bluuebunny/crossref_metadata_2025_split huggingface dataset:
Amyloid β / PKC-dependent alterations in NMDA receptor composition are detected in early stages of Alzheimer´s disease
Authors: Ortiz-Sanz Carolina , Balantzategi Uxue , Quintela-López Tania , Ruiz Asier , Luchena Celia , Zuazo-Ibarra Jone , Capetillo-Zarate Estibaliz , Matute Carlos , Zugaza José L. , Alberdi Elena 
Published: March 2022

AbstractAmyloid beta (Aβ)-mediated synapse dysfunction is an early event in Alzheimer’s disease (AD) pathogenesis and previous studies suggest that NMDA receptor (NMDAR) dysregulation may contribute to these pathological effects. Although Aβ peptides impair NMDAR expression and activity, the mechanisms mediating these alterations in the early stages of AD are unclear. Here, we observed that NMDAR subunit NR2B and PSD-95 levels were aberrantly upregulated and correlated with Aβ42 load in human postsynaptic fractions of the prefrontal cortex in early stages of AD patients, as well as in the hippocampus of 3xTg-AD mice. Importantly, NR2B and PSD95 dysregulation was revealed by an increased expression of both proteins in Aβ-injected mouse hippocampi. In cultured neurons, Aβ oligomers increased the NR2B-containing NMDAR density in neuronal membranes and the NMDA-induced intracellular Ca2+ increase, in addition to colocalization in dendrites of NR2B subunit and PSD95. Mechanistically, Aβ oligomers required integrin β1 to promote synaptic location and function of NR2B-containing NMDARs and PSD95 by phosphorylation through classic PKCs. These results provide evidence that Aβ oligomers modify the contribution of NR2B to NMDAR composition and function in the early stages of AD through an integrin β1 and PKC-dependent pathway. These data reveal a novel role of Aβ oligomers in synaptic dysfunction that may be relevant to early-stage AD pathogenesis.
Pyruvate kinase L/R links metabolism dysfunction to neuroendocrine differentiation of prostate cancer by ZBTB10 deficiency
Authors: Wen Yu-Ching , Chen Wei-Yu , Tram Van Thi Ngoc , Yeh Hsiu-Lien , Chen Wei-Hao , Jiang Kuo-Ching , Abou-Kheir Wassim , Huang Jiaoti , Hsiao Michael , Liu Yen-Nien 
Published: March 2022

AbstractNeuroendocrine differentiation (NED) frequently occurs in androgen-deprivation therapy (ADT)-resistant prostate cancer (PCa) and is typically associated with metabolic pathway alterations, acquisition of lineage plasticity, and malignancy. There is no conventional therapeutic approach for PCa patients with NED pathologic features because the molecular targets are unknown. Here, we evaluated the regulatory mechanism of NED-associated metabolic reprogramming induced by ADT. We detected that the loss of the androgen-responsive transcription factor, zinc finger, and BTB domain containing 10 (ZBTB10), can activate pyruvate kinase L/R (PKLR) to enhance a NED response that is associated with glucose uptake by PCa cells. PKLR exhibits a tumor-promoting effect in PCa after ADT, but ZBTB10 can compensate for the glucose metabolism and NED capacity of PKLR through the direct transcriptional downregulation of PKLR. Targeting PKLR by drug repurposing with FDA-approved compounds can reduce the aggressiveness and NED of ADT-resistant PCa. We demonstrated that PKLR acts as a modulator to activate NED in PCa enhancement by loss of ZBTB10, thereby enabling PCa cells to mount a glycolysis response essential for therapeutic resistance. Our findings highlight the broad relation between NED and metabolic dysfunction to provide gene expression-based biomarkers for NEPC treatment.
End-point RT-PCR based on a conservation landscape for SARS-COV-2 detection
Authors: Cruz-Rangel Armando , Gómez-Romero Laura , Cisneros-Villanueva Mireya , de Anda Jáuregui G. , Luna-Pineda Victor , Cedro-Tanda Alberto , Campos-Romero Abraham , Mendoza-Vargas Alfredo , Reyes-Grajeda J. P. , Hidalgo-Miranda Alfredo ,   COVID-19 Consortium INMEGEN, Herrera Luis A. , Hidalgo-Miranda Alfredo , Mendoza-Vargas Alfredo , Reyes-Grajeda Juan P. , Vadillo-Ortega Felipe , Cedro-Tanda Alberto , Peñaloza Fernando , Frías-Jimenez Emmanuel , Ruiz Rosaura , Angulo Ofelia , Cisneros-Villanueva Mireya , Hernandez-Morales Jose S. , Moreno Bernardo , Hernández-Cruz Irwin A. , Herrera César A. , García Francisco , González-Woge Miguel A. , Munguía-Garza Paulina , Luna-Maldonado Fernando , Sanchez-Vizcarra Antonia , Osnaya Vincent G. , Medina-Molotla Nelly , Alfaro-Mora Yair , Caceres-Gutiérrez Rodrigo E. , Tolentino-Garcia Laura , Moreno-Camacho José Luis , Rodriguez-Gallegos Jorge , Esparza Marco A. Luna-Ruiz , Rojas Miguel Ángel Fernández , Rosas-Escobar Patricia , Román-González Sergio A. , Escobar-Arrazola Marco A. , Canseco-Mendez Julio C. , Ortiz-Soriano Diana R. , Dominguez-Ortiz Julieta , Gonzalez-Barrera Ana D. , Aparicio-Bautista Diana I. , Rodriguez Martinez Griselda , Rangel Armando Cruz , Herrera Luis A. , Vadillo-Ortega Felipe 
Published: March 2022

AbstractEnd-point RT-PCR is a suitable alternative diagnostic technique since it is cheaper than RT-qPCR tests and can be implemented on a massive scale in low- and middle-income countries. In this work, a bioinformatic approach to guide the design of PCR primers was developed, and an alternative diagnostic test based on end-point PCR was designed. End-point PCR primers were designed through conservation analysis based on kmer frequency in SARS-CoV-2 and human respiratory pathogen genomes. Highly conserved regions were identified for primer design, and the resulting PCR primers were used to amplify 871 nasopharyngeal human samples with a previous RT-qPCR based SARS-CoV-2 diagnosis. The diagnostic test showed high accuracy in identifying SARS-CoV-2-positive samples including B.1.1.7, P.1, B.1.427/B.1.429 and B.1.617.2/ AY samples with a detection limit of 7.2 viral copies/µL. In addition, this test could discern SARS-CoV-2 infection from other viral infections with COVID-19-like symptomatology. The designed end-point PCR diagnostic test to detect SARS-CoV-2 is a suitable alternative to RT-qPCR. Since the proposed bioinformatic approach can be easily applied in thousands of viral genomes and over highly divergent strains, it can be used as a PCR design tool as new SARS-CoV-2 variants emerge. Therefore, this end-point PCR test could be employed in epidemiological surveillance to detect new SARS-CoV-2 variants as they emerge and propagate.
Classification of ransomware using different types of neural networks
Authors: Madani Houria , Ouerdi Noura , Boumesaoud Ahmed , Azizi Abdelmalek 
Published: March 2022

AbstractMalware threat the security of computers and Internet. Among the diversity of malware, we have “ransomware”. Its main objective is to prevent and block access to user data and computers in exchange for a ransom, once paid, the data will be liberated. Researchers and developers are rushing to find reliable and safe techniques and methods to detect Ransomware to protect the Internet user from such threats. Among the techniques generally used to detect malware are machine learning techniques. In this paper, we will discuss the different types of neural networks, the related work of each type, aiming at the classification of malware in general and ransomware in particular. After this study, we will talk about the adopted methodology for the implementation of our neural network model (multilayer perceptron). We tested this model, firstly, with the binary detection whether it is malware or goodware, and secondly, with the classification of the nine families of Ransomware by taking the vector of our previous work and we will make a comparison of the accuracy rate of the instances that are correctly classified.
A novel lipase with dual localisation in Trypanosoma brucei
Authors: Monic S.G. , Lamy A. , Thonnus M. , Bizarra-Rebelo T. , Bringaud F. , Smith T. K. , Figueiredo L. M. , Rivière L. 
Published: March 2022

AbstractPhospholipases are esterases involved in lipid catabolism. In pathogenic micro-organisms (bacteria, fungi, parasites) they often play a critical role in virulence and pathogenicity. A few phospholipases (PL) have been characterised so far at the gene and protein level in unicellular parasites including African trypanosomes (AT). They could play a role in different processes such as host–pathogen interaction, antigenic variation, intermediary metabolism. By mining the genome database of AT we found putative new phospholipase candidate genes and here we provided biochemical evidence that one of these has lipolytic activity. This protein has a unique non-canonical glycosome targeting signal responsible for its dual localisation in the cytosol and the peroxisomes-related organelles named glycosomes. We also show that this new phospholipase is excreted by these pathogens and that antibodies directed against this protein are generated during an experimental infection withT. brucei gambiense, a subspecies responsible for infection in humans. This feature makes this protein a possible tool for diagnosis.
Terrestrial arthropods broadly possess endogenous phytohormones auxin and cytokinins
Authors: Tokuda Makoto , Suzuki Yoshihito , Fujita Shohei , Matsuda Hiroki , Adachi-Fukunaga Shuhei , Elsayed Ayman Khamis 
Published: March 2022

AbstractSome herbivorous insects possess the ability to synthesize phytohormones and are considered to use them for manipulating their host plants, but how these insects acquired the ability remains unclear. We investigated endogenous levels of auxin (IAA) and cytokinins (iP and tZ), including their ribosides (iPR and tZR), in various terrestrial arthropod taxa. Surprisingly, IAA was detected in all arthropods analysed. In contrast, tZ and/or tZR was detected only in some taxa. Endogenous levels of IAA were not significantly different among groups with different feeding habits, but gall inducers possessed significantly higher levels of iPR, tZ and tZR. Ancestral state reconstruction of the ability to synthesize tZ and tZR revealed that the trait has only been acquired in taxa containing gall inducers. Our results strongly suggest critical role of the cytokinin synthetic ability in the evolution of gall-inducing habit and IAA has some function in arthropods.
Identifying and extracting bark key features of 42 tree species using convolutional neural networks and class activation mapping
Authors: Kim Tae Kyung , Hong Jeonghyun , Ryu Daun , Kim Sukyung , Byeon Si Yeon , Huh Woojin , Kim Kunhyo , Baek Gyu Heon , Kim Hyun Seok 
Published: March 2022

AbstractThe significance of automatic plant identification has already been recognized by academia and industry. There were several attempts to utilize leaves and flowers for identification; however, bark also could be beneficial, especially for trees, due to its consistency throughout the seasons and its easy accessibility, even in high crown conditions. Previous studies regarding bark identification have mostly contributed quantitatively to increasing classification accuracy. However, ever since computer vision algorithms surpassed the identification ability of humans, an open question arises as to how machines successfully interpret and unravel the complicated patterns of barks. Here, we trained two convolutional neural networks (CNNs) with distinct architectures using a large-scale bark image dataset and applied class activation mapping (CAM) aggregation to investigate diagnostic keys for identifying each species. CNNs could identify the barks of 42 species with > 90% accuracy, and the overall accuracies showed a small difference between the two models. Diagnostic keys matched with salient shapes, which were also easily recognized by human eyes, and were typified as blisters, horizontal and vertical stripes, lenticels of various shapes, and vertical crevices and clefts. The two models exhibited disparate quality in the diagnostic features: the old and less complex model showed more general and well-matching patterns, while the better-performing model with much deeper layers indicated local patterns less relevant to barks. CNNs were also capable of predicting untrained species by 41.98% and 48.67% within the correct genus and family, respectively. Our methodologies and findings are potentially applicable to identify and visualize crucial traits of other plant organs.
A viability assay combining palladium compound treatment with quantitative PCR to detect viable Mycobacterium avium subsp. paratuberculosis cells
Authors: Cechova Martina , Beinhauerova Monika , Babak Vladimir , Kralik Petr 
Published: March 2022

AbstractMycobacterium aviumsubsp. paratuberculosis(MAP) is a pathogenic bacterium causing the paratuberculosis, chronic and infectious disease common particularly in wild and domestic ruminants. Currently, culture techniques to detect viable MAP are still used most commonly, although these require a long incubation period. Consequently, a faster molecular method for assessing MAP cell viability based on cell membrane integrity was introduced consisting of sample treatment with the intercalation dye propidium monoazide (PMA) followed by quantitative PCR (qPCR). However, the PMA-qPCR assay is complicated by demanding procedures involving work in a darkroom and on ice. In this study, we therefore optimized a viability assay combining sample treatment with palladium (Pd) compounds as an alternative viability marker to PMA, which does not require such laborious procedures, with subsequent qPCR. The optimized Pd-qPCR conditions consisting of 90 min exposure to 30 µM bis(benzonitrile)dichloropalladium(II) or 30 µM palladium(II)acetate at 5 °C and using ultrapure water as a resuspension medium resulted in differences in quantification cycle (Cq) values between treated live and dead MAP cells of 8.5 and 7.9, respectively, corresponding to approximately 2.5 log units. In addition, Pd-qPCR proved to be superior to PMA-qPCR in distinguishing between live and dead MAP cells. The Pd-qPCR viability assay thus has the potential to replace time-consuming culture methods and demanding PMA-qPCR in the detection and quantification of viable MAP cells with possible application in food, feed, clinical and environmental samples.
Dissipated electroosmotic EMHD hybrid nanofluid flow through the micro-channel
Authors: Bilal M. , Asghar I. , Ramzan M. , Nisar K. S. , Aty A.-H Abdel , Yahia I. S. , Ghazwani H. A. S. 
Published: March 2022

AbstractThe main objective of the present study is to explore the effects of electromagnetohydrodynamics electroosmotic flow of hybrid nanofluid through circular cylindrical microchannels. An analysis of hybrid nanofluid consisting of four different nanomaterials i.e., single and multiwall carbon nanotubes, silver, and copper is carried out. Yamada–Ota model is employed for the single and multi wall carbon nanotubes, whereas, Xue model is used for the Silver and Copper hybrid nanofluid for specifying the thermal conductivity. The imposed pressure gradient, electromagnetic field and electroosmosis actuated the fluid flow. The flow of heat transfer and Nusselt number with the account of various effects of Joule heating and viscous dissipation under the circumstances of constant heat flux are discussed graphically. The governing system of equations is molded into a system of coupled, nonlinear ordinary differential equations. The shooting technique is used to extract the numerical solutions of the converted system of equations. Also, the outturn of different parameters like Hartman number, the strength of lateral direction electric field, EDL (electric double layer) electrokinetic width, Joule heating parameters on the temperature, and velocity are investigated. The conversion of simple fluid to hybrid nanofluid has greatly alteration in the present model. It has enhanced the thermal properties of fluid. It is also noted that $$SWCNT-MWCNT$$

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based hybrid nanofluid has most influential impact on Nusselt number, temperature distribution and velocity of the fluid. This attempt is useful for the designing of effectual electromagnetic appliances and exquisite.
Acid red 18 removal from aqueous solution by nanocrystalline granular ferric hydroxide (GFH); optimization by response surface methodology & genetic-algorithm
Authors: Hamidi Farshad , Dehghani Mohammad Hadi , Kasraee Mahboobeh , Salari Mehdi , Shiri Leila , Mahvi Amir Hossein 
Published: March 2022

AbstractThe need for fresh water is more than before by population growth, and industrial development have affected the quality of water supplies, one of the important reason for water contamination is synthetic dyes and their extensive use in industries. Adsorption has been considered as a common methods for dye removal from waters. In this study, Acid Red18 removal in batch mode by using Granular Ferric Hydroxide (GFH) was investigated. The GFH characterized by XRD, FESEM and FTIR analysis. Experiments were designed using RSM-CCD method. The maximum removal efficiency was obtained 78.59% at pH = 5, GFH dosage = 2 g/l, AR18 concentration = 77.5 mg/l and 85 min of contact time. Optimization with RSM and Genetic Algorithm carried out and is similar together. The non-linear adsorption Isotherm and kinetic fitted with Freundlich (R2 = 0.978) and pseudo-second-order (R2 = 0.989) models, respectively. Thermodynamic studies showed that the AR18 adsorption is endothermic process and GFH nature was found spontaneous.
A role for the periplasmic adaptor protein AcrA in vetting substrate access to the RND efflux transporter AcrB
Authors: Alav Ilyas , Bavro Vassiliy N. , Blair Jessica M. A. 
Published: March 2022

AbstractTripartite resistance-nodulation-division (RND) efflux pumps, such as AcrAB-TolC of Salmonella Typhimurium, contribute to antibiotic resistance and comprise an inner membrane RND-transporter, an outer membrane factor, and a periplasmic adaptor protein (PAP). The role of the PAP in the assembly and active transport process remains poorly understood. Here, we identify the functionally critical residues involved in PAP-RND-transporter binding between AcrA and AcrB and show that the corresponding RND-binding residues in the closely related PAP AcrE, are also important for its interaction with AcrB. We also report a residue in the membrane-proximal domain of AcrA, that when mutated, differentially affects the transport of substrates utilising different AcrB efflux channels, namely channels 1 and 2. This supports a potential role for the PAP in sensing the substrate-occupied state of the proximal binding pocket of the transporter and substrate vetting. Understanding the PAP’s role in the assembly and function of tripartite RND pumps can guide novel ways to inhibit their function to combat antibiotic resistance.
Long‐time target tracking algorithm based on re‐detection multi‐feature fusion
Authors: Qu Junsuo , Tang Chenxue , Zhang Yuan , Zhou Kai , Razi Abolfazl 
Published: March 2022

AbstractThis paper considers the problem of long‐term target tracking in complex scenes when tracking failures are unavoidable due to illumination change, target deformation, scale change, motion blur, and other factors. More specifically, a target tracking algorithm, called re‐detection multi‐feature fusion, is proposed based on the fusion of scale‐adaptive kernel correlation filtering and re‐detection. The target tracking algorithm trains three kernel correlation filters based on the histogram of oriented gradients, colour name, and local binary pattern features and then obtains the fusion weight of response graphs corresponding to different features based on average peak correlation energy criterion and uses weighted average to complete the position estimation of the tracked target. In order to deal with the problem that the target is occluded and disappears in the tracking process, a random fern classifier is trained to perform re‐detection when the target is occluded. After comparing the OTB‐50 target tracking dataset, the experimental results show that the proposed tracker can track the target well in the occlusion attribute video sequence in the OTB‐100 test dataset and has a certain improvement in tracking accuracy and success rate compared with the traditional correlation filter tracker.
An adaptive‐impedance fault current limiter for accelerating fault current suppression in MMC‐HVDC systems
Authors: Duan Pan , Fu Zhengzheng , Yang Ming , Sima Wenxia 
Published: March 2022

AbstractDC fault clearance is one of the critical issues for the modular‐multilevel‐converter‐based high voltage direct current (MMC‐HVDC) systems. Employing a hybrid DC circuit breaker (H‐DCCB) to isolate the faulty line is a typical method to achieve fast fault clearance. However, the H‐DCCB has to interrupt the fault current and absorb the energy up to tens of megawatts in several milliseconds. Through theoretical analysis of the interruption process using the H‐DCCB, reducing the equivalent inductance of the fault circuit during the fault falling stage is recommended to accelerate the fault current suppression for the H‐DCCBs. This paper proposes a novel adaptive‐impedance fault current limiter (AFCL), which contains two coupled DC reactors and an energy absorption branch (EAB). The proposed AFCL can automatically limit the fault current during the current rising stage and works as a DC reactor with a fixed equivalent inductance through a two‐state model analysis. Meanwhile, the AFCL contributes to accelerating the decline of the current by adaptively reducing the inductance of the discharge circuit. Consequently, the fault current suppression time and the energy absorbed by the H‐DCCB are reduced. Simulation case studies and hardware experiments are carried out to verify the performance and practicality of the proposed AFCL.
The bow‐tie antenna: Performance limitations and improvements
Authors: Gonçalves Licursi de Mello Rafael , Lepage Anne Claire , Begaud Xavier 
Published: March 2022

AbstractThe simple planar shape and wideband input impedance of the bow‐tie antenna make it suitable to diverse wideband applications. However, the radiation pattern of this kind of antenna is not stable and the gain in the broadside direction deteriorates with increasing frequencies. In this article, the operation of both the triangular and the rounded‐edge versions of the bow‐tie antenna is thoroughly investigated and the performance thereof is compared. A technique to maximise such performance, which consists of inserting radially aligned grooves in the radiators' ends, is presented. The bandwidth, defined by a broadside gain of at least 2 dBi and a reflection coefficient magnitude of less than −10 dB, is improved from 85.7% to 97.9% in simulations. Such an improvement is validated through the measurement of two prototypes, in which the presented technique also increases the broadside gain in up to 1.5 dB, with no significant change in the shapes of the radiation patterns and in the reflection coefficient magnitude.