Miracle-dz/UniFAR-FTUs huggingface dataset:
Fisher Linear Discriminant Analysis based Technique Useful for Efficient Character Recognition

This paper describes the character recognition process from printed documents containing Kannada and English text. Kannada is the fifth most popular language in India and English is the most popular language in the world. Kannada is the language spoken by more than 60 million people of South India and English is the second official language at various government organizations through out India. The proposed character recognizer is based on the Fisher linear discriminant (FLD) analysis. It is usually performed to investigate differences among multivariate classes, to determine which attributes discriminate the classes, and to determine the most parsimonious way to distinguish among classes. The proposed system is tested on various fonts, degraded characters, noisy characters of Kannada and English. The overall accuracy of the proposed system is 96.1%.
Role of the ATP-Binding Domain of the Human Papillomavirus Type 11 E1 Helicase in E2-Dependent Binding to the Origin

ABSTRACT Replication of the genome of human papillomaviruses (HPV) is initiated by the recruitment of the viral E1 helicase to the origin of DNA replication by the viral E2 protein, which binds specifically to the origin. We determined, for HPV type 11 (HPV-11), that the C-terminal 296 amino acids of E1 are sufficient for interaction with the transactivation domain of E2 in the yeast two-hybrid system and in vitro. This region of E1 encompasses the ATP-binding domain. Here we have examined the role of this ATP-binding domain, and of ATP, on E2-dependent binding of E1 to the origin. Several amino acid substitutions in the phosphate-binding loop (P loop), which is implicated in binding the triphosphate moiety of ATP, abolished E2 binding, indicating that the structural integrity of this domain is essential for the interaction. The structural constraints imposed on the E1 P loop may differ between HPV-11 and bovine papillomavirus type 1 (BPV-1), since the P479S substitution that inactivates BPV-1 E1 is tolerated in the HPV-11 enzyme. Other substitutions in the E1 P loop, or in two other conserved motifs of the ATP-binding domain, were tolerated, indicating that ATP binding is not essential for interaction with E2. Nevertheless, ATP-Mg stimulated the E2-dependent binding of E1 to the origin in vitro. This stimulation was maximal at the physiological temperature (37°C) and did not require ATP hydrolysis. In contrast, ATP-Mg did not stimulate the E2-dependent binding to the origin of an E1 protein containing only the C-terminal domain (353 to 649) or that of mutant E1 proteins with alterations in the DNA-binding domain. These results are discussed in light of a model in which the E1 ATP-binding domain is required for formation of the E2-binding surface and can, upon the binding of ATP, facilitate and/or stabilize the interaction of E1 with the origin.
Transient expression of FOXP3 in human activated nonregulatory CD4+ T cells

Foxp3 plays a key role in CD4+CD25+ Treg cell function in mice and represents a specific marker for these cells. Despite the strong association between FOXP3 expression and regulatory function in fresh human T cells, little is known about the dynamics of endogenous FOXP3 expression and its relation to the suppressive function in activated human T cells. Here, we addressed the dynamics of FOXP3 expression during human CD4+ T cell activation by plate‐bound anti‐CD3 Ab as well as the relationship between its expression and regulatory function at the single‐cell level. Our data show that FOXP3 is expressed in a high percentage of activated T cells after in vitro stimulation of human CD4+CD25– cells. FOXP3 expression is strongly associated with hyporesponsiveness of activated T cells, but is not directly correlated with their suppressive capabilities, as we demonstrate that it is also expressed in activated nonsuppressive T cells. However, in this nonsuppressive T cell population, FOXP3 expression is transient, while it is stably expressed in activated T cells that do display suppressive function, and in natural CD4+CD25++ Treg cells. These data indicate that expression of endogenous FOXP3, in humans, is not sufficient to induce regulatory T cell activity or to identify Treg cells.
Can Inner Experience Be Apprehended in High Fidelity? Examining Brain Activation and Experience from Multiple Perspectives

We discuss the historical context for explorations of “pristine inner experience,” attempts to apprehend and describe the inner experiences that directly present themselves in natural environments. There is no generally accepted method for determining whether such apprehensions/descriptions should be considered high fidelity. By analogy from musical recording, we present and discuss one strategy for establishing experiential fidelity: the examining of brain activation associated with a variety of experiential perspectives that had not been specified at the time of data collection. We beeped participants in an fMRI scanner at randomly-determined times and recorded time-locked brain activations. We used Descriptive Experience Sampling (DES) to apprehend and describe the participant's experience that was ongoing at each beep. These apprehensions/descriptions were obtained with no specific theoretical perspective or experimental intention when originally collected. If these apprehensions/descriptions were of high fidelity, then these pairings of moments of experience and brain activations should be able to be productively examined and re-examined in multiple ways and from multiple theoretical perspectives. We discuss a small set of such re-examinations and conclude that this strategy is worthy of further examination.
HIF‐Prolyl Hydroxylase 2 Inhibition Enhances the Efficiency of Mesenchymal Stem Cell‐Based Therapies for the Treatment of Critical Limb Ischemia

Upregulation of hypoxia‐inducible transcription factor‐1α (HIF‐1α), through prolyl‐hydroxylase domain protein (PHD) inhibition, can be thought of as a master switch that coordinates the expression of a wide repertoire of genes involved in regulating vascular growth and remodeling. We aimed to unravel the effect of specific PHD2 isoform silencing in cell‐based strategies designed to promote therapeutic revascularization in patients with critical limb ischemia (CLI). PHD2 mRNA levels were upregulated whereas that of HIF‐1α were downregulated in blood cells from patients with CLI. We therefore assessed the putative beneficial effects of PHD2 silencing on human bone marrow‐derived mesenchymal stem cells (hBM‐MSC)‐based therapy. PHD2 silencing enhanced hBM‐MSC therapeutic effect in an experimental model of CLI in Nude mice, through an upregulation of HIF‐1α and its target gene, VEGF‐A. In addition, PHD2‐transfected hBM‐MSC displayed higher protection against apoptosis in vitro and increased rate of survival in the ischemic tissue, as assessed by Fluorescence Molecular Tomography. Cotransfection with HIF‐1α or VEGF‐A short interfering RNAs fully abrogated the beneficial effect of PHD2 silencing on the proangiogenic capacity of hBM‐MSC. We finally investigated the effect of PHD2 inhibition on the revascularization potential of ischemic targeted tissues in the diabetic pathological context. Inhibition of PHD‐2 with shRNAs increased postischemic neovascularization in diabetic mice with CLI. This increase was associated with an upregulation of proangiogenic and proarteriogenic factors and was blunted by concomitant silencing of HIF‐1α. In conclusion, silencing of PHD2, by the transient upregulation of HIF‐1α and its target gene VEGF‐A, might improve the efficiency of hBM‐MSC‐based therapies. Stem Cells 2014;32:231–243
Learning a real time grasping strategy

Real time planning strategy is crucial for robots working in dynamic environments. In particular, robot grasping tasks require quick reactions in many applications such as human-robot interaction. In this paper, we propose an approach for grasp learning that enables robots to plan new grasps rapidly according to the object's position and orientation. This is achieved by taking a three-step approach. In the first step, we compute a variety of stable grasps for a given object. In the second step, we propose a strategy that learns a probability distribution of grasps based on the computed grasps. In the third step, we use the model to quickly generate grasps. We have tested the statistical method on the 9 degrees of freedom hand of the iCub humanoid robot and the 4 degrees of freedom Barrett hand. The average computation time for generating one grasp is less than 10 milliseconds. The experiments were run in Matlab on a machine with 2.8GHz processor.
Using Developer-Interaction Trails to Triage Change Requests

The paper presents an approach, namely iHDev, to recommend developers who are most likely to implement incoming change requests. The basic premise of iHDev is that the developers who interacted with the source code relevant to a given change request are most likely to best assist with its resolution. A machine-learning technique is first used to locate source code entities relevant to the textual description of a given change request. Ihdev then mines interaction trails (i.e., Mylyn sessions) associated with these source code entities to recommend a ranked list of developers. Ihdev integrates the interaction trails in a unique way to perform its task, which was not investigated previously. An empirical study on open source systems Mylyn and Eclipse Project was conducted to assess the effectiveness of iHDev. A number of change requests were used in the evaluated bench-mark. Recall for top one to five recommended developers and Mean Reciprocal Rank (MRR) values are reported. Furthermore, a comparative study with two previous approaches that use commit histories and/or the source code authorship information for developer recommendation was performed. Results show that iHDev could provide a recall gain of up to 127.27% with equivalent or improved MRR values by up to 112.5%.
Tetrachromacy in a butterfly that has eight varieties of spectral receptors

This paper presents the first evidence of tetrachromacy among invertebrates. The Japanese yellow swallowtail butterfly, Papilio xuthus, uses colour vision when foraging. The retina of Papilio is furnished with eight varieties of spectral receptors of six classes that are the ultraviolet (UV), violet, blue (narrow-band and wide-band), green (single-peaked and double-peaked), red and broad-band classes. We investigated whether all of the spectral receptors are involved in colour vision by measuring the wavelength discrimination ability of foraging Papilio. We trained Papilio to take nectar while seeing a certain monochromatic light. We then let the trained Papilio choose between two lights of different wavelengths and determined the minimum discriminable wavelength difference Δλ. The Δλ function of Papilio has three minima at approximately 430, 480 and 560 nm, where the Δλ values approximately 1 nm. This is the smallest value found for wavelength discrimination so far, including that of humans. The profile of the Δλ function of Papilio can be best reproduced by postulating that the UV, blue (narrow-band and wide-band), green (double-peaked) and red classes are involved in foraging. Papilio colour vision is therefore tetrachromatic.
Intensification of antiretroviral therapy with raltegravir or addition of hyperimmune bovine colostrum in HIV-infected patients with suboptimal CD4+ T-cell response: a randomized controlled trial.

BACKGROUND Despite virally suppressive combination antiretroviral therapy (cART), some HIV-infected patients exhibit suboptimal CD4(+) T-cell recovery. This study aimed to determine the effect of intensification of cART with raltegravir or addition of hyperimmune bovine colostrum (HIBC) on CD4(+) T-cell count in such patients. METHODS We randomized 75 patients to 4 treatment groups to receive raltegravir, HIBC, placebo, or both raltegravir and HIBC in a factorial, double-blind study. The primary endpoint was time-weighted mean change in CD4(+) T-cell count from baseline to week 24. T-cell activation (CD38(+) and HLA-DR(+)), plasma markers of microbial translocation (lipopolysaccharide, 16S rDNA), monocyte activation (soluble (s) CD14), and HIV-RNA (lowest level of detection 4 copies/mL) were monitored. Analysis was performed using linear regression methods. RESULTS Compared with placebo, the addition of neither raltegravir nor HIBC to cART for 24 weeks resulted in a significant change in CD4(+) T-cell count (mean difference, 95% confidence interval [CI]: 3.09 cells/μL, -14.27; 20.45, P = .724 and 9.43 cells/μL, -7.81; 26.68, P = .279, respectively, intention to treat). There was no significant interaction between HIBC and raltegravir (P = .275). No correlation was found between CD4(+) T-cell count and plasma lipopolysaccharide, 16S rDNA, sCD14, or HIV-RNA. CONCLUSION The determinants of poor CD4(+) T-cell recovery following cART require further investigation. CLINICAL TRIALS REGISTRATION ClinicalTrials.gov identifier: NCT00772590, Australia New Zealand Clinical Trials Registry: ACTRN12609000575235.
Fluctuations, Correlations and the Estimation of Concentrations inside Cells

Information transmission in cells occurs quite accurately even when concentration changes are “read” by individual binding sites. In this paper we study ligand number and site occupancy fluctuations when ligands diffuse and react going beyond the analyses that focus on their asymptotic decay. In this way we show that, for immobile binding sites, fluctuations in the number of bound molecules decay on a relatively fast scale before the asymptotic behavior kicks in. This result can explain the observed co-existence of highly fluctuating instantaneous transcriptional activities with accumulated mRNA concentrations that have relatively small noise levels. We also show that the initial stages of the decay in the bound molecule number fluctuations have one or two characteristic timescales depending on the concentration of free molecules. This transition can explain the changes in enzyme activity observed at the single molecule level.
Indoor air quality in 24 California residences designed as high-performance homes

Today's high-performance homes are reaching previously unheard of levels of airtightness and are using new materials, technologies, and strategies for which impacts on indoor air quality cannot be fully anticipated from prior studies. This research study used pollutant measurements, home inspections, diagnostic testing, and occupant surveys to assess indoor air quality in a heterogeneous sample of 24 new or deeply retrofitted homes designed to be high-performance homes in California; homes were not all built or certified to the same performance standard (e.g., California Title 24). Although the mechanically vented homes were six times as airtight as non-mechanically ventilated homes (medians of 1.1 and 6.1 ACH50, n = 11 and n = 8, respectively), their use of mechanical ventilation systems and possibly window operation meant their median air exchange rates were almost the same (0.30 versus 0.32 hr—1, n = 8 and n = 8, respectively). Pollutant levels were also similar in vented and unvented homes. Numerous faults were observed in complex mechanical ventilation systems, and they were not corrected as part of this study. More rigorous commissioning is recommended to avoid or correct these faults. Cooking exhaust systems were used inconsistently, and several suffered from design flaws. Failure to follow best practices led to indoor air quality problems in some cases. Ambient nitrogen dioxide benchmarks were exceeded or nearly so in four homes that either used gas ranges with standing pilots or in passive house-style homes that used gas cooking burners without venting range hoods. Homes without active particle filtration had particle count concentrations approximately double those in homes with enhanced filtration, though the effects could not be controlled for outside particle levels and mixing in forced-air homes. The majority of homes reported using low-emitting materials; consistent with this, formaldehyde levels were approximately half those previously measured by another study in conventional, new California homes built before 2008. Emissions of ultrafine particles (with diameters <100 nm) were about 40 times lower on induction electric cooktops compared with either gas or resistance electric models. These results indicate that high-performance homes can achieve acceptable and even enhanced indoor air quality by providing adequate general mechanical ventilation, using low-emitting materials, providing mechanical particle filtration, incorporating well-designed exhaust ventilation for kitchens and bathrooms, educating occupants to use the kitchen and bath ventilation, and possibly by installing induction cooktops.
Transcriptional Biomarkers of Steroidogenesis and Trophoblast Differentiation in the Placenta in Relation to Prenatal Phthalate Exposure

Background Phthalates can alter steroidogenesis and peroxisome proliferator–activated receptor gamma (PPARγ)–mediated transcription in rodent tissues. The placenta offers a rich source of biomarkers to study these relationships in humans. Objective We evaluated whether gestational phthalate exposures in humans were associated with altered human placental steroidogenesis and trophoblast differentiation as measured by markers of mRNA transcription. Methods We measured seven target genes in placentas collected from 54 Dominican and African-American women at delivery in New York City using quantitative real-time polymerase chain reaction (qPCR), normalized to 18S rRNA. qPCR results for the target genes were log-transformed, converted to Z-scores, and grouped into two functional pathways: steroidogenesis (aromatase, cholesterol side chain cleavage enzyme, 17β-hydroxysteroid dehydrogenase type 1, and cytochrome P450 1B1) and trophoblast differentiation (PPARγ, aryl hydrocarbon receptor, and human chorionic gonadotropin). Repeated measures models were used to evaluate the association of phthalate metabolites measured in third-trimester urine samples with each group of target genes, accounting for correlation among the genes within a pathway. Results Higher urinary concentrations of five phthalate metabolites were associated with lower expression of the target genes reflecting trophoblast differentiation. Results were less consistent for genes in the steroidogenesis pathway and suggested a nonlinear dose–response pattern for some phthalate metabolites. Conclusions We observed a significant association between prenatal exposure to phthalates and placental gene expression within two pathways. Further studies are warranted to understand the significance of this association with respect to fetal development and placental function.
Orientation of DNA Minicircles Balances Density and Topological Complexity in Kinetoplast DNA

Kinetoplast DNA (kDNA), a unique mitochondrial structure common to trypanosomatid parasites, contains thousands of DNA minicircles that are densely packed and can be topologically linked into a chain mail-like network. Experimental data indicate that every minicircle in the network is, on average, singly linked to three other minicircles (i.e., has mean valence 3) before replication and to six minicircles in the late stages of replication. The biophysical factors that determine the topology of the network and its changes during the cell cycle remain unknown. Using a mathematical modeling approach, we previously showed that volume confinement alone can drive the formation of the network and that it induces a linear relationship between mean valence and minicircle density. Our modeling also predicted a minicircle valence two orders of magnitude greater than that observed in kDNA. To determine the factors that contribute to this discrepancy we systematically analyzed the relationship between the topological properties of the network (i.e., minicircle density and mean valence) and its biophysical properties such as DNA bending, electrostatic repulsion, and minicircle relative position and orientation. Significantly, our results showed that most of the discrepancy between the theoretical and experimental observations can be accounted for by the orientation of the minicircles with volume exclusion due to electrostatic interactions and DNA bending playing smaller roles. Our results are in agreement with the three dimensional kDNA organization model, initially proposed by Delain and Riou, in which minicircles are oriented almost perpendicular to the horizontal plane of the kDNA disk. We suggest that while minicircle confinement drives the formation of kDNA networks, it is minicircle orientation that regulates the topological complexity of the network.
Preprint Accepted for Publication in the Ieee Transactions on Biomedical Engineering Beamforming in Non-invasive Brain-computer Interfaces Abstract—spatial Filtering Constitutes an Integral Part of Build- Ing Eeg-based Brain-computer Interfaces (bcis). Algorithms Frequently Used for Spatial Filterin

In this study, Beamforming is employed to construct spatial filters that extract EEG sources originating within pre-defined regions of interest (ROIs) within the brain. In this way, neuro-physiological knowledge on which brain regions are relevant for a certain experimental paradigm can be utilized to construct unsupervised spatial filters that are robust against artifactual EEG components. Beamforming is experimentally compared with CSP and Laplacian spatial filtering in a two-class motor-imagery paradigm. It is demonstrated that Beamforming outperforms CSP and Laplacian spatial filtering on noisy datasets, while CSP and Beamforming perform almost equally well on datasets with few artifactual trials. It is concluded that Beamforming constitutes an alternative method for spatial filtering that might be particularly useful for BCIs used in clinical settings, i.e., in an environment where artifact-free datasets are difficult to obtain.
Electronic cigarettes (e‐cigarettes)

As Australia’s lead agency for health and medical research, NHMRC works actively and collaboratively to promote the highest research standards and develop evidence-based health advice. The National Health and Medical Research Council Act 1992 charges NHMRC with promoting the development of individual and public health standards, fostering national consistency in health standards, supporting research and training, and fostering consideration of relevant ethical issues. This work includes developing evidence-based guidelines, health advice and companion resources that aim to improve the health and wellbeing of the Australian population.
Tumour growth inhibition and anti-metastatic activity of a mutated furin-resistant Semaphorin 3E isoform

Secreted Semaphorin 3E (Sema3E) promotes cancer cell invasiveness and metastatic spreading. The pro‐metastatic activity of Sema3E is due to its proteolytic fragment p61, capable of transactivating the oncogenic tyrosine kinase ErbB2 that associates with the Sema3E receptor PlexinD1 in cancer cells. Here, we show that a mutated, uncleavable variant of Sema3E (Uncl‐Sema3E) binds to PlexinD1 like p61‐Sema3E, but does not promote the association of PlexinD1 with ErbB2 nor activates the ensuing signalling cascade leading to metastatic spreading. Furthermore, Uncl‐Sema3E competes with endogenous p61‐Sema3E produced by tumour cells, thereby hampering their metastatic ability. Uncl‐Sema3E also acts independently as a potent anti‐angiogenic factor. It activates a PlexinD1‐mediated signalling cascade in endothelial cells that leads to the inhibition of adhesion to extracellular matrix, directional migration and cell survival. The putative therapeutic potential of Uncl‐Sema3E was validated in multiple orthotopic or spontaneous tumour models in vivo, where either local or systemic delivery of Uncl‐Sema3E‐reduced angiogenesis, growth and metastasis, even in the case of tumours refractory to treatment with a soluble vascular endothelial growth factor trap. In summary, we conclude that Uncl‐Sema3E is a novel inhibitor of tumour angiogenesis and growth that concomitantly hampers metastatic spreading.