Optimism for accelerating scientific discovery with AI continues to grow. Current applications of AI in scientific research range from training dedicated foundation models on scientific data to agentic autonomous hypothesis generation systems to AI-driven autonomous labs. The need to measure progress of AI systems in scientific domains correspondingly must not only accelerate, but increasingly shift focus to more real-world capabilities. Beyond rote knowledge and even just reasoning to actually measuring the ability to perform meaningful work. Prior work introduced the Language Agent Biology Benchmark LAB-Bench as an initial attempt at measuring these abilities. Here we introduce an evolution of that benchmark, LABBench2, for measuring real-world capabilities of AI systems performing useful scientific tasks. LABBench2 comprises nearly 1,900 tasks and is, for the most part, a continuation of LAB-Bench, measuring similar capabilities but in more realistic contexts. We evaluate performance of current frontier models, and show that while abilities measured by LAB-Bench and LABBench2 have improved substantially, LABBench2 provides a meaningful jump in difficulty (model-specific accuracy differences range from -26% to -46% across subtasks) and underscores continued room for performance improvement. LABBench2 continues the legacy of LAB-Bench as a de facto benchmark for AI scientific research capabilities and we hope that it continues to help advance development of AI tools for these core research functions. To facilitate community use and development, we provide the task dataset at https://huggingface.co/datasets/futurehouse/labbench2 and a public eval harness at https://github.com/EdisonScientific/labbench2.
Vladimir Vinarsky, Stefania Pagliari, Bacel Aldabash
et al.
Abstract Cardiac diseases are fueled by extracellular matrix (ECM) remodelling. Together with the altered ECM chemical composition, the mechanical turmoil associated with ECM maladaptive remodelling in the pathological heart drives the shuttling of Yes Associated Protein 1 (YAP1) into cardiomyocyte (CM) nuclei that results either in cell cycle re-entry or cardiomyocyte hypertrophy. The mechanism of YAP1 reactivation and factors driving qualitatively different cellular outcomes is not well understood. Here we employed mechanical actuation as a proxy reproducing ECM remodelling in vitro to trigger YAP1 nuclear shuttling in contractile cardiomyocytes derived from human embryonic and induced pluripotent stem cells (hPSCs). By using hPSC lines in which YAP1 expression has been genetically depleted, super-resolution microscopy and electrophysiological measurements, we show that ECM-triggered nuclear presence of endogenous YAP1 contributes to cardiomyocyte maturation, participates in the formation and alignment of myofibrils, as well as in the maturation of their electrophysiological properties and calcium dynamics. We eventually exploit engineered heart tissues (EHTs) to demonstrate that the net effect of YAP1 deficiency in cardiomyocytes is the inability to respond to physiological stimuli by compensatory growth that results in reduced force development. These results suggest that the re-activation of endogenous YAP1 following ECM maladaptive remodelling promotes cardiomyocyte contractility by restructuring the sarcomere apparatus and the maturation of electrophysiological properties via transcriptionally dependent and independent mechanisms.
Neoplasms. Tumors. Oncology. Including cancer and carcinogens, Cytology
A study of the Revista General de Informacion y Documentacion, from 2005 to 2022. The objective is aimed at qualifying the structure of the research field and assessing the trajectory of the thematic areas covered. Applying as methodology the analysis of co-words, the construction of bibliometric networks and the creation of scientific maps. 514 documents are extracted from the Web of Science (WoS) database. The keywords assigned by the authors of the documents are selected and divided into three subperiods: 2005-2010, 2011-2016 and 2017-2022. In the results, 1701 author keywords and 37 bibliometric networks are obtained. In the period 2005-2010, the structure of the research field is represented on the scientific map with very few central and specialized topics, considering an initial and underdeveloped organization. In the period 2011-2016, the structure of the research field is distributed on the scientific map with a more varied number of central and specialized topics, but still insufficient, considering an organization in the process of development. In the period 2017-2022, the structure of the research field is shown on the map with all kinds of family of topics (central, specialized, transversal, emerging or disappearing), being valued as a dynamic, complex and heterogeneous organization. Regarding the evolution of the thematic areas, the map shows solid progress between the last two periods. The morphology of the thematic field treated in RGID is outlined in three phases: foundation, process of development and consolidation.
Alexander Bertuccioli, Marco Cardinali, Matteo Micucci
et al.
This study investigates the efficacy of <i>Streptococcus salivarius</i> K12 in preventing upper respiratory tract infections (URTIs) in healthy adults. URTIs are a common issue, particularly in physically active individuals, leading to significant disruptions in daily life. Probiotics, such as <i>S. salivarius</i> K12, have emerged as a potential preventive strategy for these infections. This research was conducted as a randomized, double-blind, placebo-controlled trial involving 112 participants aged between 19 and 25. Participants were randomly divided into two groups: one group received a daily dose of <i>S. salivarius</i> K12, marketed as Bactoblis<sup>®</sup>, while the other received a placebo. The trial lasted for four months, during which adherence to the treatment protocol was closely monitored. The primary goal was to measure the incidence of URTIs using the Jackson Scale and the Wisconsin Upper Respiratory Symptom Survey (WURSS-11). The results indicated that higher adherence to the <i>S. salivarius</i> K12 treatment was associated with an increased number of days without URTI symptoms. Although the overall severity of symptoms did not differ significantly between the treatment and control groups, those with high adherence to <i>S. salivarius</i> K12 (greater than 90%) reported more days free from illness. In conclusion, <i>S. salivarius</i> K12 demonstrated potential as a preventive measure against URTIs, especially in individuals who adhered strictly to the treatment regimen. However, further research involving larger populations and longer follow-up periods is needed to fully confirm these findings and better understand the role of <i>S. salivarius</i> K12 in preventing respiratory infections.
Judith Owokuhaisa, Eleanor Turyakira, Frank Ssedyabane
et al.
Abstract Background Cervical cancer continues to threaten women’s health, especially in low-resource settings. Regular follow-up after screening and treatment is an effective strategy for monitoring treatment outcomes. Consequently, understanding the factors contributing to patient non-attendance of scheduled follow-up visits is vital to providing high-quality care, reducing morbidity and mortality, and unnecessary healthcare costs in low-resource settings. Methods A descriptive qualitative study was done among healthcare providers and patients who attended the cervical cancer screening clinic at Mbarara Regional Referral Hospital in southwestern Uganda. In-depth interviews were conducted using a semi-structured interview guide. Interviews were audio-recorded, transcribed verbatim, and thematically analysed in line with the social-ecological model to identify barriers and facilitators. Results We conducted 23 in-depth interviews with 5 healthcare providers and 18 patients. Health system barriers included long waiting time at the facility, long turnaround time for laboratory results, congestion and lack of privacy affecting counselling, and healthcare provider training gaps. The most important interpersonal barrier among married women was lacking support from male partners. Individual-level barriers were lack of money for transport, fear of painful procedures, emotional distress, and illiteracy. Inadequate and inaccurate information was a cross-cutting barrier across the individual, interpersonal, and community levels of the socio-ecological model. The facilitators were social support, positive self-perception, and patient counselling. Conclusions Our study revealed barriers to retention in care after cervical cancer screening, including lack of partner support, financial and educational constraints, and inadequate information. It also found facilitators that included social support, positive self-perception, and effective counselling.
Gynecology and obstetrics, Public aspects of medicine
Recent research trends in computational biology have increasingly focused on integrating text and bio-entity modeling, especially in the context of molecules and proteins. However, previous efforts like BioT5 faced challenges in generalizing across diverse tasks and lacked a nuanced understanding of molecular structures, particularly in their textual representations (e.g., IUPAC). This paper introduces BioT5+, an extension of the BioT5 framework, tailored to enhance biological research and drug discovery. BioT5+ incorporates several novel features: integration of IUPAC names for molecular understanding, inclusion of extensive bio-text and molecule data from sources like bioRxiv and PubChem, the multi-task instruction tuning for generality across tasks, and a numerical tokenization technique for improved processing of numerical data. These enhancements allow BioT5+ to bridge the gap between molecular representations and their textual descriptions, providing a more holistic understanding of biological entities, and largely improving the grounded reasoning of bio-text and bio-sequences. The model is pre-trained and fine-tuned with a large number of experiments, including \emph{3 types of problems (classification, regression, generation), 15 kinds of tasks, and 21 total benchmark datasets}, demonstrating the remarkable performance and state-of-the-art results in most cases. BioT5+ stands out for its ability to capture intricate relationships in biological data, thereby contributing significantly to bioinformatics and computational biology. Our code is available at \url{https://github.com/QizhiPei/BioT5}.
Luisa Riato, Scott G. Leibowitz, Marc H. Weber
et al.
Abstract River and stream conservation programs have historically focused on a single spatial scale, for example, a watershed or stream site. Recently, the use of landscape information (e.g., land use and land cover) at multiple spatial scales and over large spatial extents has highlighted the importance of incorporating a landscape perspective into stream protection and restoration activities. Previously, we developed a novel framework that links information about watershed‐, catchment‐, and reach‐scale integrity with stream biological condition using scatterplots and a landscape integrity map. Here we examined an application of this approach for streams in urban and other settings in King County, Washington State, United States, where we related stream macroinvertebrate condition to two indices of landscape integrity, the US Environmental Protection Agency's (USEPA) nationally available Index of Watershed Integrity (IWI) and Index of Catchment Integrity (ICI). We generated a scatterplot of IWI versus ICI for sample sites, where points represented site macroinvertebrate condition from poor to good. The same data were also visualized as a landscape integrity map that displayed catchments of King County according to the level of watershed and catchment integrity (high or low IWI/ICI). Almost three‐quarters of poor‐condition sites were associated with high‐integrity watersheds and catchments (i.e., underperforming sites), which suggested that either one or both national indicators were insufficient for this area, and that sites underperformed because of local‐scale factors. In response, we used a catchment‐scale indicator related to forest condition (PctForestCat) after examining several GIS‐based dispersal indicators from the National Hydrography Dataset and other candidates from the USEPA's StreamCat dataset. We then compared the results of the scatterplots and maps based on the current and original analyses and found that many of the sites previously classified as underperforming now performed as expected, that is, they were poor‐condition sites in poor‐condition catchments. This analysis demonstrates how results based on a national dataset can be improved by developing an alternative that represents regionally important stressors. The methods used to develop an effective landscape indicator based on StreamCat datasets, and the utility of the multiscale approach, could provide important tools for prioritizing, optimizing, and communicating stream conservation actions.
Andrea Piccioni, Federico Rosa, Sergio Mannucci
et al.
There is much evidence confirming the crucial role played by the gut microbiota in modulating the immune system in the onset of autoimmune diseases. In this article, we focus on the relationship between alterations in the microbiome and the onset of diabetes mellitus type 1 and LADA, in light of the latest evidence. We will then look at both how the role of the gut microbiota appears to be increasingly crucial in the pathogenesis of these disorders and how this aspect may be instrumental in the development of new potential therapeutic strategies that modulate the gut microbiota, such as probiotics, prebiotics, and fecal microbiota transplantation.
Cervical cancer, among the most frequent adverse cancers in women, could be avoided through routine checks. The Pap smear check is a widespread screening methodology for the timely identification of cervical cancer, but it is susceptible to human mistakes. Artificial Intelligence-reliant computer-aided diagnostic (CAD) methods have been extensively explored to identify cervical cancer in order to enhance the conventional testing procedure. In order to attain remarkable classification results, most current CAD systems require pre-segmentation steps for the extraction of cervical cells from a pap smear slide, which is a complicated task. Furthermore, some CAD models use only hand-crafted feature extraction methods which cannot guarantee the sufficiency of classification phases. In addition, if there are few data samples, such as in cervical cell datasets, the use of deep learning (DL) alone is not the perfect choice. In addition, most existing CAD systems obtain attributes from one domain, but the integration of features from multiple domains usually increases performance. Hence, this article presents a CAD model based on extracting features from multiple domains not only one domain. It does not require a pre-segmentation process thus it is less complex than existing methods. It employs three compact DL models to obtain high-level spatial deep features rather than utilizing an individual DL model with large number of parameters and layers as used in current CADs. Moreover, it retrieves several statistical and textural descriptors from multiple domains including spatial and time–frequency domains instead of employing features from a single domain to demonstrate a clearer representation of cervical cancer features, which is not the case in most existing CADs. It examines the influence of each set of handcrafted attributes on diagnostic accuracy independently and hybrid. It then examines the consequences of combining each DL feature set obtained from each CNN with the combined handcrafted features. Finally, it uses principal component analysis to merge the entire DL features with the combined handcrafted features to investigate the effect of merging numerous DL features with various handcrafted features on classification results. With only 35 principal components, the accuracy achieved by the quatric SVM of the proposed CAD reached 100%. The performance of the described CAD proves that combining several DL features with numerous handcrafted descriptors from multiple domains is able to boost diagnostic accuracy. Additionally, the comparative performance analysis, along with other present studies, shows the competing capacity of the proposed CAD.
G. D. Varsamis, I. G. Karafyllidis, K. M. Gilkes
et al.
Reference-guided DNA sequencing and alignment is an important process in computational molecular biology. The amount of DNA data grows very fast, and many new genomes are waiting to be sequenced while millions of private genomes need to be re-sequenced. Each human genome has 3.2 B base pairs, and each one could be stored with 2 bits of information, so one human genome would take 6.4 B bits or about 760 MB of storage (National Institute of General Medical Sciences). Today most powerful tensor processing units cannot handle the volume of DNA data necessitating a major leap in computing power. It is, therefore, important to investigate the usefulness of quantum computers in genomic data analysis, especially in DNA sequence alignment. Quantum computers are expected to be involved in DNA sequencing, initially as parts of classical systems, acting as quantum accelerators. The number of available qubits is increasing annually, and future quantum computers could conduct DNA sequencing, taking the place of classical computing systems. We present a novel quantum algorithm for reference-guided DNA sequence alignment modeled with gate-based quantum computing. The algorithm is scalable, can be integrated into existing classical DNA sequencing systems and is intentionally structured to limit computational errors. The quantum algorithm has been tested using the quantum processing units and simulators provided by IBM Quantum, and its correctness has been confirmed.
Henry V. Jakubowski, Henry Agnew, Bartholomew E. Jardine
et al.
Biology is perhaps the most complex of the sciences, given the incredible variety of chemical species that are interconnected in spatial and temporal pathways that are daunting to understand. Their interconnections lead to emergent properties such as memory, consciousness, and recognition of self and non-self. To understand how these interconnected reactions lead to cellular life characterized by activation, inhibition, regulation, homeostasis, and adaptation, computational analyses and simulations are essential, a fact recognized by the biological communities. At the same time, students struggle to understand and apply binding and kinetic analyses for the simplest reactions such as the irreversible first-order conversion of a single reactant to a product. This likely results from cognitive difficulties in combining structural, chemical, mathematical, and textual descriptions of binding and catalytic reactions. To help students better understand dynamic reactions and their analyses, we have introduced two kinds of interactive graphs and simulations into the online educational resource, Fundamentals of Biochemistry, a multivolume biochemistry textbook that is part of the LibreText collection. One type is available for simple binding and kinetic reactions. The other displays progress curves (concentrations vs time) for both simple reactions and more complex metabolic and signal transduction pathways, including those available through databases using systems biology markup language (SBML) files. Users can move sliders to change dissociation and kinetic constants as well as initial concentrations and see instantaneous changes in the graphs. They can also export data into a spreadsheet for further processing, such as producing derivative Lineweaver-Burk and traditional Michaelis-Menten graphs of initial velocity (v0) vs substrate concentration.
Propellant Gauging is of vital importance to a spacecraft at the end of its life. Based on the Monte Carlo Method, uncertainty analysis and the improvement of propellant gauging using gas injection have been studied. As a result of the analysis, the gauging uncertainty has weak relation to the uncertainties of the volumes of the injection room and tank, the uncertainties of the pressure, and the temperature in the injection room. Relatively, the uncertainties of the temperature and pressure in the tank have a great effect on the gauging uncertainty. By improving the uncertainties of the tank pressure and temperature within 0.04% and 0.4%, the final gauging uncertainty can be obtained within 0.4%. Ground tests have been conducted and the results came out with approximately 0.4% error, well within the theoretical analysis.
Pedro Duque, Cristina P. Vieira, Bárbara Bastos
et al.
Abstract Background Vitamin C (VC) is an indispensable antioxidant and co-factor for optimal function and development of eukaryotic cells. In animals, VC can be synthesized by the organism, acquired through the diet, or both. In the single VC synthesis pathway described in animals, the penultimate step is catalysed by Regucalcin, and the last step by l-gulonolactone oxidase (GULO). The GULO gene has been implicated in VC synthesis only, while Regucalcin has been shown to have multiple functions in mammals. Results Both GULO and Regucalcin can be found in non-bilaterian, protostome and deuterostome species. Regucalcin, as here shown, is involved in multiple functions such as VC synthesis, calcium homeostasis, and the oxidative stress response in both Deuterostomes and Protostomes, and in insects in receptor-mediated uptake of hexamerin storage proteins from haemolymph. In Insecta and Nematoda, however, there is no GULO gene, and in the latter no Regucalcin gene, but species from these lineages are still able to synthesize VC, implying at least one novel synthesis pathway. In vertebrates, SVCT1, a gene that belongs to a family with up to five members, as here shown, is the only gene involved in the uptake of VC in the gut. This specificity is likely the result of a subfunctionalization event that happened at the base of the Craniata subphylum. SVCT-like genes present in non-Vertebrate animals are likely involved in both VC and nucleobase transport. It is also shown that in lineages where GULO has been lost, SVCT1 is now an essential gene, while in lineages where SVCT1 gene has been lost, GULO is now an essential gene. Conclusions The simultaneous study, for the first time, of GULO, Regucalcin and SVCTs evolution provides a clear picture of VC synthesis/acquisition and reveals very different selective pressures in different animal taxonomic groups.
Tsung-Jang Yeh, Ching-I Yang, Chien-Tzu Huang
et al.
Infection is a major complication after allogeneic hematopoietic stem cell transplantation (allo-HSCT) especially cytomegalovirus (CMV) infection and invasive fungal infection (IFI). Taiwan is a high CMV seroprevalence area. Our study aimed to evaluate the incidence, risk factors, the impact on survival of CMV infection (including reactivation and disease) and the association of CMV infection and IFI in recipients after allo-HSCT during the first 100 days after transplantation. This was a retrospective study including 180 recipients of allo-HSCT. A total of 99 patients had CMV reactivation, and nine patients had CMV diseases. There were more mismatched donors, more ATG usage and more transplantation from CMV IgG-negative donor in patients with CMV reactivation. There was no survival difference in patients with or without CMV reactivation. A total of 34 patients had IFIs, and IFI after allo-HSCT was associated with significantly inferior survival. Patients with CMV reactivation did not increase the incidence of overall IFI, but they did result in more late-onset (>40 days) IFI (<i>p</i> = 0.056). In this study, we demonstrated real-world data of CMV infection and IFI from a high CMV seroprevalence area.
Fixed point results of Perov type mapping which satisfy generalized Tcontractive conditions in the setup of cone b-metric spaces associated with generalized c-distance are proved and illustrated by nontrivial examples.
Cell biology, since the advent of the electron microscope and sophisticated techniques of biochemical analysis and synthesis, has advanced in giant steps that find even experts in the field hard pressed to pace. With the voluminous literature of the discipline, the interested layman or scientist of a different field can easily get lost on the side-roads, losing sight of the general direction. This collection of 24 articles from Scientific American, including nine from the special September 1961 issue on the living cell, attempts to summarize the salient features of our present knowledge of cell structure and function. Each article is written by an expert in the field with the expressed intent of presenting a coherent, unified and non-intricate overview of his topic. In the effort to present the most recent theories, the authors do sometimes give the impression that these theories are thoroughly grounded in experimental fact, whereas recent experiments have already cast doubt on a few of these theories. If the reader realizes this possibility, however, it is unlikely that he will be led astray. Credit for a fine, but neither inspired nor difficult, job of selecting the articles, arranging them in logical order, and preparing short introductions to each of six sections must go to the editor, Donald Kennedy, Professor of Biology at Stanford University. The collection appears to have fulfilled its purpose admirably and should provide stimulating reading for those who would like a short review of modern developments in the study of the cell. RICHARD P. MILLS
Abstract Background BBX transcription factors are a kind of zinc finger transcription factors with one or two B-box domains, which partilant in plant growth, development and response to abiotic or biotic stress. The BBX family has been identified in Arabidopsis, rice, tomato and some other model plant genomes. Results Here, 24 CaBBX genes were identified in pepper (Capsicum annuum L.), and the phylogenic analysis, structures, chromosomal location, gene expression patterns and subcellular localizations were also carried out to understand the evolution and function of CaBBX genes. All these CaBBXs were divided into five classes, and 20 of them distributed in 11 of 12 pepper chromosomes unevenly. Most duplication events occurred in subgroup I. Quantitative RT-PCR indicated that several CaBBX genes were induced by abiotic stress and hormones, some had tissue-specific expression profiles or differentially expressed at developmental stages. Most of CaBBX members were predicated to be nucleus-localized in consistent with the transient expression assay by onion inner epidermis of the three tested CaBBX members (CaBBX5, 6 and 20). Conclusion Several CaBBX genes were induced by abiotic stress and exogenous phytohormones, some expressed tissue-specific and variously at different developmental stage. The detected CaBBXs act as nucleus-localized transcription factors. Our data might be a foundation in the identification of CaBBX genes, and a further understanding of their biological function in future studies.
Background: Most blood collection bags contain 63 mL CPDA anticoagulant which is sufficient to anticoagulant and ensures the viability of blood cells in 450 mL±10% blood for up to 28–35 days when the blood is stored at 2–8°C. Prolonged storage of blood leads to alteration in cells hematologically which may lose viability with time. Aim: The study was conducted to determine the effect of storage on CPDA-1 for varying periods on some hematological parameters. Materials and methods: The study was conducted on blood donated by 30 healthy volunteer donors. Effect of storage was analyzed at 1, 7, 14, 21and 28 days intervals. Hematological parameters were measured using Mindary PS 300 hematology analyzer. Results: There is a highly significant increase in hemoglobin concentration, packed cell volume (P.C.V. %), MCV, and also a decrease in lymphocyte, granulocyte, and platelet count. The results also showed an insignificant decrease in total white blood cell count. Conclusion: There are degenerative changes observed in blood parameters in samples collected in citrate phosphate dextrose adenine (CPDA-1).