Miracle-dz/UniFAR-FTUs huggingface dataset:
Seasonal regulation of petal number

Flowering time and floral architecture was examined in controlled environments (Environ). Flowering time was assessed by RLN (rosette leaf number), CLN (cauline leaf number), VIS (visible inflorescence meristem), BOLT (5cm stem bolt), ANTH (anthesis), and MAT (floral maturation interval) was calculated as the difference between ANTH and VIS. Petals and sepal trichomes were scored for the first 25 floral nodes. Pair-wise comparisons to control conditions (ND, 20 °C, WL) by Mann Whitney U-test. time and floral architecture following different of by and as the difference between ANTH and and for 25 nodes. Multiple comparisons by Kruskal-Wallis test with post hoc analysis using the Tukey Kramer
CLEP_A_259648 953..962

1Department of Clinical Epidemiology, Aarhus University Hospital, Aarhus, Denmark; 2Health Economics & Payer Evidence, AstraZeneca, Gothenburg, Sweden; 3Epidemiology, AstraZeneca, Cambridge, UK; 4Biometrics, AstraZeneca, Gothenburg, Sweden; 5Department of Renal Medicine, Aarhus University Hospital, Aarhus, Denmark; 6Department of Biomedicine, Aarhus University, Aarhus, Denmark Purpose: Anemia is prevalent in patients with chronic kidney disease (CKD), but the longitudinal risk of anemia in patients with newly identified CKD is unknown. We therefore examined the risks of experiencing anemia in persons with newly identified CKD. Patients and Methods: This cohort study included adult patients with newly identified CKD stages 3–5 defined by an estimated glomerular filtration rate (eGFR) level <60 mL/min/ 1.73m (at least two measurements ≥90 days apart) ascertained from a population-based registry with complete laboratory test results in Northern Denmark (population ~2.2 million) during 2009–2016. We calculated 1) cumulative incidence (risk) of anemia [hemoglobin <12/ <13 g/dl in women/men] by CKD stage, and 2) adjusted hazard ratios (HRs) of anemia using Cox regression analyses. Results: We identified 55,940 distinct individuals with newly identified CKD stages 3–5 and no prevalent anemia [n=41,958 patients in stage 3a, n=17,875 in stage 3b, n=5182 in stage 4, and n=931 in stage 5]. After one year, 42.3% (95%-confidence interval [CI]: 41.9–42.7) of patients with CKD stages 3–5 had newly measured anemia, increasing to 67.7% (95%-CI: 67.2–68.2) after five years. The absolute and relative anemia risk increased markedly with higher CKD stages. The adjusted HR of any anemia was 5.42 (95%-CI: 5.09–5.77) in patients with CKD stage 5 compared to patients with CKD stage 3a. Conclusion: Patients with newly identified CKD stages 3–5 have a substantial risk of anemia, increasing with higher CKD stages. This study underlines that clinical awareness of anemia risk is important in patients with newly identified or progressed CKD.
INCREASED CHEMICAL ACETYLATION OF PEPTIDES AND PROTEINS 1 AFTER DAILY INGESTION OF DIACETYL ANALYZED BY NANO-LC- 2 MS/MS (Q-TOF) 3

24 Background: Acetylation alters several protein properties including molecular weight, 25 stability, enzymatic activity, protein-protein interactions, and other biological functions. 26 Our previous findings demonstrating that diacetyl/peroxynitrite can acetylate L-lysine, 27 L-histidine, and albumin in vitro led us to investigate whether diacetyl-treated rats 28 suffer protein acetylation as well. 29 Methods: Wistar rats were administered diacetyl daily for 4 weeks, after which they 30 were sacrificed, and their lung proteins were extracted to be analysed by Nano-LC- 31 MS/MS (Q-TOF). A C18 reversed-phase column and gradient elution with formic 32 acid/acetonitrile solutions from 2 to 50% over 150 min were used to separate the 33 proteins. Protein detection was performed using a microTOF-Q II (QTOF) equipped 34 with captive source and an electrospray-ionization source. The data from mass 35 spectrometry were processed using a Compass 1.7 and analyzed using Protein Scape, 36 software that uses Mascot algorithms to perform protein searches. 37 Results: A set of 3162 acetylated peptides derived from 351 acetylated proteins in the 38 diacetyl-treated group was identified. Among them, 23 targeted proteins were 39 significantly more acetylated in the diacetyl-treated group than in the PBS control. 40 Protein acetylation of the group treated with 540 mg/kg/day of diacetyl was 41 corroborated by Western blotting analysis. 42 Conclusions: These data support our hypothesis that diacetyl exposure in animals may 43 lead to the generation of acetyl radicals, compounds that attach to proteins, affecting 44 their functions and triggering adverse health problems. 45
Pseudorabies Virus EP0 Antagonizes the Type I Interferon Response via Inhibiting IRF9 Transcription

Alphaherpesviruses can establish lifelong infections and cause many diseases in humans and animals. Pseudorabies virus (PRV) is a swine alphaherpesvirus that threatens pig production. ABSTRACT The alphaherpesvirus pseudorabies virus (PRV) is the etiologic agent of swine Aujeszky’s disease, which can cause huge economic losses to the pig industry. PRV can overcome a type I interferon (IFN)-induced antiviral state in host cells through its encoded EP0 protein. However, the exact role of EP0 in this process is poorly defined. Here, we report that EP0 transcriptionally represses IFN regulatory factor 9 (IRF9), a critical component in the IFN signaling pathway, thereby reducing the cellular levels of IRF9 and inhibiting IFN-induced gene transcription. This activity of EP0 is mediated by its C-terminal region independently of the RING domain. Moreover, compared with EP0 wild-type PRV, EP0-deficient PRV loses the ability to efficiently decrease cellular IRF9, while reintroducing the C-terminal region of EP0 back into the EP0-deficient virus restores the activity. Together, these results suggest that EP0 can transcriptionally modulate IRF9-mediated antiviral pathways through its C-terminal region, contributing to PRV innate immune evasion. IMPORTANCE Alphaherpesviruses can establish lifelong infections and cause many diseases in humans and animals. Pseudorabies virus (PRV) is a swine alphaherpesvirus that threatens pig production. Using PRV as a model, we found that alphaherpesvirus can utilize its encoded early protein EP0 to inhibit the IFN-induced upregulation of antiviral proteins by reducing the basal expression levels of IRF9 through repressing its transcription. Our findings reveal a mechanism employed by alphaherpesvirus to evade the immune response and indicate that EP0 is an important viral protein in pathogenesis and a potential target for antiviral drug development.
Antibiotic Exposure Leads to Reduced Phage Susceptibility in Vancomycin Intermediate Staphylococcus aureus (VISA)

In the time of antimicrobial resistance, phage therapy is frequently suggested as a possible solution for such difficult-to-treat infections. Vancomycin-intermediate Staphylococcus aureus (VISA) remains a relatively rare yet increasing occurrence in the clinic for which phage therapy may be an option. ABSTRACT In the time of antimicrobial resistance, phage therapy is frequently suggested as a possible solution for such difficult-to-treat infections. Vancomycin-intermediate Staphylococcus aureus (VISA) remains a relatively rare yet increasing occurrence in the clinic for which phage therapy may be an option. However, the data presented herein suggest a potential cross-resistance mechanism to phage following vancomycin exposure in VISA strains. When comparing genetically similar strains differing in their susceptibility to vancomycin, those with intermediate levels of vancomycin resistance displayed decreased sensitivity to phage in solid and liquid assays. Serial passaging with vancomycin induced both reduced vancomycin susceptibility and phage sensitivity. As a consequence, the process of phage infection was shown to be interrupted after DNA ejection from adsorbed phage but prior to phage DNA replication, as demonstrated through adsorption assays, lysostaphin sensitivity assays, electron microscopy, and quantitative PCR (qPCR). At a time when phage products are being used for experimental treatments and tested in clinical trials, it is important to understand possible interference between mechanisms underlying antibiotic and phage resistance in order to design effective therapeutic regimens.
Microorganisms Accelerate REE Mineralization in Supergene Environments

Understanding the role of microorganisms in the formation of regolith-hosted rare earth element (REE) deposits is beneficial for improving the metallogenic theory and deposit exploitation, given that such deposits absolutely exist in subtropical regions with strong microbial activities. Little is known of the microbial community composition and its contribution to REE mineralization in this kind of deposit. ABSTRACT Exogenic deposits are an important source of rare earth elements (REEs), especially heavy REEs (HREEs). It is generally accepted that microorganisms are able to dissolve minerals and mobilize elements in supergene environments. However, little is known about the roles of microorganisms in the formation of exogenic deposits such as regolith-hosted REE deposits that are of HREE enrichment and provide over 90% of global HREE demand. In this study, we characterized the microbial community composition and diversity along a complete weathering profile drilled from a regolith-hosted REE deposit in Southeastern China and report the striking contributions of microorganisms to the enrichment of REEs and fractionation between HREEs and light REEs (LREEs). Our results provide evidence that the variations in REE contents are correlated with microbial community along the profile. Both fungi and bacteria contributed to the accumulation of REEs, whereas bacteria played a key role in the fractionation between HREEs and LREEs. Taking advantage of bacteria strains isolated from the profile, Gram-positive bacteria affiliated with Bacillus and Micrococcus preferentially adsorbed HREEs, and teichoic acids in the cell wall served as the main sites for HREE adsorption, leading to an enrichment of HREEs in the deposit. The present study provides the first database of microbial community in regolith-hosted REE deposits. These findings not only elucidate the crucial contribution of fungi and bacteria in the supergene REE mineralization but also provide insights into efficient utilization of mineral resources via a biological pathway. IMPORTANCE Understanding the role of microorganisms in the formation of regolith-hosted rare earth element (REE) deposits is beneficial for improving the metallogenic theory and deposit exploitation, given that such deposits absolutely exist in subtropical regions with strong microbial activities. Little is known of the microbial community composition and its contribution to REE mineralization in this kind of deposit. Using a combination of high-throughput sequencing, batch adsorption experiments, and spectroscopic characterization, the functional microorganisms contributing to REE enrichment and fractionation are disclosed. For bacteria, the surface carboxyl and phosphate groups are active sites for REE adsorption, while teichoic acids in the cell walls of G+ bacteria lead to REE fractionation. The above-mentioned findings not only unravel the importance of microorganisms in the formation of supergene REE deposits but also provide experimental evidence for the bioutilization of REE resources.
Development of a sinusoidal pseudochirp material measure for the characterization of optical surface topography measuring instruments

Optical surface topography measuring instruments are used more and more widely for surface quality control in industry by enabling fast, areal and non-destructive surface topography measurements. However, due to the complexity of the interaction between the surface properties to be measured and the measuring system, their capability to accurately reproduce topographical features of a surface under test is quite often questionable. To understand and investigate the topographic measurement accuracy of different optical surface topography measuring instruments, a physical measurement standard has been developed at PTB which is intended to be used to determine the metrological characteristics of surface topography measuring instruments such as topographic spatial resolution and topography fidelity. The physical standard, fabricated by a diamond turning process, containing nine sinusoidal structures with different amplitudes from 50 nm to 10 μm and varying spatial wavelengths from 2.6 μm to 82.8 μm, is suitable for the characterization of optical instruments with different magnification and numerical apertures. The design of the chirp structures, including the wavelength series, the smallest wavelength for different amplitudes, the slope distribution and the layout are detailed in this paper. The tool path for accurately positioning the cutting tool in fabrication is also described. First measurement results of the instruments response in terms of the features’ aspect ratio, slopes and curvatures, the homogeneity of the field of view of a confocal microscope are presented.
MASTIFF: structure-aware minimum spanning tree/forest

The Minimum Spanning Forest (MSF) problem finds usage in many different applications. While theoretical analysis shows that linear-time solutions exist, in practice, parallel MSF algorithms remain computationally demanding due to the continuously increasing size of data sets. In this paper, we study the MSF algorithm from the perspective of graph structure and investigate the implications of the power-law degree distribution of real-world graphs on this algorithm. We introduce the MASTIFF algorithm as a structure-aware MSF algorithm that optimizes work efficiency by (1) dynamically tracking the largest forest component of each graph component and exempting them from processing, and (2) by avoiding topology-related operations such as relabeling and merging neighbour lists. The evaluations on 2 different processor architectures with up to 128 cores and on graphs of up to 124 billion edges, shows that Mastiff is 3.4--5.9X faster than previous works.
Robust android malware detection based on subgraph network and denoising GCN network

This paper proposes an Android malware detection model based on Android Function Call Graph (FCG) and Denoising Graph Convolutional Neural Network. This study proposes a method to simplify the FCG to reduce its size, and a new method to construct vertex feature vectors. The model uses the subgraph network to detect the underlying structural features of the FCG and discover the confusion attack. A denoising graph neural network is applied to graph convolution to reduce the impact of obfuscation attacks.
On utilizing smartphone cameras to detect counterfeit liquid food products

Counterfeit liquid food products, including olive oil, honey and alcohol, are continuing to pose severe threats to the general public as counterfeiters adulterate the authentic content with cheaper and potentially harmful substitutes, and package them in authentic bottles. Existing solutions are often impractical for the general public as they require specialized and costly equipment as well as taking liquid samples. We overcome these limitations by proposing LiquidHash, a novel detection system that only requires the use of a commodity smartphone to detect adulterated liquid products without opening the bottles. LiquidHash leverages computer vision and machine learning techniques to extract characteristics of air bubbles formed by flipping a bottle. We implement LiquidHash and evaluate its feasibility with real-world experiments and achieve an overall detection accuracy of up to 95%.
MagEar: eavesdropping via audio recovery using magnetic side channel

Speakers have been widely embedded in various electronic devices as a standard configuration. The security vulnerability of microspeakers (such as earphones) is commonly overlooked because it is often assumed that soundproof boundaries, such as walls, can prevent privacy-infringing sound leakage. In this paper, we present the prototype MagEar, an eavesdropping system that leverages magnetic side-channel signals leaked by a microspeaker to recover intelligible human speech. MagEar has sufficiently high sensitivity to detect magnetic fields on the order of nanotesla, exceeding some high-precision magnetometers. It can recover high-quality audio with 90% similarity to the original audio even at a distance of 60 cm. In addition, the MagEar prototype is portable and can be hidden in a headset shell. We have implemented MagEar as a proof-of-concept system and conducted several case studies of eavesdropping on different types of speaker-embedded devices, including earphones, and we have demonstrated the ability to successfully transcribe the recovered speech using automatic speech recognition techniques even when blocked by soundproof walls. We hope that our work can push manufacturers to rethink this security vulnerability of speakers.
TransFi: emulating custom wireless physical layer from commodity wifi

New wireless physical-layer designs are the key to improving wireless network performance. Adopting these new designs, however, requires modifications on wireless hardware and is difficult on commodity devices. In this paper, we show that this hardware modification in many cases can be avoided by TransFi, a new software technique that enables custom wireless PHY functionality on commodity WiFi transmitters via fine-grained emulation. Our basic insight is that many custom wireless signals can be emulated by manipulating the MAC payloads of WiFi MIMO streams and mixing the transmitted signals from these streams on the air. To perform such emulation, TransFi considers the target signal as a mixture of QAM constellation points on the complex plane, and reversely computes the MAC payload of each MIMO stream from one selected QAM constellation point. We implemented TransFi on commodity WiFi devices to emulate three custom wireless PHYs with diverse characteristics. Experiment results show that TransFi's accuracy of emulation is >90% when transmitting emulated data payloads at 11.4 Mbps (46x faster than existing methods), and the decoding error at this data rate is <1% (10x lower than existing methods).
Underwater messaging using mobile devices

Since its inception, underwater digital acoustic communication has required custom hardware that neither has the economies of scale nor is pervasive. We present the first acoustic system that brings underwater messaging capabilities to existing mobile devices like smartphones and smart watches. Our software-only solution leverages audio sensors, i.e., microphones and speakers, ubiquitous in today's devices to enable acoustic underwater communication between mobile devices. To achieve this, we design a communication system that in real-time adapts to differences in frequency responses across mobile devices, changes in multipath and noise levels at different locations and dynamic channel changes due to mobility. We evaluate our system in six different real-world underwater environments with depths of 2--15 m in the presence of boats, ships and people fishing and kayaking. Our results show that our system can in real-time adapt its frequency band and achieve bit rates of 100 bps to 1.8 kbps and a range of 30 m. By using a lower bit rate of 10--20 bps, we can further increase the range to 100 m. As smartphones and watches are increasingly being used in underwater scenarios, our software-based approach has the potential to make underwater messaging capabilities widely available to anyone with a mobile device. Project page with open-source code and data can be found here: https://underwatermessaging.cs. washington.edu/
Indoor navigation for visually impaired people with vertex colored graphs

Visually impaired people face many daily encumbrances. Traditional visual enhancements do not suffice to navigate indoor environments. In this paper, we explore path finding algorithms such as Dijkstra and A* combined with graph coloring to find a safest and shortest path for visual impaired people to navigate indoors. Our mobile application is based on a database which stores the locations of several spots in the building and their corresponding label. Visual impaired people select the start and destination when they want to find their way, and our mobile application will show the appropriate path which guarantees their safety.
Cloak: tolerating non-volatile cache read latency

The increased memory demands of workloads are putting high pressure on Last Level Caches (LLCs). In general, there is limited opportunity to increase the capacity of LLCs due to the area and power requirements of the underlying SRAM technology. Interestingly, emerging Non-Volatile Memory (NVM) technologies promise a feasible alternative to SRAM for LLCs due to their higher area density. However, NVMs have substantially higher read and write latencies, which offset their density benefit. Although researchers have proposed methods to tolerate NVM's higher write latency, little emphasis has been placed on the critical NVM read latency. To address this problem, this paper proposes Cloak. Cloak exploits page-level data reuse in the LLC, to hide NVM read latency. Specifically, on certain L1 DTLB misses, Cloak transfers LLC-resident data belonging to the TLB-missing page from the LLC NVM array to a set of small SRAM Page Buffers that will service subsequent requests to this page. Further, to enable the high-bandwidth, low-latency transfer of lines of a page to the page buffers, Cloak uses an LLC layout that accelerates the discovery of LLC-resident cache lines from the page. We evaluate Cloak with full-system simulations of a 4-core processor across 14 workloads. We find that, on average, a machine with Cloak is faster than one with an SRAM LLC by 23.8% and one with an NVM-only LLC by 8.9%---in both cases, with negligible change in area. Further, Cloak reduces the ED2 metric relative to these designs by 39.9% and 17.5%, respectively.
MetaSight: localizing blocked RFID objects by modulating NLOS signals via metasurfaces

It remains a challenging issue to localize blocked RFID objects. Existing solutions rely on non-line-of-sight (NLOS) signals reflected from environments, which are not reliable and cannot be accurately measured. To eliminate such limitations, this paper develops a new approach (called MetaSight) that localizes blocked objects by modulating NLOS signals via metasurfaces. More specifically, a programmable metasurface is designed such that each reflecting element can dynamically change frequencies and phases of reflected signals. With proper setting of frequencies and phases within a certain range of reflecting elements (i.e., the reflecting window) by a reflection beamforming algorithm, a unique NLOS signal path (called metasurface path or MS path) is established between an object and its reader. By shifting the reflecting window in time domain, multiple MS paths and the corresponding channel coefficients can be obtained sequentially. To make the sequential process fast, both the preamble and the payload of a frame are utilized for channel estimation. Based on the estimated channel coefficients of multiple MS paths, the 3D direction of the object viewed from the metasurface is derived through a 3D direction estimation algorithm. By consolidating the 3D directions from two separate metasurfaces, the object's 3D location is finally determined. MetaSight is implemented as a prototype system. Extensive experiments show that MetaSight can localize a blocked object with an average accuracy of 15 cm.