Miracle-dz/UniFAR-FTUs huggingface dataset:
Protein Degradation in Plants

CONTENTS INTRODUCTION . 385 FUNCTIONS OF PROTEIN DEGRADATION . 386 MECHANISMS FOR DEGRADING PROTEINS . 389 General Features . 389 Degradation of Proteins in the Cytoplasm and Nucleus . 390 Degradation of Proteins in Organelles 401 CONCLUSIONS 404
Observations on the Andean-Patagonian Component of Southeastern Brazil's Avifauna

Several birds typical of southeastern Brazil's isolated and cold mountains have most probably been derived from Andean/Patagonian ancestors following Pleistocene glaciation. Typical species endemic to that area include Itatiaia Spinetail (Schizoeaca moreirae), Long-tailed Cinclodes (Cinclodes pabsti), and Mousecolored Tapaculo (Scytalopus speluncae). Uniquely among Andean-Patagonian derivatives, Band-winged Nightjar (Caprimulgus longirostris) has also colonized lowlands, even reaching tropical, urban Rio de Janeiro. Secondary radiation has led to at least one species of Andean origin (Brasilia Tapaculo, Scytalopus novacapitalis) colonizing the central Brazil Plateau, apparently having followed the inland movement of coastal forests. Extension southward of Amazonian heat and northward of Patagonian aridity are advanced in explanation for the rupture of a formerly continuous band of vegetation linking the Andes and southeastern Brazil, with resulting isolation and speciation of landbirds. RESUMEN. Varias aves tipicas de las montanas aisladas y frias del sureste de Brasil han derivado muy probablemente de ancestros andino-patagonicos luego de las glaciaciones del pleistocene Especies endemicas tipicas de esa area incluyen Schizoeaca moreirae, Cinclodes pabsti, y Scytalopus speluncae. La chotacabra sen-ana (Caprimulgus longirostris) es unica entre los descendientes andinopatag6nicos, ya que tambien ha colonizado las tierras bajas e incluso ha llegado a las areas urbanas y tropicales en Rio de Janeiro. La radiation secundaria ha hecho que al menos una especie de origen andino (Scytalopus novacapitalis) colonice la meseta central de Brasil, aparentemente habiendo seguido las extensiones tierra adentro del bosque atlantico. La extensidn del calor amaz6nico hacia el sur y de la aridez patag6nica hacia el norte brindan una hipdtesis para explicar la ruptura de una banda de vegetaci6n que en el pasado era continua y enlazaba los Andes con el sur de Brasil, dando como resultado la aislacion y especiacidn de aves terrestres. The Itatiaia Highlands of southeastern Brazil (Fig. 1) were recognized early in the 20th century as having a peculiar flora composed largely of endemics whose closest relatives were in the Bolivian Andes (Dusen 1903). Shortly thereafter, Miranda Ribeiro (1906) extended the analysis to the area's fauna, confirming its Andean affinities. He noted among other observations that the nearest relatives of certain catfishes (Siluroidei) and some birds were not in Brazil but in the Andes, a conclusion later reached for frogs and butterflies as well (Lutz 1951; Ebert 1960). In the present paper I offer observations on the taxonomic affinities of birds that occur generally in southeastern Brazil.
A hot-potato game under transient price impact and some effects of a transaction tax

Building on observations by Sch\"oneborn (2008), we consider a Nash equilibrium between two high-frequency traders in a simple market impact model with transient price impact and additional quadratic transaction costs. We show that for small transaction costs the high-frequency traders engage in a "hot-potato game", in which the same asset position is sold back and forth. We then identify a critical value for the size of the transaction costs above which all oscillations disappear and strategies become buy-only or sell-only. Numerical simulations show that for both traders the expected costs can be lower with transaction costs than without. Moreover, the costs can increase with the trading frequency when there are no transaction costs, but decrease with the trading frequency when transaction costs are sufficiently high. We argue that these effects occur due to the need of protection against predatory trading in the regime of low transaction costs.
Association between a vasopressin receptor AVPR1A promoter region microsatellite and eating behavior measured by a self-report questionnaire (Eating Attitudes Test) in a family-based study of a nonclinical population.

OBJECTIVES Considerable evidence including twin and family studies suggests that biologic determinants interact with cultural cues in the etiology of anorexia and bulimia nervosa. A gene that makes "biologic sense" in contributing susceptibility to these disorders, and to our knowledge not previously investigated for this phenotype, is the vasopressin receptor (AVPR1A), which we have tested for association with eating pathology. METHODS We genotyped 280 families with same-sex siblings for two microsatellites in the promoter region of the AVPR1A gene. Siblings completed the 26-item Eating Attitudes Test (EAT) and the Drive for Thinness (DT) and Body Dissatisfaction (BD) subscales of the Eating Disorders Inventory (EDI). The Quantitative Transmission Disequilibrium Test program (QTDT), which employs flexible and powerful variance-components procedures, was used to test for an association between EAT scores and the two AVPR1A promoter region microsatellites, RS1 and RS3. RESULTS A significant association (p = .036) was detected between the RS3 microsatellite and EAT scores. The strongest association was between RS3 and the Dieting subscale of the EAT (p = .011). A significant association was also observed between the EDI-DT and the RS3 microsatellit (p = .0450). CONCLUSIONS We demonstrate for the first time an association between a microsatellite polymorphism in the AVPR1A promoter region and scores on the EAT as well as with the EDI-DT. The strongest association was observed between the RS3 microsatellite and the Dieting subscale of the EAT. The relevant phenotype appears to tap severe dietary restriction for weight loss purposes.
Cross-Sectional Population-Based Study of Knowledge, Attitudes, and Practices Regarding HIV/AIDS in Dakshina Kannada District of Karnataka, India

Objective: To assess HIV/AIDS-related knowledge, attitudes, and practices among the general population in South India. Methods: The 1669 participants (834 males, 835 females) aged 19-49 years were surveyed using a stratified 2-stage random sampling design with probability proportional to size. Results: Although 54% of participants knew that AIDS is caused by “HIV” virus and 44% could correctly identify all modes of transmission, 52% believed in one or more myths, 41% did not know that condoms can prevent HIV, and 18% had not heard of a condom. Higher HIV knowledge scores were significantly associated with male gender, higher education, currently married, higher frequency of reading newspapers, listening to radio or watching television, and willingness to get tested for HIV (P < .01). Thirty-four percent felt that HIV-infected individuals should be kept away from others, and 40% were not willing to accept a family member with HIV. There was a significant and positive correlation between knowledge and attitude scores (P < .01). Among respondents who ever had sexual intercourse, significantly more males declared having more than one sexual partner compared to females ( P < .01). Only16% of respondents reported that they consistently used condoms. Sixty-two percent of the respondents were willing to undergo an HIV test if provided free of cost. This willingness to opt for HIV testing increased significantly with better knowledge score, better attitude score, and higher education status (P < .01). Conclusions: HIV/AIDS prevention campaigns in India should focus on public education, stigma reduction, promotion of condom use, and risk-reduction behaviors in urban and rural communities targeted toward young adults.
Prevalence of attention deficit hyperactivity disorder and comorbid disruptive behavior disorders among school age children in Trabzon.

5 OZET: Trabzon ili ilko¤retim ca¤› cocuklar›nda dikkat eksiklii hiperaktivite bozukluu ve efllik eden y›k›c› davran›fl bozukluklar› yayg›nl›¤› Amac: Bu cal›flman›n amac› Trabzon ilinde ilko¤retim ca¤› cocuklar›nda Dikkat Eksiklii Hiperaktivite Bozukluu'nun (DEHB) ve ona efllik eden Y›k›c› Davran›fl Bozukluklar›'n›n (YDB) yayg›nl›¤›n› incelemektir. Yontem: Cal›flmada 6-12 yafl aral›¤›ndaki ilkokul o¤rencile- rinde (n=1126) DSM-IV tan› olcutlerine gore DEHB ve YDB tan›lar›n›n konulmas› amac› ile Turgay'›n Cocuk ve Ergen- lerde Davran›m Bozukluklar› icin DSM-IV'e Dayal› Tarama Olcei kullan›lm›flt›r. Bulgular: DEHB yayg›nl›¤› %8.6 (n=97) ve alt tip da¤›l›mla- r› dikkat eksiklii %1.6 (n=18), hiperaktif/ durtusel tip %6 (n=69) ve kombine %0.9 (n=10) olarak s›ralanm›flt›r. Erkek k›z oran› DEHB'nin tum alt tipleri icin 3.5/1 olarak bulun- mufltur. Orneklemde dier YDB yayg›nl›¤› %18.6 (n=209)'d›r. Karfl›t Gelme-Karfl› Olma Bozukluu'nun (KG-KOB) yayg›nl›¤› %14.1 (n=159) ve Davran›m Bozuklu- ¤u'nunki (DB) %4.4 (n=50) olarak belirlenmifltir. DEHB olan olgularda KG-KOB'nin s›kl›¤› %57.5 (n=56)ve DB'nin s›kl›¤› %20.6 (n=20)'d›r. Sonuc: Bu cal›flman›n sonuclar› DEHB yayg›nl›¤›n›n, erkek bask›nl›¤›n›n ve efllik eden YDB s›kl›¤›n›n kulturler aras›nda anlaml› bir farkl›l›k gostermedii goruflunu desteklemekte- dir. Ote yandan hiperaktif/ durtusel alt tipin da¤›l›m› litera- turde sunulan oranlardan farkl›l›k gostermektedir. Bu fark›n Turk toplumunda cocua yonelik yafla bal› tutumlar, yak- lafl›m oruntuleri ve beklentilerle iliflkili kulturel farklarla fle- killlenebilecei deerlendirilmifltir. Bu noktan›n kulturel farklara odaklanan ileri cal›flmalarla ac›klanmas› onerilmek- tedir. ABSTRACT: of attention deficit hyperactivity disorder and comorbid disruptive behavior disorders among school age children in Trabzon
Reference Manual for the Analysis and Annotation of Rhetorical Structure

2 Segmentation 3 2.1 Base Case . 3 2.2 Sentence Internal Segmentation . 3 2.2.1 Subordinate Clauses . 4 2.2.2 Relative Clauses . 4 2.2. 3 Adjuncts . 5 2.2. 4 Appositives . 7 2.2. 5 Coordination . 7
How Many Patients Are Needed to Provide Reliable Evaluations of Individual Clinicians?

PurposeThe purpose of this study was to determine how many patients are needed to provide reliable patient ratings of care at the individual clinician level. Setting and Sources of DataThe study was conducted in an academic medical center and was based on analysis of 34,985 patients who completed a 50-item survey rating the care received during a recent outpatient visit to a physician or midlevel provider. Study DesignAnalyses of patient satisfaction surveys was done to: 1) confirm the dimensions of satisfaction with outpatient care in an existing measure, and 2) determine the number of patients required to provide reliable estimates of clinician care for single items and an 11-item composite scale. Principal FindingsFactor analysis showed that the survey measured 2 dimensions of satisfaction: 1) clinician care, and 2) features of visiting the office. The 11-item clinician care scale had high reliability (Cronbach’s alpha = 0.97). The number of patients needed to achieve reliability of 0.80 at the clinician level was 66 for the 11-item scale and ranged from 52 to 91 for individual items. For primary care physicians only, the comparable number of patients per clinician was 77 for the 11-item scale and ranged from 50 to 147 across items. ConclusionsFor the survey items that we analyzed, the answer to the question “How many patients are needed to obtain useful and reliable feedback? ” is at least 50, but varies by item type (global vs. specific) and by number of items (composite scale or single-item rating) and by the conditions of use (for self-assessment and learning or reward and punishment).
palaeoenvironmental changes during the Messinian salinity crisis

Flocculent layers and bacterial mats in the mudstone interbeds of the Primary Lower Gypsum unit (Tertiary Piedmont Basin, NW Italy): archives of palaeoenvironmental changes during the Messinian salinity crisis / Dela Pierre F. ; Clari P.; Natalicchio M. ; Ferrando S. ; Giustetto R. ; Lozar F. ; Lugli S. ; Manzi V. ; Roveri M. ; Violanti D. In: MARINE GEOLOGY. ISSN 0025-3227. STAMPA. 355(2014), pp. 71-87. Original Citation: Flocculent layers and bacterial mats in the mudstone interbeds of the Primary Lower Gypsum unit (Tertiary Piedmont Basin, NW Italy): archives of palaeoenvironmental changes during the Messinian salinity crisis
Demographics, habits, and clinical presentation of oral cancer in Puducherry′s population: An institutional experience

Introduction: Oral cancer ranks among the top three of all cancers in India and accounts for over 30% of all cancers reported in the country. More than one-third of these are preventable by avoiding deleterious habits. Although the term oral cancer encompasses all malignant tumors that originate from the oral tissues, 90% of these are squamous cell carcinomas confirmed histologically. Aim and Objective: 1. To assess the demographic profile of patients with oral cancer in Puducherry′s population. 2. To evaluate if any correlation exists among the habits, primary site, and clinical presentation of oral cancer. Materials and Methods: Demographic, clinical, and histopathological data concerning oral cancer patients were retrieved from the archives of our institution from 2009 to 2014 and tabulated for further statistical analysis using Statistical Package for the Social Sciences (SPSS) version 17.0. Chi-square test was used to assess the correlation between variables (P < 0.01 significant). Results: The male-to-female ratio was 1:1.35. The mean age at presentation was 53 years; the incidence increased with age and more steeply in females. Smokeless tobacco was used in 69.3% of the cases. Mandibular alveolobuccal complex and buccal mucosa were the most common primary sites. Though no statistically significant correlation (P > 0.05) was found between habits and the primary site, the palate was more commonly involved in smokers. Clinical presentation was ulceroproliferative in 67.19% of the cases but no significant correlation (P > 0.05) was seen among age, gender, habits, and clinical presentation. 80% of the patients reported within 3 months of onset of symptoms and 66% were in TNM Stage 3. Conclusion: Through our study, we have tried to sketch the demographic profile of Puducherry′s population with oral cancer but this is just the tip of a massive upsurging iceberg in the subcontinent.
Phenomenology of Postpartum Psychosis

Background For centuries, physicians have observed a temporal relation between the occurrence of female-specific reproductive events and the symptoms of illness that traditionally have been classified as "mental". Objectives: study of phenomenology of postpartum psychosis. Methods: 60 female patients with postpartum psychosis during the first four weeks after delivery (patients group) and 30 female patents within the first four weeks after delivery not suffering any psychiatric disorders (Control group). The two groups were subjected to clinical psychiatric assessment using structured psychiatric interview of DSM -V, BPRS, HDRS and EPDS. Results: Postpartum psychosis was more in younger females than older and in primipara than multipara. The onset of symptoms of postpartum psychosis was more common in first week after delivery (mean 6.11 days), sleep disturbance, irritability and hypomanic symptoms are the most early symptoms of postpartum psychosis followed by anxiety, confusion and somatic complain. Mood congruent psychotic feature significantly more than mood non-congruent psychotic feature. Conclusion: postpartum psychosis is more common in younger and primipara females with onset of symptoms in first in first week after delivery. Sleep disturbance, irritability and hypomanic symptoms are the earliest symptoms of postpartum psychosis
Improving the application of the Integrated River Basin Management paradigm in the implementation of the EU Water Framework Directive

4 ACKNOWLEDGEMENTS . 5 CONTENTS. 6 LIST OF TABLES . 10 LIST OF FIGURES . 12 List of Abbreviations . 15 1. INRODUCTION . 16 2. Background . 18 2.1. The IRBM paradigm . 18 2.1. 1. The IWRM/IRBM in the Global political agenda . 19 2.1. 2. The IRBM: A systems approach . 22 2.2. The links of the WFD with other EU directives . 24 2.3. The GLOBAQUA project . 29 3. AIM AND OBJECTIVES . 31 3.1. Aim . 31 3.2. Objectives . 31 3.3. Thesis structure . 32 3.4. Methodology . 33
Salmonella spp. in swine - the abattoir as a link in the food chain

XIV ABBREVIATIONS . XVII • SECTION I – INTRODUCTION / LITERATURE REVIEW . 1 1.Introduction . 3 2. Salmonella – A food-borne zoonosis of increasing importance . 4 2.1. Historical aspects . 4 2.2. Characteristics, taxonomy and nomenclature of Salmonella . 5 2.3. Hosts and habitats . 7 2.4. Transmission pathways . 9 3. Salmonella in Swine as a foodborne pathogen. 10 3.1. Infection and pathogenesis . 11 3.2. Vaccination and immunity . 14 3.2.1.Interactions of other microbial agents with Salmonella . 15 3.3. Herd-level risk factors . 16 3.4. Current monitoring and control programs . 16 3.5. The EU assessment: most frequent serotypes in humans, pigs and pork . 17 3.5. 1. Portuguese slaughter swine . 19 4. Salmonella and antimicrobial resistance . 21 4.1. Resistance phenotypes . 23 4.2. Resistance determinants and transmission . 24 Salmonella spp. in swine – The abattoir as a link in the food chain XX • SECTION II – Aims of the Thesis . 27 • SECTION III – RESULTS . 31 Chapter 1. From Salmonella-carrier pigs to contaminated pork: from farm to fork. Salmonella cross-contamination in swine abattoirs in Portugal: carcasses, meat and meat handlers . 33 Chapter 2. One health: Antimicrobial Resistance entering the food chain. Clinically relevant multidrug resistant Salmonella enterica in swine, at slaughter: filling the gaps in the food chain . 41 Chapter 3. The weakest link: Meat handlers from food producing animals to public health. Meat handlers training in Portugal: a survey on Knowledge and Practice . 51 • SECTION IV – GENERAL DISCUSSION . 61 • SECTION V – CONCLUSIONS AND PERSPECTIVES . 73 • SECTION VI – REFERENCES . 77 Salmonella spp. in swine – The abattoir as a link in the food chain
From Trees to Clouds: PhageClouds for Fast Comparison of ∼640,000 Phage Genomic Sequences and Host-Centric Visualization Using Genomic Network Graphs

Background: Fast and computationally efficient strategies are required to explore genomic relationships within an increasingly large and diverse phage sequence space. Here, we present PhageClouds, a novel approach using a graph database of phage genomic sequences and their intergenomic distances to explore the phage genomic sequence space. Methods: A total of 640,000 phage genomic sequences were retrieved from a variety of databases and public virome assemblies. Intergenomic distances were calculated with dashing, an alignment-free method suitable for handling massive data sets. These data were used to build a Neo4j® graph database. Results: PhageClouds supported the search of related phages among all complete phage genomes from GenBank for a single query phage in just 10 s. Moreover, PhageClouds expanded the number of closely related phage sequences detected for both finished and draft phage genomes, in comparison with searches exclusively targeting phage entries from GenBank. Conclusions: PhageClouds is a novel resource that will facilitate the analysis of phage genomic sequences and the characterization of assembled phage genomes.
Local damage detection methods based on the stochastic modeling techniques

Problem of selection of informative frequency band (IFB) for local damage detection using vibration signal is often discussed in the literature. One of the approaches used in this context is based on the analysis of sub-signals obtained in time-frequency representation of the vibration signal. Mentioned sub-signals are analyzed using appropriate statistics (called selectors). Till now, the most popular statistic was kurtosis, one of the measures that can point out these frequency bins on time-frequency map that reveal the most impulsive nature. However for many real signals the spectral kurtosis does not give expected results because it can be sensitive for impulses not related to damage (i.e. artifacts). In this paper we extend the idea of spectral kurtosis. We propose a novel method combining time-frequency representation, namely spectrogram, dependency measure suitable for heavy-tailed distributions, statistical features for novel time-frequency representation and statistical modeling of such features. The new time-frequency representation is based on the measure of dependence appropriate for more general class of distribution, namely heavy tailed. This measure, called autocovariation, is an extension of the classical measures of dependences, namely autocovariance or autocorrelation. The new time-frequency representation was developed in order to enhance informative parts of the signal while reducing inadvisable parts of the signal like artifact or high-energy deterministic parts. Next, the Kuiper statistic is applied to novel time-frequency representation for IFB detection and we design the Alter characteristic. Moreover, we propose also the automatic procedure of filter characteristic thresholding based on the alpha-stable distribution approach.
Finite element modeling of piezoelectric bimorphs with conductive polymer electrodes

The purpose of my research has been to find a good way to solve for the mechanical and electrical behavior of piezoelectric polymer bimorphs which are electroded with a low to medium conductivity material. Traditionally, metal with very high conductivity has been used as the electrode material. Any applied voltage to an electrode will be distributed nearly instantaneously and uniformly throughout the electrode. Because of this quality, the voltage was assumed to be known and uniform for any applied voltage signal, including high frequency signals. The disadvantage of metal is that it is stiffer than polymers, and thus impedes the bending of the bimorph to a greater extent than for comparable polymer electrodes. With the modern invention of conductive polymers with acceptably high conductivities, it is now possible to manufacture piezoelectric devices with finite conductivity electrodes. For all but the very lowest frequencies of applied voltage signals, the voltage distribution cannot be assumed to be uniform throughout the electrode, nor can it be assumed to be exactly in phase. With finite conductivity electrodes there will be a loss in voltage amplitude due to resistivity, and there will also be a phase lag. The piezoelectric problem involves solving a coupled set of differential equations which involve mechanical displacement and electric potential. The electrical behavior of the electrodes is also included in the formulation, so that the voltage distribution in the electrodes is solved for simultaneously with the mechanical displacement and electric potential in the piezoelectric sheets. In this dissertation the coupled set of differential equations was solved using the Finite Element Method with quadratic Lagrange finite elements. The piezoelectric polymer which was modeled was polyvinylidene fluoride (PVDF). The conductive polymer of interest was PEDOT-PSS, although the model is valid for any type of isotropic finite conductivity material. The results of the work show that for moderate conductivity, the mechanical response of the bimorph is very good. There will not be a large phase lag within the first frequency mode. The bimorph resonates at low frequencies, and so any large effect from finite conductivity would only occur at higher modes.