Miracle-dz/UniFAR-FTUs huggingface dataset:
The Safety and Feasibility of Re-treating Patients with Severe Emphysema with Endobronchial Coils: A Pilot Study

ABSTRACT Severe emphysema patients who have been treated with endobronchial coils have been shown to initially benefit, but slowly decline in the years thereafter. Re-treating a patient with endobronchial coils could potentially lead to new improvements and may again reduce the rate of further decline. To our knowledge, until now, no results are published about patients who are re-treated. The primary aim of this study is to investigate the safety and feasibility of re-treating severe emphysema patients with endobronchial coils, using the PneumRx coil system. Furthermore, as secondary aim, we will evaluate the efficacy of re-treating these patients. Patients who at least 2 years ago were treated with endobronchial coils and responded clinically meaningful to this treatment were included in the study and re-treated. Safety was evaluated by the number of reported adverse events. Efficacy was evaluated 6 months after re-treatment, and measured by the change in quality of life, exercise capacity and pulmonary function testing. Eight patients were re-treated at a median of 1382 days (range 849–1545) after initial coil treatment with a median additional of 12 (10–15) coils per patient. During treatment, and until 6 months of follow-up, no unexpected adverse events occurred. Quality of life, exercise capacity and lung function did not change significantly 6 months after re-treatment. The results of this pilot study suggest that re-treating patients with endobronchial coils is feasible and safe. However, larger studies are needed to confirm these results and to investigate the efficacy and thus the clinical relevance.
Decreased expression of caveolin 1 in patients with systemic sclerosis: crucial role in the pathogenesis of tissue fibrosis.

OBJECTIVE Recent studies have implicated caveolin 1 in the regulation of transforming growth factor beta (TGFbeta) downstream signaling. Given the crucial role of TGFbeta in the pathogenesis of systemic sclerosis (SSc), we sought to determine whether caveolin 1 is also involved in the pathogenesis of tissue fibrosis in SSc. We analyzed the expression of CAV1 in affected SSc tissues, studied the effects of lack of expression of CAV1 in vitro and in vivo, and analyzed the effects of restoration of caveolin 1 function on the fibrotic phenotype of SSc fibroblasts in vitro. METHODS CAV1 expression in tissues was analyzed by immunofluorescence and confocal microscopy. The extent of tissue fibrosis in Cav1-knockout mice was assessed by histologic/histochemical analyses and quantified by hydroxyproline assays. Cav1-null and SSc fibroblast phenotypes and protein production were analyzed by real-time polymerase chain reaction, immunofluorescence, Western blot, and multiplexed enzyme-linked immunosorbent assay techniques. The effects of restoration of caveolin 1 function in SSc fibroblasts in vitro were also examined using a cell-permeable recombinant CAV1 peptide. RESULTS CAV1 was markedly decreased in the affected lungs and skin of SSc patients. Cav1-knockout mice developed pulmonary and skin fibrosis. Down-regulation of caveolin 1 was maintained in cultured SSc fibroblasts, and restoration of caveolin 1 function in vitro normalized their phenotype and abrogated TGFbeta stimulation through inhibition of Smad3 activation. CONCLUSION Caveolin 1 appears to participate in the pathogenesis of tissue fibrosis in SSc. Restoration of caveolin 1 function by treatment with a cell-permeable peptide corresponding to the CAV1 scaffolding domain may be a novel therapeutic approach in SSc.
Effect of Basalt Reinforcement Type and Content on the Abrasive Wear Behaviour of Polymer Composites

Basalt reinforced composites are quite recently (during last 20 years) developed materials having low density, high specific strength, good frictional, heat and chemical resistance. Natural mineral based fibres are potential alternatives to glass fibres for their strength and to carbon fibres for their lower cost. In order to use basalt reinforced composites for lightweight applications, it is necessary to perform wear characterisation. Basalt fibre, powder and scales reinforced, unsaturated polyester and epoxy resin composites were fabricated with various ratios of basalt and polymeric matrixes. The tribological behaviour of basalt reinforced composites was determined according to the ASTM G132 standard test method for pin abrasion testing. Results showed that type and content of reinforcement have a significant influence on the mechanical and tribological properties of the composites. Scanning electron microscope images are given to illustrate the wear mechanism of composites.
Innate responses to gene knockouts impact overlapping gene networks and vary with respect to resistance to viral infection

Significance Analyses of 10 cell lines from which individual genes associated with innate immunity had been knocked out revealed the following: knockout of some genes is associated with increases in the expression of overlapping networks of genes and significant loss of ability to support the replication of HSV-1; knockout of other genes is associated with decreases in the expression of overlapping networks of genes and, overall, no effect on viral replication; the phenotype of cells from which a gene was deleted reflects the sum total of the effects of genes up- or down-regulated as a consequence of the deletion; and key functions associated with innate immunity are normally repressed and must be activated in response to infection. Analyses of the levels of mRNAs encoding IFIT1, IFI16, RIG-1, MDA5, CXCL10, LGP2, PUM1, LSD1, STING, and IFNβ in cell lines from which the gene encoding LGP2, LSD1, PML, HDAC4, IFI16, PUM1, STING, MDA5, IRF3, or HDAC 1 had been knocked out, as well as the ability of these cell lines to support the replication of HSV-1, revealed the following: (i) Cell lines lacking the gene encoding LGP2, PML, or HDAC4 (cluster 1) exhibited increased levels of expression of partially overlapping gene networks. Concurrently, these cell lines produced from 5 fold to 12 fold lower yields of HSV-1 than the parental cells. (ii) Cell lines lacking the genes encoding STING, LSD1, MDA5, IRF3, or HDAC 1 (cluster 2) exhibited decreased levels of mRNAs of partially overlapping gene networks. Concurrently, these cell lines produced virus yields that did not differ from those produced by the parental cell line. The genes up-regulated in cell lines forming cluster 1, overlapped in part with genes down-regulated in cluster 2. The key conclusions are that gene knockouts and subsequent selection for growth causes changes in expression of multiple genes, and hence the phenotype of the cell lines cannot be ascribed to a single gene; the patterns of gene expression may be shared by multiple knockouts; and the enhanced immunity to viral replication by cluster 1 knockout cell lines but not by cluster 2 cell lines suggests that in parental cells, the expression of innate resistance to infection is specifically repressed.
Change in Provider Beliefs Regarding Cervical Cancer Screening Intervals After an Educational Intervention.

BACKGROUND Current cervical cancer screening guidelines include the option of lengthening the screening interval to 5 years for average-risk women aged 30-65 years when screened with Pap and human papillomavirus (HPV) test (co-test). Because many providers are reluctant to extend screening intervals, we launched an educational intervention to promote recommended screening practices. The study objective was to assess changes in provider attitudes and beliefs to extending screening intervals among low-income women. METHODS The study was conducted in 15 clinics in Federally Qualified Health Centers in Illinois. Providers in the intervention arm received a multicomponent educational intervention. Fifty-six providers (n = 29 intervention and n = 27 control) completed baseline and 12-month follow-up surveys assessing beliefs and intentions about extending screening intervals. RESULTS The 12-month assessment showed providers in the intervention arm were significantly more likely than those in the control arm to recommend a 3-year screening interval (guideline recommendation at time of study) with a normal co-test result. Providers who received the intervention were significantly more likely to agree that routine co-testing is the best way to screen for cervical cancer, that extending the screening interval would be good, easy, and beneficial, and to disagree that the increased screening interval would cause patients to lose contact with the medical system. CONCLUSION Educating providers on the natural history of HPV infection and cervical cancer and the benefits of extended intervals increased their willingness to follow guidelines. This study provides evidence that an educational intervention delivered with HPV testing materials may be effective in encouraging appropriate cervical screening intervals.
Natural Language or Not (NLoN) - A Package for Software Engineering Text Analysis Pipeline

The use of natural language processing (NLP) is gaining popularity in software engineering. In order to correctly perform NLP, we must pre-process the textual information to separate natural language from other information, such as log messages, that are often part of the communication in software engineering. We present a simple approach for classifying whether some textual input is natural language or not. Although our NLoN package relies on only 11 language features and character tri-grams, we are able to achieve an area under the ROC curve performances between 0.976-0.987 on three different data sources, with Lasso regression from Glmnet as our learner and two human raters for providing ground truth. Cross-source prediction performance is lower and has more fluctuation with top ROC performances from 0.913 to 0.980. Compared with prior work, our approach offers similar performance but is considerably more lightweight, making it easier to apply in software engineering text mining pipelines. Our source code and data are provided as an R-package for further improvements.
Chromosome Evolution in Marsupials

Marsupials typically possess very large, distinctive chromosomes that make them excellent subjects for cytogenetic analysis, and the high level of conservation makes it relatively easy to track chromosome evolution. There are two speciose marsupial families with contrasting rates of karyotypic evolution that could provide insight into the mechanisms driving genome reshuffling and speciation. The family Dasyuridae displays exceptional karyotype conservation with all karyotyped species possessing a 2n = 14 karyotype similar to that predicted for the ancestral marsupial. In contrast, the family Macropodidae has experienced a higher rate of genomic rearrangement and one genus of macropods, the rock-wallabies (Petrogale), has experienced extensive reshuffling. For at least some recently diverged Petrogale species, there is still gene flow despite hybrid fertility issues, making this species group an exceptional model for studying speciation. This review highlights the unique chromosome features of marsupial chromosomes, particularly for these two contrasting families, and the value that a combined cytogenetics, genomics, and epigenomics approach will have for testing models of genome evolution and speciation.
Comparison of scale‐up methods for dispersive mixing in twin‐screw extruders

Twin-screw extrusion processes are commonly refined on laboratory-scale extruders then scaled-up to manufacturing systems. When using twin-screw extrusion to compound filler into a polymer, the dispersion of the filler must be considered during scale-up. In this work, two scale-up methods are evaluated for how accurately they scale dispersion as measured by the Residence Stress Distribution, an experimental method that quantifies stress developed in a twin-screw extruder. The first scale-up method evaluated is the industry-standard scaling based on maintaining equivalent volumetric flow rate across extruder sizes. Volumetric scaling is compared to a second, novel scale-up method, the percent drag flow rule, which maintains the same degree of fill in the strongest dispersive screw elements on all extruder sizes. Both scale-up rules have been used to scale between three extruder sizes and have been evaluated for how accurately the larger extruders recreate the dispersive mixing of the smallest machine. Results indicate that the percent drag flow scale-up more accurately maintains dispersive mixing behavior than the volumetric scaling. Furthermore, percent drag flow scale-up resulted in all three extruder sizes behaving similarly to changes in operating conditions. These results indicate that percent drag flow scale-up is a valid technique to scale real industrial processes. POLYM. ENG. SCI., 57:345–354, 2017. © 2016 Society of Plastics Engineers
Phenotypic characteristics of Alzheimer patients carrying an ABCA7 mutation

Objective: To generate a clinical and pathologic phenotype of patients carrying rare loss-of-function mutations in ABCA7, identified in a Belgian Alzheimer patient cohort and in an autosomal dominant family. Methods: We performed a retrospective review of available data records, medical records, results of CSF analyses and neuroimaging studies, and neuropathology data. Results: The mean onset age of the mutation carriers (n = 22) was 73.4 ± 8.4 years with a wide age range of 36 (54–90) years, which was independent of APOE genotype and cerebrovascular disease. The mean disease duration was 5.7 ± 3.0 years (range 2–12 years). A positive family history was recorded for 10 carriers (45.5%). All patient carriers except one presented with memory complaints. The 4 autopsied brains showed typical immunohistochemical changes of late-onset Alzheimer disease. Conclusions: All patients carrying a loss-of-function mutation in ABCA7 exhibited a classical Alzheimer disease phenotype, though with a striking wide onset age range, suggesting the influence of unknown modifying factors.
Visualizing Reciprocal and Non-Reciprocal Relationships in an Online Community

Online communities thrive on their members' participation and contributions. There are numerous ways to visually represent information, current status, power, and acceptance of members in an online community. In this paper we present a design of a visualization representing reciprocal and non-reciprocal relationships among users, which emphasizes and hopefully triggers common bond in the community. Our future goal is to see whether the visualization triggers higher participation in an online community called "WISEtales", which currently is mostly based on common identity. If our hypothesis is confirmed, it will present one of the few examples of successful community whose members associate both by common identity and common bond.
Personalized medicine in rheumatology

In the era of the 21st century, rheumatoid arthritis (RA) is still poorly characterized. Rheumatoid arthritis is a common but heterogeneous disease, not only in the course and clinical symptoms, but also in the clinical response to treatment. Now it is known that early, correct diagnosis and starting treatment with disease-modifying drugs (DMARDs), of which methotrexate (MTX) remains the gold standard in the treatment of RA, is crucial in order to prevent joint destruction, functional disability and an unfavourable disease outcome. Early diagnosis of rheumatoid arthritis is significant in so much as the primary treatment can be started better. Pharmacogenetic and pharmacogenomic studies, which help determine the genetic profile of individual patients, may bring us closer to personalized medicine. Further studies on RA should allow for the identification of disease-specific genes at the stage when their tolerance by the organism is still preserved (before auto-aggression develops).
Production Line Technique for Autonomous Vehicle Scheduling

This paper considers the problem of scheduling autonomous vehicles in intersections. A new system is proposed that could be an additional choice to the recently introduced Autonomous Intersection Management (AIM) model. The proposed system is based on the production line technique, where the environment of the intersection, vehicles position, speeds and turning are specified and determined in advance. The goal of the proposed system is to eliminate vehicle collision and the waiting time inside the intersection. Three different patterns of the vehicles flow toward the intersection have been considered for the evaluation of the model. The system requires less waiting time (compared to the other models) in the random case where the flow is unpredictable. The KNN algorithm is used to predict the right turn vehicle. The experimental results show that there is no single chance of collision inside the intersection, however, the system requires more free space in the traffic lane.
Site-specific O-glycosylation of members of the low-density lipoprotein receptor superfamily enhances ligand interactions

The low-density lipoprotein receptor (LDLR) and related receptors are important for the transport of diverse biomolecules across cell membranes and barriers. Their functions are especially relevant for cholesterol homeostasis and diseases, including neurodegenerative and kidney disorders. Members of the LDLR-related protein family share LDLR class A (LA) repeats providing binding properties for lipoproteins and other biomolecules. We previously demonstrated that short linker regions between these LA repeats contain conserved O-glycan sites. Moreover, we found that O-glycan modifications at these sites are selectively controlled by the GalNAc-transferase isoform, GalNAc-T11. However, the effects of GalNAc-T11–mediated O-glycosylation on LDLR and related receptor localization and function are unknown. Here, we characterized O-glycosylation of LDLR-related proteins and identified conserved O-glycosylation sites in the LA linker regions of VLDLR, LRP1, and LRP2 (Megalin) from both cell lines and rat organs. Using a panel of gene-edited isogenic cell line models, we demonstrate that GalNAc-T11–mediated LDLR and VLDLR O-glycosylation is not required for transport and cell-surface expression and stability of these receptors but markedly enhances LDL and VLDL binding and uptake. Direct ELISA-based binding assays with truncated LDLR constructs revealed that O-glycosylation increased affinity for LDL by ∼5-fold. The molecular basis for this observation is currently unknown, but these findings open up new avenues for exploring the roles of LDLR-related proteins in disease.
Development and evaluation of a controlled drug delivery wound dressing based on polymeric porous microspheres

The aim of the present work was to develop and evaluate a controlled drug delivery wound dressing based on polymeric porous microspheres, which are also termed as microsponge drug delivery system. For this purpose, turmeric (drug)-based polymeric porous microspheres formulations were developed by quasi-emulsion solvent diffusion method. The production yields, actual drug content, drug entrapment efficiency, particle size, formulation of the material, and in vitro release were studied. On the basis of maximum drug released, a formulation was selected to incorporate into wound dressings with the help of a binder by spraying technique. Finally, the selected formulation and samples of wound dressings containing microsponges were subjected to scanning electron microscopy and drug release analyses. The result of in vitro release shows that microsponge drug delivery system is a versatile tool that has a potential to convert any wound dressing into a controlled drug delivery wound dressing.
Addition of MRI for CT-based pancreatic tumor delineation: a feasibility study

Abstract Purpose: To assess the effect of additional magnetic resonance imaging (MRI) alongside the planning computed tomography (CT) scan on target volume delineation in pancreatic cancer patients. Material and methods: Eight observers (radiation oncologists) from six institutions delineated the gross tumor volume (GTV) on 3DCT, and internal GTV (iGTV) on 4DCT of four pancreatic cancer patients, while MRI was available in a second window (CT + MRI). Variations in volume, generalized conformity index (CIgen), and overall observer variation, expressed as standard deviation (SD) of the distances between delineated surfaces, were analyzed. CIgen is a measure of overlap of the delineated iGTVs (1 = full overlap, 0 = no overlap). Results were compared with those from an earlier study that assessed the interobserver variation by the same observers on the same patients on CT without MRI (CT-only). Results: The maximum ratios between delineated volumes within a patient were 6.1 and 22.4 for the GTV (3DCT) and iGTV (4DCT), respectively. The average (root-mean-square) overall observer variations were SD = 0.41 cm (GTV) and SD = 0.73 cm (iGTV). The mean CIgen was 0.36 for GTV and 0.37 for iGTV. When compared to the iGTV delineated on CT-only, the mean volumes of the iGTV on CT + MRI were significantly smaller (32%, Wilcoxon signed-rank, p < .0005). The median volumes of the iGTV on CT + MRI were included for 97% and 92% in the median volumes of the iGTV on CT. Furthermore, CT + MRI showed smaller overall observer variations (root-mean-square SD = 0.59 cm) in six out of eight delineated structures compared to CT-only (root-mean-square SD = 0.72 cm). However, large local observer variations remained close to biliary stents and pathological lymph nodes, indicating issues with instructions and instruction compliance. Conclusions: The availability of MRI images during target delineation of pancreatic cancer on 3DCT and 4DCT resulted in smaller target volumes and reduced the interobserver variation in six out of eight delineated structures.
A trans-acting leader RNA from a Salmonella virulence gene

Significance The intracellular pathogen Salmonella enterica serovar Typhimurium must move toward nutrients to obtain food. However, at the same time, it has to evade the host immune system. Because bacterial flagella are required for both bacterial movement and immune detection, production of flagella must be tightly regulated during infection. Here, we establish that Salmonella produces a leader RNA from the mgtCBR virulence operon and degrades mRNAs of the fljB phase 2 flagellin gene during infection. Our finding indicates a direct link between a virulence determinant and motility via a trans-acting leader RNA derived from the virulence determinant gene in a given host environment. Bacteria use flagella to move toward nutrients, find its host, or retract from toxic substances. Because bacterial flagellum is one of the ligands that activate the host innate immune system, its synthesis should be tightly regulated during host infection, which is largely unknown. Here, we report that a bacterial leader mRNA from the mgtCBR virulence operon in the intracellular pathogen Salmonella enterica serovar Typhimurium binds to the fljB coding region of mRNAs in the fljBA operon encoding the FljB phase 2 flagellin, a main component of bacterial flagella and the FljA repressor for the FliC phase 1 flagellin, and degrades fljBA mRNAs in an RNase E-dependent fashion during infection. A nucleotide substitution of the fljB flagellin gene that prevents the mgtC leader RNA-mediated down-regulation increases the fljB-encoded flagellin synthesis, leading to a hypermotile phenotype inside macrophages. Moreover, the fljB nucleotide substitution renders Salmonella hypervirulent, indicating that FljB-based motility must be compromised in the phagosomal compartment where Salmonella resides. This suggests that this pathogen promotes pathogenicity by producing a virulence protein and limits locomotion by a trans-acting leader RNA from the same virulence gene during infection.