Miracle-dz/UniFAR-FTUs huggingface dataset:
Light-Front Dynamics and AdS/QCD Correspondence: Gravitational Form Factors of Composite Hadrons

Light-front holography is a remarkable feature of the AdS/CFT correspondence between gravity in AdS space and conformal field theories in physical space-time; it allows string modes $\ensuremath{\Phi}(z)$ in the anti-de Sitter (AdS) fifth dimension to be precisely mapped to the light-front wave functions of hadrons in physical space-time in terms of a specific light-front impact variable $\ensuremath{\zeta}$ which measures the separation of the quark and gluonic constituents within the hadron. This mapping was originally obtained by matching the exact expression for electromagnetic current matrix elements in AdS space with the corresponding exact expression for the current matrix element using light-front theory in physical space-time. In this paper we show that one obtains the identical holographic mapping using matrix elements of the energy-momentum tensor. To prove this, we show that there exists a correspondence between the matrix elements of the energy-momentum tensor of the fundamental hadronic constituents in QCD with the transition amplitudes describing the interaction of string modes in AdS space with an external graviton field which propagates in the AdS interior. The agreement of the results for electromagnetic and gravitational hadronic transition amplitudes provides an important consistency test and verification of holographic mapping from AdS to physical observables defined on the light front.
Comorbidity of five chronic health conditions in elderly community residents: determinants and impact on mortality.

BACKGROUND Comorbidity is common in elderly persons. Its extent, correlates, and life-threatening impact in representative community residents are unclear. METHODS Self-reported information of physician-diagnosed coronary artery disease (CAD), cerebrovascular disease (CVD), diabetes, and cancer was obtained annually between 1986-87 and 1992-93, and hypertension was obtained triennially from the participants of the Duke Established Populations for Epidemiologic Studies of the Elderly, a stratified multistage sample of 4,126 Black and White community residents aged 65-100, living in a five-county area of North Carolina. Date of death was obtained from death certificates identified through search of the National Death Index. Statistical procedures included descriptive statistics, logistic regression, and survival analysis. RESULTS Of this sample, 57% reported hypertension, 20% diabetes, 15% CAD, 9% cancer, and 9% CVD; 29% reported none of these conditions, whereas 29% reported two or more. Demographic characteristics were not related to comorbidity with CVD or cancer. Increased education tended to be protective. The effect of age, gender, and race varied with condition. At baseline there was substantial comorbidity among hypertension, CAD, CVD, and diabetes, but not with cancer. Hypertension, CVD, and diabetes were risk factors for CAD, whereas diabetes was a risk factor for CVD. After controlling for demographic characteristics, all health conditions except hypertension were predictive of 6-year mortality, as was the presence of comorbidity. CONCLUSION We found significant comorbidity in older persons who have hypertension, CAD, CVD, or diabetes; particular risk of developing comorbidity, particularly CAD, among those with hypertension, CVD, and diabetes; and risk of CVD in those with diabetes. With the exception of hypertension, these conditions, and comorbidity per se, are life-threatening.
Systematic Comparison of the Effects of Alpha-synuclein Mutations on Its Oligomerization and Aggregation

Aggregation of alpha-synuclein (ASYN) in Lewy bodies and Lewy neurites is the typical pathological hallmark of Parkinson's disease (PD) and other synucleinopathies. Furthermore, mutations in the gene encoding for ASYN are associated with familial and sporadic forms of PD, suggesting this protein plays a central role in the disease. However, the precise contribution of ASYN to neuronal dysfunction and death is unclear. There is intense debate about the nature of the toxic species of ASYN and little is known about the molecular determinants of oligomerization and aggregation of ASYN in the cell. In order to clarify the effects of different mutations on the propensity of ASYN to oligomerize and aggregate, we assembled a panel of 19 ASYN variants and compared their behaviour. We found that familial mutants linked to PD (A30P, E46K, H50Q, G51D and A53T) exhibited identical propensities to oligomerize in living cells, but had distinct abilities to form inclusions. While the A30P mutant reduced the percentage of cells with inclusions, the E46K mutant had the opposite effect. Interestingly, artificial proline mutants designed to interfere with the helical structure of the N-terminal domain, showed increased propensity to form oligomeric species rather than inclusions. Moreover, lysine substitution mutants increased oligomerization and altered the pattern of aggregation. Altogether, our data shed light into the molecular effects of ASYN mutations in a cellular context, and established a common ground for the study of genetic and pharmacological modulators of the aggregation process, opening new perspectives for therapeutic intervention in PD and other synucleinopathies.
Protection Against Epithelial Damage During Candida albicans Infection Is Mediated by PI3K/Akt and Mammalian Target of Rapamycin Signaling

Background. The ability of epithelial cells (ECs) to discriminate between commensal and pathogenic microbes is essential for healthy living. Key to these interactions are mucosal epithelial responses to pathogen-induced damage. Methods. Using reconstituted oral epithelium, we assessed epithelial gene transcriptional responses to Candida albicans infection by microarray. Signal pathway activation was monitored by Western blotting and transcription factor enzyme-linked immunosorbent assay, and the role of these pathways in C. albicans–induced damage protection was determined using chemical inhibitors. Results. Transcript profiling demonstrated early upregulation of epithelial genes involved in immune responses. Many of these genes constituted components of signaling pathways, but only NF-κB, MAPK, and PI3K/Akt pathways were functionally activated. We demonstrate that PI3K/Akt signaling is independent of NF-κB and MAPK signaling and plays a key role in epithelial immune activation and damage protection via mammalian target of rapamycin (mTOR) activation. Conclusions. PI3K/Akt/mTOR signaling may play a critical role in protecting epithelial cells from damage during mucosal fungal infections independent of NF-κB or MAPK signaling.
Integrative Taxonomy for Continental-Scale Terrestrial Insect Observations

Although 21st century ecology uses unprecedented technology at the largest spatio-temporal scales in history, the data remain reliant on sound taxonomic practices that derive from 18th century science. The importance of accurate species identifications has been assessed repeatedly and in instances where inappropriate assignments have been made there have been costly consequences. The National Ecological Observatory Network (NEON) will use a standardized system based upon an integrative taxonomic foundation to conduct observations of the focal terrestrial insect taxa, ground beetles and mosquitoes, at the continental scale for a 30 year monitoring program. The use of molecular data for continental-scale, multi-decadal research conducted by a geographically widely distributed set of researchers has not been evaluated until this point. The current paper addresses the development of a reference library for verifying species identifications at NEON and the key ways in which this resource will enhance a variety of user communities.
Direct Identification of Insulator Components by Insertional Chromatin Immunoprecipitation

Comprehensive understanding of mechanisms of epigenetic regulation requires identification of molecules bound to genomic regions of interest in vivo. However, non-biased methods to identify molecules bound to specific genomic loci in vivo are limited. Here, we applied insertional chromatin immunoprecipitation (iChIP) to direct identification of components of insulator complexes, which function as boundaries of chromatin domain. We found that the chicken β-globin HS4 (cHS4) insulator complex contains an RNA helicase protein, p68/DDX5; an RNA species, steroid receptor RNA activator 1; and a nuclear matrix protein, Matrin-3, in vivo. Binding of p68 and Matrin-3 to the cHS4 insulator core sequence was mediated by CCCTC-binding factor (CTCF). Thus, our results showed that it is feasible to directly identify proteins and RNA bound to a specific genomic region in vivo by using iChIP.
Improved ex vivo method for microbiocidal activity across vertebrate species

Summary The field of ecoimmunology is currently undergoing rapid expansion, whereby biologists from a wide range of ecological disciplines are increasingly interested in assessing immunocompetence in their study organisms. One of the key challenges to researchers is determining what eco-immune measures to use in a given experiment. Moreover, there are limitations depending on study species, requirements for specific antibodies, and relevance of the methodology to the study organism. Here we introduce an improved ex vivo method for microbiocidal activity across vertebrate species. The utility of this assay is that it determines the ability of an organism to remove a pathogen that could be encountered in the wild, lending ecological relevancy to the technique. The applications of this microbiocidal assay are broad, as it is readily adaptable to different types of microbes as well as a wide variety of study species. We describe a method of microbiocidal analysis that will enable researchers across disciplines to effectively employ this method to accurately quantify microbial killing ability, using readily available microplate absorbance readers.
Oncogenic viral protein HPV E7 up-regulates the SIRT1 longevity protein in human cervical cancer cells

Senescence is blocked in human cervical keratinocytes infected with high risk human papillomavirus (e.g. HPV type16). Viral oncoproteins HPV E6 and HPV E7 access the cell cycle via cellular p53 and retinoblastoma proteins respectively. Previously we have shown that HPV E7, not HPV E6, is also responsible for cervical cancer cell survival (SiHa cells; HPV type16). We now present evidence that SIRT1, an aging-related NAD-dependent deacetylase, mediates HPV E7 survival function in SiHa cervical cancer cells. Moreover, HPV E7 up-regulates SIRT1 protein when expressed in primary human keratinocytes. Conversely, SIRT1 levels decrease following RNAi-mediated silencing of HPV E7 in SiHa cells. Silencing HPV E6 has no effect on SIRT1 but, as expected, causes marked accumulation of p53 protein accompanied by p53-mediated up-regulation of p21. However, p53 acetylation (K382Ac) was barely detectable. Since p53 is a known SIRT1 substrate we propose that elevated SIRT1 levels (induced by HPV E7) attenuate p53 pro-apoptotic capacity via its de-acetylation. Our discovery that HPV E7 up-regulates SIRT1 links a clinically important oncogenic virus with the multi-functional SIRT1 protein. This link may open the way for a more in-depth understanding of the process of HPV-induced malignant transformation and also of the inter-relationships between aging and cancer.
From Stereoscopic Vision to Symbolic Representation

This paper describes a symbolic representation of the data provided by the stereo-vision system of a mobile robot. The representation proposed is constructed from qualitative descriptions of transitions in the depth information given by the stereograms. The goal of this paper is to investigate the consequences in the depth transitions of qualitative spatial events such as the relative motion between objects, spatial occlusion and object’s deformation (expansion and contraction). This causal relationship between spatial events and depth transitions forms a background theory for an abductive process of sensor data assimilation.
Using a Generative Lexicon Resource to Compute Bridging Anaphora in Italian

bridging, an aforas aso- ciativas Abstract: This article reports on a preliminary work on the use of a Generative Lexicon based lexical resource to resolve bridging anaphors in Italian. The results obtained, though not very satisfying, seem to support the use of such a resource with respect to WordNet-like ones due to the wider range of bridging anaphors which can
Abductive, Causal, and Counterfactual Conditionals Under Incomplete Probabilistic Knowledge

We study abductive, causal, and non-causal conditionals in indicative and counterfactual formulations using probabilistic truth table tasks under incomplete probabilistic knowledge (N = 80). We frame the task as a probability-logical inference problem. The most frequently observed response type across all conditions was a class of conditional event interpretations of conditionals; it was followed by conjunction interpretations. An interesting minority of participants neglected some of the relevant imprecision involved in the premises when inferring lower or upper probability bounds on the target conditional/counterfactual ("halfway responses"). We discuss the results in the light of coherence-based probability logic and the new paradigm psychology of reasoning.
Characterization of the Reductase Domain of Rat Neuronal Nitric Oxide Synthase Generated in the Methylotrophic Yeast Pichia pastoris

Rat neuronal NO synthase (nNOS) is comprised of a flavin-containing reductase domain and a heme-containing oxygenase domain. Calmodulin binding to nNOS increases the rate of electron transfer from NADPH into its flavins, triggers electron transfer from flavins to the heme, activates NO synthesis, and increases reduction of artificial electron acceptors such as cytochrome c. To investigate what role the reductase domain plays in calmodulin's activation of these functions, we overexpressed a form of the nNOS reductase domain (amino acids 724-1429) in the yeast Pichia pastoris that for the first time exhibits a complete calmodulin response. The reductase domain was purified by 2′,5′-ADP affinity chromatography yielding 25 mg of pure protein per liter of culture. It contained 1 FAD and 0.8 FMN per molecule. Most of the protein as isolated contained an air-stable flavin semiquinone radical that was sensitive to FeCN6 oxidation. Anaerobic titration of the FeCN6-oxidized reductase domain with NADPH indicated the flavin semiquinone re-formed after addition of 1-electron equivalent and the flavins could accept up to 3 electrons from NADPH. Calmodulin binding to the recombinant reductase protein increased its rate of NADPH-dependent flavin reduction and its rate of electron transfer to cytochrome c, FeCN6, or dichlorophenolindophenol to fully match the rate increases achieved when calmodulin bound to native full-length nNOS. Calmodulin's activation of the reductase protein was associated with an increase in domain tryptophan and flavin fluorescence. We conclude that many of calmodulin's actions on native nNOS can be fully accounted for through its interaction with the nNOS reductase domain itself.
Opposing Fgf and Bmp activities regulate the specification of olfactory sensory and respiratory epithelial cell fates

The olfactory sensory epithelium and the respiratory epithelium are derived from the olfactory placode. However, the molecular mechanisms regulating the differential specification of the sensory and the respiratory epithelium have remained undefined. To address this issue, we first identified Msx1/2 and Id3 as markers for respiratory epithelial cells by performing quail chick transplantation studies. Next, we established chick explant and intact chick embryo assays of sensory/respiratory epithelial cell differentiation and analyzed two mice mutants deleted of Bmpr1a;Bmpr1b or Fgfr1;Fgfr2 in the olfactory placode. In this study, we provide evidence that in both chick and mouse, Bmp signals promote respiratory epithelial character, whereas Fgf signals are required for the generation of sensory epithelial cells. Moreover, olfactory placodal cells can switch between sensory and respiratory epithelial cell fates in response to Fgf and Bmp activity, respectively. Our results provide evidence that Fgf activity suppresses and restricts the ability of Bmp signals to induce respiratory cell fate in the nasal epithelium. In addition, we show that in both chick and mouse the lack of Bmp or Fgf activity results in disturbed placodal invagination; however, the fate of cells in the remaining olfactory epithelium is independent of morphological movements related to invagination. In summary, we present a conserved mechanism in amniotes in which Bmp and Fgf signals act in an opposing manner to regulate the respiratory versus sensory epithelial cell fate decision.
Evolutionary history of almond tree domestication in the Mediterranean basin

Genetic diversity of contemporary domesticated species is shaped by both natural and human‐driven processes. However, until now, little is known about how domestication has imprinted the variation of fruit tree species. In this study, we reconstruct the recent evolutionary history of the domesticated almond tree, Prunus dulcis, around the Mediterranean basin, using a combination of nuclear and chloroplast microsatellites [i.e. simple sequence repeat (SSRs)] to investigate patterns of genetic diversity. Whereas conservative chloroplast SSRs show a widespread haplotype and rare locally distributed variants, nuclear SSRs show a pattern of isolation by distance with clines of diversity from the East to the West of the Mediterranean basin, while Bayesian genetic clustering reveals a substantial longitudinal genetic structure. Both kinds of markers thus support a single domestication event, in the eastern side of the Mediterranean basin. In addition, model‐based estimation of the timing of genetic divergence among those clusters is estimated sometime during the Holocene, a result that is compatible with human‐mediated dispersal of almond tree out of its centre of origin. Still, the detection of region‐specific alleles suggests that gene flow from relictual wild preglacial populations (in North Africa) or from wild counterparts (in the Near East) could account for a fraction of the diversity observed.
Three-Dimensional Structure and Composition of CA3→CA1 Axons in Rat Hippocampal Slices: Implications for Presynaptic Connectivity and Compartmentalization

Physiological studies of CA3→CA1 synaptic transmission and plasticity have revealed both pre- and postsynaptic effects. Understanding the extent to which individual presynaptic axonal boutons could provide local compartments for control of synaptic efficacy and microconnectivity requires knowledge of their three-dimensional morphology and composition. In hippocampal slices, serial electron microscopy was used to examine a nearly homogeneous population of CA3→CA1 axons in the middle of stratum radiatum of area CA1. The locations of postsynaptic densities (PSDs), vesicles, and mitochondria were determined along 75 axon segments (9.1 ± 2.0 μm in length). Synapses, defined by the colocalization of PSDs and vesicles, occurred on average at 2.7 μm intervals along the axons. Most varicosities (68%) had one PSD, 19% had 2–4 PSDs, and 13% had none. Synaptic vesicles occurred in 90% of the varicosities. One-half (53%) of the varicosities lacked mitochondria, raising questions about their regulation of ATP and Ca2+, and 8% of varicosities contained only mitochondria. Eleven axons were reconstructed fully. The varicosities were oblong and varied greatly in both length (1.1 ± 0.7 μm) and volume (0.13 ± 0.14 μm3), whereas the intervaricosity shafts were narrow, tubular, and similar in diameter (0.17 ± 0.04 μm) but variable in length (1.4 ± 1.2 μm). The narrow axonal shafts resemble dendritic spine necks and thus could promote biochemical compartmentalization of individual axonal varicosities. The findings raise the intriguing possibility of localized differences in metabolism and connectivity among different axons, varicosities, and synapses.
Quantum random walk on the integer lattice: examples and phenomena

We apply results from Baryshnikov, Brady, Bressler and Pemantle (2008) to compute limiting probability profiles for various quantum random walks in one and two dimensions. Using analytic machinery we show some features of the limit distribution that are not evident in an empirical intensity plot of the time 10,000 distribution. Some conjectures are stated and computational techniques are discussed as well.
HER2 as a Prognostic Marker in Gastric Cancer - A Systematic Analysis of Data from the Literature

Through the recent conduct of the ToGA trial, HER2 has shown to be predictive for the treatment with trastuzumab in advanced gastric and gastro-oesophageal cancer. When it comes to the prognostic properties the situation is different. Despite the fact that it is more than 20 years ago since the first studies demonstrating an association between a positive HER2 status and poor prognosis were published the issue is still controversial. In this current systematic review a large number of studies on HER2 and gastric cancer have been reviewed. The studies included in this review should fulfill the following two criteria. First criterion: The number of patients in each study should be ≥ 100, and the HER2 status should have been determined either by immunohistochemistry (IHC) or in situ hybridization (ISH). Second criterion: The selected articles should include an analysis of the association between the HER2 status and survival or relevant clinicopathological characteristics. Forty-two publications with a total of 12,749 patients fulfilled the two criteria and were reviewed in detail. The majority of the publications (71%) showed that a HER2-postive status measured either by IHC or ISH was associated with poor survival and/or clinicopathological characteristics, such as serosal invasion, lymph node metastases, disease stage, or distant metastases. Based on the current analysis a clear trend towards a potential role for HER2 as a negative prognostics factor in gastric cancer was shown, suggesting that HER2 overexpression and/or amplification is a molecular abnormality that might be linked to the development of gastric cancer.
The Timing and Scale of Investment Under Uncertainty

This paper studies optimal investment in sunk assets for a firm facing uncertain future demand and costs. The investment problem is decomposed into decisions over scale and timing which are influenced by convex adjustment costs and the feasibility of delaying investment. The value of the resulting real option to delay behaves as expected in response to increases in demand and cost uncertainty but has new timing and scale interpretations. The larger is the option value, the more capital would be installed if delay were not profitable. The timing of investment, however, is controlled by the expected trajectory of capital prices relative to the firm's discount rate. The analysis also suggests an empirical model for aggregate investment which explains 96% of the variation in real annual investment for Canada over the period (1981-94) using regressors formed from only three variables: business confidence, capital prices and real interest rates.