Miracle-dz/UniFAR-FTUs huggingface dataset:
Fractional Burgers Fluid Flow Due to Metachronal Ciliary Motion in an Inclined Tube

Cilia-induced flow of fractional Burgers fluid is studied in an inclined tube for both symplectic and antiplectic wave patterns. The solution of the problem is persued under the long wave length limitation. The fractional Adomian decomposition method is employed to evaluate the pressure gradient. Mathematical expressions for the axial velocity, frictional force, pressure gradient, and stream function are obtained and the influence of the main operating parameters is discussed in detail. It is noted that the velocity profile is more dominant in the case of antiplectic metachronal waves compared to symplectic ones, which confirms former results on the better capability of antiplectic waves to transport mucus, obtained with more complex numerical solvers.
Efficient implementation of the Cauchy method for automated CAD-model construction

An efficient and stable implementation of the multidimensional Cauchy method for creating high quality multivariate models of microwave circuits from electromagnetic (EM) simulation data is presented in this paper. The algorithm uses the total least squares method to solve the ill-conditioned interpolation problem and automatically determines the model order and distribution of support points in the parameter space in such a manner that instabilities are prevented. Numerical tests show that the method requires fewer support points to achieve similar accuracy as the rational function models published previously. The utility and accuracy of the technique is demonstrated on a filter design example involving three- and five-dimensional models.
Evidential multi-band common spatial pattern in brain computer interface

In electroencephalography (EEG)-based brain computer interfaces (BCI) one way to extract discriminative command-related patterns is to use common spatial pattern (CSP). Speech-imagery BCIs on the other hand, are a more recent type of BCIs in which imagination of a vowel, sound or word is detected from EEG measurements. Since the performance of CSP highly depends on the spectral filters which are previously applied to the signal, finding the appropriate frequency band seems to be a major concern. In order to overcome this problem, the novel evidential multi-band common spatial pattern (EMBCSP) is proposed. In EMBCSP, features are extracted using CSP after multiple band-pass filtering. The preliminary classification results are later given to a fusion system and then the features are labeled regarding the larger combined probability value. The performance of this method has been assessed using speech-imagery-based EEG measurements and has also been compared with some prevalent methods. The results suggest the outperforming of EMBCSP with accuracies between 75 to 96.67 percent and give rise to opportunities to apply such a method to other common types of BCIs.
Identification and Characterization of ComE and ComF, Two Novel Pilin-Like Competence Factors Involved in Natural Transformation of Acinetobacter sp. Strain BD413

ABSTRACT Although the high level of competence for natural transformation ofAcinetobacter sp. strain BD413 has been the subject of numerous studies, only two competence genes, comC andcomP, have been identified to date. By chromosomal walking analysis we found two overlapping open reading frames, designatedcomE and comF, starting 61 bp downstream ofcomC. comE and comF are expressed as stable proteins in Escherichia coli, thus proving that they are indeed coding regions, but expression was successful only with 5′-deleted genes. ComE and ComF are similar to pilins and pilin-like components. Both genes were mutated, and the phenotypes of the mutants were analyzed. Natural transformation in comF mutants is 1,000-fold reduced, whereas comE mutants exhibit 10-fold-reduced transformation frequencies. This is clear evidence thatcomE and comF are involved in natural transformation. However, ComE and ComF are specific for DNA translocation, since comE and comF defects affected neither piliation nor lipase secretion. These results suggest that the type IV pili, the general protein secretion pathway, and the DNA translocation machinery in Acinetobacter sp. strain BD413 are evolutionary related but functionally distinct systems.
Evaluating the Effect of QIIME Balanced Default Parameters on Metataxonomic Analysis Workflows With a Mock Community

Metataxonomic analysis represents a fast and cost-effective approach for acquiring informative insight into the composition of the microbiome of samples with variable diversity, such as wine samples. Nevertheless, it comprises a vast amount of laboratory procedures and bioinformatic frameworks each one associated with an inherent variability of protocols and algorithms, respectively. As a solution to the bioinformatic maze, QIIME bioinformatic framework has incorporated benchmarked, and balanced parameters as default parameters. In the current study, metataxonomic analysis of two types of mock community standards with the same microbial composition has been performed for evaluating the effectivess of QIIME balanced default parameters on a variety of aspects related to different laboratory and bioinformatic workflows. These aspects concern NGS platforms, PCR protocols, bioinformatic pipelines, and taxonomic classification algorithms. Several qualitative performance expectations have been the outcome of the analysis, rendering the mock community a useful evaluation tool.
A Software Framework for Multimodal Interactive Simulations (SoFMIS)

The development of a multimodal interactive simulation is a very elaborate task due to the various complex software components involved, which run simultaneously at very high rates with maximum CPU load. In this work, we propose a multimodal parallel simulation framework called SoFMIS to create rapid interactive simulations such as surgical simulations. Our framework offers great flexibility and customization allowing simulation developers and researchers to concentrate on the simulation logic rather than component development.
The implication of repair processes in the mechanism of DNA integration by lymphoma cells.

SummaryThe uptake and integration of exogenous 3H-IUdR labelled DNA by irradiated cultures of an IUdR resistant mutant of P338F cells has been studied by preparative CsCl density gradient centrifugation. 10−2 M hydroxyurea was found to inhibit DNA synthesis as measured by uptake of 14C cytidine, but did not inhibit the integration of the exogenous DNA. This implies that enzymes involved in integration and repair are different from those concerned with DNA synthesis. ‘Repair’ synthesis of DNA has been demonstrated after 150 and 400 rads of x-rays. The amount of DNA uptake and integration was higher in irradiated cells and increased with increasing dose. Density-gradient centrifugation of DNA integrated into irradiated cells suggests the possibility of the release of nucleases from irradiated cells. The survival of the irradiated cells was unaffected by the integration of exogenous DNA.
Hand Preference in Attention Deficit Hyperactivity Disorder

In our Outpatient Department, we studied 56 subjects (41 males, 15 females; aged 5–16 yr.) with Attention Deficit Hyperactivity Disorder (ADHD) with respect to hand use in functional tasks via parental report. Left-hand use was markedly preferred, compared to that of a control group, more for complex than simple and for external (touching food and objects) than internal (scratching, rubbing eyes) tasks, suggesting a deficit in cerebral control of right-hand use. More patients were reported to have a left-hand preference than in the non-ADHD population. Furthermore, extent of laterality was greater for complex than simple external tasks and for external than for internal.
Isolation, characterization, and nucleotide sequence of IS1202, an insertion sequence of Streptococcus pneumoniae

A comparative hybridization protocol was used to isolate a small segment of DNA present in the Streptococcus pneumoniae type 19F strain SSZ but absent from strain Rx1, a nonencapsulated derivative of the type 2 strain D39. This segment of DNA is a 1,747-bp insertion sequence, designated IS1202, flanked by 23-bp imperfect inverted repeats and containing a single open reading frame sufficient to encode a 54.4-kDa polypeptide. A 27-bp target sequence is duplicated at either end of the element. IS1202 is not related to any of the currently known insertion elements and is the first reported for S. pneumoniae. Although found predominantly in type 19F strains in up to five copies, it has also been shown to be present in the chromosomes of pneumococci belonging to other serotypes. One of the four IS1202 copies in the encapsulated strain SSZ is located 1,009 bp downstream of the dexB gene, and transformation studies reveal that it is also closely linked to the type 19F capsular polysaccharide synthesis (cps) locus.
Students as Partners in a Multi-Media Note-Taking App Development: Best Practices

This paper summarises some of the best practices learned from an extended software engineering project completed through a collaboration of multidisciplinary faculty and several teams of computer science students. The collaboration delivered an advanced multimedia note-taking application, as an open educational resource (OER), capable of supporting both students and research into note-making practices. The project lasted beyond a single academic year, thus enabling multiple student cohort participation, and took place in an English medium of instruction, Sino-foreign university in China. The experiences and reflections surrounding the project were examined, with a number of resulting ideas for best practices.
Shifts in the Composition of the Microbiota of Stored Wheat Grains in Response to Fumigation

While the wheat-associated microbiome is of major agricultural importance, little is known about the alterations in wheat grain microbial community composition during storage. Characterization of the bacterial and fungal communities in stored wheat grains revealed the impact of phosphine fumigation, one of the most effective methods to eliminate insects in stored commodities, on the composition of the wheat grain microbiome. High-throughput amplicon sequencing of the bacterial 16S rRNA gene and fungal internal transcribed spacer (ITS) region was used to analyze the wheat grain microbiome at different times over as 6 months period of storage. Higher bacterial diversity was found across the samples during the first (immediately after harvest) and second (3 months later) time points, with a predominance of Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes and Planctomycetes. A two-fold decrease in the number of bacterial operational taxonomic units (OTUs) was observed in wheat grains at the last time point (6 months later), following phosphine treatment. In contrast to the effect of phosphine on bacteria, it did not affect fungal diversity in stored grains. The majority of fungal sequences were assigned to Ascomycota, followed by Basidiomycota, Glomeromycota, and unidentified fungi, which were evenly distributed throughout the storage period. Alpha and beta diversity analyses were confirmed by examination of the cultured microbial taxa obtained from the stored wheat grains. Mycotoxin analysis of wheat grains collected after phosphine fumigation revealed the presence of Fusarium toxins, primarily deoxynivalenol (DON). Several mycotoxigenic Fusarium spp. were also detected in the same samples. Results of the present study indicate that microbiome of stored, whole wheat grains was strongly affected by phosphine fumigation, which changed the structure of the microbial community leading to shifts in species composition toward mycotoxigenic strains. A better understanding of the complex interactions within the microbial communities of stored grains will assist in the development of novel biocontrol strategies to overcome mycotoxin contamination.
Are Patients With Schizophrenia Spectrum Disorders More Prone to Manifest Nocebo-Like-Effects? A Meta-Analysis of Adverse Events in Placebo Groups of Double-Blind Antipsychotic Trials

Background: Antipsychotic clinical trials use to present adverse events (AEs) for the drug under evaluation to treat schizophrenia. Interestingly, patients who receive the placebo during antipsychotic trials often report several AEs, but little is known about the essence of these negative effects in patients with schizophrenia spectrum disorders (SCD). In the present meta-analysis, we evaluated the relationship between the level of psychiatric symptomatology expressed as Positive and Negative Syndrome Scale (PANSS) scores and the rates of AEs reported in the placebo arms of double-blind clinical trials, for commonly prescribed atypical antipsychotic medications. Methods: We selected 58 clinical trials describing AEs in SCD placebo groups, which compared atypical antipsychotic medications with placebo. A total of 6,301 placebo-treated patients were considered. AE profiles of the class were clusterized using MedDRA classification and analysed using a meta-regression approach. Results: In the placebo arms the proportions of patients with any AE was 66.3% (95% CI: 62.7–69.8%). The proportion of withdrawal of patients treated with placebo because of AEs was 7.2% (95% CI: 5.9–8.4%). Interestingly, the AEs in the placebo arms corresponded to those of the antipsychotic-atypical-medication-class against which the placebo was compared. Namely, using meta-regression analysis we found an association between the level of psychiatric symptomatology measured with PANSS scores and higher AEs reported as nervous system (p = 0.020) and gastrintestinal disorders (p = 0.004). Moreover, the level of a higher psychiatric symptomatology expressed with PANSS scores was also related with higher AEs associated with psychiatric symptoms (p = 0.017). Conclusion: These findings emphasise that the AEs in placebo arms of clinical trials of antipsychotic medications were substantial. Importantly, a higher level of psychiatric symptomatology makes SCD patients more prone to express AEs, thus contributing to possible drop-outs and to a lower adherence to treatments. These results are consistent with the expectation theory of placebo and nocebo effects.
Why We Need the Journal of Interactive Advertising

There is disclosed an incentive spirometer for measuring, as desired, the inspiratory breathing capacity and/or the expiratory breathing capacity including a freely floating piston positioned within a chamber. The piston is responsive to an inspired breath inhaled from one end of the chamber and also responsive to an exhaled breath introduced into the other end of the chamber. A novel rolling seal is provided which causes extremely minute friction losses during movement and which effectively seals the area between the external perimeter of the piston and the internal surface of the chamber.
Rhesus Cytomegalovirus Contains Functional Homologues of US2, US3, US6, and US11

ABSTRACT Human cytomegalovirus (HCMV) is a paradigm for mechanisms subverting antigen presentation by major histocompatibility complex (MHC) molecules. Due to its limited host range, HCMV cannot be studied in animals. Thus, the in vivo importance of inhibiting antigen presentation for the establishment and maintenance of infection with HCMV is unknown. Rhesus cytomegalovirus (RhCMV) is an emerging animal model that shares many of the features of HCMV infection. The recent completion of the genomic sequence of RhCMV revealed a significant degree of homology to HCMV. Strikingly, RhCMV contains several genes with low homology to the HCMV US6 gene family of inhibitors of the MHC I antigen presentation pathway. Here, we examine whether the RhCMV US6 homologues (open reading frames Rh182, -184, -185, -186, -187, and -189) interfere with the MHC I antigen-processing pathway. We demonstrate that Rh182 and Rh189 function similarly to HCMV US2 and US11, respectively, mediating the proteasomal degradation of newly synthesized MHC I. The US3 homologue, Rh184, delayed MHC I maturation. Unlike US3, MHC I molecules eventually escaped retention by Rh184, so that steady-state surface levels of MHC I remained unchanged. Rh185 acted similarly to US6 and inhibited peptide transport by TAP and, consequently, peptide loading of MHC I molecules. Thus, despite relatively low sequence conservation, US6 family-related genes in RhCMV are functionally closely related to the conserved structural features of HCMV immunomodulators. The conservation of these mechanisms implies their importance for immune evasion in vivo, a question that can now be addressed experimentally.
Hold Your Methods! How Multineuronal Firing Ensembles Can Be Studied Using Classical Spike-Train Analysis Techniques

Responses of neuronal populations play an important role in the encoding of stimulus related information. However, the inherent multidimensionality required to describe population activity has imposed significant challenges and has limited the applicability of classical spike train analysis techniques. Here, we show that these limitations can be overcome. We first quantify the collective activity of neurons as multidimensional vectors (patterns). Then we characterize the behavior of these patterns by applying classical spike train analysis techniques: peri-stimulus time histograms, tuning curves and auto- and cross-correlation histograms. We find that patterns can exhibit a broad spectrum of properties, some resembling and others substantially differing from those of their component neurons. We show that in some cases pattern behavior cannot be intuitively inferred from the activity of component neurons. Importantly, silent neurons play a critical role in shaping pattern expression. By correlating pattern timing with local-field potentials, we show that the method can reveal fine temporal coordination of cortical circuits at the mesoscale. Because of its simplicity and reliance on well understood classical analysis methods the proposed approach is valuable for the study of neuronal population dynamics.
SPKI Certificate Theory

The SPKI Working Group has developed a standard form for digital certificates whose main purpose is authorization rather than authentication. These structures bind either names or explicit authorizations to keys or other objects. The binding to a key can be directly to an explicit key, or indirectly through the hash of the key or a name for it. The name and authorization structures can be used separately or together. We use S-expressions as the standard format for these certificates and define a canonical form for those S-expressions. As part of this development, a mechanism for deriving authorization decisions from a mixture of certificate types was developed and is presented in this document.
Physical Exercise Induces Immunoregulation of TREG, M2, and pDCs in a Lung Allergic Inflammation Model

The benefits of moderate aerobic physical exercise for allergic asthma are well-known, particularly that of the anti-inflammatory effect that occurs by reducing Th2 responses and lung remodeling. However, the mechanisms of this immunoregulation are still under investigation. In this study, we investigated the possible immunoregulatory mechanisms of lung inflammation induced by moderate aerobic exercise in an experimental asthma model. BALB/c mice were distributed into Control, Exercise (EX), OVA, and OEX groups. OVA and OEX groups were sensitized with ovalbumin (OVA) on days 0, 14, 21, 28, and 42 and were challenged with OVA aerosol three times a week from days 21 to 51. The EX and OEX groups underwent moderate aerobic physical exercise from days 21 to 51 (5 d/w, 1 h/d). The mice were euthanized on day 52. We evaluated pulmonary cytokine production, serum immunoglobulin levels, and the inflammatory cell profile in lung and mediastinal lymph nodes. OVA mice showed increased expression of IL-4, IL-6, IL-10, and TGF-β and decreased macrophage type 2 (M2) recruitment. Physical exercise did not affect the increased antibody production of IgG2a, IgG1, or IgE induced by OVA. Of note, physical exercise alone markedly increased production of anti-inflammatory cytokines such as IL-10 and TGF-β. Physical exercise in OVA-mice also increased the recruitment of M2 in the lungs, as well as the influx and activation of regulatory T cells (Tregs) and CD4 and CD8 lymphocytes. In the draining lymph nodes, it was also observed that physical exercise increased the activation of CD4 T cells, regardless of the presence of OVA. Notably, physical exercise decreased common dendritic cells' (cDCs; pro-inflammatory) expression of co-stimulatory molecules such as CD80, CD86, and ICOSL in the draining lymph nodes, as well as increased ICOSL in plasmacytoid dendritic cells (pDCs; anti-inflammatory). Together, these findings show that physical exercise modulates pulmonary allergic inflammation by increasing Treg and M2 recruitment, as well as pDCs activation, which leads to an increase in anti-inflammatory cytokines and a decrease in pro-inflammatory cells and mediators.
Identification of Chemicals Inducing Cardiomyocyte Proliferation in Developmental Stage–Specific Manner With Pluripotent Stem Cells

Background—The proliferation of cardiomyocytes is highly restricted after postnatal maturation, limiting heart regeneration. Elucidation of the regulatory machineries for the proliferation and growth arrest of cardiomyocytes is imperative. Chemical biology is efficient to dissect molecular mechanisms of various cellular events and often provides therapeutic potentials. We have been investigating cardiovascular differentiation with pluripotent stem cells. The combination of stem cell and chemical biology can provide novel approaches to investigate the molecular mechanisms and manipulation of cardiomyocyte proliferation. Methods and Results—To identify chemicals that regulate cardiomyocyte proliferation, we performed a screening of a defined chemical library based on proliferation of mouse pluripotent stem cell–derived cardiomyocytes and identified 4 chemical compound groups: inhibitors of glycogen synthase kinase-3, p38 mitogen-activated protein kinase, and Ca2+/calmodulin-dependent protein kinase II, and activators of extracellular signal–regulated kinase. Several appropriate combinations of chemicals synergistically enhanced proliferation of cardiomyocytes derived from both mouse and human pluripotent stem cells, notably up to a 14-fold increase in mouse cardiomyocytes. We also examined the effects of identified chemicals on cardiomyocytes in various developmental stages and species. Whereas extracellular signal–regulated kinase activators and Ca2+/calmodulin-dependent protein kinase II inhibitors showed proliferative effects only on cardiomyocytes in early developmental stages, glycogen synthase kinase-3 and p38 mitogen-activated protein kinase inhibitors substantially and synergistically induced re-entry and progression of cell cycle in neonatal but also as well as adult cardiomyocytes. Conclusions—Our approach successfully uncovered novel molecular targets and mechanisms controlling cardiomyocyte proliferation in distinct developmental stages and offered pluripotent stem cell–derived cardiomyocytes as a potent tool to explore chemical-based cardiac regenerative strategies.