A strategy for the identification of proteins targeted by thioredoxin

Thioredoxins are 12-kDa proteins functional in the regulation of cellular processes throughout the animal, plant, and microbial kingdoms. Growing evidence with seeds suggests that an h-type of thioredoxin, reduced by NADPH via NADP-thioredoxin reductase, reduces disulfide bonds of target proteins and thereby acts as a wakeup call in germination. A better understanding of the role of thioredoxin in seeds as well as other systems could be achieved if more were known about the target proteins. To this end, we have devised a strategy for the comprehensive identification of proteins targeted by thioredoxin. Tissue extracts incubated with reduced thioredoxin are treated with a fluorescent probe (monobromobimane) to label sulfhydryl groups. The newly labeled proteins are isolated by conventional two-dimensional electrophoresis: (i) nonreducing/reducing or (ii) isoelectric focusing/reducing SDS/PAGE. The isolated proteins are identified by amino acid sequencing. Each electrophoresis system offers an advantage: the first method reveals the specificity of thioredoxin in the reduction of intramolecular vs. intermolecular disulfide bonds, whereas the second method improves the separation of the labeled proteins. By application of both methods to peanut seed extracts, we isolated at least 20 thioredoxin targets and identified 5—three allergens (Ara h2, Ara h3, and Ara h6) and two proteins not known to occur in peanut (desiccation-related and seed maturation protein). These findings open the door to the identification of proteins targeted by thioredoxin in a wide range of systems, thereby enhancing our understanding of its function and extending its technological and medical applications.

Research in speech communication.

Advances in digital speech processing are now supporting application and deployment of a variety of speech technologies for human/machine communication. In fact, new businesses are rapidly forming about these technologies. But these capabilities are of little use unless society can afford them. Happily, explosive advances in microelectronics over the past two decades have assured affordable access to this sophistication as well as to the underlying computing technology. The research challenges in speech processing remain in the traditionally identified areas of recognition, synthesis, and coding. These three areas have typically been addressed individually, often with significant isolation among the efforts. But they are all facets of the same fundamental issue--how to represent and quantify the information in the speech signal. This implies deeper understanding of the physics of speech production, the constraints that the conventions of language impose, and the mechanism for information processing in the auditory system. In ongoing research, therefore, we seek more accurate models of speech generation, better computational formulations of language, and realistic perceptual guides for speech processing--along with ways to coalesce the fundamental issues of recognition, synthesis, and coding. Successful solution will yield the long-sought dictation machine, high-quality synthesis from text, and the ultimate in low bit-rate transmission of speech. It will also open the door to language-translating telephony, where the synthetic foreign translation can be in the voice of the originating talker.

Behavioral expression of emotions and non-invasive assessment of physiological correlates in dogs (Canis familiaris)

The aim of this thesis was to validate the use of infrared thermography (IRT) to non-invasively measure emotional reactions to different situations in pet dogs (Canis familiaris). A preliminary test, aimed to evaluate the correlation between eye-temperature and rectal temperature in dog, was performed. Then, in three different situations, negative (veterinary visit), positive (palatable food rewards), and mildly stressing followed by mildly positive (separation from and reunion with the owner), variations in heat emitted from lacrimal caruncle (referred to as eye temperature) were measured with an infrared thermographic camera. In addition, heart rate and heart rate variability parameters were collected using a non-invasive heart rate monitor designed for human use and validated on dogs. All experiments were video recorded to allow behavioral coding. During the negative situation dogs’ level of activity and stress related behaviors varied across compared to the baseline and dogs showed an increase in eye temperature despite having a significant decrease in the level of activity. The positive situation was characterized by a peak in eye temperature and mean HR and dogs engaged in behaviors indicating a positive arousal, focusing on food treats and tail wagging but there were not variations in HRV during stimulation but only an increment in SDNN immediately after the stimulus. In the separation from and reunion with the owner dogs’ eye temperature and mean HR did not vary neither in the stressful nor in the positive situations, RMSSD increased after the positive episode, SDNN dropped during the two stimulations and it increased after the stimulations. During the separation from the owner dogs were mainly directed to the door or to the experimenter while during the reunion with the owner dogs were focused mainly on the owner and on the environment, exhibiting safe base effect. A different approach was used to assess the welfare of shelter dogs. Dogs were implanted with a telemeter and after implantation dogs were housed in sequence in four different situations lasting 1 week: alone, alone with toys and a stretch cot for sleeping, with an unknown, spayed, female, and alone with a daily 2-hours interaction with an experimenter. Two different approaches were tried: partially random extracted fragments from every week, behaviors from 8 a.m. to 4 p.m. were continuous during baseline and the female situation. Results showed different reactions by dogs to the different situations and interestingly not all enrichments were enjoyed by the dogs improving their welfare. Overall results suggest that IRT may represent a useful tool to investigate emotional reactions in dogs. Nevertheless, further research is needed to establish the specificity and sensivity of IRT in this context and to assess how different dogs’ characteristics, breed, previous experience and the valence and arousal elicited by the stimulus could influence the magnitude and type of the response. The role of HRV in understanding emotional valence and the one of telemeters in understanding long-term effects on sheltered dogs’ welfare is also discussed.

Efeitos da probabilidade e proporção de reforço sobre o comportamento de escolha em ratos Wistar (Rattus norvegicus)

A metacognição é processo conceituado como o julgamento que um organismo (humano ou não humano) faz sobre seu próprio saber ou não saber. Há relatos de pesquisas sobre esse processo com seres humanos e diversas espécies de não humanos. Poucos estudos, porém, discutem a ocorrência de metacognição em ratos, e os resultados são controversos, em função de questionamentos sobre os procedimentos experimentais empregados. Este estudo teve o objetivo de investigar o efeito da manipulação de diferentes proporções de reforço produzidas em duas alternativas, sendo uma probabilística e outra com reforçamento contínuo, sobre o desempenho de ratos em uma tarefa de discriminação de diferentes durações de estímulos sonoros. O procedimento empregado é uma adaptação do utilizado por Foote e Crystal (2007), que investigou a ocorrência de metacognição em ratos. Foram utilizados cinco ratos machos, da linhagem Wistar (Rattus norvegicus) mantidos a 80% de seu peso ad libitum. O aparato utilizado foi um labirinto em Ey. O procedimento consistiu de quatro fases: 1) Treino exploratório no braço em Y, no qual o animal foi exposto a alternativas que continham seis pelotas de ração; 2) Treino de discriminação de estímulos sonoros, no qual foram treinadas duas discriminações condicionais com duas durações de estímulo sonoro, uma curta (2s), e uma longa (8s), cada uma correlacionada com a escolha de uma das portas do braço em Y; 3) Treino exploratório no braço em I, no qual os animais foram expostos a uma alternativa livre, que continha três pelotas de ração; e 4) Fase de Teste, na qual foram apresentadas diferentes durações de som (2.00, 2.44, 2.97, 3.62, 4.42, 5.38, 6.56 e 8.00s), a partir das quais o animal poderia escolher entre o braço em Y (fazer o teste), e receber seis pelotas de ração caso escolhesse a porta correta (correlacionada à duração curta ou longa), ou escolher a alternativa de recusa do teste, produzindo, com certeza, a quantidade de ração estabelecida pela condição em vigor. Foi analisada a porcentagem de escolhas realizadas pelos animais nos braços Y e I em cada condição, assim como a relação entre a porcentagem de acertos e erros nos testes e recusa, para cada duração de som. Todos os sujeitos atingiram o critério de aprendizagem estabelecido na fase de treino. Na fase de testes, observou-se que o som deixou de exercer controle sobre a resposta de escolha de todos os animais. À medida que a proporção de reforço variou na alternativa de recusa, os animais alteraram o padrão de escolha, de propensão para aversão ao risco, de acordo com a condição em vigor. A escolha por uma alternativa não se mostrou sob controle da acurácia dos animais em discriminar as durações dos estímulos apresentados, mas sim da proporção e probabilidade do reforço em cada alternativa. Discute-se a necessidade de se recorrer ao conceito de metacognição para descrever o desempenho dos animais em tarefas como a empregada no presente estudo.

A parallel method for impulsive image noise removal on hybrid CPU/GPU systems

A parallel algorithm for image noise removal is proposed. The algorithm is based on peer group concept and uses a fuzzy metric. An optimization study on the use of the CUDA platform to remove impulsive noise using this algorithm is presented. Moreover, an implementation of the algorithm on multi-core platforms using OpenMP is presented. Performance is evaluated in terms of execution time and a comparison of the implementation parallelised in multi-core, GPUs and the combination of both is conducted. A performance analysis with large images is conducted in order to identify the amount of pixels to allocate in the CPU and GPU. The observed time shows that both devices must have work to do, leaving the most to the GPU. Results show that parallel implementations of denoising filters on GPUs and multi-cores are very advisable, and they open the door to use such algorithms for real-time processing.

Endophytic colonization of barley (Hordeum vulgare) roots by the nematophagous fungus Pochonia chlamydosporia reveals plant growth promotion and a general defense and stress transcriptomic response

Plant crop yields are negatively conditioned by a large set of biotic and abiotic factors. An alternative to mitigate these adverse effects is the use of fungal biological control agents and endophytes. The egg-parasitic fungus Pochonia chlamydosporia has been traditionally studied because of its potential as a biological control agent of plant-parasitic nematodes. This fungus can also act as an endophyte in monocot and dicot plants, and has been shown to promote plant growth in different agronomic crops. An Affymetrix 22K Barley GeneChip was used in this work to analyze the barley root transcriptomic response to P. chlamydosporia root colonization. Functional gene ontology (GO) and gene set enrichment analyses showed that genes involved in stress response were enriched in the barley transcriptome under endophytism. An 87.5 % of the probesets identified within the abiotic stress response group encoded heat shock proteins. Additionally, we found in our transcriptomic analysis an up-regulation of genes implicated in the biosynthesis of plant hormones, such as auxin, ethylene and jasmonic acid. Along with these, we detected induction of brassinosteroid insensitive 1-associated receptor kinase 1 (BR1) and other genes related to effector-triggered immunity (ETI) and pattern-triggered immunity (PTI). Our study supports at the molecular level the growth-promoting effect observed in plants endophytically colonized by P. chlamydosporia, which opens the door to further studies addressing the capacity of this fungus to mitigate the negative effects of biotic and abiotic factors on plant crops.

Calculations of stone work in new dining halls and chapel, [ca. 1814]

Estimate for $10,189.62 to complete stone work in University Hall. This includes the front basement, end basement, window stools, door ports, and stairs.

Journal of College Disorders, 1788-1797

This journal contains entries about various student "disorders" which occurred during Eliphalet Pearson’s tenure at Harvard. Daily entries describe a wide range of students’ rebellious conduct, which included: hissing at speakers in chapel, throwing snowballs and stones at College buildings and people (including tutors and then-President Joseph Willard), disrupting lectures by scraping chairs and feet, breaking windows, intoxication, moving and breaking furniture, stealing firewood, firing pistols, building bonfires, stealing supplies (food, cider and candles), throwing food and utensils during meals, stealing Bibles, wearing hats indoors, filling door locks with stones, drawing on lecture room walls with gravel, and silencing the morning chapel bell by filling it with molten pewter plates (stolen from the kitchen). There are also entries pertaining to more malicious offenses, including the drowning of a dog in a well. Several entries describe meetings of the College government to determine the appropriate punishments for each offense. Students were often fined, expelled, or suspended ("rusticated") for their unruly behavior.

Account book of Andrew Croswell, 1794-1802

Andrew Croswell kept this account book while an undergraduate at Harvard College. It contains entries from 1794, the year he entered, until his graduation in 1798. There is also one entry on the back cover apparently made in 1802. The entries, divided by school term, are very detailed. Croswell indicates the cost of the following, among many other expenses and purchases: transportation, most often to Hingham and Plymouth; payment for "passing the bridge"; candles; hiring a horse; wood and having it cut; laundry; quills and pencils; paper and ink; razors, haircuts, hair ribbons; a trunk; clothing and cloth for trousers; furniture; tickets to the theater; door locks; a bowl and spoon; "batts and balls" and "other necessaries"; tobacco; toothbrushes; shoe and boot repair; fruit; wine, brandy and rum; cheese; coffee and tea; butter; lemons; sugar; and wafers. There are also entries for college-related costs, including the payment of quarter bills, buttery bills, Hasty Pudding Club dues, and a fee to the President of Harvard College related to Croswell's graduation. There are also entries pertaining to the cost of celebrating various special occasions, including Election Day, Christmas Eve, "Independent Day," and George Washington's birthday.

Dunkerque, France, 1695 (Raster Image)

This layer is a georeferenced raster image of the historic paper map entitled: Plan en profil van Duynkerken : met sijn sterktens en zee-kasteelen, belegert te water, engebombardeert door de Engelse en Hollantse zee-magten, onder de Engelse admiraal Berkly en Hollantse admiraal Alemonde, op den Augustus, 1695, doen maken en uytgeven na de autentijke tekeninge van Monsieur Pamer, Ingenieur van Sijn Kon. Majest. van Groot Brittannien. It was published by Pieter Persoy, op den Dam in 1695. Scale [ca. 1:13,000]. Covers a portion of Dunkerque, France. Map in Dutch. The image inside the map neatline is georeferenced to the surface of the earth and fit to the European Datum 1950, Universal Transverse Mercator (UTM) Zone 31N projected coordinate system. All map collar and inset information is also available as part of the raster image, including any inset maps, profiles, statistical tables, directories, text, illustrations, index maps, legends, or other information associated with the principal map. This map shows features such as roads, drainage, built-up areas and selected buildings, fortifications and defenses, canals, docks, ground cover, and more. Includes also index and panorama view.This layer is part of a selection of digitally scanned and georeferenced historic maps from the Harvard Map Collection. These maps typically portray both natural and manmade features. The selection represents a range of originators, ground condition dates, scales, and map purposes.

Graubünden Region, Switzerland, 1724 (Raster Image)

This layer is a georeferenced raster image of the historic paper map entitled: Nouvelle carte du pays de Grisons : avec ses dependances la Valteline, les comtés de Chiavenne, et Bormio, dressée sur les observations du Ph. Cluvere geographe, et du Collonel Schmid de Gruenek ; Johannes van Lugtenburg gesneden ; en door Jacob Keyzer gecorrigeert. It was published by R. Ottens in 1724. Scale [ca. 1:260,000]. Covers the Kanton Graubünden region of Switzerland and portions of Liechtenstein, Italy, and Austria. Map in French.The image inside the map neatline is georeferenced to the surface of the earth and fit to the Europe Lambert Conformal Conic coordinate system. All map collar and inset information is also available as part of the raster image, including any inset maps, profiles, statistical tables, directories, text, illustrations, index maps, legends, or other information associated with the principal map. This map shows features such as drainage, cities, towns, villages, and other human settlements, territorial and administrative boundaries, shoreline features, and more. Relief shown pictorially. Includes alsoThis layer is part of a selection of digitally scanned and georeferenced historic maps from the Harvard Map Collection. These maps typically portray both natural and manmade features. The selection represents a range of originators, ground condition dates, scales, and map purposes.

Enkhuizen, Netherlands, 1734 (Raster Image)

This layer is a georeferenced raster image of the historic paper map entitled: Nieuwe afteekening van alle de banken, canaalen, tonnen en dieptens : geleegen voor de stad Enkhuysen in de Zuyder Zee, waar in aengeweesen word, hoedanig men, uyt de stad nae de vuur toren door het Voor Land gevoeglyk kan maken een nieuwe zee haven, getekent door Ian Belkmeer. It was published by Joannes van Keulen in 1734. Scale [ca. 1:9,630]. Covers Enkhuizen, Netherlands. Map in Dutch.The image inside the map neatline is georeferenced to the surface of the earth and fit to the RD_New (Rijksdriehoekstelsel), GCS Amersfoort coordinate system. All map collar and inset information is also available as part of the raster image, including any inset maps, profiles, statistical tables, directories, text, illustrations, index maps, legends, or other information associated with the principal map. This map shows features such as roads, drainage, built-up areas and selected buildings, fortifications, ground cover, canals, shoreline features, and more. Depths shown by soundings and shading. Includes inset: "Verbeelding van de mond van de Nieuwe Haven".This layer is part of a selection of digitally scanned and georeferenced historic maps from the Harvard Map Collection. These maps typically portray both natural and manmade features. The selection represents a range of originators, ground condition dates, scales, and map purposes.

Europe & Mediterranean Sea Region, 1705 (Image 1 of 2) (Raster Image)

This layer is a georeferenced raster image of the historic paper map entitled: Toonneel des oorlogs in't zuider deel van Europa, door Carel Allard = Theatre de la guerre dans l'Europe meridionale, par Charles Allard. It was published by C. Allard in 1705. Scale [ca. 1:6,800,000]. Covers a portion of Europe and the Mediterranean Sea region. This layer is image 1 of 2 total images of the two sheet source map, representing the western portion of the map. Map in Dutch and French. The image inside the map neatline is georeferenced to the surface of the earth and fit to the World Miller Cylindrical projected coordinate system. All map collar and inset information is also available as part of the raster image, including any inset maps, profiles, statistical tables, directories, text, illustrations, index maps, legends, or other information associated with the principal map. This map shows features such as drainage, cities and other human settlements, territorial boundaries, shoreline features, and more. Relief shown pictorially.This layer is part of a selection of digitally scanned and georeferenced historic maps from the Harvard Map Collection. These maps typically portray both natural and manmade features. The selection represents a range of originators, ground condition dates, scales, and map purposes.

Europe & Mediterranean Sea Region, 1705 (Image 2 of 2) (Raster Image)

This layer is a georeferenced raster image of the historic paper map entitled: Toonneel des oorlogs in't zuider deel van Europa, door Carel Allard = Theatre de la guerre dans l'Europe meridionale, par Charles Allard. It was published by C. Allard in 1705. Scale [ca. 1:6,800,000]. Covers a portion of Europe and the Mediterranean Sea region. This layer is image 2 of 2 total images of the two sheet source map, representing the eastern portion of the map. Map in Dutch and French. The image inside the map neatline is georeferenced to the surface of the earth and fit to the World Miller Cylindrical projected coordinate system. All map collar and inset information is also available as part of the raster image, including any inset maps, profiles, statistical tables, directories, text, illustrations, index maps, legends, or other information associated with the principal map. This map shows features such as drainage, cities and other human settlements, territorial boundaries, shoreline features, and more. Relief shown pictorially.This layer is part of a selection of digitally scanned and georeferenced historic maps from the Harvard Map Collection. These maps typically portray both natural and manmade features. The selection represents a range of originators, ground condition dates, scales, and map purposes.

Amsterdam, Netherlands, ca. 1780 (Raster Image)

This layer is a georeferenced raster image of the historic paper map entitled: [Plan de la grande & fameuse ville marchande d'Amsterdam = Plan van de wyd vermaarde en beroemde koop stad Amsterdam, mise au jour par Ies Iean Covens & Corneille Mortier avec privilege de Mess.rs les Etats Generaux des Provinces Unies = nieuwelks uyt gegeven door Ioannes Covens en Cornelis Mortier met previl. van de Staaten Generaal]. It was published by Iean Covens & Corneille Mortier ca. 1780. Scale [1:53,000]. Map in Dutch and French. The image inside the map neatline is georeferenced to the surface of the earth and fit to the Dutch National Grid: RD (Rijksdriehoekstelsel) GCS Amersfoort (Bessel 1841) coordinate system. All map collar and inset information is also available as part of the raster image, including any inset maps, profiles, statistical tables, directories, text, illustrations, index maps, legends, or other information associated with the principal map. This map shows features such as roads, bridges, drainage, canals, wharves, docks, built-up areas and selected buildings pictorially, fortification, water mills, and more. Relief is shown by hachures. Includes indexes. This layer is part of a selection of digitally scanned and georeferenced historic maps from The Harvard Map Collection as part of the Imaging the Urban Environment project. Maps selected for this project represent major urban areas and cities of the world, at various time periods. These maps typically portray both natural and manmade features at a large scale. The selection represents a range of regions, originators, ground condition dates, scales, and purposes.