Diagnostic application of exome sequencing in Chinese children with suspected inherited kidney diseases

Background: Inherited kidney diseases (IKDs) are a group of kidney diseases characterized by abnormal kidney structure or function caused by genetic factors, but they are not easily diagnosed in childhood due to either nonspecific symptoms and signs or clinically silent symptoms in the early stages until the progressive stages, even end-stages. Early diagnosis of IKDs is very urgent for timely treatment and improving outcomes of patients. So far, the etiological diagnosis has been accelerated with the advance of clinical genetic technology, particularly the advent of next-generation sequencing (NGS) that is not only a powerful tool for prompt and accurate diagnosis of IKDs but also gives therapy guidance to decrease the risk of unnecessary and harmful interventions.Methods: The patients presenting with urinalysis abnormalities or structural abnormalities from 149 Chinese families were enrolled in this study. The clinical features of the patients were collected, and the potentially causative gene variants were detected using exome sequencing. The clinical diagnostic utility of the genetic testing was assessed after more detailed clinical data were analyzed.Result: In total, 55 patients identified having causative variants by exome sequencing were genetically diagnosed, encompassing 16 (29.1%) autosomal dominant IKDs, 16 (29.1%) autosomal recessive IKDs, and 23 (41.8%) X-linked IKDs, with 25 unreported and 45 reported variants. The diagnostic yield was 36.9%. The utility of the exome sequencing was accessed, 12 patients (21.8%) were confirmed to have suspected IKDs, 26 patients (47.3%) discerned the specific sub-types of clinical category, and 17 patients (30.9%) with unknown etiology or lack of typical manifestations were reclassified.Conclusion: Our study supported that genetic testing plays a crucial role in the early diagnosis for children with IKDs, which affected follow-up treatment and prognostic assessment in clinical practice. Moreover, the variant spectrum associated with IKDs was expanded

Reduced NOV expression correlates with disease progression in colorectal cancer and is associated with survival, invasion and chemoresistance of cancer cells

Aberrant expression of nephroblastoma overexpressed (NOV) has been evident in certain malignancies. In the current study, we aim to investigate the role played by NOV in colorectal cancer (CRC). NOV expression was determined in a cohort of 359 CRC tissues and 174 normal colorectal tissues. Its impact on CRC cells was investigated using in vitro NOV knockdown and overexpression models. NOV transcripts were reduced in the CRC tumours compared with the paired adjacent normal colorectal tissues (p < 0.01) and was associated with distant metastases. NOV knockdown resulted in increased cell proliferation and invasion of RKO cells, whilst an opposite effect was seen in the HT115 NOV over expressing cells. A positive association between Caspase-3/-8 and NOV was seen in NOV knockdown and overexpression cell lines which contributed to the survival of serum deprived CRC cells. Further investigation showed that NOV regulated proliferation, survival and invasion through the JNK pathway. NOV knockdown in RKO cells reduced the responsiveness to 5-Fluorouracil treatment, whilst overexpression in HT115 cells exhibited a contrasting effect. Taken together, NOV is reduced in CRC tumours and this is associated with disease progression. NOV inhibits the proliferation and invasion of CRC cells in vitro. Inhibition of proliferation is mediated by a regulation of Caspase-3/-8, via the JNK pathway, which has potential for predicting and preventing chemoresistance

Functional Analysis of the Kinome of the Wheat Scab Fungus Fusarium graminearum

As in other eukaryotes, protein kinases play major regulatory roles in filamentous fungi. Although the genomes of many plant pathogenic fungi have been sequenced, systematic characterization of their kinomes has not been reported. The wheat scab fungus Fusarium graminearum has 116 protein kinases (PK) genes. Although twenty of them appeared to be essential, we generated deletion mutants for the other 96 PK genes, including 12 orthologs of essential genes in yeast. All of the PK mutants were assayed for changes in 17 phenotypes, including growth, conidiation, pathogenesis, stress responses, and sexual reproduction. Overall, deletion of 64 PK genes resulted in at least one of the phenotypes examined, including three mutants blocked in conidiation and five mutants with increased tolerance to hyperosmotic stress. In total, 42 PK mutants were significantly reduced in virulence or non-pathogenic, including mutants deleted of key components of the cAMP signaling and three MAPK pathways. A number of these PK genes, including Fg03146 and Fg04770 that are unique to filamentous fungi, are dispensable for hyphal growth and likely encode novel fungal virulence factors. Ascospores play a critical role in the initiation of wheat scab. Twenty-six PK mutants were blocked in perithecia formation or aborted in ascosporogenesis. Additional 19 mutants were defective in ascospore release or morphology. Interestingly, F. graminearum contains two aurora kinase genes with distinct functions, which has not been reported in fungi. In addition, we used the interlog approach to predict the PK-PK and PK-protein interaction networks of F. graminearum. Several predicted interactions were verified with yeast two-hybrid or co-immunoprecipitation assays. To our knowledge, this is the first functional characterization of the kinome in plant pathogenic fungi. Protein kinase genes important for various aspects of growth, developmental, and infection processes in F. graminearum were identified in this study

Data for publication: Experimental requirements for high temperature solid state electrochemical TEM experiments

This dataset was used for the our publication in Small Method "Experimental requirements for high temperature solid state electrochemical TEM experiments" authored by:Zhongtao Ma, Christodoulos Chatzichristodoulou, Waynah Lou Dacayan, Kristian Speranza Mølhave, Francesco Maria Chiabrera, Thomas Erik Lyck Smitshuysen, Christian Danvad Damsgaard, Søren Bredmose Simonsen**corresponding author: [email protected]</p

Wheat Seed Detection and Counting Method Based on Improved YOLOv8 Model

Wheat seed detection has important applications in calculating thousand-grain weight and crop breeding. In order to solve the problems of seed accumulation, adhesion, and occlusion that can lead to low counting accuracy, while ensuring fast detection speed with high accuracy, a wheat seed counting method is proposed to provide technical support for the development of the embedded platform of the seed counter. This study proposes a lightweight real-time wheat seed detection model, YOLOv8-HD, based on YOLOv8. Firstly, we introduce the concept of shared convolutional layers to improve the YOLOv8 detection head, reducing the number of parameters and achieving a lightweight design to improve runtime speed. Secondly, we incorporate the Vision Transformer with a Deformable Attention mechanism into the C2f module of the backbone network to enhance the network’s feature extraction capability and improve detection accuracy. The results show that in the stacked scenes with impurities (severe seed adhesion), the YOLOv8-HD model achieves an average detection accuracy (mAP) of 77.6%, which is 9.1% higher than YOLOv8. In all scenes, the YOLOv8-HD model achieves an average detection accuracy (mAP) of 99.3%, which is 16.8% higher than YOLOv8. The memory size of the YOLOv8-HD model is 6.35 MB, approximately 4/5 of YOLOv8. The GFLOPs of YOLOv8-HD decrease by 16%. The inference time of YOLOv8-HD is 2.86 ms (on GPU), which is lower than YOLOv8. Finally, we conducted numerous experiments and the results showed that YOLOv8-HD outperforms other mainstream networks in terms of mAP, speed, and model size. Therefore, our YOLOv8-HD can efficiently detect wheat seeds in various scenarios, providing technical support for the development of seed counting instruments

Degassing effect and grain refinement of Al-Si alloy under ultrasound field

Under different constant temperatures a Al-1%Si alloy (mass fraction) melt was treated by ultrasound field. The gas content in Al-Si melt decreased obviously when the treated time is 60 s. The grains are refined and globularization when the Al-Si melt was solidified under ultrasound but the grains only are refined when solidified at isothermal temperature in the mushy zone with ultrasonic vibrations. The results imply that the expansion and collapse of cavities which results in the formation of nuclei play the important role in the formation of fine and globular grains

Do children need a longer time to shed SARS-CoV-2 in stool than adults?

SARS-CoV-2 can be shed in the stool of patients in the recovery phase. Children show a longer shedding time than adults. We analyzed the possible causes of this finding and recommend that a negative stool sample be included in a patient's discharge criteria

Identification of the hub genes RUNX2 and FN1 in gastric cancer

This study identified key genes in gastric cancer (GC) based on the mRNA microarray GSE19826 from the Gene Expression Omnibus (GEO) database and preliminarily explored the relationships among the key genes

Fluorinated Nickel(II) Phenoxyiminato Catalysts: Exploring the Role of Fluorine Atoms in Controlling Polyethylene Productivities and Microstructures

A series of neutrally charged Ni­(II) phenoxyiminato catalysts with fluorine atoms at different positions on the <i>N</i>-terphenyl motif are synthesized, and their abilities to polymerize ethylene are compared. At 25 °C, the <i>ortho</i>-fluorinated <b>Ni-5F</b>, <b>Ni-3F</b>′, and <b>Ni-2F</b> achieve significantly higher polymerization activities than <b>Ni-3F</b> and <b>Ni-0F</b>. In addition, branch density and molecular weight of the obtained polyethylenes vary gradually in the order of <b>Ni-5F</b>, <b>Ni-3F</b>, <b>Ni-3F</b>′, <b>Ni-2F</b>, and <b>Ni-0F</b>. Based on the X-ray crystal structure and ¹⁹F NMR spectra, the <i>ortho</i> fluorine atoms are found to make terphenyl groups more rigid and bulky. Theoretical calculations suggest that the increased steric bulk of terphenyl motif leads to an increase in the ground state energy of the resting state species relative to the migratory insertion transition state, and consequently, lowered migratory insertion barriers are expected in <b>Ni-5F</b>, <b>Ni-3F</b>′, and <b>Ni-2F</b>. On the other hand, the weak hydrogen bonding between the <i>ortho</i> fluorine atoms and coordinated ethylene in insertion transition state is also proposed in favor of insertion. Similar to previous reports, polyethylene microstructure was mainly related to electronic effects of fluorine atoms