Miracle-dz/UniFAR-FTUs huggingface dataset:
Enhancing genomics-based outbreak detection of endemic Salmonella enterica serovar Typhimurium using dynamic thresholds

Salmonella enterica serovar Typhimurium is the leading cause of salmonellosis in Australia, and the ability to identify outbreaks and their sources is vital to public health. Here, we examined the utility of whole-genome sequencing (WGS), including complete genome sequencing with Oxford Nanopore technologies, in examining 105 isolates from an endemic multi-locus variable number tandem repeat analysis (MLVA) type over 5 years. The MLVA type was very homogeneous, with 90 % of the isolates falling into groups with a five SNP cut-off. We developed a new two-step approach for outbreak detection using WGS. The first clustering at a zero single nucleotide polymorphism (SNP) cut-off was used to detect outbreak clusters that each occurred within a 4 week window and then a second clustering with dynamically increased SNP cut-offs were used to generate outbreak investigation clusters capable of identifying all outbreak cases. This approach offered optimal specificity and sensitivity for outbreak detection and investigation, in particular of those caused by endemic MLVA types or clones with low genetic diversity. We further showed that inclusion of complete genome sequences detected no additional mutational events for genomic outbreak surveillance. Phylogenetic analysis found that the MLVA type was likely to have been derived recently from a single source that persisted over 5 years, and seeded numerous sporadic infections and outbreaks. Our findings suggest that SNP cut-offs for outbreak cluster detection and public-health surveillance should be based on the local diversity of the relevant strains over time. These findings have general applicability to outbreak detection of bacterial pathogens.
Effect of hygiene-sanitary management on goat milk quality in semi-extensive systems in Spain

Milk samples were collected from 28 farms, at monthly intervals during the production period (December to September). At the same time, each farmer was surveyed about specific conditions of hygiene-sanitary management at the farm. When management improvements were made, there was improvement ( P < 0.05) in both bacteria count (165,000 bacteria/ml versus 379,000 bacteria/ml in the samples taken from the tank) and somatic cell count (SCC; 1,564,000 cells/ml versus 2,354,000 cells/ml). A source ( P < 0.001) of microbial milk contamination was its handling in the time from leaving the udder (65,000 bacteria/ml) until reaching the refrigeration farm tank (in the case of machine-milking, with 362,000 bacteria/ml) or the bulk tank of the cooperative (in the case of hand-milking, with 262,000 bacteria/ml). The two study areas, characterized by the milking method, presented differences ( P < 0.001) in bacteria count and SCC (2,534,000 cells/ml with machine-milking versus 1,785,000 cells/ml with hand-milking). Farms with fewer animals ( <100 animals) that practised hand-milking had a better hygiene-sanitary quality. Month also affected SCC, with concentration lowest in December and March (1,510,000 cells/ml), and highest in August and September (3,379,000 cells/ml). This was also part of the change in SCC with stage of lactation, increasing towards its end. SCC showed a positive correlation ( P < 0.01) with % fat (r = 0.21) and % protein ( r = 0.49). No correlation was observed between the number of bacteria and SCC. It is concluded that the establishment of appropriate conditions of hygiene-sanitary management on the farms improved the bacteriological quality and enabled SCC to fall below recommended limits. © 2003 Elsevier Science B.V. All rights reserved.
New Evidence on asymmetric dependence in the returns from U.S. Real Estate Estate Investment Trusts

A robust assessment of asymmetric dependence is crucial for determining the benefits of diversification associated with including real estate in mixed-asset portfolios, but analysing asymmetric dependence is a complex, multi-dimensional problem. Using Monte Carlo simulations, we identify the most suitable metric of asymmetric dependence out of a range of methodologies commonly employed in real estate finance: the Adjusted J statistic (Alcock and Hatherley, 2010). We employ this statistic to empirically examine the dependence structures in a large sample of U.S. Real Estate Investment Trusts (REITs) and a broad range of benchmark assets over the period 1997-2010. Our results suggest that when we control for linear dependence and focus on the strength, direction and statistical significance of higher-order, asymmetric dependence, the benefits of diversification offered by REITs are stronger than sometimes reported, while the dependence with bonds appears to be more complex than previously assumed.
Genetic variability in Iranian limb‐girdle muscular dystrophy type 2B patients: An evidence of a founder effect

Dysferlinopathies are a group of autosomal recessive limb‐girdle muscular dystrophies (LGMDs) caused by mutations in DYSF (#603,009). This gene encodes a transmembrane protein called dysferlin. Since there are few reports on Iranian dysferlinopathy patients, we tried to identify the DYSF mutations in affected individuals of Iran.
Prevalence of Autism and its Comorbidities and the Relationship with Maternal Psychopathology: A National Population-Based Study.

BACKGROUND There is no clear picture regarding the prevalence rates of autism and its comorbidities among Iranian children and adolescents. The present study aimed to estimate these rates as part of a large national population-based study on epidemiology of psychiatric disorders in Iranian children and adolescents. METHODS The total sample consisted of 31000 children and adolescents between 6 to 18 years of age. The Kiddie Schedule for Affective Disorders and Schizophrenia for School-Age Present and Life time version (K-SADS-PL) was used as the diagnostic tool. RESULTS The prevalence of autism in the total sample is equal to 0.1% (10 per 10000), with a 2:1 male-to-female ratio. In total, 86% of people with autism had at least one comorbid condition. Intellectual disability, epilepsy, enuresis and attention deficit and hyperactivity disorder (ADHD) with prevalence rates of 70.3%, 29.7%, 27% and 21.62%, respectively, were the most prevalent comorbid conditions in people with autism. Maternal personality disorders were also shown to be associated with increasing risk of autism. CONCLUSION The present study shows high prevalence rates for autism and its comorbid conditions among Iranian children and adolescents. It also reveals that there is a relationship between some maternal psychiatric disorders and the risk of autism.
Age and growth parameters of the dourado Salminus brasiliensis (Cuvier, 1816) from the river Cuiabá, Mato Grosso State, Brazil

Age and growth parameters of Salminus brasiliensis (Curvier, 1816) from the Manso Reservoir and from the river Cuiaba are estimated by their fish scales. Sampling was performed between January and December 2006. There was a linear relationship between the standard length of the fish (cm) and the scale radius (mm) (r = 0.93). The coefficients of variation of standard mean lengths calculated for fish of the same age class were low (>19.0%), while temporal variation analysis of mean marginal increment showed that growth ring was annually formed in November, possibly related to the species’s reproductive period between November and January. The maximum number of rings was 12 for both sexes. The growth curve for length expressed by von Bertalanffy model was Sl = 69.0[1-e -0.21(t-(-0.86) ] for males and Sl = 77.9[1-e -0.17(t-(-0.41) ] for females. The growth curve in weight was Wt = 7334.6[1-e -0.21(t-(-0.86) ] 3.07 for males and Wt = 10226.8[1-e -0.17(t-(-0.41) ] 3.05 for females. Females attained greater length and weight than males. Since growth rate for the species was initially accelerated for both sexes, specimens attain size to start migration after the floods, avoiding predation and frequenting sites with greater food availability.
The association of exudation pattern with anatomical and functional outcomes in patients with Neovascular Age-Related Macular Degeneration

Objective. To evaluate the correlation between visual outcomes and fluid configuration observed on spectral-domain optical coherence tomography (SD-OCT) in patients with wet age-related macular degeneration (AMD). Methods. Sixty-five eyes of 53 patients with AMD who were administered intravitreal ranibizumab treatment with 12 months of follow-up were included in this retrospective study. Presence of intraretinal cystoid fluid (IRC) and pigment epithelial detachment (PED), thickness of subretinal fluid (SRF), central macular thickness (CMT), and central macular volume (CMV) were assessed. Results. Subretinal fluid was observed in 29 eyes (45%), IRC in 36 eyes (55%), and PED in 39 eyes (60%). Baseline and final best-corrected visual acuity (BCVA) were 0.69±0.4 and 0.60±0.4 logMAR in the IRC negative group and 1.17±0.5 and 0.97±0.5 logMAR in the IRC positive group. BCVA was lower in IRC positive group (baseline p=0.001 and final=0.003); however, marked improvement was detected in both groups. Anatomic improvement and increased visual acuity were observed in groups with and without PED, IRC, and SRF. An inverse correlation was detected between pre-treatment CMT, IRC and post-treatment IRC, and final BCVA. Conclusion. Significant visual and anatomic improvement was observed after one-year of ranibizumab treatment regardless of fluid configuration. However, the presence of IRC was observed to be associated with worse visual acuity. Baseline retinal fluid configuration may have prognostic effects on functional success in patients treated with ranibizumab for wet AMD. Abbreviations. AMD = Age-related macular degeneration, VEGF = Vascular endothelial growth factor, IRC = intraretinal cystoid fluid, PED = pigment epithelial detachment, SRF = subretinal fluid, SD-OCT = spectral-domain ocular coherence tomography, IVR = intravitreal ranibizumab, BCVA = best-corrected visual acuity, FFA = fundus fluorescein angiography, CMT = central macular thickness, CMV = central macular volume
Near-Zero-Cost Differentially Private Deep Learning with Teacher Ensembles

Ensuring the privacy of sensitive data used to train modern machine learning models is of paramount importance in many areas of practice. One approach to study these concerns is through the lens of differential privacy. In this framework, privacy guarantees are generally obtained by perturbing models in such a way that specifics of data used to train the model are made ambiguous. A particular instance of this approach is through a “teacher-student” model, wherein the teacher, who owns the sensitive data, provides the student with useful, but noisy, information, hopefully allowing the student model to perform well on a given task without access to particular features of the sensitive data. Because stronger privacy guarantees generally involve more significant noising on the part of the teacher, deploying existing frameworks fundamentally involves a trade-off between utility and privacy guarantee. One of the most important techniques used in previous work involves an ensemble of teacher models, which return information to a student based on a noisy voting procedure. In this work, we propose a novel voting mechanism, which we call an Immutable Noisy ArgMax, that, under certain conditions, can bear very large random noising from the teacher without affecting the useful information transferred to the student. Our mechanisms improve over the state-of-the-art methods on all measures, and scale to larger tasks with both higher utility and stronger privacy ( ≈ 0).
Ocular Surface Disease with BAK preserved Travoprost and Polyquaternium 1(Polyquad) preserved Travoprost

Introduction. The topical medications containing benzalkonium chloride (BAK) as preservative is known to induce corneal toxicity and ocular surface disease (OSD) in glaucoma patients. Newer preservatives like SofZia or polyquaternium-1 (Polyquad) have been developed to replace BAK in many medications. The present study aimed at comparing the OSD in glaucoma patients receiving BAK preserved travoprost versus travoprost with polyquad as preservative and controls not receiving any medications. Methods. This prospective, controlled, observational study was conducted on patients of primary open angle glaucoma (POAG) on medications for more than 6 months. The first group comprised of 40 patients receiving BAK preserved travoprost, the second group included 40 patients receiving polyquad preserved travoprost and 30 of control group not receiving any medical treatment. Ocular Surface Disease Index (OSDI) scores using Ocular Surface Disease Index (OSDI) Questionnaire were assessed and compared in all subjects. Results. The mean OSDI score was 29.09 ± 13.45 in BAK group, 12.4 ± 5.085 in polyquad group and 10.93 ± 7.36 in controls. The mean difference in OSDI scores between BAK and polyquad group 16.63 (p < 0.05) and between the BAK and control group was 18.96 (p < 0.05). The mean difference in OSDI scores between the polyquad and control group was 1.53 (p > 0.05). The mean IOP in the BAK group was 19.2 ± 3.5 and in polyquad group was 20.1 ± 4.2. The IOP measured at 12 months of treatment was 13.2 ± 2.1 in BAK group and 12.8 ± 3.3 in polyquad group. The IOP measured at baseline and 12 months showed statistically significant difference in both the groups (p <o.oo1, p=o.ooo, respectively). Conclusions. OSDI scores revealed significantly lesser symptoms in polyquad preserved travoprost when compared to BAK preserved travoprost. The OSDI scores in polyquad group were also comparable to the control group. Hence, for long term glaucoma management polyquad containing travoprost should be preferred over the BAK preserved travoprost.
Using morphometric traits for live body weight estimation and multivariate analysis in Central Highland and Woyto-Guji Goat Breeds, Ethiopia

The study was conducted to differentiate the Woyto-Guji and Central Highland goat breeds of Ethiopia and derive the most accurate linear regression equation for live body weight prediction. Morphological measurements were taken on randomly selected 531 adult female goats (263 from Woyto-Guji and 268 from Central Highland). Positive and highly significant (P<0.001) correlations were observed between body weight and most independent body measurement variables in both breeds. The highest relationship between chest girth and body weight were illustrated in both breeds (r=0.85 for Woyto-Guji and r=0.82 for Central Highland). The multiple regressions found five parameters to be significant (P<0.05) for Woyto-Guji (chest girth, body length, pelvic width, chest width and ramp length) and Central Highland (chest girth, body length, ramp length, horn and ear length) with R2 values of 84% and 79%, respectively. Body weight, body length, height at wither, chest width, ramp length, pelvic width, horn length and ear length had a significant (P<0.15) discriminating power on the breeds. Nearest neighbor discriminating function analysis shows that 93.23% of Woyto-Guji and 92.96% of Central Highland breeds were classified into their source population. The morphological variations obtained in this study should be consolidated with more evidence drawn from genetic analysis. Key words: Central Highland, goat, multivariate, morphometric traits, Woyto-Guji.
Resource-allocation specialization, market-recognition specialization and audit fees : evidence from the Chinese audit market

Existing literature on audit industry specialization in Anglo-American countries often measures industry specialization using firms’ market share in specific industries from market recognition perspective. This paper contributes to the audit industry specialization research by distinguishing between market recognition specialization and resource allocation specialization, and tests their different effects on audit fees in the Chinese audit market. The results support the hypotheses that market recognition specialization is likely to lead to higher audit fees in the whole audit market, resource allocation specialization is likely to lead to lower audit fees in ‘top–ten’ audit firms, and there is likely to be no effect of resource allocation specialization on audit fees in ‘non–top–ten’ audit firms. The findings have implications for the regulators both in China and globally in designing strategies to enhance the functioning of audit firms. Importantly, the findings suggest that economic, political and social contexts of a country cannot be ignored in examining audit industry specialization
Revisiting the Reverse Sural Artery Flap in Distal Lower Extremity Reconstruction: A Systematic Review and Risk Analysis.

BACKGROUND The reverse sural artery flap (RSAF) is a popular option for patients with distal lower extremity defects who are not ideal candidates for free flap reconstruction. This is the first systematic review and pooled analysis of surgical characteristics, risk factors, and outcomes of the RSAF. METHODS A systematic literature review was conducted. All studies reporting on patients undergoing RSAF reconstruction and their outcomes were included. Outcomes were pooled and analyzed using Fisher exact or χ test. RESULTS Forty-three studies (479 patients, 481 flaps) were analyzed. The majority of patients were male (70.3%), and average ± SD age was 46.9 ± 16.7 years. Rates of smoking, diabetes mellitus (DM), and peripheral vascular disease (PVD) were 34.6%, 35.4%, and 12.3%, respectively. Defect etiologies were largely traumatic (60.4%). The most common defect location was the heel (40.8%). Flap modifications were reported in 123 flaps (25.6%). The most common modification was adipofascial extension (20.3%). Overall, the partial and total flap loss rates were 15.4% and 3.1%, respectively. Partial flap loss was significantly increased in smokers (28.9% vs 12.2% in nonsmokers, P = 0.0195). Technical modifications decreased the odds of partial necrosis by almost 3-fold compared with traditional RSAF reconstruction (7.2% vs 17.9%; odds ratio, 2.8 [1.4-5.8]; P = 0.0035). Patient age, DM, and PVD were not significantly associated with flap loss. CONCLUSIONS The RSAF remains a safe salvage option for patients with DM or PVD but should be used with caution in smokers. Technical modifications to minimize pedicle compression significantly reduce rates of partial necrosis.
Corrosion Control by Aminoacetic acid(Glycine) an Overview

Glycine has the ability to control corrosion of various metals such as carbon steel, zinc, tin and copper. It behaves as an inhibitor in acid medium, neutral medium and in desecrated carbonated solution. Various techniques like weight loss method, polarization study and AC impedence spectra have been used to evaluate the corrosion inhibition efficiency of glycine. The protective film has been analysed by IR spectroscopy, atomic force microscopy, scanning electron microscopy and auger electron spectroscopy. Adsorption of glycine on metal surface obeys Langmuir, Flory- Huggins or Temkin isotherm, depending on nature of metal and corrosive environment. Polarization study reveals that glycine can function as anodic or cathodic or mixed type of inhibitor depending on nature of metal and corrosive environment.
Impact of an incentive-based prenatal smoking cessation program for low-income women in Colorado.

OBJECTIVE To assess birth outcomes and cost-savings of an incentive-based prenatal smoking cessation program targeting low-income women in Colorado. DESIGN Prospective observational cohort with nonequivalent population control groups. SAMPLE Program participants (n = 2,231) linked to the birth certificate to ascertain birth outcomes compared to two reference populations from Pregnancy Risk Assessment Monitoring System (PRAMS) and Colorado live births based on the birth certificate. MEASUREMENTS Tobacco cessation metrics in the third trimester of pregnancy, neonatal low birth weight (<2,500 g), preterm birth (birth at <37 weeks gestation), neonatal intensive care unit (NICU) admission and maternal gestational hypertension. Cost-savings and return on investment (ROI) were projected using average Medicaid reimbursement. RESULTS Infants of mothers enrolled in the program had a lower risk of low birthweight (RR = 0.86; 95% CI = 0.75, 0.97), preterm birth (PTB) (RR = 0.76; 95% CI = 0.65, 0.88) and neonatal intensive care unit (NICU) admission (RR = 0.76; 95% CI = 0.66, 0.88) compared to the birth certificate population, corresponding to a ROI of $7.73 and an individual cost savings of $6,040. Compared to PRAMS, infants of enrolled mothers had a lower risk of PTB (RR = 0.72; 95% CI = 0.53, 0.99) and NICU admission (RR = 0.45; 95% CI = 0.32, 0.62), corresponding to an ROI of $2.79 and an individual cost savings of $2,182. CONCLUSIONS We found a reduction of adverse birth outcomes, and cost savings.
THE EFFECTS OF SCIENCE BASED VERSUS MARKET BASED PARTNERS ON DIFFERENT TYPES OF INNOVATION PERFORMANCE

Accessing external knowledge is beneficial for firms’ innovation performance. External knowledge brings novelty and diversity to the firm which is less likely to be accessed internally. Therefore, firms interact with different partners inside the innovation process, such as customers, competitors, suppliers and universities. These partners can be classified as science-based and market-based partners. Science-based ones are associated with universities and research institutes whereas market-based partners are linked to customers and suppliers. These two partners become essential for firms in terms of accessing different kinds of knowledge. In particular, these partners are important for producing different kinds of innovation whether it is radical or incremental. Radical innovation requires to access novel and basic knowledge while incremental innovation requires to access market and applied knowledge since it improves and extends existing knowledge. Although previous studies have investigated the relationship between partner types and innovation performance, there is inconsistency in the literature explaining the impact of different partner types on different types of innovation performance. Hence, this study reviews the literature by discussing the characteristics of science-based and market-based partners and their effects on different types of innovation performance, such as radical and incremental. In doing so, this paper suggests two propositions that need to be further investigated by future studies. First proposition suggests that there is a link between science-based partners and radical innovation whereas second proposition suggests that there is a link between market-based partners and incremental innovation.