Miracle-dz/UniFAR-FTUs huggingface dataset:
Normal saline remodels the omentum and stimulates its receptivity for transcoelomic metastasis

The omentum contains immune cell structures called milky spots that are niches for transcoelomic metastasis. It is difficult to remove the omentum completely, and there are no effective strategies to minimize the risk of colonization of preserved omental tissues by cancer cells that circulate in the peritoneal fluid. Normal saline is commonly administered into the peritoneal cavity for diagnostic and intraoperative lavage. Here we show that normal saline, when administered into the peritoneal cavity of mice, is prominently absorbed by the omentum, exfoliates its mesothelium, and induces expression of CX3CL1, the ligand for CX3CR1, within and surrounding the omental vasculature. Studies using CX3CR1-competent and CX3CR1-deficient mice showed that the predominant response in the omentum following saline administration is an accumulation of CX3CR1+ monocytes/macrophages that expand milky spots and promote neoangiogenesis within these niches. Moreover, saline administration promoted the implantation of cancer cells of ovarian and colorectal origin onto the omentum. By contrast, these deleterious effects were not observed following i.p. administration of lactated Ringer’s solution. Our findings suggest that normal saline stimulates the receptivity of the omentum for cancer cells and that the risk of colonization can be minimized by using a biocompatible crystalloid for lavage procedures.
Heat Transfer in a Horizontal Cylinder With Eccentric Surfaces

Heat transfer in horizontal cylinders exposed to free convection and radiation is of importance in many industries. Usually this problem is treated by adopting a concentric geometry, disregarding that the external surface temperature is not uniform. If an eccentric geometry is used, the external surface temperature should have a larger variation, changing the flow around the cylinder and the heat transfer coefficient, either improving or reducing the heat transfer. A numerical analysis is presented of the heat transfer in a horizontal cylinder with an internal isothermal surface eccentric to the external surface that is exposed to air free convection and radiation. The conduction problem was solved analytically and integrated numerically, while the free convection was solved by the PHOENICS software. The parameters analyzed were the ratio of radius, the ratio between the material and air thermal conductivities, the Rayleigh number, the emissivity of the outer surface, and the eccentricity between the external and inner surfaces. The parameters of a proposed equation to estimate the total heat of an eccentric arrangement in terms of the total heat of the corresponding concentric arrangement and the ratio between the convective and conductive thermal resistances were determined for given ratios of radius and eccentricities.
Remote Controlled Entanglement

Quantum entanglement is not only one of the most puzzling features of quantum mechanics, but it is also a useful resource that can be consumed to realize tasks that would otherwise be impossible. Famous examples are quantum teleportation and quantum cryptography, which are most useful when entanglement is shared between remote parties. Although nearby entangled states can routinely be created using a host of physical systems, optical photons are the natural choice for entangling spatially separated systems. But in Physical Review Letters, Nicolas Roch, from the University of California at Berkeley, and colleagues reported realizing this feat using microwave radiation to measure, and thereby entangle, superconducting circuits separated by 1.3 meters of coaxial cable [1].
Regulatory logic of endogenous RNAi in silencing de novo genomic conflicts

Although the biological utilities of endogenous RNAi (endo-RNAi) have been largely elusive, recent studies reveal its critical role in the non-model fruitfly Drosophila simulans to suppress selfish genes, whose unchecked activities can severely impair spermatogenesis. In particular, hairpin RNA (hpRNA) loci generate endo-siRNAs that suppress evolutionary novel, X-linked, meiotic drive loci. The consequences of deleting even a single hpRNA (Nmy) in males are profound, as such individuals are nearly incapable of siring male progeny. Here, comparative genomic analyses of D. simulans and D. melanogaster mutants of the core RNAi factor dcr-2 reveal a substantially expanded network of recently-emerged hpRNA-target interactions in the former species. The de novo hpRNA regulatory network in D. simulans provides insight into molecular strategies that underlie hpRNA emergence and their potential roles in sex chromosome conflict. In particular, our data support the existence of ongoing rapid evolution of Nmy/Dox-related networks, and recurrent targeting of testis HMG-box loci by hpRNAs. Importantly, the impact of the endo-RNAi network on gene expression flips the convention for regulatory networks, since we observe strong derepression of targets of the youngest hpRNAs, but only mild effects on the targets of the oldest hpRNAs. These data suggest that endo-RNAi are especially critical during incipient stages of intrinsic sex chromosome conflicts, and that continual cycles of distortion and resolution may contribute to speciation.
Convergence of melt electrowriting and extrusion-based bioprinting for vascular patterning of a myocardial construct

To progress cardiac tissue engineering strategies closer to the clinic, thicker constructs are required to meet the functional need following a cardiac event. Consequently, pre-vascularization of these constructs needs to be investigated to ensure survival and optimal performance of implantable engineered heart tissue. The aim of this research is to investigate the potential of combining extrusion-based bioprinting (EBB) and melt electrowriting for the fabrication of a myocardial construct with a precisely patterned pre-vascular pathway. Gelatin methacryloyl (GelMA) was investigated as a base hydrogel for the respective myocardial and vascular bioinks with collagen, Matrigel and fibrinogen as interpenetrating polymers to support myocardial functionality. Subsequently, extrusion-based printability and viability were investigated to determine the optimal processing parameters for printing into melt electrowritten meshes. Finally, an anatomically inspired vascular pathway was implemented in a dual EBB set-up into melt electrowritten meshes, creating a patterned pre-vascularized myocardial construct. It was determined that a blend of 5% GelMA and 0.8 mg·ml−1 collagen with a low crosslinked density was optimal for myocardial cellular arrangement and alignment within the constructs. For the vascular fraction, the optimized formulation consisted of 5% GelMA, 0.8 mg·ml−1 collagen and 1 mg·ml−1 fibrinogen with a higher crosslinked density, which led to enhanced vascular cell connectivity. Printability assessment confirmed that the optimized bioinks could effectively fill the microfiber mesh while supporting cell viability (∼70%). Finally, the two bioinks were applied using a dual EBB system for the fabrication of a pre-vascular pathway with the shape of a left anterior descending artery within a myocardial construct, whereby the distinct cell populations could be visualized in their respective patterns up to D14. This research investigated the first step towards developing a thick engineered cardiac tissue construct in which a pre-vascularization pathway is fabricated within a myocardial construct.
Ordering taxa in image convolution networks improves microbiome-based machine learning accuracy

ABSTRACT The human gut microbiome is associated with a large number of disease etiologies. As such, it is a natural candidate for machine-learning-based biomarker development for multiple diseases and conditions. The microbiome is often analyzed using 16S rRNA gene sequencing or shotgun metagenomics. However, several properties of microbial sequence-based studies hinder machine learning (ML), including non-uniform representation, a small number of samples compared with the dimension of each sample, and sparsity of the data, with the majority of taxa present in a small subset of samples. We show here using a graph representation that the cladogram structure is as informative as the taxa frequency. We then suggest a novel method to combine information from different taxa and improve data representation for ML using microbial taxonomy. iMic (image microbiome) translates the microbiome to images through an iterative ordering scheme, and applies convolutional neural networks to the resulting image. We show that iMic has a higher precision in static microbiome gene sequence-based ML than state-of-the-art methods. iMic also facilitates the interpretation of the classifiers through an explainable artificial intelligence (AI) algorithm to iMic to detect taxa relevant to each condition. iMic is then extended to dynamic microbiome samples by translating them to movies.
Declining tree growth resilience mediates subsequent forest mortality in the US Mountain West

Climate change‐triggered forest die‐off is an increasing threat to global forests and carbon sequestration but remains extremely challenging to predict. Tree growth resilience metrics have been proposed as measurable proxies of tree susceptibility to mortality. However, it remains unclear whether tree growth resilience can improve predictions of stand‐level mortality. Here, we use an extensive tree‐ring dataset collected at ~3000 permanent forest inventory plots, spanning 13 dominant species across the US Mountain West, where forests have experienced strong drought and extensive die‐off has been observed in the past two decades, to test the hypothesis that tree growth resilience to drought can explain and improve predictions of observed stand‐level mortality. We found substantial increases in growth variability and temporal autocorrelation as well declining drought resistance and resilience for a number of species over the second half of the 20th century. Declining resilience and low tree growth were strongly associated with cross‐ and within‐species patterns of mortality. Resilience metrics had similar explicative power compared to climate and stand structure, but the covariance structure among predictors implied that the effect of tree resilience on mortality could partially be explained by stand and climate variables. We conclude that tree growth resilience offers highly valuable insights on tree physiology by integrating the effect of stressors on forest mortality but may have only moderate potential to improve large‐scale projections of forest die‐off under climate change.
Determinants of double product: a cross-sectional study of urban residents in Japan

Background The current study aimed to investigate the determinants of high double product (DP) by evaluating the association between resting DP, which is calculated as systolic blood pressure (SBP) multiplied by heart rate (HR), and blood test results and lifestyle factors. Methods This research included 973 participants in the baseline survey of the KOBE study, which included a cohort of urban residents. The possible DP determinants were identified by examining the association between lifestyle factors and laboratory findings and DP by analyzing covariance adjusted for sex and age. Logistic regression analysis was performed with high DP (SBP × HR ≥ 9145 mmHg beats/min or quintile according to sex) as outcome and DP determinants as independent variables. Results Age, hematocrit, and gamma-glutamyl transferase (log) level were positively associated with a high DP in both men and women. In addition, a high DP was positively associated with Homeostatic Model Assessment for Insulin Resistance score in women alone. Meanwhile, the amount of exercise was negatively associated with a high DP in men alone. Conclusions High DP values at rest were associated with insulin resistance, gamma-glutamyl transferase, and the amount of exercise in participants without underlying disease. Supplementary information The online version contains supplementary material available at https://doi.org/10.1265/ehpm.23-00002.
Research and therapeutic applications of silk proteins in cancer

Despite the availability of advanced treatments, cancer remains the second leading cause of death worldwide. This is due to the many challenges prevailing in the research field and cancer therapy. Resistance to therapy and side effects provide major hindrances to recovery from cancer. As a result, in addition to the aim of killing cancer cells, the focus should also be on reducing or preventing side effects of the treatment. To enhance the effectiveness of cancer treatment, many researchers are studying drug delivery systems based on silk proteins: fibroin and sericin. These proteins have high biocompatibility, biodegradability, and ease of modification. Consequently, many researchers have developed several formulations of silk proteins such as scaffolds, nanoparticles, and hydrogels by combining them with other materials or drugs. This review summarizes the use of silk proteins in various forms in cancer research and therapy. The use of silk proteins to study cancer cells, to deliver cancer drugs to a target site, in cancer thermal therapy, and as an anti-cancer agent is described here.
Tissue‐Specific RNA Localization in the Uterus During Implantation, Decidualization and Placentation: Technical Nuances of Various Labeling Approaches

In situ hybridization (ISH) is a sensitive method used to localize a specific sequence of DNA or RNA in biological samples, including cells, tissue sections or whole organs. RNA ISH can be used to determine spatial gene expression using a single‐stranded probe with a reverse‐complementary sequence. Cell‐specific gene expression has been studied using mRNA and protein levels. Signals produced by RNA probes are usually more specific than those produced by antibodies in immunostaining. Currently, ISH is the most widely used method to localize mRNA molecules. Traditionally, probes were labeled with radioactive isotopes, but the cumbersome procedures and potential health risk limit their acceptance. Recently, probes labeled with nonradioactive materials including digoxigenin, biotin and various fluorophores have been developed. The tyramide signal amplification system further enhances the sensitivity of detection. These methods have been applied in numerous studies in various tissues including reproductive organs. This article details three methods of RNA in situ hybridization: radioactive in situ hybridization, digoxigenin in situ hybridization, and digoxigenin‐tyramide signal amplification fluorescein in situ hybridization. The pros and cons of each protocol are discussed. © 2023 Wiley Periodicals LLC.
YTHDF2/m6A/NF‐κB axis controls anti‐tumor immunity by regulating intratumoral Tregs

N6‐methyladenosine (m6A) in messenger RNA (mRNA) regulates immune cells in homeostasis and in response to infection and inflammation. The function of the m6A reader YTHDF2 in the tumor microenvironment (TME) in these contexts has not been explored. We discovered that the loss of YTHDF2 in regulatory T (Treg) cells reduces tumor growth in mice. Deletion of Ythdf2 in Tregs does not affect peripheral immune homeostasis but leads to increased apoptosis and impaired suppressive function of Treg cells in the TME. Elevated tumor necrosis factor (TNF) signaling in the TME promotes YTHDF2 expression, which in turn regulates NF‐κB signaling by accelerating the degradation of m6A‐modified transcripts that encode NF‐κB‐negative regulators. This TME‐specific regulation of Treg by YTHDF2 points to YTHDF2 as a potential target for anti‐cancer immunotherapy, where intratumoral Treg cells can be targeted to enhance anti‐tumor immune response while avoiding Treg cells in the periphery to minimize undesired inflammations.
Branch Aggregation Attention Network for Robotic Surgical Instrument Segmentation

Surgical instrument segmentation is of great significance to robot-assisted surgery, but the noise caused by reflection, water mist, and motion blur during the surgery as well as the different forms of surgical instruments would greatly increase the difficulty of precise segmentation. A novel method called Branch Aggregation Attention network (BAANet) is proposed to address these challenges, which adopts a lightweight encoder and two designed modules, named Branch Balance Aggregation module (BBA) and Block Attention Fusion module (BAF), for efficient feature localization and denoising. By introducing the unique BBA module, features from multiple branches are balanced and optimized through a combination of addition and multiplication to complement strengths and effectively suppress noise. Furthermore, to fully integrate the contextual information and capture the region of interest, the BAF module is proposed in the decoder, which receives adjacent feature maps from the BBA module and localizes the surgical instruments from both global and local perspectives by utilizing a dual branch attention mechanism. According to the experimental results, the proposed method has the advantage of being lightweight while outperforming the second-best method by 4.03%, 1.53%, and 1.34% in mIoU scores on three challenging surgical instrument datasets, respectively, compared to the existing state-of-the-art methods. Code is available at https://github.com/SWT-1014/BAANet.
Determining specified intraocular lens powers when silicone oil is to be used in the vitreous chamber

Lens shape and axial length influence the required increase in specified IOL power with silicone oil placed in the vitreous chamber, with equiconvex shapes requiring increases of 8 to 9 D. Purpose: To apply a theoretical approach to determining how specified intraocular lens (IOL) powers should change when vitreous oil substitution is combined with IOL implantation. Setting: University laboratory, private Ophthalmological practice. Design: Theoretical raytracing. Methods: Raytracing was done backwards from the retina with equi-convex 20 diopters (D) and 25 D IOLs, of refractive index 1.5332, to the object side of the anterior IOL surface. The 1.336 vitreous index was replaced with a high index 1.405 silicone oil. Raytracing was repeated with increase in specified power, that power as if 1.336 index was still surrounding the IOL, so that the object reduced vergence on the anterior side of the lens matched that of the original IOL power. This was done for a range of lens shapes from plano-convex (front surface flat), through equi-convex, to plano-convex (back surface flat), and for a range of axial lengths. The true power, the power with 1.336 index on the object side and silicone oil on the image side, was also determined. Results: Replacing vitreous by silicone oil increases the necessary specified IOL power. This increase varies from approximately 14% for flat back surfaces, to 40% for equi-convex lenses, to 80% for flat front surface IOLs. True powers increase by about 15% across the range of IOL shapes. In terms of percentages, effects of changing the original IOL power and the axial length are small. Conclusions: When silicone oil is to remain in an eye after cataract surgery, biconvex IOLs require much higher specified powers than convex-plano IOLs.
Developing a telehealth medical nutrition therapy (MNT) service for adults living in rural Australia at risk of cardiovascular disease: An intervention development study

Abstract Background Receiving medical nutrition therapy (MNT) from an accredited practising dietitian (APD) can reduce diet‐related cardiovascular disease (CVD) risk factors. However, people living in rural areas of Australia experience barriers to accessing dietitians because of their remote location. Telehealth has the potential to improve dietetic access in rural areas; however, there is limited research into the development and delivery of telehealth MNT interventions specific to these areas. The present study describes the development of the Healthy Rural Hearts (HealthyRHearts) telehealth MNT intervention, which was developed as a part of the HealthyRHearts randomised control trial, set in primary care practices in rural areas of the Hunter New England and Central Coast Primary Health Network. The aim of HealthyRHearts is to improve diet‐related risk factors for CVD in rural adults at moderate to high CVD risk using a telehealth MNT intervention delivered by an APD. Methods The study describes the development of the HealthyRHearts telehealth MNT intervention, using the 14‐item GUIDance for rEporting of intervention Development (GUIDED) checklist and the Template for Intervention Description and Replication (TIDieR) framework to guide description. Results HealthyRHearts is a complex intervention that aims to translate a telehealth MNT intervention for CVD prevention into rural and remote primary care settings. The intervention is designed to be implemented across multiple sites of varying characteristics and needs, with the ability to accommodate individual complexities within the rural context and target population. Participants are adults aged 45–75 years who are assessed as moderate to high risk of CVD by their general practitioner (GP). Consenting participants are referred to the intervention by their GPs and receive five telehealth MNT consultations with an APD over 6‐months. APDs are trained in the intervention protocol including intervention materials, resources and behaviour change counselling strategies. Conclusion Using the GUIDED and TIDieR frameworks to guide description of the HealthyRHearts intervention development process facilitates detailed description of decision‐making pathways for each element of the intervention design. The comprehensive description of the intervention development process for HealthyRHearts is intended to facilitate replication, iteration and optimisation of the intervention for rural contexts.
Differences in gut microbiota and fecal bile acids between Caucasian and Hispanic children and young adults with ulcerative colitis

Ulcerative Colitis (UC) is an inflammatory bowel disease (IBD) that has been associated with gut dysbiosis. Changes in the gut microbiome lead to changes in bile acids (BA) metabolism, which changes the BA profiles in patients with UC. We conducted this study to investigate the differences in bile acids and gut microbiota between Hispanic and Caucasian children and young adults with UC. Twenty‐seven Caucasian and 20 Hispanic children and young adults with UC were enrolled in the study. BAs were extracted from the subjects' stool samples and analyzed by liquid chromatography–mass spectrometry. Microbial DNA was also extracted from the stool samples to perform 16s rRNA amplicon sequencing. The median levels of cholic acid and taurolithocholic acid were found to be significantly higher in Hispanic children and young adults with UC compared to their Caucasian counterparts. The abundance of the gut microbiota that metabolizes BAs such as Proteobacteria, Pseudomonadaceae, Pseudomonas, Ruminococcus gnavus, and Escherichia coli were also all significantly higher in Hispanic children and young adults as well. The distinct BA profile that we found in Hispanic children and young adults with UC, in addition to the unique composition of their gut microbiome, provide them with a protective gut environment against inflammation, which is contrary to the common believe that Hispanics have worse IBD.