Miracle-dz/UniFAR-FTUs huggingface dataset:
Dissecting the Genomic Diversification of Late Embryogenesis Abundant (LEA) Protein Gene Families in Plants

Abstract Late embryogenesis abundant (LEA) proteins include eight multigene families that are expressed in response to water loss during seed maturation and in vegetative tissues of desiccation tolerant species. To elucidate LEA proteins evolution and diversification, we performed a comprehensive synteny and phylogenetic analyses of the eight gene families across 60 complete plant genomes. Our integrated comparative genomic approach revealed that synteny conservation and diversification contributed to LEA family expansion and functional diversification in plants. We provide examples that: 1) the genomic diversification of the Dehydrin family contributed to differential evolution of amino acid sequences, protein biochemical properties, and gene expression patterns, and led to the appearance of a novel functional motif in angiosperms; 2) ancient genomic diversification contributed to the evolution of distinct intrinsically disordered regions of LEA_1 proteins; 3) recurrent tandem-duplications contributed to the large expansion of LEA_2; and 4) dynamic synteny diversification played a role on the evolution of LEA_4 and its function on plant desiccation tolerance. Taken together, these results show that multiple evolutionary mechanisms have not only led to genomic diversification but also to structural and functional plasticity among LEA proteins which have jointly contributed to the adaptation of plants to water-limiting environments.
Effects of agricultural management on phyllosphere fungal diversity in vineyards and the association with adjacent native forests

Agriculture is one of the main drivers of land conversion, and agriculture practices can impact on microbial diversity. Here we characterized the phyllosphere fungal diversity associated with Carménère grapevines under conventional and organic agricultural management. We also explored the fungal diversity present in the adjacent sclerophyllous forests to explore the potential role of native forest on vineyard phyllosphere. After conducting D2 and ITS2 amplicon sequencing, we found that fungal diversity indices did not change between conventional and organic vineyards, but community structure was sensitive to the agricultural management. On the other hand, we found a high proportion of shared fungal OTUs between vineyards and native forests. In addition, both habitats had similar levels of fungal diversity despite forest samples were derived from multiple plant species. In contrast, the community structure was different in both habitats. Interestingly, the native forest had more unidentified species and unique OTUs than vineyards. Forest dominant species were Aureobasidium pullulans and Endoconidioma populi, whereas Davidiella tassiana, Didymella sp. , and Alternaria eichhorniae were more abundant in vineyards. Overall, this study argues that a better understanding of the relationship native forests and agroecosystems is needed for maintaining and enhancing ecosystem services provided by natural ecosystems. Finally, knowledge of microbial communities living in the Chilean Mediterranean biome is needed for appropriate conservation management of these biomes and their classification as biodiversity hotspots.
Reliability of Whole-Exome Sequencing for Assessing Intratumor Genetic Heterogeneity

Multi-region sequencing is used to detect intratumor genetic heterogeneity (ITGH) in tumors. To assess whether genuine ITGH can be distinguished from sequencing artifacts, we whole-exome sequenced (WES) three anatomically distinct regions of the same tumor with technical replicates to estimate technical noise. Somatic variants were detected with three different WES pipelines and subsequently validated by high-depth amplicon sequencing. The cancer-only pipeline was unreliable, with about 69% of the identified somatic variants being false positive. Even with matched normal DNA where 82% of the somatic variants were detected reliably, only 36%-78% were found consistently in technical replicate pairs. Overall 34%-80% of the discordant somatic variants, which could be interpreted as ITGH, were found to constitute technical noise. Excluding mutations affecting low mappability regions or occurring in certain mutational contexts was found to reduce artifacts, yet detection of subclonal mutations by WES in the absence of orthogonal validation remains unreliable.
An RF-Powered Crystal-Less Double-Mixing Receiver for Miniaturized Biomedical Implants

In this paper, we present a low-power event-driven receiver intended for miniaturized biomedical implants. The fully integrated system can operate by power harvesting from electromagnetic fields using a radio frequency-to-dc converter or through a 0.5-V voltage supply such as a rechargeable battery. Without any external component and calibration overhead, the proposed double-mixing receiver is operating at a frequency of 915-MHz industrial, scientific, and medical band and is robust to process, supply voltage, and body temperature variations. The proof-of-concept receiver is designed and implemented in a 0.13-<inline-formula> <tex-math notation="LaTeX">$\mu \text{m}$ </tex-math></inline-formula> CMOS technology. The system occupies a silicon area of 0.75 mm<sup>2</sup> and consumes only 9.1-<inline-formula> <tex-math notation="LaTeX">$\mu \text{W}$ </tex-math></inline-formula> power while achieving a sensitivity of −48 and −39 dBm at the data rate of 1 and 100 kb/s, respectively.
Transcriptional Reprogramming of Legume Genomes: Perspective and Challenges Associated With Single-Cell and Single Cell-Type Approaches During Nodule Development

Transcriptomic approaches revealed thousands of genes differentially or specifically expressed during nodulation, a biological process resulting from the symbiosis between leguminous plant roots and rhizobia, atmospheric nitrogen-fixing symbiotic bacteria. Ultimately, nodulation will lead to the development of a new root organ, the nodule. Through functional genomic studies, plant transcriptomes have been used by scientists to reveal plant genes potentially controlling nodulation. However, it is important to acknowledge that the physiology, transcriptomic programs, and biochemical properties of the plant cells involved in nodulation are continuously regulated. They also differ between the different cell-types composing the nodules. To generate a more accurate picture of the transcriptome, epigenome, proteome, and metabolome of the cells infected by rhizobia and cells composing the nodule, there is a need to implement plant single-cell and single cell-types strategies and methods. Accessing such information would allow a better understanding of the infection of plant cells by rhizobia and will help understanding the complex interactions existing between rhizobia and the plant cells. In this mini-review, we are reporting the current knowledge on legume nodulation gained by plant scientists at the level of single cell-types, and provide perspectives on single cell/single cell-type approaches when applied to legume nodulation.
Multisensor Filtration and Fusion on a Three-Layer Architecture

Using a proposed Three-Layer Architecture, several filtration and fusion techniques are experimented using various sensors. Different scenarios were tested to validate the architecture on three different platforms; a Mobile Robot, a Four-Wheel Vehicle and a Quadcopter. The techniques investigated which yielded the best results were fusing an Infrared sensor along with an Ultrasonic sensor on a Mobile Robot through a Particle Filter and Fuzzy Logic to optimize the fusion. For the Quadcopter, an IMU was fused using Extended Kalman Filter with Fuzzy Logic to compensate for the IMU’s drift. As for the Four-Wheel Vehicle, an IMU with an Encoder was fused to estimate the odometry of the vehicle using an Extended Kalman Filter. Communication between the platforms and the signals was done on a three-layer communication system that uses multimaster package of ROS, I2C and WiFi to communicate between the platforms and the signals being sent and received.
The longitudinal links of personality traits, values, and well-being and self-esteem: A five-wave study of a nationally representative sample.

[Correction Notice: An Erratum for this article was reported online in Journal of Personality and Social Psychology on Apr 4 2019 (see record 2019-18472-001). In the article, the stability model is referred to incorrectly as trait-state error model in the abstract, twice in the main body of the article, and in the Table 2 Note. Corrected versions of the fourth sentence in the abstract, the first sentence of the Analysis Outline section, and the first sentence of the Table 2 Note are provided in the erratum. The Kenny & Zautra (1995) reference has been deleted from the text and References list, and Steyer & Schmitt (1994) was added to the text and References list. All versions of this article have been corrected. ] The existence of links between personality traits, values, and well-being and self-esteem is well established, but the nature and direction of these links have been less clearly understood. This study examines longitudinally the stability of traits and values, their mutual effects, and their effects on affective and cognitive well-being and self-esteem. We analyzed data from a nationally representative panel in The Netherlands, spanning 5 time points spread across 8 years (n = 5,159 to 7,021 per time point, total N = 11,890). We estimated latent state-trait models with autoregression and random-intercepts cross-lagged panel models to account for the trait-like, time-invariant stability of the constructs. Traits were more stable than values. The bidirectional effects tended to be significant, but could be distinguished by their relative size. Traits predicted values more strongly than they were predicted by values, and generally predicted well-being and self-esteem more strongly than values did. Traits predicted broad well-being (especially its affective aspects) more strongly than they were predicted by it; values, by contrast, were predicted by well-being (especially its cognitive aspects and self-esteem) more strongly than they predicted it. The findings highlight the central role of traits for personality functioning, while also supporting the mutual constitution of traits and other personality concepts. The results are discussed in the framework of different theoretical approaches to the composition of the broader personality system. (PsycINFO Database Record (c) 2019 APA, all rights reserved).
The transgenic expression of the β-subunit of human chorionic gonadotropin influences the growth of implanted tumor cells

The beta subunit of human chorionic gonadotropin (βhCG) is secreted by various tumors, and its presence associated with poor prognosis. Though exogenous hCG elicits the synthesis of molecules associated with angiogenesis, invasion, immune suppression and chemoresistance from responsive tumor cells in vitro, the influence of cell-extrinsic βhCG on tumorigenesis in vivo has not been adequately explored. Female C57BL/6−/− × FVBβhCG/− F1 transgenic mice demonstrated ovarian hyperplasia and pituitary adenomas; transcripts of hCG-driven, tumor-associated molecules were heightened in the pituitary. Upon the implantation of Lewis Lung Carcinoma cells (murine lung tumor cells derived from C57BL/6 mice) in transgenic mice, tumor incidence and volume were enhanced, and increased transcription and expression of hCG-driven, tumor-associated molecules was observed in excised tumors. While treatment of these mice with Cabergoline (a potent dopamine receptor agonist) had no significant effects, ovariectomy resulted in a reduction in the lag phase, accompanied by an increase in tumor incidence and volume upon Lewis Lung Carcinoma cell implantation. In tumors derived from Lewis Lung Carcinoma cell-implanted ovariectomized, transgenic mice, the transcription and expression of hCG-driven, tumor-associated molecules remained elevated and enhanced animal mortality was observed. Cell-extrinsic βhCG can therefore induce pro-tumorigenic effects in vivo (even on tumor lineages not part of the reproductive axis), with ovarian products mediating an ameliorating influence.
Parents' Perspectives and Clinical Effectiveness of Cranial-Molding Orthoses in Infants With Plagiocephaly

Objective To investigate the clinical effectiveness of and parents’ perspectives on cranial-molding orthotic treatment. Methods Medical charts were reviewed for 82 infants treated for plagiocephaly with cranial-molding orthoses in our clinic from April 2012 to July 2016 retrospectively. Infants who were clinically diagnosed with positional plagiocephaly and had a Cranial Vault Asymmetry Index (CVAI) of more than 3.5% were included. Pre- and post-treatment CVAI was obtained by three-dimensional head-surface laser scan. Parents’ perceptions of good outcome (satisfaction) were evaluated with the Goal Attainment Scale (GAS). The GAS score assessed how much the parent felt that his or her initial goal for correcting the skull asymmetry was achieved after the treatment. Results The compliance with cranial-molding orthoses was 90.2% (74 of 82 infants). There were 53 infants (65% of the 82 infants) who had adverse events with the cranial-molding orthoses during the study. Heat rash was found in 29 cases (35.4%) and was the most common adverse event. The mean GAS T-score was 51.9±10.2. A GAS T-score of 0 or more was identified for 71.6% of parents. The GAS T-score was significantly related to the age (p<0.001), the initial CVAI, and the difference of CVAI during the treatment (p<0.001). Conclusion Parents’ perception of good outcome was correlated with the anthropometric improvement in cranialmolding orthotic treatment in infants with plagiocephaly. A high percentage of parents felt that the treatment met their initial goals in spite of a high occurrence of adverse events.
Temperature response of Rubisco kinetics in Arabidopsis thaliana: thermal breakpoints and implications for reaction mechanisms

Optimization of Rubisco kinetics could improve photosynthetic efficiency, ultimatly resulting in increased crop yield. However, imprecise knowledge of the reaction mechanism and the individual rate constants limit our ability to optimize the enzyme. Membrane inlet mass spectrometery (MIMS) may offer benefits over traditional methods for determining individual rate constants of the Rubisco reaction mechanism, as it can directly monitor concentration changes in CO2, O2, and their isotopologs during assays. However, a direct comparsion of MIMS to the traditional Radiolabel method of determining Rubisco kinetic parameters has not been made. Here, the temperature responses of Rubisco kinetic parameters from Arabidopsis thaliana were measured using the Radiolabel and MIMS methods. The two methods provided comparable parameters above 25 °C, but temperature responses deviated at low temperature as MIMS derived catalytic rates of carboxylation, oxygenation, and CO2/O2 specificity showed thermal breakpoints. Here we discuss the variability and uncertainty surrounding breakpoints in the Rubisco temperature response and relavance of individual rate constants of the reaction mechanisms to potential breakpoints.
A Fully Integrated 300-MHz Channel Bandwidth 256 QAM Transceiver With Self-Interference Suppression in Closely Spaced Channels at 6.5-GHz Band

We present a fully-integrated 256 QAM single-chip transceiver (TRX) with 300-MHz channel bandwidth at the 6.5-GHz band. A novel architecture for self-interference suppression (SIS) is proposed. A noise-canceling low-noise amplifier with the embedded programmable source degeneration network based on the bond wires, manifesting the notch filtering characteristics of the self-interference signal, has been utilized to facilitate the SIS, and LC-tuned tanks further improve the interference filtering in a receiver (RX) and considerable adjacent channel leakage power ratio in a transmitter (TX). The SAW-less /duplexer-less TRX allows TDD/FDD co-operation in closely spaced channels. The RX achieves a noise figure (NF) as low as 3 dB with +17.5-dBm out-of-band IIP3. The EVM is 2.02% and 2.72% for the RX and TX, respectively, in 160-MHz bandwidth OFDM 256 QAM. In the SIS mode, the blocker P1dB is −8 dBm, and the NF of the RX degrades only 2.1 dB (from 3.0 to 5.1 dB), withstanding 0-dBm interference at 150-MHz offset. The TRX exhibits a slight EVM degradation (from 2.02% to 2.98%) when receiving a −40-dBm 160-MHz bandwidth 256 QAM desired signal, in the presence of a −15-dBm 80-MHz bandwidth self-interference signal at 300-MHz offset. The TRX has been implemented in 0.13- $\mu \text{m}$ CMOS with superior overall performances.
Okbyungpoongsan (Yupingfeng) for treating allergic rhinitis

Background: Okbyungpoongsan (OBPS) is widely used as a treatment for allergic rhinitis (AR) in Far East countries. Many clinical trials have assessed the efficacy and safety of the OBPS formula for treating AR. Here, we systematically will review the clinical evidence for and against administration of OBPS. Methods and analysis: All RCTs of decoctions or modified decoctions will be included. The methodological quality of the RCTs will be analyzed using the Cochrane Collaboration tool for assessing risk of bias, while confidence in the cumulative evidence will be evaluated using the Grading of Recommendations Assessment, Development and Evaluation (GRADE) instrument. Ethics and dissemination: This systematic review will be published in a peer-reviewed journal and will also be disseminated electronically and in print. The review will be updated to provide additional information and guide healthcare practices. Registration number: CRD42017080292.
Concise Derivation for Generalized Approximate Message Passing Using Expectation Propagation

Generalized approximate message passing (GAMP) is an efficient algorithm for the estimation of independent identically distributed random signals under generalized linear model. The sum-product GAMP has long been recognized as an approximate implementation of the sum-product loopy belief propagation. In this letter, we propose to view the message passing in a new perspective of expectation propagation (EP). Comparing with the previous methods that were based on Taylor expansions, the proposed EP method could unify the derivations for the real and the complex GAMP, with a difference only in the setup of Gaussian densities.
Are 24-hour motor activity patterns associated with continued rapid response to ketamine?

Purpose This study examined the links between 24-hour activity patterns (specifically, amplitude and timing of wrist activity) and the persisting qualities of clinical antidepressant response to the glutamatergic modulator ketamine. Methods Twenty-four-hour activity patterns were compared across 5 days of 24-hour activity rhythms in patients with major depressive disorder who displayed either a brief antidepressant response (24–48 hours), a continued antidepressant response (>72 hours), or no antidepressant response to ketamine. These postinfusion-response profiles were then used retrospectively to examine cohort-specific fitted parameters at baseline, postinfusion day 1 (D1), and postinfusion D3. Results Relative to the nonresponders, the cohort experiencing a brief antidepressant response had blunted 24-hour amplitude that extended from baseline through D3 and postketamine phase advance of activity on D1 that reverted to baseline on D3. Relative to the nonresponders, the cohort experiencing a continued antidepressant response to ketamine had phase-advanced activity at both baseline and D1, as well as increased amplitude on D1 and D3. Conclusion Taken together, the results suggest that the time course of antidepressant response to ketamine is influenced by underlying biological differences in motor activity timekeeping. These differences may provide clues that link durable mood response with the molecular machinery of the circadian system, thus leading to more effective interventions. In addition, biomarkers of preinfusion motor activity (eg, amplitude, timing) may be useful for recommending future individualized treatment interventions, to the extent that they help identify patients who may relapse quickly after treatment.
Blind Single-Channel Dereverberation Using a Recursive Maximum-Sparseness-Power-Prediction-Model

Several single-channel speech dereverberation techniques rely on a sufficiently precise estimate of the reverberation time T60. Blindly estimating the frequency dependent T60remains a challenging task, especially if only a short time section is available for the estimation. In this work, we first review an offline method which estimates both T60per frequency as well as the power spectral density (PSD) of the early reverberant speech and then derive a recursive and adaptive version thereof. These estimates can be used to suppress the late reverberation of reverberant speech signals. It is shown that the proposed algorithm can estimate the T60with a deviation of approximately ±20% w.r. t. the ground truth value. Moreover, objective quality measures show that the proposed dereverberation algorithm performs slightly better than two other existing methods.
Smooth Obstacle Avoidance Path Planning for Autonomous Vehicles

Obstacle avoidance and overtaking are important manoeuvres for autonomous driving. The collision avoidance with a vehicle, a pedestrian or any obstacle and the generation of a feasible continuous curvature trajectory represent the major problems faced by researchers to provide a safe path planning solution. This paper presents an algorithm able to avoid vehicles or obstacles by proposing a smooth local modified trajectory of a global path. The proposed method is based on the combination of a parameterized sigmoid function and a rolling horizon. The major advantage of this method is the reactivity to the obstacle motion and the generation of a smooth trajectory in a low execution time. The lateral and the longitudinal safety distances are easily parameterized when generating the avoidance trajectory. Simulation results show that the algorithm performs collision avoidance manoeuvres for static and dynamic obstacles in an effective way. The method is validated by applying the avoidance approach on real measured trajectory.
Scalable Robust Kidney Exchange

In barter exchanges, participants directly trade their endowed goods in a constrained economic setting without money. Transactions in barter exchanges are often facilitated via a central clearinghouse that must match participants even in the face of uncertainty—over participants, existence and quality of potential trades, and so on. Leveraging robust combinatorial optimization techniques, we address uncertainty in kidney exchange, a real-world barter market where patients swap (in)compatible paired donors. We provide two scalable robust methods to handle two distinct types of uncertainty in kidney exchange—over the quality and the existence of a potential match. The latter case directly addresses a weakness in all stochastic-optimization-based methods to the kidney exchange clearing problem, which all necessarily require explicit estimates of the probability of a transaction existing—a still-unsolved problem in this nascent market. We also propose a novel, scalable kidney exchange formulation that eliminates the need for an exponential-time constraint generation process in competing formulations, maintains provable optimality, and serves as a subsolver for our robust approach. For each type of uncertainty we demonstrate the benefits of robustness on real data from a large, fielded kidney exchange in the United States. We conclude by drawing parallels between robustness and notions of fairness in the kidney exchange setting.