Miracle-dz/UniFAR-FTUs huggingface dataset:
New MicroRNAs Candidates to Treat Human Colorectal Cancer; Molecular Dynamic Simulations Found a Major Down-Regulator of CLCA4 Tumor Suppressor Gene

IntroductionColorectal cancer (CRC) is one of the most common malignancies worldwide. The expression of CLCA4, a tumor suppressor gene, decreases significantly in cancer cells of CRC. In this study, we identified miRNAs target the mRNA of the CLCA4 gene. ObjectiveThe aim of this study was the identification of miRNAs involved in CRC.Material and methodsWe predicted miRNA(s) that target CLCA4 mRNA applying TargetScan v.7. Then through analysis of Gene Expression Omnibus (GEO) datasets, among them, miRNA(s) over-expressed in CRC cells were determined. To identify miRNAs with the highest potential to down-regulate CLCA4 through binding, we calculated the binding free energies of the candidate miRNA- mRNA complexes using the molecular mechanics energies combined with several solvation models: The Poisson–Boltzmann (MM/PBSA), the generalized Born (MM/GBSA), and the three-dimensional reference interaction site model with Kovalenko–Hirata closure relation (3D-RISM-KH). ResultsOur TargetScan analysis predicted that 106 miRNAs could bind to CLCA4 3' UTR mRNA. Hsa-miR-934, hsa-miR-574-5p, hsa-miR-377-3p, hsa-miR-5580-3p, hsa-miR-4775, hsa-miR-590-3p and hsa-miR-501-5p showed increased expression in CRC samples compared to normal cells. MD results found the lowest free energy changes in three hsa-miR-377-3p, hsa-miR-574-5p and hsa-miR-501-5p miRNAs. ConclusionThis research beside introducing a new fast and low cost plan to find best candidate of miRNAs to bind their targets, suggested miR-501-5p as a biomarker for early diagnosis of CRC. As well, preventing of down regulation of the CLCA4 expression through interrupting in the expression of miR-574-5p and miR-377-3p and more effectively miR-501-5p probably treat or slow down the development of colorectal cancer.
Whole-Course Conformal Radiotherapy Combined with Late-Course Accelerated Hyperfractionation Radiotherapy for Esophageal Squamous Cell Carcinoma: A Report of 110 Cases

Purpose: This retrospective study was designed to analyze the effect and prognostic factors of whole-course conformal radiotherapy and late-course accelerated hyperfractionation radiotherapy (LCAFRT) for esophageal squamous cell carcinoma (ESCC). Methods and materials: A total of 110 patients with ESCC received whole-course conformal radiotherapy and LCAFRT in Chaozhou City People’s hospital between May 2004 and January 2015. All patients received conventional conformal radiotherapy of 2 Gy per day up to 30–40 Gy, followed by accelerated hyperfractionation conformal radiotherapy using reduced fields at 1.5 Gy/fraction twice a day up to 24–39 Gy, with a total dose of 60–69 Gy.Results: Median follow-up was 85 months (2–170 months). The one-, three-, and five-year survival rates were 81.82%, 46.36%, and 41.82%, respectively. The median survival time was 31.8 months. The local control rates for the whole group at 1, 3, and 5 years were 82.73%, 70%, and 68.18%, respectively. There were no significant differences among 1-, 3-, and 5-year survival rates and local control rates between the three-dimensional conformal radiotherapy group and intensity-modulated radiotherapy group. The main reactions to acute radiotherapy were acute radiation tracheitis, esophagitis, and pneumonia. Multivariate analysis showed that the tumor location and TNM stage were independent prognostic factors.Conclusion: The results from this study showed that whole-course conformal radiotherapy and LCAFRT for ESCC can further improve survival and local control with a tolerable acute reaction compared to previous studies. Local recurrence and distant metastasis are the main failure modes of treatment.
Application of Bone Collagen Matrix combined with HUC-MSCs for Alveolar Process Cleft in a Rabbit Model

Background: Most materials used clinically for filling severe bone defects lack the ability to induce bone regeneration or low bone conversion rate, therefore, their therapeutic effects are limited. Human umbilical cord mesenchymal stem cells (HUC-MSCs) have good osteoinduction. The mechanism of heterogeneous bone collagen matrix combined with HUC-MSCs in repairing bone defects of alveolar process cleft is still unclear.Methods: Here, a rabbit alveolar process cleft model was established to evaluate the repair effect and molecular mechanism of bone collagen matrix and its combination with HUC-MSCs on critical-sized bone defects in the alveolar process. We randomly divided 48 young Japanese white rabbits (JWRs) into normal, control, material and MSCs groups. The alveolar process cleft model was established by removing the bone of equal volume at the left maxillary. Bone collagen matrix combined with HUC-MSCs that were then implanted in the defect area. X-ray analysis and blood analysis were analyzed 3 months after surgery. Skull tissues were collected for micro-focus computerized tomography (micro-CT) analysis and histochemical staining. The above experiment was repeated 6 months after surgery.Results: the main findingsResults: It was found that bone collagen matrix and HUC-MSCs showed good biocompatibility. Heterogeneous bone collagen matrix combined with HUC-MSCs significantly enhanced osteoinduction and osteoconduction. Conclusions: This experiment provides a new method for repairing alveolar process cleft.Trial registration: Not applicable.
The influence of the enhancement of the convective activities of tropical Pacific on the trend of stratospheric sudden warmings in the period of 1948-2003

The exploration of the trend of stratospheric sudden warming (SSW) in the Northern Hemisphere is conducive to predict SSWs in the future. Utilizing the National Centre for Environmental Prediction (NCEP) (1948–2017) and Japanese 55-year reanalysis data (JRA55) (1958–2017), we investigated the duration and strength of SSWs in the Northern Hemisphere winter (December-February). We found the duration of SSWs has an increasing trend and the strength of SSWs tends to strengthen from 1948 to 2003. However, after 2003, these trends did not continue. We also utilize the observed cloudiness from the International Comprehensive Ocean-Atmosphere Data Set (ICOADS) to examine the convective activities in the tropical Pacific and found that the convective activities in the tropical central Pacific are enhanced during the period of 1948–2003, and the trend of the enhancement of the convective activities ceases after 2003. The circulation anomalies caused by the enhanced convective activities propagate to the troposphere at high latitudes through wave trains. The anomalies of circulation and the climatic circulation at high latitudes interfere with each other and superimpose, which has a significant impact on planetary wave 1 (PW1). As a result, the PW1 in the troposphere also showed an increasing trend from 1948 to 2003 and a decreasing trend after 2003. After the stratosphere filters out the planetary wave with a large wavenumber, PW1 accounts for more proportion of planetary waves, which causes the trend of SSW to change synchronously.
Sequence diversity and evolution of infectious bursal disease virus in Iraq

Background: Infectious Bursal Disease (IBD) is a highly infectious disease which causes huge economic losses to the poultry industry due to the direct impact of the illness and indirect consequences such as decreasing the general immunity of the flock, leaving it naive to other diseases. In Iraq, IBD is highly prevalent despite vaccination programs, yet studies on sequence diversity of the causative virus are still rare. Methods: A sample from Bursa of Fabricius from an IBD outbreak in a flock in the city of Najaf in Iraq was smeared on an FTA card. Amplicons of targeted regions in VP1 and VP2 genes were generated and sequenced. Sequences were then compared with other local and global sequences downloaded from GenBank repositories. Sequence alignment and DNA sequence analyses were achieved using MUSCLE, UGENE and MEGAx software. The molecular clock and sequence evolutionary analyses were applied using MEGAx tools. Results: The strain sequenced in this study belongs to a very virulent Infectious Bursal Disease Virus (vvIBDV) as the DNA and phylogenetic analysis of VP1 and VP2 gene sequences showed a mutual clustering with similar sequences belonging to vvIBDV genogroup 3. Analyses of the hyper variable region of VP2 gene (hvVP2) of IBDV isolates from Iraq indicates a presence of sequence diversity. Interestingly, the two vaccine strains Ventri IBDV Plus and ABIC MB71 that showed the highest sequence similarity to the local isolates in the hvVP2 region are not used in vaccination routine against IBDV in Iraq. Conclusion: Sequences of vvIBDV in Iraq are diverse. Remarkably, some of the available vaccine strains show high sequence similarity with local strains in Iraq; however, they are not included in the routine vaccination programs. Analysis of more samples involving more geographical regions is needed to draw a detailed map of antigenic diversity of IBDV in Iraq.
A dynamic optimisation approach for a single machine scheduling problem with machine conditions and maintenance decisions

In modern production systems, considering machine conditions is becoming essential to achieving an overall optimisation of the production schedule. This paper studies a single machine scheduling problem, where the actual processing times of jobs depend on their position in the production sequence and maintenance is considered. Moreover, the machine is subject to an uncertain condition variation. There is a trade-off between rejecting a maintenance action, resulting in longer processing times, and accepting a maintenance action, leading to higher processing efficiency for future jobs. The problem is formulated as a finite-horizon Markov Decision Process. The objective is to minimise the makespan. Optimality properties are analysed, based on which a dynamic optimisation approach is developed. Computational experiments demonstrate the effectiveness of the proposed approach.
Removal of defects in CdO nanoparticle and rapid synthesis of CdO nanoflake using novel microwave technique to improve semiconductor device performance

Objective: The objective of this study is to synthesize CdO nanoparticle and nanoﬂakes both in a single way. Also the purpose of removing defects from semiconductor nanoparticles has been considered. Methods : Very small sized Cadmium oxide nanoparticles (11 – 29 nm) and nanoﬂakes of average size 70 nm were prepared by sol-gel process. Two solutions of 0.2M CdCl 2 and 0.2M NaOH were used with a mixture of 1:2 ethylene glycol and methanol. Two diﬀerent heating method of dried precipitate was adopted to observe the morphology and defect characteristics. Half of the precipitate was annealed in furnace and rest half in domestic microwave. Findings : The fcc (NaCl-type) structure has been found in the nanostructures with lattice constant varying with annealing temperature. We propose a linear relation for the change in lattice constant. HRTEM pictures show nanoﬂakes and hexagonal nanoparticles. The ratio curve of coincidence Doppler broadening spectroscopy (CDBS) found defect concentration reduction and agglomeration eﬀect on microwave irradiation in place of furnace annealing. It indicated reduction of defects inside the nanoparticles. The S and W parameter revealed the chemical surroundings and momentum distribution of the vacancy clusters varying with crystallite size. Novelty: Furnace annealing and microwave irradiation showed diﬀerent eﬀect of surface strain on lattice. Microwave irradiation has been used to reduce defects inside CdO nanocrystals for potential application and coincidence Doppler broadening spectroscopy showed potential to be a very eﬀective tool of defect characterization and electron momentum comparison. Also, this work presents how microwave radiation can be used to prepare nanoﬂakes and nanoparticles from same reactants without any substrate.
Improving Flexibility of Poly(l-lactide) by Blending with Poly(l-lactic acid) Based Poly(ester-urethane): Morphology, Mechanical Properties, and Crystallization Behaviors

Poly(l-lactide) (PLLA) is one of the most promising biobased and biodegradable polymers. However, the lack of toughness restricts its application considerably. In the present study, PLLA was successfully toughened by blending with a poly(lactic acid) based poly(ester-urethane) (PEU), which contained poly(butylene succinate) as a flexible segment. The tensile properties and notched Izod impact strength of PLLA and toughened PLLA were investigated. The flexibility of PLLA was considerably improved after introduction of PEU by the evidence of high strain and improved impact strength. The crystallization behavior was investigated by differential scanning calorimeter (DSC), polarized optical microscopy (POM), and wide-angle X-ray diffraction (WAXD). The glass transition temperature of toughened PLLA decreased with an increasing content of PEU, suggesting that the blends showed limited miscibility. POM observation showed that the crystallites of PEU uniformly distributed in the PLLA matrix after two-step crysta.
Kinetics of Water Vapor Adsorption on Single-Layer Molecular Sieve 3A: Experiments and Modeling

The objective of the current work was to shorten the gap for fundamental adsorption kinetic data required for the development of advanced adsorption unit-operation models to be incorporated into an overall plant-level model for spent nuclear fuel reprocessing. The kinetics of water-vapor adsorption on molecular sieve 3A was investigated at 25–80 °C and water dew points from −69 to 17 °C. Water uptake curves were fitted with three kinetic models including the linear-driving-force model, the shrinking-core model, and the Langmuir kinetic model. The results suggest that the water-vapor adsorption on molecular sieve 3A under the investigated experimental conditions was controlled by both external film resistance and internal macropore resistance. The contribution of the external film resistance varied from 25% to 50% of the total mass-transfer resistance depending on the adsorption temperature. It was also found that the Langmuir kinetic model fitted individual sets of kinetic data very well, but the Langmuir.
Physiological Response of Garlic (Allium Sativum) to Elevated Tropospheric Ozone in High Altitude Region of Western Ghats, Tamil Nadu, India

A pot culture study was conducted at Horticultural Research Station, Ooty to assess the effect of ground level ozone on physiology in garlic plant and to find out the suitable remedial measures against ground level ozone. The potted soil was found to be acidic in nature with very low salt concentration, very high in organic carbon, medium in nitrogen, phosphorus and high in potassium. Elevated ozone levels (150ppb and 200ppb) had significantly reduced the garlic plant chlorophyll content, stomatal conductance, photosynthetic rate, pungency and total soluble solids. The highest chlorophyll content (33.97µmolm-2) was observed under ambient ozone level (T1) and the lowest chlorophyll content (12.68µmolm-2) was observed in elevated ozone exposure at 200 ppb (T3), the highest stomatal conductance (0.45mmol m-2s-1) was recorded in Ambient Ozone level + foliar spray 3% Panchagavya (T4), and the lowest stomatal conductance (0.11mmol m-2s-1) was observed in elevated ozone exposure at 200 ppb (T3). Since, the elevated ozone had significant reduction in photosynthetic rate in garlic, the lowest was observed (0.82µmol CO2 s-1m-2) in T3- Elevated ozone exposure at 200 ppb and the highest photosynthetic rate (3.02µmol CO2 s-1m-2) was observed in treatment T4- Ambient Ozone level + foliar spray 3% Panchagavya after a week. When coming to quality of garlic bulbs, the highest pungency content was found in Ambient Ozone level + foliar spray 0.1% Ascorbic acid and the lowest was observed in Elevated ozone exposure at 200 ppb (T3) furthermore, in observing the garlic quality where total soluble solids (TSS) showed that the treatment Ambient Ozone level + foliar spray 3% Panchagavya (40.00°Brix) as highest and the treatment Elevated ozone exposure at 200 ppb (T3) recorded the lowest. Thus the tropospheric ozone has detrimental impact on physiological responses, which will reduce crop growth and yield. The ozone protectants helped in scavenging the O3 from apoplast of the crops and among the ozone protectants, neem oil acted as a good ozone scavenger followed by ascorbic acid and panchagavya to improve the physiological response of garlic plant under elevated tropospheric ozone levels.
The impact of recent and future calving events on the Larsen C ice shelf

Abstract. The Antarctic Peninsula has seen rapid and widespread changes in the extent of its ice shelves in recent decades, including the collapse of the Larsen A and B ice shelves in 1995 and 2002, respectively. In 2017 the Larsen C ice shelf (LCIS) lost around 10 % of its area by calving one of the largest icebergs ever recorded (A68). This has raised questions about the structural integrity of the shelf and the impact of any changes in its extent on the flow of its tributary glaciers. In this work, we used an ice flow model to study the instantaneous impact of changes in the thickness and extent of the LCIS on ice dynamics, and in particular on changes in the grounding line flux (GLF). We initialised the model to a pre-A68 calving state, and first replicated the calving of the A68 iceberg. We found that there was a limited impact on upstream flow – with speeds increasing by less than 10 % across almost all of the shelf – and a 0.5 % increase in GLF. This result is supported by observations of ice velocity made before and after the calving event. We then perturbed the ice-shelf geometry through idealised calving and thinning experiments of increasing magnitude. We found that significant changes to the geometry of the ice shelf, through both calving and thinning, resulted in limited changes in GLF. For example, to produce a doubling of GLF from calving, the new calving front needed to be moved to 5 km from the grounding line, removing almost the entire ice shelf. For thinning, over 200 m of the ice-shelf thickness had to be removed across the whole shelf to produce a doubling of GLF. Calculating the increase in GLF (607 %) after removing the entire ice shelf allowed us to quantify the total amount of buttressing provided by the LCIS. From this, we identified that the region of the ice shelf in the first 5 km downstream of the grounding line provided over 80 % of the buttressing capacity of the shelf. This is due to the large resistive stresses generated in the narrow, local embayments downstream of the largest tributary glaciers.
Lipid panel with Non-HDL cholesterol and total cholesterol/HDL cholesterol ratio

Amac: Calismamizda, kan lipid duzeylerinin degerlendirilmesinde, hesaplamali test olan Non-HDL kolesterol ve Total kolesterol/HDL kolesterol degerlendirilmesinin onemi incelenmistir. Yontem: Aile hekimligi polikliniginden yapilan laboratuvar istemlerinden 683 hastanin hem olculen hem de hesaplanan lipid parametreleri degerlendirildi. Rutinde calisilan lipid parametrelerine gore kabul edilebilir aralikta olup da Non-HDL kolesterol ve Total kolesterol/HDL degerine gore hedef degerlerin ustunde kalan hasta sayilari belirlendi. Bulgular: Calismamizin sonuclarina gore, 45 (%6,6) hasta yuksek Non-HDL kolesterol degerlerine ve 127 (%18,6) hasta yuksek TK/HDL-K oranina sahiptir. Tum rutin lipid parametreleri kabul edilebilir sinirlarda iken, Non-HDL kolesterol degerleri yuksek olan 11 (%1,6) hasta ve ve TK/HDL kolesterol orani yuksek olan 39 (%5,7) hasta saptandi. saptandi. Sonuc: Non-HDL kolesterol degerinin ve TK/HDL-K oraninin rutin lipit sonuclarina eklenmesi, klinisyenlere lipit bozuklugu acisindan uyari olusturabileceginden faydali olacaktir. Objective: In our study, the importance of the computational tests such as non-HDL cholesterol and Total cholesterol to HDL ratio for evaluating blood lipid levels were investigated. Method: The measured and calculated lipid parameters of 683 patients whose test inputs were done from Family Medicine Clinic were evaluated. The number of the patients were determined who had high Non-HDL cholesterol and total cholesterol / HDL cholesterol however the the routine lipid parameters were in the acceptable range. Results: According to our results, 45 (6.6%) patients had high non-HDL cholesterol values and 127 (%18,6) patients had high TC / HDL-cholesterol levels. Also, there were 11 (1.6%) patients with high non-HDL-cholesterol levels, and 39 (%5,7) patients with high TC / HDL cholesterol ratio, while all routine lipid parameters were in acceptable limits. Conclusion: The addition of Non-HDL cholesterol and TC / HDL-cholesterol ratio to routine laboratory results would be beneficial because it can create an alert to clinicians in terms of lipid disorders.
α-Linolenic Acid Induces Breast Cancer Cell Apoptosis by Down-Regulating Human Fatty Acid Synthase

Background/Aims: Fatty acid synthase (FASN) is a multi-enzyme complex that synthesizes endogenous fatty acids. The overexpression of FASN has been reported in variety of cancers, including breast, ovarian, prostrate, and colon cancers, which strongly indicates the involvement of FASN in cancer progression. α-Linolenic acid (ALA) has many biological activities, including anti-cancer effects. The aim of the present study was to investigate the inhibitory effect of ALA on fatty acid synthesis pathway and apoptosis of human breast cancer cells. Methods: Cytotoxicity of ALA in human breast cancer cells (MDA-MB-231 and MCF-7 cells) was assessed by MTT assay. Changes in protein expression were detected by immunoblot analysis. Cell migration was detected by wound healing and cell transwell assay. Apoptotic effects, mitochondrial membrane potential and cell cycle analysis were detected by flow cytometry. Molecular docking was carried out with the AutoDockTools program suite to analyze the binding abilities of ALA on thioesterase (TE) domain of FASN. Results: We found that the expression levels of FASN decreased significantly in ALA treated breast cancer cells. Compared with palmitic acid (PA), ALA reduced cell viability in a dose-dependent manner. ALA showed a higher affinity with the TE domain than PA. ALA induced breast cancer cells apoptosis, which effects were similar with the knockdown of FASN. In addition, ALA inhibited the invasion and metastasis, and arrested cell cycle in breast cancer cells. Conclusion: We propose a hypothesis that ALA could contribute to the treatment of human breast cancer by inhibiting FASN.
DenseConv for 3D point set upsampling

Recently, a data-driven approach from point cloud upsampling network (PU-Net) has been used to upsample point set, making it from sparse to dense. However, PU-Net ﬁrst needs to downsample the point set before upsampling, and extract the point features of ﬁxed-level in the sampling area. The local features are not enough to extract, and then restoring its global representation will lead to point cloud coordinates to be inaccurate. In view of the insufﬁcient local feature extraction, EdgeConv module is utilised to merge the points and the information in the local neighbourhood. In addition, a dense connection is proposed to maintain the effective transmission of information across the entire network. In this letter, EdgeConv and dense connection are combined into DenseC-onv that are nested for recursive use on PU-Net to ensure the accuracy of the generation of point cloud. The experimental results show that the average error of the proposed method is reduced by about 5% on the PU-Net dataset and about 10% on the ModelNet10 dataset, which veriﬁes the effectiveness of the proposed method.