Life Sciences

193 items

RNA Biology Sep 16, 2026
The study proposes HyLnc, a framework that first pre-trains a custom BERT model on a large corpus of metazoan RNA sequences with masked language modelling, then fine-tunes it on curated lncRNA and protein-coding transcript datasets to extract 256-dimensional deep embeddings, while computing 348 handcrafted features including ORF characteristics, UTR properties, nucleotide composition and Fickett scores; after multi-stage feature selection, multiple machine learning classifiers were evaluated, with random forest performing best and achieving 91.30% accuracy, 91.23% F1-score and 82.60 MCC on an independent validation dataset, outperforming several existing lncRNA prediction tools.
The study proposes HyLnc, a framework that first pre-trains a custom BERT model on a large corpus of metazoan RNA sequences with masked language modelling, then fine-tunes it on curated lncRNA and protein-coding transcript datasets to extract 256-dimensional deep embeddings, while computing 348 handcrafted features including ORF characteristics, UTR properties, nucleotide composition and Fickett scores; after multi-stage feature selection, multiple machine learning classifiers were evaluated, with random forest performing best and achieving 91.30% accuracy, 91.23% F1-score and 82.60 MCC on an independent validation dataset, outperforming several existing lncRNA prediction tools.
HyLnc: A Hybrid Framework Combining Deep Contextual Embeddings and Handcrafted Sequence Features for Long Non-Coding RNA Prediction
The study proposes HyLnc, a framework that first pre-trains a custom BERT model on a large corpus of metazoan RNA sequences with masked language modelling, then fine-tunes it on curated lncRNA and protein-coding transcript datasets to extract 256-dimensional deep embeddings, while computing 348 handcrafted features including ORF characteristics, UTR properties, nucleotide composition and Fickett scores; after multi-stage feature selection, multiple machine learning classifiers were evaluated, with random forest performing best and achieving 91.30% accuracy, 91.23% F1-score and 82.60 MCC on an independent validation dataset, outperforming several existing lncRNA prediction tools.
The study proposes HyLnc, a framework that first pre-trains a custom BERT model on a large corpus of metazoan RNA sequences with masked language modelling, then fine-tunes it on curated lncRNA and protein-coding transcript datasets to extract 256-dimensional deep embeddings, while computing 348 handcrafted features including ORF characteristics, UTR properties, nucleotide composition and Fickett scores; after multi-stage feature selection, multiple machine learning classifiers were evaluated, with random forest performing best and achieving 91.30% accuracy, 91.23% F1-score and 82.60 MCC on an independent validation dataset, outperforming several existing lncRNA prediction tools.
bioRxiv Sep 16, 2026
This work develops a method to infer a Corpus-Wide Causal Score (CWCS) for a gene-disease pair by integrating network-based causal signals in a gene regulatory network (CWCS-Net) with corpus-wide literature evidence from PubMed abstracts quantified by a newly developed Truth Discovery algorithm (CWCS-TD), achieving a causal class F1 score of 0.600 across ten diseases using OMIM as an external expert-curated reference, outperforming GPT-4o (0.505) and MMed-Llama 3 (0.522).
This work develops a method to infer a Corpus-Wide Causal Score (CWCS) for a gene-disease pair by integrating network-based causal signals in a gene regulatory network (CWCS-Net) with corpus-wide literature evidence from PubMed abstracts quantified by a newly developed Truth Discovery algorithm (CWCS-TD), achieving a causal class F1 score of 0.600 across ten diseases using OMIM as an external expert-curated reference, outperforming GPT-4o (0.505) and MMed-Llama 3 (0.522).
Corpus-wide causality: Algorithm design & application for aggregating gene-disease causal evidence
This work develops a method to infer a Corpus-Wide Causal Score (CWCS) for a gene-disease pair by integrating network-based causal signals in a gene regulatory network (CWCS-Net) with corpus-wide literature evidence from PubMed abstracts quantified by a newly developed Truth Discovery algorithm (CWCS-TD), achieving a causal class F1 score of 0.600 across ten diseases using OMIM as an external expert-curated reference, outperforming GPT-4o (0.505) and MMed-Llama 3 (0.522).
This work develops a method to infer a Corpus-Wide Causal Score (CWCS) for a gene-disease pair by integrating network-based causal signals in a gene regulatory network (CWCS-Net) with corpus-wide literature evidence from PubMed abstracts quantified by a newly developed Truth Discovery algorithm (CWCS-TD), achieving a causal class F1 score of 0.600 across ten diseases using OMIM as an external expert-curated reference, outperforming GPT-4o (0.505) and MMed-Llama 3 (0.522).
Nature News Sep 16, 2026
Combining mass spectrometry, RNA sequencing and ribosomal profiling on 608 post-mortem dorsolateral prefrontal cortex samples from individuals with and without Alzheimer's disease, the study identified 4,321 microproteins (3,217 of them not previously characterized in the UniProtKB/Swiss-Prot standard human protein catalogue), applied a deep-learning model to rank the mass-spectrometry identification confidence of 3,001 of them with 1,067 rated high confidence, and found dozens of microproteins with altered expression in people with Alzheimer's disease, producing what is described as the largest atlas of microproteins in Alzheimer's disease made so far and making the dataset publicly available.
Combining mass spectrometry, RNA sequencing and ribosomal profiling on 608 post-mortem dorsolateral prefrontal cortex samples from individuals with and without Alzheimer's disease, the study identified 4,321 microproteins (3,217 of them not previously characterized in the UniProtKB/Swiss-Prot standard human protein catalogue), applied a deep-learning model to rank the mass-spectrometry identification confidence of 3,001 of them with 1,067 rated high confidence, and found dozens of microproteins with altered expression in people with Alzheimer's disease, producing what is described as the largest atlas of microproteins in Alzheimer's disease made so far and making the dataset publicly available.
Map of brain 'microproteins' could offer new clues to Alzheimer's disease
Combining mass spectrometry, RNA sequencing and ribosomal profiling on 608 post-mortem dorsolateral prefrontal cortex samples from individuals with and without Alzheimer's disease, the study identified 4,321 microproteins (3,217 of them not previously characterized in the UniProtKB/Swiss-Prot standard human protein catalogue), applied a deep-learning model to rank the mass-spectrometry identification confidence of 3,001 of them with 1,067 rated high confidence, and found dozens of microproteins with altered expression in people with Alzheimer's disease, producing what is described as the largest atlas of microproteins in Alzheimer's disease made so far and making the dataset publicly available.
Combining mass spectrometry, RNA sequencing and ribosomal profiling on 608 post-mortem dorsolateral prefrontal cortex samples from individuals with and without Alzheimer's disease, the study identified 4,321 microproteins (3,217 of them not previously characterized in the UniProtKB/Swiss-Prot standard human protein catalogue), applied a deep-learning model to rank the mass-spectrometry identification confidence of 3,001 of them with 1,067 rated high confidence, and found dozens of microproteins with altered expression in people with Alzheimer's disease, producing what is described as the largest atlas of microproteins in Alzheimer's disease made so far and making the dataset publicly available.
Nature News Sep 16, 2026
This evidence bundle, comprising a Nature news feature and two bioRxiv preprints, reports progress in culturing Asgard archaea (Promethearchaeota): live-cell microscopy showed that cells of the Loki and Hodarchaea lineages drastically change shape on a minute timescale, extend and retract protrusions at 1.5 to 5.3 micrometres per minute, and crawl on glass surfaces, with actin inhibitors arresting these dynamics; separately, an Asgard archaeal virus infecting a novel strain of Ca. Lokiarchaeum ossiferum B36 was cultured for the first time, with a 16 kbp integrated provirus able to excise and replicate independently to form virus particles, placed in a new family Fylgjaviridae, while the host carries Septu, Wadjet and type II CBASS antiviral defence systems.
This evidence bundle, comprising a Nature news feature and two bioRxiv preprints, reports progress in culturing Asgard archaea (Promethearchaeota): live-cell microscopy showed that cells of the Loki and Hodarchaea lineages drastically change shape on a minute timescale, extend and retract protrusions at 1.5 to 5.3 micrometres per minute, and crawl on glass surfaces, with actin inhibitors arresting these dynamics; separately, an Asgard archaeal virus infecting a novel strain of Ca. Lokiarchaeum ossiferum B36 was cultured for the first time, with a 16 kbp integrated provirus able to excise and replicate independently to form virus particles, placed in a new family Fylgjaviridae, while the host carries Septu, Wadjet and type II CBASS antiviral defence systems.
Cultured Asgard Archaea and a Virus-Host System: Live Clues to Eukaryogenesis
This evidence bundle, comprising a Nature news feature and two bioRxiv preprints, reports progress in culturing Asgard archaea (Promethearchaeota): live-cell microscopy showed that cells of the Loki and Hodarchaea lineages drastically change shape on a minute timescale, extend and retract protrusions at 1.5 to 5.3 micrometres per minute, and crawl on glass surfaces, with actin inhibitors arresting these dynamics; separately, an Asgard archaeal virus infecting a novel strain of Ca. Lokiarchaeum ossiferum B36 was cultured for the first time, with a 16 kbp integrated provirus able to excise and replicate independently to form virus particles, placed in a new family Fylgjaviridae, while the host carries Septu, Wadjet and type II CBASS antiviral defence systems.
This evidence bundle, comprising a Nature news feature and two bioRxiv preprints, reports progress in culturing Asgard archaea (Promethearchaeota): live-cell microscopy showed that cells of the Loki and Hodarchaea lineages drastically change shape on a minute timescale, extend and retract protrusions at 1.5 to 5.3 micrometres per minute, and crawl on glass surfaces, with actin inhibitors arresting these dynamics; separately, an Asgard archaeal virus infecting a novel strain of Ca. Lokiarchaeum ossiferum B36 was cultured for the first time, with a 16 kbp integrated provirus able to excise and replicate independently to form virus particles, placed in a new family Fylgjaviridae, while the host carries Septu, Wadjet and type II CBASS antiviral defence systems.
Nature News Sep 16, 2026
By genetically engineering mice so that the precursor cells that would have formed the cerebral cortex do not survive, thereby emptying part of the brain cavity, and then implanting human brain tissue into newborn mice, the study reports that the graft expanded nearly fivefold within two to three months, filled more than 90% of the vacant space, sent projections deep into the rodents' spinal cords, and developed specialized neurons including cells similar to von Economo neurons, while behavioral tests showed no enhancement of the rodents' intellect.
By genetically engineering mice so that the precursor cells that would have formed the cerebral cortex do not survive, thereby emptying part of the brain cavity, and then implanting human brain tissue into newborn mice, the study reports that the graft expanded nearly fivefold within two to three months, filled more than 90% of the vacant space, sent projections deep into the rodents' spinal cords, and developed specialized neurons including cells similar to von Economo neurons, while behavioral tests showed no enhancement of the rodents' intellect.
Human Brain Tissue Transplanted into Mice: The Most Extensive Brain-Region Chimeric Model to Date
By genetically engineering mice so that the precursor cells that would have formed the cerebral cortex do not survive, thereby emptying part of the brain cavity, and then implanting human brain tissue into newborn mice, the study reports that the graft expanded nearly fivefold within two to three months, filled more than 90% of the vacant space, sent projections deep into the rodents' spinal cords, and developed specialized neurons including cells similar to von Economo neurons, while behavioral tests showed no enhancement of the rodents' intellect.
By genetically engineering mice so that the precursor cells that would have formed the cerebral cortex do not survive, thereby emptying part of the brain cavity, and then implanting human brain tissue into newborn mice, the study reports that the graft expanded nearly fivefold within two to three months, filled more than 90% of the vacant space, sent projections deep into the rodents' spinal cords, and developed specialized neurons including cells similar to von Economo neurons, while behavioral tests showed no enhancement of the rodents' intellect.
bioRxiv Sep 15, 2026
The work proposes that cortico-thalamic circuits are well suited to implement multi-head self- and cross-attention: layer 2/3 pyramidal cells maintain a recurrent key-value memory while layer 5 pyramidal cells decode the memory retrieved by an incoming query, the computation of keys, values and queries maps onto core and matrix thalamo-cortical projections distributed across the micro- and macro-columns of a cortical area, one cortical area forms an attention head and cortex a multi-head self-attention network, the same thalamo-cortical microcircuit also calculates sensory prediction errors guiding gradient-based synaptic plasticity, and a reward-prediction error gates via basal ganglia the cortical output and the re-activation of hippocampal memories, with the trained network aligning wit
The work proposes that cortico-thalamic circuits are well suited to implement multi-head self- and cross-attention: layer 2/3 pyramidal cells maintain a recurrent key-value memory while layer 5 pyramidal cells decode the memory retrieved by an incoming query, the computation of keys, values and queries maps onto core and matrix thalamo-cortical projections distributed across the micro- and macro-columns of a cortical area, one cortical area forms an attention head and cortex a multi-head self-attention network, the same thalamo-cortical microcircuit also calculates sensory prediction errors guiding gradient-based synaptic plasticity, and a reward-prediction error gates via basal ganglia the cortical output and the re-activation of hippocampal memories, with the trained network aligning wit
Cortico-subcortical multi-head self-attention as a substrate for cognitive performance
The work proposes that cortico-thalamic circuits are well suited to implement multi-head self- and cross-attention: layer 2/3 pyramidal cells maintain a recurrent key-value memory while layer 5 pyramidal cells decode the memory retrieved by an incoming query, the computation of keys, values and queries maps onto core and matrix thalamo-cortical projections distributed across the micro- and macro-columns of a cortical area, one cortical area forms an attention head and cortex a multi-head self-attention network, the same thalamo-cortical microcircuit also calculates sensory prediction errors guiding gradient-based synaptic plasticity, and a reward-prediction error gates via basal ganglia the cortical output and the re-activation of hippocampal memories, with the trained network aligning wit
The work proposes that cortico-thalamic circuits are well suited to implement multi-head self- and cross-attention: layer 2/3 pyramidal cells maintain a recurrent key-value memory while layer 5 pyramidal cells decode the memory retrieved by an incoming query, the computation of keys, values and queries maps onto core and matrix thalamo-cortical projections distributed across the micro- and macro-columns of a cortical area, one cortical area forms an attention head and cortex a multi-head self-attention network, the same thalamo-cortical microcircuit also calculates sensory prediction errors guiding gradient-based synaptic plasticity, and a reward-prediction error gates via basal ganglia the cortical output and the re-activation of hippocampal memories, with the trained network aligning wit
Expert Review of Hematology Sep 15, 2026
This review argues that immune reconstitution assessment after allogeneic hematopoietic cell transplantation is highly heterogeneous, which hampers the production of solid evidence and limits its potential use as a clinical endpoint, and that cross-center standardization is therefore needed, covering pre-analytical variables such as sample collection and handling as well as analytical procedures, drawing on the experience of international flow cytometry standardization consortia and achievable through existing working groups.
This review argues that immune reconstitution assessment after allogeneic hematopoietic cell transplantation is highly heterogeneous, which hampers the production of solid evidence and limits its potential use as a clinical endpoint, and that cross-center standardization is therefore needed, covering pre-analytical variables such as sample collection and handling as well as analytical procedures, drawing on the experience of international flow cytometry standardization consortia and achievable through existing working groups.
Implementation barriers of standardizing flow cytometric immune reconstitution monitoring post-allogeneic hematopoietic cell transplantation
This review argues that immune reconstitution assessment after allogeneic hematopoietic cell transplantation is highly heterogeneous, which hampers the production of solid evidence and limits its potential use as a clinical endpoint, and that cross-center standardization is therefore needed, covering pre-analytical variables such as sample collection and handling as well as analytical procedures, drawing on the experience of international flow cytometry standardization consortia and achievable through existing working groups.
This review argues that immune reconstitution assessment after allogeneic hematopoietic cell transplantation is highly heterogeneous, which hampers the production of solid evidence and limits its potential use as a clinical endpoint, and that cross-center standardization is therefore needed, covering pre-analytical variables such as sample collection and handling as well as analytical procedures, drawing on the experience of international flow cytometry standardization consortia and achievable through existing working groups.
Cancer Sep 15, 2026
This review synthesizes the clinical evidence and resistance mechanisms for immunotherapy in ovarian cancer, noting that single-agent immune checkpoint inhibitors achieve objective response rates generally below 15% in recurrent disease, that the clearest added benefit appears in chemotherapy-based combinations for PD-L1-positive platinum-resistant disease (e.g., in ENGOT-ov65/KEYNOTE-B96, median overall survival 18.2 vs 14.0 months in the CPS >=1 population, HR 0.
This review synthesizes the clinical evidence and resistance mechanisms for immunotherapy in ovarian cancer, noting that single-agent immune checkpoint inhibitors achieve objective response rates generally below 15% in recurrent disease, that the clearest added benefit appears in chemotherapy-based combinations for PD-L1-positive platinum-resistant disease (e.g., in ENGOT-ov65/KEYNOTE-B96, median overall survival 18.2 vs 14.0 months in the CPS >=1 population, HR 0.
The Evolving Role of Immunotherapy in Ovarian Cancer: From Empirical Use Toward Biology-Driven Combination and Precision Strategies
This review synthesizes the clinical evidence and resistance mechanisms for immunotherapy in ovarian cancer, noting that single-agent immune checkpoint inhibitors achieve objective response rates generally below 15% in recurrent disease, that the clearest added benefit appears in chemotherapy-based combinations for PD-L1-positive platinum-resistant disease (e.g., in ENGOT-ov65/KEYNOTE-B96, median overall survival 18.2 vs 14.0 months in the CPS >=1 population, HR 0.
This review synthesizes the clinical evidence and resistance mechanisms for immunotherapy in ovarian cancer, noting that single-agent immune checkpoint inhibitors achieve objective response rates generally below 15% in recurrent disease, that the clearest added benefit appears in chemotherapy-based combinations for PD-L1-positive platinum-resistant disease (e.g., in ENGOT-ov65/KEYNOTE-B96, median overall survival 18.2 vs 14.0 months in the CPS >=1 population, HR 0.
Clinical Cancer Research Sep 15, 2026
In 203 patients with pancreatic ductal adenocarcinoma who received neoadjuvant therapy and curative-intent resection and were restricted to minor pathologic response, an AI-enabled pipeline segmented cancer and stroma from routine H&E whole-slide images and quantified spatial composition and configuration, finding that a fragmented, interface-rich tumor-stroma ecology was independently associated with shorter disease-free survival; two spatial risk models (cancer mean shape index plus stromal shape index variability, adjusted HR 1.71, P = 0.003; mean stromal patch area plus edge density, adjusted HR 2.19, P = 0.
In 203 patients with pancreatic ductal adenocarcinoma who received neoadjuvant therapy and curative-intent resection and were restricted to minor pathologic response, an AI-enabled pipeline segmented cancer and stroma from routine H&E whole-slide images and quantified spatial composition and configuration, finding that a fragmented, interface-rich tumor-stroma ecology was independently associated with shorter disease-free survival; two spatial risk models (cancer mean shape index plus stromal shape index variability, adjusted HR 1.71, P = 0.003; mean stromal patch area plus edge density, adjusted HR 2.19, P = 0.
Spatial Configuration of Residual Pancreatic Cancer Is Associated with Recurrence Risk
In 203 patients with pancreatic ductal adenocarcinoma who received neoadjuvant therapy and curative-intent resection and were restricted to minor pathologic response, an AI-enabled pipeline segmented cancer and stroma from routine H&E whole-slide images and quantified spatial composition and configuration, finding that a fragmented, interface-rich tumor-stroma ecology was independently associated with shorter disease-free survival; two spatial risk models (cancer mean shape index plus stromal shape index variability, adjusted HR 1.71, P = 0.003; mean stromal patch area plus edge density, adjusted HR 2.19, P = 0.
In 203 patients with pancreatic ductal adenocarcinoma who received neoadjuvant therapy and curative-intent resection and were restricted to minor pathologic response, an AI-enabled pipeline segmented cancer and stroma from routine H&E whole-slide images and quantified spatial composition and configuration, finding that a fragmented, interface-rich tumor-stroma ecology was independently associated with shorter disease-free survival; two spatial risk models (cancer mean shape index plus stromal shape index variability, adjusted HR 1.71, P = 0.003; mean stromal patch area plus edge density, adjusted HR 2.19, P = 0.
Chinese medical journal Sep 15, 2026
This review systematically evaluates established and emerging non-invasive tests for detecting early-stage liver fibrosis (F1–F2), spanning serum biomarkers, molecular imaging probes, AI-based analysis of conventional imaging, alternative biofluids such as urine, exhaled breath and saliva, gut microbiota-derived biomarkers, and multiomics-integrated models, concluding that these approaches show diagnostic promise but remain constrained by limited validation, absent standardization, and unclear integration into clinical pathways, and proposing a tiered diagnostic framework as a near-term implementation route.
This review systematically evaluates established and emerging non-invasive tests for detecting early-stage liver fibrosis (F1–F2), spanning serum biomarkers, molecular imaging probes, AI-based analysis of conventional imaging, alternative biofluids such as urine, exhaled breath and saliva, gut microbiota-derived biomarkers, and multiomics-integrated models, concluding that these approaches show diagnostic promise but remain constrained by limited validation, absent standardization, and unclear integration into clinical pathways, and proposing a tiered diagnostic framework as a near-term implementation route.
Non-invasive tests for early-stage liver fibrosis: current advances and challenges
This review systematically evaluates established and emerging non-invasive tests for detecting early-stage liver fibrosis (F1–F2), spanning serum biomarkers, molecular imaging probes, AI-based analysis of conventional imaging, alternative biofluids such as urine, exhaled breath and saliva, gut microbiota-derived biomarkers, and multiomics-integrated models, concluding that these approaches show diagnostic promise but remain constrained by limited validation, absent standardization, and unclear integration into clinical pathways, and proposing a tiered diagnostic framework as a near-term implementation route.
This review systematically evaluates established and emerging non-invasive tests for detecting early-stage liver fibrosis (F1–F2), spanning serum biomarkers, molecular imaging probes, AI-based analysis of conventional imaging, alternative biofluids such as urine, exhaled breath and saliva, gut microbiota-derived biomarkers, and multiomics-integrated models, concluding that these approaches show diagnostic promise but remain constrained by limited validation, absent standardization, and unclear integration into clinical pathways, and proposing a tiered diagnostic framework as a near-term implementation route.

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