Miracle-dz/UniFAR-FTUs huggingface dataset:
Occupancy Modeling, Maximum Contig Size Probabilities and Designing Metagenomics Experiments

Mathematical aspects of coverage and gaps in genome assembly have received substantial attention by bioinformaticians. Typical problems under consideration suppose that reads can be experimentally obtained from a single genome and that the number of reads will be set to cover a large percentage of that genome at a desired depth. In metagenomics experiments genomes from multiple species are simultaneously analyzed and obtaining large numbers of reads per genome is unlikely. We propose the probability of obtaining at least one contig of a desired minimum size from each novel genome in the pool without restriction based on depth of coverage as a metric for metagenomic experimental design. We derive an approximation to the distribution of maximum contig size for single genome assemblies using relatively few reads. This approximation is verified in simulation studies and applied to a number of different metagenomic experimental design problems, ranging in difficulty from detecting a single novel genome in a pool of known species to detecting each of a random number of novel genomes collectively sized and with abundances corresponding to given distributions in a single pool.
Effects of the Gama Cuulu Radio Serial Drama on HIV-Related Behavior Change in Zambia

The Gama Cuulu radio serial drama is written and produced in Zambia's Southern Province. It promotes behavior change and service use to prevent HIV transmission. The authors evaluated the effects of Gama Cuulu on intermediate outcomes (e.g., perceived norms), as well as number of sexual partners, condom use, and HIV testing in the past year among adults between 18 and 49 years of age. The authors used a pretest/posttest assessment with a comparison group design, with Southern Province as the intervention area and Western Province as the comparison area. Approximately 1,500 in-person interviews were conducted in both provinces in 2006 (pretest), 2007, and 2008. Regression models included terms for province, time, and the interaction of the two. Outcomes improved in both provinces (e.g., by 2008, 37.6% of participants in Southern Province and 28.3% participants in Western Province tested for HIV in the past year). Pretest-to-posttest changes in condom use (from 20.2% to 29.4% in Southern Province) and 5 intermediate outcomes were significantly different in the 2 provinces. However, changes in condom use were not associated with listening to Gama Cuulu and changes in other outcomes were similar in both provinces. Weak intervention effects might be attributable to implementation challenges or the saturation of HIV programs in Zambia.
Coxiella burnetii Induces Inflammatory Interferon-Like Signature in Plasmacytoid Dendritic Cells: A New Feature of Immune Response in Q Fever

Plasmacytoid dendritic cells (pDCs) play a major role in antiviral immunity via the production of type I interferons (IFNs). There is some evidence that pDCs interact with bacteria but it is not yet clear whether they are protective or contribute to bacterial pathogenicity. We wished to investigate whether Coxiella burnetii, the agent of Q fever, interacts with pDCs. The stimulation of pDCs with C. burnetii increased the expression of activation and migratory markers (CD86 and CCR7) as determined by flow cytometry and modulated gene expression program as revealed by a microarray approach. Indeed, genes encoding for pro-inflammatory cytokines, chemokines, and type I INF were up-regulated. The up-regulation of type I IFN was correlated with an increase in IFN-α release by C. burnetii-stimulated pDCs. We also investigated pDCs in patients with Q fever endocarditis. Using flow cytometry and a specific gating strategy, we found that the number of circulating pDCs was significantly lower in patients with Q fever endocarditis as compared to healthy donors. In addition, the remaining circulating pDCs expressed activation and migratory markers. As a whole, our study identified non-previously reported activation of pDCs by C. burnetii and their modulation during Q fever.
Airway antioxidant and inflammatory responses to diesel exhaust exposure in healthy humans

Pulmonary cells exposed to diesel exhaust (DE) particles in vitro respond in a hierarchical fashion with protective antioxidant responses predominating at low doses and inflammation and injury only occurring at higher concentrations. In the present study, the authors examined whether similar responses occurred in vivo, specifically whether antioxidants were upregulated following a low-dose DE challenge and investigated how these responses related to the development of airway inflammation at different levels of the respiratory tract where particle dose varies markedly. A total of 15 volunteers were exposed to DE (100 µg·m−3 airborne particulate matter with a diameter of <10 µm for 2 h) and air in a double-blinded, randomised fashion. At 18 h post-exposure, bronchoscopy was performed with lavage and mucosal biopsies taken to assess airway redox and inflammatory status. Following DE exposure, the current authors observed an increase in bronchial mucosa neutrophil and mast cell numbers, as well as increased neutrophil numbers, interleukin-8 and myeloperoxidase concentrations in bronchial lavage. No inflammatory responses were seen in the alveolar compartment, but both reduced glutathione and urate concentrations were increased following diesel exposure. In conclusion, the lung inflammatory response to diesel exhaust is compartmentalised, related to differing antioxidant responses in the conducting airway and alveolar regions.
Higher genus universally decodable matrices (UDMG)

We introduce the notion of Universally Decodable Matrices of Genus g (UDMG), which for g=0 reduces to the notion of Universally Decodable Matrices (UDM) introduced in [8]. A UDMG is a set of L matrices over a finite field, each with K rows, and a linear independence condition satisfied by collections of K+g columns formed from the initial segments of the matrices. We consider the mathematical structure of UDMGs and their relation to linear vector codes. We then give a construction of UDMG based on curves of genus g over the finite field, which is a natural generalization of the UDM constructed in [8]. We provide upper (and constructable lower) bounds for L in terms of K, q, g, and the number of columns of the matrices. We will show there is a fundamental trade off (Theorem 5.4) between L and g, akin to the Singleton bound for the minimal Hamming distance of linear vector codes.
A Novel Time Domain Synchronous Orthogonal Frequency Division Multiple Access Scheme

Time-domain synchronous orthogonal frequency division multiplexing (TDS-OFDM) outperforms cyclic prefixed-OFDM (CP-OFDM) in spectrum efficiency at the expense of higher complexity. Up to now, TDS-OFDM has only been used in unidirectional transmission, such as broadcasting applications. The overwhelming complexity of removing the implicitly superposed interferences between the PN sequences and IDFT information blocks, caused by multiple users, hinders the application of time-domain synchronous orthogonal frequency division multiple access (TDS-OFDMA) in multi-user communication scenarios. To solve this problem, this paper proposes a novel TDS-OFDMA scheme, including joint cyclicity reconstruction and joint channel estimation, utilizing the new "time-space two-dimensional frame structure". Theoretical analysis and computer simulation show that the proposed scheme not only can achieve the purpose of multiple access but also has an even better system performance Fin mobile environment than the conventional single-user TDSOFDM system.
Corneal Hydration Control in Fuchs' Endothelial Corneal Dystrophy

Purpose To assess corneal hydration control across a range of severity of Fuchs' endothelial corneal dystrophy (FECD) by measuring the percent recovery per hour (PRPH) of central corneal thickness after swelling the cornea and to determine its association with corneal morphologic parameters. Methods Twenty-three corneas of 23 phakic FECD patients and 8 corneas of 8 healthy control participants devoid of guttae were graded (modified Krachmer scale). Effective endothelial cell density (ECDe) was determined from the area of guttae and local cell density in confocal microscopy images. Steady-state corneal thickness (CTss) and standardized central corneal backscatter were derived from Scheimpflug images. Corneal swelling was induced by wearing a low-oxygen transmissible contact lens for 2 hours in the morning. De-swelling was measured over 5 hours after lens removal or until corneal thickness returned to CTss. Percent recovery per hour was 100 × (1 – e−k), where k was determined from CT(t) = (de−kt) + CTss, and where d was the initial change from CTss. Results After contact lens wear, corneas swelled by 9% (95% CI 9–10). Percent recovery per hour was 49%/h (95% CI 41–57) in controls and 37%/h in advanced FECD (95% CI 29–43, P = 0.028). Low PRPH was associated with disease severity, low ECDe, and increased anterior and posterior corneal backscatter. Anterior backscatter was associated with PRPH in a multivariable model (R2 = 0.44). Conclusions Corneal hydration control is impaired in advanced FECD and is inversely related to anterior corneal backscatter. Anterior corneal backscatter might serve as an indicator of impaired endothelium in FECD.
Detecting and estimating the regions of activation in CBF activation studies in human brain

Many studies of brain function with positron emission tomography (PET) involve the interpretation of a subtracted PET image, usually the difference between two images of cerebral blood flow (CBF) under baseline and activation conditions. In many cognitive studies, the activation is so slight (4-8%) that the experiment must be repeated on several subjects. The images are then mapped into a standardised coordinate space to account for differences in brain size and orientation, and the subtracted images averaged to improve the signal to noise ratio. The averaged ∆CBF image is then normalised to have unit variance and the resulting t-statistic image is searched for local maxima. If the between-subject variance is not demonstrably (significantly) different across all voxels then the normalisation can be based on a pooled estimate of the between subjects variance. If this is not so then a voxel-based normalisation must be used. We describe a method for determining if the population standard deviation image has regions of high or low values. If these are detected then we give an approximate P -value for the global maximum of the voxel-based t-statistic. We propose an estimator of the number of regions of high or low standard deviation, and the number of regions of activation in the voxel-based t-statistic image. The method uses the Euler characteristic, a concept borrowed from topology. We can thus determine not only if any activation has taken place, but also how many isolated regions of activation are present.
The solution set of the mixed ls-tls problem

Although the least squares (LS) problem and the total least squares (TLS) problem have received much attention, the mixed LS-TLS problem still remains to be investigated. In this paper, we study the necessary and sufficient solvability conditions for the mixed LS-TLS problem in Frobenius norm. The solution set, the minimum Frobenius norm solution and an algorithm to obtain the solution are also given. Further we propose the mixed LS-TLS problem in spectral norm and present the solvability condition.
Following a "collapsing" wave function.

I study the quantum mechanics of a spin interacting with an apparatus. '' Although the evolution of the whole system is unitary, the spin evolution is not. The system is chosen so that the spin exhibits loss of quantum coherence, or wave function collapse,'' of the sort usually associated with a quantum measurement. The system is analyzed from the point of view of the spin density matrix (or Schmidt paths''), and also using the consistent histories approach. These two points of view are contrasted with each other. Connections between the results and the form of the Hamiltonian are discussed in detail.
Novel mutations in the Atlastin gene (SPG3A) in families with autosomal dominant hereditary spastic paraplegia and evidence for late onset forms of HSP linked to the SPG3A locus

Hereditary spastic paraplegias (HSP) comprise a genetically and clinically heterogeneous group of neurodegenerative disorders characterised by progressive spasticity and hyperreflexia of the lower limbs. Autosomal dominant hereditary spastic paraplegia linked to the SPG3A locus on chromosome 14q11‐21 accounts for approximately 10% of autosomal dominant hereditary spastic paraplegia (ADHSP). It is caused by mutations in the SPG3A gene encoding the protein atlastin. To date, only five disease‐causing mutations in the SPG3A gene have been described. We analysed 13 SPG4‐negative families for mutations in the SPG3A gene and identified a mutation in 38% (5/13). Two of the mutations are novel, c.481G>C (p.A161P) and c.740A>C (p.H247P). One of the novel mutations was found both in a family with early onset of symptoms and in a late onset family. Furthermore, we report on numerous polymorphisms detected in the SPG3A gene. © 2003 Wiley‐Liss, Inc.
The Nitric Oxide/Cyclic GMP Messenger System in Olfactory Pathways of the Locust Brain

Nitric oxide is generated by a Ca2+/calmodulin‐stimulated nitric oxide synthase and activates soluble guanylyl cyclase. Using NADPH diaphorase (NADPHd) staining as a marker for the enzyme nitric oxide synthase and an antiserum against cGMP, we investigated the cellular organization of nitric oxide donor and target cells in olfactory pathways of the brain of the locust (Schistocerca gregaria). A small subset of neuronal and glial cells expressed cGMP immunoreactivity after incubation of tissue in a nitric oxide donor. Nitric oxide‐induced increases in cGMP immunoreactivity were quantified in a tissue preparation of the antennal lobe and in primary mushroom body cell cultures. The mushroom body neuropil is a potential target of a transcellular nitric oxide/ cGMP messenger system since it is innervated by extrinsic NADPHd‐positive neurons. The mushroom body‐intrinsic Kenyon cells do not stain for NADPHd but can be induced to express cGMP immunoreactivity. The colocalization of NADPHd and cGMP immunoreactivity in a cluster of interneurons of the antennal lobe, the principal olfactory neuropil of the insect brain, suggests a role of the nitric oxide/cGMP system in olfactory sensory processing. Colocalization of NADPHd staining and cGMP immunoreactivity was also found in certain glial cells. The cellular organization of the nitric oxide/cGMP system in neurons and glia raises the possibility that nitric oxide acts not only as an intercellular but also as an intracellular messenger molecule in the insect brain.
A self-renewing division of zebrafish Müller glial cells generates neuronal progenitors that require N-cadherin to regenerate retinal neurons

Müller glia function as retinal stem cells in adult zebrafish. In response to loss of retinal neurons, Müller glia partially dedifferentiate, re-express neuroepithelial markers and re-enter the cell cycle. We show that the immunoglobulin superfamily adhesion molecule Alcama is a novel marker of multipotent retinal stem cells, including injury-induced Müller glia, and that each Müller glial cell divides asymmetrically only once to produce an Alcama-negative, proliferating retinal progenitor. The initial mitotic division of Müller glia involves interkinetic nuclear migration, but mitosis of retinal progenitors occurs in situ. Rapidly dividing retinal progenitors form neurogenic clusters tightly associated with Alcama/N-cadherin-labeled Müller glial radial processes. Genetic suppression of N-cadherin function interferes with basal migration of retinal progenitors and subsequent regeneration of HuC/D+ inner retinal neurons.
Three Degree of Freedom Robust Voltage Controller for Instantaneous Current Sharing Among Voltage Source Inverters in Parallel

Voltage controlled voltage source inverters (VCVSI) are predominantly used as an interface between source and grid in distributed generation. Modularity of system is achieved by parallel operation of several VCVSI of reduced rating. In this paper, a 3-DOF control scheme is proposed for parallel operation of three phase inverters to enable equal load sharing even during transients while tracking a common sinusoidal voltage reference. The voltage reference is either free running or derived from grid voltage and can be used to synchronize a parallel inverter module with any utility grid. The control algorithm for each inverter is identical, and it is independent of terminal parameters of other inverters, granting N+1 modularity to the system. The proposed fast inner voltage loop with second-order controller and lead compensators enable stable operation at low switching frequencies. A voltage correction is added to the reference to ensure sharing of higher order load current harmonics among inverters. A method to estimate the system tolerance to parametric uncertainties and delays is developed using μ-analysis and a method is presented to improve it. The analysis is validated with simulation and experimental results on two 110 Vac/2.5 kVA three-phase inverters, paralleled to form a stand-alone grid and feeding a nonlinear load.
Integration of electricity cost saving interventions on a water distribution utility

The efficient usage of electricity in the South African water industry has not been a priority due to the relatively low cost of electricity in the past. The situation has changed over the past years as a result of the rapid increase in electricity costs. South African water distribution utilities (WDUs) have installed capacities up to 450 MW. Not all WDUs operate efficiently. Therefore an intervention is needed to move towards efficient use of electricity in the South African water industry. Large combined installed capacity of the pumps and the large storage capacity make WDUs good candidates for load shifting projects. Due to the scale of the WDU and the complexity, the electricity cost saving approach needs to be integrated. Such an integrated approach could not be found in literature. An investigation methodology, as well as an integration strategy for the implementation of an electricity cost saving intervention is developed. The proposed integrated strategy is simulated and an optimised approach is developed. The proposed approach is implemented on a large water distribution utility in South Africa. The project realised an average electricity peak load shift of 15.4 MW. It is concluded that load shifting is possible on individual pumping stations in the water distribution utility subsystems.
A Reference Net Based Formalization of Concurrent Cognitive Decision Making

Multi-agent systems are said to possess considerable strengths like robustness, flexibility, and reliability. But their application in safety- and/or security-critical domains is often not accepted. This is because in such domains the correctness and predictability of a system must be validated by application of a huge amount of test sets or, in the worst case, verified by formal methods. However, verifying multi-agent systems can be very complex or even impossible. Note that the main problem seems not to be the distributed nature of agent-based systems but the agents' autonomy, especially when agents have to act in a non-cooperative and non-deterministic environment because such situations require the ability to reason about the current situation context and draw own decisions in order to realize individual or common group goals. In our work we propose a model that is based on the Observe-Orient-Decide-Act Loop and the Belief-Desire-Intention Model and is completely realized with Reference Nets - a special kind of Object Petri Nets. It allows for the formal specification of Cognitive Decision Making processes together with inherent concurrencies as well as causal dependencies and facilitates automatic code generation. Furthermore, it enforces modeling with constrained resources in order to allow for practical model-checking.
Expression of CDX-2 and Ki-67 in different grades of colorectal adenocarcinomas.

BACKGROUND CDX2 is a caudal homeobox gene essential for intestinal differentiation and is specifically expressed in colorectal adenocarcinomas. Its role in colorectal carcinogenesis is not fully elucidated. AIMS AND OBJECTIVES To study the expression pattern of CDX2 and Ki-67 in different grades of colorectal adenocarcinomas and to observe the relationship of their staining patterns in various tumor stages and to look for correlation if any, between Ki-67 labeling index (Ki-67 LI) and CDX2 expression. MATERIALS AND METHODS A total of 74 cases were enrolled. Detailed clinical profile, peroperative findings, histological grading and staging were noted. Immunohistochemistry for CDX2 and Ki-67 was done, and Ki-67 LI was calculated. CDX2 staining was graded semi-quantitatively, and statistical analysis was done. RESULT Age of presentation ranged from 20 to 75 years, and the male:female ratio was 1.83:1. There were 8, 47 and 13 cases of well, moderate and poorly differentiated adenocarcinomas, respectively. The mean Ki-67 LI of well, moderate and poorly differentiated adenocarcinomas were 14.25, 31.34 and 43.08 respectively, and their difference was statistically significant, correlation was also noted with stage. CDX2 expression appeared to be stronger in poorly differentiated cases, but there was no significant difference in its expression in the different grades and stages. There was no correlation between Ki-67 LI and CDX2 immunostaining pattern. The lymph node metastasis showed CDX2 positivity in all the cases. CONCLUSION Expression of CDX2 does not significantly change with the grade of colorectal adenocarcinomas. However, it is an important diagnostic marker in metastatic colonic lesions. The Ki-67 LI, on the other hand, showed a strong correlation with histopathological grades.
Moving Beyond Correlations in Assessing the Consequences of Poverty

&NA; In the United States, does growing up in a poor household cause negative developmental outcomes for children? Hundreds of studies have documented statistical associations between family income in childhood and a host of outcomes in childhood, adolescence, and adulthood. Many of these studies have used correlational evidence to draw policy conclusions regarding the benefits of added family income for children, in particular children in families with incomes below the poverty line. Are these conclusions warranted? After a review of possible mechanisms linking poverty to negative childhood outcomes, we summarize the evidence for income's effects on children, paying particular attention to the strength of the evidence and the timing of economic deprivation. We demonstrate that, in contrast to the nearly universal associations between poverty and children's outcomes in the correlational literature, impacts estimated from social experiments and quasi‐experiments are more selective. In particular, these stronger studies have linked increases in family income to increased school achievement in middle childhood and to greater educational attainment in adolescence and early adulthood. There is no experimental or quasi‐experimental evidence in the United States that links child outcomes to economic deprivation in the first several years of life. Understanding the nature of socioeconomic influences, as well as their potential use in evidence‐based policy recommendations, requires greater attention to identifying causal effects.