Miracle-dz/UniFAR-FTUs huggingface dataset:
Hardware synthesis from requirement specifications

This paper describes the theory and implementation of a novel system for hardware synthesis from requirement specifications expressed in a graphical specification language called Symbolic Timing Diagrams (STD). The system can be used together with an existing formal-verification environment for VHDL leading to a novel methodology based on the combination of synthesis and formal verification. We show the feasibility of the approach and experimental results obtained with the system on the well known example of an industrial production cell, where both FPGA and ASIC hardware implementations were successfully synthesized.
New Insights on Taxonomy, Phylogeny and Population Genetics of Leishmania (Viannia) Parasites Based on Multilocus Sequence Analysis

The Leishmania genus comprises up to 35 species, some with status still under discussion. The multilocus sequence typing (MLST)—extensively used for bacteria—has been proposed for pathogenic trypanosomatids. For Leishmania, however, a detailed analysis and revision on the taxonomy is still required. We have partially sequenced four housekeeping genes—glucose-6-phosphate dehydrogenase (G6PD), 6-phosphogluconate dehydrogenase (6PGD), mannose phosphate isomerase (MPI) and isocitrate dehydrogenase (ICD)—from 96 Leishmania (Viannia) strains and assessed their discriminatory typing capacity. The fragments had different degrees of diversity, and are thus suitable to be used in combination for intra- and inter-specific inferences. Species-specific single nucleotide polymorphisms were detected, but not for all species; ambiguous sites indicating heterozygosis were observed, as well as the putative homozygous donor. A large number of haplotypes were detected for each marker; for 6PGD a possible ancestral allele for L. (Viannia) was found. Maximum parsimony-based haplotype networks were built. Strains of different species, as identified by multilocus enzyme electrophoresis (MLEE), formed separated clusters in each network, with exceptions. NeighborNet of concatenated sequences confirmed species-specific clusters, suggesting recombination occurring in L. braziliensis and L. guyanensis. Phylogenetic analysis indicates L. lainsoni and L. naiffi as the most divergent species and does not support L. shawi as a distinct species, placing it in the L. guyanensis cluster. BURST analysis resulted in six clonal complexes (CC), corresponding to distinct species. The L. braziliensis strains evaluated correspond to one widely geographically distributed CC and another restricted to one endemic area. This study demonstrates the value of systematic multilocus sequence analysis (MLSA) for determining intra- and inter-species relationships and presents an approach to validate the species status of some entities. Furthermore, it contributes to the phylogeny of L. (Viannia) and might be helpful for epidemiological and population genetics analysis based on haplotype/diplotype determinations and inferences.
Normal Glucose Metabolism in Carnivores Overlaps with Diabetes Pathology in Non-Carnivores

Carnivores, such as the dolphin and the domestic cat, have numerous adaptations that befit consumption of diets with high protein and fat content, with little carbohydrate content. Consequently, nutrient metabolism in carnivorous species differs substantially from that of non-carnivores. Important metabolic pathways known to differ between carnivores and non-carnivores are implicated in the development of diabetes and insulin resistance in non-carnivores: (1) the hepatic glucokinase (GCK) pathway is absent in healthy carnivores yet GCK deficiency may result in diabetes in rodents and humans, (2) healthy dolphins and cats are prone to periods of fasting hyperglycemia and exhibit insulin resistance, both of which are risk factors for diabetes in non-carnivores. Similarly, carnivores develop naturally occurring diseases such as hemochromatosis, fatty liver, obesity, and diabetes that have strong parallels with the same disorders in humans. Understanding how evolution, environment, diet, and domestication may play a role with nutrient metabolism in the dolphin and cat may also be relevant to human diabetes.
Movement Patterns and Home Range Use of the Northern Watersnake (Nerodia sipedon)

Abstract The factors that influence spatial use and movement patterns in ectotherms may have important fitness consequences. To examine the effects of sex and condition on spatial use, we used radio telemetry to observe the movement of 18 adult Nerodia sipedon in a southwest Missouri lake. Snakes generally remained in close proximity (<5 m) to aquatic habitats throughout the summer. Home range size estimates differed according to calculation method. Monthly total home range sizes peaked in mid-summer, possibly in response to increased amounts of vegetative cover, although core area sizes were consistent across the season. Contrary to previous studies of snakes, mean movement rates and home range sizes of male and gravid female N. sipedon were statistically indistinguishable and highly variable. Body size and condition influenced spatial characteristics of females, but only appeared to influence movement frequency of males. When compared to other populations, we found that our population of N. sipedon tended to occupy similarly-sized shifting core areas associated with aquatic vegetation. Future studies should focus on the measurement of resource distribution to further understand the factors influencing variation in snake movements and spatial patterns.
Gene Turnover in the Avian Globin Gene Families and Evolutionary Changes in Hemoglobin Isoform Expression

The apparent stasis in the evolution of avian chromosomes suggests that birds may have experienced relatively low rates of gene gain and loss in multigene families. To investigate this possibility and to explore the phenotypic consequences of variation in gene copy number, we examined evolutionary changes in the families of genes that encode the α- and β-type subunits of hemoglobin (Hb), the tetrameric α2β2 protein responsible for blood-O2 transport. A comparative genomic analysis of 52 bird species revealed that the size and membership composition of the α- and β-globin gene families have remained remarkably constant during approximately 100 My of avian evolution. Most interspecific variation in gene content is attributable to multiple independent inactivations of the αD-globin gene, which encodes the α-chain subunit of a functionally distinct Hb isoform (HbD) that is expressed in both embryonic and definitive erythrocytes. Due to consistent differences in O2-binding properties between HbD and the major adult-expressed Hb isoform, HbA (which incorporates products of the αA-globin gene), recurrent losses of αD-globin contribute to among-species variation in blood-O2 affinity. Analysis of HbA/HbD expression levels in the red blood cells of 122 bird species revealed high variability among lineages and strong phylogenetic signal. In comparison with the homologous gene clusters in mammals, the low retention rate for lineage-specific gene duplicates in the avian globin gene clusters suggests that the developmental regulation of Hb synthesis in birds may be more highly conserved, with orthologous genes having similar stage-specific expression profiles and similar functional properties in disparate taxa.
Nerve Growth Factor Regulates Neurolymphatic Remodeling during Corneal Inflammation and Resolution

The cellular and physiologic mechanisms that regulate the resolution of inflammation remain poorly defined despite their widespread importance in improving inflammatory disease outcomes. We studied the resolution of two cardinal signs of inflammation–pain and swelling–by investigating molecular mechanisms that regulate neural and lymphatic vessel remodeling during the resolution of corneal inflammation. A mouse model of corneal inflammation and wound recovery was developed to study this process in vivo. Administration of nerve growth factor (NGF) increased pain sensation and inhibited neural remodeling and lymphatic vessel regression processes during wound recovery. A complementary in vivo approach, the corneal micropocket assay, revealed that NGF-laden pellets stimulated lymphangiogenesis and increased protein levels of VEGF-C. Adult human dermal lymphatic endothelial cells did not express canonical NGF receptors TrkA and p75NTR or activate downstream MAPK- or Akt-pathway effectors in the presence of NGF, although NGF treatment increased their migratory and tubulogenesis capacities in vitro. Blockade of the VEGF-R2/R3 signaling pathway ablated NGF-mediated lymphangiogenesis in vivo. These findings suggest a hierarchical relationship with NGF functioning upstream of the VEGF family members, particularly VEGF-C, to stimulate lymphangiogenesis. Taken together, these studies show that NGF stimulates lymphangiogenesis and that NGF may act as a pathogenic factor that negatively regulates the normal neural and lymphatic vascular remodeling events that accompany wound recovery.
A Disrupted Circumstellar Torus inside η Carinae’s Homunculus Nebula

We present thermal infrared images of the bipolar nebula surrounding η Carinae at six wavelengths from 4.8 to 24.5 μm. These were obtained with the MIRAC3 camera system at the Magellan Observatory. Our images reveal new intricate structure in the bright core of the nebula, allowing us to reevaluate interpretations of morphology seen in images with lower resolution. Complex structures in the core might not arise from a pair of overlapping rings or a cool (110 K) and very massive dust torus, as has been suggested recently. Instead, it seems more likely that the arcs and compact knots comprise a warm (200-350 K) disrupted torus at the intersection of the larger polar lobes. Some of the arcs appear to break out of the inner core region and may be associated with equatorial features seen in optical images. The torus could have been disrupted by a posteruption stellar wind or by ejecta from the Great Eruption itself if the torus existed before that event. Kinematic data are required to rule out either possibility.
Role of Oxidative Stress in Parkinson's Disease

Parkinson's disease (PD) is a progressive neurodegenerative movement disorder associated with a selective loss of the dopamine(DA)rgic neurons in the substantia nigra pars compacta and the degeneration of projecting nerve fibers in the striatum. Because there is currently no therapy that delays the neurodegenerative process, modification of the disease course by neuroprotective therapy is an important unmet clinical need. Toward this end, understanding cellular mechanisms that render the nigral neurons particularly vulnerable have been a subject of intensive research. Increasing evidence suggests that oxidative stress plays a major role. The metabolism of DA itself contributes to oxidative stress, resulting in modification of intracellular macromolecules whose functions are important for cell survival. Mitochondrial dysfunction and the consequent increase in reactive oxygen species also trigger a sequence of events that leads to cell demise. In addition, activated microglia produce nitric oxide and superoxide during neuroinflammatory responses, and this is aggravated by the molecules released by damaged DAergic neurons such as α-synuclein, neuromelanin and matrix metalloproteinase-3. Ways to reduce oxidative stress therefore can provide a therapeutic strategy. NAD(P)H:quinone reductase (NQO1) and other antioxidant enzymes, whose gene expression are commonly under the regulation of the transcription factor Nrf2, can serve as target proteins utilized toward development of disease-modifying therapy for PD.
Phases and binding of reflexives and pronouns in English

This paper proposes a distinct approach to local binding effects for reflexives and pronominals in English whereby the nature of local binding domains is a by-product of the incremental interpretation of syntactic derivations (Uriageraka 1999, Chomsky 2000, 2001), emphasizing the role of the Conceptual /Intentional interface and the computational system (i.e. bare output conditions) in shaping general principles of grammars. A significant development of the Minimalist framework is the proposal that derivations operate through phases or multiple spell outs, which allows to reduce the strict cyclicity of derivations, and related locality effects of movement, to interface (bare output) conditions and economy conditions. In this paper I propose that incremental interpretation can further capture local binding domains effects of conditions A and B of Chomsky's (1981, 1986) Binding Theory. Basically, local binding domains are shown to correspond to accessible phase domains. Our proposal hence contrasts with standard analyses (e.g. Reinhart and Reuland 1993, Pollard and Sag 1992) that define co-argumenthood as the core factor from which binding conditions are developed. Our proposal also provides a new perspective on the core contrasts between A-chain and A-bar chain w.r. t. binding and scope reconstruction effects and argues that checking of the uninterpretable feature Case is what defines potential phase domains.
Self-Construal and Forgiveness Revisited: Examining the Motivations for Forgiving Others

Evidence suggests that self-construal influences an individual’s perspective on granting forgiveness to an offender. However, there is still a lack of understanding of the intricacies of the relationships between self-construal, forgiveness, and forgiveness motivations. The current study examined the relationship between self-construal, particularly relational self-construal, and individuals’ engagement in either emotional or decisional forgiveness. In addition, I sought to understand the relationship between forgiveness behaviors and individuals’ motivations for forgiving offenders for offenses. The primary results were: 1) that relational self-construal was significantly correlated with decisional forgiveness; 2) that individuals high in relational self-construal were more likely to engage in decisional forgiveness than emotional forgiveness; and 3) that individuals who are higher in relational self-construal were more likely to endorse relationship-themed motivations for forgiveness.
Multiple Time Scales in Volatility and Leverage Correlations: An Stochastic Volatility Model

Financial time series exhibit two different type of non linear correlations: (i) volatility autocorrelations that have a very long range memory, on the order of years, and (ii) asymmetric return-volatility (or `leverage') correlations that are much shorter ranged. Different stochastic volatility models have been proposed in the past to account for both these correlations. However, in these models, the decay of the correlations is exponential, with a single time scale for both the volatility and the leverage correlations, at variance with observations. We extend the linear Ornstein-Uhlenbeck stochastic volatility model by assuming that the mean reverting level is itself random. We find that the resulting three-dimensional diffusion process can account for different correlation time scales. We show that the results are in good agreement with a century of the Dow Jones index daily returns (1900-2000), with the exception of crash days.
Noncoding origins of anthropoid traits and a new null model of transposon functionalization

Little is known about novel genetic elements that drove the emergence of anthropoid primates. We exploited the sequencing of the marmoset genome to identify 23,849 anthropoid-specific constrained (ASC) regions and confirmed their robust functional signatures. Of the ASC base pairs, 99.7% were noncoding, suggesting that novel anthropoid functional elements were overwhelmingly cis-regulatory. ASCs were highly enriched in loci associated with fetal brain development, motor coordination, neurotransmission, and vision, thus providing a large set of candidate elements for exploring the molecular basis of hallmark primate traits. We validated ASC192 as a primate-specific enhancer in proliferative zones of the developing brain. Unexpectedly, transposable elements (TEs) contributed to >56% of ASCs, and almost all TE families showed functional potential similar to that of nonrepetitive DNA. Three L1PA repeat-derived ASCs displayed coherent eye-enhancer function, thus demonstrating that the “gene-battery” model of TE functionalization applies to enhancers in vivo. Our study provides fundamental insights into genome evolution and the origins of anthropoid phenotypes and supports an elegantly simple new null model of TE exaptation.
Detectability of Changes in the Walker Circulation in 1 Response to Global Warming 2 3

Pedro N. DiNezio 4 International Pacific Research Center, School of Ocean and Earth Science and Technology, University of 5 Hawaii, Honolulu, Hawaii 6 7 Gabriel A. Vecchi 8 NOAA/Geophysical Fluid Dynamics Laboratory, Princeton, New Jersey 9 10 Amy C. Clement 11 Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, Florida 12 13 Submitted to J. Climate 14 15 16 17 18 19 20 21 22 23 24 ____________________ 25
The brightness of SN 1991T and the uniformity of decline-rate and colour corrected absolute magnitudes of supernovae Ia

We present a distance to NGC 4527, the host galaxy of the type Ia SN 1991T, measured by surface brightness fluctuations. This supernova has been labelled "peculiar"both on the grounds of its spectroscopic behaviour and its apparent overluminosity with respect to other supernovae. The distance modulus to NGC 4527 and thus to SN 1991T is $30.26\pm0.09$. This relatively short distance largely removes the discrepancy with other Ia supernovae having similar light-curve characteristics and also removes the motivation for interpreting SN 1991T as a super-Chandrasekhar explosion. However, the reddening uncertainty results in significant uncertainty of the absolute magnitudes. We show further that, although the intrinsic absolute magnitudes among Ia supernovae are quite different, their brightness, corrected for decline-rate and colour, shows a high degree of uniformity, including underluminous events like SN 1991bg and SN 1997cn. In particular, the present data do not support a significant difference between corrected SNe Ia luminosities in late-type and early-type host galaxies.
Human kallikrein 4: quantitative study in tissues and evidence for its secretion into biological fluids.

BACKGROUND Human kallikrein 4 (hK4) is a proteolytic enzyme belonging to the tissue kallikrein family of serine proteases. Previous tissue expression studies have demonstrated highest KLK4 mRNA expression in prostatic tissue, but there has been only limited evidence for the presence of hK4 protein in prostate and other tissues and in corresponding biological secretions. METHODS To investigate the concentrations of hK4 in tissues and biological fluids, we developed a new hK4-specific sandwich-type immunoassay using a monoclonal antibody as the capture reagent. RESULTS The assay has a detection limit of 0.02 microg/L and <0.1% cross-reactivity toward any of the other 14 human kallikreins. Twelve of 40 tissue extracts prepared from various human tissues contained detectable hK4 concentrations (0.68-7143 ng/g of total protein), with healthy prostate tissue containing the highest amount of hK4. Examination of 16 malignant and 18 benign prostate tissues revealed no significant differences in hK4 protein content, and the tissues contained a wide range of values (benign, <0.02 to 801 ng/g; malignant, <0.02 to 824 ng/g). Among the biological fluids tested, seminal plasma and urine contained widely varying amounts of hK4; concentrations in 54 urine samples were <0.02 to 2.6 microg/L, whereas concentrations in 58 seminal plasma samples were 0.2-202 microg/L. Affinity purification of hK4 from seminal plasma and subsequent mass spectrometry demonstrated the secreted nature of hK4 in seminal plasma. CONCLUSIONS hK4 is found primarily in prostate tissue and is secreted in seminal plasma. Its value as a novel prostatic biomarker needs to be defined further.
Competition between shocks and entropy floor: Unifying groups and clusters of galaxies

Semi-analytic models of X-ray clusters and groups of galaxies, relying on the idea that there was a non-gravitational energy injection in these systems, are able to reproduce many observed correlations, in particular the $L_{\rm X}-T$ relation and the “central entropy floor” in groups. Limiting models exist which describe the behaviour of clusters and groups separately, but no analytic modeling has yet been found to unify both mass ranges. It is the aim of this paper to provide such an analytic model. Our description relies on a now standard description of the shock thought to occur in these systems near the virial radius (Cavaliere et al. [CITE]), the isothermality and spherical symmetry of the intracluster medium, as well as the reinterpretation of observed quantities (like the X-ray luminosity, the gas mass M ICM and the central SZ effect y 0 ) in terms of the specific entropy. This allows the derivation of analytic expressions for several observed correlations ($L_{\rm X}-T$, $M_{\rm ICM}-T$, $y_0-T$,.) and their normalisation encompassing both the group and the cluster regimes . The analytic predictions compare very well with observations, as well as with more elaborated semi-analytic schemes. This agreement allows a reinterpretation of the $L_{\rm X}-T$ relation (via the quantity $L_{\rm X}/T^{7/2}$) and the $y_0-T$ relation (via $y_0/T^{5/2}$) as indirect measures of the non-gravitational entropy content of groups and clusters of galaxies. We emphasize the need for shock heating, even in the group mass range: shocks can not be completely suppressed in groups (and thus groups can not be entirely isentropic) unless an unacceptably high entropy floor is needed in order to break the self-similarity in the $L_{\rm X}-T$ relation. Our model shows that the normalisation of the entropy after the shock (which is mass-dependent) is a key ingredient and that this quantity a lone can explain the shape of the observed correlations between integrated X-ray and SZ quantities over and below 2 keV.