Miracle-dz/UniFAR-FTUs huggingface dataset:
Effects of xylanase supplementation to wheat-based diets on growth performance, nutrient digestibility and gut microbes in weanling pigs

Objective This study was designed to investigate the effects of an Aspergillus sulphureus xylanase expressed in Pichia pastoris on the growth performance, nutrient digestibility and gut microbes in weanling pigs. Methods A total of 180 weanling pigs (initial body weights were 8.47±1.40 kg) were assigned randomly to 5 dietary treatments. Each treatment had 6 replicates with 6 pigs per replicate. The experimental diets were wheat based with supplementation of 0, 500, 1,000, 2,000, and 4,000 U xylanase/kg. The experiment lasted 28 days (early phase, d 0 to 14; late phase, d 15 to 28). Results In the early phase, compared to the control, average daily gain (ADG) was higher for pigs fed diets supplemented with xylanase and there was a quadratic response in ADG (p<0.05). In the entire phase, ADG was higher for the pigs fed 1,000 or 2,000 U/kg xylanase compared to the control (p<0.05). The gain to feed ratio was higher for pigs fed diets supplemented with 1,000 or 2,000 U/kg xylanase compared to the control (p<0.05). Increasing the amount of xylanase improved the apparent total tract digestibility of dry matter, crude protein, neutral detergent fiber, calcium, and phosphorus during both periods (p<0.05). Xylanase supplementation (2,000 U/kg) decreased the proportion of Lachnospiraceae (by 50%) in Firmicutes, but increased Prevotellaceae (by 175%) in Bacteroidetes and almost diminished Enterobacteriaceae (Escherichia-Shigella) in Proteobacteria. Conclusion Xylanase supplementation increased growth performance and nutrient digestibility up to 2,000 U/kg. Supplementation of xylanase (2,000 U/kg) decreased the richness of gut bacteria but diminished the growth of harmful pathogenic bacteria, such as Escherichia-Shigella, in the colon.
DAT1 Polymorphism Is Associated with Risk Taking in the Balloon Analogue Risk Task (BART)

Twin-studies suggest that a significant portion of individual differences in the propensity to take risks resides in people’s genetic make-up and there is evidence that variability in dopaminergic systems relates to individual differences in risky choice. We examined the link between risk taking in a risk taking task (the Balloon Analogue Risk Task, BART) and a variable number tandem repeat (VNTR) polymorphism in the 3′UTR of the dopamine transporter gene (SLC6A3/DAT1). Behavior in BART is known to be associated with activity in striatal reward-processing regions, and DAT1 is assumed to modulate striatal dopamine levels. We find that carriers of DAT1 alleles, which presumably result in lower striatal dopamine availability, showed more risk taking, relative to carriers of the alleles associated with higher striatal dopamine availability. Our analyses suggest that the mechanism underlying this association is diminished sensitivity to rewards among those who take more risks. Overall, our results support the notion that a behavioral genetic approach can be helpful in uncovering the basis of individual differences in risk taking.
Genome Features of “Dark-Fly”, a Drosophila Line Reared Long-Term in a Dark Environment

Organisms are remarkably adapted to diverse environments by specialized metabolisms, morphology, or behaviors. To address the molecular mechanisms underlying environmental adaptation, we have utilized a Drosophila melanogaster line, termed “Dark-fly”, which has been maintained in constant dark conditions for 57 years (1400 generations). We found that Dark-fly exhibited higher fecundity in dark than in light conditions, indicating that Dark-fly possesses some traits advantageous in darkness. Using next-generation sequencing technology, we determined the whole genome sequence of Dark-fly and identified approximately 220,000 single nucleotide polymorphisms (SNPs) and 4,700 insertions or deletions (InDels) in the Dark-fly genome compared to the genome of the Oregon-R-S strain, a control strain. 1.8% of SNPs were classified as non-synonymous SNPs (nsSNPs: i.e., they alter the amino acid sequence of gene products). Among them, we detected 28 nonsense mutations (i.e., they produce a stop codon in the protein sequence) in the Dark-fly genome. These included genes encoding an olfactory receptor and a light receptor. We also searched runs of homozygosity (ROH) regions as putative regions selected during the population history, and found 21 ROH regions in the Dark-fly genome. We identified 241 genes carrying nsSNPs or InDels in the ROH regions. These include a cluster of alpha-esterase genes that are involved in detoxification processes. Furthermore, analysis of structural variants in the Dark-fly genome showed the deletion of a gene related to fatty acid metabolism. Our results revealed unique features of the Dark-fly genome and provided a list of potential candidate genes involved in environmental adaptation.
Bacterial Species and Antibiotic Sensitivity in Korean Patients Diagnosed with Acute Otitis Media and Otitis Media with Effusion

Changes over time in pathogens and their antibiotic sensitivity resulting from the recent overuse and misuse of antibiotics in otitis media (OM) have complicated treatment. This study evaluated changes over 5 years in principal pathogens and their antibiotic sensitivity in patients in Korea diagnosed with acute OM (AOM) and OM with effusion (OME). The study population consisted of 683 patients who visited the outpatient department of otorhinolaryngology in 7 tertiary hospitals in Korea between January 2010 and May 2015 and were diagnosed with acute AOM or OME. Aural discharge or middle ear fluid were collected from patients in the operating room or outpatient department and subjected to tests of bacterial identification and antibiotic sensitivity. The overall bacteria detection rate of AOM was 62.3% and OME was 40.9%. The most frequently isolated Gram-positive bacterial species was coagulase negative Staphylococcus aureus (CNS) followed by methicillin-susceptible S. aureus (MSSA), methicillin-resistant S. aureus (MRSA), and Streptococcus pneumonia (SP), whereas the most frequently isolated Gram-negative bacterium was Pseudomonas aeruginosa (PA). Regardless of OM subtype, ≥ 80% of CNS and MRSA strains were resistant to penicillin (PC) and tetracycline (TC); isolated MRSA strains showed low sensitivity to other antibiotics, with 100% resistant to PC, TC, cefoxitin (CFT), and erythromycin (EM); and isolated PA showed low sensitivity to quinolone antibiotics, including ciprofloxacin (CIP) and levofloxacin (LFX), and to aminoglycosides. Bacterial species and antibiotic sensitivity did not change significantly over 5 years. The rate of detection of MRSA was higher in OME than in previous studies. As bacterial predominance and antibiotic sensitivity could change over time, continuous and periodic surveillance is necessary in guiding appropriate antibacterial therapy.
Assessing Individual Change Without Knowing the Test Properties: Item Bootstrapping

Assessing significant change (or reliable change) in a person often involve comparing the responses of that person in two administrations of a test or scale. Several procedures have been proposed to determine if a difference between two observed scores is statistically significant or rather is within the range of mere random fluctuations due to measurement error. Application of those procedures involve some knowledge of the test properties. But sometimes those procedures cannot be employed because the properties are unknown or are not trustworthy. In this paper we propose the bootstrap of items procedure to create confidence intervals of the individual's scores without using any known psychometric properties of the test. Six databases containing the responses of several groups to one or more subscales have been analyzed using two methods: bootstrap of items and a classical procedure based on confidence intervals to estimate the true score. The rates of significant change obtained were very similar, suggesting that item bootstrapping is a promising solution when other methods cannot be applied.
Impact of diabetes education and peer support group on the metabolic parameters of patients with Diabetes Mellitus (Type 1 and Type 2)

Aim This study was undertaken to investigate the effect of diabetes education (DE) alone versus diabetes education plus peer support group (DE+PS) in improving metabolic parameters in patients with diabetes mellitus (DM). Methods We retrospectively included a total of 188 subjects with DM who were seen at the Diabetes Centre and Primary Care clinics at Queens Hospital Centre, Jamaica, New York. The patients were categorized into three main groups: (1) control group (n=62), who received primary care only, (2) DE group (n=63), who received primary care plus diabetes teaching from a certified diabetes nurse educator and (3) DE+PS group (n=63) who received education in diabetes and who joined a peer support group for at least two or more sessions. The mean change from baseline in hemoglobin A1C (HbA1C), weight, body mass index (BMI), systolic blood pressure (SBP), total cholesterol (TC), high density lipoprotein cholesterol (HDL-C), low density lipoprotein cholesterol (LDL-C) and triglycerides (TG-C) was calculated after 3 follow up visits. Results The patients in DE group were observed to have statistically significant decrease in mean HbA1C (mean change: -0.78%, p=0.013), TC (mean change: -16.89 mg/dL, p=0.01) and LDL-C (mean change: -11.75 mg/dL, p=0.04) from baseline to final follow. The same group also exhibited consistently significant reductions in HbA1C and LDL-C throughout from the third month to the thirteenth month of follow up. The patients in DE+PS group had a moderate decrease in HbA1C, SBP, TG-C and weight, and an increase in HDL-C, LDL-C and BMI in the final follow up, but all were not statistically significant. Conclusion The present study suggested that participation in DE may assist with optimizing metabolic parameters such as HbA1C, TC and LDL-C levels in patients with diabetes. This benefit may perpetuate through time. The addition of peer support group to DE may or may not confer additional benefit.
Input Subject Diversity Accelerates the Growth of Tense and Agreement: Indirect Benefits From a Parent-Implemented Intervention.

Purpose This follow-up study examined whether a parent intervention that increased the diversity of lexical noun phrase subjects in parent input and accelerated children's sentence diversity (Hadley et al., 2017) had indirect benefits on tense/agreement (T/A) morphemes in parent input and children's spontaneous speech. Method Differences in input variables related to T/A marking were compared for parents who received toy talk instruction and a quasi-control group: input informativeness and full is declaratives. Language growth on tense agreement productivity (TAP) was modeled for 38 children from language samples obtained at 21, 24, 27, and 30 months. Parent input properties following instruction and children's growth in lexical diversity and sentence diversity were examined as predictors of TAP growth. Results Instruction increased parent use of full is declaratives (ηp2 ≥ .25) but not input informativeness. Children's sentence diversity was also a significant time-varying predictor of TAP growth. Two input variables, lexical noun phrase subject diversity and full is declaratives, were also significant predictors, even after controlling for children's sentence diversity. Conclusions These findings establish a link between children's sentence diversity and the development of T/A morphemes and provide evidence about characteristics of input that facilitate growth in this grammatical system.
Global prevalence and economic and humanistic burden of astigmatism in cataract patients: a systematic literature review

Purpose To systematically review the published evidence on the prevalence and economic and humanistic burden of astigmatism in cataract patients. Materials and methods For this systematic literature review, the Medline, PubMed, Embase, and Cochrane databases were searched from 1996 to September 2015 for available scientific literature that met the inclusion criteria. Studies published in the English language reporting prevalence and humanistic and economic burden in patients diagnosed with cataract and astigmatism were included. Results Of 3,649 papers reviewed, 31 studies from 32 publications met the inclusion criteria of this review. Preexisting astigmatism ≥1 D was present in up to 47% of cataract eyes. The cost burden of residual uncorrected astigmatism after cataract surgery was driven by the cost of spectacles, which was estimated to range from $2,151 to $3,440 in the US and $1,786 to $4,629 in Europe over a lifetime. In cataract patients, both preexisting and postoperative residual astigmatism were associated with poor vision-related patient satisfaction and quality of life, as well as higher spectacle burden. Astigmatism correction during cataract surgery appears to improve visual outcomes and results in overall lifetime cost savings compared to astigmatism correction with postoperative vision correction. Conclusion There is a high prevalence of preexisting astigmatism in cataract patients. Although published data are limited, both preoperative astigmatism and postoperative residual astigmatism affect visual function and vision-related quality of life, resulting in increased humanistic burden. Suboptimal correction of astigmatism during cataract surgery drives the continuous need for vision correction with spectacles in the postoperative period. Patients must bear the out-of-pocket expenses, since payers often do not reimburse the cost of spectacles. Greater access to astigmatism correction during cataract surgery could improve visual outcomes and quality of life in patients. More research is required to gain a better understanding of the disease burden of astigmatism in cataract patients.
TAT-Gap19 and Carbenoxolone Alleviate Liver Fibrosis in Mice

Although a plethora of signaling pathways are known to drive the activation of hepatic stellate cells in liver fibrosis, the involvement of connexin-based communication in this process remains elusive. Connexin43 expression is enhanced in activated hepatic stellate cells and constitutes the molecular building stone of hemichannels and gap junctions. While gap junctions support intercellular communication, and hence the maintenance of liver homeostasis, hemichannels provide a circuit for extracellular communication and are typically opened by pathological stimuli, such as oxidative stress and inflammation. The present study was set up to investigate the effects of inhibition of connexin43-based hemichannels and gap junctions on liver fibrosis in mice. Liver fibrosis was induced by administration of thioacetamide to Balb/c mice for eight weeks. Thereafter, mice were treated for two weeks with TAT-Gap19, a specific connexin43 hemichannel inhibitor, or carbenoxolone, a general hemichannel and gap junction inhibitor. Subsequently, histopathological analysis was performed and markers of hepatic damage and functionality, oxidative stress, hepatic stellate cell activation and inflammation were evaluated. Connexin43 hemichannel specificity of TAT-Gap19 was confirmed in vitro by fluorescence recovery after photobleaching analysis and the measurement of extracellular release of adenosine-5′-triphosphate. Upon administration to animals, both TAT-Gap19 and carbenoxolone lowered the degree of liver fibrosis accompanied by superoxide dismutase overactivation and reduced production of inflammatory proteins, respectively. These results support a role of connexin-based signaling in the resolution of liver fibrosis, and simultaneously demonstrate the therapeutic potential of TAT-Gap19 and carbenoxolone in the treatment of this type of chronic liver disease.
How Human Brucellosis Incidence in Urban Kampala Can Be Reduced Most Efficiently? A Stochastic Risk Assessment of Informally-Marketed Milk

Background In Kampala, Uganda, studies have shown a significant incidence of human brucellosis. A stochastic risk assessment involving two field surveys (cattle farms and milk shops) and a medical record survey was conducted to assess the risk of human brucellosis infection through consumption of informally marketed raw milk potentially infected with Brucella abortus in Kampala and to identify the best control options. Methodology/Principal Findings In the cattle farm survey, sera of 425 cows in 177 herds in the Kampala economic zone were sampled and tested for brucellosis using a competitive enzyme-linked immunosorbent assay (CELISA). Farmers were interviewed for dairy information. In the milk shop surveys, 135 milk sellers in the urban areas were interviewed and 117 milk samples were collected and tested using an indirect enzyme-linked immunosorbent assay (IELISA). A medical record survey was conducted in Mulago National Referral Hospital for serological test results. A risk model was developed synthesizing data from these three surveys. Possible control options were prepared based on the model and the reduction of risk was simulated for each scenario. Overall, 12.6% (6.8–18.9: 90%CI) of informally marketed milk in urban Kampala was contaminated with B.abortus at purchase and the annual incidence rate was estimated to be 5.8 (90% CI: 5.3–6.2) per 10,000 people. The best control option would be the construction of a milk boiling centre either in Mbarara, the largest source of milk, or in peri-urban Kampala and to ensure that milk traders always sell milk to the boiling centre; 90% success in enforcing these two options would reduce risk by 47.4% (21.6–70.1: 90%CI) and 82.0% (71.0–89.0: 90%CI), respectively. Conclusion/Significance This study quantifies the risk of human brucellosis infection through informally marketed milk and estimates the incidence rate in Kampala for the first time; risk-based mitigation strategies are outlined to assist in developing policy.
Randomized Quasi-Newton Updates Are Linearly Convergent Matrix Inversion Algorithms

We develop and analyze a broad family of stochastic/randomized algorithms for calculating an approximate inverse matrix. We also develop specialized variants maintaining symmetry or positive definiteness of the iterates. All methods in the family converge globally and linearly (i.e., the error decays exponentially), with explicit rates. In special cases, we obtain stochastic block variants of several quasi-Newton updates, including bad Broyden (BB), good Broyden (GB), Powell-symmetric-Broyden (PSB), Davidon--Fletcher--Powell (DFP), and Broyden--Fletcher--Goldfarb--Shanno (BFGS). Ours are the first stochastic versions of these updates shown to converge to an inverse of a fixed matrix. Through a dual viewpoint we uncover a fundamental link between quasi-Newton updates and approximate inverse preconditioning. Further, we develop an adaptive variant of randomized block BFGS, where we modify the distribution underlying the stochasticity of the method throughout the iterative process to achieve faster convergen.
Inducible Wnt16 inactivation: WNT16 regulates cortical bone thickness in adult mice

Substantial progress has been made in the therapeutic reduction of vertebral fracture risk in patients with osteoporosis, but non-vertebral fracture risk has been improved only marginally. Human genetic studies demonstrate that the WNT16 locus is a major determinant of cortical bone thickness and non-vertebral fracture risk and mouse models with life-long Wnt16 inactivation revealed that WNT16 is a key regulator of cortical thickness. These studies, however, could not exclude that the effect of Wnt16 inactivation on cortical thickness might be caused by early developmental and/or growth effects. To determine the effect of WNT16 specifically on adult cortical bone homeostasis, Wnt16 was conditionally ablated in young adult and old mice through tamoxifen-inducible Cre-mediated recombination using CAG-Cre-ER; Wnt16flox/flox (Cre-Wnt16flox/flox) mice. First, 10-week-old Cre-Wnt16flox/flox and Wnt16flox/flox littermate control mice were treated with tamoxifen. Four weeks later, Wnt16 mRNA levels in cortical bone were reduced and cortical thickness in femur was decreased in Cre-Wnt16flox/flox mice compared to Wnt16flox/flox mice. Then, inactivation of Wnt16 in 47-week-old mice (evaluated four weeks later) resulted in a reduction of Wnt16 mRNA levels, cortical thickness and cortical bone strength with no effect on trabecular bone volume fraction. Mechanistic studies demonstrated that the reduced cortical bone thickness was caused by a combination of increased bone resorption and reduced periosteal bone formation. In conclusion, WNT16 is a crucial regulator of cortical bone thickness in young adult and old mice. We propose that new treatment strategies targeting the adult regulation of WNT16 might be useful to reduce fracture risk at cortical bone sites.
Rapid Assessment of Avoidable Blindness in the Occupied Palestinian Territories

Background There are no recent data on the prevalence and causes of blindness in the Occupied Palestinian Territories. The aim of our study was to estimate the prevalence and causes of blindness and visual impairment in the population aged 50 years and above in the Occupied Palestinian Territories using the Rapid Assessment of Avoidable Blindness (RAAB) survey method. Methods and Findings Clusters of 40 people who were 50 years and above were selected with probability proportionate to size using a multistage cluster random sampling method. Participants received a comprehensive ophthalmic examination in their homes, including visual acuity testing by one of three experienced ophthalmologists. The principal cause for visual loss was determined by an experienced ophthalmologist using portable diagnostic instruments. Information about previous cataract surgery, satisfaction with surgery and barriers to cataract surgery were collected. The prevalence of self-reported diabetes was also determined. The prevalence of bilateral blindness (VA<3/60 in the better eye with available correction) was 3.4% (95% CI: 2.7–4.0), 2.0% (95% CI: 1.4–2.5) for severe visual impairment (VA≥3/60 and <6/60), and 7.4% (95% CI: 6.4–8.3) for visual impairment (VA≥6/60 and <6/18). Avoidable causes (i.e. cataract, refractive error, aphakia, surgical complications, corneal scarring and phthysis) accounted for 80.0% of bilateral blindness, severe visual impairment (70.7%) and visual impairment (86.2%). Cataract was the main cause of blindness (55.0%). The prevalence of blindness was higher in Gaza (4.9%, 95% CI: 3.7–6.1%) than in the West Bank (2.5%, 95% CI: 1.9–3.1%) and among women (4.3%,95% CI: 3.3–5.2%) compared to men (2.2%,95%CI:1.5–2.9%). Among people who had undergone cataract surgery in the past, only 54.5% of eyes obtained a good outcome (VA≥6/18), 23.2% had a borderline outcome (VA<6/18 and ≥6/60) and 22.3% had a poor outcome (VA<6/60) with available correction. The prevalence of self-reported diabetes mellitus in ≥50 year age group was 26.4% (95% CI: 24.9–27.9). Conclusions The prevalence of blindness suggests that significant numbers of people in the Occupied Palestinian Territories exist who do not access eye care - predominantly women and those residing in Gaza. Programmes need to focus on maximizing the use of current services by these excluded groups.