Miracle-dz/UniFAR-FTUs huggingface dataset:
The Protein Data Bank : a historical perspective

The Protein Data Bank began as a grassroots effort in 1971. It has grown from a small archive containing a dozen structures to a major international resource for structural biology containing more than 40 000 entries. The interplay of science, technology and attitudes about data sharing have all played a role in the growth of this resource. The establishment of the Protein Data Bank (PDB) began in the 1970's as a grassroots effort. A group of (then) young crystallographers, including Edgar Meyer, Gerson Cohen and myself, began discussing the idea of establishing a central repository for coordinate data at an American Crystallographic Association (ACA) meeting in Ottawa, Canada, in 1970. Those conversations were continued with a larger group at the ACA meeting in Columbia, South Carolina, USA, in 1971. At that meeting, a petition was written and a proposal was submitted to the United States National Committee for Crystallography (USNCCr). Later that year, the Cold Spring Harbor (CSH) Symposium was held on 'Structure and Function of Proteins at the Three Dimensional Level' (Cold Spring Laboratory Press, 1972). This meeting, characterized by David Phillips as a 'coming of age', heralded a new era in biology. The discussions within the meeting room, on the lawn, and on the beach were exciting and intense. In an informal meeting convened by Max Perutz, protein crystallographers discussed how best to collect and distribute data. Until that point, coordinates for individual entries had only been exchanged among a few research laboratories using punched cards. Since each atom was represented by a single card, an exchange of a structure the size of myoglobin required more than 1000 cards. By providing a central repository for these data, the PDB would make such an exchange possible for anyone. Walter Hamilton was also in attendance. A chemist at Brookhaven National Laboratory (BNL) and a leader in the crystallographic community, Hamilton had begun to focus on two new science and technology projects. In collaboration with postdoctoral fellow Tom Koetzle and others, he was working on the determination of the structures of all the amino acids using neutron diffraction (Lehmann et al., 1972). In another collaboration, he was developing new computer technologies for graphics and for remote computing with Edgar Meyer (Meyer, 1997). During the CSH meeting, Hamilton was approached with the idea that had been discussed within the ACA community – a public data bank of protein structures. At an ad …
GROUND WATER NITRATE REDUCTION IN GIANT CANE AND FOREST RIPARIAN BUFFER ZONES 1

ABSTRACT: Ground water contamination by excess nitrate leaching in row‐crop fields is an important issue in intensive agricultural areas of the United States and abroad. Giant cane and forest riparian buffer zones were monitored to determine each cover type's ability to reduce ground water nitrate concentrations. Ground water was sampled at varying distances from the field edge to determine an effective width for maximum nitrate attenuation. Ground water samples were analyzed for nitrate concentrations as well as chloride concentrations, which were used as a conservative ion to assess dilution or concentration effects within the riparian zone. Significant nitrate reductions occurred in both the cane and the forest riparian buffer zones within the first 3.3 m, a relatively narrow width. In this first 3.3 m, the cane and forest buffer reduced ground water nitrate levels by 90 percent and 61 percent, respectively. Approximately 40 percent of the observed 99 percent nitrate reduction over the 10 m cane buffer could be attributed to dilution by upwelling ground water. Neither ground water dilution nor concentration was observed in the forest buffer. The ground water nitrate attenuation capabilities of the cane and forest riparian zones were not statistically different. During the spring, both plant assimilation and denitrification were probably important nitrate loss mechanisms, while in the summer nitrate was more likely lost via denitrification since the water table dropped below the rooting zone.
Iron (hydr)oxide nanocrystals in raw and burnt sienna pigments

The mineral pigments raw sienna and burnt sienna , known as bolar earths, mostly consist of iron (hydr)oxides; the two pigments, yellow and red-brown respectively, differ for thermal processing of the raw material. Sixteen bolar earth samples from a quarry in Monte Amiata and from the Accademia dei Fisiocritici Museum were investigated by XRD, SEM-EDS, TEM-EDS, thermal treatment, TG/DTA and DRIFT. Raw sienna is yellow to brown and prevalently contains goethite. Burnt sienna is red and consists of hematite obtained by dehydration of goethite at around 270°C. Chemical analyses show dominant Fe 2 O 3 (53.5–71.5 wt.%), with minor SiO 2 (3.0–24.7 wt.%) and Al 2 O 3 (0.8–7.1 wt.%). A very high arsenic content characterizes all the samples (with a mean of 5.6 wt.% As 2 O 5 ). Goethite and hematite occur as finely dispersed nanocrystals, respectively 2–10 nm and 10–40 nm in size. They are enclosed in a minor amorphous silica matrix, with arsenic adsorbed on the iron (hydr)oxide nanoparticles. Due to its high arsenic content, the ochre used to produce raw and burnt sienna is an important example of an effective natural sink for arsenic.
On the representation of the Southern Ocean water masses in an ocean climate model

In global ocean general circulation models used for climate studies, the simulated global deep ocean temperature and salinity generally appear to be lower than that observed. This may be due to an insufficient representation of the cryosphere in such models because the deep ocean thermohaline properties are strongly determined by high-latitude surface conditions. In this study, it is our aim to arrive at an improved simulation of polar water mass characteristics and distribution in the framework of an ocean climate model. As a step toward identifying the critical factors influencing the high-latitude water masses, in particular those of the Southern Ocean, we have proceeded a series of sensitivity experiments with a global sea ice-ocean model. Forcing Southern Ocean sea ice with daily instead of monthly fluctuating wind enhances brine release due to new-ice formation, which leads to a more pronounced core of Lower Circumpolar Deep Water (LCDW) in the Antarctic oceanic regime. Wider Antarctic shelf topography improves the distribution and thickness of sea ice, simultaneously providing a brine reservoir on the shelf, which is a crucial ingredient in the formation process of Antarctic Bottom Water (AABW). As a consequence, the salinity on the Antarctic shelf is increased with depth as observed. Intense southeasterly katabatic winds play a significant role in increasing the salinity, mainly off east Antarctica. It is suggested that modeled Southern Ocean water mass properties are highly sensitive to the large scale and regional forcing of Antarctic sea ice as well as the model representation of the shelf topography, the width of which is crucial to reproducing the first-order features of near-boundary convection.
Laboratory taphonomy-material loss and skeletal part profiles: The example of Saint-Germain-La-Riviere (Gironde, France)

Taphonomic studies can allow us to reconstruct the history of faunal assemblages. However, few studies concern themselves with measuring the effect of sampling problems and specific analytical procedures. Zooarchaeological study of the site of Saint-Germain-la-Riviere is instructive in this regard. Taphonomic studies suggest a loss of material during curation and storage. The study showed when unplotted specimens are not taken into account, the skeletal part profiles are modified in a significant way. In level 1, only square M21 can be used for analysis. By contrast, the quantity of specimens from level 3 in squares L21 and L22 rich in shaft fragments is so large compared to the other squares that this level can be studied in its totality.
Modelling of temperature changes during transport of fresh fish products

Temperature control is a critical parameter to retard quality deterioration of perishable foodstu , such as fresh sh, during distribution from processing to consumers. This thesis is aimed at analysing and improving the temperature management in fresh sh chill chains from processing to market by means of experiments and numerical heat transfer modelling. Ambient and product temperatures are mapped in real multi-modal distribution chains, which are both sea and air based. The results serve as a basis for simulation experiments, in which di erent packaging units and solutions are compared with respect to thermal insulation and product quality maintenance and more optimal ones are proposed. The experimental results are used to validate 3-D heat transfer models of chilled or superchilled white sh, packaged in single boxes or multiple boxes assembled on a pallet, under thermal load. Much more severe temperature control problems are measured in air transport chains, especially in passenger airplanes, compared to sea transport. However, space for improvement in sea transport chains has also been discovered. The results underline the importance of precooling white sh products before packaging for air freight and applying well distributed cooling packs inside the packaging. The results imply that product temperature di erences of up to 10.5 °C can occur in a non-superchilled fresh sh pallet load and the storage life di erence between the most and the least sensitive boxes on a full size pallet in a real air transport chain can exceed 1 1.5 days. It is demonstrated that even though a widely used expanded polystyrene (EPS) box design with sharp corners o ers better thermal insulation than a corrugated plastic (CP) box, the sharp-corner design can be signi cantly improved. Such design improvement has been accomplished by developing a numerical heat transfer model in ANSYS FLUENT resulting in a new 5-kg EPS box currently manufactured by the largest EPS box manufacturer in Iceland. Other temperature-predictive models of products, developed and validated in this thesis, consider a cooling pack on top of superchilled cod packaged in two types of EPS boxes, compared to chilled sh packaged in a CP box without a cooling pack. Finally, models are developed for pallet loads of di erent sizes containing either chilled or superchilled sh. The models are used to con rm the temperature-maintaining e ect of precooling and estimate the e ect of pallet stack size.
TR 01-040 Criterion Functions for Document Clustering : Experiments and Analysis

In recentyears,wehavewitnessedatremendousgrowth in thevolumeof text documentsavailableontheInternet, digital libraries, news sources,and company-wide intranets. This hasled to an increasedinterestin developing methodsthat can help usersto effectively navigate, summarize,and organizethis information with the ultimate goalof helpingthemto find whatthey arelooking for. Fastandhigh-qualitydocumentclusteringalgorithmsplay an importantrole towardsthisgoalasthey havebeenshown to providebothanintuitivenavigation/browsingmechanism by organizinglargeamountsof informationinto a smallnumberof meaningfulclustersaswell asto greatlyimprove theretrieval performanceeithervia cluster-driven dimensionalityreduction,term-weighting,or queryexpansion.This ever-increasingimportanceof documentclusteringandtheexpandedrangeof its applicationsled to thedevelopment of a numberof new and novel algorithmswith different complexity-quality trade-ofs. Among them, a classof clusteringalgorithmsthathave relatively low computational requirementsarethosethat treattheclusteringproblem asan optimizationprocesswhich seeksto maximizeor minimize a particularclusteringcriterion functiondefined over theentireclusteringsolution. Thefocusof thispaperis to evaluatetheperformanceof differentcriterionfunctionsfor theproblemof clustering documents.Our study involvesa total of eight different criterion functions,threeof which are introducedin this paperandfive that have beenproposedin the past. Our evaluationconsistsof both a comprehensi ve experimental evaluationinvolving fifteendifferentdatasets,aswell asan analysisof the characteristicsof the variouscriterion functionsandtheir effect on theclustersthey produce.Our experimentalresultsshow thattherearea setof criterion functionsthatconsistentlyoutperformtherest,andthatsomeof thenewly proposedcriterionfunctionleadto thebest overall results.Our theoreticalanalysisof thecriterionfunctionshows thattheir relative performancedependson (i) thedegreeto whichthey cancorrectlyoperatewhentheclustersareof differenttightness,and(ii) thedegreeto which they canleadto reasonablybalancedclusters.
CARACTERIZAÇÃO TECNOLÓGICA DA MADEIRA DE TRÊS ESPÉCIES FLORESTAIS CULTIVADAS NO AMAZONAS: ALTERNATIVA PARA PRODUÇÃO DE LENHA

Resumo As especies florestais Acacia mangium, Inga edulis e Tachigalia chrysophyllum foram pre-selecionadas para utilizacao em plantios energeticos. Com o objetivo de caracterizar essas especies, foram realizados testes a partir das variaveis densidade basica, poder calorifico e analise imediata. O experimento foi implantado na Estacao Experimental da EMBRAPA no municipio de Iranduba/AM. O delineamento foi em blocos ao acaso com tres repeticoes, perfazendo 9 parcelas compostas de 25 plantas cada. Foram retiradas cinco arvores dentre as nove centrais da area util. Destas, foram retirados os discos com 5 cm de espessura e desdobrados em corpos de prova, para se determinar a densidade basica e demais testes. Realizou-se analise de variância e teste de Tukey a 5% de probabilidade. A Acacia mangium (24,16 cm – 13,09 m) superou as demais em diâmetro e altura, respectivamente. Os dados medios obtidos para densidade basica classificam todas as especies como madeira de densidade baixa, media e levemente densa. O poder calorifico observado em Acacia mangium (4430,37 kcal/kg) foi estatisticamente superior as demais especies. Na analise imediata, as especies apresentaram resultados satisfatorios, sendo apontadas como madeiras adequadas para uso no processo da queima. Os resultados demonstram que as especies possuem qualidade para producao de lenha. Abstract Energetic characterization of native and exotic forest species cultivated at Amazonas. The forest species Acacia mangium, Inga edulis and Tachigalia chrysophyllum were pre-selected to be used at energetic crops. In order to their characterization, tests of basic density, heating power and immediate analysis were performed. The experiment was carried out at EMBRAPA’s Experimental Station, located at Iranduba/AM and was designed as randomized blocks, with three repetitions, comprising 9 plots with 25 plants each. Five trees were removed from the nine central ones of the utile area. Discs of 5 cm thick were removed from them and divided into proof bodies to evaluate basic density and other variables. Analysis of variance and Tukey test at 5% of probability were done. Acacia mangium (20.82 cm – 13.41 m) presented greater diameter and height, respectively, than the other species. The data of basic density average classified all three species as low, medium and dense-lightly density wood. The heating power observed for Acacia mangium (4430.37 kcal/kg) was statistically superior to other species. All three species presented satisfactory results at immediate analysis, being identified as suitable woods for use in burning process. Results show that the species present quality for fire wood production. Keywords: Biomass; basic density; heating power; immediate analysis; planting.
Multicomponent velocity analysis with quaternions

Multicomponent seismic data are acquired by orthogonal geophones that record a vectorial wavefield. Since the single component recordings are not independent, the processing should be performed jointly for all the components. A way to achieve this goal is to exploit quaternions, hyper‐complex numbers that due to their very nature are apt to represent multidimensional data. In fact, quaternion algebra allows us to extend coherence functionals used for scalar observations to multicomponent data. Therefore by means of quaternions we implement semblance and other methods based on matched filtering and on the data covariance properties.
Uncertainties in fPAR estimation of grass canopies under different stress situations and differences in architecture

The fraction of intercepted photosynthetic active radiation (fPAR) is a key variable used by the Monteith model to estimate the net primary productivity (NPP). This variable can be assessed by vegetation indices (VIs) derived from spectral remote sensing data but several factors usually affect their relationship. The objectives of this work were to analyse the fPAR dynamics and to describe the relationships between fPAR and several indices (normalized difference vegetation index (NDVI), optimized soil adjusted vegetation index (OSAVI), Green NDVI (GNDVI), visible atmospherically resistant index (VARI) green, VIgreen and red edge position (REP)) under different water and nutrient treatments for two species with different canopy architectures. Two C3 grass species with differences in leaf orientation (planophile and erectophile) were cultivated from seeds in pots. Four treatments were applied combining water and nitrogen availability. Every week, canopy reflectance and fPAR were measured. Aerial biomass was clipped to estimate final above-ground production for each species and treatment. Starting from reflectance values, the indices were calculated. Planophile species have a steeper (but not significantly) slope in VIs–fPAR relationships than the erectophile species. Water and nutrient deficiencies treatment showed no relationship with fPAR in any spectral index in the erectophile species. In the other species, this treatment showed significant relationship according to the index used. Analysing each species individually, treatments did not modify slopes except in one case (planophile species between both treatments with high nitrogen but differing in water availability). Among indices, GNDVI was the best estimator of fPAR for both species, followed by NDVI and OSAVI. Inaccurate results may be obtained from commonly reported spectral relationships if plants' stress factors are not taken into account.
The Environmental Setting of Erw-wen and Moel y Gerddi: Prehistoric Enclosures in Upland Ardudwy, North Wales.

The environmental setting of two late-prehistoric enclosures in upland Ardudwy, Gwynedd was investigated by pollen analysis of nearby valley mire deposits and of old ground surfaces revealed during excavation of the sites. Radiocarbon-dated pollen data indicate human influence on the local environment since Mesolithic times, with the major period of woodland clearance in the early Bronze Age. The two enclosures appear to have been constructed in an environment already substantially deforested. Remanent upland timber resources appear to have been substantially depleted during occupation of the sites, whilst soil acidification and/or climatic change may also have contributed to their eventual abandonment.
On the Need for Larger Manning's Roughness Coefficients in Depth-Integrated Tsunami Inundation Models

Manning's n values for open channel (river) flow have been studied by hydraulic engineers since the late 19th century, and a rich literature exists on the topic including large-scale laboratory experiments and actual field measurements. Both river flood models and shallow water equation tsunami inundation models incorporate the importance of varying equivalent roughness values with the large-scale roughness elements present for different land use types. However, many tsunami models (especially in Japan) use n values based on a very limited set of small-scale model laboratory experiments with inappropriate Reynolds and Weber numbers, instead of using Manning's n values from the open channel flow literature. Due to this, equivalent Manning's n values for vegetated and urban areas in these tsunami inundation models are too small, causing the mitigating effect of forests and urban regions to be underestimated. This paper presents a review of Manning's n research applied to both river flood and tsunami inundation models, and suggests values to improve the reliability of the latter.
Geochemistry of Palaeozoic–Mesozoic Pacific rim orogenic magmatism, Thurston Island area, West Antarctica

Thurston Island, and the adjacent Eights Coast and Jones Mountains, record Pacific margin magmatism from Carboniferous to Late Cretaceous times. The igneous rocks form a uniformly calc-alkaline, high-alumina, dominantly metaluminous suite; some relatively fractionated granitoids are mildly peraluminous. The magmas were hydrous, a result of subduction. Gabbros have compositions outside the range of mafic volcanic and hypabyssal rocks, as a result of cumulate processes. Trace element compositions of the mafic magmas range from a low La/Yb, Th/Ta end-member close to E-MORB in composition, perhaps contaminated by crust, to a high La/Yb, Th/Ta end-member, close to shoshonite, with strong magmatic arc trace element character. This variation may be a result of mixing of tholeiitic and shoshonitic end-members. Most silicic rocks could have been generated batch-wise from mafic magmas by fractional crystallization of a phenocryst assemblage dominated by plagioclase, pyroxene ± amphibole, as seen in the cumulates. Cessation of magmatism at about 90 Ma approximately coincided with collison of a spreading centre between the Phoenix and Pacific oceanic plates with the continent margin subduction zone. The rifting of New Zealand from West Antarctica and associated extension probably was responsible for emplacement of a coast-parallel Cretaceous dyke swarm.
Condições termodinâmicas de eventos de precipitação extrema em Belém-PA durante a estação chuvosa

As condicoes termodinâmicas de uma regiao sao muito importantes para o desenvolvimento da conveccao umida profunda, principalmente nas regioes tropicais. Portanto, o objetivo deste trabalho foi o de entender e caracterizar o papel das condicoes termodinâmicas da atmosfera durante os eventos de precipitacoes extremas na estacao chuvosa, no periodo de 1987 a 2007, em Belem (PA). Os resultados mostram que as precipitacoes extremas, em sua maioria (56%) apresentam um ambiente precursor com forte instabilidade, indicada pelos altos valores de CAPE (acima de 1000 J/kg) e valores significativos dos indices de instabilidade. Houve, contudo, eventos com baixos valores de CAPE na sondagem das 1200 UTC do dia do evento, mas valores maiores na vespera, o que indica que a chuva em questao pode ter comecado na madrugada e ter perdurado por varias horas, atravessando a hora da sondagem, explicando a queda deste parâmetro. Os indices de instabilidade K, TT e LI apresentaram uma boa representacao do ambiente, prognosticando as tempestades com chuvas fortes com indice de acerto de ate 74%, se levados em conta os eventos em que todos os indices apontavam os mesmos resultados e indicavam forte instabilidade. As condicoes termodinâmicas de forte instabilidade ajudam a promover, mas nao sao as unicas responsaveis pelas tempestades convectivas com precipitacoes extremas.