bluuebunny/crossref_metadata_2025_split huggingface dataset:
GAN-based data augmentation for transcriptomics: survey and comparative assessment
Authors: Lacan Alice , Sebag Michèle , Hanczar Blaise 
Published: June 2023

Abstract

Motivation
Transcriptomics data are becoming more accessible due to high-throughput and less costly sequencing methods. However, data scarcity prevents exploiting deep learning models’ full predictive power for phenotypes prediction. Artificially enhancing the training sets, namely data augmentation, is suggested as a regularization strategy. Data augmentation corresponds to label-invariant transformations of the training set (e.g. geometric transformations on images and syntax parsing on text data). Such transformations are, unfortunately, unknown in the transcriptomic field. Therefore, deep generative models such as generative adversarial networks (GANs) have been proposed to generate additional samples. In this article, we analyze GAN-based data augmentation strategies with respect to performance indicators and the classification of cancer phenotypes.

Results
This work highlights a significant boost in binary and multiclass classification performances due to augmentation strategies. Without augmentation, training a classifier on only 50 RNA-seq samples yields an accuracy of, respectively, 94% and 70% for binary and tissue classification. In comparison, we achieved 98% and 94% of accuracy when adding 1000 augmented samples. Richer architectures and more expensive training of the GAN return better augmentation performances and generated data quality overall. Further analysis of the generated data shows that several performance indicators are needed to assess its quality correctly.

Availability and implementation
All data used for this research are publicly available and comes from The Cancer Genome Atlas. Reproducible code is available on the GitLab repository: https://forge.ibisc.univ-evry.fr/alacan/GANs-for-transcriptomics
Coriolis: enabling metagenomic classification on lightweight mobile devices
Authors: Mikalsen Andrew J , Zola Jaroslaw 
Published: June 2023

Abstract

Motivation
The introduction of portable DNA sequencers such as the Oxford Nanopore Technologies MinION has enabled real-time and in the field DNA sequencing. However, in the field sequencing is actionable only when coupled with in the field DNA classification. This poses new challenges for metagenomic software since mobile deployments are typically in remote locations with limited network connectivity and without access to capable computing devices.

Results
We propose new strategies to enable in the field metagenomic classification on mobile devices. We first introduce a programming model for expressing metagenomic classifiers that decomposes the classification process into well-defined and manageable abstractions. The model simplifies resource management in mobile setups and enables rapid prototyping of classification algorithms. Next, we introduce the compact string B-tree, a practical data structure for indexing text in external storage, and we demonstrate its viability as a strategy to deploy massive DNA databases on memory-constrained devices. Finally, we combine both solutions into Coriolis, a metagenomic classifier designed specifically to operate on lightweight mobile devices. Through experiments with actual MinION metagenomic reads and a portable supercomputer-on-a-chip, we show that compared with the state-of-the-art solutions Coriolis offers higher throughput and lower resource consumption without sacrificing quality of classification.

Availability and implementation
Source code and test data are available from http://score-group.org/?id=smarten.
Robust reconstruction of single-cell RNA-seq data with iterative gene weight updates
Authors: Sheng Yueqi , Barak Boaz , Nitzan Mor 
Published: June 2023

Abstract

Motivation
Single-cell RNA-sequencing technologies have greatly enhanced our understanding of heterogeneous cell populations and underlying regulatory processes. However, structural (spatial or temporal) relations between cells are lost during cell dissociation. These relations are crucial for identifying associated biological processes. Many existing tissue-reconstruction algorithms use prior information about subsets of genes that are informative with respect to the structure or process to be reconstructed. When such information is not available, and in the general case when the input genes code for multiple processes, including being susceptible to noise, biological reconstruction is often computationally challenging.

Results
We propose an algorithm that iteratively identifies manifold-informative genes using existing reconstruction algorithms for single-cell RNA-seq data as subroutine. We show that our algorithm improves the quality of tissue reconstruction for diverse synthetic and real scRNA-seq data, including data from the mammalian intestinal epithelium and liver lobules.

Availability and implementation
The code and data for benchmarking are available at github.com/syq2012/iterative_weight_update_for_reconstruction.
Privacy preserving identification of population stratification for collaborative genomic research
Authors: Dervishi Leonard , Li Wenbiao , Halimi Anisa , Jiang Xiaoqian , Vaidya Jaideep , Ayday Erman 
Published: June 2023

Abstract
The rapid improvements in genomic sequencing technology have led to the proliferation of locally collected genomic datasets. Given the sensitivity of genomic data, it is crucial to conduct collaborative studies while preserving the privacy of the individuals. However, before starting any collaborative research effort, the quality of the data needs to be assessed. One of the essential steps of the quality control process is population stratification: identifying the presence of genetic difference in individuals due to subpopulations. One of the common methods used to group genomes of individuals based on ancestry is principal component analysis (PCA). In this article, we propose a privacy-preserving framework which utilizes PCA to assign individuals to populations across multiple collaborators as part of the population stratification step. In our proposed client-server-based scheme, we initially let the server train a global PCA model on a publicly available genomic dataset which contains individuals from multiple populations. The global PCA model is later used to reduce the dimensionality of the local data by each collaborator (client). After adding noise to achieve local differential privacy (LDP), the collaborators send metadata (in the form of their local PCA outputs) about their research datasets to the server, which then aligns the local PCA results to identify the genetic differences among collaborators’ datasets. Our results on real genomic data show that the proposed framework can perform population stratification analysis with high accuracy while preserving the privacy of the research participants.
KG-Hub—building and exchanging biological knowledge graphs
Authors: Caufield J Harry , Putman Tim , Schaper Kevin , Unni Deepak R , Hegde Harshad , Callahan Tiffany J , Cappelletti Luca , Moxon Sierra A T , Ravanmehr Vida , Carbon Seth , Chan Lauren E , Cortes Katherina , Shefchek Kent A , Elsarboukh Glass , Balhoff Jim , Fontana Tommaso , Matentzoglu Nicolas , Bruskiewich Richard M , Thessen Anne E , Harris Nomi L , Munoz-Torres Monica C , Haendel Melissa A , Robinson Peter N , Joachimiak Marcin P , Mungall Christopher J , Reese Justin T 
Published: June 2023

Abstract

Motivation
Knowledge graphs (KGs) are a powerful approach for integrating heterogeneous data and making inferences in biology and many other domains, but a coherent solution for constructing, exchanging, and facilitating the downstream use of KGs is lacking.

Results
Here we present KG-Hub, a platform that enables standardized construction, exchange, and reuse of KGs. Features include a simple, modular extract–transform–load pattern for producing graphs compliant with Biolink Model (a high-level data model for standardizing biological data), easy integration of any OBO (Open Biological and Biomedical Ontologies) ontology, cached downloads of upstream data sources, versioned and automatically updated builds with stable URLs, web-browsable storage of KG artifacts on cloud infrastructure, and easy reuse of transformed subgraphs across projects. Current KG-Hub projects span use cases including COVID-19 research, drug repurposing, microbial–environmental interactions, and rare disease research. KG-Hub is equipped with tooling to easily analyze and manipulate KGs. KG-Hub is also tightly integrated with graph machine learning (ML) tools which allow automated graph ML, including node embeddings and training of models for link prediction and node classification.

Availability and implementation
https://kghub.org.
O047 Registry outcomes on gasless insufflation-less laparoscopic surgery in rural North-East India
Authors: Aruparayil N , Gnanaraj J , Mishra A , Bains L , Cundill B , Gordon K , Shinkins B , Brown J , Jayne D 
Published: June 2023

Abstract

Introduction
Gasless insufflation-less laparoscopic surgery (GILLS) was introduced in rural northeast India as part of the NIHR Global Health Research Group - Surgical Technologies (GHRG-ST) project. The GILLS Registry aims to provide a reliable mechanism for monitoring the safe implementation of the GILLS technique in everyday clinical practice by the newly trained rural surgeons deemed competent in independent practice.

Methods
The GILLS Registry captured all gasless laparoscopic abdominal procedures for patients consenting to participate in the Registry and performed by trained rural surgeons. They attended the NIHR GHRG-ST TARGET training programme in March 2019 and proctorship in May 2019. Patients were recruited prospectively. Complications were reported using ISOS classification. The data were captured on REDCap from October 2019 to July 2020.

Results
Four rural surgeons from three regions of North-East India participated. Of 286 recorded procedures, 123 had general surgical and gynaecological GILLS procedures. Mean age was 34.51 (SD 11.17), 89% were female. Cholecystectomy (44%), tubal ligation (24%) and appendicectomy (16%) were the commonest procedures. More patients received regional (53%) over general anaesthesia (47%). Overall, 11% GILLS cases were converted to open and 9% to conventional laparoscopy. The intra and postoperative complication rates were both 5%. One patient died due to postoperative pancreatitis. Mean length of stay 3.02 (2.12) days.

Conclusion
GILLS procedure demonstrates favourable outcomes for patients in rural settings. This prospective Registry indicates that GILLS can be safely introduced in low resource settings and findings support wider adoption of GILLS technology in India.

Take-home message
Gas Insufflation-Less Laparoscopic Surgery (Gasless laparoscopy) can be safely introduced in low resource settings and the registry supports its wider adoption and implementation in India.
O053 An audit of the diagnostic accuracy of ultrasound-guided fine-needle aspiration of axillary lymph nodes in breast cancer, and its pathological significance to axillary nodal burden
Authors: Jalil OA 
Published: June 2023

Abstract

Introduction
Axillary lymph nodes have long been recognized as a route for breast cancer to spread systemically, thus the assessment of the axilla with ultrasound should be undertaken if suspicious findings are identified in the breast or axilla. Needle biopsy: (Fine needle aspiration (FNA) or core biopsy (CB) -under imaging guidance- is indicated if enlarged axillary nodes or a mass lesion (U2–5) is identified. Multiple meta-analyses revealed similar specificities between the two methods, however, CB appeared to be more sensitive than FNA when assessing the axilla. Our aim is to detect our breast unit's (ELHT) diagnostic accuracy of US-FNAC of axillary lymph nodes in breast cancer.

Methods
This was a retrospective audit that looked into all axillary FNAs done in the year 2019. 192 FNAs were evaluated: 23 of which were repeats and only the first FNA was accounted for, 5 were found to be breast masses and were excluded and 4 patients lost to follow up and did not have a final pathology and thus were excluded too. In total, 162 FNAs were examined.

Results
Multiple accuracy measures were calculated: The absolute sensitivity was found to be 69.69% while the specificity was 86.54% with an absolute diagnostic accuracy of 69.75%. In addition, the false-negative rate was 18.18% and the overall inadequate reports were found to be 12.3%.

Conclusion
In our breast unit, among this cohort of patients, who had FNAC-axilla, we have reported an overall lower than average sensitivity and specificity rate.

Take-home message
FNAC for axilla in our trust reported lower than average sensitivity and specificity.
Risk of chronic kidney disease in patients with acute kidney injury following a major surgery: a US claims database analysis
Authors: Ohlmeier Christoph , Schuchhardt Johannes , Bauer Chris , Brinker Meike , Kong Sheldon X , Scott Charlie , Vaitsiakhovich Tatsiana 
Published: June 2023

ABSTRACT

Background
Acute kidney injury (AKI) is a common complication after major surgery. This study assessed the risk of developing or worsening of chronic kidney disease (CKD) and other clinical outcomes in patients experiencing AKI after major surgery.

Methods
This retrospective observational study used Optum's de-identified Clinformatics Data Mart Database to investigate cardiorenal outcomes in adult patients at the first AKI event following major surgery. The primary outcome was CKD stage ≥3; secondary outcomes included myocardial infarction (MI), stroke, heart failure, all-cause hospitalization, end-stage kidney disease, need for dialysis or kidney transplant and composite measures. Follow-up was up to 3 years. Additionally, the effect of intercurrent events on the risk of clinical outcomes was assessed.

Results
Of the included patients (N = 31 252), most were male (61.9%) and White (68.9%), with a median age of 72 years (interquartile range 64–79). The event rates were 25.5 events/100 patient-years (PY) for CKD stage ≥3, 3.1 events/100 PY for end-stage kidney disease, 3.0 events/100 PY for dialysis and 0.1 events/100 PY for kidney transplants. Additionally, there were 6.9 events/100 PY for MI, 8.7 events/100 PY for stroke and 49.8 events/100 PY for all-cause hospitalization during follow-up. Patients with AKI relapses as intercurrent events were more likely to develop CKD stage ≥3 than those with just one AKI event after major surgery.

Conclusion
This analysis demonstrated that patients experiencing AKI following major surgery are at high risk of developing severe CKD or worsening of pre-existing CKD and other cardiorenal clinical outcomes such as MI and stroke.
Isochronous singing in 3 crested gibbon species (Nomascus spp.)
Authors: De Gregorio Chiara , Raimondi Teresa , Bevilacqua Valeria , Pertosa Chiara , Valente Daria , Carugati Filippo , Bandoli Francesca , Favaro Livio , Lefaux Brice , Ravignani Andrea , Gamba Marco 
Published: June 2023

Abstract
The search for common characteristics between the musical abilities of humans and other animal species is still taking its first steps. One of the most promising aspects from a comparative point of view is the analysis of rhythmic components, which are crucial features of human communicative performance but also well-identifiable patterns in the vocal displays of other species. Therefore, the study of rhythm is becoming essential to understand the mechanisms of singing behavior and the evolution of human communication. Recent findings provided evidence that particular rhythmic structures occur in human music and some singing animal species, such as birds and rock hyraxes, but only 2 species of nonhuman primates have been investigated so far (Indri indri and Hylobates lar). Therefore, our study aims to consistently broaden the list of species studied regarding the presence of rhythmic categories. We investigated the temporal organization in the singing of 3 species of crested gibbons (Nomascus gabriellae, Nomascus leucogenys, and Nomascus siki) and found that the most prominent rhythmic category was isochrony. Moreover, we found slight variation in songs’ tempo among species, with N. gabriellae and N. siki singing with a temporal pattern involving a gradually increasing tempo (a musical accelerando), and N. leucogenys with a more regular pattern. Here, we show how the prominence of a peak at the isochrony establishes itself as a shared characteristic in the small apes considered so far.
PETCH-DB: a Portal for Exploring Tissue-specific and Complex disease-associated 5-Hydroxymethylcytosines
Authors: Cai Qinyun , Zhang Zhou , Cui Xiaolong , Zeng Chang , Cai Jiabin , Cai Jiajun , Wu Kai , Zhang Xu , Shi Yixiang , Arvanitakis Zoe , Bissonnette Marc A , Chiu Brian C -H , Cheng Shi-Yuan , He Chuan , Zhang Wei 
Published: June 2023

AbstractEpigenetic modifications play critical roles in gene regulation and disease pathobiology. Highly sensitive enabling technologies, including microarray- and sequencing-based approaches have allowed genome-wide profiling of cytosine modifications in DNAs in clinical samples to facilitate discovery of epigenetic biomarkers for disease diagnosis and prognosis. Historically, many previous studies, however, did not distinguish the most investigated 5-methylcytosines (5mC) from other modified cytosines, especially the biochemically stable 5-hydroxymethylcytosines (5hmC), which have been shown to have a distinct genomic distribution and regulatory role from 5mC. Notably, during the past several years, the 5hmC-Seal, a highly sensitive chemical labeling technique, has been demonstrated to be a powerful tool for genome-wide profiling of 5hmC in clinically feasible biospecimens (e.g. a few milliliter of plasma or serum). The 5hmC-Seal technique has been utilized by our team in biomarker discovery for human cancers and other complex diseases using circulating cell-free DNA (cfDNA), as well as the characterization of the first 5hmC Human Tissue Map. Convenient access to the accumulating 5hmC-Seal data will allow the research community to validate and re-use these results, potentially providing novel insights into epigenetic contribution to a range of human diseases. Here we introduce the PETCH-DB, an integrated database that was implemented to provide 5hmC-related results generated using the 5hmC-Seal technique. We aim the PETCH-DB to be a central portal, which will be available to the scientific community with regularly updated 5hmC data in clinical samples to reflect current advances in this field.Database URL http://petch-db.org/
Unloading, ablation, bridging and transplant: different indications and treatments using the Impella 5.5 as longer-term circulatory support in one patient—an interdisciplinary case report
Authors: Volgmann Constanze , Barten Markus J , Al Assar Yousuf , Grahn Hanno , Metzner Andreas , Söffker Gerold , Schulte-Uentrop Leonie , Magnussen Christina , Kirchhof Paulus , Kluge Stefan , Doll Susanne , Doll Nicolas , Reichenspurner Hermann , Bernhardt Alexander M 
Published: June 2023

AbstractBackgroundIn patients with cardiogenic shock the clinical treatment often involves temporary mechanical circulatory support for initial haemodynamic stabilization to enable further assessment of therapeutic strategies. The surgically implanted Impella 5.5 can be used for several indications like ventricular unloading, haemodynamic support during high-risk interventions, and as a bridge-to-transplant strategy.We present an interdisciplinary managed case of using Impella 5.5 for multiple indications and treatment strategies in one patient.Case summaryA 66-year-old patient with known dilated cardiomyopathy was admitted with non-ST-elevation myocardial infarction and underwent urgent coronary bypass grafting. His native heart function did not recover and he experienced recurrent episodes of sustained ventricular tachycardia (VT) and electrical storm. He was evaluated for heart transplantation (OHT) and received a VT-ablation. However, he suffered an in-hospital cardiac arrest (IHCA) with subsequent implantation of an extracorporeal life support system (ECLS). After surgical placement of an Impella 5.5 due to left ventricular distension and pulmonary congestion, the ECLS was successfully weaned. He showed good neurological outcomes and underwent another high-risk VT-ablation. The patient was further stabilized under Impella 5.5 support in a bridge-to-transplant strategy. After 34 days he underwent a successful OHT.DiscussionIn this interdisciplinary case report the surgically implanted Impella 5.5 as temporary mechanical circulatory support was used for multiple different indications and treatment strategies like ventricular unloading, haemodynamic support during high-risk interventions, and as bridge-to-transplant strategy in one patient.
Joint association of loneliness and traditional risk factor control and incident cardiovascular disease in diabetes patients
Authors: Wang Xuan , Ma Hao , Li Xiang , Heianza Yoriko , Fonseca Vivian , Qi Lu 
Published: June 2023

Abstract

Aims
To investigate the prospective associations of the loneliness and social isolation scales with cardiovascular disease (CVD) risk in diabetes patients and compare the relative importance of loneliness and social isolation with traditional risk factors. Also, the interactions of loneliness or isolation with the degree of risk factor control in relation to CVD risk were evaluated.

Methods and results
A total of 18 509 participants diagnosed with diabetes from the UK Biobank were included. A two-item scale and a three-item scale were used to assess loneliness and isolation levels, respectively. The degree of risk factor control was defined as numbers of glycated hemoglobin (HbA1c), blood pressure (BP), low-density lipoprotein cholesterol (LDL-C), smoking, and kidney condition controlled within the target range. During a mean follow-up of 10.7 years, 3247 total CVD incidents were documented, including 2771 coronary heart disease and 701 strokes. In the fully adjusted model, compared with participants with the lowest loneliness score (zero), hazard ratios (95% confidence interval) for CVD were 1.11 (1.02 and 1.20) and 1.26 (1.11 and 1.42) for participants with a loneliness scale of 1 and 2, respectively (P-trend &lt; 0.001). No significant associations were observed for social isolation. Loneliness ranked higher in relative strength for predicting CVD than the lifestyle risk factors in diabetes patients. A significant additive interaction between loneliness and the degree of risk factor control on the risk of CVD was observed (P for additive interaction = 0.005).

Conclusion
Among diabetes patients, loneliness, but not social isolation scale, is associated with a higher risk of CVD and shows an additive interaction with the degree of risk factor control.