Miracle-dz/UniFAR-FTUs huggingface dataset:
Camouflage mismatch in seasonal coat color due to decreased snow duration

Most examples of seasonal mismatches in phenology span multiple trophic levels, with timing of animal reproduction, hibernation, or migration becoming detached from peak food supply. The consequences of such mismatches are difficult to link to specific future climate change scenarios because the responses across trophic levels have complex underlying climate drivers often confounded by other stressors. In contrast, seasonal coat color polyphenism creating camouflage against snow is a direct and potentially severe type of seasonal mismatch if crypsis becomes compromised by the animal being white when snow is absent. It is unknown whether plasticity in the initiation or rate of coat color change will be able to reduce mismatch between the seasonal coat color and an increasingly snow-free background. We find that natural populations of snowshoe hares exposed to 3 y of widely varying snowpack have plasticity in the rate of the spring white-to-brown molt, but not in either the initiation dates of color change or the rate of the fall brown-to-white molt. Using an ensemble of locally downscaled climate projections, we also show that annual average duration of snowpack is forecast to decrease by 29–35 d by midcentury and 40–69 d by the end of the century. Without evolution in coat color phenology, the reduced snow duration will increase the number of days that white hares will be mismatched on a snowless background by four- to eightfold by the end of the century. This novel and visually compelling climate change-induced stressor likely applies to >9 widely distributed mammals with seasonal coat color.
Simultaneous determination of seven pesticides in waters using multi‐walled carbon nanotube SPE and NACE

In this work, NACE with UV detection is combined with SPE using multi‐walled carbon nanotubes (MWCNT) as stationary phase to determine a group of seven pesticides (pirimicarb, pyrifenox, penconazol, carbendazim, cyromazine, pyrimethanil and cyprodinil) in mineral water samples using ametryn as internal standard. The optimized BGE, consisting of a mixture of MeOH and ACN (1:2 v/v) with 90 mM SDS and 20.5 mM HClO4, was satisfactory to get a good resolution of the seven compounds in less than 13 min. On‐line preconcentration was carried out by electrokinetic injection of the sample dissolved in 78:22 v/v MeOH/ACN, 1.11 mM HClO4. Repeatability was studied for the same day (n=4), for nine different days (n=36) and for four different capillaries. RSD values were appropriate in all cases, i.e. in the range 4.3–9.4% between different capillaries. MWCNT of 10–15 nm od, 2–6 nm id and 0.1–10 μm length were used as SPE materials for the preconcentration of these pesticides from water samples. SPE parameters influencing the enrichment were optimized and the most favorable conditions were as follows: the amount of stationary phase, eluent, sample pH and sample volume were 40 mg MWCNT, 10 mL ACN and 10 mL dichloromethane containing 5% v/v formic acid, pH 8.0, and 750 mL, respectively. Mean recovery values ranged between 53 and 94% for Milli‐Q water and between 47 and 93% for mineral waters (RSD values were in the range 2–16%). The method allowed the determination of these pesticides at concentrations below the maximum residue limits established by the European Union legislation (LOD in the range 27–58 ng/L). When the cost, amount and type of the carbon nanotubes used in this work are compared with those carbon nanotubes previously used in the literature it is clear that the proposed materials can be used as economical stationary phases, even cheaper than conventional SPE cartridges.
Communicating Visually: Videoconferencing and Remote and Rural First Nations

Videoconferencing is usually perceived as something useful for institutional reasons - primarily telehealth and distance education. First Nations are using videoconferencing not only for health and education but also in other ways for community, economic and social development. This paper discusses findings from a SSHRC-funded study of First Nations organizations that are supporting the use of video communications by rural and remote communities. The discussion explores why visual communication is important for First Nations, the prevalence and purposes of videoconferencing in non-institutional settings, and the challenges the communities experience using this technology. The central theme of this paper is that videoconferencing is a vital tool for remote and rural First Nations and in order for it to become widely used, the technology has to be a part of everyday life in communities and not just restricted to telehealth and distance education. Further, if we can find ways to increase the use of videoconferencing in non- institutional settings by everyone in First Nations communities, the technology will be used more often for institutional applications. Thus, increasing the non-institutional, everyday use of videoconferencing will have a positive impact on its use for telehealth and distance education. The paper includes recommendations for policy makers to support the more widespread use of this powerful communication technology by remote and rural First Nations.
Bacterial expression and characterization of the CREB bZip module: Circular dichroism and 2D 1H‐NMR studies

In this paper we describe the expression and purification from bacteria of the recombinant basic leucine zipper (bZip) domain of the cAMP response element binding protein, CREB327. The bZip peptide, CREB259–327, purified to near homogeneity, maintains the sequence‐specific CRE site recognition demonstrated by in vitro competition assays. Alkylation of the three cysteine residues of CREB259–327 was employed to prevent aggregation of the peptide due to cysteine oxidation. The Kd of the purified native and modified CREB259–327 for the CRE site was determined by gel retardation assays to be on the order of 10−7 M. We employed CD spectroscopy to study the folding properties of the native and modified CREB259–327. The CD analyses of the native/modified CREB259–327 peptide demonstrated a 20% increase in the α‐helical content upon binding to the cAMP response‐element. Only a 5% increase in the α‐helical content of CREB259–327 is observed upon binding to the AP‐1 site. This observation contrasts with CREB from the GCN4 protein (Weiss, M.A., et al., 1990, Nature 347, 575–578). In addition, the two‐dimensional (2D) 1H‐NMR studies of the bZip CREB peptide further support the distinct features of the CREB protein, in comparison to GCN4. Analysis by CD and 2D NMR of the dimerization domain of CREB suggests that the distinct DNA binding characteristics of CREB reside in the basic portion of the bZip module.
A double-screening method to identify reliable candidate non-synonymous SNPs from chicken EST data.

Discovery of non-synonymous single nucleotide polymorphisms (nsSNP), which cause amino acid substitutions, is important because they are more likely to alter protein function than synonymous SNPs (sSNP) or those SNPs that do not result in amino acid changes. By changing the coding sequences, nsSNP may play a role in heritable differences between individual organisms. In the chicken and many other vertebrates, the main obstacle for identifying nsSNP is that there is insufficient protein and mRNA sequence information for self-species referencing and thus, determination of the correct reading frame for expressed sequence tags (ESTs) is difficult. Therefore, in order to estimate the correct reading frame at nsSNP in chicken ESTs, a double-screening approach was designed using self- or cross-species protein referencing, in addition to the ESTScan coding region estimation programme. Starting with 23 427 chicken ESTs, 1210 potential SNPs were discovered using a phred/phrap/polyphred/consed pipeline process and among these, 108 candidate nsSNP were identified with the double screening method. A searchable SNP database (chicksnps) for the candidate chicken SNPs, including both nsSNPs and sSNPs is available at http://chicksnps.afs. udel.edu. The chicken SNP data described in this paper have been submitted to the data base SNP under National Center for Biotechnology Information assay ID ss4387050-ss4388259.
Post-transplant obstructive lung disease ("bronchiolitis obliterans"): a clinical comparative study of bone marrow and lung transplant patients.

Patients at a single pulmonary centre who developed obstructive lung disease after bone marrow transplantation (BMT) and lung transplantation (LT) were studied, in order to compare the clinical expression of post-transplant obstructive lung disease (PTOLD) (bronchiolitis obliterans) in these two conditions, which have so far been studied separately. Nine out of 179 patients surviving more than 100 days after BMT (5%) and 9 out of 44 patients surviving more than 100 days after LT (20%) developed post-transplant obstructive lung disease. This was defined by an irreversible airflow obstruction, as characterized by a forced expiratory volume in one second divided by forced vital capacity (FEV1/FVC) of less than 70%, and a FEV1 of less than 70% of predicted value. The mean interval between transplantation and the diagnosis of post-transplant obstructive lung disease was 262 days and 217 days for BMT and LT patients, respectively. In all cases, pulmonary symptoms consisted of dyspnoea and progressively productive cough. Bronchial dilatation on high-resolution computed tomography scans was the main imaging feature present in both groups of patients at the onset of post-transplant obstructive lung disease. The mean FEV1/FVC ratio was 51 and 54% for BMT and LT patients, respectively. All BMT and LT patients had normal transfer coefficient. Clinical chronic graft-versus-host disease was present in all BMT patients before or concurrent with the onset of post-transplant obstructive lung disease, and all LT patients had presented at least one episode of acute lung rejection. (ABSTRACT TRUNCATED AT 250 WORDS)
Compromised Catalysis and Potential Folding Defects in in Vitro Studies of Missense Mutants Associated with Hereditary Phosphoglucomutase 1 Deficiency*

Background: Phosphoglucomutase 1 deficiency is a newly described inherited disorder in humans. Results: In vitro studies of 13 missense variants associated with disease are presented. Conclusion: Compromised catalysis and differential effects on recombinant protein folding/stability are found. Significance: Biochemical defects are consistent with previous in vivo studies and may have clinical relevance. Recent studies have identified phosphoglucomutase 1 (PGM1) deficiency as an inherited metabolic disorder in humans. Affected patients show multiple disease phenotypes, including dilated cardiomyopathy, exercise intolerance, and hepatopathy, reflecting the central role of the enzyme in glucose metabolism. We present here the first in vitro biochemical characterization of 13 missense mutations involved in PGM1 deficiency. The biochemical phenotypes of the PGM1 mutants cluster into two groups: those with compromised catalysis and those with possible folding defects. Relative to the recombinant wild-type enzyme, certain missense mutants show greatly decreased expression of soluble protein and/or increased aggregation. In contrast, other missense variants are well behaved in solution, but show dramatic reductions in enzyme activity, with kcat/Km often <1.5% of wild-type. Modest changes in protein conformation and flexibility are also apparent in some of the catalytically impaired variants. In the case of the G291R mutant, severely compromised activity is linked to the inability of a key active site serine to be phosphorylated, a prerequisite for catalysis. Our results complement previous in vivo studies, which suggest that both protein misfolding and catalytic impairment may play a role in PGM1 deficiency.
Intrinsic Gilbert damping constant in Co/sub 2/MnAl Heusler alloy films

Intrinsic /spl alpha/-damping constants of Co/sub 2/MnAl Heusler alloy films prepared by magnetron sputtering were investigated. After deposition of Co/sub 2/MnAl films, the films were annealed at 200-400/spl deg/C to control the crystal structure and the atomic order between Co, Mn, and Al sites. Ferromagnetic resonance (FMR) technique was used to obtain /spl alpha/ values of Co/sub 2/MnAl films in this study. Out-of-plane angular dependences of the resonance field (H/sub R/) and linewidth (/spl Delta/H/sub pp/) of FMR spectra were measured and fitted using the Landau-Lifshitz-Gilbert (LLG) equation. The authors were able to fit all experimental results well because of the lack of inhomogeneities in prepared Co/sub 2/MnAl films. The /spl alpha/-damping constants obtained from the fitting results decreased with increasing annealing temperature and showed a minimum value of 0.007 at 300/spl deg/C. It was found that a degree of B2 structure order can sensitively affect /spl alpha/-damping constants of Co/sub 2/MnAl films.
Expression of Various Microtubule‐Associated Protein 2 Forms in the Developing Mouse Brain and in Cultured Neurons and Astrocytes

Abstract: A cDNA probe specific to microtubule‐associated protein 2 (MAP2) was used to study the expression of the mRNAs encoding the high‐ and low‐molecular‐weight MAP2 variants in cultured neurons and astrocytes. The timing and relative abundance of these MAP2 transcripts and of their encoded proteins were also studied in the developing cerebral hemispheres and cerebellum of the mouse. A 9‐kb mRNA, known to encode high‐molecular‐weight MAP2, was expressed in cultured astrocytes, albeit at a lower level than in neurons. The 6‐kb transcript, recently shown to encode low‐molecular‐weight MAP2 (MAP2c), was expressed in neurons and was the predominant MAP2 transcript of the astrocytes. The level of the 9‐ and 6‐kb transcripts decreased at late stages of astroglial and neuronal cell culture. The 9‐kb mRNA was detected in the cerebellum and cerebral hemispheres at every developmental stage. Although the levels of this mRNA varied slightly in the cerebral hemispheres, its expression was biphasic in the cerebellum. This might be explained by the differences in timing of development of the various neuronal cell types formed in these two brain areas. The 6‐kb transcript was detected only at early developmental stages in the two brain areas. Correlating the temporal expression of the 9‐kb mRNA to that of high‐molecular‐weight MAP2 indicates that the accumulation of this protein is in part regulated at a cytoplasmic level.
Stock Market Volatility and Returns: A Study of NSE & BSE in India

The paper examines the relationship between returns and volatility, volatility clustering, leverage effect and the persistence of volatility for the Indian stock markets viz. National Stock Exchange (NSE) and Bombay Stock Exchange (BSE) for the financial year 2005-06 to 2013-14. The GARCHM model is used to examine the volatility clustering and persistence of volatility and the relationship between returns and volatility. The EGARCH model is used to capture the asymmetric effect. The study reveals that the volatility in both the markets exhibits the characteristics like volatility clustering, asymmetry effect and persistence of volatility in their daily returns. The study finds that the recent news as well as past news both has an impact on volatility. The study also finds the existence of leverage effect indicating that the negative shocks or bad news have more impact on volatility than that of positive shocks or good news. The relationship between returns and volatility is not significant for both the markets.
Adenovirus Transforming Protein E1A Induces c-Myc in Quiescent Cells by a Novel Mechanism

ABSTRACT Previously we showed that the E1A binding proteins p300 and CBP negatively regulate c-Myc in quiescent cells and that binding of E1A to p300 results in the induction of c-Myc and thereby induction of S phase. We demonstrated that p300 and HDAC3 cooperate with the transcription factor YY1 at an upstream YY1 binding site and repress the Myc promoter. Here we show that the small E1A protein induces c-Myc by interfering with the protein-protein interaction between p300, YY1, and HDAC3. Wild-type E1A but not the E1A mutants that do not bind to p300 interfered in recruitment of YY1, p300, and HDAC3 to the YY1 binding site. As E1A started to accumulate after infection, it transiently associated with promoter-bound p300. Subsequently, YY1, p300, and HDAC3 began to dissociate from the promoter. Later in infection, E1A dissociated from the promoter as well as p300, YY1, and HDAC3. Removal of HDAC3 from the promoter correlated with increased acetylation of Myc chromatin and induction. In vivo E1A stably associated with p300 and dissociated YY1 and HDAC3 from the trimolecular complex. In vitro protein-protein interaction studies indicated that E1A initially binds to the p300-YY1-HDAC3 complex, briefly associates with it, and then dissociates the complex, recapitulating somewhat the in vivo situation. Thus, E1A binding to the C-terminal region of p300 disrupts the important corepressor function provided by p300 in repressing c-Myc. Our results reveal a novel mechanism by which a viral oncoprotein activates c-Myc in quiescent cells and raise the possibility that the oncoproteins encoded by the small-DNA tumor viruses may use this mechanism to induce c-Myc, which may be critical for cell transformation.
Operationalizing a contested concept: indicators of territorial cohesion

ABSTRACT European territorial policies increasingly refer to broad goals such as sustainability, well-being and cohesion. For their operationalization as political goals, there is a need to create indicators. But how can an indicator be meaningful in relation to a complex concept that is not well defined? If the creation of an indicator is primarily aimed at quantifying a concept and making it more operational, in the case of a contested concept (such as territorial cohesion), the process of building indicators also helps stabilize it, allowing a potential decontestation. A participatory constructivist approach – as used by the ESPON project Indicators for Territorial Cohesion (INTERCO) – is considered to be the most suitable for building indicators of contested concepts. While ensuring computability of the indicators, it allows more flexibility and reconciles the different meanings of the concept in order to stabilize it. Ultimately, the validity of indicators of contested concepts lies in pragmatic criteria: usability, usefulness and use.
EventThread: Visual Summarization and Stage Analysis of Event Sequence Data

Event sequence data such as electronic health records, a person's academic records, or car service records, are ordered series of events which have occurred over a period of time. Analyzing collections of event sequences can reveal common or semantically important sequential patterns. For example, event sequence analysis might reveal frequently used care plans for treating a disease, typical publishing patterns of professors, and the patterns of service that result in a well-maintained car. It is challenging, however, to visually explore large numbers of event sequences, or sequences with large numbers of event types. Existing methods focus on extracting explicitly matching patterns of events using statistical analysis to create stages of event progression over time. However, these methods fail to capture latent clusters of similar but not identical evolutions of event sequences. In this paper, we introduce a novel visualization system named EventThread which clusters event sequences into threads based on tensor analysis and visualizes the latent stage categories and evolution patterns by interactively grouping the threads by similarity into time-specific clusters. We demonstrate the effectiveness of EventThread through usage scenarios in three different application domains and via interviews with an expert user.
Phase Constancy in a Ladder Model of Neural Dynamics

This paper presents a novel concept of modeling biological systems by means of preserving the natural rules governing the system's dynamics, i.e., their intrinsic fractal (recurrent) structure. The purpose of this paper is to illustrate the capability of recurrent ladder networks to capture the intrinsic recurrent anatomy of neural networks and to provide a dynamic model which shows typical neuronal phenomena, such as the phase constancy. As an illustrating example, the simplified model for a neural network consisting of motor neurons is used in simulation of a recurrent ladder network. Starting from a generalized approach, it is shown that, in the steady state, the result converges to a constant-phase behavior. The outcome of this paper indicates that the proposed model is a suitable tool for specific neural models in various neuroscience applications, being able to capture their fractal structure and the corresponding fractal dynamic behavior. A link to the dynamics of EEG activity is suggested. By studying specific neural populations by means of the ladder network model presented in this paper, one might be able to understand the changes observed in the EEG with normal aging or with neurodegenerative disorders.
Effects of Lip Color on Perceived Lightness of Human Facial Skin

Whereas geometric illusions in human faces have been reported by several studies, illusions of color or lightness in faces have seldom been explored. Here, we psychophysically investigated whether lip color influences facial skin’s perceived lightness. Results of Experiment 1 demonstrated that redder lips lightened and darker lips darkened the perceived complexion. These lightness or darkness inducing effects differ from the classical illusion of lightness contrast in nonface objects for two reasons. First, illusory effects are more assimilative than contrastive. Second, the inducing area (i.e., lips) is much smaller than the influenced area (facial skin). Experiment 2 showed that the assimilative lightness induction was caused by holistic processing of faces. This is the first study to scientifically substantiate the claim of cosmetics manufacturers and makeup artists that lip colors can alter perceived facial skin color. Implications for face perception, lightness illusion, and perceptual effects of cosmetics are discussed.
Essays on Pension Finance and Dynamic Asset Allocation.

This thesis addresses a few topics in pension finance and dynamic asset allocation, including: (i) the quality of pension profile of condition indexation schemes from a life-cycle investment perspective; (ii) the valuation of conditionally indexed pension liabilities in the framework of market valuation; (iii) the optimal consumption and portfolio decision in a setting where expected returns on stocks are time-varying, but unobservable; and (iv) how to include the asset class of commodities into the traditional portfolio of stocks and bonds by investigating the implications of commodity return predictability arising from mean-reverting commodity prices.