Miracle-dz/UniFAR-FTUs huggingface dataset:
Normothermic Machine Perfusion Systems: Where Do We Go From Here?

Normothermic machine perfusion (NMP) aims to preserve organs ex vivo by simulating physiological conditions such as body temperature. Recent advancements in NMP system design have prompted the development of clinically effective devices for liver, heart, lung, and kidney transplantation that preserve organs for several hours/up to 1 d. In preclinical studies, adjustments to circuit structure, perfusate composition, and automatic supervision have extended perfusion times up to 1 wk of preservation. Emerging NMP platforms for ex vivo preservation of the pancreas, intestine, uterus, ovary, and vascularized composite allografts represent exciting prospects. Thus, NMP may become a valuable tool in transplantation and provide significant advantages to biomedical research. This review recaps recent NMP research, including discussions of devices in clinical trials, innovative preclinical systems for extended preservation, and platforms developed for other organs. We will also discuss NMP strategies using a global approach while focusing on technical specifications and preservation times.
Standardization and Interpretation of RNA-sequencing for Transplantation

RNA-sequencing (RNA-seq) is a technique to determine the order of nucleotides in an RNA segment. Modern sequencing platforms simultaneously sequence millions of RNA molecules. Advances in bioinformatics have allowed us to collect, store, analyze, and disseminate data from RNA-seq experiments and decipher biological insights from large sequencing datasets. Although bulk RNA-seq has significantly advanced our understanding of tissue-specific gene expression and regulation, recent advances in single-cell RNA-seq have allowed such information to be mapped to individual cells, thus remarkably enhancing our insight into discrete cellular functions within a biospecimen. These different RNA-seq experimental approaches require specialized computational tools. Herein, we will first review the RNA-seq experimental workflow, discuss the common terminologies used in RNA-seq, and suggest approaches for standardization across multiple studies. Next, we will provide an up-to-date appraisal of the applications of bulk RNA-seq and single-cell/nucleus RNA-seq in preclinical and clinical research on kidney transplantation, as well as typical bioinformatic workflows utilized in such analysis. Lastly, we will deliberate on the limitations of this technology in transplantation research and briefly summarize newer technologies that could be combined with RNA-seq to permit more powerful dissections of biological functions. Because each step in RNA-seq workflow has numerous variations and could potentially impact the results, as conscientious citizens of the research community, we must strive to continuously modernize our analytical pipelines and exhaustively report their technical details.
Exploring objective factors to predict successful outcomes after laparoscopic Nissen fundoplication

Background: Currently, the reported parameters that predict the resolution of symptoms after surgery are largely subjective and unreliable. Considering that fundoplication rebuilds the structural integrity of the lower esophageal sphincter (LES), the authors focused on searching for objective and quantitative predictors for the resolution of symptoms based on the anatomical issues and whether an antireflux barrier can be well established or not. Materials and methods: The authors reviewed the prospectively collected data of 266 patients with gastroesophageal reflux disease (GERD) who had undergone laparoscopic Nissen fundoplication (LNF). All patients were diagnosed with GERD using preoperative esophagogastroduodenoscopy, 24-h ambulatory esophageal pH monitoring, and high-resolution esophageal manometry. The patients received GERD symptom surveys using the validated Korean Antireflux Surgery Group questionnaire twice: preoperatively and 3 months after the surgery. Results: After excluding patients with insufficient follow-up data, 152 patients were included in the analysis. Multivariate logistic regression analyses revealed that a longer length of the LES and lower BMI determined better resolution of typical symptoms after LNF (all P<0.05). Regarding atypical symptoms, higher resting pressure of LES and DeMeester score greater than or equal to 14.7 were associated with better resolution after the surgery (all P<0.05). After LNF, typical symptoms improved in 34 out of 37 patients (91.9%) with a length of LES >greater than . 05 cm, BMI less than 23.67 kg/m2, and atypical symptoms were resolved in 16 out of 19 patients (84.2%) with resting pressure of LES greater than or equal to 19.65 mm Hg, DeMeester score greater than or equal to 14.7. Conclusion: These results show that the preoperative length and resting pressure of LES is important in the objective prediction of symptom improvement after LNF.
Multiple Routes to Bicontinuous Cubic Liquid Crystal Phases Discovered by High-Throughput Self-Assembly Screening of Multi-Tail Lipidoids.

Bicontinuous cubic phases offer advantageous routes to a broad range of applied materials ranging from drug delivery devices to membranes. However, a priori design of molecules that assemble into these phases remains a technological challenge. In this article, a high-throughput synthesis of lipidoids that undergo protonation-driven self-assembly (PrSA) into liquid crystalline (LC) phases is conducted. With this screening approach, 12 different multi-tail lipidoid structures capable of assembling into the bicontinuous double gyroid phase are discovered. The large volume of small-angle X-ray scattering (SAXS) data uncovers unexpected design criteria that enable phase selection as a function of lipidoid headgroup size and architecture, tail length and architecture, and counterion identity. Surprisingly, combining branched headgroups with bulky tails forces lipidoids to adopt unconventional pseudo-disc conformations that pack into double gyroid networks, entirely distinct from other synthetic or biological amphiphiles within bicontinuous cubic phases. From a multitude of possible applications, two examples of functional materials from lipidoid liquid crystals are demonstrated. First, the fabrication of gyroid nanostructured films by interfacial PrSA, which are rapidly responsive to the external medium. Second, it is shown that colloidally-dispersed lipidoid cubosomes, for example, for drug delivery, are easily assembled using top-down solvent evaporation methods.
Tear film microbiome in Sjogren’s and non-Sjogren’s aqueous deficiency dry eye

Purpose: To understand the bacterial microbiome changes associated with Sjogren's syndrome (SS) and non-Sjogren's syndrome (NSS) aqueous-deficient dry eyes compared to healthy eyes. Methods: Bacterial microbiome was generated from the deoxyribonucleic acid of tear film samples in healthy (n = 33), SS (n = 17), and NSS (n = 28) individuals. Sequencing of the V3-V4 region of the 16S rRNA gene was performed on the Illumina HiSeq2500 platform. Quantitative Insights Into Microbial Ecology (QIIME) pipeline was used to assign taxa to sequences. Statistical analysis was performed in R to assess the alpha diversity and beta diversity indices. Significant changes between the healthy, SS, and NSS cohorts were depicted by principal coordinate analysis (PCoA), differential abundance, and network analysis. Results: Tear microbiome was generated in healthy, SS, and NSS samples. Phyla Actinobacteria, Firmicutes, and Bacteroidetes showed significant changes in SS and NSS compared to healthy. Genera Lactobacillus and Bacillus were predominantly present in all samples. PCoA and heat map analysis showed distinct clusters for SS and NSS from the healthy cohort. Genera Prevotella, Coriobacteriaceae UCG-003, Enterococcus, Streptomyces, Rhodobacter, Ezakiella, and Microbacterium significantly increased in abundance in SS and NSS compared to a healthy cohort. Bacteria–bacteria interaction in SS, NSS, and healthy cohorts was predicted by CoNet network analysis. This analysis predicted a major hub of interaction for the pro-inflammatory bacterium Prevotella in the SS and NSS cohorts. Conclusion: The results of the study indicate significant changes in the phyla and genera in SS and NSS compared to healthy. Both discriminative analysis and network analysis indicated a possible association of predominant pro-inflammatory bacteria with SS and NSS.
An Improved Hybrid Network With a Transformer Module for Medical Image Fusion

Medical image fusion technology is an essential component of computer-aided diagnosis, which aims to extract useful cross-modality cues from raw signals to generate high-quality fused images. Many advanced methods focus on designing fusion rules, but there is still room for improvement in cross-modal information extraction. To this end, we propose a novel encoder-decoder architecture with three technical novelties. First, we divide the medical images into two attributes, namely pixel intensity distribution attributes and texture attributes, and thus design two self-reconstruction tasks to mine as many specific features as possible. Second, we propose a hybrid network combining a CNN and a transformer module to model both long-range and short-range dependencies. Moreover, we construct a self-adaptive weight fusion rule that automatically measures salient features. Extensive experiments on a public medical image dataset and other multimodal datasets show that the proposed method achieves satisfactory performance.
Reversible Recognition-Based Boronic Acid Probes for Glucose Detection in Live Cells and Zebrafish

Glucose, a critical source of energy, directly determines the homeostasis of the human body. However, due to the lack of robust imaging probes, the mechanism underlying the changes of glucose homeostasis in the human body remains unclear. Herein, diboronic acid probes with good biocompatibility and high sensitivity were synthesized based on an ortho-aminomethylphenylboronic acid probe, phenyl(di)boronic acid (PDBA). Significantly, by introducing the water-solubilizing group −CN directly opposite the boronic acid group and −COOCH3 or −COOH groups to the β site of the anthracene in PDBA, we obtained the water-soluble probe Mc-CDBA with sensitive response (F/F0 = 47.8, detection limit (LOD) = 1.37 μM) and Ca-CDBA with the highest affinity for glucose (Ka = 4.5 × 103 M–1). On this basis, Mc-CDBA was used to identify glucose heterogeneity between normal and tumor cells. Finally, Mc-CDBA and Ca-CDBA were used for imaging glucose in zebrafish. Our research provides a new strategy for designing efficient boronic acid glucose probes and powerful new tools for the evaluation of glucose-related diseases.
Prevalence estimates of major depressive disorder in 27 European countries from the European Health Interview Survey: accounting for imperfect diagnostic accuracy of the PHQ-8

Background Cut-offs on self-report depression screening tools are designed to identify many more people than those who meet criteria for major depressive disorder. In a recent analysis of the European Health Interview Survey (EHIS), the percentage of participants with Patient Health Questionnaire-8 (PHQ-8) scores ≥10 was reported as major depression prevalence. Objective We used a Bayesian framework to re-analyse EHIS PHQ-8 data, accounting for the imperfect diagnostic accuracy of the PHQ-8. Methods The EHIS is a cross-sectional, population-based survey in 27 countries across Europe with 258 888 participants from the general population. We incorporated evidence from a comprehensive individual participant data meta-analysis on the accuracy of the PHQ-8 cut-off of ≥10. We evaluated the joint posterior distribution to estimate the major depression prevalence, prevalence differences between countries and compared with previous EHIS results. Findings Overall, major depression prevalence was 2.1% (95% credible interval (CrI) 1.0% to 3.8%). Mean posterior prevalence estimates ranged from 0.6% (0.0% to 1.9%) in the Czech Republic to 4.2% (0.2% to 11.3%) in Iceland. Accounting for the imperfect diagnostic accuracy resulted in insufficient power to establish prevalence differences. 76.4% (38.0% to 96.0%) of observed positive tests were estimated to be false positives. Prevalence was lower than the 6.4% (95% CI 6.2% to 6.5%) estimated previously. Conclusions Prevalence estimation needs to account for imperfect diagnostic accuracy. Clinical implications Major depression prevalence in European countries is likely lower than previously reported on the basis of the EHIS survey.
Disruption of Dcp1 leads to a Dcp2‐dependent aberrant ribosome profiles in Aspergillus nidulans

There are multiple RNA degradation mechanisms in eukaryotes, key among these is mRNA decapping, which requires the Dcp1‐Dcp2 complex. Decapping is involved in various processes including nonsense‐mediated decay (NMD), a process by which aberrant transcripts with a premature termination codon are targeted for translational repression and rapid decay. NMD is ubiquitous throughout eukaryotes and the key factors involved are highly conserved, although many differences have evolved. We investigated the role of Aspergillus nidulans decapping factors in NMD and found that they are not required, unlike Saccharomyces cerevisiae. Intriguingly, we also observed that the disruption of one of the decapping factors, Dcp1, leads to an aberrant ribosome profile. Importantly this was not shared by mutations disrupting Dcp2, the catalytic component of the decapping complex. The aberrant profile is associated with the accumulation of a high proportion of 25S rRNA degradation intermediates. We identified the location of three rRNA cleavage sites and show that a mutation targeted to disrupt the catalytic domain of Dcp2 partially suppresses the aberrant profile of Δdcp1 strains. This suggests that in the absence of Dcp1, cleaved ribosomal components accumulate and Dcp2 may be directly involved in mediating these cleavage events. We discuss the implications of this.
Resveratrol for dry eye disease – Hope or Hype?

Dry eye disease (DED) is a multifactorial and common ophthalmic disease that has a tremendous effect on the quality of life. It is now becoming a public health concern because of our changing lifestyle and environment. The current treatment modalities, artificial tear substitutes, and anti-inflammatory therapy are directed at dry eye symptoms. One of the major drivers for DED is oxidative stress, and the polyphenol group of natural compounds has the potential to reduce the same. Resveratrol, widely found in the skin of grapes and nuts, has antioxidative and anti-inflammatory properties. It has been shown to have beneficial effects in glaucoma, age-related macular degeneration, retinopathy of prematurity, uveitis, and diabetic retinopathy. Studies have also explored the beneficial effects of resveratrol in DED, making it as a promising therapeutic molecule. Resveratrol has not yet reached clinical application because of difficulty in deliverability and low bioavailability. In this review, we explore the potential of resveratrol in DED treatment based on various in vitro and in vivo studies.
Chemsex, HIV, and Psychiatric Diagnosis in Gay or Bisexual Men in Hong Kong

Abstract Background: Psychotropic substance use, for chemsex in particular, is common in gay or bisexual men (GBM) with HIV infection. This case-control study examined the association between Axis I psychiatric disorders and active psychotropic substance use, and identified factors affecting the prevalence of psychiatric disorders in HIV-infected GBM. Methods: Participants were 62 HIV-infected self-identified GBM who reported psychotropic substance use in the past 1 year (cases), and 55 HIV-infected self-identified GBM without psychotropic substance use in the past 1 year and had negative toxicology tests at recruitment (controls). The Chinese-bilingual Structured Clinical Interview for DSM-IV (Axis I, Patient version) was followed to establish the psychiatric diagnoses. Socio-demographic data, level of social support, HIV-related data, and pattern of psychotropic substance use were collected. Results: Cases had lower level of social support, more depressive disorders (AOR 3.4, 95% CI 1.3-8.7, p=0.01) and psychotic disorders (AOR 7.2, 95% CI 1.2-41, p=0.03) but not anxiety disorders. Significant difference in the prevalence of psychiatric disorders was only evident for disorders with onset after HIV diagnosis. Methamphetamine dependence, weekly methamphetamine use for 2 years or more, using methamphetamine beyond chemsex, duration of HIV diagnosis were significant predictors for psychiatric disorders in the cases. Conclusion: Active psychotropic substance use in HIV-infected gay or bisexual men was associated with an overall 3-fold increase in Axis I psychiatric disorders. Coordinated efforts from HIV, psychiatric and substance use services are needed to prevent harms arising from chemsex and to identify those in need and facilitate treatment access.
Influence of cantilever tip geometry and contact model on AFM elasticity measurement of cells

We have measured the elastic properties of live cells by Atomic Force Microscope (AFM) using different tip geometries commonly used in AFM studies. Soft 4‐sided pyramidal probes (spring constant = 12 and 30 mN/m, radius 20 nm), 3‐sided pyramidal probes (spring constant = 100 mN/m, radius 65‐75 nm), flat (circular) probes (spring constant = 63 mN/m, radius 290 nm) and spherical probes (spring constant = 43 mN/m, radius 5 μm) have been used. Cells (3T3 fibroblasts) having elastic moduli around 0.5 kPa were investigated. We found that cell measured stiffness shows a systematic dependence on tip geometry: the sharper the tip, the higher the average modulus values. We hypothesize that the blunter the tip, the larger the contact area over which the mechanical response is measured or averaged. If there are small‐scale stiffer areas (like actin bundles) they will be easier to pick up by a sharp probe. This effect can be seen in the wider distribution of the histograms of the measured elastic moduli on cells. Furthermore, non‐linear responses of cells may be present due to the high average pressures applied by sharp probes, which would lead to an overestimation of the Young's modulus. Pressure versus contact radius simulations for the different tip geometries for a 0.5 kPa sample suggested similar average pressure for Bio‐MLCTs, PFQNM and cut tips, except spherical tips that showed much lower average pressure at the same 400 nm indentation. However, real data of the cells suggested different results. Using the same indentation depth (400 nm), PFQNM and Bio‐MLCTs showed similar average pressure and it decreased for cut and spherical tips. The calculated contact area at 400 nm cell indentation, using the obtained apparent Young's modulus for each tip geometry, showed the following distribution: Bio‐MLCTs < PFQNM < cut << spherical. In summary, tip geometry as well as average pressure and tip‐sample contact area are important parameters to take into account when measuring mechanical properties of soft samples. The larger the tip radius, the larger the contact area that will lead to a more evenly distribution of the applied pressure.
Inertial focusing of particles in curved microchannels

Since the beginning of microfluidics, the ability to control motion of particles in microchannels has always been fascinating. Microfluidic techniques such as dielectrophoresis, magnetophoresis rely on externally applied fields to separate particles while others like hydrophoresis and deterministic lateral displacement depend on low Reynolds number operation for particle manipulation. One of these techniques is inertial focusing of particles in microchannels. The particles and channel interact to cause lateral migration of particles to equilibrium positions within channel cross-section in flow regime where inertia and viscosity of fluid are finite. Inertial focusing has wide range of applications in fields of chemical synthesis, biological analysis, multiphase flows, cell biology and many more. This thesis presents the study of inertial focusing of particles in spiral microchannels. Particle focusing in curved channel depends on number of parameters such as channel crosssection, curvature of channel, size and shape of particles and flow parameters like channel Reynolds number. Effect of some of above mentioned parameters on inertial focusing of particles have been discussed in detail in this thesis. Effect of curvature of channel on inertial focusing in spiral channels has been studied. Microchannels with square and rectangular cross-section are considered in this study. Study of hydrodynamic focusing of particles in non-Newtonian fluid in curved channel is performed. The results are compared with those obtained for inertial focusing of particles in Newtonian fluids in spiral microchannel. The understanding of different factors influencing the particle behavior in spiral channels can be used to develop new and improved technologies in biomedical applications.
Sparse-to-Dense Matching Network for Large-Scale LiDAR Point Cloud Registration

Point cloud registration is a fundamental problem in 3D computer vision. Previous learning-based methods for LiDAR point cloud registration can be categorized into two schemes: dense-to-dense matching methods and sparse-to-sparse matching methods. However, for large-scale outdoor LiDAR point clouds, solving dense point correspondences is time-consuming, whereas sparse keypoint matching easily suffers from keypoint detection error. In this paper, we propose SDMNet, a novel Sparse-to-Dense Matching Network for large-scale outdoor LiDAR point cloud registration. Specifically, SDMNet performs registration in two sequential stages: sparse matching stage and local-dense matching stage. In the sparse matching stage, we sample a set of sparse points from the source point cloud and then match them to the dense target point cloud using a spatial consistency enhanced soft matching network and a robust outlier rejection module. Furthermore, a novel neighborhood matching module is developed to incorporate local neighborhood consensus, significantly improving performance. The local-dense matching stage is followed for fine-grained performance, where dense correspondences are efficiently obtained by performing point matching in local spatial neighborhoods of high-confidence sparse correspondences. Extensive experiments on three large-scale outdoor LiDAR point cloud datasets demonstrate that the proposed SDMNet achieves state-of-the-art performance with high efficiency.