Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluation of Hatchery Production from Captive and Wild-caught Sandfish (Holothuria scabra Jaeger, 1833) Broodstocks

The overexploitation of natural populations of sea cucumbers is a threat to the sustainability of sea cucumber aquaculture operations reliant on wild-caught broodstocks. Maintaining wild-caught broodstocks in captivity ensures continuous availability of suitable broodstocks. However, it remains unclear if captive broodstocks are suitable for use in hatchery production. This study evaluates hatchery production of sandfish ( Holothuria scabra Jaeger, 1833) using captive broodstock, maintained in a pond for 1 year, compared to newly wild-caught broodstock. At the end of the 40-day hatchery cycle, lengths of juvenile sandfish resulting from the wild-caught (3.26 ± 0.13 mm) and captive (3.28 ± 0.16 mm) broodstocks were comparable ( P = 0.92). Survival curves of larval and juvenile sandfish differed between the two broodstock sources ( P < 0.01), owing to differences in the onset of exponential mortality. However, survival was comparable for juvenile sandfish derived from the wild-caught (1.23 ± 0.27 %) and captive (1.34 ± 0.73 %) broodstocks ( P = 0.89) at the end of the hatchery cycle (40-days post-fertilisation). The results of the present study demonstrate that captive sandfish broodstock supported hatchery production comparable to that of wild-caught broodstock.
Author ranking in multi-author collaborative networks

Methods for ranking authors of research publications generally attach equal value to all citations obtained for the publications. The Page Rank algorithm can be applied by treating each paper as a page and a citation as a link to bring out the differential values of citations thereby over-coming this limitation. However, the twin problems of ranking of papers and ranking of authors cannot be treated separately. In this article, we present a novel Author Ranking Algorithm that interleaves the ranking of papers and authors. The algorithm puts into practice the idea that an author's rank is determined by the quality or rank of papers which cite him while the ranks of the papers in turn depend on the quality of its authors. Further, this algorithm also considers collaborative contribution by factoring in the ranks of co-authored papers. We illustrate the algorithm by applying it to an author citation network consisting of authors who published their works on Web Semantics in the year 2013-2014. We also show how this algorithm is different from previous adaptations of Page Rank for ranking of authors.
Parental wellbeing and treatment adherence for children and adolescents with Phenylketonuria (PKU)

217 Total excluding abstract, tables, figures and references: 4745 Number of figures and tables: 4 9 1.1 Abstract Phenylketonuria (PKU) i-s a rare genetic disorder in which the amino acid phenylalanine cannot be sufficiently metabolised. Although a build-up of phenylalanine causes irreversible cognitive impairment, this can be prevented through a strict, lifelong, protein-restricted diet. Despite the severe consequences of poor metabolic control, many children and adolescents have phenylalanine levels above their recommended limits. This systematic review was the first to examine studies reporting demographic and/or psychosocial influences on blood phenylalanine levels, with the aim to identify factors that were robustly linked with metabolic control. Four electronic databases were searched, yielding 1808 articles. Articles were included if they reported a statistical examination of the association between one or more demographic or psychosocial factor(s) and metabolic control (as measured by blood phenylalanine concentration) for children and adolescents with PKU. Twenty-nine studies were selected for inclusion, which examined a range of child, parent and family factors related to blood phenylalanine levels. The most reproducible association was with child age, with metabolic control worsening with increasing age. This suggests that interventions promoting treatment adherence would be particularly beneficial for adolescents. There was a paucity of studies in some areas, and the quality of included studies varied; therefore, the conclusions of this review are preliminary. Research recommendations focus on promoting the growth of the evidence base to support clinical practice.
Between-year variation in the effects of phosphorus deficiency in breeder cows grazing tropical pastures in northern Australia

Breeder herd productivity can be severely reduced by dietary phosphorus (P) deficiency. The performance of small groups of P-deficient (Pdefic) or P-supplemented (Psupp) breeder cows was studied over 5 annual cycles while grazing C4 grass-Stylosanthes pastures at a site in the seasonally dry tropics of northern Australia. Soils contained c. 4 ppm of bicarbonate extractable P. Plasma inorganic P concentrations (PIP) during the wet season indicated that the Pdefic cows were deficient in P in 4 years and marginal in one year. Annual liveweight (LW) changes ranged widely between annual cycles from −71 to +13 kg in Pdefic cows and from +4 to +44 kg/head in Psupp cows. The LW responses to increased dietary P ranged from −9 to +115 kg, were greatest in years when LW losses by the Pdefic cows were greatest, and were associated with low-rainfall years. LW gains of calves suckling Psupp cows (mean 0.86 kg/d) tended to be higher (range 0.01–0.17 kg/d; mean 0.09 kg/d) than those of calves suckling Pdefic cows, but were significantly (P = 0.03) higher in only one year. Reconception appeared to be higher in Psupp than Pdefic cows during the 2 years of lower rainfall. Overall, the results indicated that responses to P supplementation by breeders grazing P-deficient pastures can vary widely between years. Therefore, the response in any one year may not reliably indicate responses in the longer term.
Sports Performance Wearable Technology, sEMG, and Manual Muscle Testing: Practical Methods for Measuring Maximal Voluntary Contractions

PURPOSE: The development in sports performance wearable technology has allowed for the monitoring of an athletes’ internal load via surface electromyography (sEMG) based garments. These garments have been shown to be a valid tool for measuring sEMG in sports settings. However, to conduct valid comparisons of sEMG, current methods often involve referencing data from a particular movement to a maximal voluntary contraction (MVC). MVCs are typically measured using an isokinetic dynamometer (ISO); however, with the application of sEMG in a sports environment utilizing an ISO can be impractical. An alternative is the use of manual muscle testing (MMT), in which manual resistance is applied by a trained practitioner to invoke a MVC. The purpose of this study was to compare sEMG-based garment measurement of MVCs elicited using ISO versus MMT in lower extremity muscles. METHODS: Twelve healthy, physically active participants (7 males, 5 females) were recruited for this study. Participants were fitted with a sEMG-based compression short or legging embedded with sEMG sensors. Following a dynamic warm-up, participants performed, in a randomized order, either ISO or MMT normalization protocols to measure the MVC of the vastus medialis (VM), vastus lateralis (VL), bicep femoris (BF) and gluteus maximus (GM). Data were sampled at 1KHz and band pass filtered, with the peak amplitude of the MVC used for analysis. Paired samples t-tests (p < .05) were used to compare the mean peak amplitudes from each muscle between ISO and MMT protocols. Pearson’s correlations (p < .05) were conducted to evaluate the degree of the relationship of peak amplitudes obtained by the two protocols for each muscle. RESULTS: No significant differences (p = .47-.88) were found between any of the muscles when comparing mean peak amplitudes for the ISO and MMT protocols. Significant correlations indicated a positive association between peak amplitudes obtained through ISO and MMT for the VM, RF, and BF (r > 0.80, p < .001 for all) and for the GM (r = . 63, p = . 022. CONCLUSIONS: The present data demonstrated that similar sEMG MVC data for the VM, VL, BF, and GM were recorded for the ISO and MMT. This suggests that the use of MMT, when administered by a trained member of staff, could be a practical method for normalizing each of the measured muscles to the MVC in a field environment.
Robust Face Recognition based on Color and Depth Information

One of the most important advantages of automatic human face recognition is its nonintrusiveness property. Face images can sometime be acquired without user’s knowledge or explicit cooperation. However, face images acquired in an uncontrolled environment can appear with varying imaging conditions. Traditionally, researchers focus on tackling this problem using 2D gray-scale images due to the wide availability of 2D cameras and the low processing and storage cost of gray-scale data. Nevertheless, face recognition can not be performed reliably with 2D gray-scale data due to insufficient information and its high sensitivity to pose, expression and illumination variations. Recent rapid development in hardware makes acquisition and processing of color and 3D data feasible. This thesis aims to improve face recognition accuracy and robustness using color and 3D information. In terms of color information usage, this thesis proposes several improvements over existing approaches. Firstly, the Block-wise Discriminant Color Space is proposed, which learns the discriminative color space based on local patches of a human face image instead of the holistic image, as human faces display different colors in different parts. Secondly, observing that most of the existing color spaces consist of at most three color components, while complementary information can be found in multiple color components across multiple color spaces and therefore the Multiple Color Fusion model is proposed to search and utilize multiple color components effectively. Lastly, two robust color face recognition algorithms are proposed. The Color Sparse Coding method can deal with face images with noise and occlusion. The Multi-linear Color Tensor Discriminant method harnesses multi-linear technique to handle non-linear data. Experiments show that all the proposed methods outperform their existing competitors. In terms of 3D information utilization, this thesis investigates the feasibility of face recognition using Kinect. Unlike traditional 3D scanners which are too slow in speed and too expensive in cost for broad face recognition applications, Kinect trades data quality for high speed and low cost. An algorithm is proposed to show that Kinect data can be used for face recognition despite its noisy nature. In order to fully utilize Kinect data, a more sophisticated RGB-D face recognition algorithm is developed which harnesses the Color Sparse Coding framework and 3D information to perform accurate face recognition robustly even under simultaneous varying conditions of poses, illuminations, expressions and disguises.
Defining Monocyte Differentiation into Colonic and Ileal Macrophages

Monocytes are circulating short-lived macrophage precursors that are recruited on demand from the blood to sites of inflammation and challenge. In steady state, classical monocytes give rise to vasculature-resident cells that patrol the luminal side of the endothelium. In addition, classical monocytes feed macrophage compartments of selected organs, including barrier tissues, such as the skin and intestine, as well as the heart. Monocyte differentiation under conditions of inflammation has been studied in considerable detail. In contrast, monocyte differentiation under non-inflammatory conditions remains less well understood. Here we took advantage of a combination of cell ablation and precursor engraftment to investigate the generation of gut macrophages from monocytes. Collectively, we identify factors associated with the gradual adaptation of monocytes to tissue residency. Moreover, comparison of monocyte differentiation into the colon and ileum-resident macrophages revealed the graduated acquisition of gut segment-specific gene expression signatures.
The plant pathogen Pectobacterium atrosepticum contains a functional formate hydrogenlyase-2 complex

Pectobacterium atrosepticum SCRI1043 is a phytopathogenic gram-negative enterobacterium. Genomic analysis has identified that genes required for both respiration and fermentation are expressed under anaerobic conditions. One set of anaerobically expressed genes is predicted to encode an important but poorly-understood membrane-bound enzyme termed formate hydrogenlyase-2 (FHL-2), which has fascinating evolutionary links to the mitochondrial NADH dehydrogenase (Complex I). In this work, molecular genetic and biochemical approaches were taken to establish that FHL-2 is fully functional in P. atrosepticum and is the major source of molecular hydrogen gas generated by this bacterium. The FHL-2 complex was shown to comprise a rare example of an active [NiFe]-hydrogenase-4 (Hyd-4) isoenzyme, itself linked to an unusual selenium-free formate dehydrogenase in the final complex. In addition, further genetic dissection of the genes encoding the predicted membrane domain of FHL-2 established surprisingly that the majority of genes encoding this domain are not required for physiological hydrogen production activity. Overall, this study presents P. atrosepticum as a new model bacterial system for understanding anaerobic formate and hydrogen metabolism in general, and FHL-2 function and structure in particular. Significance Statement Pectobacterium atrospecticum contains the genes for the formate hydrogenlyase-2 enzyme, considered the ancient progenitor of mitochondrial respiratory Complex I. In this study, the harnessing of P. atrosepticum as a new model system for understanding bacterial hydrogen metabolism has accelerated new knowledge in FHL-2 and its component parts. Importantly, those component parts include an unusual selenium-free formate dehydrogenase and a complicated [NiFe]-hydrogenase-4 with a large membrane domain. FHL-2 is established as the major source of molecular hydrogen produced under anaerobic conditions by P. atrospectium, however surprisingly some components of the membrane domain were not essential for this activity.
Comparison of water use efficiency and biomass production in 10-year-old Populus sibirica and Ulmus pumila plantations in Lun soum, Mongolia

Abstract Although afforestation is one of the best solutions for combating desertification, it requires intensive management. To minimize management efforts in plantations in arid area, it is crucial to select suitable tree species, i.e. those with a high adaptability to xeric environments. In this study, we investigated key tree traits related to drought adaptation in Populus sibirica Hort. ex Tausch and Ulmus pumila L. , planted in the Korea-Mongolia Green Belt Plantation in Lun soum, Mongolia. We found that U. pumila had a smaller leaf size and smaller specific leaf area (SLA) than P. sibirica. In addition, the water use efficiency (WUE) of U. pumila (carbon isotope-based) was significantly higher than that of P. sibirica. Although biomass production was ∼2.5 times higher in P. sibirica than in U. pumila due to the differences in leaf area, there were no statistically significant differences in the photosynthetic characteristics on an area basis. These results indicate that U. pumila has a higher adaptive potential to dry conditions than P. sibirica due to its small leaf size, low SLA, and high WUE.
Some specific microbiological parameters and prevalence of Salmonella spp. in retail chicken meat from Erzurum province, Turkey and characterization of antibiotic resistance of isolates

Specific microbiological parameters and the presence of Salmonella spp. were investigated in 72 chicken meat samples (36 wings and 36 drumsticks) collected from markets and butcher shops. The specific microbiological parameters were determined using a conventional cultural method and the presence of Salmonella spp. in chicken samples was determined using conventional and immunomagnetic separation (IMS)-polymerase chain reaction (PCR) methods. In addition, antimicrobial susceptibility of the isolates was revealed using the Kirby-Bauer disc diffusion method. The results indicated that 30 of the 72 samples were positive for Salmonella spp. by the conventional method, and 42 of the 72 were positive by the IMS-PCR method. However, 30 of the 72 samples were positive for Salmonella spp. by both methods. The Salmonella spp. isolates were confirmed by the VITEK2 Compact System and PCR. The susceptibilities of the isolates against 10 antibiotics were determined. The results indicated that isolates (27/30) showed the highest susceptibility to gentamycin (90.00%), while the highest resistance was to nalidixic acid and tetracycline at the 100 and 93.34% levels, respectively. These results indicate a high prevalence of Salmonella spp. in poultry meat from Erzurum city, Turkey, and the antimicrobial resistance profile of these isolates should be considered for public health. The results also show that the IMS-PCR technique was superior to the conventional method for detecting Salmonella in poultry meat.
Kefir Produced from Red Rice Milk by Lactobacillus bulgaricus and Candida kefir Starter

Kefir is a dairy product commonly fermented by bacteria and yeasts. One of the potential vegetable milk materials to be used in kefir production is milk from red rice. Studies of fermentation of milk from red rice to produce kefir are barely found. This study aimed to determine the nutrient content of red rice milk kefir fermented using mixed of microorganisms, Lactobacillus bulgaricus and Candida kefir, in various concentrations of 3%, 9%, and 15%, respectively. The content of carbohydrate, fat, protein, water, and ash was measured using proximate analysis, while their content of lactic acid and alcohol was assayed using titration method. The results showed that fat, water and ash content in all resulted kefir products met standard quality of kefir, whereas carbohydrates and protein content did not. Treatment using the set mixed starters at a concentration of 9% was found to be able to produce kefir with a lactic acid content of 2.19%. Increasing alcohol content of kefir was dependent by starters. Generally, all treatments were able to produce kefir with alcohol content of 1.5% on average. As conclusion, fermentation of red rice milk at concentration of mixed starters at 9% has nutrient content which meet standard quality of kefir.
Global stability of the multi-strain Kermack-McKendrick (renewal) epidemic model

We extend a recent investigation by Meehan et al. (2019) regarding the global stability properties of the general Kermack-McKendrick (renewal) model to the multi-strain case. We demonstrate that the basic reproduction number of each strain $R_{0j}$ represents a sharp threshold parameter such that when $R_{0j} \leq 1$ for all $j$ each strain dies out and the infection-free equilibrium is globally asymptotically stable; whereas for $R_{01} \equiv \mathrm{max}_j\, R_{0j} > 1$ the endemic equilibrium point $\bar{P}^1$, at which only the fittest strain (i.e. strain 1) remains in circulation, becomes globally asymptotically stable.
Comparison between inosinic acid content of muscle in Chinese native chickens

The order of IMP content of muscle from high to low is Taihe Silkes, White earlobes chickens, Beijing fatty chickens, Xiaoshan chickens(♂)×White earlobes chickens(♀), White earlobes chickens(♂)×Xiaoshan chickens(♀), Xiaoshan chickens, Langshan chickens. IMP content of muscle in Taihe Silkes is significantly higher than that in other chickens except for White earlobes chickens and Beijing fatty chickens which is significantly higher than that in Langshan chickens (P<0.05). There is a significant difference of IMP content of muscle between female and male, IMP content of muscle of male is lower than that of female. There is a significant negative correlation (-0.3986) between IMP content of muscle and body weight (P<0.01).
Mutations in the Methylenetetrahydrofolate Reductase Gene and Methionine Metabolism in male infertility

Background and Aim: The human methylenetetrahydrofolate reductase (MTHFR) gene plays a crucial role in folate metabolism. Data regarding the influence of MTHFR gene polymorphisms on male fertility status are conflicting. The present study aimed to investigate the possible role of genetic variants of the MTHFR 677 C→T and 1298 A→C and the seminal plasma levels of S-adenosylmethionine (SAM), S-adenosylhomocysteine (SAH) in male infertility. Patients & Methods: The present study included 229 men attending the Andrology Outpatient Clinic, Mansoura University Hospital. The semen samples obtained from men were grouped according to the profile of seminogram into normozoospermic (N), oligoathenoteratozoospermia (OAT) and azoospermia (AZ). Spermatozoa were separated and the purified spermatozoa were used for assessment of acrosine activity by gelatinolysis. High Performance Liquid Chromatography equipped with a reversed-phase column-C18, and UV detector at 254 nm was used to separate SAM and SAH. Genomic DNA was isolated from peripheral blood leukocytes by Genta genomic DNA purification kit. MTHFR 677 C→T and 1298 A→C polymorphisms were analyzed using PCR, restriction enzymes and agarose gel electrophoresis. Results: The results of the current study showed that SAM, SAM/SAH ratio and acrosine activity index to be significantly decreased in OAT and AZ compared with normozoospermia. MTHR 1298AA and 677CC genotypes frequency was significantly higher in OAT and AZ groups when compared to N group.Also, SAH were significantly increased in MTHR 1298AA and 677CC genotypes. Conclusion: The polymorphisms in the MTHR A1298C and C677T gene were associated with abnormal sperm function, morphology and motility. Carrier of 1298AA and 677CC genotypes had higher level of SAH. It could be concluded that methionine metabolism is abnormal in infertile men denoted by impaired SAM and SAH levels. Further studies may be of benefit for new strategies in therapy for male infertility.
The long non-coding RNA GHSROS reprograms prostate cancer cell lines toward a more aggressive phenotype

It is now appreciated that long non-coding RNAs (lncRNAs) are important players in the orchestration of cancer progression. In this study we characterized GHSROS, a human lncRNA gene on the opposite DNA strand (antisense) to the ghrelin receptor gene, in prostate cancer. The lncRNA was upregulated by prostate tumors from different clinical datasets. Consistently, transcriptome data revealed that GHSROS alters the expression of cancer-associated genes. Functional analyses in vitro showed that GHSROS mediates tumor growth, migration, and survival and resistance to the cytotoxic drug docetaxel. Increased cellular proliferation of GHSROS-overexpressing PC3, DU145, and LNCaP prostate cancer cell lines in vitro was recapitulated in a subcutaneous xenograft model. Conversely, in vitro antisense oligonucleotide inhibition of the lncRNA reciprocally regulated cell growth and migration, and gene expression. Notably, GHSROS modulates the expression of PPP2R2C, the loss of which may drive androgen receptor pathway-independent prostate tumor progression in a subset of prostate cancers. Collectively, our findings suggest that GHSROS can reprogram prostate cancer cells toward a more aggressive phenotype and that this lncRNA may represent a potential therapeutic target.