Miracle-dz/UniFAR-FTUs huggingface dataset:
Tribolium castaneum as a model for microRNA evolution, expression and function during short germband development

MicroRNAs are well-established players in the development of multicellular animals. Most of our understanding of microRNA function in arthropod development comes from studies in Drosophila. Despite their advantages as model systems, the long germband embryogenesis of fruit flies is an evolutionary derived state restricted to several holometabolous insect lineages. MicroRNA evolution and expression across development in animals exhibiting the ancestral and more widespread short germband mode of embryogenesis has not been characterized. We sequenced small RNA libraries of oocytes and successive time intervals covering the embryonic development of the short germband model organism, the red flour beetle Tribolium castaneum. We analysed the evolution and temporal expression of the microRNA complement, and sequenced libraries of total RNA to investigate the relationships with microRNA target expression. We show microRNA maternal loading and sequence-specific 3’-end non-template oligoadenylation of maternally deposited microRNAs that is conserved between Tribolium and Drosophila. We further uncover large clusters encoding multiple paralogs from several Tribolium-specific microRNA families expressed during a narrow interval of time immediately after the activation of zygotic transcription. These novel microRNAs, together with several early expressed conserved microRNAs, target a significant number of maternally deposited transcripts. Comparison with Drosophila shows that microRNA-mediated maternal transcript targeting is a conserved phenomenon in insects, but the number and sequences of microRNAs involved in this process have diverged. The expression of fast-evolving and species-specific microRNAs in the early blastoderm of T. castaneum is consistent with previous findings in Drosophila and shows that the unique permissiveness for microRNA innovation at this stage is a conserved phenomenon.
Sex and hatching order modulate the association between MHC‐II diversity and fitness in early‐life stages of a wild seabird

Genes of the major histocompatibility complex (MHC) play a pivotal role in parasite resistance, and their allelic diversity has been associated with fitness variations in several taxa. However, studies report inconsistencies in the direction of this association, with either positive, quadratic or no association being described. These discrepancies may arise because the fitness costs and benefits of MHC diversity differ among individuals depending on their exposure and immune responses to parasites. Here, we investigated in black‐legged kittiwake (Rissa tridactyla) chicks whether associations between MHC class‐II diversity and fitness vary with sex and hatching order. MHC‐II diversity was positively associated with growth and tick clearance in female chicks, but not in male chicks. Our data also revealed a positive association between MHC‐II diversity and survival in second‐hatched female chicks (two eggs being the typical clutch size). These findings may result from condition‐dependent parasite infections differentially impacting sexes in relation to hatching order. We thus suggest that it may be important to account for individual heterogeneities in traits that potentially exert selective pressures on MHC diversity in order to properly predict MHC–fitness associations.
Skin tear prevalence and incidence in the long-term care population: a prospective study.

OBJECTIVE The World Health Organization estimates that between 2015 and 2050 the proportion of the world's population over 60 years old will nearly double from 12% to 22%. An often overlooked byproduct of ageing is the skin changes associated with it, which heighten the risk of developing skin tears. Despite this presumed increased risk, the true impact of skin tears across age groups and care settings is poorly understood. The purpose of the present study was to establish the prevalence and incidence of skin tears in the Ontario long-term care population. METHOD A prospective study design was used to explore the prevalence and incidence of skin tears. Individuals from four long-term care facilities in Ontario were followed over four weeks. The participants were examined for skin tears at the beginning of the study and at week four to determine whether skin tears had occurred and to record the skin tear type and location. RESULTS A total of 380 individuals, aged 65 years and over, took part. The study found a skin tear prevalence of 20.8% and an incidence of 18.9% within four weeks. These results provide much needed data on the burden of skin tears in the long-term care population. Conclusion: The present study is an important first step towards developing a prevention programme targeting individuals at risk for skin tears in long-term care.
Literature‐derived bioaccumulation models for earthworms: Development and validation

Estimation of contaminant concentrations in earthworms is a critical component in many ecological risk assessments. Without site‐specific data, literature‐derived uptake factors or models are frequently used. Although considerable research has been conducted on contaminant transfer from soil to earthworms, most studies focus on only a single location. External validation of transfer models has not been performed. We developed a database of soil and tissue concentrations for nine inorganic and two organic chemicals. Only studies that presented total concentrations in depurated earthworms were included. Uptake factors and simple and multiple regression models of natural‐log‐transformed concentrations of each analyte in soil and earthworms were developed using data from 26 studies. These models were then applied to data from six additional studies. Estimated and observed earthworm concentrations were compared using nonparametricWilcoxon signed‐rank tests. Relative accuracy and quality of different estimation methods were evaluated by calculating the proportional deviation ([measured ‐ estimate]/measured) of the estimate from the measured value. With the exception of Cr, significant, single‐variable (e.g., soil concentration) regression models were fit for each analyte. Inclusion of soil Ca improved model fits for Cd and Pb. Soil pH only marginally improved model fits. The best general estimates of chemical concentrations in earthworms were generated by simple ln‐ln regression models for As, Cd, Cu, Hg, Mn, Pb, Zn, and polychlorinated biphenyls. No method accurately estimated Cr or Ni in earthworms. Although multiple regression models including pH generated better estimates for a few analytes, in general, the predictive utility gained by incorporating environmental variables was marginal.
Perioperative Risk Factors Associated With Acute Kidney Injury in Patients After Brain Tumor Resection

Supplemental Digital Content is available in the text. Background: Acute kidney injury (AKI) is a serious complication after surgery. The aim of this study is to identify risk factors for postoperative AKI in patients undergoing brain tumor surgery. Methods: This single-center, retrospective, matched case-control study included patients undergoing elective brain tumor surgery between January 2016 and December 2018 at Beijing Tiantan Hospital, Capital Medical University, China. Patients developing postoperative AKI were compared with controls without AKI matched by age, sex, and date of surgery in a ratio of 1:3. AKI was defined using the Kidney Disease Improving Global Outcomes criteria. Results: A total of 9933 patients were identified for review, of which 115 (1.16%) developed AKI; 345 matched patients were included in the control group. AKI occurred most commonly within the first 24 hours (41/97, 42.3%) and 48 hours (33/94, 35.1%) after surgery. Preoperative administration of mannitol (odds ratio [OR], 1.64; 95% confidence interval [CI], 1.04-2.60; P= 0.034), American Society of Anesthesiologists physical status III or higher (OR, 5.50; 95% CI, 2.23-13.59; P<0.001), preoperative blood glucose (OR, 2.53; 95% CI, 1.23-5.22; P=0.012), craniopharyngioma (OR, 8.96; 95% CI, 3.55-22.63; P<0.001), nonsteroidal anti-inflammatory drug administration (OR, 3.74; 95% CI, 1.66-8.42; P<0.001), and intraoperative hypotension (OR, 2.13; 95% CI, 1.21-3.75; P=0.009) were independent risk factors for postoperative AKI. Conclusion: Multiple factors, including preoperative administration of mannitol, are independently associated with the development of postoperative AKI in patients undergoing brain tumor surgery.
Effect of an interval rehabilitation program with home-based, vibration-assisted training on the development of muscle and bone in children with cerebral palsy – an observational study

Abstract Objectives In children with cerebral palsy (CP), the most common cause of physical impairment in childhood, less muscle and bone growth has been reported, when compared with typically developing children. The aim of this study was to evaluate the effect of an intensive rehabilitation program including physiotherapy in combination with 6 months of home-based, vibration-assisted training on muscle and bone growth in children with CP. Methods We included children with CP, who participated in a rehabilitation program utilizing whole-body vibration (WBV). Muscle mass was quantified by appendicular lean mass index (App-LMI) and bone mass by total-body-less-head bone mineral content (TBLH-BMC) assessed by Dual-energy X-ray absorptiometry (DXA) at the beginning of rehabilitation and one year later. To assess the functional muscle-bone unit, the relation of TBLH-BMC to TBLH lean body mass (TBLH-LBM) was used. Results The study population included 128 children (52 females, mean age 11.9 ± 2.7). App-LMI assessed in kg/m2 increased significantly after rehabilitation. The age-adjusted Z-score for App-LMI showed no significant change. TBLH-BMC assessed in gram increased significantly. The Z-scores for TBLH-BMC decreased lesser than expected by the evaluation of the cross-sectional data at the beginning of rehabilitation. The parameter T B L H − B M C T B L H − L B M $\frac{TBLH-BMC}{TBLH-LBM}$ did not change relevantly after 12 months. Conclusions Muscle growth and to a lesser extent bone growth could be increased in children with CP. The intensive rehabilitation program including WBV seemed to have no direct effect on the bone, but the observed anabolic effect on the bone, may only been mediated through the muscle.
New species of Holopedium Zaddach, 1855 (Crustacea: Cladocera: Ctenopoda) from Greenland

The genus Holopedium remains poorly studied. Its nominal species H. gibberum was superficially described; later morphological differences of representatives of this taxon, especially in North America, have been recorded but not investigated in detail. The Greenlandic members of the taxon, listed for the first time in 1889, have never been precisely studied. Meanwhile, their comparative analysis resulted in the description of a new species, H. groenlandicum, which differs from H. gibberum s. l. in having a dorsally low shell and jelly envelope, shorter row of valve marginal spinules which are subdivided in groups, and comparatively longer postabdominal claws. Morphologically, the new species seems more primitive than H. gibberum. Absence of males and the presence of resting eggs may indicate a pseudosexual or another, poorly understood, mode of reproduction. Holopedium groenlandicum inhabits only permanent water bodies, mostly along the south-western and western coast of Greenland up to 71o N. This species is endemic to the island, and is most probably of relict nature.
First record of Schizymenia apoda (Schizymeniaceae, Rhodophyta) in New Zealand

The foliose red alga Schizymenia apoda (Schizymeniaceae) is reported for the first time in New Zealand waters. Its identity was confirmed by rbcL sequence data and morphological observations. This alga has been reported from both the Atlantic and the North Pacific and, although it is very variable in colour and habit, it is easily distinguished morphologically by the presence of refractive gland cells (visible in surface view), large cystocarps with a pronounced ostiole, and the lack of tetrasporophyte blades. Although not reported as an introduced species elsewhere, in New Zealand S. apoda was collected at the ferry terminal and on pontoons and pilings in the marinas of Wellington Harbour. It was also discovered in Otago Harbour. The examination of herbarium specimens and recent collections from areas outside the harbour has resulted in only a few samples that could be referred to this species, leading us to consider this a new introduction.
Comparative effects of neurally adjusted ventilatory assist and variable pressure support on lung and diaphragmatic function in a model of acute respiratory distress syndrome

Supplemental Digital Content is available in the text BACKGROUND Variable assisted mechanical ventilation has been shown to improve lung function and reduce lung injury. However, differences between extrinsic and intrinsic variability are unknown. OBJECTIVE To investigate the effects of neurally adjusted ventilatory assist (NAVA, intrinsic variability), variable pressure support ventilation (Noisy PSV, extrinsic variability) and conventional pressure-controlled ventilation (PCV) on lung and diaphragmatic function and damage in experimental acute respiratory distress syndrome (ARDS). DESIGN Randomised controlled animal study. SETTING University Hospital Research Facility. SUBJECTS A total of 24 juvenile female pigs. INTERVENTIONS ARDS was induced by repetitive lung lavage and injurious ventilation. Animals were randomly assigned to 24 h of either: 1) NAVA, 2) Noisy PSV or 3) PCV (n=8 per group). Mechanical ventilation settings followed the ARDS Network recommendations. MEASUREMENTS The primary outcome was histological lung damage. Secondary outcomes were respiratory variables and patterns, subject-ventilator asynchrony (SVA), pulmonary and diaphragmatic biomarkers, as well as diaphragmatic muscle atrophy and myosin isotypes. RESULTS Global alveolar damage did not differ between groups, but NAVA resulted in less interstitial oedema in dorsal lung regions than Noisy PSV. Gas exchange and SVA incidence did not differ between groups. Compared with Noisy PSV, NAVA generated higher coefficients of variation of tidal volume and respiratory rate. During NAVA, only 40.4% of breaths were triggered by the electrical diaphragm signal. The IL-8 concentration in lung tissue was lower after NAVA compared with PCV and Noisy PSV, whereas Noisy PSV yielded lower type III procollagen mRNA expression than NAVA and PCV. Diaphragmatic muscle fibre diameters were smaller after PCV compared with assisted modes, whereas expression of myosin isotypes did not differ between groups. CONCLUSION Noisy PSV and NAVA did not reduce global lung injury compared with PCV but affected different biomarkers and attenuated diaphragmatic atrophy. NAVA increased the respiratory variability; however, NAVA yielded a similar SVA incidence as Noisy PSV. TRIAL REGISTRATION This trial was registered and approved by the Landesdirektion Dresden, Germany (AZ 24-9168.11-1/2012-2).
Density‐dependent dispersal and the formation of range borders.

Knowledge about the mechanisms of range formation is crucial for scientifically based species conservation strategies in the face of ongoing global climate change. In recent years an increasing amount of studies have focused on the influences of density-dependent dispersal on demographic and biogeographical patterns. However, it still remains unclear, to what extent and in what ways this strategy would affect the range formation of species. In order to fill this gap, we present a study using individual-based simulations of a species with discrete generations living along a dispersal mortality gradient. We compare the evolution of range sizes for species following density-dependent and density-independent emigration. Furthermore we assess the influence of environmental stochasticity and Allee effects on range formation, as both processes are known to play an important role for dispersal evolution. We find that density-dependent dispersal always results in much wider ranges than unconditional dispersal. Increasing environmental stochasticity, a predicted consequence of climate change, can remarkably expand the ranges of species living in such connectivity gradients if dispersal decisions are based on local population density. A strong Allee effect causes range contraction for both strategies, but the effect is considerably less dramatic under density-dependent compared to density-independent emigration. We strongly recommend accounting for these findings in future attempts to model species’ range shifts due to climate change.
A new cryptic species of Aphaenops (Coleoptera: Carabidae: Trechinae) from a French Pyrenean cave: Congruence between morphometrical and geographical data confirm species isolation

Abstract A new species of cave-dwelling beetle from the pyrenean massif, Aphaenops (Cerbaphaenops) jauzioni n. sp. (Coleoptera: Carabidae), is described. Geometric morphometric analyses based on five morphological structures and comparisons with two populations of the closely related species Aphaenops (Cerbaphaenops) cerberus Dieck 1869 support the uniqueness of the new species. The specific status of the new taxon is also confirmed by the male genitalia structures. A putative scenario of population isolation is proposed.
Postmortem recovery, in vitro maturation and fertilization of fallow deer (Dama dama, Linnaeus 1758) oocytes collected during reproductive and no reproductive season.

Habitat degradation leads to small and fragmented populations, lower genetic variability and fertility overtime. Assisted reproductive techniques represent important tools to cope with the dramatic loss of biodiversity. Fallow deer (Dama dama), beyond its high commercial value and wide distribution, may represent the most suitable model to study endangered cervids. In this study, oocytes were recovered post mortem from fallow deer during the breeding and no breeding seasons and were in vitro matured (IVM). The ability of cryopreserved thawed sperm samples recovered by electroejaculation from 4 adult males was tested by in vitro fertilization of IVM oocytes. The number of oocytes collected per ovary did significantly vary across seasons from 6.2 ± 0.92 during breeding season to 10.4 ± 1.26 during no breeding season (p = 0.006). Oocytes collected during the breeding season showed higher in vitro fertilization rate compared to the no breeding season (p = 0.045). However, no embryos reached the blastocyst stage. Semen samples obtained by electroejaculation were successfully cryopreserved, although the cryopreservation process negatively affected most kinetic parameters, mainly at 2h post-thawing. Moreover, the percentage of rapid spermatozoa significantly decreased between fresh samples and at 2h post thawing, whereas the percentage of slow spermatozoa increased across the same period (p < 0.05). Our study provides the logistic steps for the application of assisted reproductive techniques in fallow deer and might be of great interest for genetic resource bank planning.
Competition between stink bug and heliothine caterpillar pests on cotton at within‐plant spatial scales

Outbreaks of non‐target pests associated with transgenic Bt cotton threaten the economic and ecological benefits of the technology in cotton‐producing countries. In the southeastern USA, stink bug pests, namely Nezara viridula L. and Euschistus servus Say (both Heteroptera: Pentatomidae), have recently become severe problems associated with Bt cotton, requiring continued insecticide use. However, the causes of non‐target pest outbreaks remain unclear. Release from competition with Bt‐susceptible pest species, in addition to other mechanisms, may contribute to increased stink bug populations in Bt cotton. We investigated the competitive interactions between the two stink bug species and the Bt‐susceptible pests Helicoverpa zea (Boddie) and Heliothis virescens Fabricius (both Lepidoptera: Noctuidae) on non‐Bt cotton. We tested for competition effects on stink bug growth rates in no‐choice experiments at two spatial scales: a single cotton boll and a branch with multiple developing bolls. Although caterpillars of the two species had equivalent effects on resource availability, they had distinct effects on stink bug growth rates. Fourth instar H. zea reduced growth rates of both stink bug species by 60% when caged on a single cotton boll and reduced growth rates of only E. servus by 36% when caged on a cotton branch. In contrast, H. virescens had no effect on stink bug growth rates. Resource competition was apparent in the interactions between H. zea and E. servus, but interference competition may have contributed to the interactions as well. Competitive release of stink bug populations in Bt cotton is possible, and should be more likely for E. servus than for N. viridula. Understanding the causes of non‐target pest outbreaks in Bt cotton will contribute to improved environmental risk assessments of future releases of Bt cotton and related transgenic crops.
White clover cryptic virus‐1 in New Zealand and eastern Australia

The distribution and abundance of cryptic viruses (Partitiviridae) in natural and agricultural systems have received little attention. White clover cryptic virus-1 (WCCV-1) was detected infecting white clover plants and seed growing in New Zealand, but was not detected in field collections and in only two of 114 seedlings grown from seed collected in eastern Australia using enzyme-linked immunosorbent assay and RT-PCR. WCCV-1 was detected at high incidences (14–48%) in the cultivars Huia, Kopu II and Tahora and at low incidences (0–7%) in Aran, Haifa, Ladino, Siral and Sustain white clovers. WCCV-1 remained viable in seed stored for 50 years. The results are compared with another group of obligate seed-transmitted pasture microbes: the fungal endophytes of perennial grasses.
The substrate‐dependent regulatory effects of the AfeI/R system in Acidithiobacillus ferrooxidans reveals the novel regulation strategy of quorum sensing in acidophiles

Summary A LuxI/R‐like quorum sensing (QS) system (AfeI/R) has been reported in the acidophilic and chemoautotrophic Acidithiobacillus spp. However, the function of AfeI/R remains unclear because of the difficulties in the genetic manipulation of these bacteria. Here, we constructed different afeI mutants of the sulfur‐ and iron‐oxidizer A. ferrooxidans, identified the N‐acyl homoserine lactones (acyl‐HSLs) synthesized by AfeI, and determined the regulatory effects of AfeI/R on genes expression, extracellular polymeric substance synthesis, energy metabolism, cell growth and population density of A. ferrooxidans in different energy substrates. Acyl‐HSLs‐mediated distinct regulation strategies were employed to influence bacterial metabolism and cell growth of A. ferrooxidans cultivated in either sulfur or ferrous iron. Based on these findings, an energy‐substrate‐dependent regulation mode of AfeI/R in A. ferrooxidans was illuminated that AfeI/R could produce different types of acyl‐HSLs and employ specific acyl‐HSLs to regulate specific genes in response to different energy substrates. The discovery of the AfeI/R‐mediated substrate‐dependent regulatory mode expands our knowledge on the function of QS system in the chemoautotrophic sulfur‐ and ferrous iron‐oxidizing bacteria, and provides new insights in understanding energy metabolism modulation, population control, bacteria‐driven bioleaching process, and the coevolution between the acidophiles and their acidic habitats.