Miracle-dz/UniFAR-FTUs huggingface dataset:
The Birth and Death of Human Single-nucleotide Polymorphisms: New Experimental Evidence and Implications for Human History and Medicine Life Cycle of a Snp

Extensive, new databases of single-nucleotide polymorphisms (SNPs) provide a powerful resource for disease gene discovery, and they will be even more useful as more frequency data become available. Interesting observed genomic patterns include SNP deserts (regions of low SNP incidence) and lengthy regions of linkage disequilibrium containing only a few haplotypes. A variety of genetic studies will benefit from SNP resources. The desire to test the promising approach of studying complex traits by genetic association has spurred the recent explosion in discovery of human single-nucleotide polymorphisms (SNPs). For Mendelian diseases with high penetrance due to mutations in a single gene, pedigree studies have been very successful in mapping the disease loci. However, for complex diseases, those caused by multiple disease genes of modest effect, the number of families required is not practical and the results obtained for the families are not additive. In theory, association studies comparing the prevalence of a set of markers in a moderate number of affected and unaffected individuals, could localize high frequency, complex disease alleles due to underlying non-random association in short stretches of the genome, if enough genetic markers were available (1). A major motivation to find human SNPs and record them in public databases was to provide freely available markers for genome-wide association studies (2). Major, successful SNP search efforts were mounted, and the past 2 years have truly been an era of SNP discovery and seen the birth of a new SNP collection. As part of the publication of the draft human genome sequence in February, 2001, 1.42 million SNPs were reported (1.69 million as of June, 2001) (3). These are available in several databases including dbSNP at NCBI The SNPs designated 'rs' (for reference SNP) in dbSNP represent a non-redundant set, since many have been found by more than one strategy. One highly efficient discovery method was to compare DNA sequences from overlapping clones sequenced for the human genome project, using statistical methods to identify candidate SNPs versus sequencing noise. If the clones were derived from the same chromosome, there should be no differences, but if derived from maternal and paternal chromosomes or from different individuals, one finds SNPs at the rate of approximately 1 per 1000 bp (4,5). The other major effort was lead by The SNP Consortium (TSC), a group formed by the Wellcome Trust and a number of companies. The TSC funded academic groups to sequence 'reduced representation' …
Identification of a Novel Small RNA Modulating Francisella tularensis Pathogenicity

Francisella tularensis is a highly virulent bacterium responsible for the zoonotic disease tularemia. It is a facultative intracellular pathogen that replicates in the cytoplasm of host cells, particularly in macrophages. Here we show that F. tularensis live vaccine strain (LVS) expresses a novel small RNA (sRNA), which modulates the virulence capacities of the bacterium. When this sRNA, designated FtrC (for Francisella tularensis RNA C), is expressed at high levels, F. tularensis replicates in macrophages less efficiently than the wild-type parent strain. Similarly, high expression of FtrC reduces the number of viable bacteria recovered from the spleen and liver of infected mice. Our data demonstrate that expression of gene FTL_1293 is regulated by FtrC. Furthermore, we show by in vitro gel shift assays that FtrC interacts specifically with FTL_1293 mRNA and that this happens independently of the RNA chaperone Hfq. Remarkably, FtrC interacts only with full-length FTL_1293 mRNA. These results, combined with a bioinformatic analysis, indicate that FtrC interacts with the central region of the mRNA and hence does not act by sterically hindering access of the ribosome to the mRNA. We further show that gene FTL_1293 is not required for F. tularensis virulence in vitro or in vivo, which indicates that another unidentified FtrC target modulates the virulence capacity of the bacterium.
Beyond Population: Everyone Counts in Development

This essay reviews important demographic trends expected to occur between 2010 and 2050, indicates some of their implications for economic and global development, and suggests some possible policies to respond these trends and implications. The century from 1950 to 2050 will have witnessed the highest global population growth rate ever, the largest voluntary fall in the global population growth rate ever, and the most enormous demographic shift ever between the more developed and less developed regions. In the coming half century, according to most demographers, the world’s population will grow older, larger (albeit more slowly), and more urban than in the 20th century, but with much variance within and across regions. No one knows what population and demographic characteristics of humans are sustainable, but it is clear that having a billion or people chronically hungry today results from collective human choices, not biophysical necessities. Concrete policy options to respond to demographic trends include providing universal primary and secondary education, eliminating unmet needs for contraception and reproductive health, and implementing demographically sensitive urban planning, particularly construction for greater energy efficiency and for an aging population.
Composición química, actividad antibacteriana y tóxica de aceites esenciales de seis especies medicinales de lamiaceae en el estado de Hidalgo

En la flora medicinal del estado de Hidalgo la familia lamiaceae ocupa el tercer lugar en cuanto al numero de especies utilizadas. Estas plantas tienen un alto contenido de aceites esenciales que pudieran ser los responsables de su efecto medicinal. Se seleccionaron seis especies de lamiaceae, hedeoma drummondii benth. , hedeoma piperitum benth. , hyptis verticillata jacq. , mentha rotundifolia (L.) huds. , salvia elegans vahl. y salvia microphylla kunth.
Periodic tilting of Saturn's plasma sheet

From the vantage of the dawn sector, the INCA instrument on Cassini imaged neutral hydrogen atoms (20–50 keV) emitted from the center of the Saturn's plasma sheet for five days during late 2004. Points along the center of the plasma sheet were found from contoured images projected onto the noon‐midnight plane; points within 20 RS of Saturn were fitted to straight lines, and the slopes of these lines were examined as a function of time at one hour resolution. The slopes vary between ∼17° and ∼24° with a period of 10.80 hours, the same as that of Saturn kilometric radiation (SKR). This periodic tilting of the plasma sheet is in phase with SKR radiation in the sense that the maximum tilt angle occurs when the maximum in the SKR power occurs, and the tilt angle periodicity has a phase angle of ∼47° in SLS‐3 longitude.
Fossil eggs and Cenozoic continental biostratigraphy of Namibia

One kind of aepyornithoid and six kinds of struthious eggshells have been found in Cenozoic deposits of Namibia. Field evidence indicates that the six struthious egg types are time successive, and they thus form a useful basis for determining the relative stratigraphic positions of sites at which they occur. Their placement in the geological time scale has been partly tied down by reference to the biostratigraphic position of mammals that occur in association with them.
Familial amyotrophic lateral sclerosis is associated with a mutation in D-amino acid oxidase

We report a unique mutation in the D-amino acid oxidase gene (R199W DAO) associated with classical adult onset familial amyotrophic lateral sclerosis (FALS) in a three generational FALS kindred, after candidate gene screening in a 14.52 cM region on chromosome 12q22-23 linked to disease. Neuronal cell lines expressing R199W DAO showed decreased viability and increased ubiquitinated aggregates compared with cells expressing the wild-type protein. Similarly, lentiviral-mediated expression of R199W DAO in primary motor neuron cultures caused increased TUNEL labeling. This effect was also observed when motor neurons were cocultured on transduced astrocytes expressing R199W, indicating that the motor neuron cell death induced by this mutation is mediated by both cell autonomous and noncell autonomous processes. DAO controls the level of D-serine, which accumulates in the spinal cord in cases of sporadic ALS and in a mouse model of ALS, indicating that this abnormality may represent a fundamental component of ALS pathogenesis.
Reactive oxygen species as mediators of organ dysfunction caused by sepsis, acute respiratory distress syndrome, or hemorrhagic shock: potential benefits of resuscitation with Ringer's ethyl pyruvate solution

Reactive oxygen species are reactive, partly reduced derivatives of molecular oxygen. Important reactive oxygen species in biological systems include superoxide radical anion, hydrogen peroxide, and hydroxyl radical. Peroxynitrite, is another important species in biological systems. A variety of enzymatic and non-enzymatic processes can generate reactive oxygen species in mammalian cells. An extensive body of experimental evidence from studies using animal models supports the view that reactive oxygen species are important in the pathogenesis of ischemia-reperfusion syndromes, sepsis, acute respiratory distress syndrome, and multiple organ dysfunction syndrome. This view is further supported by data from clinical studies that correlate biochemical evidence of reactive oxygen species-mediated stress with the development of acute respiratory distress syndrome or sepsis in patients. Ethyl pyruvate, a simple derivative of pyruvic acid, has been shown to be efficacious in several animal models of critical illness, and warrants further evaluation in this regard.
Applications of DNA barcoding to fish landings: authentication and diversity assessment

Abstract DNA barcoding methodologies are being increasingly applied not only for scientific purposes but also for diverse real-life uses. Fisheries assessment is a potential niche for DNA barcoding, which serves for species authentication and may also be used for estimating within-population genetic diversity of exploited fish. Analysis of single-sequence barcodes has been proposed as a shortcut for measuring diversity in addition to the original purpose of species identification. Here we explore the relative utility of different mitochondrial sequences (12S rDNA, COI, cyt b, and D-Loop) for application as barcodes in fisheries sciences, using as case studies two marine and two freshwater catches of contrasting diversity levels. Ambiguous catch identification from COI and cyt b was observed. In some cases this could be attributed to duplicated names in databases, but in others it could be due to mitochondrial introgression between closely related species that may obscure species assignation from mtDNA. This last problem could be solved using a combination of mitochondrial and nuclear genes. We suggest to simultaneously analyze one conserved and one more polymorphic gene to identify species and assess diversity in fish catches.
EMG-based hand gesture recognition with flexible analog front end

Conditioning and processing of biological signals represent interesting challenges for wearable electronics in health applications. Information gathering from these signals requires complex hardware circuitry and dedicated computation resources. The design of innovative analog front-end integrated circuits, combined with efficient signal processing algorithms, allows the development of platforms for monitoring, activity and gesture recognition based on embedded real-time systems. This paper describes an Electromyography pattern recognition system based on the combination of low cost passive sensors, an innovative analog front-end and a low power microcontroller. The performance of the proposed system matches state-of-the-art high-end active sensors, opening the way to the development of affordable and accurate wearable devices.
MACROSCOPIC WORKLOAD MODEL FOR ESTIMATING EN ROUTE SECTOR CAPACITY

Under ideal weather conditions, each en route sector in an air traffic management (ATM) system has a certain maximum operational traffic density that its controller team can safely handle with nominal traffic flow. We call this the design capacity of the sector. Bad weather and altered flow often reduce sector capacity by increasing controller workload. We refer to sector capacity that is reduced by such conditions as dynamic capacity. When operational conditions cause workload to exceed the capability of a sector’s controllers, air traffic managers can respond either by reducing demand or by increasing design capacity. Reducing demand can increase aircraft operating costs and impose delays. Increasing design capacity is usually accomplished by assigning more control resources to the airspace. This increases the cost of ATM. To ensure full utilization of the dynamic capacity and efficient use of the workforce, it is important to accurately characterize the capacity of each sector. Airspace designers often estimate sector capacity using microscopic workload simulations that model each task imposed by each aircraft. However, the complexities of those detailed models limit their realtime operational use, particularly in situations in which sector volumes or flow directions must adapt to changing conditions. To represent design capacity operationally in the United States, traffic flow managers define an acceptable peak traffic count for each sector based on practical experience. These subjective thresholds— while usable in decision-making—do not always reflect the complexity and geometry of the sectors, nor the direction of the traffic flow. We have developed a general macroscopic workload model to quantify the workload impact of traffic density, sector geometry, flow direction, and air-to-air conflict rates. This model provides an objective basis for estimating design capacity. Unlike simulation models, this analytical approach easily extrapolates to new conditions and allows parameter validation by fitting to observed sector traffic counts. The model quantifies coordination and conflict workload as well as observed relationships between sector volume and controller efficiency. The model can support real-time prediction of changes in design capacity when traffic is diverted from nominal routes. It can be used to estimate residual airspace capacity when weather partially blocks a sector. Its ability to identify dominant manual workload factors can also help define the benefits and effectiveness of alternative concepts for automating labor-intensive tasks.
Understanding the Relationship between Rainstorm-Related Experiences and PTSD among Chinese Adolescents after Rainstorm Disaster: The Roles of Rumination and Social Support

Posttraumatic stress disorder (PTSD) is prevalent among adolescents following natural disasters, and the trauma experiences represent a critical risk factor for PTSD. Nevertheless, the underlying mechanism of adolescents’ PTSD following trauma experiences remains unclear. Rumination appears to be a mediating factor between trauma experiences and PTSD, and social support may moderate this mediating relationship between trauma experiences, rumination, and PTSD, but few studies have examined these assumptions. Thus, this study aimed to assess the mediating role of rumination and the moderating role of social support in the relationship between rainstorm-related experiences and PTSD among adolescents, following a rainstorm in China. Nine hundred and fifty-one middle school students completed self-report questionnaires, and structural equation modeling was conducted to examine the potential moderated mediation effect. Rainstorm-related experiences had a direct and positive effect on PTSD, and also indirectly influenced PTSD via rumination. Moreover, social support work to buffer the direct effect of rainstorm-related experiences on PTSD, but not the effect of rumination on PTSD. Implications for clinical practice and research are discussed along with study limitations.
Soils of the Serengeti Woodlands Tanzania

Soils were surveyed in the woodlands of the Serengeti National Park in north-west Tanzania. The Serengeti Woodlands have been covered by volcanic deposits that have influenced chemical properties to a large extent. Physical characteristics were studied too in detail. The distribution of woodland and grassland correlated with infiltration rate and depth the moisture front reached after infiltration. A neutron probe was used for the soil moisture study. Especially in grassland areas frequented by large herds of herbivores, effective rainfall was less than half the actual rainfall. Mineralogical studies revealed that the clay fraction of the soils of the Serengeti Woodlands consisted almost entirely of X-ray amorphous material.
Enterprise Models as Drivers for IT Security Management at Runtime

This paper describes how enterprise models can be made suitable for monitoring and controlling IT security at runtime. A holistic modeling method is proposed that extends enterprise models with runtime information, turning them into dashboards for managing security incidents and risks, and supporting decision making at runtime. The requirements of such a modeling method are defined and an existing enterprise modeling language is extended with relevant security concepts that also capture runtime information to satisfy these requirements. Subsequently, the resulting modeling method is evaluated against the previously defined requirements. It is also shown that common metamodeling frameworks are not suitable for implementing a modeling environment that results in suitable IT security dashboards. This leads to suggesting implementation of the modeling environment using the eXecutable Modeling Facility.
Computational stabilization of human growth hormone

Recombinant human growth hormone (hGH) is used worldwide for the treatment of pediatric hypopituitary dwarfism and in children suffering from low levels of hGH. It has limited stability in solution, and because of poor oral absorption, is administered by injection, typically several times a week. Development has therefore focused on more stable or sustained‐release formulations and alternatives to injectable delivery that would increase bioavailability and make it easier for patients to use. We redesigned hGH computationally to improve its thermostability. A more stable variant of hGH could have improved pharmacokinetics or enhanced shelf‐life, or be more amenable to use in alternate delivery systems and formulations. The computational design was performed using a previously developed combinatorial optimization algorithm based on the dead‐end elimination theorem. The algorithm uses an empirical free energy function for scoring designed sequences. This function was augmented with a term that accounts for the loss of backbone and side‐chain conformational entropy. The weighting factors for this term, the electrostatic interaction term, and the polar hydrogen burial term were optimized by minimizing the number of mutations designed by the algorithm relative to wild‐type. Forty‐five residues in the core of the protein were selected for optimization with the modified potential function. The proteins designed using the developed scoring function contained six to 10 mutations, showed enhancement in the melting temperature of up to 16°C, and were biologically active in cell proliferation studies. These results show the utility of our free energy function in automated protein design.
Test Data and Test Time Reduction for LOS Transition Test in Multi-Mode Segmented Scan Architecture

Launch-off-Shift (LOS) is a widely used technique for delay test in scan-based design. Test data compression for LOS patterns, however, is less efficient. In this paper, we first analyze the reason for low compression rate in LOS patterns, and present an LOS test enabled scan architecture that supports three operation modes: broadcast, multicast, and serial. Efficient LOS test data compression can be achieved under this architecture with limited hardware overhead. An ATPG method for LOS test patterns under the proposed architecture is also presented. Experimental results show that most of the serial scan operations can be replaced by multicast operations, and thus achieve much better compression rate.
Structure of a DNA Glycosylase Searching for Lesions

DNA glycosylases must interrogate millions of base pairs of undamaged DNA in order to locate and then excise one damaged nucleobase. The nature of this search process remains poorly understood. Here we report the use of disulfide cross-linking (DXL) technology to obtain structures of a bacterial DNA glycosylase, MutM, interrogating undamaged DNA. These structures, solved to 2.0 angstrom resolution, reveal the nature of the search process: The protein inserts a probe residue into the helical stack and severely buckles the target base pair, which remains intrahelical. MutM therefore actively interrogates the intact DNA helix while searching for damage.
Critical Survey of the Freely Available Arabic Corpora

The availability of corpora is a major factor in building natural language processing applications. However, the costs of acquiring corpora can prevent some researchers from going further in their endeavours. The ease of access to freely available corpora is urgent needed in the NLP research community especially for language such as Arabic. Currently, there is not easy was to access to a comprehensive and updated list of freely available Arabic corpora. We present in this paper, the results of a recent survey conducted to identify the list of the freely available Arabic corpora and language resources. Our preliminary results showed an initial list of 66 sources. We presents our findings in the various categories studied and we provided the direct links to get the data when possible.
Developments in satellite radar altimetry

This paper briefly overviews the status of the research in the development of new altimeter systems presently carried out in Alenia Spazio S.p.A. in the frame of internal research activities and ESA feasibility study contracts. In particular, the concepts of synthetic aperture and interferometric altimetry or global ice/land topography are reviewed in this paper. These system designs are extremely promising, since they can overcome the limitations of the classic nadir-looking pulse limited systems. Conventional system in fact, in spite of the extremely high range accuracy achievable over oceans, are unable to provide topographic details over ice or land due to their coarse horizontal resolution, several hundreds od meters against the 100-300 m required in ice/land topography applications.