Miracle-dz/UniFAR-FTUs huggingface dataset:
Kidney modelling: status and perspectives

Mathematical models have played an essential role in elucidating various functions of the kidney, including the mech- anism by which the avian and mammalian kidney can produce a urine that is more concentrated than blood plasma, quasi- isosmotic reabsorption along the proximal tubule, and the control and regulation of glomerular filtration by the myogenic and tubuloglomerular feedback mechanisms. This review includes a brief description of relevant renal physiology, a summary of the contributions of mathematical models at various levels and describes our recent work towards the Renal Physiome. by a network of blood vessels that recovers the fluid and solutes reabsorbed from the various segments of the nephron. About 75% of the initial nephron flow is reabsorbed into the general circulation by the first part of the nephron, called the proximal convoluted tubule (PCT), situated entirely in the cortex; almost all the rest is reabsorbed from the loop of Henle and the distal parts of the nephron; the remainder (on the order of only 1% of the initial filtrate, during antidiuresis, when urine volume is minimal and its osmolality maximal) is excreted as urine from the tip of the IM (called the papillary tip) into the pelvic space, which empties into the ureter and from there into the bladder. The renal medulla is characteristic of the higher vertebrates, and the IM (which contains the portions of long loops of Henle having thin epithelium) exists only in mammals. The medulla is formed by the hairpin-turn feature of the nephrons (descending and ascending limbs) and blood vessels (called the vasa recta within the medulla), which, by counter-current
The Portals 4.3 Network Programming Interface

This report presents a specification for the Portals 4.0 network programming interface. Portals 4.0 is intended to allow scalable, high-performance network communication between nodes of a parallel computing system. Portals 4.0 is well suited to massively parallel processing and embedded systems. Portals 4.0 represents an adaption of the data movement layer developed for massively parallel processing platforms, such as the 4500-node Intel TeraFLOPS machine. Sandia's Cplant cluster project motivated the development of Version 3.0, which was later extended to Version 3.3 as part of the Cray Red Storm machine and XT line. Version 4.0 is targeted to the next generation of machines employing advanced network interface architectures that support enhanced offload capabilities. 3
Notch intracellular domain deficiency in nuclear localization activity retains the ability to enhance neural stem cell character and block neurogenesis in mammalian brain development.

Notch has a broad range of regulatory functions in many developmental processes, including hematopoiesis, neurogenesis, and angiogenesis. Notch has several key functional regions such as the RBP-Jκ/CBF1 association module (RAM) domain, nuclear localization signals (NLS), and ankyrin (ANK) repeats. However, previous reports assessing the level of importance of these domains in the Notch signaling pathway are controversial. In this study, we have assessed the level of contribution of each Notch domain to the regulation of mammalian neural stem cells in vivo as well as in vitro. Reporter assays and real-time polymerase chain reactions show that the ANK repeats and RAM domain are indispensable to the transactivation of Notch target genes, whereas a nuclear export signal (NES)-fused Notch intracellular domain (NICD) mutant defective in nuclear localization exerts a level of activity comparable to unmodified NICD. Transactivational ability appears to be tightly coupled to Notch functions during brain developmen.
Thermophilia in a tropical Australian ant of the Melophorus aeneovirens (Lowne) species‐group (Hymenoptera: Formicidae)

Observations were made on the activity of three colonies of a Melophorus species of the aeneovirens species‐group in woodland at Black Jungle, near Darwin in the monsoonal tropics of the Northern Territory. Melophorusaeneovirens displays thermophilic behaviour typical of the genus. Colony activity rates and duration varied between colonies in relation to the microclimatic conditions of the nests. The lowest nest mound temperature at which activity was initiated was 35.2°C; the highest was 45.3°C. Foraging (leaving the nest) did not occur below a threshold of 38°C. Activity levels peaked at around midday. Cessation of activity in the afternoon corresponded with temperatures between 38.3°C and 42.8°C. Activity levels differed between minor and major workers, with the latter most active prior to 10.00 h and the minors most active during the remaining hours of the day. The activity of a single colony of M. aeneovirens was strongly negatively correlated to the activity of the behaviourally dominant ant Iridomyrmex sanguineus. The average foraging time of M. aeneovirens workers was 11 min, the mean furthest displacement from the colony was 9 m and the furthest, 25 m. Melophorus aeneovirens differed from arid and semi‐arid congeners in having year‐round activity, lower initial activity levels, less random and slower foraging, and in not exploiting thermal refugia.
Compression of Medical Image Stacks using Wavelets and Zero-Tree Coding

The use of computers for handling image data in the healthcare is growing. The amount of data produced by modern image generating techniques, such as CT and MR, is vast. The amount of data might be a problem from a storage point of view or when the data is sent over a network. To overcome these problems data compression techniques adapted to these applications are needed. There are an abundant number of compression schemes for the compression of images, but few that are geared towards compression of image stacks. Though these 2D techniques can be applied to the image stacks they do not fully exploit the three-dimensional nature of the stacks. In this thesis ideas from the image compression area are extended to exploit the 3D nature of image stacks. Attention is directed to MR and CT stacks. The compression schemes in this thesis are based on the relatively new notion of wavelets, used in the JPEG2000 standard. The schemes also providea quality progressive transmission, which allows intermediate low-quality results to be constructed. Two different coders are presented in this thesis both developed for the compression of image stacks containing medical data. They are evaluated and compared and a top performer is chosen. Advantages and drawbacks of the schemes and future enhancements are also discussed.
Observations on the Reproduction in Captivity of the Mona Coqui Eleutherodactylus monensis (Anura: Leptodactylidae) from Puerto Rico

Abstract: Courtship and nesting behaviors and some reproductive parameters were reported for Eleutherodactylus monensis, a terrestrial leptdactylid frog endemic to Mona Island, Puerto Rico, for the first time on the basis of captive observations of two males and one female. The female, captured in the wild in April 1996, produced a total of 22 clutches, each consisting of 5–28 eggs (±SD: 16.2±4.55), at intervals of 14–59 days (25±15.91) from December 1997 to May 2001. Approximately five days before each oviposition, the female started digging the ground with her hind-legs to make a nest concavity. Then, the female temporarily left the concavity, during which one of the males entered therein and started digging also with his hind-legs. The nest concavity eventually got to approximately 37–43 mm in diameter and 10–15 mm in depth. Then, the male moved out of it and started amplexus by mounting and holding the female. The amplectant pair moved to the concavity and the female resumed digging with her hind-legs. She, then, laid a clutch of eggs and buried it also with her hind-legs at a depth of approximately 5 to 40 mm and diameter of approximately 30 to 45 mm. The froglets, weighing 38–67 mg (57.9±6.12), hatched 15–23 days (18.8±2.86) after oviposition.
Fertirrigação com água salina e seus efeitos na produção do pepino enxertado cultivado em ambiente protegido

A aplicacao de fertilizantes via agua de irrigacao nos cultivos protegidos, bem como a utilizacao de agua subterrânea com alta concentracao salina, tem resultado no aumento da salinidade do solo, ocasionando perdas de produtividade. Este trabalho teve o objetivo de avaliar a producao da cultura do pepino enxertado, cultivado em ambiente protegido, quando irrigado com aguas de diferentes condutividades eletricas (S1=1,54; S2=3,10 e S3=5,20 dS.m-1) e duas lâminas de irrigacao associadas as suas frequencias de aplicacao (L0=1,00.ETc; L1F1=1,25.ETc em todas as irrigacoes e L1F2=1,25.ETc quando a lâmina de agua de irrigacao acumulada em L0 atingia 100 mm), sendo ETc a evapotranspiracao da cultura. O ensaio foi conduzido em blocos casualizados com tres repeticoes e os fatores foram arranjados no esquema fatorial 3x3. O numero de frutos comerciais por planta reduziu linearmente com o aumento da salinidade, enquanto a producao total e comercial, bem como o numero total de frutos por planta e a producao de materia seca de frutos nao foram afetados significativamente pela salinidade, embora todas as caracteristicas tenham apresentado tendencia de reducao com o aumento da salinidade da agua de irrigacao. As diferentes lâminas de irrigacao nao foram suficientes para reduzir os efeitos do estresse salino, independente das suas frequencias de aplicacao.
A reliable and efficient protocol for human pluripotent stem cell differentiation into the definitive endoderm based on dispersed single cells.

Differentiation of pluripotent cells into endoderm-related cell types initially requires in vitro gastrulation into the definitive endoderm (DE). Most differentiation protocols are initiated from colonies of pluripotent cells complicating their adaption due to insufficiently defined starting conditions. The protocol described here was initiated from a defined cell number of dispersed single cells and tested on three different human embryonic stem cell lines and one human induced pluripotent stem cell line. Combined activation of ActivinA/Nodal signaling and GSK3 inhibition for the first 24 h, followed by ActivinA/Nodal signaling efficiently induced the DE state. Activation of ActivinA/Nodal signaling alone was not effective. Efficient GSK3 inhibition allowed the reduction of the ActivinA concentration during the entire protocol. A feeder-independent cultivation of pluripotent cells was preferred to achieve the high efficiency and robustness since feeder cells hindered the differentiation process. Addition.
Isozyme analysis of Galaxias species (Teleostei: Galaxiidae) from the Taieri River, South Island, New Zealand: a species complex revealed

Abstract We examined genetic differentiation among 23 samples of non-migratory river galaxias from 17 streams in the Taieri River system, South Island, New Zealand. Four major genetic types were found, two of which occur in narrow sympatry in one location. These were compared with topotypical material representing Galaxias anomalus from the Clutha system (Otago) and G. vulgaris from the Waimakariri system (Canterbury) in order to establish identity. Morphological examination of these four major genetic types revealed consistent concomitant differences. The results suggest that there are at least three species of river galaxias in the Taieri system: G. anomalus, G. vulgaris and at least one previously undescribed species. We propose that the genetic structuring and subsequent speciation of this group has been promoted by the absence of the marine juvenile phase that is found in five other members of the genus native to New Zealand. This structuring may be exacerbated by population fragmentation over the last century owing to the negative influence of introduced trout. The phylogenetic diversity within the river system mirrors the diverse flora and invertebrate fauna of the region, and has conservation implications that parallel those resulting from our improved knowledge of the New Zealand herpetofauna through the application of genetic analysis.
Increased Physical Activity and Fitness above the 50th Percentile Avoid the Threat of Older Adults Becoming Institutionalized: A Cross-sectional Pilot Study

Abstract The objective of this study was to analyze the impact of physical fitness and physical activity on the threat of older adults without cognitive impairment becoming institutionalized. This cross-sectional study involved 195 non-institutionalized (80.1 ± 4.4 years) and 186 institutionalized (83.8 ± 5.2years) participants. Cognitive impairment was assessed using Mini-Mental State Examination, measures of physical fitness were determined by the Senior Fitness Test, and physical activity was assessed using the International Physical Activity Questionnaire. Multivariate binary logistic analysis selected four main determinants of institutionalization in both genders: The likelihood of becoming institutionalized increased by +18.6% for each additional year of age, whereas it decreased by −24.8% by each fewer kg/m2 in body mass index (BMI), by −0.9% for each additional meter performed in the aerobic endurance test, and by −2.0% for each additional 100 metabolic equivalent of task (MET)-min/week of physica.
The Antiinflammatory Properties of Humic Substances: A Mini Review

Humic substances are effective in the suppression of delayed type hypersensitivity, rat paw oedema, a graft‐versus‐host reaction and contact hypersensitivity in rats. They reduce the C‐reactive protein levels of patients suffering from osteoarthritis of the knee and the wheel and flare reaction of patients suffering from hay fever. They have also been described as cardioprotective and pro‐angiogenic. Toxicity studies have indicated that potassium humate is safe in humans up to a daily dosage of 1 g/kg, whereas fulvic acid is safe in humans up to a daily dosage of 1.8 g per adult. The antiinflammatory action of potassium humate can be contributed to the inhibition of the release of inflammatory‐related cytokines, an adhesion molecule, oxidants and components of the complement system. Copyright © 2015 John Wiley & Sons, Ltd.
Integrating bio‐inorganic and analytical chemistry into an undergraduate biochemistry laboratory

Undergraduate laboratories expose students to a wide variety of topics and techniques in a limited amount of time. This can be a challenge and lead to less exposure to concepts and activities in bio‐inorganic chemistry and analytical chemistry that are closely‐related to biochemistry. To address this, we incorporated a new iron determination by atomic absorption spectroscopy exercise as part of a five‐week long laboratory‐based project on the purification of myoglobin from beef. Students were required to prepare samples for chemical analysis, operate an atomic absorption spectrophotometer, critically evaluate their iron data, and integrate these data into a study of myoglobin. © 2015 by The International Union of Biochemistry and Molecular Biology, 43(2):121–125, 2015.
Modulation of fibroblast proliferation by oxygen free radicals.

The major unexplained phenomenon in fibrotic conditions is an increase in replicating fibroblasts. In this report we present evidence that oxygen free radicals can both stimulate and inhibit proliferation of cultured human fibroblasts, and that fibroblasts themselves release superoxide (O2.-) free radicals. Fibroblasts released O2. - in concentrations which stimulated proliferation, a finding confirmed by a dose-dependent inhibition of proliferation by free radical scavengers. Oxygen free radicals released by a host of agents may thus provide a very fast, specific and sensitive trigger for fibroblast proliferation. Prolonged stimulation may result in fibrosis, and agents which inhibit free radical release may have a role in the prevention of fibrosis.
Pengaruh Jarak Tanam Terhadap Pertumbuhan Pohon dan Beberapa Sifat Fisis-Mekanis Kayu Jati Cepat Tumbuh

The aim of this study was to evaluate the effect of tree spacing or planting distance on tree growth characteristic and several physical and mechanical properties of fast growing teak ( Tectona grandis ) wood from a plantation area in West Java. Growth characteristics of all trees within the plot of each planting distance were evaluated, while physical-mechanical properties were represented by 6 selected trees of each planting distance. The results showed that growth characteristics were significantly influenced by tree spacing, while wood properties were not. The wider spacing (3 by 3 m) tends to produce bigger stem diameter, but shorter tree height, shorter clear bole height, and greater branches. Although tree spacing of 3 by 3 m is more favored by the farmers since it provides more space for agroforestry activity, such spacing is not recommended to be applied in order to produce the best timber from teak plantation.
Molecular phylogenetics of the gomphoid-phalloid fungi with an establishment of the new subclass Phallomycetidae and two new orders

Molecular phylogenetic analyses for the gomphoid-phalloid fungi were conducted based on the five gene dataset with extensive taxon sampling. The monophyly of the gomphoid-phalloid clade was strongly supported, and four well supported major subclades were recognized. Three of the four sub-clades were represented entirely by gastroid taxa, and only Gomphales contained both gastroid and non-gastroid taxa. While the gastroid morphology is derived from epigeous, nongastroid taxa in Gomphales, the topology of Phallales indicated that truffle-like form is an ancestral morphology of the stinkhorn fruiting bodies. Although basidiospore maturation occurs within the enclosed fruiting bodies of the stinkhorn, the elevation of the mature spore-producing tissue represents an independent origin of the stipe among Basidiomycota. Comparisons are made between previous and new classification schemes, which are based on the results of phylogenetic analyses. Based on the results of these analyses, a new subclass Phallomycetidae, and two new orders, Hysterangiales and Geastrales, are proposed.
Computational Modeling of Music Cognition: Problem or Solution?

The central purpose of this paper is to elaborate on the methods for computational modeling and to show how, although computational modeling should in principle be instrumental in the understanding of the structure of musical knowledge and the processes involved in music cognition, in practice it too often degenerates into a loose "if you want to understand the theory, here, look in my program" approach. We will show how many issues cannot be decided by inspecting computer programs as they are written nowadays, and we will indicate a possible solution, giving examples from the field of music cognition research.
Silagem de aveia branca em função da adubação nitrogenada e pré-murchamento

A conservacao da forragem na forma de silagem e uma forma de fornecer volumoso de qualidade em epocas de baixa oferta de pastagem, com isso, objetivou-se avaliar o efeito do pre-murchamento e da adubacao nitrogenada nos parâmetros fermentativos e valor nutritivo da silagem de aveia branca, em dois estadios de colheita. O experimento foi conduzido em 2011, na UTFPR, Dois Vizinhos-PR, em delineamento de blocos ao acaso com esquema bifatorial com tres repeticoes. Os tratamentos principais foram seis doses de nitrogenio: 0, 40, 80, 120, 160 e 200 kg ha-1, e os secundarios foram estadios de corte para ensilagem: inicio do florescimento com e sem pre-murchamento, e florescimento pleno sem pre-murchamento. Foi observado que a adubacao nitrogenada promove reducao no pH e no teor de material mineral da silagem de aveia, reduzindo os teores de fibras e elevando os de proteina bruta (PB), quando confeccionada no inicio do florescimento. O efeito de pre-murchamento no inicio de florescimento inibe a producao de efluentes e apresenta maiores teores de PB, sem efeito sobre os parâmetros de fermentacao e de valor nutritivo. A ensilagem no estadio de florescimento pleno apresenta melhores padroes de fermentacao, com pH e capacidade tampao menores, porem com menor valor nutritivo.
Mitochondrial pathology in human schizophrenic striatum: a postmortem ultrastructural study

Studies using in vivo imaging or microscopic analysis of autopsy specimens indicate abnormalities in the striatum of schizophrenics including lower striatal metabolism, a change which can be normalized by antipsychotic medication. To investigate the possibility that abnormalities in schizophrenia brain may be due, in part, to pathology in mitochondria, organelles which generate energy, postmortem brain tissue from schizophrenic and control cases was obtained from the Maryland Brain Collection. Mitochondria in electron micrographs of striatal neuropil were counted and digitized. The caudate and the putamen of the schizophrenic subjects contained significantly (P < 0.05) fewer (a decrease of approximately 20%) mitochondrial profiles throughout the neuropil than did normal controls. The numbers of mitochondrial profiles per axon terminal appeared lower in the subset of schizophrenics off‐drug as compared to either the subset of schizophrenics on‐drug or to controls, suggesting that neuroleptic treatment may normalize this measure. The structural integrity of mitochondrial profiles in the schizophrenic striata was not obviously different from that of controls. Fewer mitochondrial profiles suggest decreased energy demands or diminished capacity to respond to energy requirements in the structures that contain them. These data are consistent with other studies showing decreased metabolism in the striatum of schizophrenics and may identify, in part, the anatomical basis of this deficit. Synapse 31:67–75, 1999. © 1999 Wiley‐Liss, Inc.
Cell Wall Composition of Hyphomicrobium Species

Chemical analysis of cell walls obtained from Hyphomicrobium B-522 and from a morphologically and nutritionally distinct organism, Hyphomicrobium neptunium (ATCC 15444), showed that the organisms have a similar cell wall composition, which is typical of gram-negative bacteria. The walls of both strains contained many amino acids, including the characteristic mucopeptide components diaminopimelic acid and muramic acid. Isolation of the mucopeptide by use of sodium dodecyl sulfate was successful only with cell walls of H. neptunium, thus revealing a difference between the walls of the two strains. The mucopeptide preparation contained glucosamine, muramic acid, alanine, glutamic acid, diaminopimelic acid, and glycine in molar ratios of 1.05:1.21:1.84:1.0:1.04:0.31, respectively. The concentration of glycine was sufficiently high to suggest that it is a mucopeptide component rather than an impurity.
An implementation of a CMA adaptive array for high speed GMSK transmission in mobile communications

The hardware implementation of an adaptive array as a technique for compensating multipath fading in mobile communications is described. The number of the antenna elements is four. The target communication system is modulated by 256 kbps Gaussian-filtered minimum shift keying (MSK) and has a time-division multiplexing (TDM) architecture with 24 time slots. Based on the digital beamforming concept, all of the signals and the array weights are digital-signal processed. The constant modulus algorithm (CMA) is employed for weight optimizing. In an additive white Gaussian noise channel, this system has 5.6-dB gain in an energy-per-bit-to-noise-density ratio at a bit error rate (BER) of 1.0*10/sup -3/, compared with a single antenna system. The result of the basic field test shows that the gain at a BER of 1.0*10/sup -3/ reaches 22.3 dB in a nonselective, slow Rayleigh fading channel given a 5 Hz maximum Doppler shift. >