Miracle-dz/UniFAR-FTUs huggingface dataset:
The role of neuraminidase in the development of pneumococcal pneumonia

Streptococcus pneumoniae causes the diseases pneumonia, bacteraemia and meningitis. Among the putative virulence factors of S. pneumoniae is the enzyme neuraminidase. Neuraminidase cleaves terminal sialic acid residues from glycolipids, glycoproteins and oligosaccharides. The pneumococcus has two neuraminidase genes, nanA and nanB. This project was to study their role in pneumococcal disease. A NanA-deficient mutant (ANanA) and a NanB-deficient mutant (ANanB) were obtained in the serotype 2 strain, D39. These mutants were used to identify roles for NanA and NanB in the development of pneumonia and bacteraemia. The mean survival times of mice infected with each strain were; D39 2 days, ANanA >10 days and ANanB 4.4 days. The mutants had significantly reduced virulence compared to the wild type. After intranasal infection ANanA cells were rapidly lost from the nasopharynx, trachea and lung. The rate at which ANanA cells were removed could suggest a role for NanA in the secure adhesion of pneumococcal cells to the mucosa, to facilitate colonisation. In the nasopharynx, trachea and lung ANanB behaved in a similar way to the wild type early in infection, however, later when D39 multiplied, ANanB cells did not. The reason for this behaviour is unknown but two possibilities are; greater susceptibilty of ANanB to killing by neutrophils or NanB has a nutritional role in vivo. By cleaving sialic acids from cells of the epithelium NanB may expose sugars which could be hydrolysed by the other enzymes. Neither ANanA nor ANanB cells were recovered from the blood after intranasal infection. Whether this represents a defect in invasion or an inability to replicate in the blood remains to be seen.
Relationship of Sweetpotato Yield and Quality to Amount of Irrigation

A line-source irrigation design was used to provide continuously increasing amounts of irrigation at each application to sweetpotato [Ipomoea batatas (L.)Lam]. Marketable yields increased with applied irrigation amounts until a total water application of 76% of pan evaporation (E pan ) was reached and then decreased rapidly with applied irrigation amounts. Weight loss and decay of roots during storage showed quadratic responses to irrigation amounts and were minimal at the irrigation level of maximum yields (.)
Soil phosphorus fractionation as a tool for monitoring dust phosphorus signature underneath a Blue Pine (Pinus wallichiana) canopy in a Temperate Forest

Aims of the study: This study aims (i) to monitor the amount of dust deposition during dry season in the moist temperate forest; (ii) to study nature of P fractions in the dust samples falling on the trees in the region; (iii) to study soil P fractions as influenced by the processes of throughfall and stemflow of a Blue Pine (Pinus wallichiana) canopy and to finger print the contribution of dust towards P input in the temperate forest ecosystem.Area of study: The site used for the collection of soil samples was situated at an elevation of 6900 feet above sea levels (temperate forest in Himalaya region) in the Thandani area national forest located in the north west of Pakistan.Material and methods: For soil sampling and processing, three forest sites with three old tree plants per site were selected at approximately leveled plain for surface soil sampling. Two dust samples were collected and analyzed for different physicochemical properties along with different P fractions. First dust sample was collected from a site situated at an elevation of 4000 feet and second one was collected from an elevation of 6500 feet above sea levels. Modified Hedley procedure for the fractionation of P in the dust and soil samples were used.Main results: The input of dust was 43 and 20 kg ha-1 during drier months of the year (September-June) at lower and higher elevation sites respectively, and the dust from lower elevation site had relative more all P fractions than the other dust sample. However, HCl-Pi fraction was dominant in both samples. Both labile (water plus NaHCO3) and non-labile (NaOH plus HCl) inorganic P (Pi) fractions were significantly increased in the surface soil by both stemflow and throughfall compared to the open field soil. The buildup of NaOH and HCl-Pi pools in soils underneath the canopy might prove useful in fingerprinting the contribution of atmospheric dust towards P cycling in this temperate forest.Research highlights: The role of dust in the cycling of P in temperate forest in Himalaya region.Keywords: soil phosphorus fractions; atmospheric dust; stemflow, throughfall; temperate forest.
Comparative Fingerprinting of the Human Microbiota in Diabetes and Cardiovascular Disease

Abstract Diabetes and cardiovascular diseases are major causes of morbidity and mortality worldwide, and are associated with changes in the human gut microbiota. To better understand the relationships between diet, disease, and the colonic microbiome, we used the in vitro GIS1 system and repetitive element palindromic polymerase chain reaction (rep-PCR) to determine the microbial fingerprints in individuals with these diseases and compared them with the fingerprints in healthy controls. Clear differences were apparent in the three groups. The diabetes group showed significantly increased aerobic bacteria, increased coliforms, and reduced bifidobacteria; the balance between beneficial and pathogenic bacteria was disturbed; significant numbers of clostridia were present; and the proportions of various major bacterial groups were unstable through the length of the colon. The microbiota of the cardiovascular group had high numbers of beneficial strains and more closely resembled the control microbiota. Differ.
RESEARCH ARTICLE Effect of triptolide on reproductive output of male Bandicota bengalensis

Manuscript History: Present study was aimed to evaluate the effect of triptolide on reproductive output of wild male rodent pest species, Bandicota bengalensis for its further use in integration with chemical control for management of this pest species under field conditions. One group of rats (n =15) was kept as vehicle control and other three groups (n = 15 each) were fed on bait containing different concentrations of triptolide. Feeding of bait containing 0.15, 0.2 and 0.25% triptolide for a period of 15 days in choice with plain bait resulted in per day ingestion of 19.99 ± 2.41, 19.28 ± 2.01 and 11.42 ± 1.30 mg/kg bw of triptolide, respectively. No pregnancy was observed in female rats paired with male rats treated with 0.2 and 0.25% triptolide immediately after treatment withdrawal. No pregnancy was observed in female rats paired with male rats treated with 0.25% triptolide even after 30 days of treatment withdrawal. Autopsy of rats immediately and after 30 and 60 days of termination of treatment revealed significant effect of triptolide treatment on weights reproductive organs, sperm motility, viability, density and sperm morphology. No effect of treatment was observed on plasma levels of testosterone. The present study suggests triptolide to be a strong candidate for reducing the reproductive output of male B. bengalensis.
Ecophysiology of adonis distorta, a high-mountain species endemic of the Central Apennines

Morphological, anatomical and physiological plant and leaf traits of A. distorta , an endemic species of the Central Apennines on the Majella Massif, growing at 2,675 m a.s. l, were analyzed. The length of the phenological cycle starts immediately after the snowmelt at the end of May, lasting 128 ± 10 days. The low A. distorta height (H max = 64 ± 4 mm) and total leaf area (TLA= 38 ± 9 cm 2 ) associated to a high leaf mass area (LMA =11.8±0.6 mg cm −2 ) and a relatively high leaf tissue density (LTD = 124.6±14.3 mg cm −3 ) seem to be adaptive traits to the stress factors of the environment where it grows. From a physiological point of view, the high A. distorta photosynthetic rates ( P N =19.6 ± 2.3 µmol m −2 s −1 ) and total chlorophyll content (Chl a + b = 0.88 ± 0.13 mg g −1 ) in July are justified by the favorable temperature. P N decreases by 87% in September at the beginning of plant senescence. Photosynthesis and leaf respiration ( R D ) variations allow A. distorta to maintain a positive carbon balance during the growing season becoming indicative of the efficiency of plant carbon use. The results could be an important tool for conservation programmes of the A. distorta wild populations.
Proliferation of Falcula hyalina and Cylindrotheca closterium (Bacillariophyceae) on copepods in Bahía de La Paz, Gulf of California, Mexico

A proliferation of the epizoic diatoms Falcula hyalina and Cylindrotheca closterium occurred, respectively, on the exoskeleton of marine copepods Acartia tonsa and Paracalanus sp. Samples were collected in February and in October 2013 in Bahia de La Paz. Both represent the first proliferations of this epizoic microalgae reported in the Gulf of California. Seawater temperature was 19°C in February and 28°C in October. A short morphological description, cell measurements and distribution of both species are provided.
Hybrids between Pseudoplatystoma corruscans and P. reticulatum (Siluriformes: Pimelodidae) previously reported in the Upper Paraná River are likely escapes from aquaculture farms: evidence from microsatellite markers

The production of hybrids of the 'pintado', Pseudoplatystoma corruscans (Spix & Agassiz, 1829) and 'cachara', Pseudoplatystoma reticulatum (Eigenmann & Eigenmann, 1889) in captivity has generated many concerns about the possibility of introduction of farmed hybrids into natural environments. In the last decade, hybrids between these species, known as 'pintachara' or 'cachapinta', were reported from different regions of the Upper Parana River basin. Prospection of these hybrids is important in order to orient conservation programs for the species involved. Knowledge of the presence of these hybrids will direct conservation strategies towards prevention and/or mitigation of the effects of cross breeding in natural populations of P. corruscans (the native species of the genus) and farmed hybrids. In this study, surveyed the larval population using molecular tools to detect the presence and assess the origin (natural hybridization or escapes from fish farms) of hybrids in natural water bodies. Nine microsatellite markers were used to detect signals of hybridization and introgression of P. reticulatum in larvae and adults of P. corruscans in Upper Parana River basin, between Itaipu Dam and Porto Primavera Dam. The specimens were sampled in the Upper Parana channel and in tributaries where hybrids had been detected in the past, during two reproductive seasons. Despite of that, no sign of hybridization and introgression was found in the 171 larvae and 75 adults sampled, suggesting that the specimens detected in previous studies had originated from escapes of aquaculture farms.
A New Species of Bachia Gray 1845 (Squamata: Gymnophthalmidae) from the Eastern Guiana Shield

Abstract: A new species of Bachia of the B. heteropa group is described from the Parque Nacional Montanhas do Tumucumaque in northeastern Amazonia, Amapá State, Brazil. The new species morphologically resembles B. heteropa and B. guianensis. Nonetheless, the absence of interparietal and prefrontal scales, and the number of supraciliary scales, can distinguish the new species from its close relatives. This description increases the species diversity of the B. heteropa group after a number of decades of stasis in the taxonomy of this group in Amazonia. In addition, we present an updated key to the groups of Bachia, including the species and subspecies of the B. heteropa group.
Breakthroughs and Views Structure and regulation of Kit protein-tyrosine kinase—The stem cell factor receptor q

Signaling by stem cell factor and Kit, its receptor, play important roles in gametogenesis, hematopoiesis, mast cell development and function, and melanogenesis. Moreover, human and mouse embryonic stem cells express Kit transcripts. Stem cell factor exists as both a soluble and a membrane-bound glycoprotein while Kit is a glycoprotein receptor protein-tyrosine kinase. The complete absence of stem cell factor or Kit is lethal. Gain-of-function mutations of Kit are associated with several human neoplasms including acute myelogenous leukemia, gastrointestinal stromal tumors, mastocytomas, and nasal T-cell lymphomas. Binding of stem cell factor to Kit results in receptor dimerization and activation of protein kinase activity. The activated receptor becomes autophosphorylated at tyrosine residues that serve as docking sites for signal transduction molecules containing SH2 domains. Kit activates Akt, Src family kinases, phosphatidylinositol 3-kinase, phospholipase Cc, and Ras/mitogen-activated protein kinases. Kit exists in active and inactive conformations as determined by X-ray crystallography. Kit consists of an extracellular domain, a transmembrane segment, a juxtamembrane domain, and a protein kinase domain that contains an insert of about 80 amino acid residues. The juxtamembrane domain inhibits enzyme activity in cis by maintaining the control aC-helix and the activation loop in their inactive conformations. The juxtamembrane domain also inhibits receptor dimerization. STI-571, a clinically effective targeted protein-tyrosine kinase inhibitor, binds to an inactive conformation of Kit. The majority of human gastrointestinal stromal tumors have Kit gain-of-function mutations in the juxtamembrane domain, and most people with these tumors respond to STI-571. STI-571 binds to Kit and Bcr-Abl (the oncoprotein of chronic myelogenous leukemia) at their ATP-binding sites. 2005 Elsevier Inc. All rights reserved.
Yield, nutritional status and soil fertility cultivated with common bean in response to amino-acids foliar application

ABSTRACT Fertilization of common bean (Phaseolus vulgaris) plants with amino-acids (AAs) near the beginning of flowering may increase productivity. This procedure is aimed to avoid waste and increase nutrient use efficiency at the end of the crop cycle, improving the leaf area in the translocation of these nutrients to the common bean. In order to test this hypothesis, a field experiment was conducted on a typic Eutrortox (Oxisol) in randomized block design, with three replicates. Four rates of a solution composed of amino-acids (6.8% glycine, 4.4% proline, 3.3% glutamic acid, 2.7% alanine, 1.9% arginine, 1.7% aspartic acid, 1.3% lysine, 1.3% histidine, and 1.0% leucine) applied 45 days after plant emergence were studied. There was no interaction between years of cultivation × amino-acids. However, the productivity of common bean was significantly influenced by the AAs rates, with the highest seed yield obtained at estimated concentration in 0.0094% of the product in foliar sprays. The increases in the rates resulted in increased foliar nitrogen (N) and zinc (Zn) concentrations and decreased sulfur (S) concentration. The macronutrient uptake was nitrogen>potassium>phosphorus>magnesium > calcium > sulfur (N > K > P > Mg > Ca > S), while for micronutrients it was iron>zinc>boron>copper>manganese (Fe > Zn > B > Cu > Mn). In the soil, the concentrations of organic carbon (C) and available P were negatively affected by the AAs rates.
Behavioral responses affect distribution analyses of bowhead whales in the vicinity of seismic operations

Aerial surveys are sometimes used to assess the densities of wide-ranging whales, as well as changes in their distributions in response to human activity. Such surveys also provide data used to estimate numbers of animals exposed to different received levels of seismic sound, as required by regulators. However, estimates of abundance are often biased because they fail to account for the effects of seismic operations on the surfacing and diving behavior of whales. Our objective was to determine the extent to which analyses of the distribution of bowhead whales Balaena mysticetus are affected by changes in visual ‘availability’ caused by seismic operations. We used aerial survey data collected during seismic operations in the Alaskan Beaufort Sea from late August to early October 2008 and fit spatial density surface models to bowhead sighting data to predict whale density in an ensonified area. We also incorporated availability correction factors to determine the sensitivity of density estimates to changes in surfacing and diving behavior caused by seismic operations. The influence of altered whale behavior was then evaluated by comparing a series of realistic simulated scenarios in which models incorporated undisturbed or seismic disturbance-related correction factors. Results suggest that the numbers of bowhead whales present in the vicinity of seismic operations during the bowhead autumn migration are underestimated if the behavioral effects of seismic operations on whales are ignored. Our study highlights the importance of accounting for changes in whale behavior that can affect sightability when estimating numbers and distribution of whales in the vicinity of industrial activity.
Assessment of Microbial and Growth Response of Broilers Fed a Commercial Prebiotic

Prebiotic refers to nondigestible food ingredients that enhance the health of the host by selectively promoting one or more number of beneficial bacteria. Gibson and Roberfroid (1995) initially described prebiotics as compounds that neither hydrolyzed nor absorbed in upper part of the gastrointestinal tract, selectively stimulates growth of beneficial bacteria, enhance health of the host and able to amend microorganism population to healthier states. Prebiotics are particularly attractive supplements in animal production due to their variety of effects including production of short chain fatty acids, pH amendments and suppression of pathogen colonization. In addition, prebiotics were emphasized as antibiotic alternatives due to raise of antibiotic resistant pathogens. This thesis consists of one review and two research parts: a comprehensive literature review that covers various prebiotics used in poultry industry and microbiome quantification techniques including multiplex polymerase chain reaction (PCR), quantitative PCR, denaturing gradient gel electrophoresis (DGGE), and next generation sequencing (NGS) (chapter 1), a research manuscript involves assessment of cecal microbiota, integron, fermentation response, and Salmonella frequency in broilers fed a commercial prebiotic (chapter 2), and a research manuscript involves growth performance and microbial population assessment by NGS approach (chapter 3).
Why Morphology Matters

This chapter contains sections titled: 6.1 Introduction, 6.2 Morphology Simplifies Control, 6.3 Morphology Eases Tasks, 6.4 Morphology Increases Evolvability, 6.5 Morphology Affords New Behaviors, 6.6 Morphology Supports Self-Exploration, 6.7 Morphology Creates New Research Questions, 6.8 Morphology Supports Scalability, 6.9 Conclusions, Notes, References
Pe(ltu((($;: Emerging Techniques Confocal scanning" microscopy: three-dimensional biological imaging

Con focal scanning optical microscopy, arguably the most significant advance in biological light microscopy in this decade, enables one to obtain quantitative non-invasive optical sectior,~s through labelled biological specimens, virtually free from out-of-focus blur. A set of these optical sections collected at a series of focal levels through an object constitutes a three-dimensional image which may then be processed digitally for display as a computer reconstruction, a stereo pair or an animation sequence. Fluorescence microscopy, widely used
Passive Human Tracking based on IMM Kalman Filter using WiFi Signal

Recently, device-free indoor tracking system using WiFi signal has made significant progress. However, many studies have focused on how to high-accuracy parameter estimation and matching, ignoring the influence of localization and tracking algorithms on the results. In this paper, focusing on the irregular motion of the target, we design a passive localization and tracking system based on Interactive Multiple Model (IMM) Kalman filter. First, we use the traditional sage algorithm to extract the angle estimates about target motion and then realize target localization. Due to the irregularity of the target motion, we construct the several different motion states of the moving target and realizing continuous tracking using an IMM Kalman filter. The experimental results show that our proposed system can improve localization accuracy and achieve a median tracking error of 0.63 m.
Nuclear Localization and Mutation of β‐Catenin in Medulloblastomas

The adenomatous polyposis coli (APC) gene, a member of the Wingless/Wnt signal transduction pathway, has been implicated in the development of medulloblastomas in Turcot's syndrome. β-catenin also functions in this highly conserved signaling pathway and is instrumental in growth and development. Mutations in either APC or β-catenin can stabilize β-catenin protein. Stabilized β-catenin complexes with Tcf/Lef transcription factors and moves from the cytoplasm into the nucleus where it regulates the transcription of c-Myc and other genes. Nuclear localization of β-catenin therefore implies activation of the signaling pathway. We have analyzed the subcellular localization of β-catenin in 51 sporadic medulloblastomas and in 1 medulloblastoma arising in a patient with Turcot's syndrome. Nuclear β-catenin staining was present in 9 of the sporadic tumors (18%) and in the 1 medulloblastoma from a Turcot's patient. The remaining 41 cases did not show nuclear staining. This confirms earlier observations that Wingless/Wnt signaling is involved in a subset of sporadic medulloblastomas. We also examined 48 glial and meningeal CNS tumors, all of which were negative for nuclear β-catenin. Exon 3 of β-catenin was sequenced in 6 of the 9 sporadic medulloblastomas with nuclear β-catenin staining. Five of the 6 tumors sequenced had mutations affecting highly conserved β-catenin phosphorylation sites involved in protein stability. These data suggest a simple immunohistochemical method to screen for β-catenin mutations in medulloblastomas.
A Broadband Circularly Polarized Patch Antenna Using Characteristic Mode Analysis

A broadband circularly polarized (CP) patch antenna is proposed based on characteristic mode analysis (CMA). It's known that the bandwidth of a CP patch antenna can be enhanced by adding two or four parasitic elements. However, it's found that only one of the two characteristic modes (CM) newly introduced by parasitic patches is excited. According to the idea of “degenerate mode separation”, these same parasitic patches are adjusted as unequal length. Then both parasitic CMs can be excited well, which resulted in wider bandwidth of axial-ratio (AR) and impedance. The CMA is used for analysis and optimization of the proposed antenna. A classical prototype at 10GHz is designed to verify this concept, and its 3dB AR bandwidth can be increased from 2.8% to 6.3%, while its −10dB impedance bandwidth is improved from 10.2% to 13.4%.