Miracle-dz/UniFAR-FTUs huggingface dataset:
Semiconductor heterostructure design for non-linear optical process for quantum information technologies

Quantum information technologies require reliable sources of correlated/entangled photons. To realize and use these technologies in real life rather than just in laboratory, high efficiency and stable sources of entangled photons are needed. This work considers the design of various semiconductor heterostructures, based on Al$_x$Ga$_{1-x}$As/GaAs, that rely on intersubband transitions in the conduction or in the valence band, to deliver the second order nonlinear process, known as spontaneous parametric down-conversion (SPDC). The second-order SPDC can produce Bell state entangled photons. Second harmonic generation (SHG) is a well known and broadly discussed process, and using the fact that SHG is the reverse process of SPDC, initial studies of SHG are used to support the validity and accuracy of the methodology employed for nonlinear susceptibility calculations. In designing the heterostructures, genetic optimization is used to reduce the computational cost in finding the best structure. The heterostructures designed by considering the intersubband transitions in the conduction band constitute good sources of spectrally entangled photons. The efficiency of the process is estimated and the Schmidt number calculation shows that the structure can produce twin photons with a reasonably good degree of entanglement. Alternatively, using intersubband transitions in the valence band can deliver the polarization entangled photons, which cannot be achieved with conduction intersubband transitions. The genetic optimization is again used to design the best structures for this purpose, and the efficiency of the process is also calculated. We then extend our work to multiparticle entangled states, also known as Greenberger-Horne-Zeilinger (GHZ) states, by considering the third order nonlinear SPDC (TOSPDC) process in designing the heterostructures for this purpose. This designed structure can be a good candidate as a direct TOSPDC source, since the second order nonlinearity is here suppressed by considering symmetric structures only. The efficiency of the process is also calculated and discussed in the thesis.
Electron and proton heating by solar wind turbulence

[1] Previous formulations of heating and transport associated with strong magnetohydrodynamic (MHD) turbulence are generalized to incorporate separate internal energy equations for electrons and protons. Electron heat conduction is included. Energy is supplied by turbulent heating that affects both electrons and protons and is exchanged between them via collisions. Comparison to available Ulysses data shows that a reasonable accounting for the data is provided when (1) the energy exchange timescale is very long and (2) the deposition of heat due to turbulence is divided, with 60% going to proton heating and 40% into electron heating. Heat conduction, determined here by an empirical fit, plays a major role in describing the electron data.
Intra-individual variability of mycophenolic acid concentration according to renal function in liver transplant recipients receiving mycophenolate monotherapy

Backgrounds/Aims Mycophenolate mofetil (MMF) has wide inter- and intra-individual variability of mycophenolic acid (MPA) after liver transplantation (LT). On this study, we aimed to analyse the intra-individual variability of MPA concentration in stable adult LT recipients receiving MMF monotherapy and develop a method to determine the target level in the situation of wide intra-individual variability. Methods This retrospective cross-sectional study included 30 LT recipients. All patients received MMF monotherapy at a dose of 500 mg twice daily for ≥2 years and were divided into two groups based on renal function. MPA concentration-associated values were presented as mean with standard deviation and coefficient of variation (CV). Results The normal renal function group (n=15) showed a mean 12-hour MPA concentration of 2.5±0.5 µg/ml (range, 1.8±0.5 to 3.6±0.7 µg/ml) and a mean CV of 20.4±7.7% (range, 8.7% to 39.4%). In the renal dysfunction group (n=15), the 12-hour MPA concentration fluctuated more widely with a mean value of 3.7±0.9 µg/ml (range, 2.8±0.8 to 5.1±1.2 µg/ml) and a mean CV of 24.5±4.9% (range, 17.1% to 37.5%). The 12-hour MPA concentration was significantly higher in the renal dysfunction group, as compared to the normal renal function group (p=0.001); whereas, the CV was not significantly different between the two groups (p=0.093). Conclusions We determined the inter- and intra-individual variability of 12-hour MPA concentration after LT. The results suggested that therapeutic drug monitoring of MPA is necessary due to the inter-individual and intra-individual variability of MMF pharmacokinetics, especially in LT recipients with renal dysfunction.
New quantitative trait loci for carotid atherosclerosis identified in an intercross derived from apolipoprotein E-deficient mouse strains

Carotid atherosclerosis is the primary cause of ischemic stroke. To identify genetic factors contributing to carotid atherosclerosis, we performed quantitative trait locus (QTL) analysis using female mice derived from an intercross between C57BL/6J (B6) and BALB/cJ (BALB) apolipoprotein E (Apoe−/−) mice. We started 266 F2 mice on a Western diet at 6 wk of age and fed them the diet for 12 wk. Atherosclerotic lesions in the left carotid bifurcation and plasma lipid levels were measured. We genotyped 130 microsatellite markers across the entire genome. Three significant QTLs, Cath1 on chromosome (Chr) 12, Cath2 on Chr5, and Cath3 on Chr13, and four suggestive QTLs on Chr6, Chr9, Chr17, and Chr18 were identified for carotid lesions. The Chr6 locus replicated a suggestive QTL and was named Cath4. Six QTLs for HDL, three QTLs for non-HDL cholesterol, and three QTLs for triglyceride were found. Of these, a significant QTL for non-HDL on Chr1 at 60.3 cM, named Nhdl13, and a suggestive QTL for HDL on ChrX were new. A significant locus for HDL (Hdlq5) was overlapping with a suggestive locus for carotid lesions on Chr9. A significant correlation between carotid lesion sizes and HDL cholesterol levels was observed in the F2 population (R = −0.153, P = 0.0133). Thus, we have identified several new QTLs for carotid atherosclerosis and the locus on Chr9 may exert effect through interactions with HDL.
Computational design of a leucine-rich repeat protein with a predefined geometry

Significance Repeat proteins are used in nature to bind to proteins and peptides. The shape of their binding surfaces can vary substantially, even for proteins within the same family. This variability likely arose because they evolved to match the proteins they interact with geometrically. Repeat proteins are often engineered to develop binders specific to new target proteins. It would be highly beneficial to design repeat proteins with predefined geometrical shapes because such a method would enable development of engineered repeat proteins that are shape-optimized to their targets. Here, we demonstrate that repeat proteins with a predefined shape can be designed using a computational design method. The approach is exemplified by the design of a protein that forms a ring structure not seen in nature. Structure-based protein design offers a possibility of optimizing the overall shape of engineered binding scaffolds to match their targets better. We developed a computational approach for the structure-based design of repeat proteins that allows for adjustment of geometrical features like length, curvature, and helical twist. By combining sequence optimization of existing repeats and de novo design of capping structures, we designed leucine-rich repeats (LRRs) from the ribonuclease inhibitor (RI) family that assemble into structures with a predefined geometry. The repeat proteins were built from self-compatible LRRs that are designed to interact to form highly curved and planar assemblies. We validated the geometrical design approach by engineering a ring structure constructed from 10 self-compatible repeats. Protein design can also be used to increase our structural understanding of repeat proteins. We use our design constructs to demonstrate that buried Cys play a central role for stability and folding cooperativity in RI-type LRR proteins. The computational procedure presented here may be used to develop repeat proteins with various geometrical shapes for applications where greater control of the interface geometry is desired.
Small interfering RNA-mediated knockdown of PRL phosphatases results in altered Akt phosphorylation and reduced clonogenicity of pancreatic cancer cells

The PRL phosphatases have been implicated in cancer cell growth and metastasis in a variety of tumor types. Using cDNA microarray, we previously identified and reported PRL-1 as being highly up-regulated in pancreatic cancer cell lines. In this study, we sought to further evaluate the expression of all three PRL phosphatases in pancreatic cancer cell lines and extend our findings to in situ analysis of primary pancreatic tumors taken directly from patients. Additionally, we determine if small interfering RNA-mediated knockdown of relevant PRLs confers antitumor effects in pancreatic cancer cells. Using oligonucleotide expression arrays, mRNA levels of PRL-1 and PRL-2 but not PRL-3 were identified as up-regulated in pancreatic cancer cell lines and tumor samples taken directly from patients compared with those of normal pancreas. Focusing on PRL-1 and PRL-2, high levels of both proteins were detected in a subset of pancreatic cancer cell lines and tumor samples using Western blotting and immunohistochemistry, respectively. Small interfering RNA-mediated knockdown of PRL-1 and PRL-2 in combination resulted in a moderate reduction of cellular growth and migration in MIA PaCa-2 and PANC-1 cells. More importantly, knockdown of both PRL-1 and PRL-2 significantly inhibited colony formation of these cells in soft agar as well as serum-induced Akt phosphorylation. These data support the hypothesis that PRL phosphatases regulate key pathways involved in tumorigenesis and metastasis and that knockdown of both PRL-1 and PRL-2 is required to disrupt PRL phosphatase function in pancreatic cancer cells. [Mol Cancer Ther 2008;7(1):202–10]
An Ironic Tragedy: Are Spouses of Persons with Dementia at Higher Risk for Dementia than Spouses of Persons without Dementia?

This issue of JAGs includes a paper by Norton et al. (2010)1 that reports a 600% greater risk of dementia in spouses of persons with dementia relative to spouses of persons without dementia even after controlling for important risk factors for dementia. The authors explain their provocative finding using three arguments previously employed to understand the higher risks of health problems seen in spouses of persons with dementia relative to spouses of persons without dementia. These include assortative mating, a shared life-style, and caregiving.2 However, no caregiver data are presented to support their argument (e.g., hours of care, length of care, caregiver distress, health habits and health problems); and this study was not designed to test the hypothesis that caregiving is a risk factor for dementia. Despite these limitations, many of the spouses of persons with dementia were probably caregivers; and, although it is not possible to conduct mediation analyses to interpret this study’s result, the literature includes several caregiver outcomes that may be postulated as reasons for the observed higher dementia risk in spouses of persons with dementia.
Drosophila neuropeptide F mediates integration of chemosensory stimulation and conditioning of the nervous system by food.

The conserved neuropeptide Y (NPY) signaling pathway has been strongly implicated in the stimulation of food uptake in vertebrates as well as in the regulation of food conditioned foraging behaviors of Caenorhabditis elegans. Using in situ RNA hybridization and immunocytochemistry, we report the neuronal network of Drosophila neuropeptide F (dNPF), a human NPY homologue, in the larval central nervous system and its food-dependent modifications. We provide indications that gustatory stimulation by sugar, but not its ingestion or metabolism, is sufficient to trigger long-term, dose-dependent alterations of the dNPF neuronal circuit through both dnpf activation and increased synaptic transmission. Our results strongly suggest that the dNPF neuronal circuit is an integral part of the sensory system that mediates food signaling, providing the neural basis for understanding how invertebrate NPY regulates food response.
Model-Driven Optimization of Opportunistic Routing

Opportunistic routing aims to improve wireless performance by exploiting communication opportunities arising by chance. A key challenge in opportunistic routing is how to achieve good, predictable performance despite the incidental nature of such communication opportunities and the complicated effects of wireless interference in IEEE 802.11 networks. To address the challenge, we develop a model-driven optimization framework to jointly optimize opportunistic routes and rate limits for both unicast and multicast traffic. A distinctive feature of our framework is that the performance derived from optimization can be achieved in a real IEEE 802.11 network. Our framework consists of three key components: 1) a model for capturing the interference among IEEE 802.11 broadcast transmissions; 2) a novel algorithm for accurately optimizing different performance objectives; and 3) effective techniques for mapping the resulting solutions to practical routing configurations. Extensive simulations and testbed experiments show that our approach significantly outperforms state-of-the-art shortest-path routing and opportunistic routing protocols. Moreover, the difference between the achieved performance and our model estimation is typically within 20%. Evaluation in dynamic and uncontrolled environments further shows that our approach is robust against inaccuracy introduced by a dynamic network and it also consistently outperforms the existing schemes. These results clearly demonstrate the effectiveness and accuracy of our approach.
Serum anti-neuronal antibodies in amyotrophic lateral sclerosis

We aimed to investigate various anti-neuronal antibodies in sera of amyotrophic lateral sclerosis (ALS) patients to detect possible autoimmune encephalitis patients imitating ALS findings and to delineate the validity of routine screening of well-characterized anti-neuronal antibodies in ALS. The patients fulfilling the revised El Escorial diagnostic criteria for definite ALS were included. Their serum samples were investigated for antiganglioside (IgM/IgG) and onconeural (IgG) antibodies by immunoblotting, for ion channel antibodies (IgG) by a cell-based assay and for IgG binding patterns to the rat brain by indirect immunohistochemistry. Thirty-five patients with definite ALS and 30 healthy individuals were included. Ganglioside antibodies were detected in 2 out of 35 (5.7%) patients with ALS. The onconeural and ion channel antibodies were negative in our series. Varied serum IgG binding patterns were identified in eight (22.9%) patients. Although autoimmune encephalitis patients may occasionally present with atypical motor neuron disease findings, definite ALS patients do not appear to exhibit onconeural or ion channel antibodies, suggesting that routine analysis of these antibodies in typical ALS is not mandatory. By contrast, some ALS patients display anti-neuronal antibodies against undetermined target antigens, prompting investigation of these novel antibodies with more advanced methods.
Hydrology and Earth System Sciences Discussions Estimation of Vegetation Cover Resilience from Satellite Time Series

Papers published in Hydrology and Earth System Sciences Discussions are under open-access review for the journal Hydrology and Earth System Sciences Abstract Resilience is a fundamental concept for understanding vegetation as a dynamic component of the climate system. It expresses the ability of ecosystems to tolerate disturbances and to recover their initial state. Recovery times are basic parameters of the vegetation's response to forcing and, therefore, are essential for describing realistic 5 vegetation within dynamical models. Healthy vegetation tends to rapidly recover from shock and to persist in growth and expansion. On the contrary, climatic and anthropic stress can reduce resilience thus favouring persistent decrease in vegetation activity. In order to characterize resilience, we analyzed the time series 1982–2003 of 8 km GIMMS AVHRR-NDVI maps of the Italian territory. Persistence probability of negative 10 and positive trends was estimated according to the vegetation cover class, altitude, and climate. Generally, mean recovery times from negative trends were shorter than those estimated for positive trends, as expected for vegetation of healthy status. Some signatures of inefficient resilience were found in high-level mountainous areas and in the Mediterranean subtropical ones. This analysis was refined by aggregating pixels ac-15 cording to phenology. This multitemporal clustering synthesized information on vegetation cover, climate, and orography rather well. The consequent persistence estimations confirmed and detailed hints obtained from the previous analyses. Under the same climatic regime, different vegetation resilience levels were found. In particular, within the Mediterranean subtropical climate, clustering was able to identify features with differ-20 ent persistence levels in areas that are liable to different levels of anthropic pressure. Moreover, it was capable of enhancing reduced vegetation resilience also in the southern areas under Warm Temperate sub-continental climate. The general consistency of the obtained results showed that, with the help of suited analysis methodologies, 8 km AVHRR-NDVI data could be useful for capturing details on vegetation cover activity at 25 local scale even in complex territories such as that of the Italian peninsula.
Using Language Sampling in Clinical Assessments with Bilingual Children: Challenges and Future Directions

Current language tests designed to assess Spanish-English-speaking children have limited clinical accuracy and do not provide sufficient information to plan language intervention. In contrast, spontaneous language samples obtained in the two languages can help identify language impairment with higher accuracy. In this article, we describe several diagnostic indicators that can be used in language assessments based on spontaneous language samples. First, based on previous research with monolingual and bilingual English speakers, we show that a verb morphology composite measure in combination with a measure of mean length of utterance (MLU) can provide valuable diagnostic information for English development in bilingual children. Dialectal considerations are discussed. Second, we discuss the available research with bilingual Spanish speakers and show a series of procedures to be used for the analysis of Spanish samples: (a) limited MLU and proportional use of ungrammatical utterances; (b) limited grammatical accuracy on articles, verbs, and clitic pronouns; and (c) limited MLU, omission of theme arguments, and limited use of ditransitive verbs. Third, we illustrate the analysis of verb argument structure using a rubric as an assessment tool. Estimated scores on morphological and syntactic measures are expected to increase the sensitivity of clinical assessments with young bilingual children. Further research using other measures of language will be needed for older school-age children.
JNK1 and IKKβ: molecular links between obesity and metabolic dysfunction

Inflammation is thought to underlie the pathogenesis of many chronic diseases. It is now established that obesity results in a state of chronic low‐grade inflammation thought to contribute to several metabolic disorders' including insulin resistance and pancreatic islet dysfunction. The protein kinases JNK1 and IKKβ have been found to serve as critical molecular links between obesity, metabolic inflammation, and disorders of glucose homeostasis. The precise mechanisms of these linkages are still being investigated. However, as we discuss here, JNK1 and IKKβ are activated by almost all forms of metabolic stress that have been implicated in insulin resistance or islet dysfunction. Furthermore, both JNK1 and IKKβ are critically involved in the promotion of diet‐induced obesity, metabolic inflammation, insulin resistance, and β‐cell dysfunction. Understanding the molecular mechanisms by which JNK1 and IKKβ mediate obesity‐induced metabolic stress is likely to be of importance for the development of new treatments for a variety of obesity‐associated diseases. —Solinas, G. , Karin, M. JNK1 and IKKβ: molecular links between obesity and metabolic dysfunction. FASEB J. 24, 2596–2611 (2010). www.fasebj. org
Thermodynamic propensities of amino acids in the native state ensemble: Implications for fold recognition

An amino acid sequence, in the context of the solvent environment, contains all of the thermodynamic information necessary to encode a three‐dimensional protein structure. To investigate the relationship between an amino acid sequence and its corresponding protein fold, a database of thermodynamic stability information was assembled that spanned 2951 residues from 44 nonhomologous proteins. This information was obtained using the COREX algorithm, which computes an ensemble‐based description of the native state of a protein. It was observed that amino acid types partitioned unequally into high, medium, and low thermodynamic stability environments. Furthermore, these distributions were reproducible and were significantly different than those expected from random partitioning. To assess the structural importance of the distributions, simple fold‐recognition experiments were performed based on a 3D‐1D scoring matrix containing only COREX residue stability information. This procedure was able to recover amino acid sequences corresponding to correct target structures more effectively than scoring matrices derived from randomized data. High‐scoring sequences were often aligned correctly with their corresponding target profiles, suggesting that calculated thermodynamic stability profiles have the potential to encode sequence information. As a control, identical fold‐recognition experiments were performed on the same database of proteins using DSSP secondary structure information in the scoring matrix, instead of COREX residue stability information. The comparable performance of both approaches suggested that COREX residue stability information and secondary structure information could be of equivalent utility in more sophisticated fold‐recognition techniques. The results of this work are a consequence of the idea that amino acid sequences fold not into single, rigidly stable structures but rather into thermodynamic ensembles best represented by a time‐averaged structure.