Miracle-dz/UniFAR-FTUs huggingface dataset:
Compound Bias due to Measurement Error When Comparing Regression Coefficients

Multiple regression is often used to compare the importance of two or more predictors. When the predictors being compared are measured with error, the estimated coefficients can be biased and Type I error rates can be inflated. This study explores the impact of measurement error on comparing predictors when one is measured with error, followed by a simulation study to help quantify the bias and Type I error rates for common research situations. Two methods used to adjust for measurement error are demonstrated using a real data example. This study adds to the literature documenting the impact of measurement error on regression modeling, identifying issues particular to the use of multiple regression for comparing predictors, and offers recommendations for researchers conducting such studies.
Death feigning as an adaptive anti-predator behavior: further evidence for its evolution from artificial selection and natural populations.

Death feigning is considered to be an adaptive anti-predator behavior. Previous studies on Tribolium castaneum have shown that prey which death feign have a fitness advantage over those that do not when using a jumping spider as the predator. Whether these effects are repeatable across species or whether they can be seen in nature is, however, unknown. Therefore, the present study involved two experiments: 1) divergent artificial selection for the duration of death feigning using a related species T. freemani as prey and a predatory bug as predator, demonstrating that previous results are repeatable across both prey and predator species, and 2) comparison of the death-feigning duration of T. castaneum populations collected from field sites with and without predatory bugs. In the first experiment, T. freemani adults from established selection regimes with longer durations of death feigning had higher survival rates and longer latency to being preyed on when they were placed with predatory bugs than the adults from regimes selected for shorter durations of death feigning. As a result, the adaptive significance of death-feigning behavior was demonstrated in another prey-predator system. In the second experiment, wild T. castaneum beetles from populations with predators feigned death longer than wild beetles from predator- free populations. Combining the results from these two experiments with those from previous studies provided strong evidence that predators drive the evolution of longer death feigning.
Is the Coyote (Canis latrans) a Potential Seed Disperser for the American Persimmon (Diospyros virginiana)?

Abstract The role of carnivores in seed dispersal has only recently been studied in North American plants. We investigated the potential effectiveness of the Coyote (Canis latrans) as a seed disperser for American Persimmon (Diospyros virginiana; Ebenaceae) and tested the effect of experimental design in gut passage experiments. Germination percentage and rate and vigor of seedlings produced by D. virginiana seeds collected from Coyote scat were compared to seeds removed from or contained in whole fruit in a common garden experiment. Germination percentages for Coyote ingested seeds and whole fruit were nearly the same. Emergence was significantly faster for seedlings produced from ingested seeds compared to those seeds in whole fruit, however the quality of these seedlings was significantly poorer. Seedlings produced by seeds artificially removed from fruits had greater survival than those resulting from seeds ingested by coyotes or contained in intact fruits. Our results suggest that Coyotes can effectively disperse D. virginiana,but whether the positive aspects of dispersal outweigh the negative effects of gut passage remains an open question. Our experimental results indicate that these two species have not coevolved, as expected, since the range of Coyotes has only recently overlapped substantially with that of D. virginiana.
CHIRONOMIDAE (DIPTERA) ASSOCIATED WITH MYRIOPHYLLUM SPICATUM IN OKANAGAN VALLEY LAKES, BRITISH COLUMBIA

Eurasian water milfoil, Myriophyllum spicatum Linnaeus, was introduced into eastern North America late in the nineteenth century. It has spread and developed into a major aquatic weed in many areas of the United states and Canada (Aiken et al. 1979; Reed 1977). In British Columbia, it was first observed in the Vernon Arm of Okanagan Lake in 1970 and had spread to all major 1,akes in the Okanagan Valley by 1976 (Newroth 1979).
Etiology of Prelingual Hearing Loss in the Universal Newborn Hearing Screening Era: A Scoping Review

Objective To conduct a scoping review on etiologic investigation of prelingual hearing loss among children <2 years of age in the era of universal newborn hearing screening (UNHS). Data Sources PubMed, Embase, PsycInfo, CINAHL, and Cochrane Library databases. Review Methods We searched for articles published from January 1, 1998, to February 19, 2020. We reviewed studies that (1) included children identified with either congenital or delayed-onset hearing loss before 2 years of age among cohorts who had undergone UNHS and (2) investigated ≥1 etiologies of hearing loss. We defined hearing loss as congenital when confirmed after UNHS failure and as delayed onset when diagnosed after ≥1 assessments with normal hearing. Results Among 2069 unique citations, 115 studies met criteria for full-text assessment, and 20 met our inclusion criteria. Six studies tested children diagnosed with hearing loss for genetic etiology, 9 for congenital cytomegalovirus (CMV) infection, and 5 for both. Among 1787 children with congenital hearing loss and etiologic investigation, 933 (52.2%) were tested for genetic mutations and 1021 (57.1%) for congenital CMV infection. The proportion of congenital hearing loss cases attributable to genetic etiology ranged between 7.7% and 83.3% and to congenital CMV infection between 0.0% and 32.0%. Conclusion Data are lacking on the identification and etiology of delayed-onset hearing loss in children <2 years of age in the UNHS era. The proportion of congenital hearing loss cases attributable to genetic etiologies and congenital CMV infection appears to vary widely.
Seasonal Zinc Storage and a Strategy for Its Use in Buds of Fruit Trees1[OPEN]

Zn is deposited in stem nodes subtending axillary buds and then sequestered, probably as Zn-phytate, prior to dormancy break in spring, when Zn is released for use in budbreak and growth. Bud dormancy allows deciduous perennial plants to rapidly grow following seasonal cold conditions. Although many studies have examined the hormonal regulation of bud growth, the role of nutrients remains unclear. Insufficient accumulation of the key micronutrient zinc (Zn) in dormant buds affects the vegetative and reproductive growth of perennial plants during the subsequent year, requiring the application of Zn fertilizers in orchard management to avoid growth defects in fruit trees. However, the mechanisms of seasonal Zn homeostasis in perennial plants remain poorly understood. Here, we provide new insights into Zn distribution and speciation within reproductive and vegetative buds of apple (Malus domestica) and four other deciduous fruit trees (peach [Amygdalus persica], grape [Vitis vinifera], pistachio [Pistacia vera], and blueberry [Vaccinium spp.]) using microscopic and spectroscopic characterization techniques comprising synchrotron-based x-ray fluorescence and x-ray absorption near-edge-structure analyses. By establishing a link between bud development and Zn distribution, we identified the following important steps of Zn storage and use in deciduous plants: Zn is preferentially deposited in the stem nodes subtending apical and axillary buds; Zn may then be sequestered as Zn-phytate prior to dormancy; in spring, Zn effectively releases for use during budbreak and subsequent meristematic growth. The mechanisms of Zn homeostasis during the seasonal cycles of plant growth and dormancy described here will contribute to improving orchard management, and to selection and breeding of deciduous perennial species.
The GARDpotency Assay for Potency-Associated Subclassification of Chemical Skin Sensitizers—Rationale, Method Development, and Ring Trial Results of Predictive Performance and Reproducibility

Abstract Proactive identification and characterization of hazards attributable to chemicals are central aspects of risk assessments. Current legislations and trends in predictive toxicology advocate a transition from in vivo methods to nonanimal alternatives. For skin sensitization assessment, several OECD validated alternatives exist for hazard identification, but nonanimal methods capable of accurately characterizing the risks associated with sensitizing potency are still lacking. The GARD (Genomic Allergen Rapid Detection) platform utilizes exposure-induced gene expression profiles of a dendritic-like cell line in combination with machine learning to provide hazard classifications for different immunotoxicity endpoints. Recently, a novel genomic biomarker signature displaying promising potency-associated discrimination between weak and strong skin sensitizers was proposed. Here, we present the adaptation of the defined biomarker signature on a gene expression analysis platform suited for routine acquisition, confirm the validity of the proposed biomarkers, and define the GARDpotency assay for prediction of skin sensitizer potency. The performance of GARDpotency was validated in a blinded ring trial, in accordance with OECD guidance documents. The cumulative accuracy was estimated to 88.0% across 3 laboratories and 9 independent experiments. The within-laboratory reproducibility measures ranged between 62.5% and 88.9%, and the between-laboratory reproducibility was estimated to 61.1%. Currently, no direct or systematic cause for the observed inconsistencies between the laboratories has been identified. Further investigations into the sources of introduced variability will potentially allow for increased reproducibility. In conclusion, the in vitro GARDpotency assay constitutes a step forward for development of nonanimal alternatives for hazard characterization of skin sensitizers.
Influence of a Lubricating Gel (Orthospeed®) on Pain and Oral Health-Related Quality of Life in Orthodontic Patients during Initial Therapy with Conventional and Low-Friction Brackets: A Prospective Randomized Clinical Trial

The aim of this study was to investigate whether statistically significant differences exist regarding pain and the impact on oral quality of life of orthodontic treatment. A conventional brackets system was compared with low-friction brackets. A total of 90 patients (male = 35, female = 55) were chosen for this randomized clinical trial. Pain was assessed at 4, 8, and 24 hours and 2, 3, 4, 5, 6, and 7 days after the start of treatment using the McGill Pain Questionnaire. Oral health-related quality of life (OHRQoL) was assessed using the Oral Health Impact Profile-14 (OHIP-14) questionnaire. Oral quality of life was assessed at one month, with patients with low-friction brackets describing lower levels of pain. The patients with conventional brackets indicated a worse impact on their quality of life compared to the group with low-friction brackets. Statistically significant differences were found between the groups, with maximum pain observed between the first 24 and 48 hours, and the values of minimum pain are reached after 7 days. The pain and impact on oral quality of life was statistically worse in patients with conventional brackets compared to patients with low-friction brackets. The type of bracket system used was therefore shown to influence patients’ perceptions of pain and impact on their OHRQoL.
Designing and fabricating a novel medical insole with universal fluid layer with auto-customizability

Medical insoles play a significant role in pressure reduction, proper stress–strain distribution, and correcting some deformities in the foot. The aim of the present research is to design and fabricate new medical insoles with universal fluid layer. After fabricating two types of insoles including flat silicone insole with shore 17 and flat silicone insole with universal fluid layer (medical silicone with shore 17 and silicone gel with shore 0), PEDAR test using one person in two standing and walking positions in three conditions comprised without the use of medical insole, using of flat medical silicone insole, and flat silicone insole with universal fluid layer was performed. These insoles were also modeled and solved in Abacus software according to the results obtained from mechanical properties testing of silicone and PEDAR test. The results of the finite element analysis showed that absorption of stress and strain in the static state by the silicone insoles with universal fluid layer was 63% and 63%, and in the dynamic state was 84% and 89% more than those obtained by the flat silicone insoles, respectively. The experimental results of the PEDAR system also showed that in the standing state, the silicone insoles with universal fluid layer and the flat silicone insoles had 58% and 30% pressure reduction, respectively, in comparison with without insole condition. Also, in the gait state, the silicone insoles with fluid layer and the flat silicone insole showed 37% and 9% pressure reduction, respectively, in comparison with without insole condition. Eventually, it was found out that the silicone insoles with fluid layer reduce plantar pressure well in comparison to the flat silicone insoles.
ARTS 2.0: feature updates and expansion of the Antibiotic Resistant Target Seeker for comparative genome mining

Abstract Multi-drug resistant pathogens have become a major threat to human health and new antibiotics are urgently needed. Most antibiotics are derived from secondary metabolites produced by bacteria. In order to avoid suicide, these bacteria usually encode resistance genes, in some cases within the biosynthetic gene cluster (BGC) of the respective antibiotic compound. Modern genome mining tools enable researchers to computationally detect and predict BGCs that encode the biosynthesis of secondary metabolites. The major challenge now is the prioritization of the most promising BGCs encoding antibiotics with novel modes of action. A recently developed target-directed genome mining approach allows researchers to predict the mode of action of the encoded compound of an uncharacterized BGC based on the presence of resistant target genes. In 2017, we introduced the ‘Antibiotic Resistant Target Seeker’ (ARTS). ARTS allows for specific and efficient genome mining for antibiotics with interesting and novel targets by rapidly linking housekeeping and known resistance genes to BGC proximity, duplication and horizontal gene transfer (HGT) events. Here, we present ARTS 2.0 available at http://arts.ziemertlab. com. ARTS 2.0 now includes options for automated target directed genome mining in all bacterial taxa as well as metagenomic data. Furthermore, it enables comparison of similar BGCs from different genomes and their putative resistance genes.
Meagre Argyrosomus regius (Asso, 1801) Stem Spermatogonia: Histological Characterization, Immunostaining, In Vitro Proliferation, and Cryopreservation

Simple Summary The meagre, Argyrosomus regius, is a commercial fish species of which aquaculture production is limited due to technological bottlenecks such as inconstant reproduction in captivity. In addition, there are only a few broodstocks in European farms, which rises the problem of limited genetic variability of the cultured meagre population. The development of germ cell xenotransplantation technology might increase aquaculture production through the production of fertile meagre gametes in a host species for which farming technology is well established. Spermatogonial stem cells have the capacity to proliferate and to proceed through the spermatogenesis process, eventually giving rise to mature spermatozoa. In the present study, meagre spermatogonial stem germ cells were identified, isolated, cultured in vitro, and cryopreserved. Isolated spermatogonial stem cells proliferated, maintained their stem properties in culture, and were still viable after cryopreservation and thawing. This work represents a first step towards the development of a xenotransplantation technology that might facilitate the production of this valuable species in captivity. Abstract The meagre, Argyrosomus regius, is a valued fish species of which aquaculture production might be supported by the development of a stem germ cell xenotransplantation technology. Meagre males were sampled at a fish farm in the Ionian Sea (Italy) at the beginning and end of the reproductive season. Small and large Type A undifferentiated spermatogonia were histologically identified in the germinal epithelium. Among the tested stemness markers, anti-oct4 and anti-vasa antibodies labeled cells likely corresponding to the small single Type A spermatogonia; no labeling was obtained with anti-GFRA1 and anti-Nanos2 antibodies. Two types of single A spermatogonia were purified via density gradient centrifugation of enzymatically digested testes. Testes from fish in active spermatogenesis resulted in a more efficient spermatogonial stem cell (SSC) yield. After cell seeding, meagre SSCs showed active proliferation from Day 7 to Day 21 and were cultured up to Day 41. After cryopreservation in dimethyl-sulfoxide-based medium, cell viability was 28.5%. In conclusion, these results indicated that meagre SSCs could be isolated, characterized, cultured in vitro, successfully cryopreserved, and used after thawing. This is a first step towards the development of a xenotransplantation technology that might facilitate the reproduction of this valuable species in captivity.
Comparative effectiveness of second-line ipilimumab vs. nivolumab in combination with ipilimumab in patients with advanced melanoma who received frontline anti-PD-1 antibodies

Introduction Anti-PD-1 antibodies are commonly used as frontline therapy for patients with metastatic melanoma. Although these medications can cause long term responses, a significant number of patients will not respond or will lose response. Optimal second-line therapy after losing response to anti-PD-1 antibodies is not well established. Therefore, we retrospectively compared the overall survival of patients who lost response to anti-PD1 antibodies between patients treated with single agent ipilimumab or ipilimumab and nivolumab. Methods A de-identified U.S. nationwide electronic health record-derived database was reviewed for patients with advanced melanoma treated with single agent anti-PD1 antibodies in the frontline setting and who subsequently received second-line ipilimumab or combination ipilimumab and nivolumab. Overall survival from initiation of second-line therapy was compared using Kaplan Meier curves and log-rank analysis. Other known prognostic markers for melanoma were analyzed for correlation with survival in a similar fashion. Disease characteristics between the two groups were compared using chi-square analysis. Results A total of 842 patients with advanced melanoma who received frontline anti-PD-1 antibodies were included for analysis. Of these, 57 received either ipilimumab (n = 22) or ipilimumab in combination with nivolumab (n = 35) in the second-line setting. Median survival from second-line therapy initiation for those treated with ipilimumab alone was 6 months and was 5.6 months for those treated with combination ipilimumab and anti-PD-1 antibodies, p = 0.81. Conclusions In this small, retrospective analysis, for patients who lost response to frontline anti-PD-1 therapy, patients treated with ipilimumab had similar survival to those who received ipilimumab in combination with anti-PD-1 antibodies.
A Novel Combination of CYP51A Mutations Confers Pan-Azole Resistance in Aspergillus fumigatus

The treatment of invasive and chronic aspergillosis involves triazole drugs. Its intensive use has resulted in the selection of resistant isolates, and at present, azole resistance in Aspergillus fumigatus is considered an emerging threat to public health worldwide. The aim of this work is to uncover the molecular mechanism implicated in the azole resistance phenotype of three Aspergillus fumigatus clinical strains isolated from an Argentinian cystic fibrosis patient under long-term triazole treatment. ABSTRACT The treatment of invasive and chronic aspergillosis involves triazole drugs. Its intensive use has resulted in the selection of resistant isolates, and at present, azole resistance in Aspergillus fumigatus is considered an emerging threat to public health worldwide. The aim of this work is to uncover the molecular mechanism implicated in the azole resistance phenotype of three Aspergillus fumigatus clinical strains isolated from an Argentinian cystic fibrosis patient under long-term triazole treatment. Strain susceptibilities were assessed, and CYP51A gene sequences were analyzed. Two of the studied Aspergillus fumigatus strains harbored the TR34-L98H allele. These strains showed high MIC values for all tested triazoles (>16.00 μg/ml, 1.00 μg/ml, 1.00 μg/ml, and 2.00 μg/ml for itraconazole, isavuconazole, posaconazole, and voriconazole, respectively). The third strain had a novel amino acid change (R65K) combined with the TR34-L98H mutations. This new mutation combination induces a pan-azole MIC augment compared with TR34-L98H mutants (>16 μg/ml, 4.00 μg/ml, 4.00 μg/ml, and 8.00 μg/ml for itraconazole, isavuconazole, posaconazole, and voriconazole, respectively). The strain harboring the TR34-R65K-L98H allele showed no inhibition halo when voriconazole susceptibility was evaluated by disk diffusion. The effect of these mutations in the azole-resistant phenotype was confirmed by gene replacement experiments. Transformants harboring the TR34-L98H and TR34-R65K-L98H alleles mimicked the azole-resistant phenotype of the clinical isolates, while the incorporation of the TR34-R65K and R65K alleles did not significantly increase azole MIC values. This is the first report of the TR34-L98H allele in Argentina. Moreover, a novel CYP51A allele (TR34-R65K-L98H) that induces a pan-azole MIC augment is described.
Female preference for fast-rate, high-pitched calls in Hermann's tortoises Testudo hermanni

The courtship and mounting behavior of promiscuous tortoises is based on a multiple signaling system that includes visual, olfactory, tactile, and acoustic signals. Vocalizations related to mounting seem to be particularly intriguing because tortoises vocalize mainly at this time. Vocalizations and courtship behavior might be costly for males, and if these costs increase differentially for different males, then the potential exists for vocalizations and displays to reveal male individual quality on which females could base their mate choice. In the present study, by using individuals breeding in seminatural enclosures, we experimentally investigated whether the mounting call of male Hermann's tortoises (Testudo hermanni) represents a relevant stimulus to both males and females. We also looked for potential preference toward different acoustic stimuli in order to determine which call features, if any, played a role in attracting potential partners or deterring rivals. Females were sensitive to call playback, whereas males apparently paid little attention to playback. In addition, females showed a significant preference toward high-pitched calls emitted at high rate. Also, females exhibited a strong tendency toward short-duration calls. Because call rate is related to hematocrit in Hermann's tortoise males, by responding to fast-rate calls females are also choosing high-quality partners as sires of their offspring. This is the first study in which an attractive function of tortoise vocalizations has been documented. Copyright 2005.