Miracle-dz/UniFAR-FTUs huggingface dataset:
GENETIC POPULATION STRUCTURE OF ATLANTIC SWORDFISH: CURRENT STATUS AND FUTURE DIRECTIONS

,SUMMARY The genetic population structure of Atlantic swordfish has been studied with mitochondrial DNA (mtDNA) and nuclear DNA (nDNA) data using a variety of laboratory methodologies and analytical approaches. In here, we compare preliminary data for the nuclear genes ldhA and Calmodulin (Cam) from the South Atlantic against published data from other regions. Results from Cam, but not ldhA, confirm the partitioning of NW Atlantic and South Atlantic swordfish populations. The distribution Cam alleles and CR-I haplotypes is homogeneous throughout the entire South Atlantic (South of 5°N) and comparisons with the Indian Ocean confirm the genetic differentiation of these two basins. However, the boundary that separates the North Atlantic from the South Atlantic cannot be delineated with the present data, and additional temporal-spatial sampling is necessary to resolve this issue. It is important to note that the North Atlantic has been characterized primarily using NW Atlantic and Caribbean samples, with very limited sampling coverage of the NE Atlantic. However, because mixing with the Mediterranean swordfish may occur in the NE Atlantic, it is important to delineate the area of contact between these two regions prior to comparing NE and NW Atlantic samples. Using CRI data, we show that the mixing zone of NE Atlantic and the Mediterranean is restricted to a small zone west of Gibraltar that extends west to 10°W. Future studies of population structure in the North Atlantic should consider this evidence to avoid Type I errors. This paper also underlines other areas of research necessary to clarify the entire population structure of Atlantic swordfish.
Mass: Workload-Aware Storage Policy for OpenStack Swift

A cloud object store entails serving workloads of multi tenants. Different applications have different access characteristics and various performance requirements. Thus, it is necessary for the cloud object store to provide tenant-specific policies. OpenStack Swift develops a storage policy mechanism to enable separate storage configurations for different applications. However, the limited configurability of the policy mechanism makes it difficult to provide efficient and flexible policies to meet the evolving needs of the applications. First, original policies only control the frontend paths of the request forwarding without covering the backend paths of the request processing. Thus, they cannot provide sufficient optimizations for workload performance. Second, those policies need to be pre-defined and remain unchanged at runtime, so that they lack the flexibility to adapt to the possible workload changes during runtime. In addition, effective execution of tenant-specific policies is based on the premise that all storage layers are aware of the requests’ sources, while the storage server layer lacks the requisite information to distinguish requests from multi tenants. In this paper, we propose Mass, a programmable framework to provide the enhanced storage policies for diverse workloads based on their access characteristics. Mass intercepts the incoming requests, and collects the requisite metrics to analyze the workload characteristics and track their changes. Policies are specified to provide flexible optimizations for the workloads. By separating the policy control from the actual storage, the policies can be enforced over the full storage paths of the requests and be dynamically adjusted during runtime to adapt to the workload changes. Compared with the setup of original policies, the latency and throughput of workloads are improved by up to 81.6% and 231.5%, respectively.
Challenges on the Way of Implementing TCP Over 5G Networks

5G cellular communication, especially with its hugely available bandwidth provided by millimeter-wave, is a promising technology to fulfill the coming high demand for vast data rates. These networks can support new use cases such as Vehicle to Vehicle and augmented reality due to its novel features such as network slicing along with the mmWave multi-gigabit-per-second data rate. Nevertheless, 5G cellular networks suffer from some shortcomings, especially in high frequencies because of the intermittent nature of channels when the frequency rises. Non-line of sight state, is one of the significant issues that the new generation encounters. This drawback is because of the intense susceptibility of higher frequencies to blockage caused by obstacles and misalignment. This unique characteristic can impair the performance of the reliable transport layer widely deployed protocol, TCP, in attaining high throughput and low latency throughout a fair network. As a result, the protocol needs to adjust the congestion window size based on the current situation of the network. However, TCP is not able to adjust its congestion window efficiently, and it leads to throughput degradation of the protocol. This paper presents a comprehensive analysis of reliable end-to-end communications in 5G networks. It provides the analysis of the effects of TCP in 5G mmWave networks, the discussion of TCP mechanisms and parameters involved in the performance over 5G networks, and a survey of current challenges, solutions, and proposals. Finally, a feasibility analysis proposal of machine learning-based approaches to improve reliable end-to-end communications in 5G networks is presented.
A CRISPR Interference Platform for Selective Downregulation of Gene Expression in Borrelia burgdorferi

Gene function studies are facilitated by the availability of rapid and easy-to-use genetic tools. Homologous recombination-based methods traditionally used to genetically investigate gene function remain cumbersome to perform in B. burgdorferi, as they often are relatively inefficient. ABSTRACT The spirochete Borrelia burgdorferi causes Lyme disease, an increasingly prevalent infection. While previous studies have provided important insight into B. burgdorferi biology, many aspects, including basic cellular processes, remain underexplored. To help speed up the discovery process, we adapted a clustered regularly interspaced palindromic repeats interference (CRISPRi) platform for use in B. burgdorferi. For efficiency and flexibility of use, we generated various CRISPRi template constructs that produce different basal and induced levels of dcas9 and carry different antibiotic resistance markers. We characterized the effectiveness of our CRISPRi platform by targeting the motility and cell morphogenesis genes flaB, mreB, rodA, and ftsI, whose native expression levels span 2 orders of magnitude. For all four genes, we obtained gene repression efficiencies of at least 95%. We showed by darkfield microscopy and cryo-electron tomography that flagellin (FlaB) depletion reduced the length and number of periplasmic flagella, which impaired cellular motility and resulted in cell straightening. Depletion of FtsI caused cell filamentation, implicating this protein in cell division in B. burgdorferi. Finally, localized cell bulging in MreB- and RodA-depleted cells matched the locations of new peptidoglycan insertion specific to spirochetes of the Borrelia genus. These results therefore implicate MreB and RodA in the particular mode of cell wall elongation of these bacteria. Collectively, our results demonstrate the efficiency and ease of use of our B. burgdorferi CRISPRi platform, which should facilitate future genetic studies of this important pathogen. IMPORTANCE Gene function studies are facilitated by the availability of rapid and easy-to-use genetic tools. Homologous recombination-based methods traditionally used to genetically investigate gene function remain cumbersome to perform in B. burgdorferi, as they often are relatively inefficient. In comparison, our CRISPRi platform offers an easy and fast method to implement, as it only requires a single plasmid transformation step and isopropyl-β-d-thiogalactopyranoside (IPTG) addition to obtain potent (>95%) downregulation of gene expression. To facilitate studies of various genes in wild-type and genetically modified strains, we provide more than 30 CRISPRi plasmids that produce distinct levels of dcas9 expression and carry different antibiotic resistance markers. Our CRISPRi platform represents a useful and efficient complement to traditional genetic and chemical methods to study gene function in B. burgdorferi.
The effect of using a case study on the academic achievement of students in learning about the topic of ‘Vitamins’

Abstract This study investigates the impact of the Case-Based Learning (CBL) method for the topic of ‘B6, B9 and B12 Vitamins’ on students’ academic achievement in a biochemistry course for an associate degree level in health. To this end, a case study with the title ‘The Reasons for Depression: Do We Know What They Are? ’ was developed and implemented. The study had a one-group pre-test and post-test research design. The ‘Vitamins’ Achievement Test’ (VAT) and a Structured Interview Form were used as data collection tools. First-year students of Medical Laboratory Techniques at the Ahmet Erdogan Vocational School of Health Services at Bulent Ecevit University (N = 34) who were aged between18 and 20 made up the study group. The VAT and the Structured Interview Form were analysed using content analysis and the paired-samples t-test was used for the VAT. The results indicated that the frequency of students’ responses in the ‘clear understanding’ category improved in the VAT post-test and it was concluded that there was a significant positive difference in the post-test scores of students. The results of the structured interview indicated that most of the students had positive opinions about the method, material and case study.
Intercellular mRNA trafficking via membrane nanotubes in mammalian cells

RNAs have been shown to undergo transfer between mammalian cells, though the mechanism behind this phenomenon and its overall importance to cell physiology is not well understood. Numerous publications have suggested that RNAs (microRNAs and incomplete mRNAs) undergo transfer via extracellular vesicles (e.g. exosomes). However, in contrast to a diffusion-based transfer mechanism, we find that full-length mRNAs undergo direct cell-cell transfer via cytoplasmic extensions, called membrane nanotubes (mNTs), which connect donor and acceptor cells. By employing a simple co-culture experimental model and using single-molecule imaging, we provide quantitative data showing that mRNAs are transferred between cells in contact. Examples of mRNAs that undergo transfer include those encoding GFP, mouse β-actin, and human Cyclin D1, BRCA1, MT2A, and HER2. We show that intercellular mRNA transfer occurs in all co-culture models tested (e.g. between primary cells, immortalized cells, and in co-cultures of immortalized human and murine cells). Rapid mRNA transfer is dependent upon actin, but independent of de novo protein synthesis, and is modulated by stress conditions and gene expression levels. Hence, this work supports the hypothesis that full-length mRNAs undergo transfer between cells through a refined structural connection. Importantly, unlike the transfer of miRNA or RNA fragments, this process of communication transfers genetic information that could potentially alter the acceptor cell proteome. This phenomenon may prove important for the proper development and functioning of tissues, as well as host-parasite or symbiotic interactions. Significance Messenger RNA (mRNA) molecules convey genetic information within cells, beginning from genes in the nucleus to ribosomes in the cell body, where they are translated into proteins. Here, we show a novel mode of transferring genetic information from one cell to another. Contrary to previous publications suggesting that mRNAs transfer via extracellular vesicles, we provide visual and quantitative data showing that mRNAs transfer via membrane nanotubes and direct cell-to-cell contact. We predict that this process has a major role in regulating local cellular environments with respect to tissue development and maintenance, cellular responses to stress, interactions with parasites, tissue transplants, and the tumor microenvironment. Author contributions G.H. , A.R. and R.H. S. conceived the research and designed the experiments; C.M. E. performed and analyzed the experiments with WM983b+/-GFP, including transwell and exosomes; M.C. D. and E.E. performed and analyzed the WM983b/NIH393 co-culture experiments; G.H. performed and analyzed all other experiments; and G.H. , J.E. G, A.R. and R.H. S. wrote the paper.
Genetic variation of the nuclear sequences of mitochondrial origin associated with retrotransposon Tv1 insertions in Drosophila species of the virilis group

Mitochondrial DNA sequences integrated into chromosomes are a promising object for designing genetic markers for studies of phylogenesis and genomic instability. Mitochondrial genomes of D. virilis and other Drosophila species of the virilis group contain (AT)nmicrosatellites in the spacer region between the atp6 and cox3 genes, and this microsatellite sequence is one of the hallmarks of the virilis group. The nuclear genome of D. virilis contains many extended fragments of mitochondrial DNA, which in total are several times longer than the mitochondrial genome. These nuclear sequences of mitochondrial origin contain all types of mitochondrial sequences, including mitochondrial genes and the aforementioned microsatellite sequence. The presence of the (AT)nmicrosatellite allows insertion of retrotransposon Tv1, which can transpose into the (AT)n microsatellite in a site-specific manner. The Tv1 insertion into (AT)n, close to the atp6 or cox3 pseudogenes produces a unique sequence. This sequence is formed by retrotransposon Tv1 and pseudogenes atp6 or cox3. This unique sequence can be detected in the genome by a PCR-based method. We applied this method to the detection and analysis of the nucleotide variability of the pseudogenes atp6 and cox3 associated with Tv1 insertions in a D. virilis cell culture and in the genomes of four Drosophila species of the virilis group: D. virilis, D. montana, D. borealis, and D. lacicola. We discovered new events of mitochondrial sequence transfer to the nucleus in the transplanted cell culture of D. virilis, and new Tv1 insertions, having emerged during the passage of this cell line were detected in the genome of the D. virilis transplanted cell culture. We found atp6 and cox3 pseudogenes associated with insertions of retrotransposon Tv1 in the nuclear genomes of four Drosophila species from the virilis group. These chimeric sequences proved to be species-specific. The age of the Tv1 insertion into the atp6 and cox3 pseudogenes is estimated at 1.50 Ma for D. virilis, 1.31 Ma for D. lacicola, and 1.56 Ma for D. borealis. A specific situation was revealed for D. montana, in which Tv1 insertions with nearly identical 5' and 3' long terminal repeats (LTRs) were present in accessions of flies from Europe and Asia. The age of this insertion was about 300 thousand years, and the insertion was absent from the D. montana fly line from North America.
Inhibition of herpes simplex virus type 1 replication by novel hsa-miR-7704 in vitro

Herpes simplex virus type 1 (HSV-1) infections are one of the most common diseases in human population. HSV-1 causes subclinical, mild to severe diseases, especially in immunocompromised patients. Acyclovir has been used to reduce manifestations of HSV-1 infections. The extensive use of this drug has led to the development of resistant strains. Thus, designing a novel anti-herpes drug with different mechanisms of action is urgently needed. Cellular microRNAs (miRNAs) have direct antiviral effects in addition to their regulatory functions. In this study we used a novel miRNA (hsa-miR-7704), expressed in macrophages, to inhibit HSV-1 lytic infection in HeLa cells. Synthesized hsa-miR-7704 mimics were transfected into HSV-1 infected HeLa cell. The inhibitory effects of the miRNA were evaluated by plaque assay, real time polymerase chain reaction and the viral titers were measured by the 50% tissue culture infective dose (TCID50). The viral titer and cell cytopathic effect were dramatically decreased in HeLa cells transfected with hsa-miR-7704 (50 and 100 nM), compared with HSV-1 infected cells alone or transfected with the mock miRNA control. These results suggest that hsa-miR-7704 inhibits HSV-1 replication efficiently in vitro. This may provide an alternative mechanism to prevent HSV-1 infections.
Using the LSTM Network to Forecast the Demand for Electricity in Poland

The impact of environmental regulations introduced by the European Union is of key importance for electricity generation systems. The Polish fuel structure of electricity production is based on solid fuels. Moreover, the generating base is outdated and must gradually be withdrawn from the power system. In this context, Poland’s energy policy is undergoing a transformation as climate and environmental regulations are becoming increasingly stringent for the energy sector based on solid fuels (hard coal and lignite). However, the transformation process must be adapted to market demands, because the overriding goal is to ensure energy security by maintaining the continuity of energy supplies and an acceptable electricity price. This directly contributes to the development of the entire economy and the standard of living of the society, in accordance with the European Agreement establishing an association between the Republic of Poland and the European Communities and their Member States, signed on 16 December 1991, and the European Energy Charter, signed on 17 December 1991. Ensuring energy security is the most important goal of the energy policy. Therefore, energy companies must forecast the demand. The main goal of this article is to develop a mathematical model of electricity consumption by 2040 by all sectors of the economy: industry, transport, residential, commercial and public services, agriculture, forestry, and fishing. In order to achieve the intended goal, a model was developed by using Long Short-Term Memory (LSTM) artificial neural networks, which belong to deep learning techniques and reflect long-term relationships in time series for a small set of statistical data. The results show that the proposed model can significantly improve the accuracy of forecasts (1–3% of mean absolute percentage error (MAPE) for the analyzed sectors of the economy).
ABSSNet: Attention-Based Spatial Segmentation Network for Traffic Scene Understanding

The location information of road and lane lines is the supremely important thing for the automatic drive and auxiliary drive. The detection accuracy of these two elements dramatically affects the reliability and practicality of the whole system. In real applications, the traffic scene can be very complicated, which makes it particularly challenging to obtain the precise location of road and lane lines. Commonly used deep learning-based object detection models perform pretty well on the lane line and road detection tasks, but they still encounter false detection and missing detection frequently. Besides, existing convolution neural network (CNN) structures only pay attention to the information flow between layers, while it cannot fully utilize the spatial information inside the layers. To address those problems, we propose an attention-based spatial segmentation network for traffic scene understanding. We use the convolutional attention module to improve the network’s understanding capacity of spatial location distribution. Spatial CNN (SCNN) obtains through the information flow within one single convolutional layer and improves the spatial relationship modeling ability of the network. The experimental results demonstrate that this method effectively improves the neural network’s application ability of the spatial information, thereby improving the effect of traffic scene understanding. Furthermore, a pixel-level road segmentation dataset called NWPU Road Dataset is built to help improve the process of traffic scene understanding.
Tuning the Structure of Nylon 6,6 Electrospun Bundles to Mimic the Mechanical Performance of Tendon Fascicles

Tendon and ligament injuries are triggered by mechanical loading, but the specific mechanisms are not yet clearly identified. It is well established however, that the inflection and transition points in tendon stress-strain curves represent thresholds that may signal the onset of irreversible fibrillar sliding. This phenomenon often results in a progressive macroscopic failure of these tissues. With the aim to simulate and replace tendons, electrospinning has been demonstrated to be a suitable technology to produce nanofibers similar to the collagen fibrils in a mat form. These nanofibrous mats can be easily assembled in higher hierarchical levels to reproduce the whole tissue structure. Despite the fact that several groups have developed electrospun tendon-inspired structures, an investigation of the inflection and transition point mechanics is missing. Comparing their behavior with that of the natural counterpart is important to adequately replicate their behavior at physiological strain levels. To fill this gap, in this work fascicle-inspired electrospun nylon 6,6 bundles were produced with different collector peripheral speeds (i.e., 19.7 m s–1; 13.7 m s–1; 7.9 m s–1), obtaining different patterns of nanofibers alignment. The scanning electron microcopy revealed a fibril-inspired structure of the nanofibers with an orientation at the higher speed similar to those in tendons and ligaments (T/L). A tensile mechanical characterization was carried out showing an elastic-brittle biomimetic behavior for the higher speed bundles with a progressively more ductile behavior at slower speeds. Moreover, for each sample category the transition and the inflection points were defined to study how these points can shift with the nanofiber arrangement and to compare their values with those of tendons. The results of this study will be of extreme interest for the material scientists working in the field, to model and improve the design of their electrospun structures and scaffolds and enable building a new generation of artificial tendons and ligaments.