Miracle-dz/UniFAR-FTUs huggingface dataset:
Estimating fish abundance and biomass from eDNA concentrations: variability among capture methods and environmental conditions

Environmental DNA (eDNA) promises to ease noninvasive quantification of fish biomass or abundance, but its integration within conservation and fisheries management is currently limited by a lack of understanding of the influence of eDNA collection method and environmental conditions on eDNA concentrations in water samples. Water temperature is known to influence the metabolism of fish and consequently could strongly affect eDNA release rate. As water temperature varies in temperate regions (both seasonally and geographically), the unknown effect of water temperature on eDNA concentrations poses practical limitations on quantifying fish populations using eDNA from water samples. This study aimed to clarify how water temperature and the eDNA capture method alter the relationships between eDNA concentration and fish abundance/biomass. Water samples (1 L) were collected from 30 aquaria including triplicate of 0, 5, 10, 15 and 20 Brook Charr specimens at two different temperatures (7 °C and 14 °C). Water samples were filtered with five different types of filters. The eDNA concentration obtained by quantitative PCR (qPCR) varied significantly with fish abundance and biomass and types of filters (mixed‐design ANOVA, P < 0.001). Results also show that fish released more eDNA in warm water than in cold water and that eDNA concentration better reflects fish abundance/biomass at high temperature. From a technical standpoint, higher levels of eDNA were captured with glass fibre (GF) filters than with mixed cellulose ester (MCE) filters and support the importance of adequate filters to quantify fish abundance based on the eDNA method. This study supports the importance of including water temperature in fish abundance/biomass prediction models based on eDNA.
Breast-feeding status alters the effect of vitamin A treatment during acute diarrhea in children.

Vitamin A administration in children reduces the incidence of severe diarrhea during the subsequent few months. We therefore examined the effect of treatment with vitamin A during acute diarrhea on the episode duration and severity. In a double-blind controlled field trial, 900 children 1 to 5 y of age with acute diarrhea of < or = 7 d duration were randomly assigned to receive vitamin A (60 mg) or a placebo. Children were followed up at home every alternate day until they recovered from the diarrheal episode. In all study children, those treated with vitamin A had a significantly lower risk of persistent diarrhea [odds ratio (OR) 0.30, 95% confidence interval (CI) 0.07-0.97], but there was no effect on the mean diarrheal duration or the mean stool frequency, in the subgroup of children who were not breast-fed, the mean diarrheal duration [ratio of geometric means (GM) 0.84, 95% CI 0.72-0.97], mean number of stools passed after the intervention (ratio of GM 0.73, 95% CI 0.56-0.95), the proportion of episodes lasting > or = 14 d (P = 0.002) and the percentage of children who passed watery stools on any study day (OR 0.40, 95% CI 0.21-0.77) were significantly lower in those treated with vitamin A. We conclude that administration of vitamin A during acute diarrhea may reduce the severity of the episode and the risk of persistent diarrhea in non-breast-fed children. Similar benefit was not seen in breast-fed children.
Advance Care Planning in an Accountable Care Organization Is Associated with Increased Advanced Directive Documentation and Decreased Costs

Abstract Background: Advance care planning (ACP) documents patient wishes and increases awareness of palliative care options. Objective: To study the association of outpatient ACP with advanced directive documentation, utilization, and costs of care. Design: This was a case–control study of cases with ACP who died matched 1:1 with controls. We used 12 months of data pre-ACP/prematch and predeath. We compared rates of documentation with logit model regression and conducted a difference-in-difference analysis using generalized linear models for utilization and costs. Setting/subjects: Medicare beneficiaries attributed to a large rural-suburban-small metro multisite accountable care organization from January 2013 to April 2016, with cross reference to ACP facilitator logs to find cases. Measurements: The presence of advance directive forms was verified by chart review. Cost analysis included all utilization and costs billed to Medicare. Results: We matched 325 cases and 325 controls (51.1% female and 48.9% male, mean age 81). 320/325 (98.5%) ACP versus 243/325 (74.8%) of controls had a Healthcare Power of Attorney (odds ratio [OR] 21.6, 95% CI 8.6–54.1) and 172/325(52.9%) ACP versus 145/325 (44.6%) controls had Practitioner Orders for Life Sustaining Treatment (OR 1.40, 95% CI 1.02–1.90) post-ACP/postmatch. Adjusted results showed ACP cases had fewer inpatient admissions (−0.37 admissions, 95% CI −0.66 to −0.08), and inpatient days (−3.66 days, 95% CI −6.23 to −1.09), with no differences in hospice, hospice days, skilled nursing facility use, home health use, 30-day readmissions, or emergency department visits. Adjusted costs were $9,500 lower in the ACP group (95% CI −$16,207 to −$2,793). Conclusions: ACP increases documentation and was associated with a reduction in overall costs driven primarily by a reduction in inpatient utilization. Our data set was limited by small numbers of minorities and cancer patients.
Waist circumference and obesity-associated risk factors among whites in the third National Health and Nutrition Examination Survey: clinical action thresholds.

BACKGROUND Waist circumference (WC) is strongly linked to obesity-associated risks. However, currently proposed WC risk thresholds are not based on associations with obesity-related risk factors but rather with body mass index (BMI; in kg/m(2)). OBJECTIVE The objective was to determine the relations of WC to obesity-associated risk factors in a representative sample of US whites and to derive comparable risk thresholds for WC and BMI. DESIGN Data on 9019 white participants of the third National Health and Nutrition Examination Survey were divided into 2 groups according to the presence of >or= 1 of 4 obesity-associated risk factors: low HDL cholesterol, high LDL cholesterol, high blood pressure, and high glucose. Odds ratio (OR) equations were derived from logistic regression models for WC and BMI with the use of the 25th percentile in the study population as the reference. Receiver operating characteristic curves for identifying risk factors were computed for WC and BMI. RESULTS At BMIs of 25 and 30, ORs were 1.19 (95% CI: 1.06, 1.35) and 2.37 (95% CI: 1.33, 4.22) for men and 1.56 (95% CI: 1.29, 1.91) and 3.16 (95% CI: 1.94, 5.28) for women, respectively. The corresponding ORs for WC were at 90 and 100 cm for men and at 83 and 93 cm for women. Minima on the receiver operating characteristic curves for men were at 96 cm for WC and at 26 for BMI and for women were at 86 cm for WC and 25 for BMI. CONCLUSION WC is more closely linked to cardiovascular disease risk factors than is BMI.
THE TOURIST EXPERIENCE

This paper identifies four noteworthy conceptual developments in the study of the tourist experience: a turn from differentiation to de-differentiation of everyday life and touristic experiences; a shift from generalizing to pluralizing conceptualizations; a transformed focus from the toured objects to the tourist subjective negotiation of meanings; and a movement from contradictory and decisive statements to relative and complementary interpretations. Thus, it is suggested that contemporary conceptualizations of this subject correspond to the so-called ‘‘postmodernist’’ theorizing in the social sciences. This turn in the literature is evaluated while addressing past and future research.
Impact of First Line Antiretroviral Therapy on Clinical Outcomes Among HIV-1 Infected Adults Attending One of the Largest HIV Care and Treatment Program in Nairobi Kenya

Objective: This study evaluated the immunologic (CD4 cell count), virological (HIV RNA viral load), hepatic (alanine and aspartate aminotransferase - ALT and AST), renal (creatinine) and hematological (hemoglobin -HB, White Blood Cell - WBC, Lymphocytes - LYM and platelets - PLT) response to a six months ART treatment among HIV participants in Nairobi Kenya. Methods: Blood samples were obtained from 599 consenting HIV infected participants receiving HIV treatment in Nairobi. CD4 cell counts were measured using flow cytometer and viral load determined using real-time polymerase chain reaction. The blood hematology, liver and kidney function tests were also measured. One-way ANOVA and Linear regression analysis were conducted. Results: The median age at ART initiation was 41 years (IQR 35-47 years). The majority of participants (60.3%) were female and 56.1% started on regimens with 2 NRTIs and efavirenz based NNRTI. About 40% of the participants were failing treatment 6 month post ART initiation. The CD4 count significantly increased at the 6-month post ART initiation (301.7 ± 199.4 to 329.4 ± 305.8; P 5 times the upper limit of normal - ULN) and renal abnormalities (elevated serum creatinine levels) were all high at month 6 compared to baseline; ALT (2.5 to 10.5%), AST (5.3 to 23.4%) and creatinine (63.4 to 68.84%). Fewer participants at month 6 had anemia (29.4% verses 56.4%), leucopenia (42.4% vs. 46.9%) and thrombocytopenia (6.5% vs. 84.1%) compared to baseline. In multivariable models, baseline levels of this parameter, ART regimen and duration with HIV at ART initiation were the most important determinant of month 6 levels. Conclusion: These data demonstrate sustained immunologic/virologic response to ART among participants remaining on therapy. Anemia, leucopenia and thrombocytopenia were minimized with marginal hepatotoxicity and renal impairment seen. Interventions leading to earlier HIV diagnosis and initiation of ART could substantially improve patient outcomes in Kenya.
The use of molecular tools in invasion biology: an emphasis on freshwater ecosystems

The potential uses of molecular tools to address issues in invasion biology are reviewed, including the early detection of novel and cryptic non-native species, the identification of introduction pathways and vectors, the understanding of the drivers in successful invasions and the assessment of effective population sizes during the establishment of new populations. The usefulness of molecular tools to assess the ecological and evolutionary consequences of biological invasions is discussed using recent examples in which the latest techniques in molecular ecology (e.g. high-throughput sequencing, DNA barcoding) are employed. This review highlights the versatility of molecular tools to provide information and insights on the ecological and evolutionary causes and consequences of biological invasions at different levels of biological organisation (i.e. gene, individual, population, community and ecosystem).
Age-sex distribution of patients with high-sensitivity troponin T levels below the 99th percentile

Background Recently, very low concentrations of high-sensitivity cardiac troponin T (hs-cTnT), below the 99th percentile, have been used to immediately exclude acute myocardial infarction in certain patients without taking their age and sex into consideration. Results The hs-cTnT values below the 99th percentile (≤ 14 ng/L) were higher in men (p = 0.000) and significantly increased with age (p = 0.000) among both men and women. In addition, hs-cTnT was positively associated with age (r = 0.459, p = 0.000), myoglobin (r = 0.392, p = 0.000), and creatine kinase-MB (r = 0.133, p = 0.000). Moreover, males were younger (p = 0.001) and had higher myoglobin (p = 0.000) and creatine kinase-MB (p = 0.000) concentrations than females. Materials and Methods A total of 5585 consecutive subjects who presented with non-traumatic chest pain/discomfort to the inpatient, outpatient, or emergency department and who underwent high-sensitivity troponin T, myoglobin and creatine kinase-MB testing at presentation, with hs-cTnT below the 99thpercentile (≤ 14 ng/L), were eligible for enrollment. Conclusions We suggest that patients’ age, sex and levels of myocardial injury biomarkers should be taken into consideration when ruling out acute myocardial infarction and/or adverse prognostic implications in patients who have very low hs-cTnT concentrations.
Radiological Features of Scoliosis in Chiari I Malformation Without Syringomyelia

Study Design. A retrospective radiographic analysis. Objective. The aim of this study was to investigate the scoliosis curve patterns/features and magnetic resonance imaging (MRI) tonsillar ectopia characteristics in Chiari I malformation without syringomyelia (CMI-only). Summary of Background Data. The development of scoliosis associated with a CMI typically has been ascribed to the presence of syringomyelia. However, a subset of CMI patients with scoliosis may not have a concomitant syrinx. Scoliosis in these patients has been very poorly documented in the literature. Methods. A retrospective study was conducted on patients with a scoliosis secondary to CMI-only. The curve direction, curve pattern/features, and side of the dominant tonsillar ectopia were recorded and assessed quantitatively. On the basis of the measurement results, associations between the scoliosis curve patterns/features and MRI tonsillar ectopia characteristics were analyzed. Results. A total of 26 patients, consisting of seven males and 19 females with an average age of 15.4 years, were included in the current study. In 19 patients with asymmetrically displaced tonsils, the concordance between the dominant side of the asymmetrically displaced tonsils and curve direction was 78.9%. A statistically significant association was found between the dominant side of the tonsillar ectopia and the convex side of scoliosis according to Fisher exact test (P = 0.045). In addition, it was noted that there was a high incidence (52.9%) of atypical curve patterns in CMI-only patients. A significantly high incidence of atypical features with a superior shift of either the apical or the end vertebrae was found in 85.7% of thoracic curves and 40% of lumbar curves. Conclusion. Scoliosis associated with CMI-only was found to have atypical curve patterns in all cases, and the direction of scoliosis was highly consistent with the dominant side of asymmetrically tonsillar herniation. These findings should be considered as an argument in favor of a nonidiopathic etiology and lead to more evidence that simple tonsillar impaction can provide enough impetus to produce or exaggerate scoliotic curvature. Level of Evidence: 3
Natural laNguage geNeratioN, ParaPhrasiNg aNd summarizatioN of user reviews with recurreNt Neural Networks

Multi-Document summarization and sentence generation are important challenges in natural language processing. This paper presents recurrent neural network (RNN) architecture capable of producing abstractive document summaries, as well as generating novel paraphrases of input sentences in the same language. We demonstrate practical application of our system on the task of multiple consumer reviews summarization.
Smoothing polyhedra using trimmed bicubic patches Jorg Peters

Several efficient constructions of smooth surfaces following the outlines of a polyhedral mesh are based on three-sided patches. To demonstrate that these constructions arc compatible with existing software based on tensor-product patches, the particular scheme in [3] is expressed in terms of linearly-trimmed bicubic patches. Explicit formulas relating the coefficients of the patches to the vertices of an arbitrary input polyhedron are given. Four of these patches can be grouped together into a NURBS surface.
Mechanics of adhesion in MEMS—a review

A review is presented of the mechanics of microscale adhesion in microelectromechanical systems (MEMS). Some governing dimensionless numbers such as Tabor number, adhesion parameter and peel number for microscale elastic adhesion contact are discussed in detail. The peel number is modified for the elastic contact between a rough surface in contact with a smooth plane. Roughness ratio is introduced to characterize the relative importance of surface roughness for microscale adhesion contact, and three kinds of asperity height distributions are discussed: Gaussian, fractal, and exponential distributions. Both Gaussian and exponential distributions are found to be special cases of fractal distribution. Casimir force induced adhesion in MEMS, and adhesion of carbon nanotubes to a substrate are also discussed. Finally, microscale plastic adhesion contact theory is briefly reviewed, and it is found that the dimensionless number, plasticity index of various forms, can be expressed by the roughness ratio.
The KDM5 family is required for activation of pro-proliferative cell cycle genes during adipocyte differentiation

Abstract The KDM5 family of histone demethylases removes the H3K4 tri-methylation (H3K4me3) mark frequently found at promoter regions of actively transcribed genes and is therefore generally considered to contribute to corepression. In this study, we show that knockdown (KD) of all expressed members of the KDM5 family in white and brown preadipocytes leads to deregulated gene expression and blocks differentiation to mature adipocytes. KDM5 KD leads to a considerable increase in H3K4me3 at promoter regions; however, these changes in H3K4me3 have a limited effect on gene expression per se. By contrast, genome-wide analyses demonstrate that KDM5A is strongly enriched at KDM5-activated promoters, which generally have high levels of H3K4me3 and are associated with highly expressed genes. We show that KDM5-activated genes include a large set of cell cycle regulators and that the KDM5s are necessary for mitotic clonal expansion in 3T3-L1 cells, indicating that KDM5 KD may interfere with differentiation in part by impairing proliferation. Notably, the demethylase activity of KDM5A is required for activation of at least a subset of pro-proliferative cell cycle genes. In conclusion, the KDM5 family acts as dual modulators of gene expression in preadipocytes and is required for early stage differentiation and activation of pro-proliferative cell cycle genes.
Association of COL1A1 rs1800012 polymorphism with musculoskeletal degenerative diseases: a meta-analysis

It has been reported that the single nucleotide polymorphism (SNP) rs1800012 in COL1A1 gene might be linked to the susceptibility of musculoskeletal degenerative diseases, such as osteoarthritis (OA) and intervertebral disc degeneration (IVDD). However, the data from different studies is contradictory. Here we aimed to comprehensively summarize and clarify the relationship between the SNP and musculoskeletal degenerative diseases. Seven eligible studies including 1339 cases and 5406 controls were screened out from PubMed, Web Of Science and Cochrane library databases. Significant association was identified in sub group analysis of IVDD in homozygote model (GG versus TT: OR = 0.33, 95% CI 0.14–0.78, P = 0.012), heterozygote model (GT versus TT: OR = 0.29, 95% CI 0.11–0.72, P = 0.008) and dominant model (GG/GT versus TT: OR = 0.31, 95% CI 0.13–0.74, P = 0.008). Additionally, significant relationship was also found in sub group analysis of severe degree of IVDD in homozygote model (GG versus TT: OR = 0.37, 95% CI 0.15–0.91, P = 0.031), heterozygote model (GT versus TT: OR = 0.33, 95% CI 0.13–0.87,P = 0.024) and dominant model (GG/GT versus TT: OR = 0.36, 95% CI 0.14–0.88, P = 0.025). Although no significance was observed, there is a trend that the more G allele at COL1A1 rs1800012 site, the less possibility of IVDD and severe IVDD would happen. Our results indicate that COL1A1 rs1800012 polymorphism associates with the susceptibility of IVDD. However, this polymorphism may not be associated with OA risk.
Endogenous microbial contamination of melons (Cucumis melo) from international trade: an underestimated risk for the consumer?

BACKGROUND Fruits and vegetables have increasingly been related to foodborne outbreaks. Besides surface contamination, a possible internalization of microorganisms into edible parts of plants during growth has already been observed. To examine an actual risk for the consumer, microbial contamination of the rind and pulp of 147 muskmelons from international trade was assessed using cultural and biochemical methods, polymerase chain reaction and matrix-assisted laser desorption/ionization-time of flight mass spectrometry. RESULTS One hundred percent of the rind samples [3.69-8.92 log colony forming units (CFU) g-1 ] and 89.8% of the pulp samples (maximum load 3.66 log CFU g-1 ) were microbiologically contaminated. Among the 432 pulp isolates, opportunistic and potentially pathogenic bacteria were identified, mainly Staphylococcus spp. (48.9%), Clostridium spp. (42.9%) and Enterobacteriaceae (27.9%). Salmonella spp. , Escherichia coli and isolates of the Bacillus cereus group were found on the rind (1.4%, 0.7% and 42.9%, respectively) and in the pulp (0.7%, 1.4% and 4.7%). Clostridium perfringens was isolated from the rind of seven melons. CONCLUSION The present study revealed a regularly occurring internal contamination of melons. Possible health risks for consumers because of an occurrence of microorganisms in melon pulp should be considered in future food safety assessments. © 2018 Society of Chemical Industry.
A Stream Database Server for Sensor Applications

We present a framework for stream data processing that incorporates a stream database se11Jer as a fundamental component. The server operates as the stream control iflterjace between arrays of distributed data stream sources and end-user clients thaJ access and analyze the streams. The underlying framework provides novel stream managemem and query processing mechanisms to support the online acquisition, management, storage, non-blocking query. and imegration ofdata streams for distributed muLti-sensor networks. In this paper, we define OUT stream model and stream representation for the stream database, and we describe the functionality alld implementation of key components of the stream processing framework, including the query processing interface for source streams, the stream manager, the stream buffer manager, non-blocking query execution, and a new class ofjoin aLgorithms for joining multipLe data streams constrained by a sliding time window. We conduct experiments using real data streams to evaluate the performance of the new aLgoritluns against traditional stream join aLgorithms. The experiments show significant performance improvements and aLso demonstrate the flexibility of our system ;n handling data streams. A muLti-sensor network appLicatioll for the intelligent detection of lwzardous materials ;s presented to illustrate the capabilities ofourframework. Index tenns: Multi-sensor processing framework, Stream database, Stream manager, Stream query processing, Stream scan, Window-join.
Latent VariabLe Hybrids Overview of Old and new Models

The conference that this book builds upon contained many different special topics within the general area of modeling with categorical latent variables, also referred to as mixture modeling. The many different models addressed at that conference and within this volume may overwhelm a newcomer to the field. In fact, however, there are really only a small number of variations on a common theme. This chapter aims to distinguish the different themes, show how they relate to each other, and give some key references for further study. Some new mixture models are also proposed. Table 1.1 gives a summary of different types of latent variable models. An overview discussion of the models of Table 1.1 was presented in Muthén (2002). The entries of the table are types of models, with the rows dividing the models into cross-sectional and longitudinal and the columns dividing models into traditional models with continuous latent variables, models