Miracle-dz/UniFAR-FTUs huggingface dataset:
Diabetes association of polyps and colon cancer.

AIM The aim of the study was to retrospectively assess the relationship between the occurrence of polyps and colon cancer in patients with type 2 diabetes. METHODS In 2014-2015, 976 colonoscopies were performed in patients. We compared the number of polyps with high-grade dysplasia and colorectal cancers in patients with and without diabetes. In addition, in the diabetic group we documented the relationship between HbA1C and the occurrence of polyps with high-grade dysplasia, and colon cancer. The data were statistically analyzed. RESULTS 1. Patients with diabetes show a higher incidence of polyps with high-grade dysplasia/carcinoma - 32/91 (35.16%) in comparison to patients without diabetes - 136/885 (15.37%), P < 0.001; 2. Patients with diabetes show a higher incience of polyps with cancer - 9/91 (9.89%) as compared to patients without diabetes - 18/885 (2.03%), P < 0.001. 3) Colorectal cancer occurred significantly more often in uncontrolled diabetes (P = 0.022). CONCLUSION The conducted study shows a significant association between type 2 diabetes and the incidence of colorectal adenomas. These findings may lead to a conclusion that diabetic patients are at a higher risk of developing colorectal cancer, thus are in higher need for controlled colonoscopy. Therefore, it may be worth considering a scheme for screening patients in the above-mentioned group with colonoscopy.
Neck height ratio is an important anthropometric predictor in metabolic syndrome

Introduction: Neck height ratio (NHtR) and NC (neck circumference) have been suggested to measure of upper body adiposity. NHtR has the advantage over NC, as it adjusts for the differences in height. The aim of this study was to evaluate the role of NC and NHtR as an independent predictor of MetS (metabolic syndrome) among Indians Materials and Methods: Present study is a cross sectional observational study, undertaken at Rajarajeshwari Medical College and Hospital, Bangalore, included 50 individuals, 30-80 years age, without comorbidities who gave informed consent underwent clinical, anthropometric and biochemical assessment, presence of MetS was ascertained using ( NCEP ATP) 3 criteria. Results: Patients with MetS in both sexes had significantly higher NC, NHtR, glycated HBA1C dyslipidaemia (elevated triglycerides, decreased HDL). The highest tertile of NC had significantly higher BMI, hypertriglyceridemia and MetS . BMI had the largest area under curve (AUC) for predicting MetS in males. NHtR had the highest AUC for predicting MetS in females. A logistic regression analysis, using MetS as the dependent variable, showed that the relationship between NC and MetS after adjusting for sex and age was statistically significant. NC of>32 cm/m and NHtR of >20 cm/m for both the genders were the best values in identifying MetS, it also showed that the relationship between NHtR and MetS was more significant. Conclusion: NC and NHtR are important predictors of metabolic syndrome and neck height ratio has a higher predictive potential than NC.
A Energy-Saving Path-Shared Protection Based on Diversity Network Coding for Multi-rate Multicast in WDM Mesh Networks

Abstract For improving the survivability and energy saving of multi-rate multicast, a novel energy-saving path-shared protection based on diversity network coding (EPP-DNC) for multi-rate multicast in wavelength division multiplexing (WDM) mesh networks is proposed in the paper. In the EPP-DNC algorithm, diversity network coding on the source node for multi-rate multicast is adopted to reduce the coding energy consumption by avoiding network coding on the network’s intermediate nodes. To decrease the transmission energy, shortest path shared based on heuristic is proposed to transmit the protection information for the request. To provision request’s working paths efficiency, the working paths are routed on the preselected P-cycles with minimum required links and minimum energy consumption. Simulation results show that the proposed EPP-DNC can save energy consumption and improve bandwidth utilization.
A restriction enzyme reduced representation sequencing approach for low-cost, high-throughput metagenome profiling

Microbial community profiles have been associated with a variety of traits, including methane emissions in livestock, however, these profiles can be difficult and expensive to obtain for thousands of samples. The objective of this work was to develop a low-cost, high-throughput approach to capture the diversity of the rumen microbiome. Restriction enzyme reduced representation sequencing (RE-RRS) using ApeKI or PstI, and two bioinformatic pipelines (reference-based and reference-free) were compared to 16S rRNA gene sequencing using repeated samples collected two weeks apart from 118 sheep that were phenotypically extreme (60 high and 58 low) for methane emitted per kg dry matter intake (n=236). DNA was extracted from freeze-dried rumen samples using a phenol chloroform and bead-beating protocol prior to sequencing. The resulting sequences were used to investigate the repeatability of the rumen microbial community profiles, the effect of host genetics, laboratory and analytical method, and the genetic and phenotypic correlations with methane production. The results suggested that the best method was PstI RE-RRS analyzed with the reference-free approach via a correspondence analysis, with estimates for repeatability of 0.62±0.06, heritability 0.31±0.29, and genetic and phenotypic correlation with methane emissions of 0.88±0.25 and 0.64±0.05 respectively for the first component of correspondence analysis. The reference-free approach assigned 62.0±5.7% of reads to common 65 bp tags, much higher than the reference-based approach of 6.8±1.8% of reads assigned. Sensitivity studies suggested approximately 2000 samples could be sequenced in a single lane on an Illumina HiSeq 2500, therefore the current work of 118 samples/lane and future proposed 384 samples/lane are well within that threshold. Our approach is now being used to investigate host factors affecting the rumen and its association with a variety of production and environmental traits. With minor adaptations, our approach could be used to obtain microbial profiles from other metagenomic samples.
Observations of novel invasive ant-scale insect interactions on the threatened vine Tecomanthe speciosa in Auckland

Tecomanthe speciosa, once referred to as "undoubtedly the rarest vine of New Zealand", was first discovered in 1945 by G.T. Baylis on the Great King Island, Three Kings Is. as a single specimen. It has since been propagated through cuttings in urban gardens across New Zealand. Nevertheless, it has continued to maintain its position on the Nationally Critical (under Acutely Threatened; in the wild) list of Threatened plants of New Zealand. Currently it is one of 91 endemic New Zealand plants in this category, which contains taxa that face an extremely high probability of extinction in the wild, within the immediate future. Despite the critically threatened status of this plant, little research has been done so far to understand its ecology in the wild. Browsing by goats introduced to the Three Kings islands has previously driven this species to near extinction, such that only a single specimen to date exists in the wild. This particular individual has not seeded in the last 64 years despite the removal of goats in 1946. Artificial propagation of this species has been undertaken on the Great King Island, however, none of the propagated plants have set seed in the wild. Nevertheless, across other parts of New Zealand after decades of propagation, the vines have set seed and can now be cultivated from seed. Despite that, the original pool of genes is derived from a single parent plant, leaving the species defenceless against a successful pest/pathogen.
An investigation of dead-zone pattern matching algorithms

Pattern matching allows us to search some text for a word or for a sequence of characters—a popular feature of computer programs such as text editors. Traditionally, three distinct families of pattern matching algorithms exist: the Boyer-Moore (BM) algorithm, the Knuth-Morris-Pratt (KMP) algorithm, and the Rabin-Karp (RK) algorithm. The basic algorithm in all these algorithmic families was developed in the 1970s and 1980s. However a new family of pattern matching algorithms, known as the Dead-Zone (DZ) family of algorithms, has recently been developed. In a previous study, it was theoretically proven that DZ is able to pattern match a text with fewer match attempts than the wellknown Horspool algorithm, a derivative of the BM algorithm. The main aim of this study was to provide empirical evidence to determine whether DZ is faster in practice. A benchmark platform was developed to compare variants of the DZ algorithm to existing pattern matching algorithms. Initial experiments were performed with four C implementations of the DZ algorithm (two recursive and two iterative implementations). Subsequent to this, DZ variants that make use of different shift functions as well as two parallel variants of DZ (implemented with Pthreads and CUDA) were developed. Additionally, the underlying skeleton of the DZ algorithm was tweaked to determine whether the DZ code was optimal. The benchmark results showed that the C implementation of the iterative DZ variants performed favourably. Both iterative algorithms beat traditional pattern matching algorithms when searching natural language and genome texts, particularly for short patterns. When different shift functions were used, the only time a DZ implementation performed better than an implementation of the traditional algorithm was for a pattern length of 65536 characters. Contrary to our expectations, the parallel implementation of DZ did not always provide a speedup. In fact, the Pthreaded variants of DZ were slower than the non-threaded DZ implementations, although the CUDA DZ variants were consistently five times faster than a CPU implementation of Horspool. By using a cache-friendly DZ algorithm, which reduces cache misses by about 20%, the the original DZ can be improved by approximately 5% for relatively short patterns (up to 128 characters with a natural language text). Moreover, a cost of recursion and the impact of information sharing were observed for all DZ variants and have thus been identified as intrinsic DZ characteristics. ii Stellenbosch University https://scholar.sun.ac.za
Controlling swelling and release of hyaluronic acid during aqueous storage by in situ cross-linking during spray drying with alginate

The success of hyaluronic acid in over-the-counter cosmetics has been limited by its poor storage stability in aqueous environments due to premature swelling and hydrolysis. Here, hyaluronic acid was prepared in dry microparticles, encapsulated by spray-drying in patented in situ calcium cross-linked alginate microcapsules (CLAMs) to minimize swelling and release in aqueous formulations. CLAMs prepared with 61% (d.b.) hyaluronic acid (HA-CLAMs) demonstrated restricted plumping, limited water absorption capacity, and reduced leaching; retaining up to 49 % hyaluronic acid after 2 hrs in water. A new method using chelated soluble calcium resulted in particles with significantly improved hyaluronic acid retention in water. ‘Chelate HA-CLAMs’ exhibited nearly full retention of hyaluronic acid over 2 hr incubation in water, and remained visibly insoluble after 1 year of storage in water at 4°C. Successful hyaluronic acid retention in CLAMs is likely due to the ability of hyaluronic acid to participate in calcium cross-linking.
Effect of Hyperbaric Oxygen on Hematopoietic Stem Cell Transplantation

In this chapter the accumulated evidence that supports the role of hyperbaric oxygen therapy (HBOT) in improving the process of hematopoietic stem/ progenitor cell (HSPC) homing, engraftment, and immune-reconstitution will be reviewed. The underlying mechanism by which HBO modulates erythropoietin (EPO)/EPOR signaling to improve HSPC homing and engraftment will be described. Also the pre-clinical evidence and pilot clinical trial evidence that supports HBO role in improving HSPC homing and engraftment will be examined. Current and future clinical trial studies that stem from this concept will be detailed. Finally, areas that need future investigations to optimally utilize HBO in the field of HSPC transplantation will be described.
Quantifying the effects of light quantity and quality on culinary herb physiology

Lighting influences plant growth and development on a quantity and quality basis, promoting the production of both primary and secondary metabolites. While the amount of light necessary for culinary herb production is species-specific, with growth curves for increasing daily light integrals (DLI), the specific spectra of incidental light absorbed plays a role in photosynthetic efficiency, biomass partitioning, and secondary metabolites related health and nutrition. The two primary objectives of this research were to 1) Quantify morphological growth of culinary herbs under increasingly higher DLI, and 2) Identify the morphological, physiological, and phytochemical responses of selected herbs to the spectral composition of light sources and blue light fraction from either supplemental or sole-source lighting. Biomass increased with increasing DLI, and the relationship was either linear or quadratic, depending upon saturating DLI. Additionally, the proportions of light spectra affected plant height, biomass, gas exchange, photosynthetic efficiency, and phenolic accumulation by alteration of blue light fraction, or use of broad-spectrum lighting. By identifying responses of plants to light quantity and quality, the goal of this research was to 1) Provide information on light quantity optimization in food crop production, and 2) Improve the quality of food crops produced by emphasizing the promotion of plant photoprotective compounds that increase both production efficiency and food nutrition.
Quantitative PCR primer design affects quantification of dsRNA‐mediated gene knockdown

Abstract RNA interference (RNAi) is a powerful tool for studying functions of candidate genes in both model and nonmodel organisms and a promising technique for therapeutic applications. Successful application of this technique relies on the accuracy and reliability of methods used to quantify gene knockdown. With the limitation in the availability of antibodies for detecting proteins, quantitative PCR (qPCR) remains the preferred method for quantifying target gene knockdown after dsRNA treatment. We evaluated how qPCR primer binding site and target gene expression levels affect quantification of intact mRNA transcripts following dsRNA‐mediated RNAi. The use of primer pairs targeting the mRNA sequence within the dsRNA target region failed to reveal a significant decrease in target mRNA transcripts for genes with low expression levels, but not for a highly expressed gene. By contrast, significant knockdown was detected in all cases with primer pairs targeting the mRNA sequence extending beyond the dsRNA target region, regardless of the expression levels of the target gene. Our results suggest that at least for genes with low expression levels, quantifying the efficiency of dsRNA‐mediated RNAi with primers amplifying sequences completely contained in the dsRNA target region should be avoided due to the risk of false‐negative results. Instead, primer pairs extending beyond the dsRNA target region of the mRNA transcript sequences should be used for accurate and reliable quantification of silencing efficiency.
Propagação in vitro de Limonium latifolium Kuntze (Plumbaginaceae)

Limonium latifolium Kuntze is a cut flower commercialy propagated in vitro. To develop and improve the micropropagation protocol, a sequence of assays was developed to evaluate performance of node explants; effect of cytokinins concentration (kinetin-KlN and 6-benzyl-aminopurin-BA) on the regeneration rate; the presence of BA during the multiplication phase; concentration of naphthaleneacetic acid-NAA and indole3-butyric acid-IBA on the rooting phase and procederes for the acciimatiwtion in vitro. The micropropagation was done at commercial levei using inflorescence nades explants. By the regeneration phase the best results were obtained with BA at 0.7mg/l for 35 days in MS medium. The multiplication phase takes 35 days and shows satisfactory results with BA at 0.2mg/l , with the rate of 4 plantiets/explant. The rooting phase is takes 30 days in MS medium with IBA at 1mg/l , with good survival scores after transfer to in vivo. The acciimatiwtion has made under plastic covering, inside greenhouse with room temperature and intermitent mist, using flats with 242 cells of 10cm3 each, filled with sterilized carbonized rice hulis. Every two weeks the plants were fertigated with commercial fertilizer (15:5:15 + micronutrients) at 0.5g/l . The in vitro process takes 100 - 120 days and one explant originates 15 - 30 plants.
Epidemiologia y patologia de las coccidiosis en cefalopodos

En esta memoria se recoge el primer estudio sobre el rango hospedador y la distribucion geografica mundial de los coccidios del genero Aggregata parasitas del tracto digestivo de una amplia variedad de hospedadores cefalopodos.Ademas, se ha realizado la descripcion de 12 nuevas especies del genero Aggregata mediante tecnicas clasicas de diagnostico utilizando microscopia optica, se amplia el rango hospedador y la distribucion del genero a 14 nuevas especies hospedadoras definitivas y 7 hospedadoras intermediarias. Asimismo, se incrementa a 17 nuevas localidades el rango de distribucion geografica del hospedador difinitivo y a una nueva localidad el del intermediario. Mediante la aplicacion de tecnicas ultraestructurales (MEB, MET, MFA y microanalisis de rayos X), asi como moleculares y bioquimicas (analisis del contenido relativo de ADN mediante citometria de flujo, electroforesis SDS-Page y perfil enzimatico), para lo que fue imprescindible el desarrollo de un protocolo adecuado para el aislamiento y la purificacion de los esporoquistes de las especies del genero Aggregata, se ha redescrito A. Octopiana y A. Eberthi en aguas de Europa, aisgnandose A. Spinosa como sinonimia de A. Octopiana. El estudio ultraestructural y molecular ha permitido incrementar los caracteres de diagnostico de las especies del genero Aggregata, como son el espesor de la pared de la cubierta del es por quiste, su topologia superficial y el valor de rugosidad RMS de dicha cubiertas, asi como el contenido relativo de ADN. El estudio epidemiologico realizado en Octopus vulgaris y Sepia officinalis de las costas del Atlantico nororienta pertenecientes a Galicia, Portugal y, en el caso de O. Vulgaris tambien a Canarias, mostro la existencia de una variabilidad intra e interespecifica.Como estas coccidiosis son infecciones adquiridas por la dieta, se realizo un analisis de la relacion entre la estructura talla-peso-madurez del h
Staphylococcus aureus and Streptococcus agalactiae: prevalence, resistance to antimicrobials, and their relationship with the milk quality of dairy cattle herds in Minas Gerais state, Brazil

ABSTRACT: Bovine mastitis is the most frequent disease worldwide in dairy herds, causing high economic losses to producers and industry, as well as having implications for public health due to the zoonotic potential of some agents involved in its etiology and the increased risk of antimicrobial residues in milk and its derivatives. Considering the multifactorial aspect of this disease, knowledge of the agents involved in its etiology and their antimicrobial susceptibility profiles is very important. This study was conducted with 306 dairy herds from the Campo das Vertentes region, located in the south of Minas Gerais state, whose owners were milk suppliers to a dairy in the same region. The study involved approximately 34,000 dairy cows and covered an area of approximately 12,564 km2. In these herds, prevalence rates of Staphylococcus aureus and Streptococcus agalactiae and their relationship with bulk milk somatic cell counts (BMSCC), total bacterial counts (TBC), and daily production were evaluated. In addition, analyses of resistance of these pathogens to the antimicrobials most commonly used in the treatment of mastitis in dairy herds were performed. Microbiological analyses of milk samples from collect from bulk milk tanks were performed aiming to evaluate the prevalence of S. aureus and S. agalactiae. For these proposes, the modified Baird-Parker Agar medium was used for detection of S. aureus and the modified Edwards Agar medium, enriched with 5% defibrinated sheep blood, was used for detection of S. agalactiae. The disc diffusion technique was applied to evaluate antimicrobial resistance. Results show high prevalence rates of S. aureus (70.3%) and S. agalactiae (67.0%) in the dairy farms studied, with 47.71% of the herds showing both pathogens. Associations between BMSCC and the presence of pathogens S. aureus and S. agalactiae and between TBC and the presence of S. agalactiae were observed, demonstrating the influence of these pathogens in milk quality. No variation was observed in the distribution of S. aureus and S. agalactiae in the different strata of daily production. High levels of resistance and multi-resistance were observed among the pathogens S. aureus and S. agalactiae. The results indicate the need for more effective control measures for mastitis caused by S. aureus and S. agalactiae in the dairy herds of the region studied and more judicious use of antimicrobials in order to reduce the problem of resistance to them.
Identification of Novel Transcription Factors Regulating Recovery of the Endothelial Lineage in Avascular Mutants

CHRISTOPHER SCHMITT: Identification of Novel Transcription Factors Regulating Recovery of the Endothelial Lineage in Avascular Mutants (Under the direction of Dr. Suk-Won Jin) Multiple mesodermal tissues are known to give rise to endothelial cells during development. Furthermore, markers for functionally distinct endothelium are well established. Therefore, it is likely that multiple distinct populations of endothelial cells exist during development and into adulthood. Two zebrafish mutants, cloche and groom of cloche provide a unique opportunity to interrogate the heterogeneous origin of the endothelial lineage. Homozygous mutant embryos lack the majority of the endothelial lineage at early developmental stages, however, generate rudimentary vessels at later stages, indicating that they retain the ability to generate endothelial cells despite this initial lack of early endothelial progenitors. To delineate the developmental source of the endothelial cells in these avascular mutant embryos, we first performed lineage tracing from early gastrula to determine the fate of mesoderm. Consistent with their phenotype, we found an increase of kdrl unspecified mesoderm, indicating that much of the mesoderm apportioned to become angioblasts fails to become specified. Conversely, endothelial differentiation from the tailbud, a proposed secondary source of endothelial cells during development, was largely unperturbed. Consistent with this finding, the majority of the early kdrl cells found in avascular mutant embryos are specified from tailbud. To better elucidate the molecular basis of endothelial recovery in avascular mutant embryos, we analyzed the gene expression profile using microarray analysis on isolated mutant endothelial cells. We find that the expression of the genes characteristic of other mesodermal lineages are substantially elevated in kdrl cells isolated from avascular mutant embryos. Subsequent validation identified two transcription factors, sox11b and pax9, both of which have not previously implicated in vascular development. Yet, we confirmed that both genes