bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gene network modeling and pathway analysis of maize transcriptomes in response to Maize Iranian mosaic virus
Authors: Ghorbani Abozar , Rostami Mahsa , Izadpanah Keramatollah 
Published: November 2022

Abstract
Maize Iranian mosaic virus (MIMV, family Rhabdoviridae) is one of the factors limiting cereal production in Iran. MIMV can affect maize transcriptome, alternative splicing, circular RNAs and miRNA profiles during infection and active biological pathways in the maize cells. In the present study, we sought to find critical genes and key pathways involved in MIMV infection and analyzed gene networks, pathways and promoters using transcriptome data. We determined the hub genes involved in pathways related to the proteasome and ubiquitin. These hub genes played a key role in the response to MIMV infection. Gene ontology (GO) and pathway analysis showed that metabolic processes are most affected in MIMV infection. In addition, the results showed the important role of the cellular endoplasmic reticulum in MIMV infection. Network cluster analysis confirmed the result of GO and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. Potential miRNAs were identified as target hub genes using the psRNATarget server. The discovered miRNAs belonged to miR166, miR167, miR169, miR395, miR399, miR408 and miR482 families, which are involved in various pathogenicity or resistance processes against MIMV or other viruses. The results of this study provide a list of hub genes, important pathways and new insights for future development of virus-resistant transgenic crops and clarify the basic mechanism of plant response. They may also be a source of information on the role of key genes and the pathway controlling the responses.
Monkeypox outbreak 2022 – an overview of all cases reported to the Cologne Health Department
Authors: Kröger Sophia Toya , Lehmann Max Christian , Treutlein Melanie , Fiethe Achim , Kossow Annelene , Küfer-Weiß Annika , Nießen Johannes , Grüne Barbara 
Published: November 2022

Abstract
Purpose:
The international monkeypox outbreak in May 2022 marks the occurrence of another previously atypical infectious disease in Europe. This study’s objective was to present a comprehensive overview based on data gathered by the Health Department of the city of Cologne.
Methods:
In this retrospective observational study, 368 individuals reported to the Cologne Health Department as PCR-positive for monkeypox were included. Data were collected in structured telephone interviews and digitally processed.
Results:
The first monkeypox case in Cologne was recorded on May 24, 2022. The local outbreak lasted approximately 4 months and reached its peak in July. The last reported case in Cologne occurred on September 17. Transmissions mostly occurred through sexual contacts (67.4 %) or other close physical contacts (4.6 %) between men, but also through fomites, in the context of events or occasionally in the work environment. In 21.5 % of cases, no route of infection could be determined. The mean incubation period was 8.2 days. Clinically, monkeypox infections usually presented with skin and/or mucosal lesions accompanied by general symptoms. In 74.8 % of cases, a prodromal stage was absent. Initially, the rash often had an unspecific appearance, but in the further clinical course, it usually passed through the typical stages. Most infections resolved spontaneously under home care. In 3.5 % of cases, however, inpatient hospitalisation was required.
Conclusions:
Most transmissions occurred through sexual contact. Although the majority of infections in Cologne affected the MSM community, there were also cases outside this context. The observed average incubation period was shorter than initially assumed. Mucosal involvement and associated symptoms occur in a relevant number of cases and can lead to more severe clinical courses. In the case of an unclear rash or symptoms suggesting mucosal involvement, monkeypox should be considered as a differential diagnosis.
The surveillance data collected in the health authorities provided important information for adapting the public health measures taken against the spread of monkeypox in the population.
KDM6B protects T-ALL cells from NOTCH1-induced oncogenic stress
Authors: Issa Nancy , Bjeije Hassan , Wilson Elisabeth , Krishnan Aishwarya , Dunuwille Wangisa , Parsons Tyler , Zhang Christine , Han Wentao , Young Andrew , Ren Zhizhong , Ge Kai , Wang Eunice , Weng Andrew , Cashen Amanda , Spencer David , Challen Grant 
Published: November 2022

Abstract
T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive hematopoietic neoplasm resulting from the malignant transformation of T-cell progenitors. While activating NOTCH1 mutations are the dominant genetic drivers of T-ALL, epigenetic dysfunction plays a central role in the pathology of T-ALL and can provide alternative mechanisms to oncogenesis in lieu of or in combination with genetic mutations. The histone demethylase enzyme KDM6A (UTX) is also recurrently mutated in T-ALL patients and functions as a tumor suppressor. However, its gene paralog, KDM6B (JMJD3), is never mutated and can be significantly overexpressed, suggesting it may be necessary for sustaining the disease. Here, we used mouse and human T-ALL models to show that KDM6B is required for T-ALL development and maintenance. Using NOTCH1 gain-of-function retroviral models, mouse cells genetically deficient for Kdm6b were unable to propagate T-ALL. Inactivating KDM6B in human T-ALL patient cells by CRISPR/Cas9 showed KDM6B-targeted cells were significantly outcompeted over time. The dependence of T-ALL cells on KDM6B was proportional to the oncogenic strength of NOTCH1 mutation, with KDM6B required to prevent stress-induced apoptosis from strong NOTCH1 signaling. These studies identify a crucial role for KDM6B in sustaining NOTCH1-driven T-ALL and implicate KDM6B as a novel therapeutic target in these patients.
Novel Plasmodium falciparum K13 Gene Polymorphisms from Kisii County, Kenya during an era of Artemisinin-Based Combination Therapies (ACTs) deployment
Authors: Maniga Josephat Nyabayo , Adeyemo Rasheed Omotayo , Samuel Mong’are , John Odda , Rael Masai , Bwogo Pacifica , Martin Odoki , Sankarapandian Vidya , Wilberforce Mfitundinda , Muchiri Jacqueline Njeri , Albert Ochweri , Onkoba Sarah Kemuma , Adebayo Ismail Abiola , Akinola Saheed Adekunle 
Published: November 2022

Abstract
Background
Currently, Chemotherapy stands out as the major malaria intervention strategy, however, antimalarial resistance may hamper global elimination programs. Artemisinin Combined Therapies (ACTs) stands as the drug of choice for treatment of Plasmodium falciparum malaria. P. falciparum Kelch13 gene mutations are associated with artemisinin resistance. Thus, this study was aimed at evaluating the circulation of P. falciparum K13 Gene Polymorphisms from Kisii County, Kenya during an era of ACTs deployment.
Methods
Participants suspected to have malaria were recruited. P. falciparum was confirmed using microscopy method. Malaria-positive patients were treated with Artemether-Lumefantrine (AL). Blood was withdrawn from participants who tested positive for parasites after day 3 and kept in blood filter papers (ET31CHR; Whatman Limited, Kent, UK). DNA was extracted using chelex-suspension method. A nested polymerase chain reaction (PCR) was conducted and the second-round products were sequenced using Sanger’s method. Sequenced products were analyzed using DNAsp 5.10.01 software and then blasted on to the NCBI for K13 propeller gene sequence identity using the Basic Local Alignment Search Tool (BLAST). To assess the selection pressure in P. falciparum parasite population, Tajima’ D statistic and Fu & Li’s D test in DnaSP software 5.10.01 was used.
Results
Out of 275 enrolled participants, 231 completed the follow-up schedule. 13 (5.6%) had parasites on day 28 hence characterized for recrudescence. Out of the 13 samples suspected for recrudescence, 5 (38%) samples were positively amplified as P. falciparum, with polymorphisms in the K13-propeller gene detected. Polymorphisms at codon 539, 458, 561, 431 and 671 were detected. The sequences have been deposited in NCBI with bio-project number PRJNA885380 and accession numbers SAMN31087430, SAMN31087431, SAMN31087432, SAMN31087433, and SAMN31087434 for Marani, Nyamache, and Bonchari samples, respectively.
Conclusions
Validated WHO resistant Polymorphisms in the K13-propeller gene previously reported to be associated with artemisinin resistance were not detected in the P. falciparum isolates from Kisii County, Kenya. However, some previously reported un-validated K13 resistant Single Nucleotide Polymorphisms were reported in this study but with limited occurrences. The study has also reported new SNPs. More studies need to be carried out in the entire country to understand the association of reported mutations if any, with ACTs resistance.
Feature Correlation Transformer for Estimating Ambiguous Optical Flow
Authors: Fang Guibiao , Chen Junhong , Liang Dayong , Reeth Frank Van , Claesen Luc , Yang Zhenguo , Liu Wenyin 
Published: November 2022

Abstract
Cost volume is widely used to establish correspondences in optical flow estimation. However, when dealing with low-texture and occluded areas, it is difficult to estimate the cost volume correctly. Therefore, we propose a replacement: feature correlation transformer (FCTR), a transformer with self-and cross-attention alternations for obtaining global receptive fields and positional embedding for establishing correspondences. With global context and positional information, FCTR can produce more accurate correspondences for ambiguous areas. Using positional embedding allows the removal of the context network; the positional information can be aggregated within ambiguous motion boundaries, and the number of model parameters can be reduced. To speed up network convergence and strengthen robustness, we introduce a smooth L1 loss with exponential weights in the pre-training step. At the time of submission, our method achieves competitive performance with all published optical flow methods on both the KITTI-2015 and MPI-Sintel benchmarks. Moreover, it outperforms all optical flow and scene flow methods in KITTI-2015 foreground-region prediction.
Controllable transmission of chirped cosh-Gaussian beams in parabolic potential
Authors: Song Lijun , Fang Lizhi , Liu Shujie , Chen Shengjie 
Published: November 2022

Abstract
In our study, based on the normalized linear Schrödinger equation, we have analytically and numerically investigated the propagation dynamics of chirped cosh-Gaussian beams in a medium with parabolic potential. The obtained results show that cosh-Gaussian beams perform a periodic auto-focusing behavior and the parabolic potential determines the focusing ability, including the focal distance as well as peak intensity at the focus. Especially, the intensity distributions and waveform of cosh-Gaussian beam are related to the initial parameter of cosh function. Furthermore, we also demonstrate the effect of chirp factors on the beam and find that the periodic oscillating behavior caused by linear chirp can be used to manipulated the propagation trajectory of beam, but linear chirp does not affect the focal intensity. While the quadratic chirp can enhance the focusing ability and peak intensity of beam on the axis, which indicates that the quadratic chirp factor plays a significant role in the modulation of the energy localization.
Effect of osmotic and salt stresses on germination and phenolic compounds of Eruca vesicaria subs. sativa L.
Authors: Barris Selma , TOUMI Mohamed , BELKEBIR Aicha 
Published: November 2022

Abstract
Rocket is a plant well adapted to the different climates in Algeria. It is known for its ability to grow in marginal conditions. It produces protein- and oil-rich seeds as well as edible leaves. Rocket and other members of the Brassicaceae plant family have been shown to contribute beneficial, health promoting phytochemicals to the human diet. However, little is known about its physiological response to water and salt stress. In this study, we sought to investigate the osmotic and salt stress effect on rocket seeds at the germination level and monitor phenolic compounds accumulation during this process. Our findings show that at an osmotic potential of -0.75 MPa, 33.33% of the seeds exposed to polyethylene glycol germinated which suggests that rocket seeds displayed tolerance to water stress. When decreasing the osmotic potential to -1.44 MPa of sodium chloride, the seed germination rate decreased to 21.33% which indicates that rocket seeds were resistant to salt stress. Quantitative analysis of seed’s phenolic compounds showed an increase in polyphenols, flavonoids and anthocyanins content. As expected, the biggest increases were observedin the highest levels of osmotic and salt stress exposures. This accumulation during germination could explain rocket seed’s ability to resist drought and salinity.
The closed-form solutions of a compartmental epidemic model for Covid-19 with the Asymptomatic population
Authors: Naz Rehana , Torrisi Mariano 
Published: November 2022

Abstract
We developed a Susceptible-Asymptomatic-Infectious-Quarantined (SAIQ) model with a Quarantine-Adjusted (QA) incidence to investigate the emergence and containment of COVID-19. The closed-form solutions of system of four nonlinear first order ordinary differential equations (ODEs) are established. The Epidemic Peak (EP), Force of Infection (FOI) and Rate of Infection (ROI) are the important indicators for the control and prevention of disease.We examined these indicators using closed-form solutions and particular parameter values. Different disease-control scenarios are thoroughly examined.
Exploring Household Financial Self-Efficacy Amid MCO
Authors: Ong Hway-Boon 
Published: November 2022

The outbreak of the covid-19 pandemic had forced economies to implement movement restrictions that resulted in income shock to households. This study aims to gauge the impact of income shock due to movement control order (MCO). This study examined the factors that affect Malaysian household financial self-efficacy due to movement restrictions. A survey was conducted online from 1 April 2020 to 30 June 2020 to gather responses from households. Data collected were analysed using the KMO sampling adequacy test, Bartlett’s test, reliability, and factor analysis. More than 46% of the respondents’ income was significantly decreased or somewhat decreased due to MCO. Financial tools, lifestyle adaptation, contingency plan and realisation of the impact of MCO had significantly affected household financial efficacy.
Crystallization and preliminary x-ray analysis of β-amylase from bacillus cereus var. mycoides
Authors: Oyama Takuji , Kusunoki Masami , Kishimoto Yoji , Takasaki Yoshiyuki , Nitta Yasunori 
Published: November 2022

Abstract:
Crystals of the P-amylase from Bacillus cereus var. mycoides were grown by the vapor diffusion method with polyethylene glycol 6000 as the precipitant. These crystals belong to the monoclinic system, space group C2 with a=177.9 A, b = 112.9 A, c = 146.2 A and /J=105.8 °. They diffracted well to 2.0 A resolution on a
synchrotron radiation source, a full data set being collected to 2.2 A resolution. On the basis of the Matthews'
parameter (Vm), at least four molecules are estimated to be in the asymmetric unit.
Insights into the Structural Complexities of SARS-CoV-2 for Therapeutic
and Vaccine Development
Authors: AlMatar Manaf , Mazila Ramli Aizi Nor , Albarri Osman , Yi Choong Xin 
Published: November 2022

Abstract:
SARS-CoV-2 is a disease that endangers both human life and the economy. There was an 11-
month period of relative evolutionary standstill following the appearance of SARS-CoV-2 in late 2019.
However, the emergence of clusters of mutations known as' variants of concern 'with variable viral properties
such as transmissibility and antigenicity defined the evolution of SARS-CoV-2. Several efforts
have been made in recent months to understand the atomic level properties of SARS-CoV-2. A review
of the literature on SARS-CoV-2 mutations is offered in this paper. The critical activities performed by
different domains of the SARS-CoV-2 genome throughout the virus's entry into the host and overall viral
life cycle are discussed in detail. These structural traits may potentially pave the way for the development
of a vaccine and medication to combat the SARS-CoV-2 sickness.
Polyaromatic Hydrocarbon Specific Ring Hydroxylating Dioxygenases:
Diversity, Structure, Function, and Protein Engineering
Authors: Sharma Pushpender Kumar , Kaur Tanjot , Lakhawat Sudarshan Singh , Kumar Vikram , Sharma Vinay , Neeraj Ravi Ranjan Kumar 
Published: November 2022

Abstract:
Polycyclic aromatic hydrocarbons (PAHs) are ubiquitously present in the environment. These
compounds have demonstrated both mutagenic and carcinogenic properties. In the past few decades,
scientists have constantly been looking for a possible route to their biological degradation. Bacterial
ring hydroxylating dioxygenases (RHDs) implicated in the polycyclic aromatic hydrocarbon degradation
comprise a large family of enzymes. RHD catalyzes the stereospecific oxidation of PAHs by incorporating
molecular oxygen into inert aromatic nuclei. These biocatalysts hold the potential to completely
transform and mineralize toxic forms of these compounds into non-toxic forms. RHDsmediated
oxygenation produces cis-dihydrodiols, a chiral compound used in pharmaceutical industries.
The Molecular investigation of 16S rRNA and key functional genes involved in pollutant degradation
have revealed the dominant occurrence of phylum proteobacteria and actinobacteria in hydrocarbonpolluted
environments. The present review is aimed at narrating the diversity, distribution, structural
and functional characteristics of RHDs. The review further highlights key amino acids participating in
RHDs catalysis. It also discusses the robustness of protein engineering methods in improving the structural
and functional activity of the ring hydroxylating dioxygenases.
Co-administration of Pterocarpus marsupium Extract and Glibenclamide
Exhibits Better Effects in Regulating Hyperglycemia and Associated
Changes in Alloxan-induced Diabetic Mice
Authors: Sharma Neha , Kar Anand , Panda Sunanda , Yadav Dhananjay 
Published: November 2022

Background:
Diabetes mellitus (DM) is a well-known global metabolic disorder. For its treatment, glibenclamide (GLB) is very often prescribed. However, herbal drugs are considered effective and better alternatives due to their low risk of side effects. This study was conducted to determine the combined effects of GLB and Pterocarpus marsupium (PM, a commonly available Indian herb) extract for the effective and safe treatment of hyperglycemia in the mouse model.

Methods:
Healthy adult male mice were distributed into five groups (n=7 in each group). Group I acted as the control, whereas groups II, III, IV, and V were considered experimental groups which received a single dosage (150 mg/kg body weight) of alloxan (ALX) intraperitoneally (i.p.). In addition, groups III, IV, and V received a pre-standardized dose of GLB (500 µg/kg body weight), PM extract (150 mg/kg body weight), and GLB+PM, respectively, at the same doses as used in individual treatment, after the seventh day of ALX administration for 15 days and the alterations in different DM related parameters were evaluated.

Results:
ALX-induced hyperglycemia and other adverse effects were nearly normalized by GLB and PM co-treatment as evidenced by marked suppression in glucose, triglyceride, total-cholesterol, lipid-peroxidation, and lipid-hydroperoxides with an increase in antioxidants status and liver glycogen content. The positive effects were more pronounced when both GLB and PM were given, as compared to that of either of the drugs, administered alone. Liver ultra-structure, analyzed through histology and transmission electron microscopy revealed normalization of the ALX-induced damaged hepatocytes. The presence of epicatechin, the major phytoconstituent of the PM extract, as confirmed by high-performance liquid chromatography (HPLC), is responsible for its antioxidative and glucose-lowering activities.

Conclusion:
These findings reveal that PM, along with GLB, exhibits synergistic and better effects than the individual drug in regulating hyperglycemia and associated changes in alloxan-induced mice.
New Strategies in the Treatment of Diseases Caused by Acanthamoeba
Based on Nanoparticles: A Systematic Review
Authors: Shakib Pegah , Kalani Hamed , Tahir Aleem Muhammad , Faridnia Roghiyeh , Zebardast Pour Mustafa , Moradpour Kobra , Cheraghipour Kourosh 
Published: November 2022

Background:
Acanthamoeba is one of the opportunistic parasites with a global prevalence.
Currently, due to the side effects and the emergence of drug resistance to this parasite, much research
has been performed on the use of nano-drugs to treat Acanthamoeba-caused diseases. Therefore, this
systematic review study aims to evaluate new strategies for treating diseases caused by Acanthamoeba
based on nanoparticles (NPs).

Methods:
We designed a systematic review based on the articles published in English between 2000
and 2022. Our search strategy was based on syntax and specific tags for each database, including ScienceDirect,
PubMed, Scopus, Ovid, and Cochrane. From the articles, those that had inclusion criteria
were selected, and their data were extracted and analyzed.

Results:
In this study, 26 studies were selected. Metallic nanoparticles were mostly used against the
Acanthamoeba species (80.7%). 19.2% of the studies used polymeric nanoparticles, and 3.8% used
emulsion nanoparticles. Most studies (96.1%) were performed in vitro, and only one study (3.8%) was
carried out in vivo. Silver NPs were the most used metallic nanoparticles in the studies. The best effect
of the anti-Acanthamoeba compound was observed for green synthesized nanoparticles based on
stabilization by plant gums, loaded with citrus fruits flavonoids hesperidin (HDN) and naringin (NRG)
with a 100% growth inhibition at a concentration of 50 μg/mL.

Conclusion:
This study showed that chlorhexidine and other plant metabolites loaded with silver and
gold nanoparticles increase the anti-Acanthambae activity of these nanoparticles. However, green
synthesized nanoparticles based on stabilization by plant gums, loaded with citrus fruits flavonoids
hesperidin (HDN) and naringin (NRG), showed the best anti-Acanthambae effect. Nevertheless, further
studies should be performed to determine their safety for human use.