Miracle-dz/UniFAR-FTUs huggingface dataset:
Development of Lactococcus lactis Biosensors for Detection of Diacetyl

Some secondary metabolites of fermentative bacteria are desired compounds for the food industry. Examples of these compounds are diacetyl and acetaldehyde, which are produced by species of the lactic acid bacteria (LAB) family. Diacetyl is an aromatic compound, giving the buttery flavor associated with dairy products, and acetaldehyde is the compound responsible for the yogurt flavor and aroma. The quantification of these compounds in food matrices is a laborious task that involves sample preparation and specific analytical methods. The ability of bacteria to naturally sense metabolites has successfully been exploited to develop biosensors that facilitate the identification and quantification of certain metabolites (Mahr and Frunzke, 2016). The presence of a specific metabolite is sensed by the biosensors, and it is subsequently translated into the expression of one or more reporter genes. In this study we aimed to develop fluorescence-based biosensors to detect diacetyl and acetaldehyde. Since the metabolic pathways for production and degradation of these compounds are present in Lactococcus lactis, the sensing mechanisms in this bacterium are expected. Thus, we identified diacetyl and acetaldehyde responsive promoters by performing transcriptome analyses in L. lactis. The characterization of the biosensors showed their response to the presence of these compounds, and a further analysis of the diacetyl-biosensors (its dynamics and orthogonality) was performed. Moreover, we attempted to produce natural diacetyl from producer strains, namely L. lactis subsp. lactis biovar diacetylactis, to benchmark the performance of our biosensors. The diacetyl-biosensors responded linearly to the amounts of diacetyl obtained in the bacterial supernatants, i.e., the increases in GFP expression were proportional to the amounts of diacetyl present in the supernatants of L. lactis subsp. lactis biovar diacetylactis MR3-T7 strain. The biosensors developed in this study may eventually be used to engineer strains or pathways for increased diacetyl and acetaldehyde production, and may facilitate the detection of these metabolites in complex food matrices.
Genetic Biocontrol for Invasive Species

Invasive species are increasingly affecting agriculture, food, fisheries, and forestry resources throughout the world. As a result of global trade, invasive species are often introduced into new environments where they become established and cause harm to human health, agriculture, and the environment. Prevention of new introductions is a high priority for addressing the harm caused by invasive species, but unfortunately efforts to prevent new introductions do not address the economic harm that is presently manifested where invasive species have already become established. Genetic biocontrol can be defined as the release of organisms with genetic methods designed to disrupt the reproduction of invasive populations. While these methods offer the potential to control or even eradicate invasive species, there is a need to ensure that genetic biocontrol methods can be deployed in a way that minimizes potential harm to the environment. This review provides an overview of the state of genetic biocontrol, focusing on several approaches that were the subject of presentations at the Genetic Biocontrol for Invasive Species Workshop in Tarragona, Spain, March 31st, 2019, a workshop sponsored by the OECD’s Co-operative Research Program on Biological Resource Management for Sustainable Agricultural Systems. The review considers four different approaches to genetic biocontrol for invasive species; sterile-release, YY Males, Trojan Female Technique, and gene drive. The different approaches will be compared with respect to the efficiency each affords as a genetic biocontrol tool, the practical utility and cost/benefits associated with implementation of the approach, and the regulatory considerations that will need to be addressed for each. The opinions expressed and arguments employed in this publication are the sole responsibility of the authors and do not necessarily reflect those of the OECD or of the governments of its Member countries.
Root morphology and aerenchyma formation as indicators for the flood-tolerance of Rumex species

(1) Rumex species are zoned along a gradient of elevation in the river ecosystem in The Netherlands. (2) Plants of R. thyrsiflorus, R. acetosa, R. obtusifolius, R. crispus, R. conglomeratus and R. maritimus were flooded to identify and quantify any relevant adaptive features and to test whether their distribution might be caused by a differential response to flooding in the growing season. (3) Most Rumex species have a tap-root from which the laterals originate. As a response to flooding, new laterals are formed. (4) The number, place of origin, growth direction and formation rate of new laterals differed between the species. (5) The number and formation rate of new roots were associated with the elevational distribution of the species: as a response to flooding, low-elevation species formed more new roots, and faster, than high-elevation species. (6) The high-elevation species had root porosity values lower than 10%; the intermediateand low-elevation species had values higher than 10%. (7) Schizogenous aerenchyma was constitutively formed by the low-elevation and floodtolerant R. maritimus, and not by the high-elevation and flood-intolerant species R. thyrsiflorus. In the intermediate-elevation species R. crispus it was induced in stagnant hypoxic solution cultures. (8) The results indicate that aerenchyma formation is closely connected with the growth rate of new roots. It appears that development of aerenchyma in the new roots is the main determinant in the flood-tolerance of Rumex species.
Effects of Tolypocladium cylindrosporum and its secondary metabolites, efrapeptins, on the immune system of Galleria mellonella larvae

Interactions between Tolypocladium cylindrosporum (Deuteromycetes), its metabolite, efrapeptins, and the insect immune defense were investigated in vivo and in vitro. In the different phagocytosis studies, Bacillus cereus spores which had been labelled with fluorescein-isothiocyanate (FITC) were used. In vitro studies showed that efrapeptins inhibit phagocytic activity of Galleria mellonella (Lepidoptera: Pyralidae) haemocytes. The response was dose-related. Efrapeptins significantly reduced the number of nodules formed in response to an injection of zymosan supernatant. Phenoloxidase (PO) activation system contained in haemocyte lysate (HLS) was not affected by efrapeptins. In vivo studies when larvae were injected with efrapeptins also revealed that efrapeptins did not affect PO activities and total haemocyte count (THC) after 1 and 6 h post-injection. However, 12 h post-injection there was a significant inhibition of PO activities in HLS. There was also no significant reduction of PO activities and THC when larvae were injected with Tolypocladium cylindrosporum spores until 24 h post-injection. However, PO activities were suppressed and THC reduced 48 h post-treatment of larvae with spores. This study suggests that efrapeptins may interfere with the ligand-receptor interactions that are likely to occur at the plasma membrane of specific haemocytes.
Spontaneous Perforation of a Malignified Corrosive Stricture of the Esophagus and Subsequent Perforation of a Giant Duodenal Stress ULCUS

Abstract Surgical interventions for corrosive stricture of the esophagus are extremely difficult and technically challenging. In this manuscript, we present a patient with esophagectomy due to perforation of a corrosive stricture of the esophagus that underwent malignant transformation and subsequent perforation of a giant duodenal stress ulcus, which occurred 12 days after the intervention. We performed a total esophagectomy, pharyngo- and gastrostomy, suture of the duodenal perforation but the postoperative period was challenging and despite our efforts, the patient died on the 50th postoperative day due to respiratory and renal failure.
Multidrug resistance proteins (MRPs) and implication in drug development

The multidrug resistance protein (MRP)‐related ABCC family (MRP1, MRP2, MRP3, MRP4, MRP5, MRP6, MRP7, MRP8, and MRP9) belongs to the ATP‐binding cassette (ABC) superfamily of transport proteins. They are capable of transporting a structurally diverse array of endo‐ and xenobiotics and their metabolites across cell membranes. These transporters play an important role in the absorption, disposition, and elimination of these compounds in the body. In particular, increased expression of these drug transporters in tumor cells is associated with resistance to a number of important chemotherapeutic agents. This review highlights the biochemical and pharmacological properties of MRP1‐9 and their implications in drug development. A detailed study on the biochemical function and regulation of MRPs is important in drug development, as this may help to avoid drug toxicity, drug resistance, and drug‐drug interactions and to optimize cancer chemotherapy. Drug Dev. Res. 64:1–18, 2005. © 2005 Wiley‐Liss, Inc.
A COMPARISON OF LEAF AND TILLER GROWTH IN SEVEN PERENNIAL GRASSES AS INFLUENCED BY NITROGEN AND TEMPERATURE

Leaf and tiller development along the main shoot of cocksfoot, ryegrass, timothy, Hordeum bulbosum, meadow fescue, S170 tall fescue and an Algerian tall fescue are described. Comparisons between plants grown at two levels of applied nitrogen, and in a heated and an unheated glasshouse, from January to April, 1961, showed that timothy, cocksfoot and, to a lesser extent, H. bulbosum and ryegrass, generally developed leaves faster than the fescues. Numbers of live leaves per shoot, and numbers of actively-elongating leaves per shoot declined in a similar varietal order. Despite this, the large leaves of the fescues resulted in their having a leaf area per main shoot equal to, or exceeding that of, the other grasses for most of the experiment. In general, rate of leaf appearance, number of live leaves, number of actively-elongating leaves and leaf length were increased by a high level of N and high temperature, but high tesnperature reduced leaf width and, in some instances, tiller numbers.
Summer Phytoplankton Variability in the Lower St. Lawrence Estuary

The study involved two data series, a weekly sampling program at a single station near Rimouski from June through September, 1974, during which semidiurnal tidal effects were considered, and a 5-d survey of the lower St. Lawrence estuary during July 1975. The biomass and species composition distributions during the survey appeared to be a function of the residual circulation and mixing characteristics of the lower estuary. Active growth in phytoplankton populations was limited to a 2-mo midsummer period. The impoverishment up to late June was probably due to high turbidity, the 1% light level being about 4 m in depth, rather than due to advective flushing. Strong temporal fluctuations in water column phytoplankton biomass and production were similar to the distribution in density stratification. The confidence limits of the derived parameters [photosynthesis at light saturation normalized by chlorophyll (θ) and by carbon (μpot), and the carbon/chlorophyll ratio] were broad with respect to their seasonal r.
The flight of the dipterous fly Muscina stabulans Fallén

As a preliminary step in the study of a system consisting of a flying insect and the air surrounding it, a comparison is made between the system under natural conditions of free flight and under experimental conditions (when the insect is held stationary), in order to ascertain under what conditions conclusions reached with the insect held stationary would hold for free flight. To avoid the difficulty of making this comparison directly in respect of each of the many factors involved, the resultant force which, acting continuously on the body of the insect, would most nearly replace those cyclicly changing forces that normally maintain or modify the state of motion in flight, is taken as an index of what is occurring in the system. When the insect is held stationary in ‘still air’ it is found in most cases that this resultant, though of sufficient magnitude to support the insect in flight, does not act through the centre of gravity: the line of action of the resultant intersects the body axis at some point behind the centre of gravity. The position of this point depends on the amplitude of wing beat. W hen the insect is exposed in a wind tunnel to a stream of air of appropriate speed and direction, however, the resultant acts through the centre of gravity, as in free flight. The forward displacement of the point of intersection between the line of action of the resultant and the body axis, when the insect is exposed to a stream of air, is analysed further, and it is found: (1) that the effect of the stream of air on the body of the insect is negligible in this connexion as compared with the effect on the wings; (2) that changes in amplitude of wing beat do not account for the forward displacement of the resultant; and (3) that when the insect is exposed to a stream of air the path travelled by the wing tip on its downward beat is displaced forwards along the body axis in a direction which would tend to produce the observed displacement of the resultant force. This forward displacement of the path travelled by the wing on its downward beat converts the elliptical course, characteristic of wing movements when the insect is held stationary in ‘still air’, into the figure of ‘8’ course commonly associated with insect flight, and is dependent on the movement or position of the third antennal joint relative to the second, which in turn is determined by the action of the stream of air on the third joint with its arista. The characteristic attitude of the legs in flight, and the continued vibration of the wings when air is blown at the insect from in front also depend on the sensory inflow from the antennae. The maintenance of the figure of ‘8’ path involves the interaction of the sensory inflow both from the antennae and from the halteres.
Effects of High Pressure on the Gelatin Properties and Molecular Structure of Peanut Protein Isolates

何轩辉,刘红芝,刘丽,胡晖,王强 (农业部农产品加工与质量控制重点开放实验,中国农业科学院农产品加工研究所,北京 100193) 摘要:本文研究了质量浓度为 5%的花生分离蛋白(PPI)在 50~200 MPa 压力范围处理 5 min 后的热凝胶硬度、弹性和粘结力的 变化情况,并对处理前后的 PPI进行了 SDS-PAGE、圆二色谱(CD)、质谱和分子结构模拟分析。 SDS-PAGE 电泳结果表明,PPI 中 分子量为 61.0 ku的亚基对压力最敏感,对此亚基进行质谱分析,结果表明压力处理后,此亚基的氨基酸序列未发生变化,含 580 个 氨基酸,实际分子量为 66.5 ku,为伴花生球蛋白II的电泳条带,在此基础上进行分子模拟,发现其空间构象在 100 MPa 处理后发生 了显著变化。 CD 结果表明,高压处理后,PPI 的二级构象发生了显著变化。 PPI 热凝性结果表明,100 MPa 处理后其形成的热凝胶硬 度最大,为 172 g,比未处理提高了 49.6%,弹性和粘结力与未处理相当。 以上结果说明压力处理使得 PPI热凝胶特性得到了改善。 关键词:花生分离蛋白;高压影响;分子结构;凝胶 文章篇号:1673-9078(2013)8-1810-1815
Speech vocal clustering methods

The problem of increasing the clustering efficiency of vocal speech sounds is considered. Centroid and medoid clustering methods that use normalized distances which increases the efficiency of clustering, are proposed. Characteristics and quality criteria based on them are suggested for these methods. These methods have been investigated on TIMIT database and are intended for intelligent biometric identification systems.
Role of Natural Interferon-α Producing Cells (Plasmacytoid Dendritic Cells) in Autoimmunity

The type I interferons (IFNs) have antiviral, cytostatic and prominent immunomodulatory effects, which all are of great importance during viral infections. However, prolonged exposure of the immune system to type I IFN can break tolerance and initiate an autoimmune reaction, eventually leading to autoimmune disease. Recent observations in patients with systemic lupus erythematosus (SLE) have revealed that such individuals have endogenous IFN-α inducers, causing an ongoing IFN-α production and consequently a continuous stimulation of the immune system. These IFN-α inducers consist of small immune complexes (IC) containing DNA or RNA and act on the principal IFN-α producing cell, the natural IFN-α producing cell (NIPC), also termed the plasmacytoid dendritic cell (PDC). The NIPC/PDC is a key cell in both the innate and adaptive immune response but can also, either directly or via produced IFN-α, have a pivotal role in autoimmunity. In this review we summarize recent data concerning NIPC/PDC, including their activation, regulation, function and possible role in autoimmune diseases, especially SLE.
Docker container based PaaS cloud computing comprehensive benchmarks using LAPACK

Platform as a Service (PaaS) cloud computing model becomes wide-spread implemented within Docker Containers. Docker uses operating system level virtualization to deliver software in packages called containers. Containers are isolated from one another and comprise all the required software, including operating system API, libraries and configuration files. With such advantageous integrity one can doubt on Docker performance. The present paper applies packet LAPACK, which is widely used for performance benchmarks of super-computers, to collect and compare benchmarks of Docker on Linux Ubuntu and MS Windows platforms. After a brief overview of Docker and LAPACK, a series of Docker images containing LAPACK is created and run, abundant benchmarks obtained and represented in tabular and graphical form. From the final discussion, we conclude that Docker runs with nearly the same performance on both Linux and Windows platforms, the slowdown does not exceed some ten percent. Though Docker performance in Windows is essentially limited by the amount of RAM allocated to Docker Engine.
Bagging-based instance selection for instance-based classification

The task of reducing marked large size samples for building diagnostic and recognizing models by precedents is considered. The method allowing to reduce essentially the size of a training sample increasing at the same time its efficiency, through removal of irrelevant and redundant instances is proposed. The given method provides an opportunity to estimate each instance of a training sample by synthesis of an ensemble of weak classifiers using a bagging model, and to create a reduced sample of the most significant instances by estimations. Software is developed to implement the proposed method. This software has been experimentally investigated in solving the task of reducing synthetic and real world data. The results of the conducted experiments allow recommending the use of the developed method and its software realization for solving the task in the sphere of technical diagnostics.
Experimental research of optimizing the Apache Spark tuning: RDD vs data frames

In this paper results and analysis of experimental research for determining the effectiveness of changing the parameters (as compared to standard values) of tuning Apache Spark for minimizing application execution time have been presented. The structure of a test dataset has been developed using RDD and Data Frames, based on which it is possible to create during a minimal time text files with a size greater than 4 GB having properties (characteristics) set up for testing. A peculiarity of test data is the fact that they often reflect basic properties of real world problems. The investigation includes 2 stages: at the first stage a comparative analysis of RDD and Data Frames is carried out for the standard settings of Apache Spark; at the second stage experiments for different sizes of an input test dataset for assessing the influence of parallelism levels, a block size in HDFS and the parameter spark.sql. shuffle.partitions in Spark Data Frames have been conducted. The obtained results substantiate the influence of the spark.sql. shuffle.partitions value on the test task execution performance. For this parameter ranges and change trends have been found. Also, levels of parallelism that maximally influence the execution time have been determined. It has been proven that for certain sizes of input test files the size of an HDFS block can be set up by default. Results of computational experiments have been demonstrated in tables and graphs. They confirm the effectiveness of the suggested changes to the Apache Spark settings as compared with the standard ones for different sizes of tested files.
Multi-layer model and training method for information-extreme malware traffic detector

Model-based on multilayer convolutional sparse coding feature extractor and information-extreme decision rules for malware traffic detection is presented in the paper. Growing sparse coding neural gas algorithms for unsupervised pre-training of the feature extractor are used. Random forest regression model as a student in knowledge distillation from sparse coding layers is proposed for speed up inference mode. Information-extreme learning method based on binary encoding with tree ensembles and class separation with radial basis function in binary Hamming space are proposed. Information-extreme classifier is characterized by low computational complexity and high generalization ability for small labeled training sets. Simulation results with an optimized model on test open datasets confirm the suitability of proposed algorithms for practical application.
Leaf blotch of Poplar caused by a new species of Septotinia.

For several years a conspicuous leaf blotch on plantation trees of hybrid poplar clones has been under observation in the eastern United States. The symptoms differ from those resulting from infection by the leaf fungi common on native poplars in that area and the causal organism has only recently been identified as a spe? cies of Septotinia. This genus was established by Whetzel (5) in the subfamily Ciborioideae of the Helotiaceae, based on 5*. podophyllina Whetzel, the only species then known in the genus.
Information technology of hot-metal ladle car handwritten numbers recognition from photo image

The paper presents the results of the construction and testing of an information system for recognizing ladle car numbers drawn up of handwritten digits. The latest publications on solving problems of recognition and analysis of texts by their images were analyzed, a selected range of application libraries for creating a program for experiments are Keras, TensorFlow, Theano, Pandas, Matplotlib and others. Two variants of recognition technology were analyzed and tested: using fuzzy logic and using deep learning neural networks. To construct and train neural networks, a well-known and rather complete base of handwritten digits MNIST was chosen. Two types of neural networks were considered: sequential and convolutional. The training of neural networks was carried out using a variable number of steps (epochs). Recognition images were scaled to a size of 28x28 (784 cells in a one-dimensional representation). Preliminary processing of images (filtering, scaling, etc.) was carried out using the OpenCV library. For recognition, each image of the digit was converted to a 28x28 size and fed to the input of a pre-trained neural network. A technique to select the area of interest in photographs containing hand-written digits for further recognition has been worked out. For handwritten digit recognition, the best recognition accuracy is provided by a convolutional neural network, with which 97.6% of car ladle digits were correctly recognized.