PS4: a next-generation dataset for protein single-sequence secondary structure prediction
We present PS4, a dataset of 18,731 nonredundant protein chains and their respective secondary structure labels. Each chain is identified, and the dataset is nonredundant against other secondary structure datasets commonly seen in the literature. We perform ablation studies by training secondary structure prediction algorithms on the PS4 training set and obtains state-of-the-art accuracy on the CB513 test set in zero shots.PMID:37997848 | DOI:10.2144/btn-2023-0024 (Source: BioTechniques)
Source: BioTechniques - November 24, 2023 Category: Biotechnology Authors: Omar Peracha Source Type: research
Automated method for quantification of 20 amino acids in cell culture media during biopharmaceutical development
Biotechniques. 2023 Nov 24. doi: 10.2144/btn-2023-0068. Online ahead of print.ABSTRACTHerein, a step-by-step protocol for simultaneous detection of 20 amino acids commonly present in cell culture media is described. The protocol facilitates detection of both primary and secondary amino acids through a two-step precolumn derivatization strategy using ortho-phthalaldehyde and 9-fluorenylmethyl chloroformate as derivatizing agents. The separation of derivatized amino acids with varying hydrophobicity is achieved through reverse-phase chromatography. The amino acids are simultaneously detected in a single workflow through the ...
Source: BioTechniques - November 24, 2023 Category: Biotechnology Authors: Ankita Dubey Srishti Joshi Kratika Upadhyay Ansuman Mahato Anurag S Rathore Source Type: research
PS4: a next-generation dataset for protein single-sequence secondary structure prediction
We present PS4, a dataset of 18,731 nonredundant protein chains and their respective secondary structure labels. Each chain is identified, and the dataset is nonredundant against other secondary structure datasets commonly seen in the literature. We perform ablation studies by training secondary structure prediction algorithms on the PS4 training set and obtains state-of-the-art accuracy on the CB513 test set in zero shots.PMID:37997848 | DOI:10.2144/btn-2023-0024 (Source: BioTechniques)
Source: BioTechniques - November 24, 2023 Category: Biotechnology Authors: Omar Peracha Source Type: research
Automated method for quantification of 20 amino acids in cell culture media during biopharmaceutical development
Biotechniques. 2023 Nov 24. doi: 10.2144/btn-2023-0068. Online ahead of print.ABSTRACTHerein, a step-by-step protocol for simultaneous detection of 20 amino acids commonly present in cell culture media is described. The protocol facilitates detection of both primary and secondary amino acids through a two-step precolumn derivatization strategy using ortho-phthalaldehyde and 9-fluorenylmethyl chloroformate as derivatizing agents. The separation of derivatized amino acids with varying hydrophobicity is achieved through reverse-phase chromatography. The amino acids are simultaneously detected in a single workflow through the ...
Source: BioTechniques - November 24, 2023 Category: Biotechnology Authors: Ankita Dubey Srishti Joshi Kratika Upadhyay Ansuman Mahato Anurag S Rathore Source Type: research
PS4: a next-generation dataset for protein single-sequence secondary structure prediction
We present PS4, a dataset of 18,731 nonredundant protein chains and their respective secondary structure labels. Each chain is identified, and the dataset is nonredundant against other secondary structure datasets commonly seen in the literature. We perform ablation studies by training secondary structure prediction algorithms on the PS4 training set and obtains state-of-the-art accuracy on the CB513 test set in zero shots.PMID:37997848 | DOI:10.2144/btn-2023-0024 (Source: BioTechniques)
Source: BioTechniques - November 24, 2023 Category: Biotechnology Authors: Omar Peracha Source Type: research
Automated method for quantification of 20 amino acids in cell culture media during biopharmaceutical development
Biotechniques. 2023 Nov 24. doi: 10.2144/btn-2023-0068. Online ahead of print.ABSTRACTHerein, a step-by-step protocol for simultaneous detection of 20 amino acids commonly present in cell culture media is described. The protocol facilitates detection of both primary and secondary amino acids through a two-step precolumn derivatization strategy using ortho-phthalaldehyde and 9-fluorenylmethyl chloroformate as derivatizing agents. The separation of derivatized amino acids with varying hydrophobicity is achieved through reverse-phase chromatography. The amino acids are simultaneously detected in a single workflow through the ...
Source: BioTechniques - November 24, 2023 Category: Biotechnology Authors: Ankita Dubey Srishti Joshi Kratika Upadhyay Ansuman Mahato Anurag S Rathore Source Type: research
PS4: a next-generation dataset for protein single-sequence secondary structure prediction
We present PS4, a dataset of 18,731 nonredundant protein chains and their respective secondary structure labels. Each chain is identified, and the dataset is nonredundant against other secondary structure datasets commonly seen in the literature. We perform ablation studies by training secondary structure prediction algorithms on the PS4 training set and obtains state-of-the-art accuracy on the CB513 test set in zero shots.PMID:37997848 | DOI:10.2144/btn-2023-0024 (Source: BioTechniques)
Source: BioTechniques - November 24, 2023 Category: Biotechnology Authors: Omar Peracha Source Type: research
Three-dimensional visualization and analysis of dendritic spines in human brain tissue
Biotechniques. 2023 Nov 23. doi: 10.2144/btn-2023-0078. Online ahead of print.ABSTRACTWe developed a simple yet powerful technique to visualize neuronal morphology in human brain tissues. By ballistically shooting DiI (1,1'-dioctadecyl-3,3,3'3'-tetramethylindocarbocyanine perchlorate)-coated tungsten particles to randomly label neurons, then clearing tissues with OPTIClear, we demonstrated the tracing of branched dendritic trees and spines in three dimensions. High-resolution imaging revealed dendrites up to 300 μm long and spine necks down to 200 nm across. Quantitative analyses of 1304 dendritic spines showed no decreas...
Source: BioTechniques - November 23, 2023 Category: Biotechnology Authors: Haitao Sun Hei Ming Lai Wutian Wu Source Type: research
Decoding disease: Scott Patterson's perspectives on the power of biomarkers in drug development
Biotechniques. 2023 Nov 23. doi: 10.2144/btn-2023-0108. Online ahead of print.ABSTRACTScott Patterson (Gilead Sciences Inc., CA, USA) speaks to Ashling Cannon, Journal Development Editor at BioTechniques, about his career. Patterson is a biochemist and proteomics and biomarker/translational expert with over 30 years of industry experience following 13 years in an academic setting. Patterson earned his BSc and PhD in Physiology and Pharmacology from the University of Queensland (Australia) while working full time in the Department of Physiology and Pharmacology, rising to a Senior Research Officer. Throughout his career, Pa...
Source: BioTechniques - November 23, 2023 Category: Biotechnology Authors: Scott D Patterson Source Type: research
Three-dimensional visualization and analysis of dendritic spines in human brain tissue
Biotechniques. 2023 Nov 23. doi: 10.2144/btn-2023-0078. Online ahead of print.ABSTRACTWe developed a simple yet powerful technique to visualize neuronal morphology in human brain tissues. By ballistically shooting DiI (1,1'-dioctadecyl-3,3,3'3'-tetramethylindocarbocyanine perchlorate)-coated tungsten particles to randomly label neurons, then clearing tissues with OPTIClear, we demonstrated the tracing of branched dendritic trees and spines in three dimensions. High-resolution imaging revealed dendrites up to 300 μm long and spine necks down to 200 nm across. Quantitative analyses of 1304 dendritic spines showed no decreas...
Source: BioTechniques - November 23, 2023 Category: Biotechnology Authors: Haitao Sun Hei Ming Lai Wutian Wu Source Type: research
Decoding disease: Scott Patterson's perspectives on the power of biomarkers in drug development
Biotechniques. 2023 Nov 23. doi: 10.2144/btn-2023-0108. Online ahead of print.ABSTRACTScott Patterson (Gilead Sciences Inc., CA, USA) speaks to Ashling Cannon, Journal Development Editor at BioTechniques, about his career. Patterson is a biochemist and proteomics and biomarker/translational expert with over 30 years of industry experience following 13 years in an academic setting. Patterson earned his BSc and PhD in Physiology and Pharmacology from the University of Queensland (Australia) while working full time in the Department of Physiology and Pharmacology, rising to a Senior Research Officer. Throughout his career, Pa...
Source: BioTechniques - November 23, 2023 Category: Biotechnology Authors: Scott D Patterson Source Type: research
Cradle cultures: growing stem cell-derived developmental cell models < em > in vitro < /em >
Biotechniques. 2023 Nov 16. doi: 10.2144/btn-2023-0100. Online ahead of print.ABSTRACTHow are three stem cell-derived developmental cell models furthering our understanding of post-implantation human embryo development? And why have recent advancements in these human embryo-like models spurred ethical discussion and the need to refine our definition of 'embryo'? [Formula: see text].PMID:37968924 | DOI:10.2144/btn-2023-0100 (Source: BioTechniques)
Source: BioTechniques - November 16, 2023 Category: Biotechnology Authors: Beatrice Bowlby Source Type: research
Cradle cultures: growing stem cell-derived developmental cell models < em > in vitro < /em >
Biotechniques. 2023 Nov 16. doi: 10.2144/btn-2023-0100. Online ahead of print.ABSTRACTHow are three stem cell-derived developmental cell models furthering our understanding of post-implantation human embryo development? And why have recent advancements in these human embryo-like models spurred ethical discussion and the need to refine our definition of 'embryo'? [Formula: see text].PMID:37968924 | DOI:10.2144/btn-2023-0100 (Source: BioTechniques)
Source: BioTechniques - November 16, 2023 Category: Biotechnology Authors: Beatrice Bowlby Source Type: research
Cradle cultures: growing stem cell-derived developmental cell models < em > in vitro < /em >
Biotechniques. 2023 Nov 16. doi: 10.2144/btn-2023-0100. Online ahead of print.ABSTRACTHow are three stem cell-derived developmental cell models furthering our understanding of post-implantation human embryo development? And why have recent advancements in these human embryo-like models spurred ethical discussion and the need to refine our definition of 'embryo'? [Formula: see text].PMID:37968924 | DOI:10.2144/btn-2023-0100 (Source: BioTechniques)
Source: BioTechniques - November 16, 2023 Category: Biotechnology Authors: Beatrice Bowlby Source Type: research
Cradle cultures: growing stem cell-derived developmental cell models < em > in vitro < /em >
Biotechniques. 2023 Nov 16. doi: 10.2144/btn-2023-0100. Online ahead of print.ABSTRACTHow are three stem cell-derived developmental cell models furthering our understanding of post-implantation human embryo development? And why have recent advancements in these human embryo-like models spurred ethical discussion and the need to refine our definition of 'embryo'? [Formula: see text].PMID:37968924 | DOI:10.2144/btn-2023-0100 (Source: BioTechniques)
Source: BioTechniques - November 16, 2023 Category: Biotechnology Authors: Beatrice Bowlby Source Type: research
