Miracle-dz/UniFAR-FTUs huggingface dataset:
Licochalcone C Inhibits the Growth of Human Colorectal Cancer HCT116 Cells Resistant to Oxaliplatin

Licochalcone C (LCC; PubChem CID:9840805), a chalcone compound originating from the root of Glycyrrhiza inflata, has shown anticancer activity against skin cancer, esophageal squamous cell carcinoma, and oral squamous cell carcinoma. However, the therapeutic potential of LCC in treating colorectal cancer (CRC) and its underlying molecular mechanisms remain unclear. Chemotherapy for CRC is challenging because of the development of drug resistance. In this study, we examined the antiproliferative activity of LCC in human colorectal carcinoma HCT116 cells, oxaliplatin (Ox) sensitive and Ox-resistant HCT116 cells (HCT116-OxR). LCC significantly and selectively inhibited the growth of HCT116 and HCT116-OxR cells. An in vitro kinase assay showed that LCC inhibited the kinase activities of EGFR and AKT. Molecular docking simulations using AutoDock Vina indicated that LCC could be in ATP-binding pockets. Decreased phosphorylation of EGFR and AKT was observed in the LCC-treated cells. In addition, LCC induced cell cycle arrest by modulating the expression of cell cycle regulators p21, p27, cyclin B1, and cdc2. LCC treatment induced ROS generation in CRC cells, and the ROS induction was accompanied by the phosphorylation of JNK and p38 kinases. Moreover, LCC dysregulated mitochondrial membrane potential (MMP), and the disruption of MMP resulted in the release of cytochrome c into the cytoplasm and activation of caspases to execute apoptosis. Overall, LCC showed anticancer activity against both Ox-sensitive and Ox-resistant CRC cells by targeting EGFR and AKT, inducing ROS generation and disrupting MMP. Thus, LCC may be potential therapeutic agents for the treatment of Ox-resistant CRC cells.
Deep Learning Approach to Semantic Segmentation in 3D Point Cloud Intra-oral Scans of Teeth

Accurate segmentation of data, derived from intra-oral scans (IOS), is a crucial step in a computer-aided design (CAD) system for many clinical tasks, such as implantology and orthodontics in modern dentistry. In order to reach the highest possible quality, a segmentation model may process a point cloud derived from an IOS in its highest available spatial resolution, especially for performing a valid analysis in finely detailed regions such as the curvatures in border lines between two teeth. In this paper, we propose an end-to-end deep learning framework for semantic segmentation of individual teeth as well as the gingiva from point clouds representing IOS. By introducing a non-uniform resampling technique, our proposed model is trained and deployed on the highest available spatial resolution where it learns the local fine details along with the global coarse structure of IOS. Furthermore, the point-wise cross-entropy loss for semantic segmentation of a point cloud is an ill-posed problem, since the relative geometrical structures between the instances (e.g. the teeth) are not formulated. By training a secondary simple network as a discriminator in an adversarial setting and penalizing unrealistic arrangements of assigned labels to the teeth on the dental arch, we improve the segmentation results considerably. Hence, a heavy post-processing stage for relational and dependency modeling (e.g. iterative energy minimization of a constructed graph) is not required anymore. Our experiments show that the proposed approach improves the performance of our baseline network and outperforms the state-of-the-art networks by achieving 0.94 IOU score.
Electrophysiological and behavioral responses of Bradysia odoriphaga (Diptera: Sciaridae) to volatiles from its Host Plant, Chinese Chives (Allium tuberosum Rottler ex Spreng)

Abstract Bradysia odoriphaga Yang et Zhang is a serious belowground pest of Chinese chives (Allium tuberosum). Our previous studies have indicated that B. odoriphaga females prefer to oviposit near the roots of Chinese chives rather than the roots of other plants, and that the performance (longevity and fecundity) of B. odoriphaga offspring was better on Chinese chives than on Lettuce (var. ramosa Hort.), Onion (Allium cepa) and Potato (Solanum tuberosum) but little is known about how the volatiles released by Chinese chives affect the host-finding and oviposition behaviors of B. odoriphaga. Here, we used gas chromatography-mass spectrometry and determined that Chinese chives releases the following volatiles: methyl allyl disulfide, β-myrcene, cis-ocimene, diallyl disulfide, nonane, n-dodecane, n-tetradecane, and n-hexadecane; quantities released were highest for methyl allyl disulfide and diallyl disulfide. In addition to eliciting strong responses in females in electroantennography assays, the latter two sulfur compounds and their mixtures attracted females in Y-tube olfactometer assays. The addition of methyl allyl disulfide, diallyl disulfide, or a mixture of the two compounds at a 1:5 ratio to chive plants increased oviposition when compared to control plants. These results indicate that methyl allyl disulfide and diallyl disulfide, either alone or in combination, influence the host-seeking behavior of B. odoriphaga.
Tornadic waterspout event in Split (Croatia) - analysis of meteorological environment

The aim of this paper is the waterspout in Split (φ 43.51 °N, λ 16.45 °E, h = 0 m) observed on January 6, 2016, which swept over the city at 15:40–16:00 CET (14:4015:00 UTC). There were convective developments in upper-level south-west flow within the cloudiness which followed the low-level cyclone and associated frontal disturbances. There was an intense thermodynamic instability in lower and mid layers of the atmosphere-the passage of the cold front as a main synoptic feature over the warm Adriatic water, pronounced directional and speed wind shear, as well as the presence of jet stream and a pronounced horizontal field of positive divergence above the observed area. The aim of this paper is to investigate synoptic and mesoscale situation, and meteorological conditions which created favourable thermodynamic environment which preceded the waterspout development.
Influence of ENSO, ENSO Modoki, and the IPO on tropical cyclogenesis: a spatial analysis of the southwest Pacific region

Tropical cyclones (TCs) pose a significant risk to the nations and territories of the southwest Pacific (SWP). The spatio‐temporal variability of TCs makes it challenging to forecast where and when a TC is likely to develop. Therefore, the aim of this study is to better understand the link between large‐scale climatic variability, the environmental conditions required for tropical cyclogenesis (TC genesis), and the spatial variability of TC activity. Three modes of climate variability are investigated: (1) El Niño/Southern Oscillation (ENSO), (2) ENSO Modoki, and (3) the Interdecadal Pacific Oscillation (IPO); along with TC genesis parameters: sea surface temperature; 700 hPa relative humidity; 700 hPa vorticity; and vertical wind shear (difference between 200 hPa and 850 hPa winds). Our findings reaffirm the well‐established northeast/southwest modulation of TC activity according to El Niño (EN)/La Niña (LN) using an extended TC dataset (1945–2011). In addition, new insights into how ENSO Modoki and the IPO modulate TC activity according to phase and season are identified. Importantly, we show that depending on phase, the IPO can enhance or alter the spatial modulation of TC genesis during ENSO/ENSO Modoki events, in favour of the northeast/southwest modulations typical of IPO positive/negative events. This is particularly the case during the latter half of the SWP TC season. For example, EN events that occur within IPO positive (negative) epochs result in a shift of TC activity up to 1087 km (1288 km) further east (west) during February to April, compared to the typical location of TC activity during EN events. Importantly, these statistical relationships are also associated with anomalously favourable genesis parameters, providing some insights into the physical mechanisms behind the modulations. The findings of this study provide baseline metrics with which to compare climate model simulations and may also facilitate improved seasonal outlooks and better quantification of TC‐related risks for the vulnerable island nations and territories of the SWP.
Visualisation of microalgal lipid bodies through electron microscopy

In this study, transmission electron microscopy (TEM) and cryo‐scanning electron microscopy (cryo‐SEM) were evaluated for their ability to detect lipid bodies in microalgae. To do so, Phaeodactylum tricornutum and Nannochloropsis oculata cells were harvested in both the mid‐exponential and early stationary growth phase. Two different cryo‐SEM cutting methods were compared: cryo‐planing and freeze‐fracturing. The results showed that, despite the longer preparation time, TEM visualisation preceded by cryo‐immobilisation allows a clear detection of lipid bodies and is preferable to cryo‐SEM. Using freeze‐fracturing, lipid bodies were rarely detected. This was only feasible if crystalline layers in the internal structure, most likely related to sterol esters or di‐saturated triacylglycerols, were revealed. Furthermore, lipid bodies could not be detected using cryo‐planing. Cryo‐SEM is also not the preferred technique to recognise other organelles besides lipid bodies, yet it did reveal chloroplasts in both species and filament‐containing organelles in cryo‐planed Nannochloropsis oculata samples.
Dioxin(-like)-Related Biological Effects through Integrated Chemical-wide and Metabolome-wide Analyses

Dioxin(-like) exposures are linked to adverse health effects, including cancer. However, metabolic alterations induced by these chemicals remain largely unknown. Beyond known dioxin(-like) compounds, we leveraged a chemical-wide approach to assess chlorinated co-exposures and parent compound products [termed dioxin(-like)-related compounds] among 137 occupational workers. Endogenous metabolites were profiled by untargeted metabolomics, namely, reversed-phase chromatography with negative electrospray ionization (C18-negative) and hydrophilic interaction liquid chromatography with positive electrospray ionization (HILIC-positive). We performed a metabolome-wide association study to select dioxin(-like) associated metabolic features using a 20% false discovery rate threshold. Metabolic features were then characterized by pathway enrichment analyses. There are no significant features associated with polychlorinated dibenzo-p-dioxins (PCDDs), a subgroup of known dioxin(-like) compounds. However, 3,110 C18-negative and 2,894 HILIC-positive features were associated with at least one of the PCDD-related compounds. Abundant metabolic changes were also observed for polychlorinated dibenzofuran-related and polychlorinated biphenyl-related compounds. These metabolic features were primarily enriched in pathways of amino acids, lipid and fatty acids, carbohydrates, cofactors, and nucleotides. Our study highlights the potential of chemical-wide analysis for comprehensive exposure assessment beyond targeted chemicals. Coupled with advanced endogenous metabolomics, this approach allows for an in-depth exploration of metabolic alterations induced by environmental chemicals.
Colicins and T6SS-based competition systems enhance enterotoxigenic E. coli (ETEC) competitiveness

ABSTRACT Diarrheal diseases are still a significant problem for humankind, causing approximately half a million deaths annually. To cause diarrhea, enteric bacterial pathogens must first colonize the gut, which is a niche occupied by the normal bacterial microbiota. Therefore, the ability of pathogenic bacteria to inhibit the growth of other bacteria can facilitate the colonization process. Although enterotoxigenic Escherichia coli (ETEC) is one of the major causative agents of diarrheal diseases, little is known about the competition systems found in and used by ETEC and how they contribute to the ability of ETEC to colonize a host. Here, we collected a set of 94 fully assembled ETEC genomes by performing whole-genome sequencing and mining the NCBI RefSeq database. Using this set, we performed a comprehensive search for delivered bacterial toxins and investigated how these toxins contribute to ETEC competitiveness in vitro. We found that type VI secretion systems (T6SS) were widespread among ETEC (n = 47). In addition, several closely related ETEC strains were found to encode Colicin Ia and T6SS (n = 8). These toxins provide ETEC competitive advantages during in vitro competition against other E. coli, suggesting that the role of T6SS as well as colicins in ETEC biology has until now been underappreciated.
Range extension for Duttaphrynus kotagamai (Amphibia: Bufonidae) and a preliminary checklist of herpetofauna from the Uda Mäliboda Trail in Samanala Nature Reserve, Sri Lanka

—Uda Mäliboda Trail is an unstudied, remarkable forest located in the northwest region of Samanala Nature Reserve (SNR) in Sri Lanka’s wet zone. Here we report the first record of D. kotagamai from Uda Mäliboda Trail and the lowest elevation records of four highland Rhacophorid frogs: Pseudophilautus alto, P. asankai, P. femoralis, and Taruga eques. Further, we present results of a preliminary study of herpetofaunal diversity in Uda Mäliboda Trail. Thirty-four amphibian (26 endemic and 19 Threatened) and 59 reptile (32 endemic and 19 Threatened) species were observed. This wet zone forest supports high herpetofaunal diversity; however activities such as deforestation, human encroachment, mining, agriculture, dumping, road construction, and a hydroelectric power station threaten the ecology of this biologically diverse forest.
Characteristics and outcome of systemic treatment for metastatic or unresectable thymic carcinoma: A single institution experience

Abstract Background Thymic carcinoma is a rare disease with an incidence of around 0.5 cases per million with a poor prognosis. The aim of this study was to assess patient outcomes with advanced thymic carcinoma receiving first‐line chemotherapy. Methods In our retrospective cohort study, we included patients who underwent treatment for metastatic thymic carcinoma between January 2013 to December 2019 in our hospital. Overall survival, progression‐free survival (PFS), objective response rates (ORR) and chemotherapy regimens were assessed and analyzed. Results A total of 27 patients were retrospectively analyzed. All patients received a platinum (cisplatin or carboplatin) based regimen as first‐line chemotherapy (29.6% received ADOC, 11.1% received PE, 40.7% received CP, 14.8% received CAP). The median PFS on first‐line chemotherapy was 199 days. The response rate was 40.7%. Median overall survival (OS) was 585 days. Positive CD5 staining was associated with better PFS. Conclusion We highlight the critical role of platinum‐based chemotherapy agents as a primary treatment modality in advanced thymic carcinoma, underscoring the efficacy of platinum as a first‐line option for recurrent disease, even in cases previously treated with platinum. Additionally, our findings indicate that CD5 positivity could be associated with improved PFS, suggesting its potential as a prognostic marker.
Evolution of plum culture; constrains and perspectives

European plum (Prunus domestica) and Japanese plum (Prunus salicina and hybrids) culture are facing a relative critical period world wide. In the last two decades the annual world plum production went up to more then 7 million tones, which has 2 to 5% increase over the 1970-1990 period, although large variation from one year to another were recorded. The European plum type production is 5.5 to 5.6 million tons per year and the Japanese type plums represent 1.5 to 1.6 million tons (21 to 23% of the total plum production). The plum culture situation is dependent on the human society demands either for fresh consumption plums or processed plums. Decrease of demands for plums are due to the competitively with other fruits (apples, peaches, oranges, bananas, etc.) and availability of those all year long as result of trade globalization. The morphological characteristics of plum fruits (size, shape, and color), taste, storage ability, etc., are only several elements that contribute to decrease of demand. Advertising and information on plum consumption benefits for healthy and balanced diet are less and less present. Investments in new plum orchards in the traditional plum growing countries like Romania, Serbia, Bulgaria, Hungary and Moldova or in Greece are very low; this can be explained by the last period economical situation of these countries which is continuing due to the financial crisis. In order to have perspectives in favor of plum culture improvements have to be done regarding cultivar assortment and behavior to virus diseases, rootstocks and orchard management. The cultivar assortment needs commercial valuable and productive genotypes, which produce large and tasty fruits that can be stored and shipped extensively. Plum rootstocks are necessary to be more available, especially those of low vigor and having good compatibility with many cultivars. Issues regarding virus infection and their reaction on plums have to be solved as soon as possible. Plum orchard management requires modernizing from all points of vue especially for the super-intensive culture.
The long-term effect of bariatric/metabolic surgery versus pharmacologic therapy in type 2 diabetes mellitus patients: A systematic review and meta-analysis

Background: Metabolic/bariatric surgery as a treatment for obesity and related diseases, such as type 2 diabetes mellitus (T2DM), has been increasingly recognized. However, the long-term effect ([≥] five years) of metabolic surgery in T2D patients is still unclear compared with conventional pharmacologic therapy. This study aims to evaluate the diabetes remission rate, diabetic microvascular complications incidence, macrovascular complications incidence, and mortality in T2D patients who received metabolic surgery versus pharmacologic therapy more than five years after the surgery. Methods: Searching the database, including PubMed, Embase, Web of Science, and Cochrane Library from the inception to recent (2022), for randomized clinical trials (RCTs) or cohort studies comparing T2D patients treated with metabolic surgery versus pharmacologic therapy reporting on the outcomes of the diabetes remission rate, diabetic microvascular complications, macrovascular complications, or mortality over five years or more. Results: A total of 13 articles with a total of 68,280 patients with T2D were eligible for review and meta-analysis in this study. There is a significant long-term increase in diabetes remission for metabolic surgery compared with conventional medical therapy in the overall pooled estimation and RCT studies or cohort studies separately (overall: OR = 8.39, 95%CI: 3.58-19.67, P<0.001). Significant long-term decreases showed in the pooled results of microvascular complications incidence (HR = 0.43, 95%CI: 0.37-0.49, P<0.001), macrovascular complications incidence (HR = 0.60, 95%CI: 0.48-0.75, P<0.001) and mortality (HR = 0.44, 95%CI: 0.37-0.49, P<0.001). Conclusion: Metabolic surgery showed more significant long-term effects than pharmacologic therapy on diabetes remission, macrovascular complications, microvascular complications incidence, and all-cause mortality in patients with T2D using currently available evidence. More high-quality evidence is needed to validate the long-term effects of metabolic surgery versus conventional treatment in the management of diabetes.
Utilising patient and public involvement to increase the acceptability of brief CBT for OCD in young people

Abstract Obsessive-compulsive disorder (OCD) is a common and debilitating disorder that frequently begins in childhood and adolescence. Previous work (Bolton et al., 2011) has demonstrated that brief CBT (5 sessions), supplemented by therapeutic workbooks, is as effective as more traditional length (12 sessions) therapist-delivered treatment for adolescents with OCD. However, as was typical at the time, the treatment was developed with very limited patient and public involvement (PPI) and was delivered in the context of a randomised controlled trial which might affect translation to routine child and adolescent mental health services (CAMHS). To be able to implement such treatment within routine clinical services, it is crucial that it acceptable to young people, their families and the clinicians delivering the treatment. The aim of this project was to improve the acceptability of the brief treatment through PPI and consultation with clinicians, and consider issues relating to implementation. This was done through written feedback, interviews and focus groups with five adolescents and two parents, and a focus group and a half-day workshop with 12 clinicians. This led to revisions to the workbooks and materials to improve (a) acceptability by updating the design through changes to wording, language and images, and to ensure that they were consistent with values of equality, diversity and inclusion, and (b) usability by clarifying, adding, removing content, and organising the materials in new ways. We emphasise the importance of continued PPI throughout the project to maximise the translation of findings into practice. Key learning aims (1) To understand the issues surrounding the delivery of brief CBT to young people with OCD. (2) To understand ways of reviewing, developing and improving the CBT materials with a range of young people, their parents, and clinicians. (3) To understand how to consult with clinicians in relation to the implementation of the treatment. (4) To consider how the process of this type of work can assist in the next steps of implementing a manualised intervention in routine CAMHS.
PharmoCo: a graph-based visualization of pharmacogenomic plausibility check reports for clinical decision support systems

Abstract The first approaches in recent years for the integration of pharmacogenomic plausibility checks into clinical practice show both a promising improvement in the drug therapy safety, but also difficulties in application. One of the difficulties is the meaningful interpretation of the text-based results by the medical practitioner. We propose here as an appropriate and sensible solution to avoid misunderstandings and to include evidence-based, pharmacogenomic recommendations in prescriptions, which should be the graph-based visualization of the reports. This allows for a plausible interpretation and relate complex, even contradictory guidelines. The improved overview over the pharmacogenomics (PGx) guidelines using the graphical visualization makes the medical practitioner’s choice of dose and medication more patient-specific, improves the treatment outcome and thus, increases the drug therapy safety.
Learning-Augmented K-Means Clustering Using Dimensional Reduction

Learning augmented is a machine learning concept built to improve the performance of a method or model, such as enhancing its ability to predict and generalize data or features, or testing the reliability of the method by introducing noise and other factors. On the other hand, clustering is a fundamental aspect of data analysis and has long been used to understand the structure of large datasets. Despite its long history, the k-means algorithm still faces challenges. One approach, as suggested by Ergun et al. [8], is to use a predictor to minimize the sum of squared distances between each data point and a specified centroid. However, it is known that the computational cost of this algorithm increases with the value of k, and it often gets stuck in local minima. In response to these challenges, we propose a solution to reduce the dimensionality of the dataset using Principal Component Analysis (PCA). It is worth noting that when using k values of 10 and 25, the proposed algorithm yields lower cost results compared to running it without PCA. "Principal component analysis (PCA) is the problem of fitting a low-dimensional affine subspace to a set of data points in a high-dimensional space. PCA is well-established in the literature and has become one of the most useful tools for data modeling, compression, and visualization. "[18]