Gene Family Abundance Visualization based on Feature Selection Combined Deep Learning to Improve Disease Diagnosis

Advancements in machine learning in general and in deep learning in particular have achieved great success in numerous fields. For personalized medicine approaches, frameworks derived from learning algorithms play an important role in supporting scientists to investigate and explore novel data sources such as metagenomic data to develop and examine methodologies to improve human healthcare. Some challenges when processing this data type include its very high dimensionality and the complexity of diseases. Metagenomic data that include gene families often have millions of features. This leads to a further increase of complexity in processing and requires a huge amount of time for computation. In this study, we propose a method combining feature selection using perceptron weight-based filters and synthetic image generation to leverage deep-learning advancements in order to predict various diseases based on gene family abundance data. An experiment was conducted using gene family datasets of five diseases, i.e. liver cirrhosis, obesity, inflammatory bowel diseases, type 2 diabetes, and colorectal cancer. The proposed method provides not only visualization for gene family abundance data but also achieved a promising performance level

OXIDIZED MAIZE STARCH: CHARACTERIZATION AND EFFECT OF IT ON THE BIODEGRADABLE FILMS I. CHARACTERIZATION OF MAIZE STARCH OXIDIZED BY SODIUM HYPOCHLORITE

The effects of hypochlorite level, i.e. 0.5; 1 and 2 active chlorine g/100g starch, on the structures and physicochemical properties of oxidized maize starch were investigated. The obtained results shown that oxidation degree grew up with increasing hypochlorite concentration, specially, the carboxyl content saw higher increased than the content of carbonyl. SEM images indicated that surface of oxidized maize starches were rougher than native starch. The surface of oxidized starches saw rougher with increasing hypochlorite level. However, the DSC results illustrated that there was no significant difference of gelatinization temperature between the native starch and oxidized starches

Effect of Silica Nanoparticles on Properties of Coatings Based on Acrylic Emulsion Resin

Effect of nanosilica size on physic-mechanical properties, thermal stability and weathering durability of coating based on acrylic emulsion. Nanocomposite coating formulas were filled by 2 wt.% nanosilica particles which were used in this study, namely: nanosilica from Sigma (15-20nm), nansilica from rice husk (~70-200 nm) and nanosilica from Arosil – Belgium (7-12 nm). Obtained results showed that viscosity flow of coating formula containing nanosilica from Arosil saw the highest flow-time while coating formulas filled other nanosilica and unfilled nanosilica experienced similar flow-time. In presence of nanosilica, coating properties were improved in comparison with neat coating. However, coating filled by nanosilica from rice husk indicated the best properties in studied coating formula. It may explained that size of nanosilica from rice husk was the largest in studied nanosilica particles and thus easily dispersing into coating formula

The Order of Limiting Amino Acids in a Wheat–Sorghum-Based Reduced-Protein Diet for Laying Hens

Understanding the order of limiting amino acids (AA) in reduced-protein (RP) diets for laying hens will facilitate precise feed formulation and ensure that AA requirements are met costeffectively. The order of the first three limiting AAs—lysine (Lys), methionine (Met), and threonine (Thr)—has been well established in RP laying hen diets. This study aimed to determine the priority order of eight additional limiting AAs (critically important AAs) when formulating wheat–sorghumbased RP diets for laying hens: tryptophan (Trp), valine (Val), isoleucine (Ile), arginine (Arg), leucine (Leu), histidine (His), phenylalanine (Phe), and glycineequivalent (Gly). A total of 330 Hy-Line Brown laying hens were randomly assigned to 11 dietary treatments (30 replicates of individual birds per treatment) from 20 to 39 weeks of age (WOA). Treatments were a standard-protein (17.24% CP) diet as the control (SP)" a reduced-protein (15.00% CP) diet with sufficient levels of Lys, Met, and Thr but insufficient levels of the eight experimental essential AA (RP)" a reduced-protein diet with sufficient levels of all essential AAs (RP-EAA)" and eight subsequent dietary treatments of the RP-EAA diet with one of the experimental essential AAs removed: Trp (RP-EAA-Trp), Val (RP-EAA-Val), Ile (RP-EAA-Ile), Arg (RP-EAA-Arg), Leu (RP-EAA-Leu), His (RP-EAA-His), Phe (RP-EAA-Phe), and Gly (RP-EAA-Gly). Eggs were collected and weighed daily, and feed intake and feed conversion ratio (FCR) were calculated weekly. External and internal egg quality was measured at 29 and 39 WOA. Nutrient digestibility, serum uric acid concentration, caecal microbiota composition, and tibia parameters were measured at 40 WOA. Overall, hens fed the RP-EAA-Val, RP-EAA-Ile, and RP diets presented significantly lower egg mass compared to hens fed the SP, RP-EAA-His, and RP-EAA-Gly diets (

New insights into arginine and arginine-sparing effects of guanidinoacetic acid and citrulline in broiler diets

Chickens have a high dietary Arg requirement compared to mamma-lians as they have an incomplete urea cycle and therefore cannot synthesise Arg. Arginine is important for protein synthesis and is also involved in immunity being converted to nitric oxide (NO) at the macrophage level. Nitric oxide is secreted as a free radical during an immune response and is toxic to bacteria, intracellular parasites and also has strong anti-viral and anti-cancer properties. Also, NO serves as a regulating factor for intestinal blood flow, integrity, secretion, and epithelial cell migration. As Arg is a limiting factor for NO synthesis, the increased availability of Arg following dietary supplementation of Arg and/or its metabolites could increase the NO production and subse-quent immune status in birds. Such improvements on bird health may become useful for antibiotic growth promoter-free poultry production. The Arg requirement in birds has received special interest due to its large variation in different dietary conditions. Growing evidence sug-gests that increasing the dietary Arg level and Arg to Lys ratio above currently accepted levels may be necessary to maximise the productive potential of modern broiler strains due to the modulatory effect of Arg on energy and protein metabolism. Also, literature evidence has indi-cated that crystalline Arg, guanidinoacetic acid (GAA), and citrulline (Cit) can provide Arg activity in chicken diets and are all commercially available. Furthermore, the use of Cit could escape the degradation of enzyme arginase in the intestine and liver resulting in higher Arg levels in the bloodstream and NO production compared to Arg supplemen-tation. The addition of GAA may also provide additional benefits on increasing creatine level and energy metabolism in broiler chickens compared to Arg. This paper will provide new insights into Arg and Arg-sparing effects of GAA and Cit in the broiler diets with a special focus on the supplementation of Arg in reduced protein diets

Feeding methionine hydroxyl analogue chelated trace minerals reduces mineral excretion to the environment in broiler chickens

This study investigated the effects of feeding mineral methionine hydroxyl analogue chelates (MMHAC) zinc (Zn), copper (Cu) and manganese (Mn) (MINTREX® Zn:Cu:Mn, Novus International, Inc.) and high dietary inorganic Cu level on growth performance, nutrient digestibility, carcass yield, excreta nitrogen (N) and mineral level, environmental conditions, bone parameters and welfare status of Ross 308 males. A total of 384 one-day-old chicks were randomly distributed to four dietary treatments with eight replicates of 12 birds per pen per treatment. The treatments consisted of (1) ITM ZnSO4 110 ppm, CuSO4 16 ppm, MnO 120 ppm (ITM), (2) MMHAC Zn 40 ppm, Cu 10 ppm, Mn 40 ppm (MMHAC10), (3) ITM ZnSO4 110 ppm, TBCC 125 ppm, MnO 120 ppm (TBCC125), and (4) MMHAC Zn 40 ppm, Cu 30 ppm, Mn 40 ppm (MMHAC30). There were three feeding phases, including starter (days 0-10), grower (days 10-21) and finisher (days 21-42). Growth performance was calculated per feeding phase. Data were analysed using R Commander with P-value ≤ 0.05 considered significant. The results showed that broilers fed the MMHAC10, MMHAC30 and TBCC125 diets tended to have higher FI with the highest FI observed for TBCC125 treatment (P = 0.052), and higher weight gain with the highest weight gain observed for MMHAC30 group (P = 0.063) compared to the ITM control group over the entire study. Although, a significant difference was not obtained, birds fed MMHAC10 had numerically higher overall liveability and European productivity index (EPI) over the entire study compared to the other groups. Thigh and drumstick weight were higher in birds fed MMHAC30 compared to the ITM control group at day 42 (P = 0.050). At days 10, 16, 21, 28 and 42, feeding MMHAC at both levels significantly decreased Zn and Mn levels while feeding TBCC125 increased Cu level in the excreta compared to the other dietary treatments (

Production, consumption status and economic efficiency of Dong Tao chicken production

peer reviewedThis study was conducted to provide informations of the growth performance of Dong Tao chicken raising under household conditions in Dong Tao commune, Khoai Chau district, Hung Yen province. A total of 250 Dong Tao chickens were observed from 1 day old to 24 weeks old among 5 families with following traits: body weight, relative growth rate, average daily gain, survival rate, feed intake and feed conversion rate. Dong Tao is one of the native chicken breeds with a heavy weight. The body weights of the cock and hen were 2.6 kg and 2.2 kg respectively at 24 weeks old. The average daily gain increased gradually from the first weeks old, peaking and stability in the period to 10 weeks old (21.24g and 20.26g for cock and hen respectively) then it began to decline from the weeks old thereafter. Whereas the relative growth rate decreased gradually by weeks old. Feed conversion rate was 4,38kg based on the whole growth period. These results could be used to dertermine the characteristics of this purebred breed which would contribute to conserve and develop in a sustainable way

Impact of Arginine, Citrulline and Guanidinoacetic Acid Supplementation in Reduced Protein Diets for Chickens

Reducing dietary protein has received increasing interest in poultry production due to lower water intake, improved litter quality, and reduced ammonia production resulting in diminished breast blistering and footpad lesions and their sequela. Four experiments were conducted to investigate the effects of supplementing arginine (Arg), guanidinoacetic acid (GAA), and citrulline (Cit) in reduced protein wheat-based basal diets on the performance of broilers and laying hens. Chickens have a high dietary Arg requirement compared to mammalians as they have an incomplete urea cycle and therefore cannot synthesise arginine. Supplementation of arginine becomes crucial in situations where reduced protein diets are used as it has been considered as an essential component of these diets. The work completed in this thesis provides new insights into the effects of Arg, GAA, and Cit supplementation in reduced protein wheat-based diets and may help to develop optimal feeding programs for broilers and laying hens. The first experiment (chapter 3) investigated the effects of Arg source (Arg, GAA or Cit) and level on broiler performance, nutrient digestibility, and carcass quality. The dietary treatments were: normal protein (NP), low protein deficient in Arg (LP) and LP with two levels of either Arg (0.238 and 0.476%), GAA (0.309 and 0.618%), or Cit (0.238 and 0.476%). The LP was 5 percentage points lower in protein level than the NP. Compared to NP, birds fed LP had reduced feed intake (FI), reduced body weight gain (BWG), and increased feed conversion ratio (FCR) from day 0 to 35. Additions of Arg or Cit to the LP at both levels resulted in increased BWG and reduced FCR. Birds fed LP with GAA added had lower FCR but not higher BWG compared to the LP observed from day 0 to 35. Supplementation of Arg, Cit, and the low level of GAA to LP resulted in increased carcass yield but did not increase ileal energy or nitrogen digestibility. The findings indicate that high levels of Arg in low protein pre-starter diets may have a negative effect on performance perhaps because of marginal deficiencies of histidine or phenylalanine. The results suggest that Cit is an efficacious source of Arg in Arg-deficient diets. Supplementation of GAA to broiler diets at the low level (0.309%) was effective in sparing the Arg deficiency but at the higher level (0.618%) was toxic. This information is of importance to the industry. The second experiment (chapter 4) was undertaken to determine the impact of Arg deficiency on laying hen performance, egg quality, and nutrient digestibility in reduced protein diets and the efficacy of adding it to the diet as either Arg, GAA, or Cit. Treatments were: standard protein (17% protein diet; SP), reduced protein diet deficient in Arg (13% protein diet; RP) and RP with added Arg (0.35%, RP-Arg), GAA (0.46% equivalent to 0.35% Arg, RP-GAA) or Cit (0.35%, RP-Cit) to the level of SP. The birds offered RP had reduced egg and albumin weights, lower yolk color score, lower protein intake and excretion than those offered SP. When Arg or Cit was added to RP to make them equivalent in Arg to the SP, FI and egg production were not different than those of RP. The birds offered RP-GAA had decreased FI and egg mass compared to those offered RP. The addition of Arg, Cit, or GAA to the RP did not affect egg quality parameters and protein and energy digestibility. However, birds offered the RP-Cit diet tended to have higher Haugh units and lower shell breaking strength compared to all other treatments while those offered RP-GAA had higher energy digestibility than all other groups but RP. The results suggest that reduction of 4 percentage points crude protein from 17% to 13% is excessive in practical wheat-based diets for laying hens. The lack of effect for Arg, GAA, and Cit supplementation on laying performance in RP diets was possibly due to excessive reduction of dietary CP resulting in the deficiency of some essential and non-essential amino acids and other components of soybean meal in the diets. Citrulline showed more positive effects than the other sources of Arg on internal egg quality in laying hens while GAA was ineffective. The third experiment (chapter 5) explored the effects of Arg or Cit supplementation in broilers fed a reduced protein diet deficient in Arg under cyclic warm temperature (WT). The reductions in protein were not as drastic as the previous two experiments. The treatments were: normal protein (NP) 22.3% and 20.9% crude protein in grower and finisher, respectively, reduced protein (RP) 2.5% lower protein and deficient in Arg, and RP supplemented with 0.28% Arg (RP-Arg) or 0.28% Cit (RP-Cit). A factorial arrangement of treatments was applied during the finisher phase (21 to 35 days). Factors were: diet (four diets above); and temperature, thermo-neutral (NT, 24°C) or cyclic WT (33°C ± 1oC for 6 hours per day) with 6 replicate pens per treatment. During 7 to 35 days and 21 to 35 days, the birds fed the RP diet had lower BWG and higher FCR compared to the NP diet. The addition of Arg or Cit to RP decreased FCR compared to RP. During 21 to 35 days, the birds exposed to cyclic WT had lower FI, lower BWG but similar FCR compared to birds exposed to NT. Diet by temperature interactions were not observed for performance parameters during the period of WT. Birds fed RP had a lower yield of thigh and drumstick and higher fat pad on day 35 but higher nitrogen digestibility on day 21 compared to those offered NP. The results from this study suggest that feeding the NP diets is necessary to maintain growth performance in broilers regardless of the temperature conditions. Finally, the fourth experiment examined the effect of dietary protein level and the replacement of crystalline Arg with Cit in the reduced protein diet on performance, gut health, immunological parameters, and gene expression in the broilers challenged with subclinical necrotic enteritis (NE). The treatments were: standard protein without NE challenge (SP-); with NE challenge (SP+); reduced protein (2 percentage points lower crude protein) without NE challenge (RP-); with NE challenge (RP+); RP+ plus added Arg (103% of RP, RPA+) and RPC+ where supplemental Arg in RPA+ was replaced with Cit. The first 4 treatments were considered as a 2 × 2 factorial arrangement with factors being NE (- or +) and protein level (SP or RP). In addition, all 6 treatments were also analysed by one-way ANOVA. The challenge model consisted of oral inoculation of Eimeria strains on day 9 and Clostridium (C.) perfringens (EHE-NE18 strain) on day 14. The results of this experiment were written in chapters 6, 7, and 8 corresponding to three manuscripts submitted for publication. Chapter 6 investigated the effects of Arg and Cit supplementation to RP diets on growth performance, carcass traits, internal organ weights, serum uric acid, and intestinal lesion score of broilers growing under NE challenge. Feeding RP diets increased FI, increased BWG, and reduced FCR during the grower phase compared to SP diets when birds were challenged with NE. Birds in the RPC+ treatment had lower overall FCR compared to those in the SP+ treatment. Birds in the RPA+ treatment had similar FI, BWG, and FCR compared to those in the RP+ treatment. The results show protective effects of replacing the supplemental Arg with Cit against NE in RP diets as indicated by higher performance during and after challenge. Chapter 7 assessed the effects of Arg and Cit supplementation on intestinal morphology, short-chain fatty acid (SCFA), microbiota count, gut permeability, and pH in broilers fed RP diets and raised under NE challenge. Necrotic enteritis × protein interactions were detected for gut permeability as assessed by serum fluorescein isothiocyanate dextran (FITC-d) level after gavage, C. perfringens count in the ceca, and acetic acid and total SCFA concentrations in the ileum on day 16. Feeding the RP diet reduced serum FITC-d level, reduced the number of C. perfringens in the ceca, and increased acetic acid and total SCFA concentrations in the ileum compared to the SP group only in birds challenged with NE. Birds in the RPC+ treatment had greater jejunal villus height, and lower cecal C. perfringens and Enterobacteriaceae compared to those in the SP+ treatment. The results indicate a benefit to gut health of broilers during NE challenge when replacing crystalline Arg with Cit in RP diets. Chapter 8 investigated the effects of Arg and Cit supplementation on serum immunological parameters, serum mineral composition, and gene expression in broilers fed reduced RP diets during the NE challenge. The NE × protein interactions indicated that serum Na level decreased, and serum K level increased in birds fed the SP diets while serum Ca level decreased in birds fed the RP diets only when challenged with NE. The NE × protein interactions showed that the NE challenge downregulated the mRNA expression of jejunal y+ L amino acid transporter-2, and mucin 2 only in birds fed the RP diets. Feeding the RP decreased serum alpha-1 acid glycoprotein, ovotransferrin, expression of catenin-alpha-1 but increased expression of claudin-5 and tight junction protein genes compared to the SP. Birds in the RPA+ treatment had decreased peptide transporter-2 expression compared to the RP+ treatment (P The findings from this study are industry-relevant and may improve performance and general health condition of broilers and laying hens fed moderately lower protein diets. Also, feeding reduced protein diets with the addition of Arg, GAA or Cit will benefit the environment by limiting nitrogenous waste from poultry production resulting from greater nitrogen digestibility. Furthermore, the results reported in this thesis may help reduce feeding of excess protein and improve performance in antibiotic growth promoter-free situations. This will benefit sustainable poultry production

Effects of L-arginine and L-citrulline supplementation in reduced protein diets for broilers under normal and cyclic warm temperature

Heat stress causes significant economic losses in the broiler industry. Dietary supplementation of arginine (Arg) and citrulline (Cit) might increase the performance of broilers raised under warm temperature due to vasodilation effects. This study investigated the effects of L-Arg or L-Cit supplementation in broilers fed a reduced protein wheat-based diet deficient in Arg under thermoneutral (NT) and cyclic warm temperature (WT). Ross 308 cockerels (n = 720) were randomly allocated to 4 dietary treatments with 12 replicates of 15 birds per pen from d 7 to 21. The 4 treatments were: normal protein (NP), i.e., 22.3% and 20.9% crude protein in grower and finisher, respectively; reduced protein (RP), i.e., 2.5% lower protein and deficient in Arg; and RP supplemented with 0.28% Arg (RP-Arg) or 0.28% Cit (RP-Cit). A factorial arrangement of treatments was applied during the finisher phase (21 to 35 d). Factors were: diet (4 diets above); and temperature, NT (24 C) or cyclic WT (33 ± 1 C for 6 h per day) with 6 replicate pens per treatment. During 7 to 35 d and 21 to 35 d, the birds fed the RP diet had lower body weight gain (BWG) and higher FCR compared to the NP diet (P P P P > 0.05) compared to birds exposed to NT. Diet by temperature interactions were not observed for performance parameters during the period of WT ( 0.05) compared to birds exposed to NT. Diet by temperature interactions were not observed for performance parameters during the period of WT (P > 0.05). On d 35, the RP-fed birds had a lower yield of thigh and drumstick, higher fat pad, lower femur ash, and breaking strength but similar serum uric acid level and higher nitrogen digestibility on d 21 compared to those offered NP ( 0.05). On d 35, the RP-fed birds had a lower yield of thigh and drumstick, higher fat pad, lower femur ash, and breaking strength but similar serum uric acid level and higher nitrogen digestibility on d 21 compared to those offered NP (P