Miracle-dz/UniFAR-FTUs huggingface dataset:
Evidence of genetic distinction and long‐term population decline in wolves (Canis lupus) in the Italian Apennines

Historical information suggests the occurrence of an extensive human‐caused contraction in the distribution range of wolves (Canis lupus) during the last few centuries in Europe. Wolves disappeared from the Alps in the 1920s, and thereafter continued to decline in peninsular Italy until the 1970s, when approximately 100 individuals survived, isolated in the central Apennines. In this study we performed a coalescent analysis of multilocus DNA markers to infer patterns and timing of historical population changes in wolves surviving in the Apennines. This population showed a unique mitochondrial DNA control‐region haplotype, the absence of private alleles and lower heterozygosity at microsatellite loci, as compared to other wolf populations. Multivariate, clustering and Bayesian assignment procedures consistently assigned all the wolf genotypes sampled in Italy to a single group, supporting their genetic distinction. Bottleneck tests showed evidences of population decline in the Italian wolves, but not in other populations. Results of a Bayesian coalescent model indicate that wolves in Italy underwent a 100‐ to 1000‐fold population contraction over the past 2000–10 000 years. The population decline was stronger and longer in peninsular Italy than elsewhere in Europe, suggesting that wolves have apparently been genetically isolated for thousands of generations south of the Alps. Ice caps covering the Alps at the Last Glacial Maximum (c. 18 000 years before present), and the wide expansion of the Po River, which cut the alluvial plains throughout the Holocene, might have provided effective geographical barriers to wolf dispersal. More recently, the admixture of Alpine and Apennine wolf populations could have been prevented by deforestation, which was already widespread in the fifteenth century in northern Italy. This study suggests that, despite the high potential rates of dispersal and gene flow, local wolf populations may not have mixed for long periods of time.
Knowing and Designing: Understanding Information Use in Open Source Design Through the Lens of Information Archetypes

The early phases of the product design process are crucial to the success of design outcomes. While information utilized during idea development has tremendous potential to impact the final design, there is a lack of understanding about the types of information utilized in industry, making it challenging to develop and teach methodologies that support the design of competitive products. As a first step in understanding this process, this study focuses on developing a framework of Information Archetypes utilized by designers in industry. This was accomplished through in-depth analysis of qualitative interviews with large software engineering companies. The results reveal two archetypes of information utilized by decision-makers within these companies during the development of new products and services. The findings of this study allow for future research that investigates the role of information during the product design process.
Unnoticed in the tropics: phylogenomic resolution of the poorly known arachnid order Ricinulei (Arachnida)

Ricinulei are among the most obscure and cryptic arachnid orders, constituting a micro-diverse group with extreme endemism. The 76 extant species described to date are grouped in three genera: Ricinoides, from tropical Western and Central Africa, and the two Neotropical genera Cryptocellus and Pseudocellus. Until now, a single molecular phylogeny of Ricinulei has been published, recovering the African Ricinoides as the sister group of the American Pseudocellus and providing evidence for the diversification of the order pre-dating the fragmentation of Gondwana. Here, we present, to our knowledge, the first phylogenomic study of this neglected arachnid order based on data from five transcriptomes obtained from the five major mitochondrial lineages of Ricinulei. Our results, based on up to more than 2000 genes, strongly support a clade containing Pseudocellus and Cryptocellus, constituting the American group of Ricinulei, with the African Ricinoides nesting outside. Our dating of the diversification of the African and American clades using a 76 gene data matrix with 90% gene occupancy indicates that this arachnid lineage was distributed in the South American, North American and African plates of Gondwana and that its diversification is concordant with a biogeographic scenario (both for pattern and tempo) of Gondwanan vicariance.
Immunohistochemical Comparison of Markers for Wound Healing on Plastic-Embedded and Frozen Mucosal Tissue

Immunohistologic investigations of wound healing in human oral mucosa require specific cell biological markers as well as consecutive small biopsies. Small specimens are ideally embedded in plastic (methylmethacrylate, MMA) resin due to their miniature size. This limits the use of antibodies for these markers. In this immunohistochemical study, the distribution of wound healing markers, e.g. cytokeratin (CK), laminin, collagen IV, vimentin, vinculin and fibronectin, were compared between semithin sections of plastic-embedded tissue and frozen sections of mucosal tissue in order to assess their use for future investigations. The antibodies against laminin, collagen IV and CK 1/2/10/11, 5/6, 13, 14, 17, 19 gave comparable staining patterns on cryostat sections of attached mucosa and on semithin sections of MMA-embedded attached mucosa. In the epithelial cell layers, the following distribution of CK immunostaining was observed: The basal cell layer was positive for CK 5/6, CK 14 and CK 19; the intermediate cell layer for CK 13, CK 17 and CK 1/2/10/11, and the superficial cell layer for CK 13 and CK 1/2/10/11. For most of these antibodies, enzyme digestion with 0.1% trypsin was adequate for demasking the antigens, except for anti-CK 14, anti-CK 17 and anti-laminin; predigestion with 0.4% pepsin in 0.01 N HCl gave similar staining results. The antibodies against vimentin, vinculin, fibronectin and CK 4 showed no affinity or a reciprocal reaction on the semithin sections. Therefore, the antibodies against CK 1/2/10/11; 5/6; 13; 14; 17, and 19, as well as the basement proteins laminin and collagen IV are deemed markers suitable on semithin sections of plastic-embedded attached oral mucosa.
Composable M&S Web Services for Net-Centric Applications

Service-oriented architectures promise easier integration of functionality in the form of web services into operational systems than is the case with interface-driven system-oriented approaches. Although the Extensible Markup Language (XML) enables a new level of interoperability among heterogeneous systems, XML alone does not solve all interoperability problems users contend with when integrating services into operational systems. To manage the basic challenges of service interoperation, we developed the Levels of Conceptual Interoperability Model (LCIM) to enable a layered approach and gradual solution improvements. Furthermore, we developed methods of model-based data engineering (MBDE) for semantically consistent service integration as a first step. These methods have been applied in the U.S. in collaboration with industry resulting in proofs of concepts. The results are directly applicable in a net-centric and net-enabled environment.
Pediatric MMR Vaccination Safety

TMeasles, mumps and rubella are viral infections that have the potential to result in globally destructive disorders. Measles, mumps and rubella (MMR) vaccine has helped to dramatically reduce the number of cases of measles, mumps and rubella infection, as well as to reduce the amount of pain and suffering associated with each of these natural infections. The purpose of this study was to analyze the incidence of serious neurologic disorders in a comparative examination between MMR vaccine and a vaccine control group. The Vaccine Adverse Events Reporting System (VAERS) database was analyzed for the incidence rate of permanent brain damage, cerebellar ataxia, autism and mental retardation reported following MMR vaccine and diphtheria, tetanus and whole-cell pertussis (DTwcP) containing-vaccines from 1994 through 2000 in the US. Statistically significant increases in the incidence of serious neurologic disorders following pediatric MMR vaccine in comparison to DTwcP vaccine were found. The potentially globally destructive effects of natural measles, mumps and rubella infections means that continued vaccination is necessary, but improvements in MMR vaccines are needed to improve its safety. Int Pediatr. 2003;18(2):203-208.
Human Umbilical Cord Blood Stem Cells Differentiate into Keratinocytes under In Vitro Conditions and Culturing Differentiated Cells on Bacterial Cellulose Film

Mesenchymal stem cells (MSC) are capable of self renewing and differentiating into other cell types. Human umbilical cord blood (HUCB) has been investigated as an alternative source to bone marrow. The aim of our examinations was to investigate MSC of HUCB could differentiate into keratinocytes under in vitro conditions. In this study, we examined the differentiation with chemical compounds, then to identify the stem cells are differentiated or not, PCR by using the expression of gene cytokeratin 18 was performed and to examine the proliferation characteristic of differentiated keratinocyte from HUCBMSCs, cultured them on cellulose film. Analysis of PCR confirmed the expression of cytokeratin 18 in keratinocytes; results of our study show that cellulose film isn’t a compatible substrate for differentiated keratinocytes. And growth factor, BMP4, with hydrocortisone and ascorbic acid with specific amounts is an appropriate induction factor for inducing of differentiation into keratinocytes.
Adsorption of tetracycline on Fe (hydr)oxides: effects of pH and metal cation (Cu2+, Zn2+ and Al3+) addition in various molar ratios

Iron (Fe) (hydr)oxides control the mobility and bioavailability of tetracycline (TC) in waters and soils. Adsorption of TC on Fe (hydr)oxides is greatly affected by polyvalent metals; however, impacts of molar metal/TC ratios on TC adsorptive behaviours on Fe (hydr)oxides remain unclear. Results showed that maximum TC adsorption on ferrihydrite and goethite occurred at pH 5–6. Such TC adsorption was generally promoted by the addition of Cu2+, Zn2+ and Al3+. The greatest increase in TC adsorption was found in the system with molar Cu/TC ratio of 3 due to the formation of Fe hydr(oxide)–Cu–TC ternary complexes. Functional groups on TC that were responsible for the complexation with Cu2+shifted from phenolic diketone groups at Cu/TC molar ratio < 1 to amide groups at Cu/TC molar ratio ≥ 1. For the addition of Al3+, the complexation only took place with phenolic diketone groups, resulting in the enhanced TC adsorption at a molar Al/TC ratio of 1. However, TC adsorption decreased for Al/TC molar ratio > 1 as excess Al3+ led to the competitive adsorption with Al/TC complexes. For the Zn2+ addition, no significant correlation was found between TC adsorption capacity and molar Zn/TC ratios.
Dose response of selected ion chambers in applied homogeneous transverse and longitudinal magnetic fields.

PURPOSE The magnetic fields of an integrated MR-Linac system will alter the paths of electrons that produce ions in the ionization chambers. The dose response of selected ion chambers is evaluated in the presence of varying transverse and longitudinal magnetic fields. The investigation is useful in calibration of therapeutic x-ray beams associated with MR-Linac systems. METHODS The Monte Carlo code PENELOPE was used to model the irradiation of NE2571, and PR06C ionization chambers in the presence of a transverse and longitudinal (with respect to the photon beam) magnetic fields of varying magnitude. The long axis of each chamber was simulated both parallel and perpendicular to the incident photon beam for each magnetic field case. The dose deposited in each chamber for each case was compared to the case with zero magnetic field by means of a ratio. The PR06C chamber's response was measured in the presence of a transverse magnetic field with field strengths ranging from 0.0 to 0.2 T to compare to simulated results. RESULTS The simulations and measured data show that in the presence of a transverse magnetic field there is a considerable dose response (maximum of 11% near 1.0 T in the ion chambers investigated, which depends on the magnitude of magnetic field, and relative orientation of the magnetic field, radiation beam, and ion chamber. Measurements made with the PR06C chamber verify these results in the region of measurement. In contrast, a longitudinal magnetic field produces only a slight increase in dose response (2% at 1.5 T) that rises slowly with increasing magnetic field and is seemingly independent of chamber orientation. Response trends were similar for the two ion chambers and relative orientations considered, but slight variations are present from chamber to chamber. CONCLUSIONS Care must be taken when making ion chamber measurements in a transverse magnetic field. Ion chamber responses vary not only with transverse field strength, but with chamber orientation and type, and can be considerable. Longitudinal magnetic fields influence ion chamber responses relatively little (2% at 1.5 T), and only at field strengths in excess of 1.0 T.
‘ ‘ Biphasic ’ ’ fevers often consist of more than two phases

Romanovsky, Andrej A. , Christopher T. Simons, and Vladimir A. Kulchitsky. ‘‘Biphasic’’ fevers often consist of more than two phases. Am. J. Physiol. 275 (Regulatory Integrative Comp. Physiol. 44): R323–R331, 1998. —This paper disproves the common belief that all doses of lipopolysaccharide (LPS) that are commonly referred to as biphasic fever inducing ($2 μg/kg) cause truly biphasic responses. A catheter was implanted into the right jugular vein of several strains of adult male rats, and the animals were habituated to the experimental conditions. At an ambient temperature of 30.0°C, loosely restrained animals were injected with a 10 μg/kg dose of LPS (various preparations), and their colonic (Tc) and tail skin temperatures were monitored (from $1 h before to $7 h after the injection). The results are presented as time graphs and phase-plane plots; in the latter case the rate of change of Tc is plotted against Tc. In experiment 1 the intravenous injection of LPS (from Escherichia coli 0111:B4, phenol extract) into the rats (Bkl:Wistar) induced a triphasic febrile response, as is obvious from time graphs of Tc (3 peaks), time graphs of effector activity (3 waves of tail skin vasoconstriction), and phase-plane plots (3 complete loops); the injection of saline (control) induced no Tc changes. We analyzed whether the triphasic pattern was due to some peculiarities of the experimental design, i.e., the pyrogen preparation used (experiment 2) or the rat strain tested (experiment 3) or whether this pattern reflects a more general law. In experiment 2 we used the same (phenol) preparation of different LPS (from Shigella flexneri 1A and Salmonella typhosa) and a different preparation (TCA extract) of the same LPS (E. coli). Regardless of the LPS used, rats of the Bkl:Wistar strain responded to the 10 μg/kg dose with the triphasic fever. In experiment 3, rats of other strains [Bkl: Sprague-Dawley and Sim:(LE)fBR(Black-hooded)] were tested. Again, all animals responded to the 10 μg/kg dose of E. coli LPS (phenol extract) with the triphasic fever. Because all fevers caused by four different LPS preparations in three rat strains were triphasic, the triphasic pattern is likely to constitute an intrinsic characteristic of the febrile response.
Do the effects of subjective frequency and age of acquisition survive better word frequency norms?

Megastudies with processing efficiency measures for thousands of words allow researchers to assess the quality of the word features they are using. In this article, we analyse reading aloud and lexical decision reaction times and accuracy rates for 2,336 words to assess the influence of subjective frequency and age of acquisition on performance. Specifically, we compare newly presented word frequency measures with the existing frequency norms of Kučera and Francis (1967), HAL (Burgess & Livesay, 1998), Brysbaert and New (2009), and Zeno, Ivens, Millard, and Duvvuri (1995). We show that the use of the Kučera and Francis word frequency measure accounts for much less variance than the other word frequencies, which leaves more variance to be “explained” by familiarity ratings and age-of-acquisition ratings. We argue that subjective frequency ratings are no longer needed if researchers have good objective word frequency counts. The effect of age of acquisition remains significant and has an effect size that is of practical relevance, although it is substantially smaller than that of the first phoneme in naming and the objective word frequency in lexical decision. Thus, our results suggest that models of word processing need to utilize these recently developed frequency estimates during training or setting baseline activation levels in the lexicon.
Quantitative assessment of computational models for retinotopic map formation

Molecular and activity‐based cues acting together are thought to guide retinal axons to their terminal sites in vertebrate optic tectum or superior colliculus (SC) to form an ordered map of connections. The details of mechanisms involved, and the degree to which they might interact, are still not well understood. We have developed a framework within which existing computational models can be assessed in an unbiased and quantitative manner against a set of experimental data curated from the mouse retinocollicular system. Our framework facilitates comparison between models, testing new models against known phenotypes and simulating new phenotypes in existing models. We have used this framework to assess four representative models that combine Eph/ephrin gradients and/or activity‐based mechanisms and competition. Two of the models were updated from their original form to fit into our framework. The models were tested against five different phenotypes: wild type, Isl2‐EphA3ki/ki, Isl2‐EphA3ki/+, ephrin‐A2,A3,A5 triple knock‐out (TKO), and Math5−/− (Atoh7). Two models successfully reproduced the extent of the Math5−/− anteromedial projection, but only one of those could account for the collapse point in Isl2‐EphA3ki/+. The models needed a weak anteroposterior gradient in the SC to reproduce the residual order in the ephrin‐A2,A3,A5 TKO phenotype, suggesting either an incomplete knock‐out or the presence of another guidance molecule. Our article demonstrates the importance of testing retinotopic models against as full a range of phenotypes as possible, and we have made available MATLAB software, we wrote to facilitate this process. © 2014 The Authors Developmental Neurobiology Published by Wiley Periodicals, Inc. Develop Neurobiol 75: 641–666, 2015
Expression of Hoxa‐11 and Hoxa‐13 in the pectoral fin of a basal ray‐finned fish, Polyodon spathula: implications for the origin of tetrapod limbs

Summary Paleontological and anatomical evidence suggests that the autopodium (hand or foot) is a novel feature that distinguishes limbs from fins, while the upper and lower limb (stylopod and zeugopod) are homologous to parts of the sarcopterygian paired fins. In tetrapod limb development Hoxa‐11 plays a key role in differentiating the lower limb and Hoxa‐13 plays a key role in differentiating the autopodium. It is thus important to determine the ancestral functions of these genes in order to understand the developmental genetic changes that led to the origin of the tetrapod autopodium. In particular it is important to understand which features of gene expression are derived in tetrapods and which are ancestral in bony fishes. To address these questions we cloned and sequenced the Hoxa‐11 and Hoxa‐13 genes from the North American paddlefish, Polyodon spathula, a basal ray‐finned fish that has a pectoral fin morphology resembling that of primitive bony fishes ancestral to the tetrapod lineage. Sequence analysis of these genes shows that they are not orthologous to the duplicated zebrafish and fugu genes. This implies that the paddlefish has not duplicated its HoxA cluster, unlike zebrafish and fugu. The expression of Hoxa‐11 and Hoxa‐13 in the pectoral fins shows two main phases: an early phase in which Hoxa‐11 is expressed proximally and Hoxa‐13 is expressed distally, and a later phase in which Hoxa‐11 and Hoxa‐13 broadly overlap in the distal mesenchyme of the fin bud but are absent in the proximal fin bud. Hence the distal polarity of Hoxa‐13 expression seen in tetrapods is likely to be an ancestral feature of paired appendage development. The main difference in HoxA gene expression between fin and limb development is that in tetrapods (with the exception of newts) Hoxa‐11 expression is suppressed by Hoxa‐13 in the distal limb bud mesenchyme. There is, however, a short period of limb bud development where Hoxa‐11 and Hoxa‐13 overlap similarly to the late expression seen in zebrafish and paddlefish. We conclude that the early expression pattern in tetrapods is similar to that seen in late fin development and that the local exclusion by Hoxa‐13 of Hoxa‐11 from the distal limb bud is a derived feature of limb developmental regulation.
Examining moisture pathways and extreme precipitation in the U.S. Intermountain West using self‐organizing maps

Self‐organizing maps (SOMs) were used to explore relationships between large‐scale synoptic conditions, especially vertically integrated water vapor transport (IVT), and extreme precipitation events in the U.S. Intermountain West (IMW). By examining spatial patterns in the IVT, pathways are identified where moisture can penetrate into the IMW. A substantial number of extreme precipitation events in the IMW are associated with infrequently occurring synoptic patterns. The transition frequency between each of the SOM nodes, which indicate temporal relationships between the patterns, identified two synoptic settings associated with extreme precipitation in the IMW: (1) a landfalling, zonally propagating trough that results in a concentrated IVT band that moves southward as the system moves inland and (2) a southwesterly storm track associated with strong ridging over the coast that results in persistent IVT transport into the Pacific Northwest that can last for several days.
Matching radiative transfer models and radiosonde data from the EPS/Metop Sodankylä campaign to IASI measurements

Abstract. Radiances observed from IASI are compared to calculated ones. Calculated radiances are obtained using several radiative transfer models (OSS, LBLRTM v11.3 and v11.6) on best estimates of the atmospheric state vectors. The atmospheric state vectors are derived from cryogenic frost point hygrometer and humidity dry bias corrected RS92 measurements flown on sondes launched 1 h and 5 min before IASI overpass time. The temperature and humidity best estimate profiles are obtained by interpolating or extrapolating these measurements to IASI overpass time. The IASI observed and calculated radiances match to within one sigma IASI instrument noise in the spectral region where water vapour is a strong absorber (wavenumber, ν, in the range of 1500 ≤ ν ≤ 1570 and 1615 ≤ ν ≤ 1800 cm−1).