Miracle-dz/UniFAR-FTUs huggingface dataset:
Cystic fibrosis: A worldwide analysis of CFTR mutations—correlation with incidence data and application to screening

Although there have been numerous reports from around the world of mutations in the gene of chromosome 7 known as CFTR (cystic fibrosis transmembrane conductance regulator), little attention has been given to integrating these mutant alleles into a global understanding of the population molecular genetics associated with cystic fibrosis (CF). We determined the distribution of CFTR mutations in as many regions throughout the world as possible in an effort designed to: 1) increase our understanding of ancestry–genotype relationships, 2) compare mutational arrays with disease incidence, and 3) gain insight for decisions regarding screening program enhancement through CFTR multi‐mutational analyses. Information on all mutations that have been published since the identification and cloning of the CFTR gene’s most common allele, ΔF508 (or F508del), was reviewed and integrated into a centralized database. The data were then sorted and regional CFTR arrays were determined using mutations that appeared in a given region with a frequency of 0.5% or greater. Final analyses were based on 72,431 CF chromosomes, using data compiled from over 100 original papers, and over 80 regions from around the world, including all nations where CF has been studied using analytical molecular genetics. Initial results confirmed wide mutational heterogeneity throughout the world; however, characterization of the most common mutations across most populations was possible. We also examined CF incidence, ΔF508 frequency, and regional mutational heterogeneity in a subset of populations. Data for these analyses were filtered for reliability and methodological strength before being incorporated into the final analysis. Statistical assessment of these variables revealed that there is a significant positive correlation between ΔF508 frequency and the CF incidence levels of regional populations. Regional analyses were also performed to search for trends in the distribution of CFTR mutations across migrant and related populations; this led to clarification of ancestry–genotype patterns that can be used to design CFTR multi‐mutation panels for CF screening programs. From comprehensive assessment of these data, we offer recommendations that multiple CFTR alleles should eventually be included to increase the sensitivity of newborn screening programs employing two‐tier testing with trypsinogen and DNA analysis. Hum Mutat 19:575–606, 2002. © 2002 Wiley‐Liss, Inc.
Forecasting meteorological time series using soft computing methods: an empirical study

The interest of researchers in different fields of science towards mo dern soft computing data driven methods for time series forecasting has grown in recent years. Modeling and forecasting hydrometeorological variables is an important step in understanding climate change. The application of modern methods instead of traditional statistical techniques has lead to great improvement in past studies on meteorological time series. In this paper, we employ Support Vector Regression (SVR) and automatic model induction by means of Adaptive Gene Expression Programming (AdaGEP) for modeling and short term forecasting of real world hydrometeorological time series. The investigated time series datasets cover annual, respectively monthly data, on temperature and precipitation, measured at several meteorological stations in the Black Se a region. Two performance measures were used to assess the efficiency of the models obtained for forecasting, alongside statistical tes ting of the goodness of fit via the Kolmogorov-Smirnov test. Based on the results of rigourous experiments, we conclude that the models obtained by the AdaGEP algorithm are more competent in forecasting the time series considered in this paper than the models produced with the SVR algorithm.
Stem cells in acute myocardial infarction: the good, the bad, and the ugly.

Any new form of treatment, when based on solid experimental observations, initially generates a lot of enthusiasm among researchers as well as among patients (when media get involved). If the initial positive results in observational studies are then confirmed in small randomized trials with surrogate endpoints and finally in large randomized trials with clinical endpoints, the new treatment gains momentum and becomes common practice when incorporated in guidelines (for instance, the use of ACE inhibitors in patients with heart failure). At the other extreme, if the initial positive results are not confirmed in controlled randomized trials, the new treatment is quickly forgotten (for instance, the use of positive inotropic agents in patients with heart failure). As clinicians, we know, however, that we have to accept the grey area where things can remain uncertain for years or even decades. A good example is offered by lipid-lowering drugs: in spite of compelling evidence in the sixties that hypercholesterolaemia is a key atherogenic stimulus, statins have entered guidelines in the nineties only. The simple reason for this prolonged hovering in the grey area is that lipid-lowering drugs used prior to statins were able to significantly reduce cholesterol levels, but this reduction was not large enough to translate into a significant reduction of clinical endpoints. More recently, growing attention has been paid to the issue of safety. For instance, non-steroidal anti-inflammatory drugs are under close scrutiny because of an increased risk of thrombotic complications which went unnoticed during the last few decades. The interpretation of the growing number of trials of cell-based therapy following acute myocardial infarction (AMI) has to be considered in this broad context. After the seminal observation in 2001 by Anversa et al . 1 that the human heart is not a post-mytotic organ, several studies in experimental models have confirmed that … *Corresponding author. Tel: +39 630154187; fax: +39 63055535. E-mail address : filippo.crea{at}rm.unicatt. it
Loss of genetic diversity in the endemic Hector's dolphin due to fisheries-related mortality

The endemic New Zealand Hector's dolphin is considered the rarest species of marine dolphin with a total abundance of less than 4000. The species is listed as vulnerable because of fisheries‐related mortality due to entanglement in set nets.The vulnerability of this species is further increased by its fidelity to local natal ranges and the genetic isolation of regional populations. Here we present evidence, based on 108 contemporary samples and 55 historical samples dating back to 1870, of a significant loss of mitochondrial DNA (mtDNA) diversity in two regional populations of Hector's dolphin. The haplotype diversity (h) was calculated from sequences of a 206 bp fragment in the mtDNA control region, designed to identify 13 out of the 14 known maternal lineages. Over the last 20 years, the North Island population has been reduced from at least three lineages (h=0.41) to a single lineage (h=0; p<0.05). Given its small size, reproductive isolation and reduced genetic diversity, this population is likely to become extinct. The diversity of the East Coast South Island population has declined significantly from h=0.65 to h=0.35 (p<0.05). Based on trend analysis of the mtDNA diversity, we predict that the East Coast population will lose all mtDNA diversity within the next 20 years. This time‐series of reduction in genetic variation provides independent evidence of the severity of population decline and habitat contraction resulting from fisheries and perhaps other human activities.
The yeast heat shock response is induced by conversion of cells to spheroplasts and by potent transcriptional inhibitors

We report here that procedures commonly used to measure transcription and mRNA decay rates in Saccharomyces cerevisiae induce the heat shock response. First, conversion of cells to spheroplasts with lyticase, a prerequisite for nuclear runoff transcription, induces the expression of HSP70 and HSP90 heat shock genes. The transcript levels of the non-heat-shock gene ACT1 are slightly depressed, consistent with the general yeast stress response. Second, the DNA intercalator, 1,10-phenanthroline, widely employed as a general transcriptional inhibitor in S. cerevisiae, enhances the mRNA abundance of certain heat shock genes (HSP82, SSA1-SSA2) although not of others (HSC82, SSA4, HSP26). Third, the antibiotic thiolutin, previously demonstrated to inhibit all three yeast RNA polymerases both in vivo and in vitro, increases the RNA levels of HSP82 5- to 10-fold, those of SSA4 greater than 25-fold, and those of HSP26 greater than 50-fold under conditions in which transcription of non-heat-shock genes is blocked. By using an episomal HSP82-lacZ fusion gene, we present evidence that lyticase and thiolutin induce heat shock gene expression at the level of transcription, whereas phenanthroline acts at a subsequent step, likely through message stabilization. We conclude that, because of the exquisite sensitivity of the yeast heat shock response, procedures designed to measure the rate of gene transcription or mRNA turnover can themselves impact upon each process.
BEHAVIOR AND BLADDER DISTURBANCE OF ENURETIC CHILDREN: A RATIONAL CLASSIFICATION OF A COMMON DISORDER

A group of 126 enuretic children were evaluated as to their psychiatric and neurological states, functional bladder volume and environmental circumstances. Few differences were found when the children were grouped according to presence or absence of social disadvantage, the presence of a family history of enuresis, or the nature of onset of enuresis. No classification differentially predicted response to treatment. However. children with an associated psychiatric disorder had significantly lower bladder volumes and had more developmental delays. It is concluded that the classifications of primary or secondary enuresis, or familial or non‐familial, etc., are of little practical value. When psychiatric disorder is found, it is probably related to other constitutional abnormalities. Rather than there being two separate groups of enuretic children with behavior disorder and low functional bladder volume, these two abnormalities are found in conjunction.
Simulation for assessing statistical methods of biologic terrorism surveillance.

INTRODUCTION Multiple systems have been developed that use surveillance of health-care encounters to provide early warning of a terrorist attack. Limited practical experience and the absence of adequate theoretical assessments have precluded determining which alarm-generating algorithms should be preferred. In the absence of practical and theoretical results, choosing a particular statistical algorithm can be difficult. One way to evaluate algorithms is through simulation. OBJECTIVES This report describes conceptual features of an example simulation based on the dispersal of anthrax spores and presents results based on the example simulation. METHODS A simulation was implemented based on the dispersal of anthrax spores from a crop-dusting plane. Simulated cases were then included into an observed data stream. Detection approaches included SaTScan trade mark and small area regression and testing (SMART) scores. An evaluation metric was developed for comparison of results. In addition, a simulation of a separate data stream was added; and then separate and combined surveillance data were compared. RESULTS In the simulation in which a single data stream was used, the two statistical approaches were substantially similar in performance. The combined surveillance based on two data streams is superior to surveillance based on either stream separately. CONCLUSION The other potential uses of such a system are considered. These uses include the comparison of different data sources (e.g., outpatient versus emergency department and evaluating the impact of potential changes to the surveillance system, and increasing the population under surveillance). Simulation is a valuable technique for evaluating and planning for syndromic surveillance.
Experimental study of POS lever-arm error compensation

The Position and Orientation measurement System (POS) is an important part of airborne remote sensing system, it is mainly used to measure and compensate the motion errors of airborne sensors. As a kind of high accuracy measurement system, compensation of dynamic errors is an important part to improve the accuracy of POS. Inner lever-arm error which called size effect is a typical dynamic error, in this paper, theoretical analysis of size effect and how to deal with different kind of size effect error is presented, through simulation analysis and experimental study, the relationship between size effect and system vibration input characteristic is illustrated, finally, after the comparison of position navigation errors in different frequency and amplitude vibration input condition, the rationality of analysis in this paper is validated.
Sparse Poisson Latent Block Model for Document Clustering

Over the last decades, several studies have demonstrated the importance of co-clustering to simultaneously produce groups of objects and features. Even to obtain object clusters only, using co-clustering is often more effective than one-way clustering, especially when considering sparse high dimensional data. In this paper, we present a novel generative mixture model for co-clustering such data. This model, the Sparse Poisson Latent Block Model (SPLBM), is based on the Poisson distribution, which arises naturally for contingency tables, such as document-term matrices. The advantages of SPLBM are two-fold. First, it is a rigorous statistical model which is also very parsimonious. Second, it has been designed from the ground up to deal with data sparsity problems. As a consequence, in addition to seeking homogeneous blocks, as other available algorithms, it also filters out homogeneous but noisy ones due to the sparsity of the data. Experiments on various datasets of different size and structure show that an algorithm based on SPLBM clearly outperforms state-of-the-art algorithms. Most notably, the SPLBM-based algorithm presented here succeeds in retrieving the natural cluster structure of difficult, unbalanced datasets which other known algorithms are unable to handle effectively.
Clinical Diagnosis of Dementia with Lewy Bodies in a Japanese Dementia Registry

We found 15 patients with dementia with Lewy bodies (DLB) and 232 patients with Alzheimer’s disease (AD) among 327 consecutive patients with mild to moderate dementia in a Japanese dementia registry, using the clinical criteria of the Consortium on DLB International Workshop. The percentage of females was significantly lower in DLB than in AD (p < 0.01), while age at examination, Mini-Mental State Examination score and duration of cognitive symptoms were comparable between the two diseases. Eight of the 15 DLB patients (53%) had spontaneous parkinsonism, which was observed in 6 of the 232 AD patients (2.6%). Visual hallucinations were reported by 11 of the 15 DLB patients (73%) and 8 of the 232 AD patients (3.4%). Cognitive fluctuation was positive in 13 of the 15 DLB patients (87%). We found two types of episodic cognitive deterioration: one was characterized by pronounced disturbances of attention and alertness (inattention type), and the other was characterized by marked and bizarre disturbances of orientation in time and places, and misidentification of persons (disorientation type). Systematized delusion was observed in 8 DLB patients, and 5 patients showed neuroleptic sensitivity. Patients with DLB have a unique dementia syndrome even in the stage of mild to moderate cognitive impairments. Further studies are recommended to establish diagnosis, treatment and management.
A control method for soft robots based on artificial musles

This paper describes simply a method how to control air muscles of lower limbs of an artificial life body developed recently(called "Ichiro"), at the Artificial Life and Robotics Laboratory of Oita University, Japan, by using compressed air controllers. The number of total air muscles is 22 where 11 air muscles are arranged in each leg. The experimental video results for controlling 24 air muscles of lower limes of "Ichiro" from stand up position to sit down position on a chair and from the sit down position on the chair to the stand up position are shown. Also, The experimental video data of a standing up on one leg and various leg movement are shown. The paper gives the brief description of the proposed control method.
A View from the other side: engaging retailers in tobacco point-of-sale reform in Allegheny County

Tobacco use disproportionately affects African Americans in Allegheny County, Pennsylvania compared to both the national rate of African Americans and that of Whites in Allegheny County, with many implications for adverse chronic disease health outcomes. Tobacco industry targeted marketing practices have historically resulted in legislation that shifted tobacco marketing to retail stores at the point-of-sale, where storeowners are uniquely situated as stakeholders in the retail environment and the community. This original investigation analyzes interviews with storeowners (n=6) of different types of corner stores in Allegheny County to inform and recommend future programming and policy approaches for the Allegheny County Health Department (ACHD) and partners that reduce tobacco exposure and marketing in the community. The findings indicate that storeowners in the sample determine their product mix and the inclusion or exclusion of tobacco products based on a dynamic interaction between business planning, customer input, and individual decision-making processes. Storeowners highlighted that many opportunities exist to reform the corner stores in Allegheny County through partnerships, store facade and interior improvements, incentives, and community engagement. An integration of these approaches can act to provide assistance such as improvements to the product mix, produce sourcing, and targeted marketing and advertising outreach to increase foot traffic through stores, all while engaging storeowners in the reform process. Tobacco control programs and policies that aim to reduce tobacco exposure in our communities must acknowledge that the built environment has an enormous impact on public health, and improvements have the ability to contribute to more equitable opportunities to be healthy.
Portable checkpointing and recovery

This paper presents a checkpointing scheme that was implemented in a parallel library that runs on top of CHIMP/MPI. The main goals of the checkpointing mechanism are portability and efficiency. It runs on every platform supported by MPI in a machine-independent way. The scheme allows the migration of checkpoints and offers a flexible recovery mechanism based on data-reconfiguration. Some performance results will be presented at the end of the paper together with some techniques that can be used to increase the efficiency of the checkpointing mechanism.
Age‐Associated Alteration in the Expression of Synapsin I mRNA in the Rat Central Nervous System

Aging is characterized by a decline in the neuroplastic responses in the brain which, in turn, may account for the age-associated deterioration of cerebral function. Spatial memory, a form of episodic memory severely affected in human dementia, is also impaired in aged rodents. Although many areas of the brain have been implicated in spatial memory processes, a main role has been ascribed to the hippocampal formation and its main afferent systems, the cholinergic septohippocampal and glutamatergic entorhinodentate pathways. ],* The molecular basis of learning and memory are still far from being understood. A crucial role is likely played by proteins that participate in synaptic function, such as B-50.3 B-50 is a presynaptic phosphoprotein that is considered a marker for neuronal plasticity. In the rat hippocampus, changes in B-50 pho~phorylat ion~ have been correlated with long-term potentiation, a measure of synaptic plasticity. Moreover, B-50 has been shown to play a role in neurotransmitter r e l e a ~ e , ~ possibly by acting in concert with the synaptic vesicole-associated protein Synapsin I (Syn I). The relation between B-50 and Syn I is still speculative and is thought to be mediated by protein kinase C and Ca2+-calmodulin-dependent phosphorylation. In the aged rat hippocampus the decrement in B-50 phosphorylation6 and content’ may be correlated with the age-associated decline in neurotransmitter release. In this study we assessed whether old animals with spatial memory deficits had reduced levels of B-50 and Syn I mRNA and whether these parameters were influenced by chronic phosphatidylserine (PS) administration. Young adult (5 months) and aged (24 months) Sprague-Dawley rats were tested in a water maze for spatial memory. Aged rats with spatial memory impairment (old impaired) were given PS in the drinking water for 3 months, starting 1 week after the screening test. At the age of 27 months, the animals were sacrificed, and total mRNA extracted from the neocortex and hippocampus was processed for Northern blot analysis and autoradiography. B-50-mRNA levels were not significantly different in cortical areas of both aged impaired and nonimpaired rats (FIG. 1). This finding suggests that the reported age-associated decline in protein content might be related to alterations in the neuronal machinery involved in mRNA translation, protein synthesis, or both. Significant loss of Syn I mRNA was observed in the frontoparietal cortex of old animals with spatial memory deficits (FIG. 2). This could be linked to synaptic loss that occurs with aging in the neocortex and/or to the age-associated decrement in synaptic function.
Streptococcus pneumoniae forms surface-attached communities in the middle ear of experimentally infected chinchillas.

BACKGROUND Streptococcus pneumoniae (pneumococcus) causes respiratory and systemic infections that are a major public health problem worldwide. It has been postulated that pneumococci persist in vivo in biofilm communities. METHODS In this study, we analyzed whether pneumococci form biofilms in vivo, and if so, whether biofilms correlated with bacterial persistence. Chinchillas were infected with S. pneumoniae TIGR4 and euthanized at varying times after infection, after which the superior ear bullae were excised and examined by culture and microscopy. RESULTS Dense material, resembling the biofilms of other otitis media pathogens, was visible in the middle ear as late as 12 days after infection. Scanning electron microscopy revealed bacteria within an electron-dense matrix, similar to pneumococcal biofilms formed in vitro. Viability staining revealed groups of viable diplococci, as well as viable and nonviable host cells, attached to a fibrous matrix that was positive when stained with propidium iodide. Cryosections of biofilms were treated with polyclonal antibodies against the pneumococcal surface components pneumococcal surface protein A family 2, pneumococcal surface protein C, choline-binding protein, and neuraminidase, coupled with appropriate secondary antibody conjugates. Immunofluorescent staining showed the presence of pneumococcal communities within the material recovered from the middle ear chamber. CONCLUSIONS On the basis of these data, we conclude that pneumococci form biofilms in vivo and that this process may be intertwined with the formation of neutrophil extracellular traps. These findings provide new insights into the potential causes of antibiotic treatment failure and bacterial persistence in chronic pneumococcal otitis media.