Miracle-dz/UniFAR-FTUs huggingface dataset:
Alterations in the fecal microbiota of patients with spinal cord injury

Objectives Spinal cord injury (SCI) is associated with severe autonomic dysfunction. Patients with SCI often suffer from a lack of central nervous system control over the gastrointestinal system. Therefore, we hypothesized that patients with SCI would cause intestinal flora imbalance. We investigated alterations in the fecal microbiome in a group of patients with SCI. Methods Microbial communities in the feces of 23 patients and 23 healthy controls were investigated using high-throughput Illumina Miseq sequencing targeting the V3-V4 region of the 16S ribosomal RNA (rRNA) gene. The relative abundances between the fecal microbiota at the genus level in patients with SCI and healthy individuals were determined using cluster analysis. Results The structure and quantity of fecal microbiota differed significantly between patients with SCI and healthy controls, but the richness and diversity were not significantly different. A two-dimensional heatmap showed that the relative abundances of forty-five operational taxonomic units (OTUs) were significantly enriched either in SCI or healthy samples. Among these, 18 OTUs were more abundant in healthy controls than in patients with SCI, and 27 OTUs were more abundant in the SCI group than in healthy controls. Conclusion Our study showed that patients with SCI exhibited microbiome dysbiosis.
Understanding the efficacy of influent waste water on microbial community structure of activated sludge process

The assembling of microbial consortia in wastewater treatment facilities is a significance of environmental conditions. In the present research work, activated sludge from different wastewater treatment plants (WWTPs) were exploited at a molecular level to determine the influence of the complexity of the influent composition on the species structure and the diversity of bacterial consortia. The community fingerprints and technological data were subjected to the canonical correspondence and correlation analyses. The number of separated biological processes realized in the treatment line and the presence of industrial wastewater in the influent were the key factors determining the species structure of total and ammonia-oxidizing bacteria in biomass. The N2O-reducers community composition depended significantly on the design of the facility; the highest species richness of denitrifiers was noted in the WWTPs with separated denitrification tanks. The contribution of industrial streams to the inflow affected the diversity of total and denitrifying bacterial consortia and diminished the diversity of ammonia oxidizers. The obtained data are valuable for engineers since they revealed the main factors, including the design of wastewater treatment plant, influencing the microbial groups critical for the stability of purification processes. Key words: Denitrification, waste water treatment plant, bacteria, influent.
The Impact of the Deepwater Horizon Oil Spill upon Lung Health—Mouse Model-Based RNA-Seq Analyses †

We used a transcriptomic approach to interrogate the effects of a saline-accommodated fraction from the Macondo 252 well (MC252) oil and Corexit dispersants on lung tissue. Wild-type C57BL/6 male and female mice were exposed on days 0, 7 and 13 by oropharyngeal aspiration to saline accommodated fractions (SAF) of crude oil from the Macondo (MC252) well, Corexit 9500, Corexit 9527, 9500+oil and 9527+oil or a saline solution as the vehicle control. These treatments did not cause overt toxicity, with the exception of the Corexit exposures which caused brief weight loss after the first exposure. On day 14, total RNA was isolated from the left lung for RNA-seq analyses. KEGG-pathway-based differential expression revealed that Corexit 9527 elicited the strongest changes involving the upregulation of 19 KEGG pathways (FDR < 0.10), followed by Corexit 9500 with the upregulation of seven pathways (FDR < 0.10). As an important signature, pathways related to a response to DNA damage (e.g., p53 signaling and mismatch repair) dominate those upregulated by Corexit 9527 and Corexit 9500. In addition, pro-inflammatory pathways (e.g., cytokine-cytokine receptor interaction, IL-17 signaling pathway and TNF signaling pathways) were upregulated selectively in oil-treated male mice. Surprisingly, oil + dispersant combinations caused lesser effects than the individual treatments at the transcriptomic level. Overall, these findings support potential genotoxicity, inflammation and cell death due to dispersant or oil exposures. Similar exposures to lung tumor bearing K-RasLA1 mice provided evidence for tumor promotion by oil and Corexit dispersant treatments. Our mouse RNA-seq analyses may be relevant to the pulmonary health hazards of MC252 oil and dispersants experienced in exposed populations.
Predicting the Role of DNA Polymerase β Alone or with KRAS Mutations in Advanced NSCLC Patients Receiving Platinum-Based Chemotherapy

Clinical data suggest that only a subgroup of non-small cell lung cancer (NSCLC) patients has long-term benefits after front-line platinum-based therapy. We prospectively investigate whether KRAS status and DNA polymerase β expression could help identify patients responding to platinum compounds. Prospectively enrolled, advanced NSCLC patients treated with a first-line regimen containing platinum were genotyped for KRAS and centrally evaluated for DNA polymerase β expression. Overall survival (OS), progression-free survival (PFS), and the objective response rate (ORR) were recorded. Patients with KRAS mutations had worse OS (hazard ratio (HR): 1.37, 95% confidence interval (95% CI): 0.70–2.27). Negative DNA polymerase β staining identified a subgroup with worse OS than patients expressing the protein (HR: 1.43, 95% CI: 0.57–3.57). The addition of KRAS to the analyses further worsened the prognosis of patients with negative DNA polymerase β staining (HR: 1.67, 95% CI: 0.52–5.56). DNA polymerase β did not influence PFS and ORR. KRAS may have a negative role in platinum-based therapy responses in NSCLC, but its impact is limited. DNA polymerase β, when not expressed, might indicate a group of patients with poor outcomes. KRAS mutations in tumors not expressing DNA polymerase β further worsens survival. Therefore, these two biomarkers together might well identify patients for whom alternatives to platinum-based chemotherapy should be used.
Hydrogel as a Biomaterial for Bone Tissue Engineering: A Review

Severe bone damage from diseases, including extensive trauma, fractures, and bone tumors, cannot self-heal, while traditional surgical treatment may bring side effects such as infection, inflammation, and pain. As a new biomaterial with controllable mechanical properties and biocompatibility, hydrogel is widely used in bone tissue engineering (BTE) as a scaffold for growth factor transport and cell adhesion. In order to make hydrogel more suitable for the local treatment of bone diseases, hydrogel preparation methods should be combined with synthetic materials with excellent properties and advanced technologies in different fields to better control drug release in time and orientation. It is necessary to establish a complete method to evaluate the hydrogel’s properties and biocompatibility with the human body. Moreover, establishment of standard animal models of bone defects helps in studying the therapeutic effect of hydrogels on bone repair, as well as to evaluate the safety and suitability of hydrogels. Thus, this review aims to systematically summarize current studies of hydrogels in BTE, including the mechanisms for promoting bone synthesis, design, and preparation; characterization and evaluation methods; as well as to explore future applications of hydrogels in BTE.
Structure Correction for Robust Volume Segmentation in Presence of Tumors

CNN based lung segmentation models in absence of diverse training dataset fail to segment lung volumes in presence of severe pathologies such as large masses, scars, and tumors. To rectify this problem, we propose a multi-stage algorithm for lung volume segmentation from CT scans. The algorithm uses a 3D CNN in the first stage to obtain a coarse segmentation of the left and right lungs. In the second stage, shape correction is performed on the segmentation mask using a 3D structure correction CNN. A novel data augmentation strategy is adopted to train a 3D CNN which helps in incorporating global shape prior. Finally, the shape corrected segmentation mask is up-sampled and refined using a parallel flood-fill operation. The proposed multi-stage algorithm is robust in the presence of large nodules/tumors and does not require labeled segmentation masks for entire pathological lung volume for training. Through extensive experiments conducted on publicly available datasets such as NSCLC, LUNA, and LOLA11 we demonstrate that the proposed approach improves the recall of large juxtapleural tumor voxels by at least 15% over state-of-the-art models without sacrificing segmentation accuracy in case of normal lungs. The proposed method also meets the requirement of CAD software by performing segmentation within 5 seconds which is significantly faster than present methods.
Hard Attention Net for Automatic Retinal Vessel Segmentation

Automated retinal vessel segmentation is among the most significant application and research topics in ophthalmologic image analysis. Deep learning based retinal vessel segmentation models have attracted much attention in the recent years. However, current deep network designs tend to predominantly focus on vessels which are easy to segment, while overlooking vessels which are more difficult to segment, such as thin vessels or those with uncertain boundaries. To address this critical gap, we propose a new end-to-end deep learning architecture for retinal vessel segmentation: hard attention net (HAnet). Our design is composed of three decoder networks: the first of which dynamically locates which image regions are “hard” or “easy” to analyze, while the other two aim to segment retinal vessels in these “hard” and “easy” regions independently. We introduce attention mechanisms in the network to reinforce focus on image features in the “hard” regions. Finally, a final vessel segmentation map is generated by fusing all decoder outputs. To quantify the network's performance, we evaluate our model on four public fundus photography datasets (DRIVE, STARE, CHASE_DB1, HRF), two recent published color scanning laser ophthalmoscopy image datasets (IOSTAR, RC-SLO), and a self-collected indocyanine green angiography dataset. Compared to existing state-of-the-art models, the proposed architecture achieves better/comparable performances in segmentation accuracy, area under the receiver operating characteristic curve (AUC), and f1-score. To further gauge the ability to generalize our model, cross-dataset and cross-modality evaluations are conducted, and demonstrate promising extendibility of our proposed network architecture.
Gain-Phase Errors Calibration for a Linear Array Based on Blind Signal Separation

In this paper, a non-iterative blind calibration algorithm for gain-phase errors is proposed. A mixing matrix is first obtained from the received observation data through blind signal separation. The mixing matrix is the product of the gain-phase error matrix and the ideal array manifold matrix. Then, a spatial spectrum is constructed by using the estimated mixed matrix. The direction corresponding to the maximum point of the spectral function is proved to be the azimuth of a certain source. Therefore, after the direction-of-arrival (DOA) is obtained by a one-dimensional spectrum search, the active calibration method can be used to estimate the gain-phase errors. The proposed algorithm is not limited to the calibration for uniform linear array (ULA), but also applicable to a non-uniform linear array. Moreover, the estimation performance of the algorithm will not be affected by the magnitude of the gain errors. Some simulations are given to verify the effectiveness and performance of the algorithm.
In Vitro Propagation of Coryphantha macromeris

Cacti are asexually propagated by offsets and cuttings or sexually via seeds (Johnson and Emino, 1979a). However, many species are slow-growing and do not produce offsets. Seeds are sometimes difficult to obtain (Mauseth, 1977) and seedlings are susceptible to damping-off (Mauseth, 1979). As onefourth of all cacti native to the United States are rare or in danger of extinction (Benson, 1977), in vitro propagation of cacti is an attractive alternative for multiplication and maintenance of valuable germplasm. Callus induction (Ault and Blackmon, 1987; Johnson and Emino, 1979a; Mauseth, 1977; Steinhart, 1962) and in vitro growth regulation (Mauseth and Halperin, 1975; Minocha and Mehra, 1974) have been investigated for some cacti species. Johnson and Emino (1979a, 1979b) reported successful in vitro propagation of Mammillaria elongata DC. , Opuntia polyacantha Haw. P. and Hylocereus calcaratus (A. Berger) Britt & Rose. However, each cactus species required a different auxin: cytokinin balance for shoot induction (Johnson and Emino, 1979b). Ault and Blackmon (1987) reported in vitro shoot proliferation from Ferocactus acanthodes (Lemaire) Britt. & Rose. We describe an in vitro propagation method for Coryphantha macromeris (Engelm.) Lem. from callus culture. Seeds were surface sterilized in 1.05% (w/ v) NaOCl for 10 rein, rinsed in sterile water, and then aseptically germinated on Murashige and Skoog (1962) (MS) inorganic salts, pH 5.9, and solidified with 6 g Bacto agar/ liter. All cultures were maintained under a 24 μmol·s -1·m -2 light intensity (Sylvania Grow Lux wide spectrum fluorescent bulbs) for 16 h daily at 26 ± 3C. Shoot explants from the aseptically grown seedlings were cultured on MS medium supplemented with (per liter) 0.4 mg thiamine·HCI, 100 i-inositol, 20 g sucrose, 44
Demo‐genetic analysis of a recovering population of otters in Central Sweden

We performed a demo‐genetic population viability analysis on a recovering population of otters Lutra lutra in Central Sweden, using data on population size, survival and genetic data from microsatellites. Population data were obtained from genotyping faeces. At present, the size and genetic variability of the population is increasing. We found that survival to first reproduction was the most crucial demographic parameter, and that even slight changes downward in this parameter, might lead to a declining population trajectory. Human factors that can affect mortality are traffic, fishing equipment and traps, and we argue that efforts to minimize road kills by means of safe passages as well as careful fishing efforts in streams and lakes would reduce the risk of extinction. In general, even though the population is now growing and has no inbreeding problem, its small abundance could make it vulnerable to chance events and environmental perturbations.
Few Layered Oxidized h-BN as Nanofiller of Cellulose-Based Paper with Superior Antibacterial Response and Enhanced Mechanical/Thermal Performance

In this study, hexagonal boron nitride nanosheets enriched with hydroxyl groups (h-BN-OH) were successfully grafted on the surface of cellulose fibers after the simple and effective exfoliation and oxidation of bulk h-BN. OH groups of h-BN-OH and the ones presented on the surface of cellulose fibers interacted via hydrogen bonding. Both spectroscopic (FT-IR, XRD) and microscopic (TEM, SEM, and atomic force microscopy (AFM)) methods results proved the successful functionalization of the cellulose fibers with the nanomaterial. Modified cellulose fibers were used to prepare paper sheets samples with different concentrations of the nanomaterial (1 wt %, 2 wt %, and 3 wt %). All the samples were tested for the antibacterial properties via the colony forming unit method and exhibited good performance against both Gram-negative (E. coli) and Gram-positive (S. epidermidis) model bacteria. Additionally, the influence of the volume of working bacterial suspension on the antibacterial efficiency of the obtained materials was examined. The results showed significantly better antibacterial performance when the volume of bacterial suspension was reduced. Mechanical properties of the paper samples with and without nanofiller were also characterized. Tensile strength, tearing strength, and bursting strength of the paper samples containing only 2 wt % of the nanofiller were improved by 60%, 61%, and 118% in comparison to the control paper samples, respectively. Furthermore, the nanofiller improved the thermal properties of the composite paper—the heat release rate decreased by up to 11.6%. Therefore, the composite paper can be further explored in a wide range of antibacterial materials, such as packaging or paper coatings
Comparing eating behaviours, and symptoms of depression and anxiety between Spain and Greece during the COVID‐19 outbreak: Cross‐sectional analysis of two different confinement strategies

Abstract Objective We compared eating behaviours, and depressive and anxiety symptoms in two countries with different confinement strictness strategies and different levels of COVID‐19 pandemic. Method A web‐based cross‐sectional survey was administered during and shortly after the COVID‐19 related lockdown in Spain and Greece. Multivariable linear regression analyses were performed to identify country differences associated with eating behaviour, and symptoms of depression and anxiety. Results This study included 1,002 responders in Spain and 839 in Greece. The mean ± SD of restraint, emotional and external eating was 2.5 ± 0.79, 2.1 ± 0.81 and 2.6 ± 0.65 in Spain, whereas 2.7 ± 0.85, 2.3 ± 0.99 and 2.9 ± 0.74 in Greece. Spanish participants had lower average scores of restraint and external eating compared to Greek participants (p < .001), but no difference was seen for emotional eating. In Spain, 13.6%, and 12.3% of the survey respondents reported moderate to severe depressive and anxiety symptoms, respectively, whereas in Greece the respective values were 18.8 and 13.2%. After adjusting for several risk factors, a higher prevalence of anxiety symptoms was observed in Spain compared to Greece (p = .001), but no difference was seen for depressive symptoms. Conclusions This study demonstrated high scores of inappropriate eating behaviours and a high frequency of depressive and anxiety symptoms in two Mediterranean countries during the COVID‐19 outbreak. Our findings revealed that compared to Greek participants, Spanish participants, that faced more severe COVID‐19 pandemic and stricter lockdown measures, were associated with lower restraint and external eating and increased anxiety symptoms, but not with depressive symptoms or emotional eating.
Prediction of haemodynamics after interatrial shunt for heart failure using the generalized circulatory equilibrium

Interatrial shunting (IAS) reduces left atrial pressure in patients with heart failure. Several clinical trials reported that IAS improved the New York Heart Association score and exercise capacity. However, its effects on haemodynamics vary depending on shunt size, cardiovascular properties, and stressed blood volume. To maximize the benefit of IAS, quantitative prediction of haemodynamics under IAS in individual patients is essential. The generalized circulatory equilibrium framework determines circulatory equilibrium as the intersection of the cardiac output curve and the venous return surface. By incorporating IAS into the framework, we predict the impact of IAS on haemodynamics.
Green Processing, Germinating and Wet Milling Brown Rice (Oryza sativa) for Beverages: Physicochemical Effects

Plant-based beverage consumption is increasing markedly. Value-added dehulled rice (Oryza sativa) germination was investigated to improve beverage qualities. Germinating brown rice has been shown to increase health-promoting compounds. Utilizing green processing, wholesome constituents, including bran, vitamins, minerals, oils, fiber and proteins should should convey forward into germinated brown rice beverages. Rapid visco-analyzer (RVA) data and trends established that brown rice, preheated brown rice and germinated brown rice had higher pasting temperatures than white rice. As pasting temperature in similar samples may be related to gelatinization, RVA helped guide the free-flowing processing protocol using temperatures slightly above those previously reported for Rondo gelatinization. Particle size analysis and viscometric evaluations indicate that the developed sprouted brown rice beverage is on track to have properties close to commercial samples, even though the sprouted brown rice beverage developed has no additives, fortifications, added oils or salts. Phenolics and γ-aminobutyric acid increased slightly in germinated brown rice, however, increases were not maintained throughout most stages of processing. Significantly lower inorganic arsenic levels (113 ng/g) were found in germinated (sprouted) brown rice, compared to Rondo white and brown rice, which is far below the USA threshold level of 200 ng/g.
The Short Overview on the Relevance of Fatty Acids for Human Cardiovascular Disorders

This review presents existing evidence of the influence of saturated and unsaturated fatty acids on cardiovascular diseases (CVD). Data are discussed regarding the roles of the most relevant fatty acids, such as myristic (C14:0), palmitic (C16:0), stearic (C18:0), palmitoleic (C16:1), oleic (C18:1), linoleic (C18:2), α-linolenic (C18:3, ω-3), γ-linolenic (C18:3, ω-6), arachidonic (C20:4), eicosapentaenoic (C20:5), docosahexaenoic (C22:6), and docosapentaenoic (C22:5) acid. The accumulated knowledge has expanded the understanding of the involvement of fatty acids in metabolic processes, thereby enabling the transition from basic exploratory studies to practical issues of application of these biomolecules to CVD treatment. In the future, these findings are expected to facilitate the interpretation and prognosis of changes in metabolic lipid aberrations in CVD.
Towards the Inhibition of Protein–Protein Interactions (PPIs) in STAT3: Insights into a New Class of Benzothiadiazole Derivatives

Signal transducer and activator of transcription 3 (STAT3) is a validated anticancer target due to the relationship between its constitutive activation and malignant tumors. Through a virtual screening approach on the STAT3-SH2 domain, 5,6-dimethyl-1H,3H-2,1,3-benzothiadiazole-2,2-dioxide (1) was identified as a potential STAT3 inhibitor. Some benzothiadiazole derivatives were synthesized by employing a versatile methodology, and they were tested by an AlphaScreen-based assay. Among them, benzosulfamide 1 showed a significant activity with an IC50 = 15.8 ± 0.6 µM as a direct STAT3 inhibitor. Notably, we discovered that compound 1 was also able to interact with cysteine residues located around the SH2 domain. By applying mass spectrometry, liquid chromatography, NMR, and UV spectroscopy, an in-depth investigation was carried out, shedding light on its intriguing and unexpected mechanism of interaction.