bluuebunny/crossref_metadata_2025 huggingface dataset:
Germline FOXJ2 overexpression causes male infertility via aberrant autophagy activation by LAMP2A upregulation
Authors: Bai Fu-Rong , Wu Qi-Qian , Wu Yu-Jie , Hu Yan-Qin , Jiang Zhi-Xuan , Lv Hao , Qian Wen-Zhe , Cai Chang , Wu Jing-Wen
Published: July 2022

Spermatogenesis is a complex biological process that produces haploid spermatozoa and requires precise regulation by many tissue-specific factors. In this study, we explored the role and mechanism of Fork head box J2 (FOXJ2, which is highly expressed in spermatocytes) in the regulation of spermatogenesis using a germline-specific conditional Foxj2 knock-in mouse model (Stra8-Cre; Foxj2tg/tg mouse). Foxj2 overexpression in mouse testes led to spermatogenesis failure, which started at the initiation of meiosis, and resulted in male infertility. Lysosomes and autophagy-related genes were upregulated in Stra8-cre; Foxj2tg/tg mouse testes and the number of autolysosomes in the spermatocytes in Stra8-cre; Foxj2tg/tg mice was increased. Chromatin immunoprecipitation-PCR and Dual-luciferase reporter assays showed that Lamp2 (encoding lysosome‐associated membrane protein‐2) was a target of FOXJ2. Foxj2 overexpression increased the expression levels of Lamp2a and Hsc70 (70-kDa cytoplasmic heat shock protein) in the Stra8-cre; Foxj2tg/tg mouse testes. Our results suggested that Foxj2 overexpression in the germ cells of mouse testes affects chaperone-mediated autophagy by upregulating LAMP2A, leading to spermatogenesis failure at the initiation of meiosis, thus resulting in male infertility. Our findings provide a new insight into the function of FOXJ2 in spermatogenesis and the significance of autophagy regulation in spermatogenesis.
Sestrin2 remedies podocyte injury via orchestrating TSP-1/TGF-β1/Smad3 axis in diabetic kidney disease
Authors: Song Shan , Shi Chonglin , Bian Yawei , Yang Zhaohua , Mu Lin , Wu Haijiang , Duan Huijun , Shi Yonghong
Published: July 2022

Sestrin2 is identified as a stress-induced protein and could functionate in many aspects. In our study, we investigated the latent impact of Sestrin2 on podocyte injury and its molecular mechanism in vivo and in vitro in diabetic kidney disease (DKD). Sestrin2 was low-expressed in renal biopsies from individuals with DKD, the glomeruli from diabetic mice, and mouse podocytes exposed to high glucose (HG). Sestrin2 overexpression ameliorated HG-induced phenotypic alterations, apoptosis, and oxidative stress in conditionally immortalized mouse podocytes and modulated the activity of Thrombospondin-1 (TSP-1)/transforming growth factor (TGF-β1)/Smad3 pathway in podocytes. Moreover, TSP-1 inhibitor LSKL or TGF-β blocker Pirfenidone arrested podocyte injury induced by HG. Streptozotocin (STZ) was employed to render equivalent diabetes in B6-TgN (CMV-Sestrin2) (TgN) and wild-type (WT) control mice. Sestrin2 alleviated increased levels of 24‐h urinary protein, blood urea nitrogen, serum creatinine and triglyceride, and urine 8-OHdG in diabetic mice. Podocyte phenotypic alterations, increased expression of apoptosis-associated proteins and podocyte loss were observed in WT but not in diabetic TgN mice, as well as oxidative stress. Additionally, TSP-1/TGF-β1/Smad3 signaling pathway was also suppressed in glomeruli of diabetic TgN mice. Thus, Sestrin2 mitigates podocyte injury in DKD via orchestrating TSP-1/TGF-β1/Smad3 pathway, underlining Sestrin2 as a promising therapeutic target for DKD.
CDC-like kinase 4 deficiency contributes to pathological cardiac hypertrophy by modulating NEXN phosphorylation
Authors: Huang Jian , Wang Luxin , Shen Yunli , Zhang Shengqi , Zhou Yaqun , Du Jimin , Ma Xiue , Liu Yi , Liang Dandan , Shi Dan , Ma Honghui , Li Li , Zhang Qi , Chen Yi-Han
Published: July 2022

Kinase-catalyzed phosphorylation plays a crucial role in pathological cardiac hypertrophy. Here, we show that CDC-like kinase 4 (CLK4) is a critical regulator of cardiomyocyte hypertrophy and heart failure. Knockdown of Clk4 leads to pathological cardiomyocyte hypertrophy, while overexpression of Clk4 confers resistance to phenylephrine-induced cardiomyocyte hypertrophy. Cardiac-specific Clk4-knockout mice manifest pathological myocardial hypertrophy with progressive left ventricular systolic dysfunction and heart dilation. Further investigation identifies nexilin (NEXN) as the direct substrate of CLK4, and overexpression of a phosphorylation-mimic mutant of NEXN is sufficient to reverse the hypertrophic growth of cardiomyocytes induced by Clk4 knockdown. Importantly, restoring phosphorylation of NEXN ameliorates myocardial hypertrophy in mice with cardiac-specific Clk4 deletion. We conclude that CLK4 regulates cardiac function through phosphorylation of NEXN, and its deficiency may lead to pathological cardiac hypertrophy. CLK4 is a potential intervention target for the prevention and treatment of heart failure.
Unexpected steric hindrance failure in the gas phase F− + (CH3)3CI SN2 reaction
Authors: Lu Xiaoxiao , Shang Chenyao , Li Lulu , Chen Rongjun , Fu Bina , Xu Xin , Zhang Dong H.
Published: July 2022

Base-induced elimination (E2) and bimolecular nucleophilic substitution (SN2) reactions are of significant importance in physical organic chemistry. The textbook example of the retardation of SN2 reactivity by bulky alkyl substitution is widely accepted based on the static analysis of molecular structure and steric environment. However, the direct dynamical evidence of the steric hindrance of SN2 from experiment or theory remains rare. Here, we report an unprecedented full-dimensional (39-dimensional) machine learning-based potential energy surface for the 15-atom F− + (CH3)3CI reaction, facilitating the reliable and efficient reaction dynamics simulations that can reproduce well the experimental outcomes and examine associated atomic-molecular level mechanisms. Moreover, we found surprisingly high “intrinsic” reactivity of SN2 when the E2 pathway is completely blocked, indicating the reaction that intends to proceed via E2 transits to SN2 instead, due to a shared pre-reaction minimum. This finding indicates that the competing factor of E2 but not the steric hindrance determines the small reactivity of SN2 for the F− + (CH3)3CI reaction. Our study provides new insight into the dynamical origin that determines the intrinsic reactivity in gas-phase organic chemistry.
Single cell transcriptome sequencing of inspiratory neurons of the preBötzinger complex in neonatal mice
Authors: David Caroline K. , Sugimura Yae K. , Kallurkar Prajkta S. , Picardo Maria Cristina D. , Saha Margaret S. , Conradi Smith Gregory D. , Del Negro Christopher A.
Published: July 2022

Neurons in the brainstem preBötzinger complex (preBötC) generate the rhythm and rudimentary motor pattern for inspiratory breathing movements. We performed whole-cell patch-clamp recordings from inspiratory neurons in the preBötC of neonatal mouse slices that retain breathing-related rhythmicity in vitro. We classified neurons based on their electrophysiological properties and genetic background, and then aspirated their cellular contents for single-cell RNA sequencing (scRNA-seq). This data set provides the raw nucleotide sequences (FASTQ files) and annotated files of nucleotide sequences mapped to the mouse genome (mm10 from Ensembl), which includes the fragment counts, gene lengths, and fragments per kilobase of transcript per million mapped reads (FPKM). These data reflect the transcriptomes of the neurons that generate the rhythm and pattern for inspiratory breathing movements.
The ProMotion LMU dataset (2022 edition), prostate intra-fraction motion recorded by transperineal ultrasound
Authors: Ballhausen Hendrik , Kortmann Elena , Belka Claus , Li Minglun
Published: July 2022

Infra-fraction motion of the prostate was recorded during 2.385 fractions of image guided radiotherapy (IGRT) in 126 patients, 14 of which were treated by intensity modulated radiation therapy (IMRT), and 112 of which were treated by volumetric arc therapy (VMAT). The prostate was imaged by three-dimensional and time-resolved transperineal ultrasound (4D-US) of type Clarity by Elekta, Stockholm, Sweden. The prostate volume was registered and the prostate position (center of volume) was recorded at a frequency of 2.0 samples per second. This raw data set contains a total of 1.138.024 prostate and patient couch positions over a time span of 158 hours, 25 minutes and 50 seconds of life radiotherapy as exported by the instrument software. This data set has been used for the validation of models of prostate intra-fraction motion and for the estimation of the dosimetric impact of actual intra-fraction motion on treatment quality and side effects. We hope that this data set may be reused by other groups for similar purposes.
Juvenile depletion of microglia reduces orientation but not high spatial frequency selectivity in mouse V1
Authors: Velez Dario X. Figueroa , Arreola Miguel , Huh Carey Y. L. , Green Kim , Gandhi Sunil P.
Published: July 2022

Microglia contain multiple mechanisms that shape the synaptic landscape during postnatal development. Whether the synaptic changes mediated by microglia reflect the developmental refinement of neuronal responses in sensory cortices, however, remains poorly understood. In postnatal life, the development of increased orientation and spatial frequency selectivity of neuronal responses in primary visual cortex (V1) supports the emergence of high visual acuity. Here, we used the colony-stimulating factor 1 receptor (CSF1R) inhibitor PLX5622 to rapidly and durably deplete microglia in mice during the juvenile period in which increased orientation and spatial frequency selectivity emerge. Excitatory and inhibitory tuning properties were measured simultaneously using multi-photon calcium imaging in layer II/III of mouse V1. We found that microglia depletion generally increased evoked activity which, in turn, reduced orientation selectivity. Surprisingly, microglia were not required for the emergence of high spatial frequency tuned responses. In addition, microglia depletion did not perturb cortical binocularity, suggesting normal depth processing. Together, our finding that orientation and high spatial frequency selectivity in V1 are differentially supported by microglia reveal that microglia are required normal sensory processing, albeit selectively.
Curcumin piperidone derivatives induce anti-proliferative and anti-migratory effects in LN-18 human glioblastoma cells
Authors: Razali Nur Syahirah Che , Lam Kok Wai , Rajab Nor Fadilah , A. Jamal A. Rahman , Kamaluddin Nurul Farahana , Chan Kok Meng
Published: July 2022

Curcumin has demonstrated potential cytotoxicity across various cell lines despite its poor bioavailability and rapid metabolism. Therefore, our group have synthesized curcuminoid analogues with piperidone derivatives, FLDP-5 and FLDP-8 to overcome these limitations. In this study, the analogues were assessed on LN-18 human glioblastoma cells in comparison to curcumin. Results from cytotoxicity assessment showed that FLDP-5 and FLDP-8 curcuminoid analogues caused death in LN-18 cells in a concentration-dependent manner after 24-h treatment with much lower IC50 values of 2.5 µM and 4 µM respectively, which were more potent compared to curcumin with IC50 of 31 µM. Moreover, a significant increase (p < 0.05) in the level of superoxide anion and hydrogen peroxide upon 2-h and 6-h treatment confirmed the oxidative stress involvement in the cell death process induced by these analogues. These analogues also showed potent anti-migratory effects through inhibition of LN-18 cells’ migration and invasion. In addition, cell cycle analysis showed that these analogues are capable of inducing significant (p < 0.05) S-phase cell cycle arrest during the 24-h treatment as compared to untreated, which explained the reduced proliferation indicated by MTT assay. In conclusion, these curcuminoid analogues exhibit potent anti-cancer effects with anti-proliferative and anti-migratory properties towards LN-18 cells as compared to curcumin.
Clinically focused multi-cohort benchmarking as a tool for external validation of artificial intelligence algorithm performance in basic chest radiography analysis
Authors: Rudolph Jan , Schachtner Balthasar , Fink Nicola , Koliogiannis Vanessa , Schwarze Vincent , Goller Sophia , Trappmann Lena , Hoppe Boj F. , Mansour Nabeel , Fischer Maximilian , Ben Khaled Najib , Jörgens Maximilian , Dinkel Julien , Kunz Wolfgang G. , Ricke Jens , Ingrisch Michael , Sabel Bastian O. , Rueckel Johannes
Published: July 2022

Artificial intelligence (AI) algorithms evaluating [supine] chest radiographs ([S]CXRs) have remarkably increased in number recently. Since training and validation are often performed on subsets of the same overall dataset, external validation is mandatory to reproduce results and reveal potential training errors. We applied a multicohort benchmarking to the publicly accessible (S)CXR analyzing AI algorithm CheXNet, comprising three clinically relevant study cohorts which differ in patient positioning ([S]CXRs), the applied reference standards (CT-/[S]CXR-based) and the possibility to also compare algorithm classification with different medical experts’ reading performance. The study cohorts include [1] a cohort, characterized by 563 CXRs acquired in the emergency unit that were evaluated by 9 readers (radiologists and non-radiologists) in terms of 4 common pathologies, [2] a collection of 6,248 SCXRs annotated by radiologists in terms of pneumothorax presence, its size and presence of inserted thoracic tube material which allowed for subgroup and confounding bias analysis and [3] a cohort consisting of 166 patients with SCXRs that were evaluated by radiologists for underlying causes of basal lung opacities, all of those cases having been correlated to a timely acquired computed tomography scan (SCXR and CT within < 90 min). CheXNet non-significantly exceeded the radiology resident (RR) consensus in the detection of suspicious lung nodules (cohort [1], AUC AI/RR: 0.851/0.839,p = 0.793) and the radiological readers in the detection of basal pneumonia (cohort [3], AUC AI/reader consensus: 0.825/0.782,p = 0.390) and basal pleural effusion (cohort [3], AUC AI/reader consensus: 0.762/0.710,p = 0.336) in SCXR, partly with AUC values higher than originally published (“Nodule”: 0.780, “Infiltration”: 0.735, “Effusion”: 0.864). The classifier “Infiltration” turned out to be very dependent on patient positioning (best in CXR, worst in SCXR). The pneumothorax SCXR cohort [2] revealed poor algorithm performance in CXRs without inserted thoracic material and in the detection of small pneumothoraces, which can be explained by a known systematic confounding error in the algorithm training process. The benefit of clinically relevant external validation is demonstrated by the differences in algorithm performance as compared to the original publication. Our multi-cohort benchmarking finally enables the consideration of confounders, different reference standards and patient positioning as well as the AI performance comparison with differentially qualified medical readers.
Application of acidic deep eutectic solvents in green extraction of 5-hydroxymethylfurfural
Authors: Karimi Sabah , Shekaari Hemayat
Published: July 2022

The extraction of the 5-hydroxymethylfurfural (5-HMF), as building block for many applications, from aqueous solutions has been became an indispensable challenge. Consequently, this study investigated the extraction ability of acidic deep eutectic solvent-based aqueous two-phase system (ATPS), choline chloride as hydrogen bond acceptor (HBA) and lactic acid, oxalic acid and citric acid as hydrogen bond donor (HBD), countering polypropylene glycol 400 at T = 298.15 K. Two semi-empirical Zafarani-Moattar et al. and Merchuk equations were used to fit the measured binodal data. Further, the NRTL and UNIQUAC models were used for correlating of tie-line data. The consistency of the experimental tie-line data was determined by utilizing the Bachman-Brown and Hand correlations. Also, the performance of these ATPSs to partitioning of 5-HMF, were investigated by calculation of extraction efficiencies, EE% and partition coefficients, K. This strategy indicates DES-based ATPSs have the acceptable extraction efficiency of the 5-HMF in a single-step extraction. A greenness assessment tool, Analytical GREEnness metric (AGREE), was tested to evaluate of greenness of analytical protocol.
Disentangling structural and functional responses of native versus alien communities by canonical ordination analyses and variation partitioning with multiple matrices
Authors: Sîrbu Ioan , Benedek Ana-Maria , Brown Bryan L. , Sîrbu Monica
Published: July 2022

Freshwaters are under accelerated human pressure, and mollusk communities are among its most sensitive, threatened, and valuable components. To the best of our knowledge, the overall effects of damming, environment, space, time, and invasive alien mollusk species, on structural and functional responses of native mollusk communities were not yet compared. Using historical information and recent data from a river, we aimed to investigate and disentangle these effects and evaluate the differences in structural and functional responses of natives and alien invasives to the same predictors. Variation partitioning showed that alien species were as important predictors as were environmental factors and time in explaining species composition of native freshwater mollusk communities. Aliens were more independent of environmental conditions than natives and responded to different drivers, partially explaining their invasion success. The increased abundance of some alien gastropods was positively related to taxonomic diversity, while certain alien bivalves were negatively associated with the functional diversity of native communities. We introduce a cumulative variation partitioning with multiple response (native and alien) and predictor matrices, along with a diagram to show their relations, advocating for a conceptual shift in future community ecology, from “variables to matrices” and from “multivariate analyses to multi-matrix statistical modeling”.
The coupled photocycle of phenyl-p-benzoquinone and Light-Harvesting Complex II (LHCII) within the biohybrid system
Authors: Łazicka Magdalena , Palińska-Saadi Adriana , Piotrowska Paulina , Paterczyk Bohdan , Mazur Radosław , Maj-Żurawska Magdalena , Garstka Maciej
Published: July 2022

The combination of trimeric form of the light-harvesting complex II (LHCII3), a porous graphite electrode (GE), and the application of phenyl-p-benzoquinone (PPBQ), the quinone derivative, allow the construction of a new type of biohybrid photoactive system. The Chl fluorescence decay and voltammetric analyzes revealed that PPBQ impacts LHCII3 proportionally to accessible quenching sites and that PPBQ forms redox complexes with Chl in both ground and excited states. As a result, photocurrent generation is directly dependent on PPBQ-induced quenching of Chl fluorescence. Since PPBQ also undergoes photoactivation, the action of GE-LHCII3-PPBQ depends on the mutual coupling of LHCII3 and PPBQ photocycles. The GE-LHCII3-PPBQ generates a photocurrent of up to 4.5 µA and exhibits considerable stability during operation. The three-dimensional arrangement of graphite scraps in GE builds an active electrode surface and stabilizes LHCII3 in its native form in low-density multilayers. The results indicate the future usability of such designed photoactive device.
A two-layer mono-objective algorithm based on guided optimization to reduce the computational cost in virtual screening
Authors: Ferrández Miriam R. , Puertas-Martín Savíns , Redondo Juana L. , Pérez-Sánchez Horacio , Ortigosa Pilar M.
Published: July 2022

Virtual screening methods focus on searching molecules with similar properties to a given compound. Molecule databases are made up of large numbers of compounds and are constantly increasing. Therefore, fast and efficient methodologies and tools have to be designed to explore them quickly. In this context, ligand-based virtual screening methods are a well-known and helpful tool. These methods focus on searching for the most similar molecules in a database to a reference one. In this work, we propose a new tool called 2L-GO-Pharm, which requires less computational effort than OptiPharm, an efficient and robust piece of software recently proposed in the literature. The new-implemented tool maintains or improves the quality of the solutions found by OptiPharm, and achieves it by considerably reducing the number of evaluations needed. Some of the strengths that help 2L-GO-Pharm enhance searchability are the reduction of the search space dimension and the introduction of some circular limits for the angular variables. Furthermore, to ensure a trade-off between exploration and exploitation of the search space, it implements a two-layer strategy and a guided search procedure combined with a convergence test on the rotation axis. The performance of 2L-GO-Pharm has been tested by considering two different descriptors, i.e. shape similarity and electrostatic potential. The results show that it saves up to 87.5 million evaluations per query molecule.
Isolation, characterization and complete genome analysis of a novel bacteriophage vB_EfaS-SRH2 against Enterococcus faecalis isolated from periodontitis patients
Authors: Pazhouhnia Setareh , Bouzari Majid , Arbabzadeh-Zavareh Farahnaz
Published: August 2022

Periodontitis is a chronic inflammatory condition that can damage soft tissues and supporting teeth.Enterococcus faecalisis an opportunistic pathogen usually living in the oral cavity and plays a critical role in apical periodontitis that significantly threatens human health. The use of bacteriophages as an alternative way to eliminate bacterial infections is a promising approach.E. faecaliswas isolated from the depth of dental packets of patients with periodontitis. Antimicrobial susceptibility was tested using 16 antimicrobial agents. Also, a specific virulent bacteriophage (vB_EfaS-SRH2) with an irregular pentagonal morphology of the head and a non-contractile tail belonging to theSiphoviridae,was isolated from wastewater in East of Isfahan, Iran, and its physiological and genomic specifications were investigated. The genome was double-strand DNA with 38,746 bp length and encoded 62 putative ORFs. In addition, eight Anti-CRISPERs and 30 Rho-dependent terminators were found. No tRNA was found. It had a short latent period of 15 min and a large burst size of~125. No undesirable genes (antibiotic resistance, lysogenic dependence, and virulence factors) were identified in the genome. Based on physiological properties and genomic characteristics, this phage can be used as a suitable choice in phage therapy for periodontitis and root canal infection.
An ANN-based advancing double-front method for automatic isotropic triangle generation
Authors: Lu Peng , Wang Nianhua , Chang Xinghua , Zhang Laiping , Wu Yadong , Zhang Hongying
Published: July 2022

The advancing front method (AFM) is one of the widely used unstructured grid generation techniques. However, the efficiency is relatively low because only one cell is generated in the advancing procedure. In this work, a novel automatic isotropic triangle generation technique is developed by introducing an artificial neural network (ANN) based advancing double-front method (ADFM) to improve the mesh generation efficiency. First, a variety of different patterns are extracted from the AFM mesh generation method and extended to the ADFM method. The mesh generation process in each pattern is discussed in detail. Second, an initial isotropic triangular mesh is generated by the traditional mesh generation method, and then an approach for automatic extraction of the training dataset is proposed. The preprocessed dataset is input into the ANN to train the network, then some typical patterns are obtained through learning. Third, after inputting the initial discrete boundary as initial fronts, the grid is generated from the shortest front and adjacent front. The coordinates of the points contained in the dual fronts and the adjacent points are sent into the neural network as the grid generation environment to obtain the most possible mesh generation pattern, the corresponding methods are used to update the advancing front until the whole computational domain is covered by initial grids, and finally, some smoothing techniques are carried out to improve the quality initial grids. Several typical cases are tested to validate the effectiveness. The experimental results show that the ANN can accurately identify mesh generation patterns, and the mesh generation efficiency is 50% higher than that of the traditional single-front AFM.
Modulation of dielectric properties in low-loss polypropylene-based composites at GHz frequencies: theory and experiment
Authors: Wilczyński Konrad , Wróblewska Anna , Daniszewska Agata , Krupka Jerzy , Mrozowski Michał , Zdrojek Mariusz
Published: July 2022

Polymer composites with high dielectric constant and low loss tangent are highly regarded as substrates for modern high-speed electronics. In this work, we analyze the high-frequency dielectric properties of two types of composites based on polypropylene infused with high-dielectric-constant microparticles. Two types of fillers are used: commercial ceramics or titanium oxide (TiO2) with different concentrations. The key observation is that adding the fillers causes an increase of dielectric constants by around 100% (for highest loading) up to 4.2 and 3.4, for micro-ceramics and TiO2 based composites, respectively. Interestingly, for the TiO2 composite, the loss tangent depends on the filler loading volume, whereas the other composite has a slightly increasing tendency, however, being at the level ~ 10–3. To explain the experimental results, a theoretical model determined by microwave reflection and transmission through a representative volume element is proposed, which allows the investigation of the impact of volume ratio, grain shape, aggregation, and size on the loss tangent and permittivity evolution. This approach could be used for modeling other low dielectric loss materials with inclusions.
Risk assessment for the native anurans from an alien invasive species, American bullfrogs (Lithobates catesbeianus), in South Korea
Authors: Park Hye-Rin , Rahman Md Mizanur , Park Seung-Min , Choi Jae-Hyeok , Kang Hee-Jin , Sung Ha-Cheol
Published: July 2022

The invasive species are of global concern, and the Invasive American Bullfrog (IAB;Lithobates catesbeianus) is one of the worst invasive amphibian species worldwide. Like other countries, South Korea is also facing challenges from IAB. Although many studies indicated impacts of IAB on native anurans in Korea, the actual risk at the specific level is yet to evaluate. Considering the putative invasiveness of IAB, it is hypothesized that any species with the possibility of physical contact or habitat sharing with them, will have a potential risk. Thus, we estimated and observed their home range, preferred habitats, morphology, behavior, and ecology. Then, comparing with existing knowledge, we assessed risks to the native anurans. We found a home range of 3474.2 ± 5872.5 m2and identified three types of habitats for IAB. The analyses showed at least 84% of native anurans (frogs and toads) were at moderate to extreme risks, which included all frogs but only 33% of toads. Finally, we recommended immediate actions to conserve the native anurans based on our results. As this study is the first initiative to assess the specific risk level from the invasiveness ofL. catesbeianus, it will help the managers to set conservation priorities and strategies.
Integrated genomic sequencing in myeloid blast crisis chronic myeloid leukemia (MBC-CML), identified potentially important findings in the context of leukemogenesis model
Authors: Kazemi-Sefat Golnaz Ensieh , Keramatipour Mohammad , Vaezi Mohammad , Razavi Seyed Mohsen , Kavousi Kaveh , Talebi Amin , Rostami Shahrbano , Yaghmaie Marjan , Chahardouli Bahram , Talebi Saeed , Mousavizadeh‬ Kazem
Published: July 2022

Chronic myeloid leukemia (CML) is a model of leukemogenesis in which the exact molecular mechanisms underlying blast crisis still remained unexplored. The current study identified multiple common and rare important findings in myeloid blast crisis CML (MBC-CML) using integrated genomic sequencing, covering all classes of genes implicated in the leukemogenesis model. Integrated genomic sequencing via Whole Exome Sequencing (WES), Chromosome-seq and RNA-sequencing were conducted on the peripheral blood samples of three CML patients in the myeloid blast crisis. An in-house filtering pipeline was applied to assess important variants in cancer-related genes. Standard variant interpretation guidelines were used for the interpretation of potentially important findings (PIFs) and potentially actionable findings (PAFs). Single nucleotide variation (SNV) and small InDel analysis by WES detected sixteen PIFs affecting all five known classes of leukemogenic genes in myeloid malignancies including signaling pathway components (ABL1, PIK3CB, PTPN11), transcription factors (GATA2, PHF6, IKZF1, WT1), epigenetic regulators (ASXL1), tumor suppressor and DNA repair genes (BRCA2, ATM, CHEK2) and components of spliceosome (PRPF8). These variants affect genes involved in leukemia stem cell proliferation, self-renewal, and differentiation. Both patients No.1 and No.2 had actionable known missense variants on ABL1 (p.Y272H, p.F359V) and frameshift variants on ASXL1 (p.A627Gfs*8, p.G646Wfs*12). The GATA2-L359S in patient No.1, PTPN11-G503V and IKZF1-R208Q variants in the patient No.3 were also PAFs. RNA-sequencing was used to confirm all of the identified variants. In the patient No. 3, chromosome sequencing revealed multiple pathogenic deletions in the short and long arms of chromosome 7, affecting at least three critical leukemogenic genes (IKZF1, EZH2, and CUX1). The large deletion discovered on the short arm of chromosome 17 in patient No. 2 resulted in the deletion of TP53 gene as well. Integrated genomic sequencing combined with RNA-sequencing can successfully discover and confirm a wide range of variants, from SNVs to CNVs. This strategy may be an effective method for identifying actionable findings and understanding the pathophysiological mechanisms underlying MBC-CML, as well as providing further insights into the genetic basis of MBC-CML and its management in the future.
Identification of Daboia siamensis venome using integrated multi-omics data
Authors: Saethang Thammakorn , Somparn Poorichaya , Payungporn Sunchai , Sriswasdi Sira , Yee Khin Than , Hodge Kenneth , Knepper Mark A. , Chanhome Lawan , Khow Orawan , Chaiyabutr Narongsak , Sitprija Visith , Pisitkun Trairak
Published: July 2022

Snakebite, classified by World Health Organization as a neglected tropical disease, causes more than 100,000 deaths and 2 million injuries per year. Currently, available antivenoms do not bind with strong specificity to target toxins, which means that severe complications can still occur despite treatment. Moreover, the cost of antivenom is expensive. Knowledge of venom compositions is fundamental for producing a specific antivenom that has high effectiveness, low side effects, and ease of manufacture. With advances in mass spectrometry techniques, venom proteomes can now be analyzed in great depth at high efficiency. However, these techniques require genomic and transcriptomic data for interpreting mass spectrometry data. This study aims to establish and incorporate genomics, transcriptomics, and proteomics data to study venomics of a venomous snake, Daboia siamensis. Multiple proteins that have not been reported as venom components of this snake such as hyaluronidase-1, phospholipase B, and waprin were discovered. Thus, multi-omics data are advantageous for venomics studies. These findings will be valuable not only for antivenom production but also for the development of novel therapeutics.
Mechanical strength and shape accuracy optimization of polyamide FFF parts using grey relational analysis
Authors: Shakeri Zohreh , Benfriha Khaled , Zirak Nader , Shirinbayan Mohammadali
Published: July 2022

This paper investigates the effect of different additive manufacturing process parameters such as chamber temperature, Printing temperature, layer thickness, and print speed on five essential parameters that characterize the manufactured components: cylindricity, circularity, strength, and Young’s modulus, and deformation by Gray Relational Analysis method simultaneously. Taguchi method was used to design the experiments, and the PA6 cylindrical parts were fabricated using a German RepRap X500® 3D printer. Then the Gray Relational Grade (GRG) values were calculated for all experiments. In the 8th trial, the highest value of GRG was observed. Then, to discover the optimal parameters, the GRG data were analyzed using ANOVA and S/N analysis, and it was determined that the best conditions for enhancing GRG are 60 °C in the chamber temperature, 270 °C in the printing temperature, 0.1 mm layer thickness, and 600 mm/min print speed. Finally, by using optimal parameters, a verification test was performed, and new components were investigated. Finally, comparing the initial GRG with the GRG of the experiments showed an improvement in the gray relational grade (14%) which is accompanying with improving of GRG value.
Managed pollination is a much better way of increasing productivity and essential oil content of dill seeds crop
Authors: Meena Narottam Kumar , Meena Ram Swaroop , Singh Ravindra , Verma Arvind Kumar , Choudhary Sharda , Singh Balraj , Meena Ram Dayal , Y Ravi , Meena Murlidhar
Published: July 2022

Dill seeds (Anethumgraveolens L.) is the most valuable medicinal seed spice crop of Apiaceae. It bears small yellow flowers in the form of umbels. Being a cross-pollinated crop, floral visitors play vital role in pollination and seed sets. Hence, the present study was conducted at the ICAR-National Research Centre on Seed Spices, Ajmer (Rajasthan), India to discover the pollinator’s community, foraging behaviour and abundance of most frequent pollinators and different modes of pollination on seed yield and quality of this seed spice crop. The insect visitors community of dill seeds was composed of 28 insect species belonging to 14 families of 6 orders. Most of floral visitors started their foraging activity at 8.00 h, reached peak activity between 12.00 and 14.00 h and their activity ceased at 18.00 h. Apisflorea,A.dorsata,A.mellifera, solitary bee, Halictus sp. and two unidentified species of Hymenoptera; Episyrphusbalteatus (DeGeer), Episyrphus sp., Eristalis sp and two other Musca species of Diptera were identified as potential and regular floral visitors of dill seeds. The highest seed yield of 1505.63 kg/ha was recorded in the treated plots provided with only 10% jaggery solution and was at par with the open pollination. A lower seed yield of 1432.5 kg/ha was recorded in plots pollinated only with A.mellifera inside insect cages. Open pollination with 10% jaggery solution spray increased the seed yield of dill seed crop by 57%, one-thousand seed test weight by 96% and the essential oil content by 27% over control plots. These results show that managed pollination is a much better way to enhance yields and quality of dill seed crop than other treatments including only honeybee-based pollination.
Calorie restriction has no effect on bone marrow tumour burden in a Vk*MYC transplant model of multiple myeloma
Authors: Bradey Alanah L. , Fitter Stephen , Duggan Jvaughn , Wilczek Vicki , Williams Connor M. D. , Cheney Emma AJ. , Noll Jacqueline E. , Tangseefa Pawanrat , Panagopoulos Vasilios , Zannettino Andrew C. W.
Published: July 2022

Multiple myeloma (MM) is an incurable haematological malignancy, caused by the uncontrolled proliferation of plasma cells within the bone marrow (BM). Obesity is a known risk factor for MM, however, few studies have investigated the potential of dietary intervention to prevent MM progression. Calorie restriction (CR) is associated with many health benefits including reduced cancer incidence and progression. To investigate if CR could reduce MM progression, dietary regimes [30% CR, normal chow diet (NCD), or high fat diet (HFD)] were initiated in C57BL/6J mice. Diet-induced changes were assessed, followed by inoculation of mice with Vk*MYC MM cells (Vk14451-GFP) at 16 weeks of age. Tumour progression was monitored by serum paraprotein, and at endpoint, BM and splenic tumour burden was analysed by flow cytometry. 30% CR promoted weight loss, improved glucose tolerance, increased BM adiposity and elevated serum adiponectin compared to NCD-fed mice. Despite these metabolic changes, CR had no significant effect on serum paraprotein levels. Furthermore, endpoint analysis found that dietary changes were insufficient to affect BM tumour burden, however, HFD resulted in an average two-fold increase in splenic tumour burden. Overall, these findings suggest diet-induced BM changes may not be key drivers of MM progression in the Vk14451-GFP transplant model of myeloma.
Ym155 localizes to the mitochondria leading to mitochondria dysfunction and activation of AMPK that inhibits BMP signaling in lung cancer cells
Authors: Mondal Arindam , Jia Dongxuan , Bhatt Vrushank , Akel Moumen , Roberge Jacques , Guo Jessie Yanxiang , Langenfeld John
Published: July 2022

The imidazolium compound Ym155 was first reported to be a survivin inhibitor. Ym155 potently induces cell death of many types of cancer cells in preclinical studies. However, in phase II clinical trials Ym155 failed to demonstrate a significant benefit. Studies have suggested that the cytotoxic effects of Ym155 in cancer cells are not mediated by the inhibition of survivin. Understanding the mechanism by which Ym155 induces cell death would provide important insight how to improve its efficacy as a cancer therapeutic. We demonstrate a novel mechanism by which Ym155 induces cell death by localizing to the mitochondria causing mitochondrial dysfunction. Our studies suggest that Ym155 binds mitochondrial DNA leading to a decrease in oxidative phosphorylation, decrease in TCA cycle intermediates, and an increase in mitochondrial permeability. Furthermore, we show that mitochondrial stress induced by Ym155 and other mitochondrial inhibitors activates AMP-activated kinase leading to the downregulation to bone morphogenetic protein (BMP) signaling. We provide first evidence that Ym155 initiates cell death by disrupting mitochondrial function.
Exome sequencing revealed comparable frequencies of RNF43 and BRAF mutations in Middle Eastern colorectal cancer
Authors: Siraj Abdul Khalid , Bu Rong , Masoodi Tariq , Parvathareddy Sandeep Kumar , Iqbal Kaleem , Al-Haqawi Wael , Al-Dossari Hassan , Azam Saud , Qadri Zeeshan , Annaiyappanaidu Padmanaban , Al-Dayel Fouad , Al-Kuraya Khawla Sami
Published: July 2022

Mutation-induced activation of Wnt-β Catenin signaling pathway is frequent in CRC. The E3 ubiquitin ligase, RNF43, has been reported to negatively regulate the Wnt signaling pathway and RNF43 mutations are frequently seen in CRC. However, its role in Middle Eastern CRC remains unclear. Therefore, we employed Exome and Sanger sequencing technology to assess the frequency of RNF43 mutations and its association with other clinico-pathological features in Middle Eastern CRC. RNF43 mutations were found in 5.9% (13/220) of CRC cases and was inversely correlated to APC and TP53 mutations. A strong association of RNF43 mutations with right sided and sporadic microsatellite instable (MSI) CRC was observed. No association was identified between RNF43 mutation and other clinico-pathological features including BRAF mutation, age, tumor histological subtype, tumor grade or patients’ prognosis. Multivariate logistic regression analysis revealed that MSI status and wild type APC were independent predictor of RNF43 mutation. We conclude that RNF43 mutations occur in Middle Eastern CRC at comparable frequencies with BRAF mutations and represent a distinct molecular subtype which further enhances our understanding of how different mutational subsets of Wnt tumor suppressor genes link to distinct tumor characteristics, which might be considered for treatment strategies for CRC patients.
Retinal small vessel dilatation in the systemic inflammatory response to surgery
Authors: Grogan Alexander , Barclay Karen , Colville Deb , Hodgson Lauren , Savige Judy
Published: August 2022

Retinal microvascular calibre has been proposed as a predictor of cardiac events. Surgery is a major stimulus for inflammation which potentially affects small vessel calibre. This study examined the effects of surgery on retinal, and thus systemic, small vessel size, and the potentially confounding effect of surgery when retinal vessel calibre is used to predict cardiac risk in hospital patients. Consecutive participants were recruited from a preoperative assessment clinic at a teaching hospital. They provided demographic and clinical details, and underwent retinal imaging before and again, within 3 days after surgery, with a non-mydriatic retinal camera. Images were graded for vessel calibre using semi-automated software based on the Parr-Hubbard formula with Knudtson’s modification (IVAN, U Wisconsin). Differences were examined using Fisher’s exact test or a paired t-test, and calibre determinants identified from univariate and multiple linear regression analysis (STATA version 11.2). Sixty-eight participants (23 men, 34%) with a mean age of 55 ± 14.5 years, were recruited. Fourteen (21%) underwent a laparotomy which was considered major surgery and 54 (79%) had Other surgery. Mean C-reactive protein (CRP) levels increased post-operatively from 7.8 ± 20.2 mg/L to 43.9 ± 55.1 mg/L (p < 0.01), and mean serum albumin decreased from 38.9 ± 4.4 g/L to 33.9 ± 5.5 g/L (p < 0.01). Mean central retinal arteriole and venular equivalent calibre (CRAE, CRVE) increased post-operatively (142.4 ± 13.3 µm to 146.4 ± 13.0 µm, p < 0.01 and 213.1 ± 16.8 µm to 217.9 ± 18.3 µm, p < 0.01, respectively). The systemic microvasculature dilates post-operatively possibly secondary to inflammation and endothelial dysfunction. These changes were present within 3 days of surgery and may confound the use of small vessel calibre to predict cardiac risk in surgical inpatients. Microvascular dilatation in response to other inflammatory stimuli such as pneumonia is a known potential confounder in hospital patients.
Theaflavin 3-gallate inhibits the main protease (Mpro) of SARS-CoV-2 and reduces its count in vitro
Authors: Chauhan Mahima , Bhardwaj Vijay Kumar , Kumar Asheesh , Kumar Vinod , Kumar Pawan , Enayathullah M. Ghalib , Thomas Jessie , George Joel , Kumar Bokara Kiran , Purohit Rituraj , Kumar Arun , Kumar Sanjay
Published: July 2022

The main protease (Mpro) of SARS-CoV-2 has been recognized as an attractive drug target because of its central role in viral replication. Our previous preliminary molecular docking studies showed that theaflavin 3-gallate (a natural bioactive molecule derived from theaflavin and found in high abundance in black tea) exhibited better docking scores than repurposed drugs (Atazanavir, Darunavir, Lopinavir). In this study, conventional and steered MD-simulations analyses revealed stronger interactions of theaflavin 3-gallate with the active site residues of Mpro than theaflavin and a standard molecule GC373 (a known inhibitor of Mproand novel broad-spectrum anti-viral agent). Theaflavin 3-gallate inhibited Mproprotein of SARS-CoV-2 with an IC50value of 18.48 ± 1.29 μM. Treatment of SARS-CoV-2 (Indian/a3i clade/2020 isolate) with 200 μM of theaflavin 3-gallate in vitro using Vero cells and quantifying viral transcripts demonstrated reduction of viral count by 75% (viral particles reduced from Log106.7to Log106.1). Overall, our findings suggest that theaflavin 3-gallate effectively targets the Mprothus limiting the replication of the SARS-CoV-2 virus in vitro.
The influence of electrocardiogram (ECG) filters on the heights of R and T waves in children
Authors: Hirokawa Jun , Hitosugi Takashi , Miki Yoichiro , Tsukamoto Masanori , Yamasaki Fumiyasu , Kawakubo Yoshifumi , Yokoyama Takeshi
Published: August 2022

Anesthesiologists often compare intraoperative and preoperative electrocardiogram (ECG) waveforms in patients undergoing general anesthesia. In addition, many intraoperative ECG monitors have filters for removing electrocautery noise. In pediatric anesthesiology practice, we often note the appearance of elevated T waves—specifically, an increase in their height—with the use of such filters, even though no actual clinical change has occurred, which possibly leads to misdiagnosis. We investigated changes in R and T wave heights and in the T/R ratio according to the use of the strong (S) versus the diagnostic (D) filtering mode during pediatric anesthesiology. Primary outcomes were the dependence of the heights of the R and T waves on the filter mode and the correlation between rates of change in the R- and T-wave heights and heart rate (HR). In the S mode, the height of the R wave was lower (p = 0.013, η2 = 0.28) and the T/R ratio was higher than the corresponding values in the D mode (χ2 = 20.46, p < 0.001). The T/R ratios were also higher in the S mode than in the D mode, and when the D mode was changed to the S mode during tachycardia, there was a strong correlation between the rate of reduction in the R wave and HR (r = 0. 573, p = 0.041). Significant differences in the heights of the R wave and in the T/R ratio occur when using different intraoperative ECG filtering modes. Specifically, in S mode, a greater relative increase in T wave height may occur due to a significant decrease in R wave height. To avoid spurious diagnoses, anesthesiologists should be familiar with these potentially purely filter-driven changes whenever ECG is intraoperatively monitored.
Cynomolgus monkey’s choroid reference database derived from hybrid deep learning optical coherence tomography segmentation
Authors: Maloca Peter M. , Freichel Christian , Hänsli Christof , Valmaggia Philippe , Müller Philipp L. , Zweifel Sandrine , Seeger Christine , Inglin Nadja , Scholl Hendrik P. N. , Denk Nora
Published: August 2022

Cynomolgus monkeys exhibit human-like features, such as a fovea, so they are often used in non-clinical research. Nevertheless, little is known about the natural variation of the choroidal thickness in relation to origin and sex. A combination of deep learning and a deterministic computer vision algorithm was applied for automatic segmentation of foveolar optical coherence tomography images in cynomolgus monkeys. The main evaluation parameters were choroidal thickness and surface area directed from the deepest point on OCT images within the fovea, marked as the nulla with regard to sex and origin. Reference choroid landmarks were set underneath the nulla and at 500 µm intervals laterally up to a distance of 2000 µm nasally and temporally, complemented by a sub-analysis of the central bouquet of cones. 203 animals contributed 374 eyes for a reference choroid database. The overall average central choroidal thickness was 193 µm with a coefficient of variation of 7.8%, and the overall mean surface area of the central bouquet temporally was 19,335 µm2 and nasally was 19,283 µm2. The choroidal thickness of the fovea appears relatively homogeneous between the sexes and the studied origins. However, considerable natural variation has been observed, which needs to be appreciated.