Miracle-dz/UniFAR-FTUs huggingface dataset:
High PHD Finger Protein 19 (PHF19) expression predicts poor prognosis in colorectal cancer: a retrospective study

Background Colorectal cancer (CRC) is the third most common cancer all around the world, and it seriously threats human health. PHF19 has been proved to be closely related to the prognosis of patients in a variety of malignant tumors, but the effect of PHF19 on the prognosis evaluation of CRC patients has not been confirmed. Methods In our study, we used GEO, TCGA database and IHC to verify the PHF19 expression in CRC samples. Survival analysis of PHF19 based on TCGA, GEO series, and our own CRC sample were performed. Cox regression was performed to reveal the relationship between PHF19 and prognosis. Co-expression was performed to find genes related to PHF19 expression. GO/KEGG enrichment analysis and GSEA analysis were used to confirm the most relevant signal pathway to PHF19. Next, cell experiments were performed to verify the effect of PHF19 on the proliferation, invasion and metastasis of CRC. Then, Western blot was used to verify the protein expression of the above two phenotypes. Finally, tumor formation experiments in nude mice were used to verify the role of PHF19 of tumor proliferation in vivo. Results We found that PHF19 was significantly over-expressed in tumors compared with normal tissues. Kaplan–Meier (K–M) analysis indicated that high PHF19 in CRC associated with poor overall survival (OS) in CRC patients. Clinical correlation analysis showed that high expression of PHF19 was closely related to t umor progression in CRC patients, especially infiltration and metastasis. Bioinformatics revealed that PHF19 might affect tumor malignant phenotype by regulating the cell cycle in CRC. CCK-8 and clonal formation experiment showed that the proliferative ability of tumor cells was promoted. Flow cytometry showed that the cell cycle accelerated the transition from G1 to S phase. Western blot found that Cyclin D1, CDK4, and CDK6 expression were up-regulated. Transwell and wound-healing experiment found that invasive and migratory abilities was promoted after the over-expression of PHF19. Western blot showed that the expression of key proteins of Epithelial-Mesenchymal Transition (EMT) changed. Tumor formation experiments in nude mice showed that overexpression of PHF19 could promote tumor proliferation in vivo. Conclusion Our research proved that PHF19 could be an independent prognostic factor for CRC, PHF19 promoted the proliferative ability and the invasion and metastasis of CRC by up-regulating the expression of key molecules related to cell cycle and EMT pathway in vitro, promoting tumor proliferation in vivo.
Prickle morphogenesis in rose is coupled with secondary metabolite accumulation and governed by canonical MBW transcriptional complex

Abstract Rose is an economically important flowering plant that holds an essential place in cut flower, medicinal, and aromatic industries. The presence of prickles, epidermal outgrowths resembling trichomes, on rose is highly undesirable as these make harvesting and transportation difficult. Attempts were made for generating rose varieties lacking prickles via breeding and natural selections; however, these approaches obtained only chimeric and genetically unstable prickle‐less mutants. The alternative way to get rid of prickles is via genetic manipulations, but the molecular mechanisms of prickle initiation and development in rose are almost unexplored. Therefore, the present study was carried out to understand the morphological, molecular, and correlated metabolic changes underlining prickle morphogenesis in a prickle‐bearing Rosa hybrida L. cv. “First Red (FR)”. The histological and metabolomic analyses at three distinct stages of the prickle morphogenesis, namely, emerging tiny initiating prickles, partially greenish soft prickles, and brownish hard prickles, demonstrated a gradually increasing deposition of phenolic compounds and lignification with development. Corresponding RNAseq analysis revealed an upregulation of the genes involved in secondary metabolism, especially in the phenylpropanoid biosynthetic pathway. A set of genes encoding a transcriptional network similar to the one regulating epidermal cell differentiation leading to phenylpropanoid accumulation and trichome development, was also upregulated. Differential expression of this transcriptional network in prickle‐less R. hybrida L. cv. “Himalayan Wonder” compared to prickly FR plants substantiated its involvement in prickle morphogenesis. The results collectively supported the proposition that prickles are evolved from trichomes and provided molecular clues towards engineering prickle‐less roses. Significance statement Prickles, the vasculature less epidermal outgrowths resembling trichomes, are defense organs protecting plants against herbivory. Despite biological significance, the mechanism of prickle morphogenesis remains obscure. Here, we show that like trichomes, prickles accumulate secondary metabolites, especially lignin and flavonoids, during morphogenesis. Cognate transcriptome analysis demonstrated that upregulation of a hormone‐regulated transcriptional activation–inhibition network, known to govern trichome morphogenesis, likely triggers the differentiation of epidermal cells to outgrow into prickle.
Symptomatic Os Subtibiale Following Injury: A Case Report of Failed Conservative Treatment, Leading to Differential Diagnosis Made Intraoperatively

Introduction: Os subtibiale is a rare accessory bone found adjacent to the distal tibia and is mostly asymptomatic. Differentiating it from a medial malleolar fracture is challenging. Most cases of acute ankle trauma that presents with an Os subtibiale are initially diagnosed as fractures by treating physicians at emergency centers. It is therefore critical for an orthopedic surgeon who gets referral for such cases to consider complete history of such patients to understand the cause of their symptoms. The goal is to avoid unnecessary surgical treatment and to realize that a symptomatic Os subtibiale can be successfully managed by conservative means. Nonetheless, certain cases may require surgical treatment if conservative treatment options fail. This is a case report of a patient that was diagnosed as a case of symptomatic Os subtibiale intraoperatively, after conservative options were unsuccessful. Case Presentation: An 18-year-old patient with an injured right ankle was referred to our clinic after failed attempts to resolve his symptoms conservatively. Based on our initial clinical and radiographic examination, the patient was continued on a conservative treatment plan assuming, it was a case of unsuccessful fracture union. After almost a year of failed conservative treatments, surgery was offered to the patient, with the understanding that the bone fragment might either be fused or completely removed based on intraoperative diagnosis. At surgery, it was observed that the bone fragment had the characteristic of an Os subtibiale. It presented as a round, smooth structure with well-formed cortical boundaries, and minimal attachment to the distal tibia. A diagnosis of symptomatic Os subtibiale was made intraoperatively, which was then successfully excised using standard orthopedic instrumentation. The patient healed uneventfully and reported a pain free, normal ankle range of motion at latest follow-up of 18 months. Conclusion: Accurate diagnosis of Os subtibiale continues to present a learning challenge for most orthopedic physicians as these cases are extremely rare and often asymptomatic. Our patient failed to respond to conservative treatment, which led to surgery and intraoperative diagnosis of Os subtibiale that was the pain causing agent.
Effect of Hydration and Base Contaminants on Sulfuric Acid Diffusion Measurement: A Computational Study

We used quantum chemical formation free energies of hydrated sulfuric acid-containing molecular clusters and a dynamic model to simulate a flow tube measurement, and determined the effective diffusion coefficient of sulfuric acid as a function of relative humidity. This type of measurement was performed by Hanson and Eisele, who presented and applied a fitting method to obtain equilibrium constants K1 and K2 for the formation of sulfuric acid mono- and dihydrates, respectively, from the experimentally determined diffusion coefficients. The fit is derived assuming that only H2SO4 molecules hydrated by up to two water molecules are present. To study the sensitivity of the results to this assumption, we implemented the same fit to the modeled diffusion coefficient data, computed including also larger H2SO4 hydrates with more than two waters. We show that according to quantum chemical equilibrium constants, the larger hydrates are likely to be present in nonnegligible amounts, which affects the effective diffusion coefficient. This results in the fitted value obtained for K1 being lower and for K2 being higher than the actual values. The results are further altered if contaminant base molecules, such as amines, capable of binding to H2SO4 molecules, are able to enter the system, for example, with the water vapor. The magnitude and direction of the effect of the contaminants depends not only on the contaminant concentration, but also on the H2SO4 concentration and on the hygroscopicity of the H2SO4–base clusters. Copyright 2014 American Association for Aerosol Research
Psychobiotics for Patients with Chronic Gastrointestinal Disorders Having Anxiety or Depression Symptoms

Purpose Using psychobiotics to modify the gut microbiome has been shown to improve the anxiety and depression situation of patients with chronic gastrointestinal (GI) symptoms. This study evaluated changes in depression, anxiety, GI symptomss and side effects when patients used a multispecies probiotics product. Patients and Methods A single-center uncontrolled trial was conducted in patients with chronic GI symptoms, anxiety and depression who used a multispecies probiotics product. The patients were screened for anxiety and depression symptoms using the Hospital Anxiety and Depression Scale (HADS). Those who had a component score of 8 or higher were given the multispecies probiotics product for 2 months and followed up after 1 and 2 months. All data are collected and managed in a case report form. Results Eighty-three patients were enrolled, with a mean age (SD) of 43.9 (12.3) years; 73.5% of the patients were female. Of these patients, 8 met the Rome IV criteria for irritable bowel syndrome. The HADS scores displayed significant improvement at follow-up. The mean (SD) total HADS scores were 20.0 (6.3), 7.2 (5.4), and 4.9 (5.1) at baseline, 1 month, and 2 months, respectively. Quality of life also improved significantly. A small proportion (<5%) of patients developed mild symptoms, including fullness, diarrhea, and sleep complaints. Conclusion After 2 months using the probiotic product, the symptoms of anxiety and depression improved significantly. Mild gastrointestinal or constitutional symptoms developed in some patients.
Transcriptome analysis of Sonneratia caseolaris seedlings under chilling stress

Sonneratia caseolaris is a native mangrove species found in China. It is fast growing and highly adaptable for mangrove afforestation, but suffered great damage by chilling event once introduced to high latitude area. To understand the response mechanisms under chilling stress, physiological and transcriptomic analyses were conducted. The relative electrolyte conductivity, malondialdehyde (MDA) content, soluble sugar content and soluble protein content increased significantly under chilling stress. This indicated that S. caseolaris suffered great damage and increased the levels of osmoprotectants in response to the chilling stress. Gene expression comparison analysis of S. caseolaris leaves after 6 h of chilling stress was performed at the transcriptional scale using RNA-Seq. A total of 168,473 unigenes and 3,706 differentially expressed genes (DEGs) were identified. GO and KEGG enrichment analyses showed that the DEGs were mainly involved in carbohydrate metabolism, antioxidant enzyme, plant hormone signal transduction, and transcription factors (TFs). Sixteen genes associated with carbohydrate metabolism, antioxidant enzyme, phytohormones and TFs were selected for qRT-PCR verification, and they indicated that the transcriptome data were reliable. Our work provided a comprehensive review of the chilling response of S. caseolaris at both physiological and transcriptomic levels, which will prove useful for further studies on stress-responses in mangrove plants.
Modeling Adsorption of Cadmium Ions on Thiol-Functionalized Mesoporous Molecular Sieve from Aqueous Solutions

Transportation of cadmium ions from aqueous solutions to MP- MCM- 41 is a continuous physical and chemical process. The SEM analysis showed that the particle was highly porous and composed of plate- like " grains" . It provided the physical basis for establishing the liquid- solid reaction model applicable for mesoporous solid: P- G model. The calculated curves from the models were in line well with the experimental results.
Visual–Tactile Fused Graph Learning for Object Clustering

Object clustering has received considerable research attention most recently. However, 1) most existing object clustering methods utilize visual information while ignoring important tactile modality, which would inevitably lead to model performance degradation and 2) simply concatenating visual and tactile information via multiview clustering method can make complementary information to not be fully explored, since there are many differences between vision and touch. To address these issues, we put forward a graph-based visual–tactile fused object clustering framework with two modules: 1) a modality-specific representation learning module <inline-formula> <tex-math notation="LaTeX">$M_{R}$ </tex-math></inline-formula> and 2) a unified affinity graph learning module <inline-formula> <tex-math notation="LaTeX">$M_{U}$ </tex-math></inline-formula>. Specifically, <inline-formula> <tex-math notation="LaTeX">$M_{R}$ </tex-math></inline-formula> focuses on learning modality-specific representations for visual–tactile data, where deep non-negative matrix factorization (NMF) is adopted to extract the hidden information behind each modality. Meanwhile, we employ an autoencoder-like structure to enhance the robustness of the learned representations, and two graphs to improve its compactness. Furthermore, <inline-formula> <tex-math notation="LaTeX">$M_{U}$ </tex-math></inline-formula> highlights how to mitigate the differences between vision and touch, and further maximize the mutual information, which adopts a minimizing disagreement scheme to guide the modality-specific representations toward a unified affinity graph. To achieve ideal clustering performance, a Laplacian rank constraint is imposed to regularize the learned graph with ideal connected components, where noises that caused wrong connections are removed and clustering labels can be obtained directly. Finally, we propose an efficient alternating iterative minimization updating strategy, followed by a theoretical proof to prove framework convergence. Comprehensive experiments on five public datasets demonstrate the superiority of the proposed framework.
Heart rate and startle responses in diving, captive harbour porpoises (Phocoena phocoena) exposed to transient noise and sonar

ABSTRACT Anthropogenic noise can alter marine mammal behaviour and physiology, but little is known about cetacean cardiovascular responses to exposures, despite evidence that acoustic stressors, such as naval sonars, may lead to decompression sickness. Here, we measured heart rate and movements of two trained harbour porpoises during controlled exposure to 6–9 kHz sonar-like sweeps and 40 kHz peak-frequency noise pulses, designed to evoke acoustic startle responses. The porpoises initially responded to the sonar sweep with intensified bradycardia despite unaltered behaviour/movement, but habituated rapidly to the stimuli. In contrast, 40 kHz noise pulses consistently evoked rapid muscle flinches (indicative of startles), but no behavioural or heart rate changes. We conclude that the autonomous startle response appears decoupled from, or overridden by, cardiac regulation in diving porpoises, whereas certain novel stimuli may motivate oxygen-conserving cardiovascular measures. Such responses to sound exposure may contribute to gas mismanagement for deeper-diving cetaceans.
Spatiotemporally confined red light-controlled gene delivery at single-cell resolution using adeno-associated viral vectors

Engineered red light-responsive OptoAAV system allows spatiotemporally controlled gene transfer at single-cell resolution. Methodologies for the controlled delivery of genetic information into target cells are of utmost importance for genetic engineering in both fundamental and applied research. However, available methods for efficient gene transfer into user-selected or even single cells suffer from low throughput, the need for complicated equipment, high invasiveness, or side effects by off-target viral uptake. Here, we engineer an adeno-associated viral (AAV) vector system that transfers genetic information into native target cells upon illumination with cell-compatible red light. This OptoAAV system allows adjustable and spatially resolved gene transfer down to single-cell resolution and is compatible with different cell lines and primary cells. Moreover, the sequential application of multiple OptoAAVs enables spatially resolved transduction with different transgenes. The approach presented is likely extendable to other classes of viral vectors and is expected to foster advances in basic and applied genetic research.
Molecular docking assisted 3D-QSAR study of benzylidene-2,4-thiazolidinedione derivatives as PTP-1B inhibitors for the management of Type-2 diabetes mellitus

Insulin resistance is the pathophysiological factor behind the etiology and progression of Type 2 diabetes mellitus (T2DM), a metabolic syndrome that is continuously increasing in prevalence worldwide, associated with the overexpression of protein tyrosine phosphatase (PTP-1B). PTP-1B acting as a negative regulator of insulin as well as leptin signaling pathways, contributing to insulin and leptin resistance, which are both responsible for ‘diabesity’, i.e. diabetes with obesity. The marketed antihyperglycemic drug pioglitazone is a benzyl-2,4-thiazolidinedione derivative with substitution on the phenyl ring. The literature also shows that benzylidene-2,4-thiazolidinedione derivatives exhibit selective and potent PTP-1B inhibitory activity. Therefore, there is an urge to investigate the pharmacophoric features of the widely explored scaffold benzylidene-2,4-thiazolidinedione against PTP-1B for its selectivity and potency using computer aided drug design tools. In the present study, a molecular docking assisted three dimensional quantitative structure activity relationship (3D-QSAR) study was performed on a diverse series of benzylidene-2,4-thiazolidinedione derivatives with wide range of PTP-1B inhibitory activity. Molecular docking explores the binding interactions between the lowest energy conformations of the molecules and the key amino acid residues present in the binding site of PTP-1B. The present study generates spatial fingerprints, which will be useful for future pharmacophoric amendments of benzylidene-2,4-thiazolidinedione derivatives towards the development of novel PTP-1B inhibitors.
Density‐Dependent Metabolic Costs of Copper Exposure in a Coastal Copepod

Traditional ecotoxicology methods involving copepods have focused on exposure of pooled individuals and averaged responses, but there is increasing awareness of the importance of individual variation. Many biological traits are density dependent, and decisions to use single‐individual or pooled exposure may affect responses to anthropogenic stressors. We investigated how conspecific density as a biotic stressor affects behavioral and respiratory responses to copper (Cu) exposure in the coastal copepod Tigriopus brevicornis. Adults were incubated at densities of 1, 2, or 4 individuals per replicate in 3.2 mL of exposure medium (23 µg Cu L–1 or control). Our results show an interaction of Cu exposure and density on respiration. The Cu exposure increased respiration, but this effect diminished with increasing density. We also found reduced swimming activity with increasing density. We propose 2 nonexclusive alternative explanations for the density‐dependent respiratory increase of Cu exposure: 1) a behavioral stress response to low conspecific density, or 2) increased Cu exposure due to increased swimming activity. We emphasize the importance of considering density‐dependency in responses when designing and interpreting ecotoxicology studies. Environ Toxicol Chem 2021;40:2538–2546. © 2021 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.
Nervous Necrosis Virus Coat Protein Mediates Host Translation Shutoff through Nuclear Translocalization and Degradation of Polyadenylate Binding Protein

Globally, more than 200 species of aquacultured and wild marine fish are susceptible to NNV infection. Devastating outbreaks of this virus have been responsible for massive economic damage in the aquaculture industry, but the molecular mechanisms by which NNV affects its host remain largely unclear. ABSTRACT Nervous necrosis virus (NNV) belongs to the Betanodavirus genus of the Nodaviridae family and is the main cause of viral nervous necrosis disease in marine fish larvae and juveniles worldwide. The NNV virion contains two positive-sense, single-stranded RNA genomes, which encode RNA-dependent RNA polymerase, coat protein, and B2 protein. Interestingly, NNV infection can shut off host translation in orange-spotted grouper (Epinephelus coioides) brain cells; however, the detailed mechanisms of this action remain unknown. In this study, we discovered that the host translation factor, polyadenylate binding protein (PABP), is a key target during NNV takeover of host translation machinery. Additionally, ectopic expression of NNV coat protein is sufficient to trigger nuclear translocalization and degradation of PABP, followed by translation shutoff. A direct interaction between NNV coat protein and PABP was demonstrated, and this binding requires the NNV coat protein N-terminal shell domain and PABP proline-rich linker region. Notably, we also showed that degradation of PABP during later stages of infection is mediated by the ubiquitin-proteasome pathway. Thus, our study reveals that the NNV coat protein hijacks host PABP, causing its relocalization to the nucleus and promoting its degradation to stimulate host translation shutoff. IMPORTANCE Globally, more than 200 species of aquacultured and wild marine fish are susceptible to NNV infection. Devastating outbreaks of this virus have been responsible for massive economic damage in the aquaculture industry, but the molecular mechanisms by which NNV affects its host remain largely unclear. In this study, we show that NNV hijacks translation in host brain cells, with the viral coat protein binding to host PABP to promote its nuclear translocalization and degradation. This previously unknown mechanism of NNV-induced host translation shutoff greatly enhances the understanding of NNV pathogenesis and provides useful insights and novel tools for development of NNV treatments, such as the use of orange-spotted grouper brain cells as an in vitro model system.