Miracle-dz/UniFAR-FTUs huggingface dataset:
More affordable and effective noninvasive SNP genotyping using high-throughput amplicon sequencing

Non-invasive genotyping methods have become key elements of wildlife research over the last two decades, but their widespread adoption is limited by high costs, low success rates, and high error rates. The information lost when genotyping success is low may lead to decreased precision in animal population densities which could misguide conservation and management actions. Single nucleotide polymorphisms (SNPs) provide a promising alternative to traditionally used microsatellites as SNPs allow amplification of shorter DNA fragments, are less prone to genotyping errors, and produce results that are easily shared among laboratories. Here, we outline a detailed protocol for cost-effective and accurate noninvasive SNP genotyping using highly multiplexed amplicon sequencing optimized for degraded DNA. We validated this method for individual identification by genotyping 216 scats, 18 hairs and 15 tissues from coyotes (Canis latrans). Our genotyping success rate for scat samples was 93%, and 100% for hair and tissue, representing a substantial increase compared to previous microsatellite-based studies at a cost of under $5 per PCR replicate (excluding labor). The accuracy of the genotypes was further corroborated in that genotypes from scats matching known, GPS-collared coyotes were always located within the territory of the known individual. We also show that different levels of multiplexing produced similar results, but that PCR product cleanup strategies can have substantial effects on genotyping success. By making noninvasive genotyping more affordable, accurate, and efficient, this research may allow for a substantial increase in the use of noninvasive methods to monitor and conserve free-ranging wildlife populations.
Domestic radon exposure and risk of childhood leukemia: A meta-analysis.

PURPOSE This meta-analysis evaluated the potential influence of environmental radon exposure on childhood leukemia. METHODS We searched comprehensive electronic databases from PubMed, EMBASE, and Cochrane Library to identify studies evaluating the association between radon and leukemia. RESULTS Ten eligible studies published from 1995 to 2014 were enrolled. Of these 10 studies, 8 were case-control studies (involving 10803 cases and 16202 controls) and 2 were cohort studies (involving 1,428 cases). Overall results as odds ratio (OR) with the corresponding 95% confidence intervals (95%CI) for case-control studies and fully adjusted hazard ratio (HR) with corresponding 95%CI for cohort studies were identified. A positive but weak association was found between radon exposure and childhood leukemia in case-control studies (summary OR 1.22, 95%CI 1.01-1.42) rather than cohort studies (summary HR 0.97, 95%CI 0.81-1.15). Heterogeneity or publication bias was not observed. Moreover, overall ORs were not changed by removing any single study, suggesting the stability and reliability of conclusions. CONCLUSIONS Future prospective studies with well-controlled confounders are needed to verify the conclusion.
The Cascade of Care From Routine Point-of-Care HIV Testing at Birth: Results From an 18-Months Pilot Program in Eswatini

Background: HIV testing at birth may improve early treatment, but concerns remain about feasibility and retention of infants in care. In 2017, point-of-care (POC) HIV birth testing was introduced into routine care at 3 high-volume maternity health facilities in Eswatini. Methods: POC birth testing was offered to HIV-exposed infants (HEI) born at, or presenting to, 3 maternities within 3 days of birth. Data were collected from a project-specific EID test request form and routine registers on all tests conducted from August 1, 2017 to November 30, 2018, including retesting at 6–8 weeks for infants testing negative at birth and six-month retention in HIV care and viral load suppression among infants testing HIV-positive at birth. Results: Of 4322 eligible HEI, 3311 (76.6%) were tested. Twenty-six HIV-infected infants were identified (positivity rate 0.8%) and 25 initiated on antiretroviral therapy (ART) (96.1%). The median time from sample collection to ART initiation was 20.50 days (IQR 14–45). Twenty-one (84%) ART-initiated infants were on ART at 6 months after initiation. Nineteen infants (90.5%) had viral load test information at 6 months and 16 (84.2%) were virally suppressed. Of 3126 HEI testing negative at birth, 3004 (96.1%) were linked to laboratory databases and 2744 (91.3%) were retested at 6–8 weeks, with 9 (0.3%) additional infants testing HIV-positive. Conclusions: Uptake of POC birth testing was high in Eswatini with low HIV positivity. Almost all infants identified HIV-positive at birth were initiated on ART, with high retention in care and viral suppression. Birth testing did not seem to significantly reduce subsequent 6–8-week testing.
Use of Fitbit Technology Does Not Impact Health Biometrics in a Community of Older Adults.

Introduction: To evaluate if the offering of Fitbit technology led to changes in cardiovascular health metrics in a cohort of older adults. Methods: A retrospective cohort study was developed in two community-embedded health monitoring sites, located in aggregate housing communities for older adults in Westchester County, NY. Participants included older adults (55 years or older) enrolled in the Telehealth Intervention Programs for Seniors (TIPS) initiative, a community-embedded remote patient monitoring initiative. Weekly blood pressure, heart rate, weight, and blood oxygenation were taken on all participants. For participants who accepted a Fitbit Zip device, a weekly step count was also collected. Results: Ninety-four TIPS participants were offered Fitbit technology. Thirty participants accepted the technology and used it for a minimum of 6 months. No significant differences in any of the regularly acquired biometrics were noted between Fitbit users and non-Fitbit users. Across all participants, regardless of Fitbit use, there was a significant decrease in systolic blood pressure (SBP) over time. Conclusions: Neither Fitbit Zip ownership or compliance to Fitbit Zip usage influenced any of the biometrics taken as part of the TIPS. However, participation in the TIPS initiative may have an overall positive effect on SBP in older adults.
Trace element and vitamin deficiency: quantum medicine or essential prescription?

PURPOSE OF REVIEW In critical care, micronutrients remain perceived as 'quantum' part, that is, a little pertinent component of therapy. Some micronutrients have attracted more attention because of their antioxidant properties. During the last decade, some large size trials have tested their therapeutic potential, generally as 'single high-dose micronutrient intervention', with variable success. This review aims at taking stock of most recent. RECENT FINDINGS Micronutrient blood levels are generally low in ICU patients, which has prompted the concept of replenishing or compensating deficits, or even realizing a pharmacological action. Single micronutrient trials have been conducted in large cohorts with selenium (≥1000 μg/day), with limited success but no harm. Other trials have tested high-dose vitamin D (>400 000 IU), with nonconvincing results despite selecting patients with very low blood levels. High-dose vitamin C has been tested in septic shock (+/- thiamine, hydrocortisone) with variable results. A problem encountered in all studies is definition of deficiency based on blood levels as majority of the patients suffer inflammation, which causes redistribution of the micronutrients away from the circulating compartment in the absence of real deficiency. SUMMARY Micronutrients are essential in the ICU. Due to their antioxidant properties and to the high prevalence of low blood concentrations suggestive of deficiency, several large-size RCTs have been conducted with variable success. Further research must clarify the respective importance of deficiency and inflammation.
Water-Stress-Induced Changes in the Pattern of Protein Synthesis in Maize Seedling Mesocotyls: A Comparison with the Effects of Heat Shock

Cut segments from the growing and non-growing regions of 4-d-old maize seedling mesocotyls exhibit reduced protein synthesis when subjected to water-stress imposed directly by incubation in solutions of polyethylene glycol. Growing mesocotyl tissue can recover full protein synthesis upon return to a fully-hydrated condition following stress to -0-5 MPa, while non-growing tissue recovers well from greater stresses (-0-75 to -1-0 MPa), and in lesser time. Using two-dimensional electrophoresis and fluorography of de novo synthesized proteins in vivo it was possible to follow changes in protein synthesis in the non-growing tissue under water-stress and upon subsequent recovery. The synthesis of several proteins was reduced by stress, although that of others intensified. Those proteins exhibiting reduced synthesis under stress were synthesized at control levels (i.e. the same levels as in unstressed tissue) when the stress was relieved. Some proteins whose synthesis was intensified under stress retained this intensification upon return to full hydration. No unique proteins were synthesized in response to water-stress, in contrast to the 'heat-shock' proteins induced when the mesocotyls were subjected to high temperature. Hence water-stress induces quantitative rather than qualitative changes in the pattern of protein synthesis.
Trend analyses of breast cancer incidence and mortality in Vojvodina.

PURPOSE Breast cancer is the most common type of malignant tumor in women and one of the most significant public health problems in the world. The purpose of this work was to determine breast cancer epidemiology in the Autonomous Province of Vojvodina in a 20-year period (1993 to 2012) by determining breast cancer incidence and mortality in female population and analyzing the trend in the specified period. METHODS The research involved the population of women in Vojvodina in the period from 1993 to 2012. Data were obtained from the Register for malignant neoplasms of Vojvodina. Incidence and mortality trends were analyzed by a joinpoint regression analysis. RESULTS A total of 20,242 cases of breast cancer were registered in the observed period. Standardized incidence ratio in 2012 was 71.2/100,000. The trend of incidence increased with an average annual percentage of growth of 2.10. A total 10,062 deaths due to breast cancer were documented. Standardized incidence ratio in 2012 was 28.6/100,000. An increase of mortality rate by 1.70% per year was recorded in the period from 1992 to 2006 and a decline in the mortality rate by 1.56% was noticed afterwards. The highest percentage of deaths due to breast cancer was recorded in a group aged 60-69 years (26.7%).
Study on Essential Derivation in Maize: III. Selection and Evaluation of a Panel of Single Nucleotide Polymorphism Loci for Use in European and North American Germplasm

Pairwise distance data for maize (Zea mays L.) inbred lines generated using sets of single nucleotide polymorphisms (SNPs) selected from a 50k Infinium array were compared with pairwise distances generated using a set of 163 simple sequence repeat (SSR) loci previously identified to help determine essentially derived variety (EDV) status (UPOV, 1991). Final comparisons were made using 26,874 SNPs after discarding SNPs with insufficient data quality or vulnerability to ascertainment bias. Inbred lines developed in the United States or in western Europe that had been previously published to establish SSR-based thresholds provided the means to determine equivalent SNP-based protocols. Use of 3072 SNPs selected to provide even genomic coverage according to genetic and physical maps provided robust, precise, high discrimination among inbred lines with consistent zonal classification with up to 20% missing data. Comparisons of intercepts and slopes for SSR and SNP inbred pairwise distance data translated the 82% SSR green-orange similarity threshold to 91% using SNPs and the 90% SSR orange-red threshold to 95% using SNPs. Information required to conduct analyses using these 3072 SNPS is presented.
A role for mast cells in geographic atrophy

Mast cells (MCs) are the initial responders of innate immunity and their degranulation contribute to various etiologies. While the abundance of MCs in the choroid implies their fundamental importance in the eye, little is known about the significance of MCs and their degranulation in choroid. The cause of geographic atrophy (GA), a progressive dry form of age‐related macular degeneration is elusive and there is currently no therapy for this blinding disorder. Here we demonstrate in both human GA and a rat model for GA, that MC degranulation and MC‐derived tryptase are central to disease progression. Retinal pigment epithelium degeneration followed by retinal and choroidal thinning, characteristic phenotypes of GA, were driven by continuous choroidal MC stimulation and activation in a slow release fashion in the rat. Genetic manipulation of MCs, pharmacological intervention targeting MC degranulation with ketotifen fumarate or inhibition of MC‐derived tryptase with APC 366 prevented all of GA‐like phenotypes following MC degranulation in the rat model. Our results demonstrate the fundamental role of choroidal MC involvement in GA disease etiology, and will provide new opportunities for understanding GA pathology and identifying novel therapies targeting MCs.
Genetic variation of the relict and endangered population of Chamaedaphne calyculata (Ericaceae) in Poland.

Chamaedaphne calyculata is rare and endangerded species of Polish flora. The genetic variation within and among ten polish population of leatherleaf was analysed by ISSR and ISJ markers. The analysis revealed a total of 160 loci with an average of 13.3 bands per primer. We expected a low level of genetic diversity of this narrowly distributed species in Poland, but our results indicate that Ch. calyculata revealed a high level of genetic diversity at species level (P=88.7% of polymorphic loci, AE=1.468, HE=0.290). At the population level, the variation of Ch. calyculata was significantly lower (P=27.6%, AE=1.140, HE=0.098). There was significant correlation between ecological properties (population size; number of flowering ramets) and genetic diversity parameters. Analysis of molecular variance showed that most of variation (62%) in Ch. calyculata occurred among population. Gene flow (Nm) between the ten studied populations, determined based on the GST index, was very low at 0.239. It indicated that the fragmentation and isolation of populations might result from specific evolutionary history of this plant and postglacial recolonization. Additional key words: Chamaedaphne calyculata, genetic diversity, ISSR and ISJ, conservation, rare and endan-
Continuous Glucose Monitoring Decreases Hypoglycemia Avoidance Behaviors, but Not Worry in Parents of Youth With New Onset Type 1 Diabetes

Background: Existing research shows that hypoglycemia fear (HF) is common in parents of children with established type 1 diabetes (T1D). We examined parental HF in the T1D recent-onset period and evaluated whether continuous glucose monitoring (CGM) adoption relates to improved outcomes of parental HF. Methods: In TACKLE-T1D, a prospective study of five- to nine-year olds with recent-onset T1D, parents completed the Hypoglycemia Fear Survey-Parents (HFS-P) at baseline (T1) and 6 (T2) and 12 (T3) months post-baseline. The HFS-P measures worry about hypoglycemia (HFS-Worry score) as well as hypoglycemia avoidance behaviors (HFS-Behavior score). We recorded CGM start dates for youth during the same time period through medical record review. Results: Between T1 and T2, 31 youth (32.3%) initiated CGM therapy, and between T2 and T3, an additional 17 youth (17.7%) began using CGM, leaving 48 youth who never initiated CGM therapy (50%) in the recent-onset period. Parents reported moderate HFS-Worry scores at T1 (32.9 ± 11.9), which increased between T1 and T2 (37.6 ± 11.4, P < .001) and plateaued between T2 and T3 (37.7 ± 12.4, P = .89). In contrast, parental HFS-Behavior scores decreased between T1 (33.1 ± 5.8) and T2 (32.2 ± 6.0, P = .005) and plateaued between T2 and T3 (32.2 ± 6.0, P = .95). Baseline HFS-Behavior and Worry scores were associated with increased adoption of CGM between T1-T2 and T2-T3, respectively. Parents of children initiating CGM therapy between T1 and T2 showed the largest decrease in HFS-Behavior (P = .03). Conclusions: Initiating CGM therapy within the first 12 months of T1D may help reduce parents’ use of hypoglycemia avoidance behaviors, but has little effect on parents’ hypoglycemia worry.
Effect of diets with fruit oils supplements on rumen fermentation parameters, fatty acid composition and methane production in vitro.

Effects of diets supplemented with fruit seed oils on fermentation parameters, ciliated protozoan population, and fatty acid composition of the rumen fluid of dairy cows were studied in 24 h batch cultures. Two diets, one containing lucerne plus wheat meal (60:40%) and the other containing of meadow hay plus wheat meal (60:40%), were supplemented with either grape oil or black currant oil (50 g . kg -1 of dry matter). The control diet contained no oil supplementation. The oils were selected due to high content of linoleic acid (grape oil, 696 g . kg -1 of fatty acids; black currant oil, 586 g . kg -1 of fatty acids). Oil supplements did not affect the basal parameters of rumen fermentation. Interactions between the diets and oil supplements affected rumen methane production and either the total or the majority of rumen ciliate species examined. Although the diets had no effect on the total content of volatile fatty acids, the proportions of n-butyrate and iso-valerate were significantly affected. The concentration of polyunsaturated fatty acids was higher in the meadow hay diet than in the lucerne diet, whereas addition of oils increased polyunsaturated fatty acids content. Black currant oil supplementation proved to be more efficient in enhancing polyunsaturated fatty acids content in rumen fluid when compared to grape oil. In conclusion, both oil supplements considerably decreased methane production when lucerne was used as the diet, what could be the effect of detrimental influence of the type of diet and oil supplement on protozoa population. However, the supplements did not negatively affect other rumen parameters, hence may be considered as valuable supplements in ruminant nutrition.
Seasonal changes in the numerical responses of predators to cyclic vole populations

Theoretical models predict that a delayed density-dependent mortality factor with a time lag of ca 9 months is able to drive 3-5-yr population cycles of northern voles. We studied numerical responses of predators in western Finland during 1986-92, in an area with 3-yr population cycles of voles. Abundances of small mammals were monitored in several farmland areas (each 3 km2) by snap-trapping in April, June, August, and October (only in 1986-90), and the abundances of avian, mammalian, and reptilian predators by visual censuses during trapping occasions. The 3-yr cycle studied was a cycle of Microtus voles (field vole M. agrestis and sibling vole M. rossiaemeridionalis) and their small-sized predators (small mustelids and vole-eating birds of prey). The numerical responses of both migratory avian predators and small mustelids to changes in vole densities were more alike than different. In late summer (August), the time lag in the numerical response of all main predators was short (0-4 months), whereas longer time lags prevailed from spring to early summer. The length of the time lag in spring appeared to be related to the length of the winter, which indicates that strong seasonality may create longer time lags to the numerical response of predators at northern latitudes than at more southern latitudes. Our results suggest that, from spring to early summer, predation by migratory avian predators may act in concordance with mustelid predation to produce the long time lag necessary to drive the 3-yr cycle of voles, whereas almost direct density-dependent predation by all major predators in late summer may dampen spatial variation in prey densities.
Soil microbial populations, activity, and community structure in continuous corn or forage systems under organic or inorganic fertilization in eastern Canada

Succession of soil microbial communities proceeds interdependently with crop development under the control of edaphic, agricultural, and climatic conditions. Soil microbial community composition and activity were characterized in two managed cropping systems (continuous corn or mixed forage) receiving liquid hog manure (LHM) or inorganic fertilization (IF) since 1989. Microbial community composition was determined from patterns of phospholipid fatty acids (PLFA). Soil microbial biomass C, enzymatic activity, and total phospholipids were greater under forage than under continuous corn. Principal component analysis (PCA) revealed a high degree of variation in PLFA composition and microbial community structure due to treatments and time of sampling. The first two PCA axes explained 80 to 90% of the variability on all sampling dates. Two main groups were created along the first component, the first comprising all forage treatments and a second with LHM-treated continuous corn. The IF and control-treated conti.
The Role of Chitosan in Emulsion Formation and Stabilization

This article reviews the basic principles of emulsion formation and stabilization through the electrosteric function of chitosan. Chitosan, which is a polycationic biopolymer, may act as an emulsifier and emulsion stabilizer through adsorption of the protective layer at oil-water interfaces, viscosity enhancement, and interaction with surface-active agents (e.g., surfactants, proteins, and polysaccharides). The interaction of chitosan at droplet interfaces can be associated with flocculation or electrosteric stabilization, depending on the nature and concentration of the chitosan, emulsifier characteristics, and the pH and ionic strength of solution.
Applied use of alternate stable state modeling in restoration ecology.

The concept of alternate stable states is important in ecological theory and models, but the application and implementation of these models have the potential to make significant future advances in the field of patterned landscapes. The bi-stable, ridge and slough landscape is a central feature of Everglades restoration and provides an important opportunity to test stable state theory with multistate transition models. We used these models to estimate environmental parameters associated with state changes (water depths, edaphic factors, etc.) to develop a quantitative method to measure resilience and stability. The multistate model indicates that long-term, local hydrology (15-year mean maximums and 15-year mean amplitude) and edaphic factors control the local scale shifts between ridge and slough states. We show that multistate models can provide hydrologic envelopes for managers, produce a tool to help assess future water management scenarios, and address issues of sustainability, resilience, and restoration for any bi-stable system.