Miracle-dz/UniFAR-FTUs huggingface dataset:
Extensions of the UNIX File Command and Magic File for File Type Identification

File format identification is a core requirement for digital archives. The UNIX file command is among the most promising technologies for file type identification. This report describes extensions to the file command and magic file that enhance their utility for file format identification in archival systems. A File Format Library (database) has been created to manage information about file formats. This information includes file format name, MIME type, PRONOM Universal Identifier and file signature tests. There is a one-to-one correspondence between file formats and file signature tests. Precedence relations between file signature tests are explicitly expressed in the database. Published specifications for file formats are also collected in the library and are used to determine file signatures for the formats. When specifications have not been published for a file format, samples for files in those formats have been collected and analyzed to determine possible file signatures. File signature tests have been created for more than 800 file formats. Sample files for more than 500 of the file formats in the library have been created or collected for testing of the file signatures. These examples are included in the library The Library includes links to file format software resources that are needed in archival processing of digital records. These include: file viewers/players, archive extractors, file format converters, password recovery software and repairers for damaged files. The File Format Library supports the creation of a magic file from the file signature tests in the Library. The GTRI File Type Identifier is a graphical user interface to the file command and the magic file created from the File Format Library. The file command and magic tests have been applied to examples of 500+ file formats from the File Format Library. These tests have led to refinement of the file signature tests and discovery of the precedence relationships among file signature tests. The National Archives (TNA) of the UK provides a public registry of file format information (PRONOM). This information includes file signature patterns expressed as regular expressions. TNA also provides a tool (DROID) that uses these file signature patterns for file format identification. This approach to file type identification is also promising and seems to be primarily limited by the small number of file signature patterns in the PRONOM registry. GTRI is collaborating with TNA to enhance the content of the registry and the performance of the DROID file format identifier.
High-Resolution Analysis of Cytosine Methylation in Ancient DNA

Epigenetic changes to gene expression can result in heritable phenotypic characteristics that are not encoded in the DNA itself, but rather by biochemical modifications to the DNA or associated chromatin proteins. Interposed between genes and environment, these epigenetic modifications can be influenced by environmental factors to affect phenotype for multiple generations. This raises the possibility that epigenetic states provide a substrate for natural selection, with the potential to participate in the rapid adaptation of species to changes in environment. Any direct test of this hypothesis would require the ability to measure epigenetic states over evolutionary timescales. Here we describe the first single-base resolution of cytosine methylation patterns in an ancient mammalian genome, by bisulphite allelic sequencing of loci from late Pleistocene Bison priscus remains. Retrotransposons and the differentially methylated regions of imprinted loci displayed methylation patterns identical to those derived from fresh bovine tissue, indicating that methylation patterns are preserved in the ancient DNA. Our findings establish the biochemical stability of methylated cytosines over extensive time frames, and provide the first direct evidence that cytosine methylation patterns are retained in DNA from ancient specimens. The ability to resolve cytosine methylation in ancient DNA provides a powerful means to study the role of epigenetics in evolution.
Levodopa in combination with carbidopa does not affect plasma arginine vasopressin levels in treatment-naïve older patients with Parkinson's disease: A before-after study.

OBJECTIVE Several cases of syndrome of inappropriate antidiuresis (SIAD) induced by antiparkinson agents have been reported. Our previous study demonstrated that in some patients with Parkinson's disease (PD), pergolide and pramipexole stimulate elevations of plasma arginine vasopressin (AVP) levels even at doses that are lower than the ordinary maintenance dose. Although mean plasma AVP levels are significantly higher in treated PD patients than in treatment-naïve patients, neither disease severity nor levodopa/carbidopa dosage (range, 300/30-850/85 mg) correlates with plasma AVP levels. However, the effects of levodopa/carbidopa monotherapy on plasma AVP levels in older patients remain unknown. To address this issue, a 14-day before-after study was conducted. METHODS Subjects in this study were consecutive treatment-naïve patients with a diagnosis of possible PD who visited our clinic from November 2008 to September 2009. Patients had no conditions that could be associated with high plasma AVP levels. Twenty-five patients were treated with levodopa/carbidopa (100/10 mg) 3 times a day. A paired t-test was used to compare plasma AVP levels before and 14 days after initiation of treatment. RESULTS Five patients dropped out of this study. In the remaining 20 patients (8 males and 12 females), no significant differences were observed between mean plasma AVP levels before and during treatment with levodopa/carbidopa. CONCLUSION Monotherapy with levodopa/carbidopa (300/30 mg/day) does not affect plasma AVP levels in older PD patients and seems less likely to cause SIAD.
Exhumation, crustal deformation, and thermal structure of the Nepal Himalaya derived from the inversion of thermochronological and thermobarometric data and modeling of the topography

duplex initiated at 9.8 ± 1.7 Ma, leading to an increase of uplift rate at front of the High Himalaya from 0.9 ± 0.31 to 3.05 ± 0.9 mm yr −1 . We also run 3‐D models by coupling PECUBE with a landscape evolution model (CASCADE). This modeling shows that the effectoftheevolvingtopographycanexplainafractionofthescatterobservedinthedatabut not all of it, suggesting that lateral variations of the kinematics of crustal deformation and exhumationarelikely.Ithasbeenarguedthatthesteepphysiographictransitionatthefootof the Greater Himalayan Sequence indicates OOS thrusting, but our results demonstrate that the best fit duplex model derived from the thermochronological and thermobarometric data reproduces the present morphology of the Nepal Himalaya equally well.
The Interplay Between Goal Intentions and Implementation Intentions

Two studies tested whether action control by implementation intentions is sensitive to the activation and strength of participants’ underlying goal intentions. In Study 1, participants formed implementation intentions (or did not) and their goal intentions were measured. Findings revealed a significant interaction between implementation intentions and the strength of respective goal intentions. Implementation intentions benefited the rate of goal attainment when participants had strong goal intentions but not when goal intentions were weak. Study 2 activated either a task-relevant or a neutral goal outside of participants’ conscious awareness and found that implementation intentions affected performance only when the relevant goal had been activated. These findings indicate that the rate of goal attainment engendered by implementation intentions takes account of the state (strength, activation) of people’s superordinate goal intentions.
Protein function influences frequency of encoded regions containing VNTRs and number of unique interactions

Proteins encoded by genes containing regions of variable number tandem repeats (VNTRs) are known to be polymorphic within species but the influence of their instability in molecular interactions remains unclear. VNTRs are overrepresented in encoding sequence of particular functional groups where their presence could influence protein interactions. Using human consensus coding sequence, this work examines if genomic instability, determined by regions of VNTRs, influences the number of protein interactions. Findings reveal that, in relation to protein function, the frequency of unique interactions in human proteins increase with the number of repeated regions. This supports experimental evidence that repeat expansion may lead to an increase in molecular interactions. Genetic diversity, estimated by Ka/Ks, appeared to decrease as the number of protein-protein interactions increased. Additionally, G+C and CpG content were negatively correlated with increasing occurrence of VNTRs. This may indicate that nucleotide composition along with selective processes can increase genomic stability and thereby restrict the expansion of repeated regions. Proteins involved in acetylation are associated with a high number of repeated regions and interactions but a low G+C and CpG content. While in contrast, less interactive membrane proteins contain a lower number of repeated regions but higher levels of C+G and CpGs. This work provides further evidence that VNTRs may provide the genetic variability to generate unique interactions between proteins.
Dose Related Absorption of JP-8 Jet Fuel Hydrocarbons Through Porcine Skin with Quantitative Structure Permeability Relationship Analysis

The effects of dosage on the percutaneous absorption of jet fuel hydrocarbons is not clear, yet is essential for human risk assessment. The present study is an ongoing approach to assess the dose-related percutaneous absorption of a number of aliphatic and aromatic hydrocarbons. The first treatment (1X) was comprised of mixtures containing undecane (4.1%), dodecane (4.7%), tridecane (4.4%), tetradecane (3%), pentadecane (1.6%), naphthalene (1.1%), and dimethyl naphthalene (1.3% of jet fuels) in hexadecane solvent using porcine skin flow through diffusion cell. Other treatments (n = 4 cells) were 2X and 5X concentrations. Perfusate samples were analyzed with gas chromatography-flame ionization detector (GC-FID) using head space solid phase micro-extraction fiber technique. We have standardized the assay to have a good linear correlation for all the tested components in media standards. Absorption parameters including diffusivity, permeability, steady state flux, and percent dose absorbed were estimated for all the tested hydrocarbons. This approach provides a baseline to access component interactions among themselves and with the diluent (solvents). A quantitative structure permeability relationship (QSPR) model was derived to predict the permeability of unknown jet fuel hydrocarbons in this solvent system by using their physicochemical parameters. Our findings suggested a dose related increase in absorption for naphthalene and dimethyl naphthalene (DMN).
Contributions of Letter-Speech Sound Learning and Visual Print Tuning to Reading Improvement: Evidence from Brain Potential and Dyslexia Training Studies

We use a neurocognitive perspective to discuss the contribution of learning letter-speech sound (L-SS) associations and visual specialization in the initial phases of reading in dyslexic children. We review findings from associative learning studies on related cognitive skills important for establishing and consolidating L-SS associations. Then we review brain potential studies, including our own, that yielded two markers associated with reading fluency. Here we show that the marker related to visual specialization (N170) predicts word and pseudoword reading fluency in children who received additional practice in the processing of morphological word structure. Conversely, L-SS integration (indexed by mismatch negativity (MMN)) may only remain important when direct orthography to semantic conversion is not possible, such as in pseudoword reading. In addition, the correlation between these two markers supports the notion that multisensory integration facilitates visual specialization. Finally, we review the role of implicit learning and executive functions in audiovisual learning in dyslexia. Implications for remedial research are discussed and suggestions for future studies are presented.
Color Constancy for RGB and Multispectral Images

The problem of inferring the light color for a scene is called Illuminant Estimation. This step forms the first task in many workflows in the larger task of discounting the effect of the color of the illuminant, which is called Color Constancy. Illuminant Estimation is typically used as a pre-processing step in many computer vision tasks. In this thesis, we tackle this problem for both RGB and multispectral images. First, for RGB images we extend a moments based method in several ways: firstly by replacing the standard expectation value, the mean, considering moments that are based on a Minkowski p-norm; and then secondly by going over to a float value for the parameter p and carrying out a nonlinear optimization on this parameter; and finally by considering a different expectation value, generated by using the geometric mean. We show that these strategies can drive down the median and maximum error of illuminant estimates. And then for multispectral images, we formulate a multiple-illuminants estimation problem as a Conditional Random Field (CRF) optimization task over local estimations. We then improve local illuminant estimation by incorporating spatial information in each local patch.
Polynomial Wigner-Ville distributions and their relationship to time-varying higher order spectra

The Wigner-Ville distribution (WVD) has optimal energy concentration for linear frequency modulated (FM) signals. This paper presents a generalization of the WVD in order to effectively process nonlinear polynomial FM signals. A class of polynomial WVD's (PWVD's) that give optimal concentration in the time-frequency plane for FM signals with a modulation law of arbitrary polynomial form are defined. A class of polynomial time-frequency distributions (PTFD's) are also defined, based on the class of PWVD's. The optimal energy concentration of the PWVD enables it to be used for estimation of the instantaneous frequency (IF) of polynomial FM signals. Finally, a link between PWVD's and time-varying higher order spectra (TVHOS) is established. Just as the expected value of the WVD of a nonstationary random signal is the time-varying power spectrum, the expected values of the PWVD's have interpretations as reduced TVHOS
The Role of Hypoxia in Glioblastoma Invasion

Glioblastoma multiforme (GBM), a grade IV astrocytoma, is the most common and deadly type of primary malignant brain tumor, with a patient’s median survival rate ranging from 15 to 17 months. The current treatment for GBM involves tumor resection surgery based on MRI image analysis, followed by radiotherapy and treatment with temozolomide. However, the gradual development of tumor resistance to temozolomide is frequent in GBM patients leading to subsequent tumor regrowth/relapse. For this reason, the development of more effective therapeutic approaches for GBM is of critical importance. Low tumor oxygenation, also known as hypoxia, constitutes a major concern for GBM patients, since it promotes cancer cell spreading (invasion) into the healthy brain tissue in order to evade this adverse microenvironment. Tumor invasion not only constitutes a major obstacle to surgery, radiotherapy, and chemotherapy, but it is also the main cause of death in GBM patients. Understanding how hypoxia triggers the GBM cells to become invasive is paramount to developing novel and more effective therapies against this devastating disease. In this review, we will present a comprehensive examination of the available literature focused on investigating how GBM hypoxia triggers an invasive cancer cell phenotype and the role of these invasive proteins in GBM progression.
Combined hyperlipidemia: familial but not (usually) monogenic

Purpose of review Combined hyperlipidemia (CHL) is a complex phenotype that is commonly encountered clinically and is often associated with the expression of early heart disease. The affixed adjective ‘familial’ gives the impression that the trait is monogenic, like familial hypercholesterolemia. But despite significant efforts, genetic studies have yielded little evidence of single gene determinants of CHL. Recent findings Sophisticated linkage studies suggest that individual lipid components of the CHL phenotype – such as elevated LDL and triglyceride – each have several determinants that segregate independently in families. Furthermore, DNA sequencing shows that rare large-effect variants in genes such as LDL receptor (LDLR) and lipoprotein lipase are found in some CHL patients, explaining the elevated LDL cholesterol and triglyceride components, respectively. In addition, multiple common small-effect lipid-altering variants accumulate in an individual's genome, raising the LDL cholesterol and/or triglyceride components by multiple mechanisms. Finally, secondary factors, such as poor diet, obesity,fatty liver or diabetes further modulate the expression of the biochemically defined CHL phenotype. Summary Given the current state of genetic understanding, CHL may be best conceptualized as a syndrome with common clinical presentation but multigenic causes, similar to other common conditions such as type 2 diabetes.
Sexual Reproduction of Interior Spruce (Pinaceae). I. Pollen Germination to Archegonial Maturation

Stages of normal sexual reproduction between pollen germination and egg maturation are described for interior spruce. These prezygotic stages were studied by light and electron microscopy in more detail than was possible in previous studies, and new observations have been made. Sperm (male gametes) formation and the organelles that accompany the sperm within the pollen tube are described. The pollen tube grows toward a lipid secretion that originates in the neck region of the archegonium. Megagametophyte development was followed from the early cellular stage through the series of mitoses that result in neck cells, the ventral canal cell, the central cell, and ultimately the egg. Maturation of the egg includes formation of modified plastids (formerly described as large inclusions) and small inclusions that are membrane‐bound regions of cytoplasm. At egg maturation, modified plastids are excluded from the mitochondria‐rich perinuclear zone that surrounds the nucleus. Small inclusions occupy the periphery of the cell so that the egg nucleus and perinuclear zone are centrally located. A second article in this series describes pollen tube entry into the archegonium, delivery of sperm to the egg, gamete fusion, and proembryo and embryo formation.
Providing end-to-end statistical delay guarantees with earliest deadline first scheduling and per-hop traffic shaping

This paper develops a framework for statistically guaranteeing end-to-end delay bounds to leaky-bucket-constrained flows transporting real-time traffic in a network of switches using earliest deadline first (EDF) packet scheduling and per-hop traffic shaping. We first analyze the delay-bound violation probabilities at an isolated EDF scheduler fed by fluid source processes generating extremal dual-leaky-bucket-regulated traffic. We compute a close upper bound by applying the Benes approach to an equivalent hypothetical system derived from the real one. We then extend the analysis to the end-to-end scenario in the presence of traffic re-shaping at each node in the network. We compare the analytical results with simulations, and show that the match is very close. We also investigate the advantages of smoothing the traffic at the ingress to the network, and propose a simple choice of smoothing parameters, which perform very well. Using realistic traffic parameters, we compare the schedulable region of our statistical framework with that of the corresponding deterministic framework, and demonstrate that the statistical framework allows tremendous improvements in network utilization, even for very low delay-violation probabilities. The framework developed in this paper is therefore highly useful in practical packet networks to provide quality of service to real-time applications in the form of statistical, rather than deterministic, end-to-end delay bounds.
Merging Satellite Retrievals and Reanalyses to Produce Global Long-Term and Consistent Surface Incident Solar Radiation Datasets

Surface incident solar radiation (Rs) is a key parameter in many climatic and ecological processes. The data from satellites and reanalysis have been widely used. However, for reanalysis, Rs data has been shown to have substantial spatial bias, and the time span of reliable satellite Rs is too short for climatic and ecological studies. Combining reanalysis and satellite data would be an effective method for generating long-term and consistent Rs datasets. Here, we apply a cumulative probability density function-based (CPDF) method to merge eight reanalyses with the latest available satellite Rs data from Clouds and Earth’s Radiant Energy System Energy Balanced and Filled (CERES EBAF) surface retrievals. The CPDF method not only reduces the spatial bias of the reanalysis Rs data, but also makes the Rs datasets in a global, long-term and consistent way. The observed Rs data collected at 54 Baseline Surface Radiation Network (BSRN) stations from 1992 to 2016 are used to evaluate the method. Results show that the CPDF method could reduce the mean absolute biases (MAB) of the reanalysis Rs effectively by 21.24–64.36%. The European Centre for Medium-Range Weather Forecasts Re-Analysis interim (ERA-interim) reanalysis Rs data, which are available for 1979 onward, perform the best before MAB = 13.20 W·m−2 and after MAB = 10.40 W·m−2 merging. This small post-merging MAB of the ERA-interim reanalysis is caused by the MAB of 9.90 W·m−2 in the satellite Rs retrievals. The Japanese 55-year reanalysis provides Rs values back to 1958, and CPDF can reduce its MAB by 32.87%, to 11.17 W·m−2. The National Oceanic and Atmospheric Administration (NOAA)-CIRES twentieth-century reanalysis (CIRES) and the ECMWF twentieth-century reanalysis (ERA20CM) provide century-long Rs estimates. CIRES performs better after merging. The MAB of CIRES can be reduced by 32.10%, to 12.99 W·m−2, while ERA20CM’s can be reduced by 12.51%, to 16.40 W·m−2.