELOC), the essential adapter protein of CRL5 complexes, for polyubiquitination and degradation. We showed that the ubiquitin ligase function of CRL4AMBRA1 is required to disrupt the assembly and attenuate the ligase activity of human CRL5SOCS3 and HIV‐1 CRL5VIF complexes as AMBRA1 depletion leads to hyperactivation of both CRL5 complexes. Moreover, CRL4AMBRA1 modulates interleukin‐6/STAT3 signaling and HIV‐1 infectivity that are regulated by CRL5SOCS3 and CRL5VIF, respectively. Thus, by discovering a substrate of CRL4AMBRA1, ELOC, the shared adapter of CRL5 ubiquitin ligases, we uncovered a novel CRL cross‐regulation pathway.
Substrate Moisture Affects the Development of Megaselia scalaris (Diptera: Phoridae): An Implication of the Growth Circumstances of the Fly in Forensic Entomology

Abstract Megaselia scalaris (Loew) (Diptera: Phoridae) provides great evidential value in estimating the postmortem interval (PMI) compared with other dipterans due to its common occurrence on human corpses both indoors and in concealed environments. Studies have focused on the effect of temperature, larval diet, and photoperiod on the development of the species; however, knowledge of M. scalaris development at different moisture levels is insufficient. This study aimed to investigate the effects of substrate moisture on the larval development time, pupal recovery, pupal weight, adult emergence, and adult head width of M. scalaris. The larvae were reared in five replicates on substrates with six moisture levels ranging from 50 to 90%. Larvae and puparia were sampled daily, and the collection time, number, and weight were recorded, measured, and then compared using multivariate analysis of variance with a post hoc least significant difference test. Larvae developed most quickly (3.75 ± 0.04 d) at 50% substrate moisture; the larvae were able to survive in extremely wet substrates (90% moisture), but the development time was significantly longer (6.48 ± 0.19 d). Moisture greatly influenced the pupation rate and adult emergence but showed a weak effect on the pupae weight and adult head width. Due to the significance of moisture on the development of M. scalaris, PMI estimation using M. scalaris with cadavers of different moisture content must be carefully conducted to avoid inaccuracy.