bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deep metric learning improves lab of origin prediction of genetically engineered plasmids
Authors: Soares Igor , Camargo Fernando , Marques Adriano , Crook Oliver 
Published: December 2021

Abstract
Genome engineering is undergoing unprecedented development and is now becoming widely available. To ensure responsible biotechnology innovation and to reduce misuse of engineered DNA sequences, it is vital to develop tools to identify the lab-of-origin of engineered plasmids. Genetic engineering attribution (GEA), the ability to make sequence-lab associations, would supportforensic experts in this process. Here, we propose a method, based on metric learning, that ranks the most likely labs-of-origin whilstsimultaneously generating embeddings for plasmid sequences and labs. These embeddings can be used to perform various downstreamtasks, such as clustering DNA sequences and labs, as well as using them as features in machine learning models. Our approach employsa circular shift augmentation approach and is able to correctly rank the lab-of-origin90%of the time within its top 10 predictions -outperforming all current state-of-the-art approaches. We also demonstrate that we can perform few-shot-learning and obtain76%top-10 accuracy using only10%of the sequences. This means, we outperform the previous CNN approach using only one-tenth of the data. We also demonstrate that we are able to extract key signatures in plasmid sequences for particular labs, allowing for an interpretable examination of the model’s outputs.CCS Concepts: Information systems→Similarity measures; Learning to rank.
DDX3X mediates EGFR-TKI resistance through VEGFR signaling
Authors: Ohtsubo Aya , Kagamu Hiroshi , Watanabe Satoshi , Shono Kunihiro , Masuda Takaaki , Sekiya Tomoki , Suzuki Ryo , Yanagimura Naohiro , Shoji Satoshi , Nozaki Koichiro , Tanaka Tomohiro , Saida Yu , Kondo Rie , Shima Kenjiro , Kimura Yosuke , Hokari Satoshi , Aoki Nobumasa , Ohshima Yasuyoshi , Koya Toshiyuki , Kikuchi Toshiaki 
Published: December 2021

Abstract
Although epidermal growth factor receptor (EGFR)-tyrosine kinase inhibitors (TKIs) are remarkably effective against non-small-cell lung cancer (NSCLC) with EGFR-activating mutations, lung cancer cells acquire resistance to EGFR-TKIs without exception. Several mechanisms of EGFR-TKI resistance have been reported, but there are many aspects that remain to be clarified. We previously identified DDX3X as an immunogenic protein preferentially expressed in murine melanoma with a cancer stem cell (CSC)-like phenotype. DDX3X induced epithelial-mesenchymal transition and reduced the sensitivity to EGFR-TKIs in PC9 cells, human lung cancer cells harboring EGFR exon 19 deletion. We also reported that there was a small nonadherent subpopulation of parental PC9 cells that highly expressed DDX3X and had CSC properties. In this study, we found that VEGFR2 was upregulated in lung cancer cells that strongly expressed DDX3X and that these cells were addicted to VEGFR signaling. The blockade of both EGFR and VEGFR signaling reduced the phosphorylation of downstream signals in the cells with DDX3X that acquired EGFR-TKI resistance. The addition of VEGFR-TKIs or anti-VEGF antibodies to EGFR-TKIs significantly inhibited the progression of EGFR-mutated NSCLC in a xenograft mouse model. These data suggest that the blockade of VEGFR signaling enhances the antitumor effects of EGFR-TKIs by eradicating cancer stem cells, which mediate resistance to EGFR-TKIs.
Hepatitis E Virus (HEV) in Imported and Domestic Camels in Saudi Arabia – A Cross-Sectional Descriptive Molecular Study
Authors: El-Kafrawy Sherif A. , Hassan Ahmed M. , El-Daly Mai M. , Al-Hajri Mohammed , Farag Elmoubashar , Elnour Fatimah Ahmed , Khan Anas , Tolah Ahmed M. , Alandijany Thamir A. , Othman Noura A. , Memish Ziad A , Corman Victor M. , Drosten Christian , Zumla Alimuddin , Azhar Esam I. 
Published: December 2021

Abstract
Camels gained attention since the discovery of MERS-CoV as intermediary hosts for potentially epidemic zoonotic viruses. DcHEV is a novel zoonotic pathogen associated with camel contact. This study aimed to genetically characterize DcHEV in domestic and imported camels in Saudi Arabia. DcHEV was detected by RT-PCR in serum samples, PCR-positive samples were subjected to sequencing and phylogenetic analyses. DcHEV was detected in 1.77% of samples with higher positivity in domestic DCs. All positive imported dromedaries were from Sudan with age declining prevalence. Domestic DcHEV sequences clustered with sequences from Kenya, Somalia, and UAE while imported sequences clustered with one DcHEV isolate from UAE and both sequences clustered away from isolates reported from Pakistan. Full-genome sequences showed 24 amino acid difference with reference sequences. Our results confirm the detection of DcHEV in domestic and imported DCs. Further investigations are needed in human and camel populations to identify DcHEV potential zoonosis threat.
High-throughput analysis of magnetic phase transition by combining table-top sputtering, photoemission electron microscopy, and Landau theory
Authors: Kotsugi Masato , Nishio Tadashi , Yamamoto Masahiro , Ohkochi Takuo , Nanasawa Daigo , Foggiatto Alexandre 
Published: December 2021

Abstract
Recent progress in materials informatics has triggered growing interest in combinatorial experimental systems for materials development. We demonstrate a novel high-throughput experiment combining compact materials synthesis, synchrotron radiation measurements, and statistical data analysis. This technique focuses on not only drawing phase diagrams but also analysing phase transitions for exploring the functions of magnetic materials. This study involved the rapid preparation of a composition-gradient Fe–Co–Cr ternary thin film using a table-top sputtering system and 3D printer, followed by measurement of the chemical components and magnetic contrast by photoemission electron microscopy, through the acquisition of one million spectral datasets within 10 min. The ternary magnetic phase diagram of Fe–Co–Cr obtained by statistical analysis of the magnetic circular dichroism (MCD) contrast images was in perfect agreement with previous studies. The MCD histogram was fitted based on Landau theory, and the estimated critical exponent β (0.36 ± 0.028) showed excellent agreement with previous theoretical and experimental studies. This study successfully demonstrates universal physical parameter analysis that characterizes magnetic properties by a high-throughput approach combined with a simple experimental apparatus.
Regressional Optimizations of Cotton Spun Yarn by Controlling its Process Parameters
Authors: Zeeshan Muhammad Ali , Abro Zamir Ahmed , Rehan Abdul Malik , Shah Ahmer Hussain , Khoso Nazakat Ali , Tariq Syed Qutaba Bin 
Published: December 2021

Abstract
Cotton is the most commonly used natural fiber and has a significant contribution to the production of yarn manufacturing. This yarn is subsequently utilized for the production of fabrics, garments, and other textile products. The quality of the end product depends on the selection of an appropriate spinning process and output parameters. Numerous methods and processes are involved in the production of yarn. Ring spinning machine is most commonly used for the production of cotton spun yarn. It is necessary to optimize the process parameters of ring-spun yarn without compromising on quality and production. In this research work; these parameters have been optimized by applying the multiple linear regression analysis. The process parameters (especially spindle speed, twist and yarn diameter) and their effect on yarn quality have been discussed in detail. Total 135 ring-spun yarn samples have been produced under three different levels of spindle speed, twist, and linear density. These yarn samples are categorized as 8 Ne, 16 Ne, and 24 Ne at three different Twist multipliers (3.8, 4.0, and 4.2) and different revolutions per minute of the spindle (9500 rpm, 10500rpm, and 11500 rpm). The models have been designed to predict the quality of ring-spun by utilizing USTER evenness tester data. The Count of yarn, yarn twist, and spindle speed were selected as a predictor. The multiple regression method has been used to find out the relation between the process parameters and yarn quality characteristics. The high values of R2 (the coefficient of determination) showed the relationships in the prediction model.
Effects of Water Stress on Vegetative and Reproductive Traits of Three Commercial Cotton Varieties in Field Conditions in Central Iran
Authors: AREFI ALI NADERI , TAVAKOLI AlIREZA 
Published: December 2021

Abstract
Backgroundwater scarcity is one of the most important factors that restricts crop production specially, cotton which must planted in areas without cold temperature limitation. Most of such area in Iran encounters drought events, hot temperatures and high atmospheric evaporative demand. So, understanding of stress severity and cultivar responses will help to better management of crop in stress conditions. Our previous study showed that cultivar responses in view of some physiological and morphological aspects were highly different in water stress condition. In this study we focused on yield formatting traits.Results Three cotton commercial varieties; Khorshid, Khordad and Varamin studied in sever, mild and without water stress. In normal condition zero type cultivar, the khorshid, produced the highest seed cotton yield. Varamin cultivar had more and longer sympodial branches which could raise it’s yield. Also, Varamin cultivar’s seed cotton yield was higher than the others (3617 kg -1 ha compared with 2477 and 3060 for khordad and khorshid, respectively). Khorshid was superior to the others at sever water stress.ConclusionSeed cotton yield showed high correlation whit boll number and boll weight and vegetative aspects such as plant height, node number and sympodial branches number. Management for developing more sympodial branches results in higher bud and flower and will increase the yield. Totally, we recommend Khorshid and Varamin cultivars for normal condition and Khorshid for sever stress conditions.
Effects of Non-Darcy Mixed Convection Over a Horizontal Cone With Different Convective Boundary Conditions Incorporating Gyrotactic Microorganisms On Dispersion
Authors: Ferdows M. , Alshuraiaan Bader , Nima Nayema Islam 
Published: December 2021

Abstract
This paper discusses an investigation of the influence of dispersion impact on mixed convection flow over a horizontal cone within a non-Darcy porous medium subjected to convective boundary conditions. By imposing appropriate similarity transformations, the nonlinear partial differential equations governing flow, temperature, concentration, and microbe fields are reduced to a system of ordinary differential equations, which are then solved using the MATLAB BVP4C function. In a few circumstances, the research is brought to a strong conclusion by comparing the findings of the current study to previously published works. Mixed convection parameter λ, buoyancy parameters N1,N2, Lewis parameter Le, bioconvection lewis parameter Lb, Bioconvection peclet number Pe, Biot number Bi, Biot number of Mass transfer Bi,m and also Biot number of motile microorganism transfer Bi,n are all numerically calculated for various values of the dimensionless parameters of the problem. The results also reveal that, in the presence of dispersion effects, these parameters greatly influence the heat, mass, and motile microorganism transfer rates, as well as the corresponding velocity, temperature, concentration, and motile microorganism profiles.
Site-Specific Variation in Bacterial Loads of Wooden Nest Boxes in the Pre-Breeding Period
Authors: Zabłotni Agnieszka , Kaliński Adam , Bańbura Mirosława , Glądalski Michał , Markowski Marcin , Skwarska Joanna , Wawrzyniak Jarosław , Bańbura Jerzy 
Published: December 2021

Abstract
Among environmental factors affecting life - history traits of birds breeding in nest boxes, an influence of microbial communities is relatively poorly understood. In this study, nest boxes used for breeding by great tit (Parus major) and blue tit (Cyanistes caeruleus) were sampled before the start of the breeding season to assess the bacterial loads of the nest box. Samples from the entrance hole and the interior of the nest box were taken at two different study sites: an urban parkland and a natural forest. Nest boxes were sampled to check if their bacterial loads differed between habitats. The second objective of this study was to check whether the occupancy of the nest boxes during the previous season would influence the bacterial load of the nest box. To verify this prediction, two categories of nest boxes were sampled at both study sites: nest boxes occupied by any of the two tit species in the previous season for breeding and nest boxes that had remained empty that year. The bacterial load of the nest box was significantly higher in the forest study area in both the occupied and unoccupied nest boxes. The nest boxes used for breeding in the previous season had significantly higher bacterial loads, but only in the forest area. Our results suggest that the bacterial load of the nest box can vary between habitats and may be positively related to the presence of the nests in the previous breeding season.
Reducing the Number of Measuring Points of the LED-Based Colorimetric Probe
Authors: Arbanas Milos , Batinic Branislav , Bajic Jovan , Vasiljevic-Toskic Marko , Brkic Miodrag , Rajs Vladimir 
Published: December 2021

Abstract
In this paper, reducing the number of necessary measuring points for estimating a reflected electromagnetic spectrum of a printed color patch is presented. In our previous work, a machine learning-based method was proven to be superior to Cubic Hermite interpolation in estimating spectrum based on six measured values. Now, the new hypothesis is that the number of measuring points could be decreased without the significant loss of the spectrum estimation. The ECI2002 test chart was used to create the dataset, which was further divided into training and test subset. For all the colors on the test chart, the measurements were performed on printed patches with the device proposed in our previous work, as well as with the commercial spectrophotometer X-Rite i1 Publish Pro2, which were then used as the ground truth, or reference values. The Artificial Neural Networks were trained to estimate spectrums based on measurements acquired with our device. The results proved satisfactory even when the number of measuring points is reduced from six to three.
Structural and Dynamic Properties of Hydrophobic Eutectic Solvents Based on Menthol and Fatty Acids: a Molecular Dynamics Simulation Study
Authors: Pour Samaneh Barani , Sardroodi Jaber Jahanbin , Ebrahimzadeh Alireza Rastkar 
Published: December 2021

Abstract
The structural and dynamical properties of the binary mixture of Menthol (MEN) and Fatty acids (FAs) were investigated using molecular dynamics simulations. We focused on the relationship between the structural and dynamical properties of the eutectic mixtures of MEN and FAs with different molar percentages of FAs. Structural properties of the eutectic mixtures were characterized by calculating the combined distribution functions(CDFs), the radial distribution functions (RDFs), and the angular distribution functions (ADFs), and the Hydrogen bonding network between species and Spatial distribution functions (SDF). Further interaction between menthol and Caprylic acid molecules was confirmed by the results of these analyzes. Also, the transport properties of the mixtures were investigated by using the mean square displacement (MSD) of the centers of mass of the species, self-diffusion coefficients and vector reorientation dynamics (VRD) of bonds. The simulation results indicated that intermolecular interactions have a significant effect on the dynamic properties of species.
Is Dynamic Spino-Pelvic Alignment During Gait Associated with Quality of Life in Patients with Degenerative Lumbar Spinal Canal Stenosis?
Authors: Miura Takuya , Tominaga Ryoji , Sato Keita , Endo Tatsuya , Iwabuchi Masumi , Ito Toshikazu , Shirado Osamu 
Published: December 2021

Abstract
This study aims to investigate the relationship between dynamic alignment of the spine and pelvis during gait and quality of life (QOL) in lumbar spinal canal stenosis (LSS) patients. We evaluated QOL using the Oswestry Disability Index (ODI), trunk and hip muscle strength as physical function, static spinal alignment, and dynamic spinal/pelvic alignment during gait. The relationship between the ODI score and physical function or static and dynamic alignment were examined. A total of 30 preoperative patients with LSS were participated in this study. ODI score significantly correlated with trunk extension strength (r = -0.559, p = 0.002), hip extension strength (r = -0.473, p = 0.011), maximum flexion angle of spine during gait (r = -0.551, p = 0.002) and maximum anterior tilt angle of pelvis (r = 0.528, p = 0.004). Multiple regression analysis showed that trunk extension strength (standardized β; - 0.35), maximum spinal flexion angle (standardized β; - 0.51) and hip extension strength (standardized β; - 0.40) significantly affected the ODI score, with adjusted coefficient of determination of 0.62. The results of this study showed that the LSS patients with weak hip or trunk extensor muscles, a greater angle of pelvic tilt or a less spinal flexion during gait had a lower QOL.
WITHDRAWN: Neonatal Circumcision: Public Health Necessity or Ethical Dilemma? – Systematic Review
Authors: Morris Brian J. , Rivin Beth , Krieger John N. 
Published: December 2021

Abstract
Male circumcision (MC) is common in many countries. Despite clear health benefits, ethical arguments have been invoked opposing MC, especially when performed neonatally (NMC). NMC is when most MCs are performed in developed countries. Here we provide the first PRISMA-compliant systematic review of the disparate evidence of ethical and legal arguments concerning NMC and MC of older boys. Searches were performed of PubMed, Embase and Scopus for publications relevant to ethical and legal aspects of MC in developed Anglophone and European countries. This led to retrieval of 48 articles meeting the inclusion criteria. A further 18 articles and 16 Internet publications were identified from searches of bibliographies of articles retrieved. Two more were supplied by a legal academic colleague. In total 84 publications were reviewed. The literature revealed arguments by some that parent-approved MC of a nonconsenting child is unethical. But parental consent also applies to vaccination and all other medical therapies in children. Strong data support a conclusion that: (1) NMC is low risk, (2) NMC provides immediate and lifetime medical and health benefits, and (3) NMC has no adverse effect on sexual function and pleasure. The United Nations Convention on the Rights of the Child articulates the right to health and focuses on the best interests of the child as its guiding principle. Discouraging or denying MC to neonates is arguably unethical, given the overwhelming health benefits. Legal scholars regard case-law as supporting the legality of NMC. Ethical and legal arguments support the rights of males of all ages to lifetime protection against infection and diseases caused by lack of MC. Arguments opposing NMC generally involve distortion of the medical evidence, poorly designed studies and opinions. Opposition to NMC goes against the principles of evidence-based medicine used in reviews conducted to develop pediatric policies in support of optimum public health, sexual health, mental health, and human rights.
GTSception: A Deep Learning EEG Emotion Recognition Model Based on Fusion of Global, Time Domain and Frequency Domain Feature Extraction
Authors: Zhao Jian , Zhang ZhiWei , Qiu Jinping , Shi Lijuan , KUANG Zhejun , Jing Weipeng , Zhu Zhan-peng 
Published: December 2021

Abstract
With the rapid development of deep learning in recent years, automatic electroencephalography (EEG) emotion recognition has been widely concerned. At present, most deep learning methods do not normalize EEG data properly and do not fully extract the features of time and frequency domain, which will affect the accuracy of EEG emotion recognition. To solve these problems, we propose GTScepeion, a deep learning EEG emotion recognition model. In pre-processing, the EEG time slicing data including channels were pre-processed. In our model, global convolution kernels are used to extract overall semantic features, followed by three kinds of temporal convolution kernels representing different emotional periods, followed by two kinds of spatial convolution kernels highlighting brain hemispheric differences to extract spatial features, and finally emotions are dichotomy classified by the full connected layer. The experiments is based on the DEAP dataset, and our model can effectively normalize the data and fully extract features. For Arousal, ours is 8.76% higher than the current optimal emotion recognition model based on Inception. For Valence, the best accuracy of our model reaches 91.51%.
Explicit Modelling of Multi-Period Setup Times in Proportional Lot-Sizing Problem with Constant Capacity
Authors: Kaczmarczyk Waldemar 
Published: December 2021

Abstract
The planning horizon of small bucket models is often divided into many fictitious micro-periods, with non-zero demand only in the last micro-period of each real (macro-)period. On the one hand, such models ensure schedules with short cycle times and low work-in-process inventory in multilevel systems; on the other, they make setup times that are longer than a single period more likely. This paper presents a new mixed-integer programming model for the case with setup operations that overlap multiple periods. The new model assumes that the capacity is constant in the whole planning horizon and explicitly determines the entire schedule of each changeover. Moreover, a two-level MIP heuristic is presented that uses model-specific cuts to fix a priori some minor decisions. The results of the computational experiments show that the new model and MIP heuristic require a substantially smaller computational effort from a standard MIP solver than the known models.MSC Classification: 90B30 , 90C11
Soil Microcosms for Bioaugmentation With Fungal Isolates to Remediate Petroleum Hydrocarbon-contaminated Soil
Authors: Daâssi Dalel , Almaghribi Fatimah Qabil 
Published: December 2021

Abstract
The aim of this work was to isolate indigenous PAH degrading-fungi from petroleum contaminated soil and exogenous ligninolytic strains from decaying-wood, with the ability to secrete diverse enzyme activity. A total of ten ligninolytic fungal isolates and two native strains, has been successfully isolated, screened and identified. The phylogenetic analysis revealed that the indigenous fungi (KBR1 and KB8) belong to the genus Aspergillus niger and tubingensis. While the ligninolytic exogenous PAH-degrading strains namely KBR1-1, KB4, KB2 and LB3 were affiliated to different genera like Syncephalastrum sp, Paecilomyces formosus, Fusarium chlamydosporum, and Coniochaeta sp., respectively. Basis on the taxonomic analysis, enzymatic activities and the hydrocarbons removal rates, single fungal culture employing the strain LB3, KB4, KBR1 and the mixed culture (LB3+KB4) were selected to be used in soil microcosms treatments. The Total petroleum hydrocarbons (TPH), fungal growth rates, BOD5/COD ratios and GC-MS analysis, were determined in all soil microcosmos treatments (SMT) and compared with those of the control (SMU). After 60 days of culture incubation, the highest rate of TPH degradation was recorded in SMT[KB4] by approximately 92±2.35% followed by SMT[KBR1] then SMT[LB3+KB4] with 86.66±1.83% and 85.14±2.21%, respectively.