Miracle-dz/UniFAR-FTUs huggingface dataset:
The “Little Iron Waltz”: The Ternary Response of Paracoccidioides spp. to Iron Deprivation

Paracoccidioides is a genus of thermodimorphic fungi that causes paracoccidioidomycosis. When in the host, the fungus undergoes several challenges, including iron deprivation imposed by nutritional immunity. In response to the iron deprivation triggered by the host, the fungus responds in a ternary manner using mechanisms of high affinity and specificity for the uptake of Fe, namely non-classical reductive iron uptake pathway, uptake of host iron proteins, and biosynthesis and uptake of siderophores. This triple response resembles the rhythmic structure of a waltz, which features three beats per compass. Using this connotation, we have constructed this review summarizing relevant findings in this area of study and pointing out new discoveries and perspectives that may contribute to the expansion of this “little iron waltz”.
Primer Transferability Analysis on SSR and EST-SSR Markers from Triticum aestivum to Bromus inermis

Bromus inermis Leyss. ( bromegrass) is a species of the Bromeae tribe,Poaceae. It has the advantages of high nutritional value,high yield,strong adaptability,and long growing season,and it is tolerant to abiotic stresses such as drought,cold,salinity,and infertile soils. In this paper,203 pairs of SSR and 46 pairs of EST-SSR primers,designed from genomes A,B,and D of Triticum aestivum,were employed to evaluate primer transferability in the genomes of B. inermis. Results showed that 137( 67. 49%) pairs of SSR and 30( 65. 22%) pairs of EST-SSR primers were successfully amplified in the genomic DNA of B. inermis. The average numbers of bands per primer in B. inermis were 2. 8 for SSR primers and 2. 5 for EST-SSR primers. This indicated that a higher transferability of SSR and EST-SSR primers might exist between T. aestivum and B. inermis. The study also found that primers from genome B and homologous chromosome group 5 of T. aestivum had the lowest effective amplification ratio and average amplified bands in B. inermis,which suggested that genome B and homologous chromosome group 5 of T. aestivum might have a homologous relationship with the genomes of B. inermis. This research has certain reference value to exploit the specific genetic marker,and estimate the genetic diversity of B. inermis.
Magnetogasdynamic boundary condition for a self-consistent solution to the closed magnetopause.

The conventional numerical inviscid blunt-body problem is used as an analog for the problem of the solar plasma flow around the geomagnetic cavity. The approach of Spreiter and Jones is extended (using the identical solution of Inouye and Lomax) for an assumed teardrop magnetospheric boundary. After the macroscopic flow properties are defined in the absence of an interplanetary field, the simplest case of a radial interplanetary magnetic field as suggested by Lees is considered together with a quiet Alfven Mach number in order to find a firstorder approximation to the exact magnetic field configuration for an infinitely conducting neutral plasma. The sum of both gasdynamic and magnetic pressures along the assumed boundary is then proposed as a necessary first step in a self-consistent iterative solution of the inner and outer time-independent magnetospheric problem. Exact post shock magnetic magnitudes and directions are compared with the first-order solution when the analogderived shock is assumed to be the exact fast magnetogasdynamic shock wave. This comparison indicates the validity of the approximate solution. The energy dissipated in the shock wave is found to be ^10 ergs/sec, which is approximately 20% of the proton energy flux through a circle with the diameter of the magnetosphere. An example of the threedimensional magnetic field topology also is considered for the case where the interplanetary field is perpendicular to the solar wind direction.
Further studies of energy exchange between the zonal flow and the eddies

The present study describes the results of calculations of transports of sensible heat and momentum and of exchanges of available potential energy and kinetic energy between the zonal flow and the eddies in the wave number regime. The study is based on five levels of data for the months of April, July, October 1962 and January 1963, while only two levels of data (850 and 500 mb) were available for the months of January 1959 and April, July, October 1961. The heat and momentum transport calculations in the wave number regime show that a very large fraction of the total heat and momentum transport is carried out by the very long waves during winter while a smaller percentage of the total heat and momentum transport is accounted for by these waves during the remaining part of the year. The exchange from zonal to eddy available potential energy shows a marked variation during the year with maxima during the winter and minima during the summer. The spectral distributions are such that we find a maximum for wave numbers 2 or 3 during the winter. This maximum disappears during summer, when we find the maximum at much smaller wave lengths. This energy exchange is positive in all months thus far investigated not only for the total conversion but also for the individual wave numbers. The interchange from eddy to zonal kinetic energy has a different behavior. It differs from the annual variation of the potential energy exchanges in that we find the maximum value during fall. The spectra are very irregular with no clearly defined maxima and minima. This energy exchange is positive for all months investigated so far except for January 1963, but the average values are always much smaller than the average exchanges between the two forms of available potential energy. It is demonstrated that a very large fraction of the total (negative) interchange during January 1963 is accounted for by wave number 3. The results of our calculations are compared with those of other investigators showing fair qualitative agreement. DOI: 10.1111/j.2153-3490.1964. tb00158.x
First report of Rhipicephalus appendiculatus, Echidnophaga gallinacea and Ctenocephalides felis on African pygmy hedgehogs (Atelerix albiventris) captured in Morogoro, Tanzania.

Article history Received: 8 Aug, 2015 Revised: 6 Sep, 2015 Accepted: 7 Sep, 2015 Abstract A study was conducted to determine ectoparasites infesting the African pygmy hedgehog, Atelerix albiventris (Wagner, 1841; Erinaceomorpha; Erinaceidae). This species is widespread throughout Africa, and can be found in steppes, savannas, grasslands, bushy areas as well as around human premises. In human settlement, they are found in abandoned houses, livestock enclosures and other agricultural fields. In this study, 22 wild-collected hedgehogs from grassland and bush areas were examined for the presence of various ectoparasites. The hedgehogs were captured by using pitfall and intensive searching methods. Thorough examination in the laboratory revealed high infestation rates with Haemaphysalis leachi (100%), Rhipicephalus appendiculatus (27.3%), Echidnophaga gallinacea (31.8%), and Ctenocephalides felis (54.5%). The intensity of parasite infestation per animal was 19.1 for Haemaphysalis leachi, 13.4 for Echidnophaga gallinacea 3.5 for Ctenocephalides felis and 2.6 for Rhipicephalus appendiculatus. These findings added to the knowledge of parasites affecting the African pygmy hedgehog.
On the momentum diffusion over multiphase surfaces with meshless methods

This work investigates the effects of the choice of momentum diffusion operator on the evolution of multiphase fluid systems resolved with Meshless Lagrangian Methods (MLM). Specifically, the effects of a non-zero viscosity gradient at multiphase interfaces are explored. This work shows that both the typical Smoothed Particle Hydrodynamics (SPH) and Generalized Finite Difference (GFD) diffusion operators under-predict the shear divergence at multiphase interfaces. Furthermore, it was shown that larger viscosity ratios increase the significance of this behavior. A multiphase GFD scheme is proposed that makes use of a computationally efficient diffusion operator that accounts for the effects arising from the jump discontinuity in viscosity. This scheme is used to simulate a 3D bubble submerged in a heavier fluid with a density ratio of 2:1 and a dynamic viscosity ratio of 100:1. When comparing the effects of momentum diffusion operators, a discrepancy of 57.2% was observed in the bubble's ascent velocity.
Caryopsis Micromorphology of Eleusine Gaertn. (Poaceae) and Its Systematic Implications

Caryopsis micromorphological characteristics of nine species of Eleusine were studied using the scanning electron microscopy(SEM). The results showed that there were three types of ventral shapes in caryopses including oval,lanceolate,and oblong,two types of compression including dorsiventral and lateral,two types of ventral faces including flat and concave.The embryo proportion ranged from 0.29 to 0.58,and hilum proportion from 0.10 to 0.24. There were two types of surface sculpture including the verrucate simple sculpture and the compound reticulate sculpture composed by the regular spread of verrucae.The mean diameter of caryopsis foveola ranged from 0.57 μm to 1.31 μm with a density from 30 to 200 in 100 μm2. It can be concluded that caryopsis ventral shape,sculpture,and foveola are very useful characteristics for the identification of species and the inference of interspecific relationships in Eleusine.Because of the flat and concave ventral face,caryopses of Eleusine have relatively small bulk,therefore possibly aiding rapid development and maturation.All characters seem to be particularly valuable in climates of East Africa seasonal drought.
(Extended Version) World Age in Julia Optimizing Method Dispatch in the Presence of Eval

Dynamic programming languages face semantic and performance challenges in the presence of features, such as eval , that can inject new code into a running program. The Julia programming language introduces the novel concept of world age to insulate optimized code from one of the most disruptive side-effects of eval : changes to the definition of an existing function. This paper provides the first formal semantics of world age in a core calculus named Juliette, and shows how world age enables compiler optimizations, such as inlining, in the presence of eval . While Julia also provides programmers with the means to bypass world age, we found that this mechanism is not used extensively: a static analysis of over 4,000 registered Julia packages shows that only 4–7% of packages bypass world age. This suggests that Julia’s semantics aligns with programmer expectations.
A Discovery of Anomozamites with Reproductive Organs

Anomozamites haifanggouensis (Kimura et al .) Zheng et Zhang comb. nov. is a characteristic Bennettitalean plant in Middle Jurassic flora. Only one specimen was collected from Haifanggou Formation (Middle Jurassic) in Daohugou village, Shantou town, Ningcheng County, Nei Mongol Autonomous Region, China. The stem of plant is slender and repeatedly branches as a dichasial system with a fertile shoot in the fork, forming equal and widely divergent branches, on the branches born with the fronds of Anomozamites type. Its reproductive organs consists of some microsporophylls and a few of the bracteoid small leaves (or receptacular leaves). Some scattered bracteoid leaves and microsporophylls were formerly considered by Pan as dicots. Since then, they were proposed to be a non_committal genus Pankuangia and described them as P. haifanggouensis by Kimura et al . In this study, we discover that these bracteoid small leaves and microsporophylls should be of Anomozamites . This discovery provides strong evidence for the “ Pankuangia " determination of the taxonomical position.
Effects of mangiferin on MAPK pathway and serum cytokines in rats with chronic inflammation induced by lipopolysaccharide

Objective To investigate the regulation of mangiferin on mitogen-activated protein kinases(MAPK) pathway and the serum cytokines expression patterns in chronic lipopolysaccharide(LPS)-induced chronic inflammation of rats.Methods The rat model with chronic inflammation was established by iv low dose(200 μg/kg) intermittent LPS injection via the caudal vein.Rats were randomly divided into model,Prednisone(PNS,5 mg/kg),and mangiferin high-,mid-,low-dose(200,100,and 50 mg/kg) groups.The rats were ig administered with the predetermined drugs once a day within four weeks.At the end of the 4th week,the RT-PCR was applied to evaluate the gene expression of p38,ERK,and JNK in the MAPK pathway,while the Western blotting was executed to detect their protein phosphorylation levels.The protein antibody microarray chip was employed for serum cytokine expression pattern measurement.Results Compared with the model group,both of the expression of ERK,JNK,and the protein phosphorylation of ERK were markedly inhibited in mangiferin high-dose group.The levels of intercellular adhesion molecule 1(ICAM-1),monocyte chemoattractant protein 1(MCP-1),cytokine-induced neutrophil chemoattractant 1(INC-1),and platelet-derived growth factor(PDGF) were significantly lowered.Conclusion Mangiferin could simultaneously regulate the gene expression of ERK,JNK,and the protein phosphorylation of ERK in the MAPK pathway and decrease the serum chemotactic cytokines level.
Quasi-Experimentation

"action research" for the less rigorous aspects of educational investigations. Will quasi-experimentation become another educational fad, misunderstood and misused for a while before being dropped in favor of some new false panacea? Is much of the quasi-experimentation being stirred up by the Campbell-Stanley Handbook chapter, despite its warnings, in fact pseudo-experimentation that would be treated better in a frankly associational framework? Some recent talk about finding ready-made quasi-experiments in extant collections of data makes me fearful. Let us, therefore, consider certain aspects of "quasi-" versus "true" experimentation and precautions that need to be observed.
ESCAPE: Countering Systematic Errors from Machine’s Blind Spots via Interactive Visual Analysis

Classification models learn to generalize the associations between data samples and their target classes. However, researchers have increasingly observed that machine learning practice easily leads to systematic errors in AI applications, a phenomenon referred to as “AI blindspots. ” Such blindspots arise when a model is trained with training samples (e.g., cat/dog classification) where important patterns (e.g., black cats) are missing or periphery/undesirable patterns (e.g., dogs with grass background) are misleading towards a certain class. Even more sophisticated techniques cannot guarantee to capture, reason about, and prevent the spurious associations. In this work, we propose ESCAPE, a visual analytic system that promotes a human-in-the-loop workflow for countering systematic errors. By allowing human users to easily inspect spurious associations, the system facilitates users to spontaneously recognize concepts associated misclassifications and evaluate mitigation strategies that can reduce biased associations. We also propose two statistical approaches, relative concept association to better quantify the associations between a concept and instances, and debias method to mitigate spurious associations. We demonstrate the utility of our proposed ESCAPE system and statistical measures through extensive evaluation including quantitative experiments, usage scenarios, expert interviews, and controlled user experiments.
Application of 16S rDNA amplification and sequencing for detection of fish and shrimp bacterial pathogens

Detection of fish and shrimp bacterial pathogens based on 16S rDNA amplification and sequencing was carried out in this study. Bacteria from live and dead fish, water samples from fish and shrimp rearing systems were isolated and their 16S rDNA were amplified by polymerase chain reaction (PCR) using universal primers. The PCR amplified products were sequenced and the sequence information was compared with the sequences in the GenBank of National Centre for Biotechnological Information (NCBI) using BLAST program. Their maximum identity showed that the bacterial isolates from live fish, dead fish, water samples from fish and shrimp rearing systems were Aeromonas hydrophila, Salmonella sp, Pseudomonas aeruginosa and Vibrio harveyi, respectively. 16S rDNA technique is a valuable tool for rapid and accurate detection of bacteria which can replace conventional, time-consuming biochemical identification methods.
The Response of the Corbiculidae (Mollusca: Bivalvia) to Osmotic Stress: The Cellular Response

When Polymesoda was transferred from 10‰ to fresh water, the free amino acid (FAA) pool decreased by 70% in 24 h; alanine accounted for 85% of the decrease. In Polymesoda blood, FAA doubled within 10 h after hypoosmotic stress; between 10 and 24 h the FAA decreased by 24%. Most of the increase and subsequent decrease were accounted for by alanine. In Corbicula, transferred from 5‰ to fresh water, the FAA pool decreased by 87% in 48 h; alanine accounted for 73% of the decrease. Upon transfer from fresh water to 10‰, the free amino acid (FAA) pool of Polymesoda foot muscle increased from 27 to 176 μmol/g dry weight during the first 36 h; between 36 and 73 h the FAA pool increased only to 187 μmol/g dry weight. Alanine accounted for 56% of the increase before 36 h and 77% after 36 h. When Corbicula was transferred from fresh water to 5‰ the FAA pool increased from 20 to 115 μmol/g dry weight; between 70 h and 30 days the pool increased to 197 μmol/g dry weight. Alanine accounted for 78% of the initial increase in the FAA pool.
ITS sequence analysis of Amomum villosum

Object To identity Amomum villosum Lour. from different producing area by ITS sequence analysis.Methods Firstly, total DNA of A. villosum from different producing area was extracted and it's succedaneum or fake was extracted. Secondly, the ITS sequence was amplified by PCR with universal primer of ITS and sequencing ITS on PCR product was directly sequenced after purification.Results The total length of ITS sequence is 626 bp in the different samples. The ITS sequence can be divided into three fragments: the length of ITS-1 is 248 bp, 5.8 S is 155 bp and ITS-2 is 223 bp respectively. In all the samples, 5.8 S has the same sequence. Six A. villosum from different producing area and Luqiao amomum have the same ITS-2 sequence. But ITS-1 fragment has bigger diversity in base sequence among the various specimens.Conclusion ITS-1 sequence can be used to confirm producing area of A.villosum, and find out its fake.
The Effect of Deficit Irrigation and Crop Load on Leaf and Fruit Nutrition of Fertigated ‘Ambrosia’/‘M.9’ Apple

Mature, fruiting ‘Ambrosia’/‘M.9’ apple [ Malus 3 sylvestris (L.) Mill. var. domestica (Borkh.) Mansf. ] trees were subjected over three growing seasons to a split-plot experimental design involving four irrigation main plot treatments and three subplot crop load treatments with six replicates. This semiarid production region is traditionally irrigated 01 May to 01 Oct. during which time an average of ’’ 15 cm of precipitation occurs. Irrigation treatments were applied through 2 3 4 L · h L 1 emitters per tree and included I1: daily application of 100% evapotranspiration (ET); or I2: 50% daily ET; or I3: 50% ET applied to one side; and I4: 50%, 25%, or 18% ET-application, applied every second day, 2007–09, respectively. Crop load treatments were imposed annually ’’ 4 to 5 weeks after full bloom to create low (2.5, 3, and 3.75 fruits/cm 2 trunk cross-sectional area (TCSA), medium (4.5, 6, and 7.5 fruits/cm 2 TCSA), and high crop loads (9, 12, and 15 fruits/cm 2 TCSA), 2007–09, respectively. Leaf and fruit nutrient concentration was affected more by
Rapid evolution or preadaptation in invasive Jacobaea vulgaris

Several theories have been developed to explain why invasive species are very successful and develop into pest species in their new area. The shifting defence hypothesis (SDH) argues that invasive plant species quickly evolve towards new defence levels in the invaded area because they lack their specialist herbivores but are still under attack by local (new) generalist herbivores. The SDH predicts that plants should increase their cheap, toxic defence compounds and lower their expensive digestibility reducing compounds. As a net result resources are saved that can be allocated to growth and reproduction giving these plants a competitive edge over the local plant species. We conducted a literature study to test whether general toxic defence compounds in the invaded area are increased and that digestibility reducing compounds are lowered. We specifically studied the levels of pyrrolizidine alkaloids, a toxin which is known for its beneficial and detrimental impact against specialists and generalists respectively. Digestibility reducers did not show a clear trend which might be due to the small number of studies and traits measured. The meta analysis showed that toxic compounds in general and pyrrolizidine alkaloid levels specifically, increased significantly in the invaded area, supporting the predictions of the SDH that a fast evolution takes place in the allocation towards defence.
Plaque Assay in SARS-CoV Titration

Objective To optimize and assess the method of plaque assay of severe acute respiratory syndrome(SARS)-associated coronavirus(SARS-CoV) for pathogenesis studies and monitor the viral titers for quantifying the amounts of SARS-CoV.Method A series of 10-fold dilutions of viruses were added into Vero-E6 cells seeded plates.The plates were overlaid with DMEM containing 1% methylcellulose 4,000 CP.The Vero-E6 cells were fixed with 4% formaldehyde,and stained with 0.5% crystal violet.Plaques were counted after the plates were air dried.Result The viral titer was 6.57 Lg pfu/mL.Clear plaques were formed in wells infected with SARS-CoV.Conclusion This procedure is useful for SARS-CoV titration and has less risk of SARS-CoV handling hazards in bio-safety laboratory.The plates can be kept for a longer time than other assays.This improved plaque formation technique can also be used and applied to measure the neutralizing antibody activities against SARS-CoV infection.
Unity

lived in the seventeenth-century [sic] , so more than three hundred years ago. And he is claimed by great people as an a ṃ śāvatāra [partial incarnation] of Lord Śiva himself. And then Nīlaka ṇṭ ha Dīk ṣ ita was his brother’s grandson—brother’s son’s son. And he is also one of the greatest people who lived later in the seventeenth century. And he’s acclaimed to be an a ṃ śāvatāra of Parāśakti. So we have descended from these great people.
Structure-based function inference using protein family-specific data

We describe a method to assign a protein structure to a functional family using family-specific fingerprints. Fingerprints represent amino acid packing patterns that occur in most members of a family but are rare in the background, a nonredundant subset of PDB; their information is additional to sequence alignments, sequence patterns, structural superposition, and active-site templates. Fingerprints were derived for 120 families in SCOP using Frequent Subgraph Mining. For a new structure, all occurrences of these family-specific fingerprints may be found by a fast algorithm for subgraph isomorphism; the structure can then be assigned to a family with a confidence value derived from the number of fingerprints found and their distribution in background proteins. In validation experiments, we infer the function of new members added to SCOP families and we discriminate between structurally similar, but functionally divergent TIM barrel families. We then apply our method to predict function for several structural genomics proteins, including orphan structures. Some predictions have been corroborated by other computational methods and some validated by subsequent functional characterization.