Miracle-dz/UniFAR-FTUs huggingface dataset:
Decoding the energy landscape: extracting structure, dynamics and thermodynamics

Describing a potential energy surface in terms of local minima and the transition states that connect them provides a conceptual and computational framework for understanding and predicting observable properties. Visualizing the potential energy landscape using disconnectivity graphs supplies a graphical connection between different structure-seeking systems, which can relax efficiently to a particular morphology. Landscapes involving competing morphologies support multiple potential energy funnels, which may exhibit characteristic heat capacity features and relaxation time scales. These connections between the organization of the potential energy landscape and structure, dynamics and thermodynamics are common to all the examples presented, ranging from atomic and molecular clusters to biomolecules and soft and condensed matter. Further connections between motifs in the energy landscape and the interparticle forces can be developed using symmetry considerations and results from catastrophe theory.
Automatic ASET sensitivity evaluation of a custom-designed 180nm CMOS technology operational amplifier

This work presents a SPICE-based automatic SET sensitivity evaluation of a 180nm CMOS full-custom Operational Amplifier. The set-up uses the well known double exponential current law to inject SET into every sensitive node in the circuit hierarchy. The pulse parameters are obtained according to a previously generated population of particles with randomly assigned energies and species, the node bias condition at the instant of the strike and an empirical model obtained through TCAD simulations. The circuit is evaluated transistor-wise for each ion of the generated database and the output waveforms are processed in time and frequency domain to obtain figures of merit of the hardness of the proposed design on a given radioactive environment. Results allow to identify the most sensitive devices and the expected error rate for the projected application, allowing to conduct hardening techniques during early design stages.
DFT-Based Channel Estimation and Noise Variance Estimation Techniques for Single-Carrier FDMA

Practical frequency domain equalization (FDE) systems generally require knowledge of the channel and the noise variance to equalize the received signal in a frequency-selective fading channel. Accurate channel estimate and noise variance estimate are thus desirable to improve receiver performance. In this paper we investigate the performance of the denoise channel estimator and the approximate linear minimum mean square error (A-LMMSE) channel estimator with channel power delay profile (PDP) mismatch and noise variance estimation errors for a single carrier frequency division multiple access (SC-FDMA) system. A windowed DFT-based noise variance estimator is also presented in this paper to improve A-LMMSE channel estimation as well as to facilitate the MMSE-FDE design. Results show that the proposed noise variance estimator remains unbiased up to a SNR of 50dB.
A Dictionary Based Indexing Approach for Music Information Retrieval

With the rapid progress of storage technologies and communication networks, there has been an explosive growth of digital music information. How to organize and search large scale music collection is one of the most fundamentally challenging research problems. According to the musical form structure and repetition rule of musical theme, repeating patterns can be regarded as the representation of musical themes. Statistical analysis indicates that repeating patterns in music collection also follow Zipf's law. Therefore we introduce a dictionary based indexing approach to organize and index music collection, where the musical dictionary comprises repeating patterns. Then all music melodies are partitioned into words using forward or backward word segmentation method with the musical dictionary. Experimental results reveal that the proposed indexing method can be applied to music information retrieval effectively, and possesses obvious advantages when the scale of music collection increases drastically.
The lifecycle of semidiurnal internal tides over the northern Mid-Atlantic Ridge

AbstractThe life cycle of semidiurnal internal tides over the Mid-Atlantic Ridge (MAR) sector south of the Azores is investigated using in situ, a high-resolution mooring and microstructure profiler, and satellite data, in combination with a theoretical model of barotropic-to-baroclinic tidal energy conversion. The mooring analysis reveals that the internal tide horizontal energy flux is dominated by mode 1 and that energy density is more distributed among modes 1–10. Most modes are compatible with an interpretation in terms of standing internal tides, suggesting that they result from interactions between waves generated over the MAR. Internal tide energy is thus concentrated above the ridge and is eventually available for local diapycnal mixing, as endorsed by the elevated rates of turbulent energy dissipation e estimated from microstructure measurements. A spring–neap modulation of energy density on the MAR is found to originate from the remote generation and radiation of strong mode-1 internal tides fr.
The ABCIT research platform

We present a portable, binaural, real-time research platform for cochlear implant devices. The platform consists of hardware and software parts. The research hardware is responsible for the 4-channel input audio signal as well as for the electric stimulation of the cochlea. The software includes a highly flexible research environment for the development of sound pre-processing (“speech processing”) and stimulation strategies. The interface between hardware and software is fully bi-directional, supporting recording capabilities of objective measures specific to the connected implant device. Hence, this platform enables the researchers to perform a diversity of experiments related to cochlear implant research.
Production, purification, 14C labeling, and bioavailability of fumonisin B1 produced by Fusarium proliferatum strain M-5991

vii CHAPTER 1. GENERAL INTRODUCTION I A. Introduction 1 B. Dissertation Organization 1 C. References 2 CHAPTER 2. LITERATURE REVIEW 3 A. Why Study Fumonisins? 3 B. Fumonisins in Com 7 1. Fusarium strains and toxins 7 2. Occurrence of Fusarium fungi and FBs in foods 8 3. Detoxification of FBs 11 C. Growth Parameters of Fusarium Fungi 14 1. Solid growth media 14 2. Liquid growth medium 15 D. Fumonisin Analysis 16 1. Fluorometry 16 2. ELISA 19 3. Other analytical methods 20 E. Fumonisin Clean-Up 21 1. Solid matrices 21 F. Fumonisin Purification 22 1. Solid matrices 22 2. Liquid matrices 24 G. Isotope Labeling of Fumonisin B, 24 1. Deuterium labeling 24 2. '^C Labeling 25 3. '"C Labeling 25 H. Fumonisin Toxicity 27 1. History 27 2. Alteration of sphinganine and sphingosine metabolism 31 3. Liver and kidney toxicity 33 4. Developmental toxicity 37 5. Cytotoxicity 38 6. Carcinogenicity 42 7. Atherosclerotic effects of FBs 44 I. Bioavailability of Fumonisin in Rats 44 J. References 49
Nonlinear Cuffless Blood Pressure Estimation of Healthy Subjects Using Pulse Transit Time and Arrival Time

This paper presents a novel blood pressure (BP) estimation method based on pulse transit time (PTT) and pulse arrival time (PAT) to estimate the systolic BP (SBP) and the diastolic BP (DBP). A data acquisition hardware is designed for high-resolution sampling of phonocardiogram (PCG), photoplethysmogram, and electrocardiogram (ECG). PCG and ECG perform as the proximal timing reference to obtain PTT and PAT indices, respectively. In order to derive a BP estimator model, a calibration procedure, including a supervised physical exercise, is conducted for each individual, which causes changes in their BP, and then, a number of reference BPs are measured alongside the acquisition of the signals per subject. It is suggested to use a force-sensing resistor that is placed under the cuff of the BP reference device to mark the exact moments of reference BP measurements, which are corresponding to the inflation of the cuff. Additionally, a novel BP estimator nonlinear model, based on the theory of elastic tubes, is introduced to estimate the BP using PTT/PAT values precisely. The proposed method is evaluated on 32 subjects. Using the PTT index, the correlation coefficients for SBP and DBP estimation are 0.89 and 0.84, respectively. Using the PAT index, the correlation coefficients for SBP and DBP estimation are 0.95 and 0.84, respectively. The results show that the proposed method, exploiting the introduced nonlinear model with the use of PAT index or PTT index, provides a reliable estimation of SBP and DBP.
Intervening Effects of Knowledge, Morality, Trust, and Benefits on Support for Animal and Plant Biotechnology Applications

Data from a regional Southwest telephone survey in the United States (N= 432) were used to examine the intervening effects of knowledge, morality, trust, and benefits on support for animal and plant biotechnology applications. Results showed that perceptions of agricultural biotechnologies varied by the two applications—animals and plants. Respondents reported higher opposition to the genetic modification of animals, which is consistent with prior research. Results also indicated that morality and perceived benefits directly affected support for both animal and plant applications, but trust and knowledge only had indirect effects. Morality and perceived benefits accounted for most of the variance explained among the intervening variables. The effects of trust were mediated through perceived benefits. The effects of knowledge on support were mediated primarily through trust. The influence of sociodemographic and consumer behavior variables varied by application. Results lend support to several theoretical notions. First, the significance of perceived benefits supports that there is an inverse relationship between benefits and risks. Second, moral objections may outweigh perceived benefits for specific applications, and the genetic modification of animals is deemed to be more morally unacceptable than the genetic modification of plants. These findings demonstrate the need to understand more thoroughly the moral and ethical issues surrounding novel technologies. Third, this research supports the claim that trust is not a powerful predictor of perceptions of technological products, which is contrary to most risk perception research.
Folliculin Contributes to VHL Tumor Suppressing Activity in Renal Cancer through Regulation of Autophagy

Von Hippel-Lindau tumor suppressor (VHL) is lost in the majority of clear cell renal cell carcinomas (ccRCC). Folliculin (FLCN) is a tumor suppressor whose function is lost in Birt-Hogg-Dubé syndrome (BHD), a disorder characterized by renal cancer of multiple histological types including clear cell carcinoma, cutaneous fibrofolliculoma, and pneumothorax. Here we explored whether there is connection between VHL and FLCN in clear cell renal carcinoma cell lines and tumors. We demonstrate that VHL regulates expression of FLCN at the mRNA and protein levels in RCC cell lines, and that FLCN protein expression is decreased in human ccRCC tumors with VHL loss, as compared with matched normal kidney tissue. Knockdown of FLCN results in increased formation of tumors by RCC cells with wild-type VHL in orthotopic xenografts in nude mice, an indication that FLCN plays a role in the tumor-suppressing activity of VHL. Interestingly, FLCN, similarly to VHL, is necessary for the activity of LC3C-mediated autophagic program that we have previously characterized as contributing to the tumor suppressing activity of VHL. The results show the existence of functional crosstalk between two major tumor suppressors in renal cancer, VHL and FLCN, converging on regulation of autophagy.
Immersive VR: a non-pharmacological analgesic for chronic pain?

This paper describes the research work being carried out by the Transforming Pain Research Group -- the only group whose work is entirely focused on the use of immersive VR for chronic pain management. Unlike VR research for acute or short-term pain, which relies on pain "distraction," this research posits a new paradigm for the use of VR. In addition to providing an overview of our work, the present paper also describes one of our current works in detail: the Virtual Meditative Walk.
Optimized protocol for the 2‐DE of extracellular proteins from higher basidiomycetes inhabiting lignocellulose

Basidiomycetes inhabiting lignocellulose comprise an important class of filamentous fungi with ecological and biotechnological relevance. Extracellular enzymes of wood‐degrading fungi such as laccases, manganese‐dependent (or independent) peroxidases, cellulases and xylanases are of considerable interest for biotechnological applications. Still, proteomic studies of fungal secretomes based on 2‐DE can be very challenging due to low protein concentrations and variable amounts of fungal metabolites. Comparison of different standard methods for protein precipitation has demonstrated their limited applicability to fungal secretomes. The extracellular metabolites impair standard methods for protein quantification and can result in a strong overestimation of total protein. We have developed an optimized protocol for the precipitation of extracellular proteins from liquid cultures of Coprinopsis cinerea growing in an exponential phase on a complex media. We found that a considerable amount of gelatinous material can be removed from the liquid culture supernatants by high‐speed centrifugation. Fungal proteins can be effectively enriched by TCA precipitation and coprecipitated metabolites hampering 2‐DE can be removed through the application of Tris/acetone. Following our protocol makes it possible to concentrate proteins from culture supernatants and to simultaneously remove most of the impeding compounds from a given sample. We have applied this procedure in the 2‐DE of secretomes from the model organism C. cinerea as well as other basidiomycetes such as Pleurotus ostreatus, Phanerochaete chrysosporium, Polyporus brumalis and Schizophyllum commune.
Dinâmica de energia, água e carbono em área de pastagem no semiárido pernambucano

Com os cenarios de mudancas climaticas apontando aumento da temperatura do ar, com previsao de reducao dos recursos hidricos de varias regioes do mundo, a exemplo do semiarido nordestino, em decorrencia do crescente aumento da emissao de gases de efeito estufa, dentre eles o dioxido de carbono (CO2), estudos que investiguem a relacao entre os fluxos de agua, energia e CO2 de ecossistemas agricolas sao de fundamental importância para se compreender o efeito das mudancas climaticas na agricultura. A covariância dos vortices turbulentos (Eddy Covariance – EC) e um metodo que fornece alta resolucao temporal de medicoes fluxos de energia, agua e CO2 entre a superficie e a atmosfera e nos ultimos anos tem sido considerado a ferramenta padrao desse tipo de estudo. Desse modo o presente trabalho teve como objetivos i) avaliar a variacao sazonal dos fluxos de energia, agua e carbono; ii) verificar o particionamento energia e agua iii) quantificar o grau com que os fatores ambientais afetam os padroes diarios e sazonais da evapotranspiracao iv) relacionar o fluxo de CO2 com o crescimento vegetal e v) determinar os componentes do balanco hidrico. Entre janeiro de 2012 e dezembro de 2013, medidas de fluxos de calor sensivel (H), calor latente (LE) e dioxido de carbono FCO2 foram realizados pelo metodo da covariância de vortices turbulentos em uma area de pastagem no semiarido de Pernambuco. Alem dessas medidas, foram realizados os monitoramento da precipitacao pluviometrica (P), da variacao no armazenamento de agua (DA) e do escoamento superficial (ES) para determinacao do balanco hidrico. Medidas de planta e o NDVI (Indice de Vegetacao por Diferenca Normalizada) foram quantificados para acompanha as mudancas na fenologia e a atividade da vegetacao. Analises de regressao foram realizadas para avaliar a relacao entre as variaveis. Os valores de P nos dois anos de estudo foram inferiores a normal climatologica da regiao. A temperatura media do ar em 2013 aumentou 0,66 ◦C em comparacao a 2012. Foi observado que a fracao H/Rn aumentou do periodo umido para o periodo seco, e em todos os periodos H foi superior ao LE, com excecao dos periodos com ocorrencia de significativos eventos de P. A constante de Priestley-Taylor (a) indicou que o armazenamento de agua no solo controlou a evapotranspiracao (ET) durante quase todo momento. A maior parte de P foi transferida para a atmosfera via ET, seguida do escoamento superficial (ES), que juntos somaram mais de 77% de P. A integracao dos dados do fluxo de carbono indicou uma absorcao media pelo ecossistema equivalente a 2,15 Mg C ha−1 ano−1.
Analysis of Protein Sequences Using Time Frequency and Analysis of Protein Sequences Using Time Frequency and Kolmogorov-Smirnov Methods Kolmogorov-Smirnov Methods Analysis of Protein Sequences Using Time Frequency and Kolmogorov-Smirnov Methods

The plethora of genomic data currently available has resulted in a search for new algorithms and analysis techniques to interpret genomic data. In this two-fold study we explore techniques for locating critical amino acid residues in protein sequences and for estimating the similarity between proteins. We demonstrate the use of the Short-Time Fourier Transform and the Continuous Wavelet Transform together with amino acid hydrophobicity in locating important amino acid domains in proteins and also show that the Kolmogorov-Smirnov statistic can be used as a metric of protein similarity.
Effect of physical and chemical methods of homogenization on inflammatory mediators in sputum of asthma patients.

BACKGROUND Dithiothreitol (DTT), which is used for sputum homogenization, may split S-S bonds of the bronchial mucins as well as other proteins and, thus, may have a detrimental effect on inflammatory mediators that are present in sputum. OBJECTIVE To evaluate the effects of physical sputum homogenization, using ultrasonic and chemical (ie, DTT) means, on the concentrations of eosinophil cationic protein (ECP), eosinophil protein X (EPX), eosinophil peroxidase (EPO), and myeloperoxidase (MPO) in the sputum of patients with asthma. METHODS The collection of sputum samples from nine patients with asthma was induced by their inhaling a sterile 3% saline solution for 10 min from an ultrasonic nebulizer. One half of the sputum sample was homogenized by ultrasound, and the other half was liquefied by DTT. The supernatant of the ultrasonically homogenized specimen was divided into the following three portions: (1) immediately frozen; (2) stored for 15 min at 37 degrees C; and (3) additionally treated with DTT. The supernatant of the sputum sample that was liquefied by DTT was divided into the following two portions: (1) immediately frozen; and (2) additionally subjected to ultrasound. The concentrations of ECP, EPO, EPX, and MPO in the sputum samples were measured using immunoassays. RESULTS Statistically significant differences were found between the ultrasonically homogenized specimens that had been either processed immediately or stored at 37 degrees C and those treated by DTT, but only for concentrations of EPO and MPO (p < 0.005). No effect of temperature on the mediators in the ultrasonically homogenized specimens could be detected. Ultrasonic homogenization had no influence on the mediators in the samples liquefied by DTT. However, the addition of DTT to the cell-free supernatant of the ultrasonically homogenized sputum samples caused a significant fall in measured EPO and MPO concentrations. CONCLUSIONS The sputum processing by DTT caused a statistically significant fall in EPO and MPO concentrations but did not significantly influence the measured concentrations of ECP and EPX.
Disproportionate Realities: The Climate Justice Implications of Mitigation Policies Across Scales

Global climate change will have disproportionate effects on low-income and minority communities around the world producing important justice challenges. As national governments increasingly rely on local governments, civil society, and private transnational actors to establish and implement climate actions policies, it is important to assess whether and how these newly emergent actors can address these justice challenges. First this thesis examines concepts of justice in relation to climate change across different scales in order to develop a comprehensive conceptual framework of climate justice. This conceptual framework expands the scale of the international climate justice movement address local concerns. Further, the framework is used as an analytical tool for examining the justice implications of urban climate change initiatives in a database of 627 experiments within 100 global cities. The results reveal that the vast majority of climate experiments at the local-level are predominantly led by local governments. However, experiments led by community based organizations, NGOs, and private actors were much more likely to include climate justice concerns. As cities and local governments become leaders in implementing climate actions, concerns for climate justice should be included within the creation of climate policy.
A Comparison of the Nitrogen Requirements of the Eastern Pygmy Possum, Cercartetus nanus, on a Pollen and on a Mealworm Diet

The eastern pygmy possum, Cercartetus nanus, is known to feed both on flower products and on invertebrates. This study compares its ability to meet its nitrogen requirements on pollen and on insect larvae. Captive C. nanus were fed diets in which nitrogen was provided either by Eucalyptus pollen or by the mealworm Tenebrio molitor. The apparent digestibility of the nitrogen from both sources was high, with a mean value of 76% for the pollen and 73% for the mealworms. This was much higher than would have been inferred from the common practice of measuring the percentage of empty pollen grains in fecal samples. The truly digestible maintenance nitrogen requirements of C. nanus on pollen were exceptionally low: 2.6 mg N d−1 compared with 9.5 mg N d−1 on mealworms. The value for pollen is the lowest yet recorded for any mammal. The difference between the requirements of C. nanus on the two diets appeared to be related to the composition of the mealworm and pollen protein. The biological value of the pollen nitrogen was exceptionally high for a plant protein, at 72%, whereas the biological value of the mealworm nitrogen was only 42%. This suggests that the amino acid composition of the pollen corresponded more closely to the requirements of C. nanus than the composition of the mealworm protein did. Pollen is an excellent source of nitrogen for C. nanus, and it should be considered as a potential nitrogen source for other flower‐feeding animals.
Why ecocentrism is the key pathway to sustainability

Ecocentrism is the broadest term for worldviews that recognize intrinsic value in all lifeforms and ecosystems themselves, including their abiotic components. Anthropocentrism, in contrast, values other lifeforms and ecosystems insofar as they are valuable for human well-being, preferences and interests. Herein, the authors examine the roots of ecocentrism and discuss its mixed history of international recognition. They argue that non-human nature has intrinsic value irrespective of human preferences or valuation, and they refute the claim that ecocentrism is misanthropic. They then summarize four key examples from the academic literature in which anthropocentrism fails to provide an ethic adequate for respecting and protecting planet Earth and its inhabitants. The authors conclude that ecocentrism is essential for solving our unprecedented environmental crisis, arguing its importance from four perspectives: ethical, evolutionary, spiritual and ecological. They contend that a social transformation towards ecocentrism is not only an ethical but a practical imperative, and they urge support for ecocentric understanding and practices. https://www.ecologicalcitizen. net/article.php? t=why-ecocentrism-key-pathway-sustainability https://www.linkedin. com/in/helenkopnina/