Miracle-dz/UniFAR-FTUs huggingface dataset:
Angiogenesis' related genetic variants alter clinical features and prognosis of diffuse large B-cell lymphoma patients.

OBJECTIVES Single nucleotide variants (SNVs) in vascular endothelial growth factor A (VEGFA) and VEGFA receptor (KDR) genes confer different inherited abilities in angiogenesis (AG) pathway. We aimed in the present study to evaluate influence of six VEGFA and four KDR SNVs in clinical features and survival of diffuse large B-cell lymphoma (DLBCL) patients. METHODS One hundred and sixty-eight DLBCL patients diagnosed between June 2009-September 2014 were enrolled in the study. Patients were homogeneously treated with R-CHOP. Genotypes were identified in genomic DNA by real-time polymerase chain reaction. RESULTS Patients with VEGFA -634CC and +936CT or TT genotypes were at increased risk of showing grade III / IV toxicities and not achieving complete remission with treatment, and shorter event-free and overall survival were seen in patients with VEGFA -1154GA or AA genotype and VEGFA ATAGCC haplotype. CONCLUSION Our data suggest that inherited abnormalities in AG's gene modulate clinical features and prognosis of DLBCL patients homogeneously treated with R-CHOP.
Electro-conductive carbon nanofibers containing ferrous sulfate for bone tissue engineering

The application of electroactive scaffolds can be promising for bone tissue engineering applications. In the current paper, we aimed to fabricate an electro-conductive scaffold based on carbon nanofibers (CNFs) containing ferrous sulfate. FeSO4·7H2O salt with different concentrations 5, 10, and 15 wt%, were blended with polyacrylonitrile (PAN) polymer as the precursor and converted to Fe2O3/CNFs nanocomposite by electrospinning and heat treatment. The characterization was conducted using SEM, EDX, XRD, FTIR, and Raman methods. The results showed that the incorporation of Fe salt did not induce an adverse effect on the nanofibers’ morphology. EDX analysis confirmed that the Fe are uniformly dispersed throughout the CNF mat. FTIR spectroscopy showed the interaction of Fe salt with PAN polymer. Raman spectroscopy showed that the incorporation of FeSO4·7H2O reduced the ID/IG ratio, indicating more ordered carbon in the synthesized nanocomposite. Electrical resistance measurement depicted that, although the incorporation of ferrous sulfate reduced the electrical conductivity, the conductive is suitable for electrical stimulation. The in vitro studies revealed that the prepared nanocomposites were cytocompatible and only negligible toxicity (less than 10%) induced by CNFs/Fe2O3 fabricated from PAN FeSO4·7H2O 15%. These results showed that the fabricated nanocomposites could be applied as the bone tissue engineering scaffold.
A Biomimetic In Vitro Model of the Kidney Filtration Barrier Using Tissue‐Derived Glomerular Basement Membrane

The glomerular filtration barrier (GFB) filters the blood to remove toxins while retaining high molecular weight proteins in the circulation. The glomerular basement membrane (GBM) and podocytes, highly specialized epithelial cells, are critical components of the filtration barrier. The GBM serves as a physical barrier to passage of molecules into the filtrate. Podocytes adhere to the filtrate side of the GBM and further restrict passage of high molecular weight molecules into the filtrate. Here, a 3D cell culture model of the glomerular filtration barrier to evaluate the role of the GBM and podocytes in mediating molecular diffusion is developed. GBM is isolated from mammalian kidneys to recapitulate the composition and mechanics of the in vivo basement membrane. The GFB model exhibits molecular selectivity that is comparable to the in vivo filtration barrier. The GBM alone provides a stringent barrier to passage of albumin and Ficoll. Podocytes further restrict molecular diffusion. Damage to the GBM that is typical of diabetic kidney disease is simulated using hypochlorous acid and results in increased molecular diffusion. This system can serve as a platform to evaluate the effects of GBM damage, podocyte injury, and reciprocal effects of altered podocyte–GBM interactions on kidney microvascular permeability.
Relationship Between Body Mass Index and Survival Among Critically Ill Patients With Cirrhosis

Background: Obesity paradox is a phenomenon in which obesity increases the risk of obesity-related chronic diseases but paradoxically is associated with improved survival among obese patients with these diagnoses. Objectives: The aim of this study was to explore the obesity paradox among critically ill patients with cirrhosis admitted to the Intensive Care Unit. Methods: A retrospective cohort of 1,143 consecutive patients with cirrhosis admitted to the ICU between January of 2006 and December of 2015 was analyzed. Primary outcome of interest was in-hospital mortality with secondary end points including ICU and short-term mortality at 30 days post ICU admission. Results: Logistic regression with generalized additive models was used, controlling for clinically relevant and statistically significant factors to determine the adjusted relationship between body mass index (BMI) and ICU, post-ICU in-hospital, and 30 day mortality following ICU discharge. ICU and hospital length of stay was similar across all BMI classes. Adjusted ICU mortality was also similar when stratified by BMI. However, a significant reduction in post-ICU hospital mortality was observed in class I and II obese patients with cirrhosis (BMI 30-39.9 kg/m2) compared to normal BMI (OR = 0.41; 95% CI, 0.20 to 0.83; P = 0.014). Similarly, overweight (BMI 25-29.9 kg/m2) and class I and II obese patients with cirrhosis had significantly lower 30-day mortality following ICU discharge (OR = 0.52, 95% CI 0.31 to 0.87; P = 0.014; OR = 0.50, 95% CI 0.29 to 0.86; P = 0.012, respectively) compared to those with normal BMI. Conclusion: The signal of obesity paradox is suggested among critically ill patients with cirrhosis.
Transcriptome analysis and identification of candidate genes involved in glyphosate resistance in the fungus Fusarium verticillioides

Abstract Glyphosate is a broad-spectrum herbicide that has been widely used for nonselective weed control in soybean fields. In the present study, RNA-seq of an Fusarium verticillioides isolate exhibiting resistance to 120 mM glyphosate revealed gene expression occurring in the presence of glyphosate and led to the identification and screening of candidate genes. A transcriptome analysis revealed 5,548 and 5,361 differentially expressed genes (DEGs) in the glyphosate resistant (GR) Fusarium verticillioides isolate treated with 45 and 90 mM glyphosate, respectively. The gene ontology (GO) pathways associated with these differentially expressed genes primarily included metabolic process, amine metabolic process, cellular aromatic compound metabolism and stress response. The primary Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathways included biosynthesis of secondary metabolites, carbon metabolism, glycolysis/gluconeogenesis, and nitrogen metabolism. The glyphosate degradation-related gene fv04, which belongs to the 3-isopropylalate dehydratase of the aconitase superfamily, was cloned to generate the prokaryotic expression vector pET-29b-fv04, which could be stably expressed in E. coli and promote the degradation of 52.3% of 500 mg/L glyphosate in 72 h. The results of the present study provide new ideas and insights for the acquisition of glyphosate resistance resources.
Morphological properties of the axon initial segment‐like process of AII amacrine cells in the rat retina

Signal processing within the retina is generally mediated by graded potentials, whereas output is conveyed by action potentials transmitted along optic nerve axons. Among retinal neurons, amacrine cells seem to be an exception to this general rule, as several types generate voltage‐gated Na+ (Nav) channel‐dependent action potentials. The AII, a narrow‐field, bistratified axon‐less amacrine cell found in mammalian retinas, displays a unique process that resembles an axon initial segment (AIS), with expression of Nav channels colocalized with the cytoskeletal protein ankyrin‐G, and generates action potentials. As the role of spiking in AIIs is uncertain, we hypothesized that the morphological properties of the AIS‐like process could provide information relevant for its functional importance, including potential pre‐ and/or postsynaptic connectivity. For morphological analysis, we injected AII amacrine cells in slices with fluorescent dye and immunolabeled the slices for ankyrin‐G. Subsequently, this enabled us to reliably identify AII‐type processes among ankyrin‐G‐labeled processes in wholemount retina. We systematically analyzed the laminar localization, spatial orientation, and distribution of the AIS‐like processes as a function of retinal eccentricity. In the horizontal plane, the processes displayed no preferred orientation and terminal endings were randomly distributed. In the vertical plane, the processes displayed a horizontal preference, but also ascended and descended into the inner nuclear layer and proximal inner plexiform layer, respectively. These results suggest that the AII amacrine AIS‐like process is unlikely to take part in conventional synaptic connections, but may instead be adapted to respond to volume neurotransmission by means of extrasynaptic receptors.
The potential for person-centred planning to support the community participation of adults with an intellectual disability

Person-centred planning (PCP) puts individuals with an intellectual disability at the centre of service and support planning, identifying how individuals wish to live their lives and what is needed to make that possible. PCP has been identified as having the potential to facilitate improved social inclusion and community participation. A mixed-methods approach combined quantitative analyses with qualitative case studies of individuals with severe-profound intellectual disability to assess the impact of PCP on community participation for adults with an intellectual disability at a disability service in Dublin. We conclude that PCP may provide a good basis to plan community participation and, with the right supports in place, may provide opportunities for people with complex needs to improve their community participation. Supports including familiar staff and family are critical to the success of PCP for people with complex needs, and their absence may undermine the best intentions of PCP for this population.
Non-invasive electrical brain stimulation for vision restoration after stroke: An exploratory randomized trial (REVIS)

Background: Occipital strokes often cause permanent homonymous hemianopia leading to significant disability. In previous studies, non-invasive electrical brain stimulation (NIBS) has improved vision after optic nerve damage and in combination with training after stroke. Objective: We explored different NIBS modalities for rehabilitation of hemianopia after chronic stroke. Methods: In a randomized, double-blinded, sham-controlled, three-armed trial, altogether 56 patients with homonymous hemianopia were recruited. The three experiments were: i) repetitive transorbital alternating current stimulation (rtACS, n = 8) vs. rtACS with prior cathodal transcranial direct current stimulation over the intact visual cortex (tDCS/rtACS, n = 8) vs. sham (n = 8); ii) rtACS (n = 9) vs. sham (n = 9); and iii) tDCS of the visual cortex (n = 7) vs. sham (n = 7). Visual functions were evaluated before and after the intervention, and after eight weeks follow-up. The primary outcome was change in visual field assessed by high-resolution and standard perimetries. The individual modalities were compared within each experimental arm. Results: Primary outcomes in Experiments 1 and 2 were negative. Only significant between-group change was observed in Experiment 3, where tDCS increased visual field of the contralesional eye compared to sham. tDCS/rtACS improved dynamic vision, reading, and visual field of the contralesional eye, but was not superior to other groups. rtACS alone increased foveal sensitivity, but was otherwise ineffective. All trial-related procedures were tolerated well. Conclusions: This exploratory trial showed safety but no main effect of NIBS on vision restoration after stroke. However, tDCS and combined tDCS/rtACS induced improvements in visually guided performance that need to be confirmed in larger-sample trials. NCT01418820 (clinicaltrials.gov)
Liaison and diversion services in South East London: Referral patterns over a 25-year period

Criminal justice liaison and diversion services identify people with mental health needs and ensure they receive appropriate support. We describe a 25-year period of one such service that deals with a population of 864,540 in South East London that was set up in 1991. We used data from three time periods. A diagnosis of a mental illness was recorded in 70.0–80.3% of court liaison and diversion referrals. The proportion receiving a hospital order declined from 15.4% in 1991/1992 to 1.1% in 2015/2016; 54/199 (27.1%) of referrals to the police liaison and diversion service were detained in hospital. Although the service is designed to support any individual with a mental health issue, these results suggest that it has dealt mainly with people who have severe mental illness. Further research is required to understand how best to benefit a wider range of people with mental health issues who attend the lower (Magistrates’) courts, and whether screening for mental disorders can be applied in liaison and diversion settings to aid the implementation of national policy. We also need to understand how disposal decisions are made, and which are most effective.
Predicting breast cancer response to neoadjuvant chemotherapy using ensemble deep transfer learning based on CT images.

OBJECTIVE To develop an ensemble a deep transfer learning model of CT images for predicting pathologic complete response (pCR) in breast cancer patients undergoing neoadjuvant chemotherapy (NAC). METHODS The data were obtained from the public dataset 'QIN-Breast' from The Cancer Imaging Archive (TCIA). CT Images were gathered before and after the first cycle of NAC. CT images of 121 breast cancer patients were used to train and test the model. Among these patients, 58 achieved a pCR and 63 showed a non-pCR based pathology examination of surgical results after NAC. The dataset was split into training and testing subsets with a ratio of 7:3. In addition, the number of training samples in the dataset was increased from 656 to 1,968 by performing an image augmentation method. Two deep transfer learning models namely, DenseNet201 and ResNet152V2, and the ensemble model with a concatenation of two models, were trained and tested using CT images. RESULTS The ensemble model obtained the highest accuracy of 100% on the testing dataset. Furthermore, we received the best performance of 100% in recall, Precision and f1-score value for the ensemble model. This supports the fact that the ensemble model results in better-generalized model and leads to efficient framework. Although a 0.004 and 0.003 difference were seen between the AUC of two base models (DenseNet201 and ResNet152V2) and the proposed ensemble, this increase in the model quality is critical in medical research. T-SNE revealed that in the proposed ensemble, no points were clustered into the wrong class. These results expose the strong performance of the proposed ensemble. CONCLUSION The study concluded that the ensemble model can increase the ability to predict breast cancer response to first-cycle NAC than two DenseNet201 and ResNet152V2 models.
Latent Profile Analysis of Cognition in a Non-Demented Diverse Cohort: A Focus on Modifiable Cardiovascular and Lifestyle Factors.

BACKGROUND Cognitively-defined subgroups are well-documented within neurodegeneration. OBJECTIVE We examined such profiles in diverse non-demented older adults and considered how resulting subgroups relate to modifiable factors associated with neurodegeneration. METHODS 121 non-demented (MMSE = 28.62) diverse (46%non-Latino Black, 40%non-Latino White, 15%Latino) community-dwelling adults (age = 67.7 years) completed cognitive, cardiovascular, physical activity, and diet evaluations. Latent profile analyses (LPA) employed six cognitive scores (letter fluency, letter-number sequencing, confrontational naming, 'animal' fluency, list-learning delayed recall, and recognition discriminability) to characterize cognitively-defined subgroups. Differences between resulting subgroups on cardiovascular (composite scores of overall health; specific health components including fasting blood levels) and lifestyle (sedentary behavior; moderate-to-vigorous physical activity; Mediterranean diet consumption) factors were examined using ANCOVAs adjusting for relevant confounders. RESULTS Based on sample means across cognitive scores, LPA resulted in the following cognitive subgroups: 1) high-average cognition, 55%non-Latino White and 64%female participants; 2) average cognition, 58%non-Latino Black and 68%male participants; 3) lower memory, 58%non-Latino Black participants; and 4) lower executive functioning, 70%Latinos. The high-average subgroup reported significantly higher Mediterranean diet consumption than the average subgroup (p = 0.001). The lower executive functioning group had higher fasting glucose and hemoglobin A1c than all other subgroups (p-values<0.001). CONCLUSION LPA revealed two average subgroups reflecting level differences in cognition previously reported between non-Latino White and Black adults, and two lower cognition subgroups in domains similar to those documented in neurodegeneration. These subgroups, and their differences, suggest the importance of considering social determinants of health in cognitive aging and modifiable risk.
NMR structure of the Vibrio vulnificus ribosomal protein S1 domains D3 and D4 provides insights into molecular recognition of single-stranded RNAs

Abstract The ribosomal S1 protein (rS1) is indispensable for translation initiation in Gram-negative bacteria. rS1 is a multidomain protein that acts as an RNA chaperone and ensures that mRNAs can bind the ribosome in a single-stranded conformation, which could be related to fast recognition. Although many ribosome structures were solved in recent years, a high-resolution structure of a two-domain mRNA-binding competent rS1 construct is not yet available. Here, we present the NMR solution structure of the minimal mRNA-binding fragment of Vibrio Vulnificus rS1 containing the domains D3 and D4. Both domains are homologues and adapt an oligonucleotide-binding fold (OB fold) motif. NMR titration experiments reveal that recognition of miscellaneous mRNAs occurs via a continuous interaction surface to one side of these structurally linked domains. Using a novel paramagnetic relaxation enhancement (PRE) approach and exploring different spin-labeling positions within RNA, we were able to track the location and determine the orientation of the RNA in the rS1–D34 bound form. Our investigations show that paramagnetically labeled RNAs, spiked into unmodified RNA, can be used as a molecular ruler to provide structural information on protein-RNA complexes. The dynamic interaction occurs on a defined binding groove spanning both domains with identical β2-β3-β5 interfaces. Evidently, the 3′-ends of the cis-acting RNAs are positioned in the direction of the N-terminus of the rS1 protein, thus towards the 30S binding site and adopt a conformation required for translation initiation.
Conservation of Epithelial-to-Mesenchymal Transition Process in Neural Crest Cells and Metastatic Cancer

Epithelial to mesenchymal transition (EMT) is a highly conserved cellular process in several species, from worms to humans. EMT plays a fundamental role in early embryogenesis, wound healing, and cancer metastasis. For neural crest cell (NCC) development, EMT typically results in forming a migratory and potent cell population that generates a wide variety of cell and tissue, including cartilage, bone, connective tissue, endocrine cells, neurons, and glia amongst many others. The degree of conservation between the signaling pathways that regulate EMT during development and metastatic cancer (MC) has not been fully established, despite ample studies. This systematic review and meta-analysis dissects the major signaling pathways involved in EMT of NCC development and MC to unravel the similarities and differences. While the FGF, TGFβ/BMP, SHH, and NOTCH pathways have been rigorously investigated in both systems, the EGF, IGF, HIPPO, Factor Receptor Superfamily, and their intracellular signaling cascades need to be the focus of future NCC studies. In general, meta-analyses of the associated signaling pathways show a significant number of overlapping genes (particularly ligands, transcription regulators, and targeted cadherins) involved in each signaling pathway of both systems without stratification by body segments and cancer type. Lack of stratification makes it difficult to meaningfully evaluate the intracellular downstream effectors of each signaling pathway. Finally, pediatric neuroblastoma and melanoma are NCC-derived malignancies, which emphasize the importance of uncovering the EMT events that convert NCC into treatment-resistant malignant cells.
Extraction of flavonoids from cherry seed and its antioxidant activity

The bioactive flavonoid compounds of cherry seed were extracted by ethanol and the optimal extraction conditions were investigated by orthogonal test.The optimal conditions were as followed: temperature 65℃,alcohol concentration 65%vol,extraction time 2 h and the solid-liquid ratio 1∶32.Under these conditions,the extraction yield of cherry seed flavonoids reached 0.856%. The extract exhibited strong antioxidant activity.
The Performance of Digital Monitoring Devices for Oxygen Saturation and Respiratory Rate in COPD: A Systematic Review

Abstract Healthcare access and delivery for individuals with chronic obstructive pulmonary disease (COPD) who live in remote areas or who are susceptible to contracting communicable diseases, such as COVID-19, may be a challenge. Telehealth and remote monitoring devices can be used to overcome this issue. However, the accuracy of these devices must be ensured before forming healthcare decisions based on their outcomes. Therefore, a systematic review was performed to synthesize the evidence on the reliability, validity and responsiveness of digital devices used for tracking oxygen saturation (SpO2) and/or respiratory rate (RR) in individuals with COPD, in remote settings. Three electronic databases were searched: MEDLINE (1996 to October 8, 2020), EMBASE (1996 to October 8, 2020) and CINAHL (1998 to October 8, 2020). Studies were included if they aimed to evaluate one or more measurement properties of a digital device measuring SpO2 or RR in individuals with COPD. Six-hundred and twenty-five articles were identified and after screening, 7 studies matched the inclusion criteria; covering 11 devices measuring SpO2 and/or RR. Studies reported on the reliability (n = 1), convergent validity (n = 1), concurrent validity (n = 2) and predictive validity (n = 2) of SpO2 devices and on the convergent validity (n = 1), concurrent validity (n = 1) and predictive validity (n = 1) of RR devices. SpO2 and RR devices were valid when compared against other respiration monitoring devices but were not precise in predicting exacerbation events. More well-designed measurement studies are needed to make firm conclusions about the accuracy of such devices. Supplemental data for this article is available online at https://doi.org/10.1080/15412555.2021. 1945021 .