bluuebunny/crossref_metadata_2025_split huggingface dataset:
Schizothorax richardsonii dsRNA dependent protein kinase has three double-stranded RNA binding motifs with a promoter lacking conserved kinase sequence
Authors: Saxena Ankur , Belwal Kiran , Chaturvedi Preeti , Pande Amit 
Published: November 2019

Abstract
Background: Double stranded RNA (dsRNA) dependent protein kinase (PKR) is an interferon (IFN) stimulated antiviral protein. It inhibits protein synthesis by phosphorylation of the eukaryotic translation initiation factor 2-alpha (eIF2-α) by its serine-threonine kinase activity that prevents virus replication. This is the first report on the in silico analysis of PKR coding region and its promoter from a Coldwater fish of the Indian Himalayan region. Snow trout, Schizothorax richardsonii is an important Coldwater food fish. It is being over fished and therefore requires conservation. Being a vulnerable species it is listed under the red list of IUCN. Here we discuss the identification, cloning and sequencing of PKR coding region and its promoter. Results: We have revealed the complete coding region of dsRNA dependent protein kinase (PKR) and its promoter from Schizothorax richardsonii , one of the several species of snow trout inhabiting sub-Himalayan fresh water bodies. An amplicon of 2884bp containing 5ʹ and 3ʹ untranslated regions (UTR) of 234 and 558 bases was obtained while the deduced open reading frame (ORF) of 2076 bases encoded a polypeptide of 691 amino-acids. Snow trout PKR protein contains three double stranded RNA binding motifs (dsRBM) at N terminal, besides possessing a serine/threonine protein kinase and a C terminal catalytic domain. Moreover, a stretch of 791 nucleotide bases was identified as the promoter upstream the ORF. The identified promoter has two interferon stimulated response elements (ISRE) besides the presence of core promoter elements. Moreover, the snow trout PKR promoter has a TATA box but lacks kinase conserved sequence (KCS) that is present in mammalian PKR promoters. Conclusion: The promoter of snow trout was identified as a stretch of 791 nucleotide bases. It has two interferon-stimulated response elements (ISRE) besides core promoter elements. Intriguingly, unlike the mammalian PKR promoter, the snow trout PKR promoter has a TATA box but lacks the conserved kinase sequence (KCS) present in human counterpart. Keywords: Schizothorax richardsonii , Interferon Stimulated Genes, PKR protein, Antiviral state, Homology modeling, dsRNA binding protein kinase
Evidence of pathogenic zoonotic tick-borne Rickettsia and Borrelia spp. in some communal farms in the Eastern Cape Province, South Africa
Authors: ADELABU OLUSESAN , Iweriebor Benson Chuks , Obi Larry Chikwelu , Okoh Anthony Ifeanyi 
Published: November 2019

Abstract
The abundance of tick populations in South Africa represents a probable risk for both animal and human health. Rickettsia and Borrelia are well-known significant agents of emerging human tick-borne infectious diseases throughout the world. Nevertheless, the epidemiology of their infections has been underreported in South Africa, Therefore, the aim of this study was to profile for zoonotic Rickettsia and Borrelia species from ticks infesting domesticated animals in the Eastern Cape, South Africa. Morphological and molecular identification techniques were conducted on 1,200 tick samples collected from domestic animals before screening for the target bacterial pathogens. The molecular identification of the tick samples was based on the amplification of the 12S rRNA mitochondrial DNA while those of Rickettsia and Borrelia species were carried out by amplifying fragments of glt A, omp A and omp B genes for Rickettsia and fla B gene for Borrelia spp. Thereafter, the positive ticks, Borrelia and Rickettsia omp B amplicons were sequenced and further analysed. Eight species of ticks belonging to three genera; Rhipicephalus, Amblyomma, and Haemaphysalis were identified. A total of 320 (27%) samples were confirmed positive for Rickettsia out of which 74 (23%) were positive for both omp A and omp B genes. Phylogenetic analysis of omp B revealed a high homology to rickettsial reference strains from GenBank, while there was no positive result for Borrelia. The generated sequences showed 99.1 to 100% homology with R. africae -KX227790 (100%), R. parkeri - KY113111 (99.8%), R .peacock (99.3%) and R. slovaca - KJ675445, JX683122 (99.1%) representative sequences in GenBank. The findings from this study revealed that ticks collected from domesticated animals were parasitized by Rickettsia species with possible zoonotic potential, which is detrimental to human health if bitten by infected ticks.
Agronomic Responses of Maize Hybrids to Row Spacing and Plant Population in the Summer and Winter Seasons in Brazil
Authors: Dias Fagner Souto , Rezende Wemerson Mendonça , Zuffo Leandro Tonello , Caixeta Diego Gonçalves , Massensini Mateus André , Ribeiro José Ivo , DeLima Rodrigo Oliveira 
Published: November 2019

Brazil has two growing seasons for maize (Zea mays L.) production: summer and winter. The additional maize produced in the winter and the high‐yielding opportunities in the summer season make it important to understand responses of maize hybrids to row spacing and plant population across the two annual Brazilian growing seasons. In the 2015 to 2016 summer season and the 2016 winter season, maize response to plant population, ranging from 60,000 to 90,000 plants ha−1, was evaluated for three hybrids in 0.45‐, 0.60‐, 0.75‐, and 0.90‐m row spacing. Plant architecture traits, grain yield and yield components did not differ with row spacing, and their responses to plant population were not affected by hybrid type and/or row spacing. The DKB390PRO2 hybrid (single cross) demonstrated better grain yield performance in the summer, whereas the BG7049YH hybrid (three‐way cross) had the highest yield in the winter. Plant and ear height increased linearly in response to plant population in the summer season, whereas other plant architecture traits, ear leaf chlorophyll concentration, and grain yield components decreased linearly with increasing plant populations in both seasons. There was a quadratic response in maize grain yield to plant population, and it was maximized with 78,688 plants ha−1 in the summer, and 71,206 plants ha−1 in the winter. Our results show preliminary evidence that regardless of row spacing, maize grain yield can be maximized with DKB390 hybrid (single cross) with 78,500 plants ha−1 in the summer, and BG7049YH hybrid (three‐way) with 71,000 plants ha−1 in the winter season.Core Ideas

Regardless of summer or winter seasons, hybrid performance was not affected by row spacing.
Maize hybrids exhibited similar yield responses to row spacing and plant population.
Most of the yield components and plant architecture traits decreased linearly with increasing plant population.
The maximum grain yield occurring at lower plant population (71,000 plants ha−1) in the winter than in the summer season (78,500 plants ha−1).
Layer stacking disorder in Mg-Fe chlorites based on powder X-ray diffraction data
Authors: Luberda-Durnaś Katarzyna , Szczerba Marek , Lempart Małgorzata , Ciesielska Zuzanna , Derkowski Arkadiusz 
Published: November 2019

AbstractThe primary aim of this study was the accurate determination of unit-cell parameters and description of disorder in chlorites with semi-random stacking using common X-ray diffraction (XRD) data for bulk powder samples. In the case of ordered chlorite structures, comprehensive crystallographic information can be obtained based on powder XRD data. Problems arise for samples with semi-random stacking, where due to strong broadening of hkl peaks with k ≠ 3n, the determination of unit-cell parameters is demanding. In this study a complete set of information about the stacking sequences in chlorite structures was determined based on XRD pattern simulation, which included determining a fraction of layers shifted by ±1/3b, interstratification with different polytypes and 2:1 layer rotations.A carefully selected series of pure Mg-Fe tri-trioctahedral chlorites with iron content in the range from 0.1 to 3.9 atoms per half formula unit cell was used in the study. In addition, powder XRD patterns were carefully investigated for the broadening of the odd-number basal reflections to determine interstratification of 14 and 7 Å layers. These type of interstratifications were finally not found in any of the samples. This result was also confirmed by the XRD pattern simulations, assuming interstratification with R0 ordering.Based on h0l XRD reflections, all the studied chlorites were found to be the IIbb polytype with a monoclinic-shaped unit cell (β ≈ 97°). For three samples, the hkl reflections with k ≠ 3n were partially resolvable; therefore, a conventional indexing procedure was applied. Two of the chlorites were found to have a monoclinic cell (with α, γ = 90°). Nevertheless, among all the samples, the more general triclinic (pseudomonoclinic) crystal system with symmetry C1 was assumed, to calculate unit-cell parameters using Le Bail fitting.A detailed study of semi-random stacking sequences shows that simple consideration of the proportion of IIb-2 and IIb-4/6 polytypes, assuming equal content of IIb-4 and IIb-6, is not sufficient to fully model the stacking structure in chlorites. Several, more general, possible models were therefore considered. In the first approach, a parameter describing a shift into one of the ±1/3b directions (thus, the proportion of IIb-4 and IIb-6 polytypes) was refined. In the second approach, for samples with slightly distinguishable hkl reflections with k ≠ 3n, some kind of segregation of individual polytypes (IIb-2/4/6) was considered. In the third approach, a model with rotations of 2:1 layers about 0°, 120°, 240° was shown to have the lowest number of parameters to be optimized and therefore give the most reliable fits. In all of the studied samples, interstratification of different polytypes was revealed with the fraction of polytypes being different than IIbb ranging from 5 to 19%, as confirmed by fitting of h0l XRD reflections.
Measurement of gross alpha and beta activity concentration in groundwater of Jordan: groundwater quality, annual effective dose and lifetime risk assessment
Authors: Alomari Ahmad Hussein , Saleh Muneer Aziz , Hashim Suhairul , Alsayaheen Amal , Abdeldin Ismail , Bani khalaf Refaat 
Published: November 2019

Abstract
The current study was conducted to measure the activity concentration of the gross alpha and beta in 87 groundwater samples collected from the productive aquifers that constitute a major source of groundwater to evaluate the annual effective dose and the corresponding health impact on the population and to investigate the quality of groundwater in Jordan. The mean activity concentration of gross alpha and beta in groundwater ranges from 0.26 ± 0.03 to 3.58 ± 0.55 Bq L−1 and from 0.51 ± 0.07 to 3.43 ± 0.46 Bq L−1, respectively. A very strong relationship was found between gross alpha and beta activity concentrations. The annual effective dose for alpha and beta was found in the range of 0.32–2.40 mSv with a mean value of 0.89 mSv, which is nine times higher than the World Health Organization (WHO) recommended limit and one and half times higher than the national regulation limit. The mean lifetime risk was found to be 45.47 × 10−4 higher than the Jordanian estimated upper-bound lifetime risk of 25 × 10−4. The data obtained in the study would be the baseline for further epidemiological studies on health effects related to the exposure to natural radioactivity in Jordan.
Delivery of HIV-1 Polyepitope Constructs Using Cationic and Amphipathic Cell Penetrating Peptides into Mammalian Cells
Authors: Namazi Fatemeh , Bolhassani Azam , Sadat Seyed Mehdi , Irani Shiva 
Published: November 2019

Background:
An effective vaccine against human immunodeficiency virus 1 (HIV-1) is
an important global health priority. Despite many efforts in the development of the HIV-1 vaccine,
no effective vaccine has been approved yet. Recently, polyepitope vaccines including several immunogenic
and conserved epitopes of HIV-1 proteins have received special attention.

Methods:
In this study, HIV-1 Nef, Tat, Gp160 and P24 proteins were considered for selection of
immunodominant and conserved epitopes due to their critical roles in the viral life cycle and pathogenesis.
At first, the Nef60-84-Nef126-144-Tat29-49-Gp16030-53-Gp160308-323-P248-151 DNA construct was
designed using in silico studies. Then, the DNA construct was subcloned in pEGFP-N1 and pET-
24a (+) expression vectors and the rNef-Tat-Gp160-P24 polyepitope peptide was generated in E.coli
expression system for in vitro delivery using novel cell-penetrating peptides (CPPs), LDP-NLS and
CyLoP-1, in a non-covalent manner. Also, the HR9 and MPG CPPs were used to transfer the DNA
construct.

Results:
Our results showed that the recombinant polyepitope peptide generated in Rosetta strain
migrated as a clear band of ~31 kDa in SDS-PAGE. The SEM data confirmed the formation of stable
nanoparticles with a size below 250 nm. MTT assay revealed that the complexes did not represent
any considerable cytotoxic effect compared to untreated cells. The results of fluorescence microscopy,
flow cytometry and western blotting indicated that these CPPs successfully delivered polyepitope
constructs into HEK-293T cell line.

Conclusion:
These data suggested that these CPPs can be used as a promising approach for the development
of the HIV-1 vaccine.
Characterization of Venoms of Deinagkistrodon acutus and Bungarus multicinctus Using Proteomics and Peptidomics
Authors: Zhang Yaqiong , Jia Zhiping , Liu Yunyang , Zhou Xinwen , Kong Yi 
Published: November 2019

Background:
Deinagkistrodon acutus (D. acutus) and Bungarus multicinctus (B. multicinctus)
as traditional medicines have been used for hundreds of years in China. The venoms of these two
species have strong toxicity on the victims.

Objective:
The objective of this study is to reveal the profile of venom proteins and peptides of
D. acutus and B. multicinctus.

Method:
Ultrafiltration, SDS-PAGE coupled with in-gel tryptic digestion and Liquid Chromatography-
Electrospray Ionization-Tandem Mass Spectrometry (LC-ESI-MS/MS) were used to characterize
proteins and peptides of venoms of D. acutus and B. multicinctus.

Results:
In the D. acutus venom, 67 proteins (16 protein families) were identified, and snake venom metalloproteinases
(SVMPs, 38.0%) and snake venom C-type lectins (snaclecs, 36.7%) were dominated proteins.
In the B. multicinctus venom, 47 proteins (15 protein families) were identified, and three-finger toxins
(3FTxs, 36.3%) and Kunitz-type Serine Protease Inhibitors (KSPIs, 32.8%) were major components.
In addition, both venoms contained small amounts of other proteins, such as Snake Venom Serine Proteinases
(SVSPs), Phospholipases A2 (PLA2s), Cysteine-Rich Secreted Proteins (CRISPs), 5'nucleotidases
(5'NUCs), Phospholipases B (PLBs), Phosphodiesterases (PDEs), Phospholipase A2 Inhibitors (PLIs),
Dipeptidyl Peptidases IV (DPP IVs), L-amino Acid Oxidases (LAAOs) and Angiotensin-Converting Enzymes
(ACEs). Each venom also had its unique proteins, Nerve Growth Factors (NGFs) and Hyaluronidases
(HYs) in D. acutus, and Cobra Venom Factors (CVFs) in B. multicinctus. In the peptidomics,
1543 and 250 peptides were identified in the venoms of D. acutus and B. multicinctus, respectively.
Some peptides showed high similarity with neuropeptides, ACE inhibitory peptides, Bradykinin-
Potentiating Peptides (BPPs), LAAOs and movement related peptides.

Conclusion:
Characterization of venom proteins and peptides of D. acutus and B. multicinctus will be
helpful for the treatment of envenomation and drug discovery.
Design and Synthesis of 4(1H)-quinolone Derivatives as Autophagy Inducing Agents by Targeting ATG5 Protein
Authors: Jia Yifan , Yu Difei , Huang Qiuhua , Zhang Xiaodong , Qiu Liqin , Cao Rihui , Du Runlei , Liu Wenbin 
Published: November 2019

Background:
Quinolines have been characterized as a class of potential antitumor agents,
and a large number of natural and synthetic quinolines acting as antitumor agents were reported.

Methods:
A series of 7-chloro-4(1H)-quinolone derivatives were synthesized. The antiproliferative
effect of these compounds was evaluated by MTT assay against five human tumor cell lines. The
mechanism of action of the selected compound 7h was also investigated.

Results and Discussion:
Most of the compounds had more potent antiproliferative activities than
the lead compound 7-chloro-4(1H)-quinolone 6b. Compound 7h was found to be the most potent
antiproliferative agent against human tumor cell lines. Further investigation demonstrated that compound
7h triggered ATG5-dependent autophagy of colorectal cancer cells by promoting the functions
of LC3 proteins.

Conclusion:
These results were useful for designing and discovering more potent novel antitumor
agents endowed with better pharmacological profiles.
LabVIEW Based Performance Assessment of Backup Emergency Power Supply for Critical Medical Equipment
Authors: G. Pandiaraj , Muralidharan S. 
Published: November 2019

Introduction:
In the recent past, the requirement of backup sources has increased exponentially
and necessitated massive energy storage devices like lead-acid batteries, and supercapacitors.

Materials and Methods:
Especially these power backup resources become inevitable, while installing
critical diagnostic and lifesaving equipment. The storage system, usually lead-acid battery
bank, needs to be connected to the electrical appliances through a converter station where the energy
conversion takes place. Such practices are involved in medical emergency appliances of uninterrupted
power supply. The devices like monitoring instruments, patient’s artificial respiratory
systems, light loads in operation theaters, motor loads and other electronic devices of laptop &
desktop computers act as a source of harmonics. Apart from these, the sine wave / square wave
inverter also introduces harmonics as well as micro ripples on the battery side. These micro frequency
components have certain impacts on the storage system performance, efficiency, and utilization
of electrical energy.

Results and Conclusion:
This work investigates the impact of micro frequency components on
the lead-acid storage battery when it is operating with a sine wave inverter supplying Resistive
load and RLE load. In order to perform the investigation, a hardware test bench was created. The
results of laboratory tests on a lead-acid battery show that batteries lose capacity and the utilization
gets reduced by the frequent use. This manuscript opens up a new direction of research in the
medical emergency backup system operating with a 12V DC system.
Melatonin Induces Apoptosis and Inhibits the Proliferation of Cancer Cells via Reactive Oxygen Species-mediated MAPK and mTOR Pathways
Authors: Kasi Reena , Yeo Pei Ling , Yen Ng. Khuen , Koh Rhun Yian , Ponnudurai Gnanajothy , Tiong Yee Lian , Chye Soi Moi 
Published: November 2019

Background:Recent human and animal studies have demonstrated the oncostatic properties of N-acetyl-5-methoxytryptamine (melatonin) in different types of cancer. However, in few cancer cell lines including colorectal cancer cell line (HT-29), acute T cell leukemia cell line (JURKAT) and cervical cancer cell line (HeLa), precise oncostatic mechanism induced by melatonin is yet to be described.Objectives:The aim of this study is to investigate the effects of melatonin in HT-29, JURKAT and HeLa cells and to determine the underlying molecular mechanism.Methods:Cell viability was determined by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay while cell cycle, apoptosis and membrane potential were analysed by flow cytometry. Reactive oxygen species (ROS) was detected by 2',7'.dichlorofluorescein diacetate(DCFH-DA) staining. Protein expressions were determined by Western blot.Results:Our results showed that melatonin suppressed cell proliferation, increased the number of sub G1 hypodiploid cells and cell cycle arrest in HT-29, JURKAT and HeLa cells. Besides, melatonin also induced early and late apoptosis, although there were marked variations in responses between different cell lines (sensitivity; HeLa > HT-29 >JURKAT). Apart from that, staining with DCHF-DA demonstrated ROS production that was induced in a dose-dependent manner in HeLa, HT-29 and JURKAT cells. Moreover, the apoptotic process and oncostatic effect of melatonin were seen to be associated with extracellular-signal-regulated kinase (ERK) and stress-activated protein kinase/c-Jun NH (2)-terminal kinase (SAPK-JNK) signalling cascades in HeLa cells. In HT-29 and JURKAT cells, melatonin induced apoptosis via activation of p38 mitogen-activated protein kinases (p38), ERK and SAPK-JNK signalling pathways. In all three cell lines, the apoptotic event was triggered by the mammalian target of rapamycin (mTOR)-mediated activation of the downstream target rapamycininsensitive companion of mTOR (RICTOR) and/or regulatory-associated protein of mTOR (RAPTOR) proteins.Conclusions:Our findings confirm that melatonin induces apoptosis through reactive oxygen speciesmediated dysregulated mitogen-activated protein kinase (MAPK) and mTOR signalling pathways in these cancer cell lines.
Quantitative Analysis and Evaluation of Tractor Gear Shifting Comfort with Entropy-Based Matter-Element Model
Authors: Jiang Wei , Xu Hongmei , Zhong Wenjie , Dong Jiajun , Shang Yujun 
Published: November 2019

Background:
The gear shifting comfort of tractors is affected by various factors, which
make it extremely difficult to accurately and quantitatively describe the handling comfort through
objective physical quantities. However, the calculation and evaluation processes of the index of manipulation
comfort mostly involve the operation of matrix form, and the numerical operation is one
of the powerful core functions of MATLAB.

Objective:
This study aims to take the gear shifting process of tractors as the research object and uses
MATLAB /GUI toolbox to develop the shifting comfort evaluation system, thereby improving the
gear shifting comfort.

Methods:
The procedures of holistic assessment, element subdivision, and detailed tracking were
adopted as the analysis method. Thus, the operation process was divided into four action units, including
pedal free travel, separation travel, gear change, and joint travel, according to the concept of
“differentiation” and manipulation behavior. Based on the matter-element model, the process of
clutch operation was described by the coupling of action elements. The closeness between the actual
model and the target model was used to measure the degree of handling comfort. Then, the results
were compared with those of the multi-index comprehensive evaluation.

Results:
It was shown that separation travel has the greatest influence on handling comfort. Taking
vehicle 1 as an example, the matter-element analysis model provided the overall comfort value of
the carrier (0.8359), which is close to the value of the multi-index comprehensive evaluation
(0.8156). Moreover, the evaluation results presented the score of each action unit, which could directly
reflect the action units with the lowest level of comfort. The evaluation results of matterelement
model can not only reflect the handling comfort of different components, but also locate the
negative aspects of the whole operation.

Conclusion:
This method is effective in overcoming the ambiguity of the concept of comfort and
the generality of overall evaluation as well as avoiding the uncertainty of subjective evaluation.