Miracle-dz/UniFAR-FTUs huggingface dataset:
Conservation of the Grassy White Box Woodlands: Rangewide Floristic Variation and Implications for Reserve Design

Grassy white box (Eucalyptus albens Benth.) woodlands once covered several million hectares of the wheat-sheep belt of south-eastern Australia. The pre-European floristic composition of these woodlands is little-known, as almost all of them were rapidly cleared for cropping or modified by livestock grazing. Woodland remnants were surveyed across NSW, to describe rangewide variation in the woodland flora, and to provide a basis for reserve design. As far as could be detected from current remnants, some of the major features of the original grassy white box woodland understorey appear to have been relatively constant across NSW: on a wide variety of soils and parent materials from southern to northern NSW, the dominant native grasses in little-disturbed sites were generally Themeda australis (R.Br.) Stapf andor Poa sieberiana Sprengel, and many of the subsidiary herbs and grasses occurred across this range. There were, however, several natural patterns of variation requiring consideration in conservation planning: about half of the subsidiary herb and grass species showed a relationship with latitude, probably relating to a climatic gradient; the understorey became more shrubby, with a sparser and more varied grass component, on soils classed as being 'unsuitable for agriculture'; and on basalt parent materials of the Inverell Plateau, Dichanthium sericeum (R.Br.) A.Camus may have been a more prominent component of the understorey. Natural floristic variation was overlain by patterns resulting from European disturbance, as indicated by floristic distinctions between sites of differing landuse. While these distinctions were partly related to poorer soil resource class in State Forests and Nature Reserves, grazing by livestock and tree clearing are likely to to have contributed to them. Reserves in ine whire box woodiands are presentiy few, and are not representative of the naturai variation. ~ o s t existing reserves occur on soils unsuited to agriculture, compared with the grazing or arable land of typical grassy woodland. Cemetery remnants, rail easements, Travelling Stock Reserves and roadsides provide the best opportunities for conservation on higher-quality soils. Remnant quality declined significantly in southern NSW, indicating a need for greater conservation effort in southern areas.
Effect of neuromuscular electrical stimulation on skeletal muscle size and function in patients with breast cancer receiving chemotherapy.

Exercise has numerous benefits for patients with cancer, but implementation is challenging because of practical and logistical hurdles. This study examined whether neuromuscular electrical stimulation (NMES) can serve as a surrogate for classical exercise by eliciting an exercise training response in skeletal muscle of women diagnosed with breast cancer undergoing chemotherapy. Patients (n=22) with histologically-confirmed, stage I, II or III breast cancer scheduled to receive neoadjuvant or adjuvant chemotherapy were randomized to 8 weeks of bilateral neuromuscular electrical stimulation (NMES; 5 days/week) to their quadriceps muscles or control. Biopsy of the vastus lateralis was performed at baseline and after 8 weeks of intervention to assess muscle fiber size, contractility and mitochondrial content. Seventeen patients (8 control/9 NMES) completed the trial and were included in analyses. NMES promoted muscle fiber hypertrophy (P<0.001), particularly in fast-twitch, myosin heavy chain (MHC) IIA fibers (P<0.05), and tended to induce fiber type shifts in MHC II fibers. The effects of NMES on single muscle fiber contractility were modest and it was unable to prevent declines in function in MHC IIA fibers. NMES did not alter intermyofibrillar mitochondrial content/structure, but was associated with reductions in subsarcolemmal mitochondria. Our results demonstrate that NMES induces muscle fiber hypertrophy and fiber type shifts in MHC II fibers, but had minimal effects on fiber contractility and promoted reductions in subsarcolemmal mitochondria. Further studies are warranted to evaluate the utility of NMES as an exercise surrogate in cancer patients and other conditions.
Exercise based assessment of cardiac autonomic function in type 1 versus type 2 diabetes mellitus

Background Cardiac autonomic neuropathy (CAN) is a complication of diabetes mellitus (DM) that is associated with increased mortality. Exercise-based assessment of autonomic function has identified diminished parasympathetic reactivation after exercise in type 2 DM. It is postulated herein, that this would be more prominent among those with type 1 DM. Methods Sixteen subjects with type 1 DM (age 32.9 ± 10.1 years), 18 subjects with type 2 DM (55.4 ± 8.0 years) and 30 controls (44.0 ± 11.6 years) underwent exercise-based assessment of autonomic function. Two 16-min submaximal bicycle tests were performed followed by 45 min of recovery. On the second test, atropine (0.04 mg/kg) was administered near end-exercise so that all of the recovery occurred under parasympathetic blockade. Plasma epinephrine and norepinephrine levels were measured at rest, during exercise, and during recovery. Results There were no differences in resting or end-exercise heart rates in the three groups. Parasympathetic effect on RR-intervals during recovery (p < 0.03) and heart rate recovery (p = 0.02) were blunted in type 2 DM. Type 1 DM had higher baseline epinephrine and norepinephrine levels (p < 0.03), and exhibited persistent sympathoexcitation during recovery. Conclusions Despite a longer duration of DM in the study patients with type 1 versus type 2 DM, diminished parasympathetic reactivation was not noted in type 1 DM. Instead, elevation in resting plasma catecholamines was noted compared to type 2 DM and controls. The variable pathophysiology for exercise-induced autonomic abnormalities in type 1 versus type 2 DM may impact prognosis.
Research note: The short‐term effect of fire on the woody component of the Sourish Mixed Bushveld

Abstract The short‐term effect of an early‐spring, moderately hot fire on the woody component of the Sourish Mixed Bushveld was monitored before, directly after, and for two successive seasons following the fire. The average height of trees less than three metres was reduced due to severe topkill, but trees higher than three metres were unaffected by the fire. Tree volume, leaf volume, total biomass and available browse initially decreased, but recovered within two seasons. Fire damage and regeneration depended on the structure of the woody component. Biomass production and woody seedling establishment was stimulated by the fire.
Demography and Ecology of Mangrove Diamondback Terrapins in a Wilderness Area of Everglades National Park, Florida, USA

Abstract Diamondback Terrapins (Malaclemys terrapin) are distributed in brackish water habitats along the U.S. east coast from Massachusetts to Texas, but many populations may be in decline. Whereas ample morphological, behavioral, and reproductive information has been collected for terrapins living in temperate salt marsh habitats, comparatively little is known about mangrove terrapins. To understand population structure of mangrove M. terrapin living in a wilderness area, we conducted a capture–recapture study in the remote, protected Big Sable Creek complex of Everglades National Park, Florida. The goals of the study were to collect baseline demographic data and to compare population structure and growth rates of mangrove terrapins with what is known for more well studied salt marsh terrapins in locations that experience human-imposed threats. We marked 300 terrapins; the sex ratio was 1 female:1.2 males. Considerable sexual size dimorphism was apparent, with reproductively mature females three times larger (by mass) than mature males. Eighty percent of females and 94% of males were classified as mature, based on straight plastron length (SPL). For a subset of terrapins not yet at maximum size (n = 39), we measured growth as a change in straight carapace length over time of 0.3–26.4 mm/yr for females (n = 26) and 0.9–14.5 mm/yr for males (n = 13). Our study presents the first demographic data on mangrove M. terrapin in the coastal Everglades.
Role of the microRNA-214/Bax axis in the progression of acute liver failure

Acute liver failure (ALF) is a fatal liver disease characterized by severe hepatocyte destruction. MicroRNAs (miRNAs/miRs) have been reported to serve a key role in a number of liver diseases. Therefore, the aim of the present study was to investigate the role and underlying mechanism of miR-214 in ALF. ALF murine and hepatocyte models were established using D-galactosamine (D-GalN) and lipopolysaccharide (LPS) or D-GalN + tumor necrosis factor (TNF)-α, respectively. The expression levels of miR-214 and Bax were detected by reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and/or western blotting. Furthermore, an automatic biochemical analyzer was used to measure the levels of aspartate aminotransferase (AST) or alanine aminotransferase (ALT). The levels of TNF-α and interleukin (IL)-6 were detected by ELISA and RT-qPCR. In addition, TUNEL staining and flow cytometry were used to analyze cell apoptosis, and the protein expression of caspase-3 was determined by western blotting. It was identified that the levels of AST and ALT were increased and that hepatocyte apoptosis was enhanced in the D-GalN/LPS-stimulated group compared with the control. Furthermore, higher expression of caspase-3 was observed in the D-GalN/LPS-stimulated group. In addition, it was demonstrated that miR-214 was downregulated, while Bax was upregulated in D-GalN/LPS-stimulated mice and D-GalN/TNF-α-stimulated BNLCL2 cells. Moreover, in D-GalN/TNF-α-stimulated BNLCL2 cells, miR-214 overexpression suppressed apoptosis and decreased TNF-α and IL-6 levels, and these effects were reversed by the Bax plasmid. It was also identified that overexpression of miR-214 significantly decreased Bax mRNA and protein expression levels in vitro. Collectively, the present results suggested that miR-214 inhibited hepatocyte apoptosis during ALF development via targeting Bax, thus indicating that miR-214 may be a potential target for ALF treatment.
The search for yield predictors for mature field-grown plants from juvenile pot-grown cassava (Manihot esculenta Crantz)

Cassava is the 6th most important source of dietary energy in the world but its root system architecture (RSA) had seldom been quantified. Ability to select superior genotypes at juvenile stages can significantly reduce the cost and time for breeding to bridge the large yield gap. This study adopted a simple approach to phenotyping RSA traits of juvenile and mature cassava plants to identify genotypic differences and the relationships between juvenile traits and harvest index of mature plants. Root classes were categorised and root and shoot traits of eight (8) juvenile pot-grown cassava genotypes, were measured at 30 and 45 days after planting (DAP). The same or related traits were measured at 7 months after planting of the same genotypes grown in the field while yield and yield components were measured in 12-months old field-grown plants. The field experiment was done in 2017 and repeated in 2018. Differences between genotypes for the measured traits were explored using analysis of variance (ANOVA) while traits in juvenile plants were correlated or regressed onto traits measured in 7- and 12-months old plants. The results show significant genotypic variations for most of the traits measured in both juvenile and 7-months old plants. In the 12-months old plants, differences between genotypes were consistent for both 2017 and 2018. Broad-sense heritability was highest for the number of commercial roots (0.87) and shoot fresh weight (0.78) and intermediate for the total number of roots (0.60), harvest index (0.58), fresh weight of roots (0.45). For all the sampling time points or growth stages, there were greater correlations between traits measured at a particular growth stage than between the same traits at different growth stages. However, some juvenile-mature plant trait relationships were significant, positive and consistent for both 2017 and 2018. For example, total root length and the total number of roots in 30 DAP, and branching density of upper nodal roots in 45 DAP, positively correlated with harvest index of 12-months old plants in both 2017 and 2018. Similarly, the diameter of nodal roots, for example, had a negative, significant correlation with fresh shoot biomass of mature plants in both 2017 and 2018. Regression of traits measured in 30 DAP explained up to 22% and 36% of the variation in HI of mature plants in 2017 and 2018, respectively. It is concluded that the simple, rapid, inexpensive phenotyping approach adopted in this study is robust for identifying genotypic variations in juvenile cassava using root system traits. Also, the results provide seminal evidence for the existence of useful relationships between traits of juvenile and mature cassava plants that can be explored to predict yield and yield components.
Habitat variables affecting nest predation rates at small ponds: a case study of the Little Crake Porzana parva and Water Rail Rallus aquaticus

Capsule Nest survival of Water Rail and Little Crake nesting at small, midfield ponds was determined by vegetation density and proximity to the shore, respectively. Aims To determine which habitat variables affect nest predation for two rallid species inhabiting small ponds. Methods Habitat variables describing nest location (water depth, distance to the shore and distance to open water) and nest concealment (density and height of vegetation) were measured for natural and artificial nests. All nests were monitored to determine their fate and to identify nest predators. We used generalized linear models to assess nest survival rates and to evaluate the influence of particular variables. Results Little Crake nest success was negatively correlated with distance to shore (the land-water edge). The survival of Water Rail nests and artificial nests was positively correlated with vegetation density. During three breeding seasons, predation rates on Little Crake nests varied from 22% to 58%, and on Water Rail nests from 36% to 91%. The main predator of natural and artificial nests was the Marsh Harrier (responsible for about 50% of natural and artificial nest failures). Conclusion High Marsh Harrier predation rates (attacks from the air) may explain why water depth did not affect the survival rate of natural and artificial nests and why nest concealment was a factor positively influencing the nest success of the Water Rail and artificial nests. Little Crakes nest successfully closer to the shore, where vegetation is usually denser. Terrestrial mammals could more easily access Water Rail nests, which were situated in shallower water than Little Crake nests, and this may have contributed to the higher rate of nest loss in this species.
Omics for Bioprospecting and Drug Discovery from Bacteria and Microalgae

“Omics” represent a combinatorial approach to high-throughput analysis of biological entities for various purposes. It broadly encompasses genomics, transcriptomics, proteomics, lipidomics, and metabolomics. Bacteria and microalgae exhibit a wide range of genetic, biochemical and concomitantly, physiological variations owing to their exposure to biotic and abiotic dynamics in their ecosystem conditions. Consequently, optimal conditions for adequate growth and production of useful bacterial or microalgal metabolites are critically unpredictable. Traditional methods employ microbe isolation and ‘blind’-culture optimization with numerous chemical analyses making the bioprospecting process laborious, strenuous, and costly. Advances in the next generation sequencing (NGS) technologies have offered a platform for the pan-genomic analysis of microbes from community and strain downstream to the gene level. Changing conditions in nature or laboratory accompany epigenetic modulation, variation in gene expression, and subsequent biochemical profiles defining an organism’s inherent metabolic repertoire. Proteome and metabolome analysis could further our understanding of the molecular and biochemical attributes of the microbes under research. This review provides an overview of recent studies that have employed omics as a robust, broad-spectrum approach for screening bacteria and microalgae to exploit their potential as sources of drug leads by focusing on their genomes, secondary metabolite biosynthetic pathway genes, transcriptomes, and metabolomes. We also highlight how recent studies have combined molecular biology with analytical chemistry methods, which further underscore the need for advances in bioinformatics and chemoinformatics as vital instruments in the discovery of novel bacterial and microalgal strains as well as new drug leads.
The possibilities of the use of N-of-1 and do-it-yourself trials in nutritional research

Background N-of-1 designs gain popularity in nutritional research because of the improving technological possibilities, practical applicability and promise of increased accuracy and sensitivity, especially in the field of personalized nutrition. This move asks for a search of applicable statistical methods. Objective To demonstrate the differences of three popular statistical methods in analyzing treatment effects of data obtained in N-of-1 designs. Method We compare Individual-participant data meta-analysis, frequentist and Bayesian linear mixed effect models using a simulation experiment. Furthermore, we demonstrate the merits of the Bayesian model including prior information by analyzing data of an empirical study on weight loss. Results The linear mixed effect models are to be preferred over the meta-analysis method, since the individual effects are estimated more accurately as evidenced by the lower errors, especially with lower sample sizes. Differences between Bayesian and frequentist mixed models were found to be small, indicating that they will lead to the same results without including an informative prior. Conclusion For empirical data, the Bayesian mixed model allows the inclusion of prior knowledge and gives potential for population based and personalized inference.
GREB1L variants in familial and sporadic hereditary urogenital adysplasia and Mayer‐Rokitansky‐Kuster‐Hauser syndrome

Congenital uterine anomalies (CUA) may have major impacts on the health and social well‐being of affected individuals. Their expressivity is variable, with the most severe end of the spectrum being the absence of any fully or unilaterally developed uterus (aplastic uterus), which is a major feature in Mayer‐Rokitansky‐Kuster‐Hauser syndrome (MRKH). So far, etiologies of CUA remain largely unknown. As reports of familial occurrences argue for strong genetic contributors in some cases, we performed whole exome sequencing in nine multiplex families with recurrence of uterine and kidney malformations, a condition called hereditary urogenital adysplasia. Heterozygous likely causative variants in the gene GREB1L were identified in four of these families, confirming GREB1L as an important gene for proper uterine and kidney development. The apparent mode of inheritance was autosomal dominant with incomplete penetrance. The four families included fetuses with uterovaginal aplasia and bilateral renal agenesis, highlighting the importance to investigate GREB1L in such phenotypes. Subsequent sequencing of the gene in a cohort of 68 individuals with MRKH syndrome or uterine malformation (mostly sporadic cases) identified six additional variants of unknown significance. We therefore conclude that heterozygous GREB1L variants contribute to MRKH syndrome and this probably requires additional genetic or environmental factors for full penetrance.
HARVESTING DISRUPTS BIOLOGICAL CONTROL OF HERBIVORES IN A SHORT-ROTATION COPPICE SYSTEM

Disturbances such as harvesting often interfere with the ecological processes that lead to the biological control of insect pests. For willows, grown as short-rotation coppice crops harvested every third to fifth year, it has been suggested that high plant quality in the resprouting shoots after harvesting may explain observed high densities of herbivorous insects, especially leaf beetles (Coleoptera: Chrysomelidae), in the plantations. In this study, we show that generalist predators may be important as regulators of leaf beetle populations. All three leaf beetle species, which were studied for five years in 12 plantations, showed a negative correlation between the population growth rate from spring to fall and the abundance of the most common generalist predator Orthotylus marginalis (Heteroptera: Miridae). For the most abundant leaf beetle, Phratora vulgatissima, we also found a significant positive correlation between its population growth rate and egg survival, indicating an overall effect of predation on herbivore population growth. Harvesting, which takes place during the winter, had a negative effect on the abundance of leaf beetles and predators. However, the first year after harvesting, all three leaf beetle species regained this loss with a very high population growth rate. A reason for the better ability of the herbivores to recover from the disturbance may be that they, unlike the predators, mainly overwinter outside the plantations. All three leaf beetles peaked in density three years after harvesting whereas the density of generalist natural enemies increased or leveled off during the five-year period after harvesting. We conclude that predation by generalist predators is potentially important for population control of leaf beetles in willow coppice, but that the intermediate disturbance regime of around five years between harvests, appears to be too short to avoid disruption of biological control. Alternatives for more efficient biological control in short-rotation coppice systems may be a longer period between harvests that enables the predators to fully respond numerically, to leave natural enemies refuges at harvest, or to harvest adjacent plantations asynchronously.