Miracle-dz/UniFAR-FTUs huggingface dataset:
The effect of passive leg-raising maneuver on hemodynamic stability during anesthesia induction for adult cardiac surgery

Introduction Some cardiac patients do not tolerate the intravenous fluid load commonly administered before anesthesia induction. This study investigated preinduction passive leg-raising maneuver (PLRM) as an alternative method to fluid loading before cardiac anesthesia. Methods and materials During a 6-month period, 120 adult elective heart surgery patients were enrolled in this study and allocated into 2 groups: PLRM group vs control group (n=60). Anesthesia was induced using midazolam, fentanyl, and cisatracurium. Initially, 250 mL of fluid was administrated intravenously in all of patients before anesthesia induction. Then in the PLRM group, PLRM was performed starting 2 minutes before anesthesia induction and continued for 20 minutes after tracheal intubation. In the control group, anesthesia was induced in a simple supine position. Heart rate, invasive mean arterial blood pressure (MAP), and central venous pressure (CVP) were recorded before PLRM, before anesthetic induction, before laryngoscopy, and at 5, 10, and 20 minutes after tracheal intubation. The hypotension episode rate (MAP <70 mmHg) and CVP changes were compared between the 2 groups. The predictive value of the ≥3 mmHg increase in CVP value in response to PLRM for hypotension prevention was defined. Results Hypotension rates were lower in the PLRM group (63.3% vs 81.6%; P-value 0.04), and MAP was higher among PLRM patients immediately before anesthetic injection, before laryngoscopy, and 20 minutes after intubation, compared to the control group. PLRM increased CVP by 3.57±4.9 mmHg (from 7.50±2.94 to 11.05±3.55 mmHg), which required several minutes to reach peak value, returning to baseline after 15 minutes. This change did not correlate to subsequent MAP changes; an increase in the CVP value ≥3 mmHg decreased the postinduction hypotension rate by 62.50%. Conclusion Preinduction PLRM can provide a more stable hemodynamic status in adult cardiac surgery patients and decreases anesthesia-induced hypotension rates by 62.50%. Rate of the changes in the CVP value caused by PLRM is not predictive of subsequent MAP changes.
SAFL: Increasing and Accelerating Testing Coverage with Symbolic Execution and Guided Fuzzing

Mutation-based fuzzing is a widely used software testing technique for bug and vulnerability detection, and the testing performance is greatly affected by the quality of initial seeds and the effectiveness of mutation strategy. In this paper, we present SAFL, an efficient fuzzing testing tool augmented with qualified seed generation and efficient coverage-directed mutation. First, symbolic execution is used in a lightweight approach to generate qualified initial seeds. Valuable explore directions are learned from the seeds, thus the later fuzzing process can reach deep paths in program state space earlier and easier. Moreover, we implement a fair and fast coverage-directed mutation algorithm. It helps the fuzzing process to exercise rare and deep paths with higher probability. We implement SAFL based on KLEE and AFL and conduct thoroughly repeated evaluations on real-world program benchmarks against state-of-the-art versions of AFL. After 24 hours, compared to AFL and AFLFast, it discovers 214% and 133% more unique crashes, covers 109% and 63% more paths and achieves 279% and 180% more covered branches. Video link: https://youtu.be/LkiFLNMBhVE
Assisted Discovery of Software Vulnerabilities

As more aspects of our daily lives rely on technology, the software that enables the technology must be secure. Developers rely on practices such as threat modeling, static and dynamic analyses, code review, and fuzz and penetration testing to engineer secure software. These practices, while effective at identifying vulnerabilities in software, are limited in their ability to describe the potential reasons for the existence of vulnerabilities. In order to overcome this limitation, researchers have proposed empirically validated metrics to identify factors that may have led to the introduction of vulnerabilities in the past. Developers must be made aware of these factors so that they can proactively consider the security implications of each line of code that they contribute. The goal of our research is to assist developers in engineering secure software by providing a technique that generates scientific, interpretable, and actionable feedback on security as the software evolves. In this paper, we provide an overview of our proposed approach to accomplish this research goal through a series of three research studies in which we (1) systematize the knowledge on vulnerability discovery metrics, (2) leverage the metrics to generate feedback on security, and (3) implement a framework for providing automatically generated feedback on security using code reviews as a medium.
Tackling Plant Meiosis: From Model Research to Crop Improvement

Genetic engineering and traditional plant breeding, which harnesses the natural genetic variation that arises during meiosis, will have key roles to improve crop varieties and thus deliver Food Security in the future. Meiosis, a specialized cell division producing haploid gametes to maintain somatic diploidy following their fusion, assures genetic variation by regulated genetic exchange through homologous recombination. However, meiotic recombination events are restricted in their total number and their distribution along chromosomes limiting allelic variations in breeding programs. Thus, modifying the number and distribution of meiotic recombination events has great potential to improve and accelerate plant breeding. In recent years much progress has been made in understanding meiotic progression and recombination in plants. Many genes and factors involved in these processes have been identified primarily in Arabidopsis thaliana but also more recently in crops such as Brassica, rice, barley, maize, or wheat. These advances put researchers in the position to translate acquired knowledge to various crops likely improving and accelerating breeding programs. However, although fundamental aspects of meiotic progression and recombination are conserved between species, differences in genome size and organization (due to repetitive DNA content and ploidy level) exist, particularly among plants, that likely account for differences in meiotic progression and recombination patterns found between species. Thus, tools and approaches are needed to better understand differences and similarities in meiotic progression and recombination among plants, to study fundamental aspects of meiosis in a variety of plants including crops and non-model species, and to transfer knowledge into crop species. In this article, we provide an overview of tools and approaches available to study plant meiosis, highlight new techniques, give examples of areas of future research and review distinct aspects of meiosis in non-model species.
Differentiation of umbilical cord mesenchymal stem cells into hepatocytes in comparison with bone marrow mesenchymal stem cells

Mesenchymal stem cells (MSCs) are considered to be an ideal source for the cell therapy of end-stage liver diseases. Umbilical cord (UC)-MSCs can be obtained via a non-invasive procedure and can be easily cultured, making them potentially superior candidates for cell transplantation when compared with MSCs from other sources. In the present study, UC-MSCs were induced to differentiate into hepatocytes and were compared with bone marrow (BM)-MSCs for their hepatic differentiation potential. UC-MSCs showed significantly higher proliferation than BM-MSCs. Under hepatic induction, UC-MSCs and BM-MSCs could differentiate into hepatocytes. Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) analysis revealed that a higher expression of the hepatocyte-specific genes albumin, cytochrome P450 3A4 (CYP3A4), tyrosine-aminotransferase, glucose-6phosphate, α1 antitrypsin and α-fetoprotein was detected in differentiated UC-MSCs when compared with differentiated BM-MSCs. The results of ELISA and western blotting were in accordance with those of RT-qPCR. Theses results indicated that UC-MSCs had higher hepatic differentiation potential than BM-MSCs. Therefore, UC-MSCs may be advantageous over BM-MSCs for the treatment of end-stage liver disease.
σI from Bacillus subtilis: Impact on Gene Expression and Characterization of σI-Dependent Transcription That Requires New Types of Promoters with Extended −35 and −10 Elements

In bacteria, σ factors are essential for transcription initiation. Knowledge about their regulons (i.e., genes transcribed from promoters dependent on these σ factors) is the key for understanding how bacteria cope with the changing environment and could be instrumental for biotechnologically motivated rewiring of gene expression. Here, we characterize the σI regulon from the industrially important model Gram-positive bacterium Bacillus subtilis. We reveal that σI affects expression of ∼130 genes, of which 16 are directly regulated by σI, including genes encoding proteins involved in iron homeostasis. Detailed analysis of promoter elements then identifies unique sequences important for σI-dependent transcription. This study thus provides a comprehensive view on this underexplored component of the B. subtilis transcription machinery. ABSTRACT The σI sigma factor from Bacillus subtilis is a σ factor associated with RNA polymerase (RNAP) that was previously implicated in adaptation of the cell to elevated temperature. Here, we provide a comprehensive characterization of this transcriptional regulator. By transcriptome sequencing (RNA-seq) of wild-type (wt) and σI-null strains at 37°C and 52°C, we identified ∼130 genes affected by the absence of σI. Further analysis revealed that the majority of these genes were affected indirectly by σI. The σI regulon, i.e., the genes directly regulated by σI, consists of 16 genes, of which eight (the dhb and yku operons) are involved in iron metabolism. The involvement of σI in iron metabolism was confirmed phenotypically. Next, we set up an in vitro transcription system and defined and experimentally validated the promoter sequence logo that, in addition to −35 and −10 regions, also contains extended −35 and −10 motifs. Thus, σI-dependent promoters are relatively information rich in comparison with most other promoters. In summary, this study supplies information about the least-explored σ factor from the industrially important model organism B. subtilis. IMPORTANCE In bacteria, σ factors are essential for transcription initiation. Knowledge about their regulons (i.e., genes transcribed from promoters dependent on these σ factors) is the key for understanding how bacteria cope with the changing environment and could be instrumental for biotechnologically motivated rewiring of gene expression. Here, we characterize the σI regulon from the industrially important model Gram-positive bacterium Bacillus subtilis. We reveal that σI affects expression of ∼130 genes, of which 16 are directly regulated by σI, including genes encoding proteins involved in iron homeostasis. Detailed analysis of promoter elements then identifies unique sequences important for σI-dependent transcription. This study thus provides a comprehensive view on this underexplored component of the B. subtilis transcription machinery.
ThUnderVolt: Enabling Aggressive Voltage Underscaling and Timing Error Resilience for Energy Efficient Deep Learning Accelerators

Hardware accelerators are being increasingly deployed to boost the performance and energy efficiency of deep neural network (DNN) inference. In this paper we propose Thundervolt, a new framework that enables aggressive voltage underscaling of high-performance DNN accelerators without compromising classification accuracy even in the presence of high timing error rates. Using post-synthesis timing simulations of a DNN accelerator modeled on the Google TPU, we show that Thundervolt enables between 34%–57% energy savings on state-of-the-art speech and image recognition benchmarks with less than 1% loss in classification accuracy and no performance loss. Further, we show that Thundervolt is synergistic with and can further increase the energy efficiency of commonly used run-time DNN pruning techniques like Zero-Skip.
Phosphorus Dynamics and Availability in the Nearshore of Eastern Lake Erie: Insights From Oxygen Isotope Ratios of Phosphate

Blooms of filamentous benthic algae that plagued Lake Erie in the 1950s through 1970s were largely reduced through reductions of phosphorus (P) loading from point sources. Since the mid-1990s, these blooms have returned despite a period of relatively stable external P inputs. While increased loadings of dissolved P have been causally linked to cyanobacterial blooms in some parts of the lake, the impacts of ecosystem changes such as the effect of invasive species on nutrient cycling and availability have not been fully elucidated, leading to uncertainty as to the effectiveness of additional non-point P management actions. Here we use the oxygen isotope ratios (18OP) of phosphate in concert with measures of water quality along the northern shore of the east basin of Lake Erie to identify sources and pathways of P cycling and infer potential importance in relation to annual blooms of Cladophora that foul the shorelines of eastern Lake Erie. 18OP data indicate that potential external source signatures are rapidly overprinted by biological cycling of P by the plankton community and that much of the available phosphate in the nearshore waters is derived from hydrolysis of dissolved organic P compounds. Near the dreissenid-colonized lake bed, 18OP was persistently and significantly enriched in 18O relative to 18OP measured in surface waters and was similar to 18OP of phosphate excreted by dreissenid mussels in incubations. These results implicate dreissenid mussels as key agents in nearshore P cycling and highlight the importance of considering ecosystem changes in the development of nutrient management strategies designed to ameliorate symptoms of eutrophication.
Trimmed Event Recognition ( Moments in Time ) : Submission to ActivityNet Challenge 2018

In this paper, a brief description is provided of the method used for the task of trimmed event recognition (Moments in Time). A set of TRN models were used to train video classification models for the 200 action categories of the Moment in Time Mini Database,and the P3D feature is also used to further enhance the model diversity, finally we propose a simple yet effective method to combine different modalities together for action prediction.
Canonical Computation without Canonical Representation

A representation of a Boolean function is canonical if, given a variable order, only one instance of the representation is possible for the function. A computation is canonical if the result depends only on the Boolean function and a variable order, and does not depend on how the function is represented and how the computation is implemented.In the context of Boolean satisfiability (SAT), canonicity of the computation implies that the result (a satisfying assignment for satisfiable instances and an abstraction of the unsat core for unsatisfiable instances) does not depend on the functional representation and the SAT solver used.This paper shows that SAT-based computations can be made canonical, even though the SAT solver is not using a canonical data structure. This brings advantages in EDA applications, such as irredundant sum of product (ISOP) computation, counter-example minimization, etc, where the uniqueness of solutions and/or improved quality of results justify a runtime overhead.
Incorporating Chinese Characters of Words for Lexical Sememe Prediction

Sememes are minimum semantic units of concepts in human languages, such that each word sense is composed of one or multiple sememes. Words are usually manually annotated with their sememes by linguists, and form linguistic common-sense knowledge bases widely used in various NLP tasks. Recently, the lexical sememe prediction task has been introduced. It consists of automatically recommending sememes for words, which is expected to improve annotation efficiency and consistency. However, existing methods of lexical sememe prediction typically rely on the external context of words to represent the meaning, which usually fails to deal with low-frequency and out-of-vocabulary words. To address this issue for Chinese, we propose a novel framework to take advantage of both internal character information and external context information of words. We experiment on HowNet, a Chinese sememe knowledge base, and demonstrate that our framework outperforms state-of-the-art baselines by a large margin, and maintains a robust performance even for low-frequency words.
Proteomics Reveals Scope of Mycolactone-mediated Sec61 Blockade and Distinctive Stress Signature*

Mycolactone is a bacteria-derived macrolide that blocks the biogenesis of a large array of secretory and integral transmembrane proteins (TMP) through potent inhibition of the Sec61 translocon. Here, we used quantitative proteomics to delineate the direct and indirect effects of mycolactone-mediated Sec61 blockade in living cells. In T lymphocytes, dendritic cells and sensory neurons, Sec61 substrates downregulated by mycolactone were in order of incidence: secretory proteins (with a signal peptide but no transmembrane domain), TMPs with a signal peptide (Type I) and TMPs without signal peptide and a cytosolic N terminus (Type II). TMPs without a signal peptide and the opposite N terminus topology (Type III) were refractory to mycolactone inhibition. This rule applied comparably to single- and multi-pass TMPs, and extended to exogenous viral proteins. Parallel to its broad-spectrum inhibition of Sec61-mediated protein translocation, mycolactone rapidly induced cytosolic chaperones Hsp70/Hsp90. Moreover, it activated an atypical endoplasmic reticulum stress response, differing from conventional unfolded protein response by the down-regulation of Bip. In addition to refining our mechanistic understanding of Sec61 inhibition by mycolactone, our findings thus reveal that Sec61 blockade induces proteostatic stress in the cytosol and the endoplasmic reticulum.
High CO2 Under Nutrient Fertilization Increases Primary Production and Biomass in Subtropical Phytoplankton Communities: A Mesocosm Approach

The subtropical oceans are home to one of the largest ecosystems on Earth, contributing to nearly one third of global oceanic primary production. Ocean warming leads to enhanced stratification in the oligotrophic ocean but also intensification in cross-shore wind gradients and thus in eddy kinetic energy across eastern boundary regions of the subtropical gyres. Phytoplankton thriving in a future warmer oligotrophic subtropical ocean with enhanced CO2 levels could therefore be patchily fertilized by increased mesoscale and submesoscale variability inducing nutrient pumping into the surface ocean. Under this premise, we have tested the response of three size classes (0.2-2, 2-20, and > 20 μm) of subtropical phytoplankton communities in terms of primary production, chlorophyll and cell biomass, to increasing CO2 concentrations and nutrient fertilization during an in situ mesocosm experiment in oligotrophic waters offof the island of Gran Canaria. We found no significant CO2-related effect on primary production and biomass under oligotrophic conditions (phase I). In contrast, primary production, chlorophyll and biomass displayed a significant and pronounced increase under elevated CO2 conditions in all groups after nutrient fertilization, both during the bloom (phase II) and post-bloom (phase III) conditions. Although the relative increase of primary production in picophytoplankton (250%) was 2.5 higher than in microphytoplankton (100%) after nutrient fertilization, comparing the high and low CO2 treatments, microphytoplankton dominated in terms of biomass, contributing > 57% to the total. These results contrast with similar studies conducted in temperate and cold waters, where consistently small phytoplankton benefitted after nutrient additions at high CO2, pointing to different CO2-sensitivities across plankton communities and ecosystem types in the ocean.
A Controlled Fermented Samjunghwan Herbal Formula Ameliorates Non-alcoholic Hepatosteatosis in HepG2 Cells and OLETF Rats

Hepatosteatosis (HS), a clinical feature of fatty liver with the excessive intracellular accumulation of triglyceride in hepatocytes, is manifested by perturbation of the maintenance of liver lipid homeostasis. Samjunghwan (SJH) is an herbal formula used mostly in Korean traditional medicine that is effective against a number of metabolic diseases, including obesity. Herbal drugs, enriched with numerous bioactive substances, possess health-protective benefits. Meanwhile, fermented herbal products enriched with probiotics are known to improve metabolic processes. Additionally, current lines of evidence indicate that probiotics-derived metabolites, termed as postbiotics, produce the same beneficial effects as their precursors. Herein, the anti-HS effects of 5-weeks naturally fermented SJH (FSJH) was investigated with FSJH-mixed chow diet in vivo using Otsuka Long-Evans Tokushima Fatty (OLETF) and Long-Evans Tokushima Otsuka (LETO) rats as animal models of HS and controls, respectively. In parallel, the anti-HS effects of postbiotic-metabolites of three bacterial strains [Lactobacillus brevis (LBB), Lactococcus lactis (LCL) and Lactobacillus plantarum (LBP)] isolated from FSJH were also evaluated in vitro using the FFAs-induced HepG2 cells. Feeding OLETF rats with FSJH-diet effectively reduced body, liver, and visceral adipose tissue (VAT) weights, produced marked hypolipidemic effects on serum and hepatic lipid parameters, decreased serum AST and ALT levels, and upregulated the HMGCOR, SREBP, and ACC, and downregulated the AMPK and LDLR gene expressions levels. Additionally, exposure of FFAs-induced HepG2 cells to postbiotic metabolic media (PMM) of bacterial strains also produced marked hypolipidemic effects on intracellular lipid contents and significantly unregulated the HMGCOR, SREBP, and ACC, and downregulated the AMPK and LDLR genes expressions levels. Overall, our results indicate that FSJH enriched with fermented metabolites could be an effective anti-HS formulation.
Inhibition of LPS-induced inflammatory responses by Satureja hortensis extracts in J774.1 macrophages

ABSTRACT Macrophages are among the main cells involved in generation of inflammation. To investigate the anti-inflammatory effect of Satureja hortensis (summer savory), lipopolysaccharide (LPS)-activated J774.1 macrophages were treated with various extracts, and the expression and release of various inflammatory molecules by macrophages were examined. We showed that dichloromethane and hexane extracts reduced nitric oxide (NO) production more efficiently than other extracts. Both extracts decreased gene expression of inducible NO synthase (iNOS) (<0.44 fold of control), cyclooxygenase (COX)-2 (<0.29 fold), interleukin (IL)-1β (<0.41 fold), IL-6 (<0.25 fold) and tumor necrosis factor (TNF)-α (<0.2 fold). The extracts reduced IL-6 and IL-1β proteins production from macrophages. Surface intensity of expression of intercellular adhesion molecule (ICAM)-1 decreased to 845 ± 28.1 (dichloromethane) and 715 ± 48.6 (hexane) compared to the control (902 ± 73.1). These findings showed that Satureja hortensis, by influencing macrophages and related mediators, could contribute to reduction of inflammation and might be useful as an anti-inflammatory agent.