bluuebunny/crossref_metadata_2025_split huggingface dataset:
ChatGPT in medical literature – a concise review and SWOT analysis
Authors: Gödde Daniel , Nöhl Sophia , Wolf Carina , Rupert Yannik , Rimkus Lukas , Ehlers Jan , Breuckmann Frank , Sellmann Timur 
Published: May 2023

SummaryBackgroundChatGPT (Chat Generative Pre-trained Transformer) has initiated widespread conversation across various human sciences. We here performed a concise review combined with a SWOT (strengths, weaknesses, opportunities, threats) analysis on ChatGPT potentials in natural science including medicine.MethodsThis is a concise review of literature published in PUBMED from 01.12.2022 to 31.03.2023. The only search term used was “ChatGPT”. Publications metrics (author, journal, and subdisciplines thereof) as well as findings of the SWOT analysis are presented.FindingsOf 178 studies in total, 160 could be evaluated. The average impact factor was 4,423 (0 – 96,216), average publication speed was 16 days (0-83 days). Of all articles, there were 77 editorials, 43 essays, 21 studies, six reviews, six case reports, six news, and one meta-analyses. Strengths of ChatGPT include well-formulated expression as well as the ability to formulate general contexts flawlessly and comprehensibly, whereas the time-limited scope as well as the need for correction by experts were identified as weaknesses and threats. Opportunities include assistance in formulating medical issues for non-native speakers as well as the chance to be involved in the development of such AI in a timely manner.InterpretationArtificial intelligences such as ChatGPT will revolutionize more than just the medical publishing landscape. One of the biggest dangers in this is uncontrolled use, so we would do well to establish control and security measures at an early stage.Research in contextEvidence before this studySince its release in 11/ 2022, only a few randomized controlled trials using ChatGPT have been published. To date, the majority of data stems from short notes or communication. Given the enormous interest (and also potential for misuse), we conducted a PUBMED literature search to create the most comprehensive evidence base currently available. We searched PUBMED for publications including the quote “ChatGPT” in English or German from 01.12.2022 until 31.03.2023. In order not risk any bias of evidence all related publications were screened initially.Added value of this studyThis is the most concise review for ChatGPT up to date. By means of a SWOT analysis, readers and researchers gain comprehensive insight to strengths, weaknesses, opportunities and threats of ChatGPT especially in the context of medical literature.Implications of all the available evidenceOur review may well serve as origin for further research related to the topic in order to create more evidence, strict regulations and policies in dealing with ChatGPT.
SanPy: A whole-cell electrophysiology analysis pipeline
Authors: Guarina Laura , Le Johnson Tran , Griffith Theanne N , Santana Luis Fernando , Cudmore Robert H 
Published: May 2023

AbstractThe analysis of action potentials and other membrane voltage fluctuations provide a powerful approach for interrogating the function of excitable cells. Yet, a major bottleneck in the interpretation of this critical data is the lack of intuitive, agreed upon software tools for its analysis. Here, we present SanPy, a Python-based open-source and freely available software pipeline for the analysis and exploration of whole-cell current-clamp recordings. SanPy provides a robust computational engine with an application programming interface. Using this, we have developed a cross-platform graphical user interface that does not require programming. SanPy is designed to extract common parameters from action potentials including threshold time and voltage, peak, half-width, and interval statistics. In addition, several cardiac parameters are measured including the early diastolic duration and rate. SanPy is built to be fully extensible by providing a plugin architecture for the addition of new file loaders, analysis, and visualizations. A key feature of SanPy is its focus on quality control and data exploration. In the desktop interface, all plots of the data and analysis are linked allowing simultaneous data visualization from different dimensions with the goal of obtaining ground truth analysis. We provide documentation for all aspects of SanPy including several use cases and examples. To test SanPy, we have performed analysis on current-clamp recordings from heart and brain cells. Taken together, SanPy is a powerful tool for whole-cell current-clamp analysis and lays the foundation for future extension by the scientific community.News and NoteworthyWhole-cell current-clamp recording is a critical technique to understand detailed biophysical mechanisms at the cellular and network levels. Yet, the analysis of this data is by no means standardized. Here, we present SanPy, a Python based open-source software pipeline for the exploration and analysis of current-clamp recordings. SanPy provides a powerful computational engine with an application programming interface. Finally, SanPy provides a cross-platform point-and-click graphical user interface that does not require programming.
Genome-scale analysis of interactions between genetic perturbations and natural variation
Authors: Hale Joseph J. , Matsui Takeshi , Goldstein Ilan , Mullis Martin N. , Roy Kevin R. , Ville Chris Ne , Miller Darach , Wang Charley , Reynolds Trevor , Steinmetz Lars M. , Levy Sasha F. , Ehrenreich Ian M. 
Published: May 2023

AbstractInteractions between genetic perturbations and segregating loci can cause perturbations to show different phenotypic effects across genetically distinct individuals. To study these interactions on a genome scale in many individuals, we used combinatorial DNA barcode sequencing to measure the fitness effects of 7,700 CRISPRi perturbations targeting 1,712 distinct genes in 169 yeast cross progeny (or segregants). We identified 460 genes whose perturbation has different effects across segregants. Several factors caused perturbations to show variable effects, including baseline segregant fitness, the mean effect of a perturbation across segregants, and interacting loci. We mapped 234 interacting loci and found four hub loci that interact with many different perturbations. Perturbations that interact with a given hub exhibit similar epistatic relationships with the hub and show enrichment for cellular processes that may mediate these interactions. These results suggest that an individual’s response to perturbations is shaped by a network of perturbation-locus interactions that cannot be measured by approaches that examine perturbations or natural variation alone.
Endogenous fine-mapping of functional regulatory elements in complex genetic loci
Authors: Zhao Ke , Zhou Yao , Wu Chengyue , Wang Jianhua , Yao Hongcheng , Cheng Xin , Zhao Lin , Wang Wei , Chu Xinlei , Yi Xianfu , Chen Yupeng , Li Miaoxin , Lu Wange , Chen Kexin , Sham Pak Chung , Li Mulin Jun 
Published: May 2023

AbstractThe vast majority of genetic loci associated with polygenic complex traits are located in non-coding regions of the human genome. However, many of these regions exhibit high- order gene regulatory relationships and complicated linkage disequilibrium (LD) configurations, which bring challenges to accurately identify causal variants and their target genes controlling specific molecular processes or traits. We employed multiplexed single-cell CRISPR interference and activation perturbations to explore the links betweencis-regulatory element (CRE) and target gene expression within tight LD in the endogenous chromatin context. We validated the prevalence of multiple causality in perfect LD (pLD) for independent expression quantitative trait locus (eQTL), and revealed fine-grained genetic effects on gene expression within pLD. These effects are difficult to decipher using conventional eQTL fine-mapping or to predict via existing computational methods. We found that nearly half of the casual CREs lack classical epigenetic markers, potentially affecting gene expression through hidden regulatory mechanisms. Integrative analysis on different types of perturbation effects suggested a high regulatory plasticity of the human genome. These findings will propel further in-depth exploration of functional genomic elements, facilitating a more comprehensive understanding of gene expression regulatory patterns and the development of complex traits.
Apposed networks of interacting TCRs and BCRs exhibiting mosaicked CDR3 sequences made of fixed junctional motifs
Authors: Ahmed Rizwan , Majety Neha , Chan Kevin C. , Giwa Adebola , Heinemann Joseph , Zhang Hao , Margolick Joseph , Al-Hallaf Rafid , Paul Prajita , Bell David R. , Song Yi , Lee Sangyun , Zhou Ruhong , Wolfe Risa M , Donner Thomas , Jie Chunfa , Hamad Abdel Rahim A 
Published: May 2023

AbstractT and B cells are the two arms of the adaptive immune system that mediate cellular and humoral immunity, respectively, using highly diverse repertoires of antigen receptors. T cells recognize antigens using the T cell receptor (TCR), whereas B cells use the B cell receptor (BCR or surface immunoglobulin). Complementary determining regions (CDR3) of TCRs and BCRs are randomly generated through somatic VDJ recombination and nucleotide deletions and insertions at the V-D and D-J junctions. Contrary to this paradigm, here we describe two networks of millions of TCRβ and IGH clonotypes that are made from only two CDR3 sequences and associated with more 63 diseases. The TCRβ network members bore either the prototypic signature CDR3 sequence (CASSPGTEAFF), its N-terminal VD motif (CASSPGT) recombined with various Jβ segments (CASSPGT-Jβx) or its DJβ motif recombined with various Vβ (Vβx-PGTEAFF). The BCR network members exhibit one signature CDR3 sequence (CARx1-4DTAMVYYFYDW) made from an invariant DJH motif (DTAMVYYFDYW) combined with various VH genes. The prototypes of the two networks are apparently teleogically related as they were dually expressed on the rare population of dual expresser (DE) lymphocytes and molecular dynamic simulations show that they were interacting partners. We conclude that members of the two networks represent a core set of evolutionary-conserved primordial antigen receptors that play fundamental roles in host defense and autoimmune diseases.
Swimming ability of theCarybdea marsupialis(Cnidaria: Cubozoa: Carybdeidae): implications for its spatial distribution
Authors: Bordehore Cesar , Manchado-Pérez Sara , Fonfría Eva S. 
Published: May 2023

ABSTRACTAlthough usually considered part of the plankton, cubozoans are strong swimmers. The aim of this study was to determine the influence of the active swimming ability of the box jellyfishCarybdea marsupialison the spatial distribution of a well-studied population off Dénia (NW Mediterranean) where adults and juveniles do not overlap geographically. To achieve this aim, we analyzed the swimming speed, proficiency, effective velocity, and effective displacement index (EDI) of 27 individuals with diagonal bell widths (DBW) ranging from 1.1 to 36 mm. The laboratory analysis utilized conventional video recordings and the video analysis tool Tracker. Mean swimming speed for small juveniles (DBW ≤ 5 mm), medium juveniles (5 mm < DBW< 15 mm) and adults (DBW ≥ 15 mm) were 9.65 ± 0.76 mm-1, 21.91 ± 2.29 mm-1and 43.10 ± 1.78 mm-1(mean ± s.e.m.), respectively. Comparing these results with the local currents obtained from drifting buoys analyzed in the area over the course of three years, adults would be able to swim strongly enough to overcome almost 70% of the currents, whereas the small juveniles would not reach 17%. This allows larger individuals to select their habitat, while smaller individuals are left dependent on advection. Although experiments adding currents in aquaria would be necessary to confirm these theoretical results, the data obtained would be useful in improving the performance of bio-mathematical models used to predict jellyfish blooms since, even though the sting ofC. marsupialisis non-fatal, it may produce systemic effects in sensitive swimmers.Summary statementThe analysis of the swimming ability ofC. marsupialiselucidates its key role in the spatial distribution of a northwestern Mediterranean population.
Temporal Dynamics of Brain Activity Predicting Sense of Agency over Muscle Movements
Authors: Veillette John P. , Lopes Pedro , Nusbaum Howard C. 
Published: May 2023

AbstractOur muscles are the primary means through which we affect the external world, and the sense of agency (SoA) over the action through those muscles is fundamental to our self-awareness. However, SoA research to date has focused almost exclusively on agency over action outcomes rather than over the musculature itself, as it was believed that SoA over the musculature could not be manipulated directly. Drawing on methods from human-computer interaction and adaptive experimentation, we use human-in-the-loop Bayesian optimization to tune the timing of electrical muscle stimulation so as to robustly elicit a sense of agency over electrically-actuated muscle movements in male and female human subjects. We use time-resolved decoding of subjects’ EEG to estimate the time course of neural activity which predicts reported agency on a trial-by-trial basis. Like paradigms which assess SoA over action consequences, we found that the late (post-conscious) neural activity predicts SoA. Unlike typical paradigms, however, we also find patterns of early (sensorimotor) activity with distinct temporal dynamics predicts agency over muscle movements, suggesting that the “neural correlates of agency” may depend on the level of abstraction (i.e., direct sensorimotor feedback vs. downstream consequences) most relevant to a given agency judgement. Moreover, fractal analysis of the EEG suggests that SoA-contingent dynamics of neural activity may modulate the sensitivity of the motor system to external input.Significance StatementThe sense of agency – the feeling of “I did that” – when directing one’s own musculature is a core feature of human experience. We show that we can robustly manipulate the sense of agency over electrically actuated muscle movements, and we investigate the time course of neural activity that predicts the sense of agency over these actuated movements. We find evidence of two distinct neural processes – a transient sequence of patterns that begins in the early sensorineural response to muscle stimulation and a later, sustained signature of agency. These results shed light on the neural mechanisms by which we experience our movements as volitional.
Prevalence of short peer reviews in leading general medical journals: a study of peer-review length at The BMJ, PLOS Medicine, and BMC Medicine
Authors: Geldsetzer Pascal , Heemann Markus , Tikka Pauli , Wang Grace , Cusick Marika Mae , Lenjani Ali , Krishnan Nandita 
Published: May 2023

AbstractBackgroundHigh-quality peer reviews are often thought to be essential to ensuring the integrity of the scientific publication process but measuring peer review quality is challenging. Although imperfect, review word count could serve as a simple, objective metric of review quality. We aimed to examine the prevalence of very short reviews and how often they inform editorial decisions on research articles in leading general medical journals.MethodsWe compiled a data set of peer reviews from published full-length original research articles in The BMJ, BMC Medicine, and PLOS Medicine for the years 2003 to 2022. In our primary analyses, we used a threshold of <200 words to calculate the prevalence of very short reviews. In secondary analyses, we also used thresholds of <100 and <300 words. In addition to disaggregating results by journal and year, we plotted the proportion of articles for which the first editorial decision was made based on a set of peer reviews in which very short reviews constituted 100%, ≥50%, ≥33%, or ≥20% of the reviews.ResultsIn this sample of 11,466 reviews corresponding to 4,038 published articles, the median review word count was 425 (Interquartile Range=253–675), and the mean was 520 (Standard Deviation=401). The overall prevalence of very short (<200 words) reviews was 17.1% [95% CI: 16.4%–17.8%]. Across the three journals, 20.9% [95% CI: 19.6%–22.2%] of initial editorial decisions were based on review sets containing ≥50% very short reviews. The prevalence of very short reviews and share of editorial decisions based on review sets containing ≥50% very short reviews was highest for BMC Medicine at 26.8% [95% CI: 25.1%–28.5%] and lowest for The BMJ at 7.3% [95% CI: 5.7%–8.9%].ConclusionsA substantial proportion of initial editorial decisions for published articles in these three leading general medical journals was based on peer reviews of such short length that they were unlikely to be of high quality. Future research should determine whether monitoring peer review length is a useful approach to improving the quality of the peer review process and which interventions, such as incentives and norm-based interventions, are most effective in soliciting more detailed reviews.
RaMALDI: enabling simultaneous Raman and MALDI imaging of the same tissue section
Authors: Yang Ethan , Kim Jeong Hee , Tressler Caitlin M. , Shen Xinyi Elaine , Brown Dalton R. , Johnson Cole C. , Barman Ishan , Glunde Kristine 
Published: May 2023

AbstractMultimodal tissue imaging techniques that integrate two complementary modalities are powerful discovery tools for unraveling biological processes and identifying biomarkers of disease. Combining Raman spectroscopic imaging (RSI) and matrix-assisted laser-desorption/ionization (MALDI) mass spectrometry imaging (MSI) to obtain fused images with the advantages of both modalities has the potential of providing spatially resolved, sensitive, and specific biomolecular information, but has so far involved two separate, consecutive tissue sections for RSI and MALDI MSI, resulting in images from two separate entities with inherent disparities. We have developed RaMALDI, a streamlined, integrated, multimodal imaging workflow of RSI and MALDI MSI, performed on a single tissue section with one sample preparation protocol. We show that RaMALDI imaging of various tissues effectively integrates molecular information acquired from both RSI and MALDI MSI of the same sample.Table of ContentsWe demonstrate for the first time RaMALDI imaging, a streamlined, integrated multimodal imaging workflow of Raman spectroscopy imaging (RSI) and matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI), which is performed on a single sample and uses one sample preparation protocol. RaMALDI imaging of various tissues effectively integrates molecular information acquired from both RSI and MALDI MSI of the same sample.
Cellular visualization of G-quadruplex RNA via fluorescence lifetime imaging microscopy
Authors: Robinson Jenna , Stenspil Stine G. , Maleckaite Karolina , Bartlett Molly , Di Antonio Marco , Vilar Ramon , Kuimova Marina K. 
Published: May 2023

ABSTRACTOver the last decade, appreciation of the roles of G-quadruplex (G4) structures in cellular regulation and maintenance have rapidly grown, making the establishment of robust methods to visualize G4s increasingly important. Fluorescent probes are commonly used for G4 detectionin vitro, however, achieving sufficient selectivity to detect G4s in a dense and structurally diverse cellular environment is challenging. The use of fluorescence probes for G4 detection is further complicated by variations of probe uptake into cells, which may affect fluorescence intensity independently of G4 abundance. In this work, we report an alternative small-molecule approach to visualize G4s that does not rely on fluorescence intensity switch-on and thus, does not require the use of molecules with exclusive G4 binding selectivity. Specifically, we have developed a novel thiazole orange derivative, TOR-G4, that exhibits a unique fluorescence lifetime when bound to G4s compared to other structures, allowing G4 binding to be sensitively distinguished from non-G4 binding, independently of local probe concentration. Furthermore, TOR-G4 primarily co-localizes with RNA in the cytoplasm and nucleoli of cells, making it the first lifetime-based probe validated for exploring the emerging roles of RNA G4sin cellulo.Abstract Figure
A transmission chain linkingMycobacterium ulceranswithAedes notoscriptusmosquitoes, possums and human Buruli ulcer cases in southeastern Australia
Authors: Mee Peter T. , Buultjens Andrew H. , Oliver Jane , Brown Karen , Crowder Jodie C. , Porter Jessica L. , Hobbs Emma C. , Judd Louise M. , Taiaroa George , Puttharak Natsuda , Williamson Deborah A. , Blasdell Kim R. , Tay Ee Laine , Feldman Rebecca , Muzari Mutizwa Odwell , Sanders Chris , Larsen Stuart , Crouch Simon R. , Johnson Paul D. R. , Wallace John R. , Price David J. , Hoffmann Ary A. , Gibney Katherine B. , Stinear Timothy P. , Lynch Stacey E. 
Published: May 2023

AbstractIn temperate southeastern Australia over the past two decades there has been a marked progressive increase in human cases of Buruli ulcer, an infection of subcutaneous tissue caused byMycobacterium ulcerans. Native possums are the major local environmental reservoir ofM. ulceransas they not only develop Buruli lesions but they also shedM. ulceransin their excreta. However the way humans acquireM. ulceransfrom possums has not been determined. Previous case-control studies, insect field surveys and vector competence studies have suggested a role for mosquitoes inM. ulceranstransmission between possums and humans. To explore these links we conducted an extensive, 4-month structured mosquito field survey and fourad hocfield surveys across an area of 350km2on the Mornington Peninsula, an area endemic for Buruli ulcer to the south of the major metropolitan city of Melbourne. We then compared spatial and temporal patterns ofM. ulcerans-positive mosquito occurrence withM. ulcerans-positive possums (established by previous possum excreta surveys) and human Buruli ulcer cases across the region. We used metabarcoding to assess mosquito blood-feeding host preference and to reconstructM. ulceransgenomes from positive mosquitoes to test epidemiological inferences. We collected 66,325 mosquitoes spanning 26 different species from 180 repeatedly sampled traps over a 4-month period.Culex molestusandAedes notoscriptuswere the dominant species (42% and 35% of trapped mosquitoes, respectively). PCR screening 25% of trapped mosquitoes revealed a significant association betweenM. ulceransandAe. notoscriptus(p<0.0001) with a maximum likelihood estimate (MLE) of 5.88M. ulceranspositive mosquitoes per 1,000 tested. Using spatial scanning statistics, we also observed significant overlap between clusters ofM. ulcerans-positiveAe. notoscriptus,M. ulcerans-positive possum excreta and human Buruli ulcer cases. Metabarcoding analyses of blood-fedAe. notoscriptusshowed individual mosquitoes had fed both on humans and native possums. Enrichment genome sequencing from PCR-positive mosquitoes confirmed sharedM. ulceransgenome single-nucleotide polymorphism (SNP) profiles between mosquitoes, possum excreta and clinical human isolates within the same regions. These findings indicate thatAe. notoscriptuslikely transmitM. ulceransin southeastern Australia and highlight mosquito control as a plausible means to control the Buruli ulcer epidemic in our region.