Miracle-dz/UniFAR-FTUs huggingface dataset:
Automated Code Generation for Lattice QCD Simulation

Quantum Chromodynamics (QCD) is the theory of strong nuclear force, responsible of the interactions between sub-nuclear particles. QCD simulations are typically performed through the lattice gauge theory approach, which provides a discrete analytical formalism called LQCD (Lattice Quantum Chromodynamics). LQCD simulations usually involve generating and then processing data on petabyte scale which demands multiple teraflop-years on supercomputers. Large parts of both, generation and analysis, can be reduced to the inversion of an extremely large matrix, the so-called Wilson-Dirac operator. For this purpose, and because this matrix is always sparse and struc-tured, iterative methods are definitely considered. Therefore, the procedure of the application of this operator, resulting in a vector-matrix product, appears as a critical computation kernel that should be optimized as much as possible. Evaluating the Wilson-Dirac operator involves symmetric stencil calculations where each node has 8 neighbors. Such configuration is really hindering when it comes to memory accesses and data exchanges among processors. For current and future generation of supercomputers the hierarchical memory structure make it next to impossible for a physicist to write an efficient code. Addressing these issues in other to harvest an acceptable amount of computing cycles for the real need, which means reaching a good level of efficiency, is the main concern of this paper. We present here a Domain Specific Language and corresponding toolkit, called QIRAL, which is a complete solution from symbolic notation to simulation code.
Structural analysis of the GLUT1 facilitative glucose transporter

The structure of the human erythrocyte facilitative glucose transporter (GLUT1) has been intensively investigated using a wide array of chemical and biophysical approaches. Despite the lack of a crystal structure for any of the facilitative monosaccharide transport proteins, detailed information regarding primary and secondary structure, membrane topology, transport kinetics, and functionally important residues has allowed the construction of a sophisticated working model for GLUT1 tertiary structure. The existing data support the formation of a central aqueous channel formed by the juxtaposition of several amphipathic transmembrane-spanning α-helices. The results of extensive mutational analysis of GLUT1 have elucidated many of the structural determinants of the glucose permeation pathway. Continued application of currently available technologies will allow further refinement of this working model. In addition to providing insights into the molecular basis of both normal and disordered glucose homeostasis, this detailed understanding of structure/function relationships within GLUT1 can provide a basis for understanding transport carried out by othermembers of the major facilitator super family.
Maternal Influences on Variation in Egg Sizes in Temperate Marine Fishes

SYNOPSIS. We examine the variation in egg sizes of marine teleosts and evaluate the maternal contribution to this variability. At the species level, egg sizes in 309 North Atlantic fishes range from 0.3 to 18.0 mm diameter (median = 1.1), size at hatching varies directly with egg size, and large adult size is associated with large eggs but the relationship is weak. Within populations, egg sizes are distributed normally with a median coefficient of variation of 4% (n = 56 species). Egg size varied among females in all cases for which female-level data were found. Estimates of the variance components of egg size due to females were found for three species and, as a percentage of total variance, are 71 % for capelin, Mallotus villosus , 46% for winter flounder, Pleuronectes americanus , and 35% for Atlantic cod, Gadus morhua . For cod, which spawn multiple egg batches per year, an additional batches-within-females component was estimated to be 26%. Size at hatching also differs among sibgroups and is generally directly related to egg size at the individual level. We modelled fish growth by allowing individuals to grow at exponential rates from a normal distribution of initial sizes. Comparing size variation in model fish to empirical evidence suggests that variation in initial sizes, propagated by growth, could account for a large fraction of the size variation observed months after hatching in natural populations. We view size variation in young marine fishes to be largely of maternal origin and environmentally modulated, which if true has special consequences for fisheries and aquaculture.
Comparison between reconstituted and fresh skim milk chemical and electrochemical acidifications

The aim of this study was to compare the electrochemical and chemical acidification of reconstituted and fresh skim milk in terms of electrodialytic parameters, precipitation kinetics, chemical composition and physicochemical and functional properties of isolates produced by bipolar membrane electro acidification (BMEA). The electrodialytic parameters were not influenced by the type of milk when both milks were compared at a similar protein and salt content. The difference in precipitation kinetics observed between the two milks, whatever the acidification procedure, can be explained mainly by a difference in salt content. Isolates produced by BMEA showed similar physicochemical and functional properties (except for foaming capacity) to isolates produced chemically. The main factor affecting the composition and the physicochemical and functional properties was the pre-treatment of milk prior to acidification: it had a higher impact on the functional properties than the acidification treatment itself. Copyright © 2002 Crown in the right of Canada. Published for SCI by John Wiley & Sons, Ltd
Frost hardiness and production of Opuntia forage clones in the Mendoza plain, Argentina

Abstract Frost resistance of Opuntia forage clones was evaluated for different plant ages after freezes of −16 and −17°C. Above-ground biomass production of 3-year-old clones established in a dune was also estimated. Frost damage was visually estimated, integrating the individual cladode damage over the entire plant. Biomass was based on a total above-ground harvest of typical plants of each species. Young cladodes from 9-month-old plants had damage higher than 85%. The 3-year-old plants exhibited mean frost damage that ranged from 0.3% in O . paraguayensis K. Sch. to 34% in O. ficus-indica L. f. inermis (Web.) Le Houer. (San Juan accession). O. spinulifera Salm-Dyck f. nacuniana Le Houer. f. nov . appears to be the most promising species for extremely cold winter areas. The 3-year-old plants of this species had 5% mean frost damage, a dry biomass production of 2 kg plant −1 and 6.5% crude protein content in young cladodes.
Progress report: Results of a long‐range captive breeding program for the bottlenose dolphin, Tursiops truncatus and Tursiops truncatus gilli

There have been 36 bottlenose dolphins born in breeding colonies at Sea World, California, and Sea World, Florida, from 1978–1985. Significant features of this successful reproductive program are construction of a compatible breeding colony, early hormonal detection of pregnancy, pre- and postnatal association of inexperienced mothers with experienced females and their calves, and minimized handling of the mothers and calves until the calves are over 1 year of age. Inclusion in the breeding colonies of males old enough to be effective breeders is stressed. Females in the colonies have successfully bred from 8–9 years of age to 23–24 years of age. Calving intervals in the colonies vary from 2 to over 3 years. Calves are born all year round, with some peaking in calving activity in the spring and fall months. Serum progesterone levels greater than 6,000 pg/ml, maintained over a 4–6-week period, are considered indicative of pregnancy. Progesterone levels vary from less than 10,000 to over 50,000 pg/ml during gestation, averaging 25,000 pg/ml. The need for further study of variation in the pattern of progesterone levels during pregnancy is emphasized. A gestation period for Tursiops of 11.5 to 12 months is consistent with our cumulative progesterone data.
Immunolocalization of Alzheimer β‐amyloid peptide precursor to cellular membranes in baculovirus expression system

One characteristic of Alzheimer's disease (Aβ disease) is the accumulation of amyloid deposits within the extracellular space of the brain and meninges. A 40 amino acid peptide called β‐peptide or A4 protein is the subunit of the amyloid fibrils found in these deposits. The sequence of β‐peptide is contained within those of a family of larger proteins called the Alzheimer β‐amyloid peptide precursor (APP). These APPs contain, in addition to a signal sequence, a hydrophobic sequence that is believed to span cell membranes. Although biochemical studies indicate that some APPs have properties of integral membrane proteins, morphological confirmation of this has not been reported. We recently described an expression system in which human APP751 cDNA was placed under the transcriptional regulation of the polyhedrin gene promoter in the baculovirus Autographica californica infecting a Spodoptera frugiperda cell line (Ramakrishna et al., Biochem Biophys Res Commun 174:983–989, 1991). As part of a larger biochemical and molecular biological study of APP, we have carried out an immunocytochemical study using antibodies directed against several epitopes within APP to reveal, at both the light and the electron microscopic levels, the cellular localization of APP in the baculovirus expression system. These studies demonstrate that APP751 is abundantly synthesized and inserted into certain of the membrane compartments of the cell. As early as 24 hr postinfection, APP751 is found associated with all membrane compartments excepting mitochondrial membranes. The patterns of immunolabeling are consistent with our biochemical findings that the protein is processed in these cells so as to release the extracellular domain and to retain a transmembrane and intracellular segment. These data provide the first morphological demonstration of the membrane location of APP751 its posttranslational processing to a secreted fragment, and its exclusion from the mitochondrial membranes. This system is especially valuable for identifying conditions under which antibodies raised against APP or appropriate synthetic peptides will react with native APP.
Extractable Soil Water and Transpiration Rate of Soybean on Sandy Soils

Substantial consistency has been obtained in describing plant response to drying soil by expressing plant performance as a function of the fraction of soil water that can be used by the plants. Generally, there is no decrease in plant activity until the soil water has been decreased to the level where only about 0.3 of the water that can be extracted by the plants remains in the soil. There is, however, ambiguity as to whether this relationship is appropriate for sandy soils. The objective of this research was to compare methods for describing extractable soil water by soybean [Glycine max (L.) Merr. ] plants grown in pots with soils differing in sand content. The two methods tested were based on thermodynamic and physiological definitions of the upper and lower end-points of extractable soil water. While differences existed in the volumetric soil water content for the two definitions of the lower end-point of extractable soil water, these differences were small. In contrast, very large differences existed in defining the volumetric soil water of the upper end-point either thermodynamically (commonly assumed to be -10 kPa for sands) or physiologically (pot capacity). As a consequence, there were large differences in the response curves obtained based on the two expressions of extractable soil water. The threshold for transpiration expressed as an absolute volumetric soil water was of course independent of the determination of the end-points. Instead of relying on a relative transpiration response to extractable soil water, for sandy soils it may be necessary to use the volumetric soil water content determined under controlled conditions to interpret crop response under any particular field situation.
Body composition and nutritional requirements of protein and energy for body weight gain of lambs browsing in a tropical semiarid region

Este trabalho foi realizado com o objetivo de avaliar a composicao corporal em gordura, proteina e energia e as exigencias nutricionais para ganho de peso em cordeiros em sistema de pastejo na regiao semi-arida. Foram utilizados 32 cordeiros Santa Ines, castrados, com peso inicial de 15,8 kg ± 1,4 kg e idade variando entre 3 e 4 meses. Desses animais, oito cordeiros foram abatidos no inicio do experimento, como animais-referencia, para determinacao da composicao corporal inicial na metodologia do abate comparativo. Os 24 animais remanescentes foram utilizados em delineamento em blocos casualizados, com tres tratamentos e oito blocos. Cada um dos oito blocos experimentais foi composto inicialmente de tres cordeiros de 15 kg, aos quais foram aplicados os tratamentos (0,0, 1,0 e 1,5% do peso vivo do animal de suplementacao diaria com mistura concentrada composta de fuba de milho, farelo de soja e mistura mineral, ajustada para ganho de peso medio diario estimado em 200 g) aleatoriamente designados. Quando um dos animais de cada lote atingiu 30 kg de peso, os tres animais do lote foram abatidos. Os valores estimados de composicao corporal variaram de 171,59 a 145,84 g de proteina/kg de peso do corpo vazio (PCV); 0,53 a 319 g de gordura/kg de PCV; e 2,06 a 3,90 Mcal/kg de PCV para animais de 15 a 30 kg de PCV. As exigencias liquidas para ganho medio de 200 g/dia variaram de 25,99 a 22,09 g de proteina e de 0,311 a 0,591 Mcal de energia para animais de 15 a 30 kg de PV, respectivamente. Cordeiros Santa Ines em pastejo na regiao semi-arida necessitam de mais proteina e menos energia que cordeiros confinados em regioes temperadas ou confinados em areas tropicais como reportado na literatura.
Effects of yeast and maltose concentration on ultrasonic velocity and attenuation coefficient and its application for process monitoring

Monitoring substrate and cell concentration is important for controlling yeast propagation and fermentation processes. This usually requires two instruments, a density meter, and an optical turbidity meter. This paper presents a method for simultaneously determining yeast and maltose concentration with a single ultrasonic sensor. Ultrasonic velocity and attenuation were measured at varying maltose and yeast cell concentrations from 0 to 4 wt%. Ultrasonic velocity increased linearly with both yeast (R2 = 0.999) and maltose concentration (R2 = 0.996). In contrast, while attenuation coefficient depended linearly on yeast concentration (R2 = 0.998), it did not significantly depend on maltose concentration (R2 = 0.476). To draw conclusions about the main mechanisms of attenuation, the measured attenuation coefficients for yeast cells at 2 MHz were compared to predicted values. With a mean absolute percentage error of 0.25%, intrinsic absorption, thermal effects, and, to a lesser extent, viscous effects were identified as the main reason for damping. These results support the feasibility of combining ultrasonic velocity and attenuation measurements for estimating yeast cell and maltose concentration.
Estimating single-tree branch biomass of Norway spruce with terrestrial laser scanning using voxel-based and crown dimension features

Abstract Many remote sensing-based methods estimating forest biomass rely on allometric biomass models for field reference data. Terrestrial laser scanning (TLS) has emerged as a tool for detailed data collection in forestry applications, and the methods have been proposed to derive, e.g. tree position, diameter-at-breast-height, and stem volume from TLS data. In this study, TLS-derived features were related to destructively sampled branch biomass of Norway spruce at the single-tree level, and the results were compared to conventional allometric models with field measured diameter and height. TLS features were derived following two approaches: one voxel-based approach with a detailed analysis of the interaction between individual voxels and each laser beam. The features were derived using voxels of size 0.1, 0.2, and 0.4 m, and the effect of the voxel size was assessed. The voxel-derived features were compared to features derived from crown dimension measurements in the unified TLS point cloud data. TLS-derived variables were used in regression models, and prediction accuracies were assessed through a Monte Carlo cross-validation procedure. The model based on 0.4 m voxel data yielded the best prediction accuracy, with a root mean square error (RMSE) of 32%. The accuracy was found to decrease with an increase in voxel size, i.e. the model based on the 0.1 m voxel yielded the lowest accuracy. The model based on crown measurements had an RMSE of 34%. The accuracies of the predictions from the TLS-based models were found to be higher than from conventional allometric models, but the improvement was relatively small.
Human impacts in soft-sediment assemblages at Casey Station, East Antarctica: Spatial variation, taxonomic resolution and data transformation

Differences between marine soft-sediment assemblages at disturbed (two waste dumps, a sewage outfall and a wharf) and control locations were found at Casey Station, Antarctica. These differences were significant against considerable background spatial variability. Core samples were collected by divers using a hierarchical, spatially nested sampling design incorporating four scales: (i) locations (thousands of metres apart); (ii) sites (hundreds of metres apart); (iii) plots (tens of metres apart); and (iv) among replicates within plots (approximately 1 metre apart). Control locations had greater species richness and diversity than disturbed locations and there were many taxa found at control locations that were not recorded at disturbed locations. Assemblages at disturbed locations were less variable than those at control locations. In contrast, populations of some dominant species were more variable at disturbed locations than at control locations. Significant variation in populations of individual taxa was also found at all scales and although greatest at the level of location, variation was also large at the smallest scale, between replicate cores, indicating significant small-scale patchiness in populations of taxa. Patterns of assemblage structure were similar at fine (77 taxa) and medium (aggregated to 33 taxa) levels of taxonomic resolution, but changed at coarse levels of resolution (nine phyla). Soft-sediment assemblages at Casey Station are markedly different from those reported from other areas of Antarctica. Assemblages at Casey are almost completely dominated by crustaceans (up to 99% total abundance) and polychaetes are rare or in very low abundances in most areas investigated in the region. This is also the first demonstration that small Antarctic research stations (population 20-50 people) may cause impacts that are detectable in the adjacent marine environment.
Artspezifische Muster der Zugunruhe bei Laubsängern und ihre mögliche Bedeutung für die Beendigung des Zuges im Winterquartier

Zusammenfassung In dieser Arbeit wird die mogliche Bedeutung der endogenen Jahresperiodik fur das Auffinden des arttypischen Winterquartiers von Zugvogeln untersucht. Fruhere Untersuchungen hatten Argumente fur eine Hypothese geliefert, nach welcher ein Zugvogel, der allein zur Richtungsorientierung befahigt ist, sein Winterquartier mit Hilfe eines endogenen Zeitprogrammes auffinden konnte. Diese Hypothese nimmt an, das wahrend der Herbstzugzeit insgesamt gerade so viel Zugunruhe aktiviert wird, wie zum Erreichen des Zielortes notig ist (Gwinner 1968). Sie wird hier durch einen Versuch gepruft, bei welchem die im Registrierkafig gemessene nachtliche Zugunruhe zweier nah verwandter Vogelarten mit unterschiedlich weiten Zugwegen (Zilpzalp, Phylloscopus collybita und Fitis, P. trochilus, vgl. Abb. 1) in identischen Versuchsbedingungen verglichen wird. Das Ergebnis stutzt diese Hypothese: die normalerweise weiter ziehenden Fitise blieben wesentlich langer zugunruhig und entwickelten insgesamt mehr Zugunruhe als die Zilpzalpe. Diese Unterschiede waren in einer Versuchsgruppe, die in den naturlichen Lichtbedingungen ihrer Brutheimat gehalten wurde, groser als in einer Gruppe, die ab Ende September einem kunstlichen 12: 12-Std. -Tag ausgesetzt gewesen war (Abb. 2, 3). Die interindividuelle Variabilitat von Dauer, Menge und maximaler Amplitude der Zugunruhe war beim Fitis wesentlich kleiner als beim Zilpzalp (Abb. 4, Tab. 2). Dies spricht dafur, das die Zugunruhe beim fernziehenden Fitis starrer endogen festgelegt ist als beim Zilpzalp, dessen Zugunruhe mehr von Auseneinflussen abhangig sein konnte. Der zeitliche Verlauf der Zugunruhe beider Arten zeigt charakteristische Unterschiede, die wenigstens zum Teil Unterschieden im Zugablauf beider Arten entsprechen durften.
Structure and Stress-Strain Relationship of Soft Tissues

The mechanical properties of a soft tissue are related to its structure. Weshall illustrate this by the properties of the arteries and the lung. Viscoelasticity, strain rate effects, pseudo-elasticity, and constitutive equations ar discussed. The mecahnical properties of an organ is, however, not only based onthe tissues of the organ, but also on its geometry and relationship to the neighboring organs. A typical example is the blood vessel. The capillary blood vessels of the mesentery are “rigid”; those in the bat's wing are “distensible”; whereas the capillaries of the lung are “sheet” like: rigid in one plane, and compliant in another. The stress-strain relationship of the systemic arteries is highly nonlinear, stiffening exponentially with increasing strains; yet that of the pulmonary arteries in the lung is linear. The systemic veins are easily collapsible; yet the pulmonary veins in the lung are not: they remain patent when the blood pressure falls below the alveolargas pressure. The explanation of these differences lies in the varied interactions between the blood vessels and the surrounding tissues in different organs. The implications of these differences on blood circulation are pointed out. Therole of ultrastructure is discussed.
Lands for Long‐Term Research in Conservation Biology

Success in conservation biology depends upon a synergistic combination of short-term tactics and long-term strategies. Although the former are often necessary to fore- stall immediate habitat losses, the latter provide the critical framework of understanding needed to develop effective short-term priorities. Although many conservation biologists now emphasize short-term tactics, prudence dictates the con- comitant establishment of long-term research projects aimed at answering fundamental ecological questions. One deterrent to amassing such long-term data bases, asidefrom time andfunding, is a lack of suitable sites where such studies can be conducted on a large scale. We describe two established major land-holding networks in the United States that could serve as appropriate places to develop long- term studies: the National Science Foundation's Long-Term