Miracle-dz/UniFAR-FTUs huggingface dataset:
Bioinformatics Methods For Studying Intra-Host and Inter-Host Evolution Of Highly Mutable Viruses

Understanding viral disease progression is vital to the detection of outbreaks and subsequent planning for public health actions. Bioinformatics methods are extremely useful for this purpose through a range of applications among which the analysis of viral next-generation sequencing (NGS) data, tracing virus evolution and reconstruction of transmission networks have been explored in this research. The first part of this research focuses on the processing of NGS data where quantification methods are proposed to describe the robustness and reproducibility of the output of bioinformatics tools. This research shows the importance of assessing the reliability of genomic tools. The second part of this study is the application of processed NGS data to investigate the intra-host evolution of Hepatitis C Virus (HCV) to diagnose and detect new and incident HCV cases. A computational method based on Machine Learning algorithms is proposed to solve this problem. This genomic multi feature-based model not only aims to predict the stage of infection but also aims to understand the evolution of HCV and its underlying complex mechanism. The third part of this research aims to reconstruct transmission networks for new cases which were identified during the aforementioned research. In this part the inter-host evolution of highly mutable viruses is studied. A Maximum Likelihood approach consisting of Uncapacitated Facility Location Algorithm is proposed to solve this problem. Finally, the last part of this dissertation focuses on the inference of the global transmission network of SARS-CoV-2 prior to the pandemic state. INDEX WORDS: Robustness, Quasispecies, Transmission Network, Machine Learning, Hepatitis C Virus, SARS-CoV-2 BIONFORMATICS METHODS FOR STUDYING INTRA-HOST AND INTER-HOST EVOLUTION OF HIGHLY MUTABLE VIRUSES
Approximating Lower-and Upper-Bounded (Connected) Facility Location via LP Rounding

We consider a lower-and upper-bounded generalization of the classical facility location problem, where each facility has a capacity (upper bound) that limits the number of clients it can serve and a lower bound on the number of clients it must serve if it is opened. We develop an LP rounding framework that exploits a Voronoi diagram-based clustering approach to derive the ﬁrst bicriteria constant approximation algorithm for this problem with non-uniform lower bounds and uniform upper bounds. This naturally leads to the the ﬁrst LP-based approximation algorithm for the lower bounded facility location problem (with non-uniform lower bounds). We also demonstrate the versatility of our framework by extending this and presenting the ﬁrst constant approximation algorithm for some connected variant of the problems in which the facilities are required to be connected as well.
More With Less: Exploring How to Use Deep Learning Effectively through Semi-supervised Learning for Automatic Bug Detection in Student Code

Automatically detecting bugs in student program code is critical to enable formative feedback to help students pin-point errors and resolve them. Deep learning models especially code2vec and ASTNN have shown great success for large-scale code classiﬁcation. It is not clear, however, whether they can be eﬀectively used for bug detection when the amount of labeled data is limited. In this work, we investigated the eﬀectiveness of code2vec and ASTNN against classic machine learning models by varying the amount of labeled data from 1% up to 100%. With a few exceptions, the two deep learning models outperform the classic models. More interestingly, our results showed that when the amount of labeled data is small, code2vec is more eﬀective, while ASTNN is more eﬀective with more training data; for both code2vec and ASTNN, the more labeled data, the better. To further improve their eﬀectiveness, we investigated the potential of semi-supervised learning which can leverage a large amount of unlabeled data to improve their performance. Our results showed that semi-supervised learning is indeed beneﬁcial especially for ASTNN.
Window detection in aerial texture images of the Berlin 3D CityGML Model

This article explores the usage of the state-of-art neural network Mask R-CNN to be used for window detection of texture files from the CityGML model of Berlin. As texture files are very irregular in terms of size, exposure settings and orientation, we use several parameter optimisation methods to improve the precision. Those textures are cropped from aerial photos, which implies that the angle of the facade, the exposure as well as contrast are calibrated towards the mean and not towards the single facade. The analysis of a single texture image with the human eye itself is challenging: A combination of window and facade estimation and perspective analysis is necessary in order to determine the facades and windows. We train and detect bounding boxes and masks from two data sets with image size 128 and 256. We explore various configuration optimisation methods and the relation of the Region Proposal Network, detected ROIs and the mask output. Our final results shows that the we can improve the average precision scores for both data set sizes, yet the initial AP score varies and leads to different resulting scores.
That-trace effects are yet to be explained away: challenges for prosody-based accounts

That-trace effects in English have been treated as violations of prosodic wellformedness conditions (Kandybowicz 2006a; Sato & Dobashi 20160): the C head and the trace cannot be parsed in the same prosodic phrase. Satisfying this condition allows for amelioration effects induced by sentitial adverbs and narrow focus on the embedded verb. However, I argue that a [C t] prosodic parse should never be predicted since it goes against the Lexical Category Conditon (Truckenbrodt 1999) or Prosodic Vacuity (Kandybowicz 2015): function words always require a (lexical) host in the Phonological Phrase they belong to. On the one hand, I provide a set of empirical arguments based on the phrasing of subject pronouns and relative clauses, and the availability of certain phonological processes. Besides, I question the application of the focus rules and their corresponding phrasing to get the desired amelioration. On the other, I question the assumption that traces are important for the system of prosodic phrasing. In fact, the system should not have access to traces at all assuming if occurs late at PF after Vocabulary Insertion.
Immediate-Early Gene Inducible by v-Fps, Epidermal Growth Factor, and Platelet-Derived Growth

A set of genes is rapidly inducible when quiescent fibroblasts are stimulated by growth factors or by the activation of temperature-sensitive retroviral protein-tyrosine kinases. Most of these so-called immediate-early genes were cloned by differential cDNA hybridization. DNA sequence analysis identified many of them as putative members of the growth factor or of the transcription factor gene family, suggesting a role in signal transmission during the Go-to-G1 transition. In this study, we identified one of the genes that are rapidly inducible by the retroviral protein-tyrosine kinases v-Src and v-Fps of Rous sarcoma virus and FuiJinami sarcoma virus, respectively, as the rhoB gene, a member of the ras gene superfamily whose products are GTPbinding proteins. rhoB is transiently activated at the transcriptional level by v-Fps and by epidermal growth factor. Its labile RNA is inducible in the presence of cycloheximide but not of actinomycin D. rhoB is strongly induced by epidermal growth factor and by platelet-derived growth factor both in subconfluent, serum-starved and in density-arrested Rat-2 fibroblasts. Fetal calf serum is a poor inducer, particularly in density-arrested cells, and phorbol esters do not increase rhoB expression at all. These data suggest that rhoB is inducible by protein-tyrosine kinases through a pathway not involving the activation of protein kinase C. Neither the closely related rhoC and rhoA genes nor the distantly related c-H-ras gene is rapidly inducible by mitogens. Thus, rhoB is the first known member of the small GTP-binding proteins among the immediate-early genes.
Benchmarking plant operation and instrumentation, control and automation in the wastewater industry

Benchmarking is an effective tool to compare the performance of full-scale wastewater treatment plant operation. In this study, 29 wastewater treatment plants from eight countries were surveyed with the aim of developing some key performance indicators, which may be used for benchmarking purposes. The level of utilisation of instrumentation, control and automation (ICA) has also been measured. The study of ICA utilisation revealed that on average only 23% of all sensors are used for online control. For most parameters, ICA is not the single dominant factor determining performance, although it is the factor that has the highest potential to improve performance. Eighty percent of the participating plants had implemented new control during the last five years leading to improvements in nitrogen and phosphorous removal, energy efficiency and ease of operation. The survey has quantified how "non-standardised" wastewater treatment plant operational practice is. Some simple key performance indicators are derived that relate the level of removal of ammonium, total nitrogen, phosphorous and suspended solids to the resources needed for their removal, i.e. volume, energy, organic matter and precipitation chemicals. Several indicators are suggested for each substance. The indicators show a great difference from the best to the poorest performance indicating that improvement potentials exist at many plants.
A. L. R.

Various concerns suggest looking for internal co-categories in categories with strong logical structure. It turns out that in any coherent category E , all cocategories are co-equivalence relations. 0.1. Definition. Let E be any category. An (internal) co-category Q in E is an internal category in E, i.e. objects and morphisms in E
Towards selective electrochemical conversion of glycerol to 1,3-propanediol

1,3-propanediol (1,3-PD) is a bulk chemical with myriad applications in polymers, lubricants, cosmetics, foods industries and in the synthesis of heterocyclic compounds. Current commercial production of 1,3-PD involves a thermocatalytic process using acrolein (DuPont) and ethylene oxide (Shell) as starting feedstock. These feedstocks are petroleum-based and there are many efforts at using glycerol as low cost biomass-derived feedstock for 1,3-PD production. A number of catalyst designs and bacterial & fungal strains are being explored for respective catalytic and fermentation routes to glycerol-to-1,3-PD. However, the electrochemical method received little attention for the purpose. In this work, in order to explore the possibility of using partly refined glycerol byproduct of biodiesel production as feedstock, we investigated conversion and 1,3-PD selectivity of glycerol electrolysis in chloride media. We demonstrated selective glycerol-to-1,3-PD conversion using Pt or RuO2-based dsa as anode and Zn or Pb as cathode in NaCl and KCl at pH 1. This electrochemical glycerol-to-1,3-PD conversion is not only green, it is a potential process network loop between biodiesel production and chlor-alkali industry.
Application of fractal theory to estimation of equivalent diameters of airborne carbon nanotube and nanofiber agglomerates

ABSTRACT Understanding transport characteristics of airborne nanotubes and nanofibers is important for assessing their fate in the respiratory system. Typically, diffusion and aerodynamic diameters capture key deposition mechanisms of near-spherical particles such as diffusion and impaction in the submicrometer size range. For nonspherical particles with high aspect ratios, such as aerosolized carbon nanotubes, these diameters can vary widely, requiring their independent measurement. The objective of this study was to develop an approach to provide approximate estimates of aerodynamic- and diffusion-equivalent diameters of airborne carbon nanotubes (CNTs) and carbon nanofibers (CNFs) using their morphological characteristics obtained from electron micrographs. The as-received CNT and CNF materials were aerosolized using different techniques such as dry dispersion and nebulization. Mobility and aerodynamic diameters of test aerosol were directly deduced from tandem measurement of particle mobility and mass. The same test aerosol was mobility-classified and subsequently collected on a microscopy grid for transmission electron microscopy (TEM) analysis. TEM micrographs were used to obtain projected area, maximum projected length, and two-dimensional (2-D) radius of gyration of test particles. Estimates of the aerodynamic diameter and the diffusion diameter were obtained by applying the fractal theory developed for aerosol agglomerates of primary spherical particles. After accounting for the particle dynamic shape factor, estimated aerodynamic diameters agreed with those from the direct measurements (using tandem mobility-mass technique) within 30–40% for the agglomerates with relatively open structures while the diffusion diameters agreed within 40–50%. The uncertainty of these estimates mainly depends on degree of overlapping structures in the microscopy image and nonuniformity in tube diameter. The approach could be useful in calculating approximate airborne properties from microscopy images of CNT and CNF agglomerates with relatively open structures. This article not subject to US copyright law
Changes in Length and Sequence

The third and fourth AUG codons in GCN4 mRNA efficiently repress translation of the GCN4-coding sequences under normal growth conditions. The first AUG codon is -30-fold less inhibitory and is required under amino acid starvation conditions to override the repressing effects of AUG codons 3 and 4. lacZ fusions constructed to functional, elongated versions of the first and fourth upstream open reading frames (URFs) were used to show that AUG codons 1 and 4 function similarly as efficient translational start sites in vivo, raising the possibility that steps following initiation distinguish the regulatory properties of URFs 1 and 4. In accord with this idea, we observed different consequences of changing the length and termination site of URF1 versus changing those of URFs 3 and 4. The latter were lengthened considerably, with little or no effect on regulation. In fact, the function of URFs 3 and 4 was partially reconstituted with a completely heterologous URF. By contrast, certain mutations that lengthen URF1 impaired its positive regulatory function nearly as much as removing its AUG codon did. The same mutations also made URF1 a much more inhibitory element when it
IMOBILISASI PROPANOLOL HCL PADA HIDROGEL POLI(VINIL ALKOHOL) - NATRIUM ALGINAT DENGAN TEKNIK RADIASI

Penelitian ini bertujuan memanfaatkan hidrogel sebagai matriks imobilisasi obat dengan teknik iradiasi gamma untuk mengontrol laju pelepasan obat terkendali. Imobilisasi propanolol HCl dalam hidrogel poli(vinil alkohol) (PVA)-g-natrium alginat (NaAlg) telah dilakukan. Larutan PVA/NaAlg (5/0,5, %berat) yang mengandung propanolol HCl (8 mg sampai dengan 16 mg), dibeku-lelehkan (3 siklus) dan diradiasi dengan variasi dosis (10 kGy sampai dengan 30 kGy). Hidrogel dikarakterisasi dengan spectrophotometer Fourier Transform-Infra Red ( FT-IR ) dan Scanning Electron Microscope ( SEM ). Fraksi gel dan daya serap air ditentukan secara gravimetri. Uji pelepasan propanolol HCl dari hidrogel dilakukan dalam larutan encer fosfat (pH 6,8) pada suhu 37 °C diukur dengan spectrofotomer Ultraviolet Visible ( UV-Vis ). Hasil evaluasi menunjukkan peningkatan dosis iradiasi dari 10 kGy hingga 30 kGy, peningkatan fraksi gel hidrogel, dan kemampuan menyerap air hidrogel relatif turun. Pelepasan kumulatif obat dari matriks hidrogel dengan meningkatnya dosis iradiasi hingga 30 kGy relatif turun. Pengamatan menggunakan SEM , menunjukkan hidrogel PVA-NaAlg mempunyai struktur pori yang tidak teratur. Hidrogel PVA-g-NaAlg selayaknya dapat digunakan sebagai matriks pelepasan obat.
Resilience-oriented Comprehensive Planning Strategy of Distributed Generator in Power Distribution System

Power distribution system resilience is not considered in traditional planning of distributed generator (DG), which leads to severe power outages and economic losses during extreme weather event. To address this issue, this paper proposes a resilience-oriented comprehensive planning strategy of DG in power distribution system. The problem is formulated as a two-stage stochastic mixed-integer second-order cone programming (SMISOCP). The objective of the first stage is to determine the number, location and capacity of DG and obtain the economic cost of power distribution system. The second stage minimizes the resilience cost under uncertain failure scenarios. First, sufficient failure scenarios are generated by the Monte Carlo method. Then the failure scenarios are reduced to the most representative scenarios by using the K-means clustering algorithm to reduce computational burden. Finally, the two-stage SMISOCP is solved based on the reduced failure scenarios. The simulation results of the IEEE 33-bus test systems illustrate the effectiveness of the proposed two-stage strategy.
Nucleotide Sequence of the Large Double-Stranded RNA Segment of Bacteriophage +6: Genes

The genome of the lipid-containing bacteriophage +6 contains three segments of double-stranded RNA. We determined the nucleotide sequence of cDNA derived from the largest RNA segment (L). This segment specifies the procapsid proteins necessary for transcription and replication of the +6 genome. The coding sequences of the four proteins on this segment were identified on the basis of size and the correlation of predicted N-terminal amino acid sequences with those found through analysis of isolated proteins. This report completes the sf quence analysis of +6. This constitutes the first complete sequence of a double-stranded RNA genome virus.
Formation of Intracellular gpl60-CD4 Complexes

precursor glycoprotein, gpl60, proceeds via the endoplasmic reticulum and Golgi complex and involves proteolytic processing of gpl60 into the mature virion components, gpl20 and gp4l. We found that coexpression of gpl60 and human CD4 in HeLa cells severely impaired gpl20 production due to the formation of intracellular gpl60-CD4 complexes. This CD4-mediated inhibition of gpl60 processing was alleviated by coexpression of the HIV-1-encoded Vpu protein. The coexpression of Vpu and CD4 in the presence of gpl60 resulted in increased degradation of CD4. Although the precise mechanism(s) responsible for the Vpu effect is presently unclear, our findings suggest that Vpu may destabilize intracellular gpl60-CD4 complexes.
IJNSNS 2021; aop

A reaction–diffusion system governing the prey–predator interaction with Allee effect on the predators, already introduced by the authors in a previous work is reconsidered with the aim of showing destabilization mechanisms of the biologically meaning equilibrium and detecting some aspects for the eventual oscillatory pattern formation. Extensive numerical simulations, depicting such complex dynamics, are shown. In order to complete the stability analysis of the coexistence equilibrium, a nonlinear stability result is shown.
Group A Rotaviruses Associated with Diarrhea in Dairy and Beef Calvest

The genome electropherotyping technique was used to examine group A rotaviral infections of diarrheic calves ranging from 1 to 85 days of age in 2 beef and 27 dairy herds. Coelectrophoresis studies demonstrated 38 distinct bovine group A rotavirus genome electropherotypes; all were long genome electropherotypes, and none had extra segments or unusual segment rearrangements. Genome electropherotypes in fecal specimens from diarrheic calves previously inoculated orally with a commercial, modified-live group A rotavirus vaccine differed from the vaccine genome electropherotype. Generally, when fecal specimens for genome electropherotyping were collected from two or more different calves within the same herd over a relatively short time, only
Double-Stranded RNA-Dependent eIF-2a Kinase in 3T3-F442A Fibroblasts

The interferon-induced double-stranded RNA-dependent eIF-2oa kinase (dsI) has an established role in mediating part of interferon's antiviral effects. Numerous studies have suggested that dsl also has regulatory functions in cells not infected with virus. Our previous results have indicated that the activation of this kinase may be an important regulatory signal in controlling growth arrest of mouse 3T3-F442A fibroblasts prior to their subsequent differentiation to adipocytes. Here, we report that extracts from 3T3-F442A cells cultured under conditions nonpermissive for differentiation exhibit significantly reduced dsl activity and that this reduction is due, at least in part, to the presence of elevated levels of a novel inhibitor of dsl activation (dRF). This inhibitor is also detected in reduced amounts in extracts from cells cultured under conditions which are permissive for differentiation. We have achieved a 1,000-fold purification of dRF activity, and highly purified dRF preparations were found to be greatly enriched for a 15-kDa protein that was greater than 90% pure. Our results indicate that dRF is not a protein phosphatase or protease but a reversible inhibitor of dsI autophosphorylation. In addition, our results imply that dRF is a physiologic regulator of dsI, since dRF activity correlates with the ability of 3T3-F442A cells to undergo adipose conversion.
Calcium Carbonate Polymorphs Growing in the Presence of Sericin: A New Composite Mimicking the Hierarchic Structure of Nacre

Bioinspired self-assembled composite materials are appealing both for their industrial applications and importance in natural sciences, and represent a stimulating topic in the area of materials science, biology, and medicine. The function of the organic matrix has been studied from the biological, chemical, crystallographic, and engineering point of view. Little attention has been paid to the effect of one of the two main components of the organic matrix, the sericin fraction, on the growth morphology of calcium carbonate polymorphs. In the present work, we address this issue experimentally, emphasizing the morphological effects of sericin on calcite and aragonite crystals, and on the formation of a sericin-aragonite-calcite self-assembled composite with a hierarchic structure comparable to that of natural nacre.
High Mobility Anisotropic Black Phosphorus Nanoribbon Field‐Effect Transistor

Achieving excellent electrostatic control and immunity to short channel effects are the formidable challenges in ultrascaled devices. 3D device architectures, such as nanoribbon, have successfully mitigated these problems by achieving uniform top‐ and side‐wall control of the channel. Here, by leveraging on the merits of 3D structure, high‐mobility black phosphorus nanoribbon field‐effect transistors (BPNR‐FET) are demonstrated and the anisotropic transport properties are systematically investigated. A simple top‐down reactive ion etching method is used to realize both armchair‐ and zigzag‐oriented nanoribbons with various widths down to 60 nm. The mobility of BPNR‐FET is found to be width‐ and thickness‐dependent, with the highest hole mobility of ≈862 cm2 V−1 s−1 demonstrated in armchair‐oriented device at room temperature by combining high‐κ gate dielectric and hydrogen treatment to reduce sidewall scattering. Furthermore, hydrogenation effectively passivates the nanoribbon dangling bonds, leading to hysteresis and contact resistance improvement. This work unravels the superior electrical performance underscore a conceptually new device based on BP nanoribbons, paving the way toward the development of nonplanar devices on 2D materials platform.