Addressing genome scale design tradeoffs in Pseudomonas putida for bioconversion of an aromatic carbon source by Deepanwita Banerjee, Javier Menasalvas, Yan Chen, Jennifer W. Gin, Edward E. K. Baidoo, Christopher J. Petzold, Thomas Eng, Aindrila Mukhopadhyay

“…While a complete implementation of the design was achieved, this study highlights the challenge of completely inactivating metabolic reactions encoded by under-characterized proteins, especially in the context of multi-gene edits.…”
Get full text

Cross-Modal Augmented Transformer for Automated Medical Report Generation by Yuhao Tang, Ye Yuan, Fei Tao, Minghao Tang

“…During the generation phase, CAT utilizes a multi-modality encoder to reinforce the correlation between generated keywords, retrieved terminologies and regions. …”
Get full text

Expression study of Wnt/β-catenin signaling pathway associated lncRNAs in schizophrenia by Fatemeh Manafzadeh, Behzad Baradaran, Seyed Gholamreza Noor Azar, Kamran Javidi Aghdam, Reza Dabbaghipour, Asghar Shayannia, Soudeh Ghafouri-Fard

“…The objective of this study was to examine the expression levels of Wnt/β-catenin-related lncRNAs, namely CCAT2, SNHG5, PTCSC3, and DANCR, as well as the CTNNB1 gene encoding beta-catenin protein in two groups of schizophrenia patients (drug-naïve and medicated) compared with healthy individuals. …”
Get full text

Biology, genetics, and ecology of the cosmopolitan ectomycorrhizal ascomycete Cenococcum geophilum by Huayong Wang, Annegret Kohler, Francis M. Martin, Francis M. Martin

“…Notably, this genome encodes a large set of repeated sequences and effector-like small secreted proteins. …”
Get full text

Phage display as a tool for identifying HIV-1 broadly neutralizing antibodies by A. N. Chikaev, A. P. Rudometov, Yu. A. Merkulyeva, L. I. Karpenko

“…Each phage particle in a library displays peptides or proteins fused to its coat protein and simultaneously carries the DNA sequence encoding the displayed peptide/protein in its genome. …”
Get full text

Forecasting Foreign Exchange Volatility Using Deep Learning Autoencoder-LSTM Techniques by Gunho Jung, Sun-Yong Choi

“…Our hybrid model utilizes an LSTM model as an encoder and decoder inside an autoencoder network. …”
Get full text

Plasmodium falciparum surf4.1 in clinical isolates: From genetic variation and variant diversity to in silico design immunopeptides for vaccine development. by Nitchakarn Noranate, Jariya Sripanomphong, Fingani Annie Mphande-Nyasulu, Suwanna Chaorattanakawee

“…The surf4.1 gene showed extensive genetic variation with total of 447 polymorphic sites with maximum of three variants as well as singlet/triplet bases indels and mini/microsatellites in the coding sequence. The exon1 encoding extracellular region exhibited higher variation compared to exon2 which coding for intracellular domain. …”
Get full text

Rare variants in previously identified linkage regions associated with carotid plaque in Dominican Republic families. by Nicole D Dueker, Ashley Beecham, Liyong Wang, Chuanhui Dong, Ralph L Sacco, Susan H Blanton, Tatjana Rundek

“…The rs61751342 missense variant is an eQTL for SCUBE2 in the atrial appendage. Notably, SCUBE2 encodes a protein which interacts with vascular endothelial growth factor (VEGF) receptor 2 to regulate VEGF-induced angiogenesis, thus providing biologic plausibility for this gene in atherosclerosis. …”
Get full text

Sarco(endo)plasmic Reticulum Ca2+-ATPase-2 Gene: Structure and Transcriptional Regulation of the Human Gene by Angel Zarain-Herzberg, Georgina Alvarez-Fernandez

“…The sarco(endo)plasmic reticulum Ca2+-ATPases (SERCAs) belong to a family of active calcium transport enzymes encoded by the SERCA1, 2, and 3 genes. In this study, we describe the complete structure of the human SERCA2 gene and its 5’ -regulatory region. …”
Get full text

Map Floodwater Radar Imagery using Machine Learning Algorithms by Thanh-Nghi Doan, Duc-Ngoc Le-Thi

“…Different blocks of the U-Net encoder architecture were fine-tuned to identify the most efficient fine-tuned model, and their results were compared. …”
Get full text

Polymorphism of CLE gene sequences in potato by M. S. Gancheva, M. R. Losev, A. A. Gurina, L. O. Poliushkevich, I. E. Dodueva, L. A. Lutova

“…In this regard, the identification and study of the CLE genes encoding the peptides of this group in cultivated plants are of great practical interest. …”
Get full text

Single Nucleotide Polymorphisms in PPARD Associated with Systemic Lupus Erythematosus in Chinese Populations by Yuan-yuan Qi, Ya-ling Zhai, Xin-ran Liu, Xiao-xue Zhang, Ya-fei Zhao, Xiang-hui Ning, Zhan-Zheng Zhao

“…Systemic lupus erythematosus (SLE) is a multifactorial autoimmune disease characterized by apoptotic clearance deficiency provoking autoimmune responses and leading to multiple organ damage. PPAR-δ, encoded by the PPARD gene, was induced in macrophages promoting the timely disposal of apoptotic cells. …”
Get full text

Intra- and Interspecies Conjugal Transfer of Plasmids in Gram-Negative Bacteria by Julia R. Savelieva, Daria A. Kondratieva, Maria V. Golikova

“…The aim of this study is to investigate the frequency of transfer of carbapenemase-encoding plasmids from <i>K. pneumoniae</i> to <i>E. coli</i> and <i>P. aeruginosa</i>. …”
Get full text

Phytoalexin deficient 4 is associated with the lesion mimic trait in watermelon clalm mutant (Citrullus lanatus) by Jiale Shi, Congji Yang, Yuanyuan Qin, Qingqing Liu, Shengqi Hua, Defeng Wu, Wei Dong

“…The predicted target gene, ClCG04G001930, encodes a Phytoalexin deficient 4 (PAD4), a protein that plays an important regulatory role in leaf senescence in many plant species. …”
Get full text

Automated Phenotypic Analysis of Mature Soybean Using Multi-View Stereo 3D Reconstruction and Point Cloud Segmentation by Daohan Cui, Pengfei Liu, Yunong Liu, Zhenqing Zhao, Jiang Feng

“…This network enhances feature extraction capabilities through the integration of point cloud and voxel convolution, as well as an orientation-encoding (OE) module. Finally, phenotypic parameters such as stem diameter, pod length, and pod width are extracted and validated against manual measurements. …”
Get full text

MSC-Derived Extracellular Vesicle-Delivered L-PGDS Inhibit Gastric Cancer Progression by Suppressing Cancer Cell Stemness and STAT3 Phosphorylation by Benshuai You, Can Jin, Jiaxin Zhang, Min Xu, Wenrong Xu, Zixuan Sun, Hui Qian

“…EVs-L-PGDS were generated from MSCs transfected with adenovirus encoding L-PGDS. Cell colony-forming, migration, invasion, and flow cytometry assays were used to show the inhibitory effects of EVs on tumor cells in vitro, and the nude mouse subcutaneous tumor model was performed to show the inhibitory effect of EVs on tumor progression in vivo. …”
Get full text

Engineering of Dihydroxy Biphenyl Dioxygenase Enzyme to Improve Its Performance In Removing PCBs: A Molecular Docking Study by Susan Yazdankhah, Alireza Zakeri, Saeed Khalili, Abolfazl Jahangiri, ZahraalSadat Hashemi, Alireza Heidari

“…One of these enzymes is called DHBD (2,3-dihydroxy biphenyl 1,2-dioxygenase) and is encoded by the BphC gene. Enhancing the function of the enzyme and reducing the binding affinity of the enzyme to the inhibitor (tert-butanol) will improve the function of the enzyme and increase its efficiency. …”
Get full text

CD8+ T cells from SIV elite controller macaques recognize Mamu-B*08-bound epitopes and select for widespread viral variation. by John T Loffredo, Thomas C Friedrich, Enrique J León, Jason J Stephany, Denise S Rodrigues, Sean P Spencer, Alex T Bean, Dominic R Beal, Benjamin J Burwitz, Richard A Rudersdorf, Lyle T Wallace, Shari M Piaskowski, Gemma E May, John Sidney, Emma Gostick, Nancy A Wilson, David A Price, Esper G Kallas, Helen Piontkivska, Austin L Hughes, Alessandro Sette, David I Watkins

“…<h4>Conclusions</h4>Together, our data suggest that Mamu-B*08-restricted CD8+ T cell responses effectively control replication of pathogenic SIV(mac)239. All seven regions encoding Mamu-B*08-restricted CD8+ T cell epitopes also exhibit amino acid replacements typically seen only in the presence of Mamu-B*08, suggesting that the variation we observe is indeed selected by CD8+ T cell responses. …”
Get full text

IHSCR: Energy-efficient clustering and routing for wireless sensor networks based on harmony search algorithm by Bing Zeng, Yan Dong, Xinyu Li, Liang Gao

“…Then, a new energy-efficient clustering algorithm is designed based on several improvements made to harmony search algorithm: (1) a discrete encoding scheme of a harmony for clustering is proposed; (2) a roulette wheel selection method is designed to choose a gateway for a regular sensor node to join, which is employed by two steps (i.e. initialization of harmony and improvisation of a new harmony); (3) the dynamically changed harmony memory considering rate is designed for improvisation of a new harmony; (4) a local search scheme is proposed to improve the best harmony within the harmony memory in iterations. …”
Get full text

Transfer of optogenetic vectors into the brain of neonatal animals to study neuron functions during subsequent periods of development by D. A. Lanshakov, U. S. Drozd, T. A. Zapara, N. N. Dygalo

“…Expression of opsins in the cell membrane, followed by the acquisition by the cell of the sensitivity to light is achieved by means of viral vectors, often created on the basis of lentiviral or adeno-associated (AAV) viruses bearing the nucleotide sequence encoding the photo-channel proteins. Inclusion of the cell-specific promoter of interest into the transgene-expression cassette allows opsin to be produced only in the target cells. …”
Get full text