Miracle-dz/UniFAR-FTUs huggingface dataset:
Hindcasting the impacts of land-use changes on bird communities with species distribution models of Bird Atlas data.

Habitat loss and degradation induced by human development are among the major threats to biodiversity worldwide. In this study, we tested our ability to predict the response of bird communities (128 species) to land-use changes in southern Quebec (~483,100 km2 ) over the last 30 yr (between 1984-1989 and 2010-2014) by using species distribution models (299,302 occurrences in 30,408 locations) from a hindcasting perspective. Results were grouped by functional guilds to infer potential impacts on ecosystem services, and to relate model transferability (i.e., ability of our models to be generalized to other times and scales) to specific functional and life-history traits. Overall, our models were able to accurately predict, both in space and time, habitat suitability for 69% of species, especially for granivorous, nonmigrant, tree-nesting species, and species that are tied to agricultural areas under intensive use. These findings indicate that model transferability depends upon specific functional and life-history traits, providing further evidence that species' ecologies affect the ability of models to accurately predict bird distributions. Declining bird species were mostly short-distance migrants that were associated with open habitats (agricultural and nonproductive forest) with aerial insectivorous or granivorous diets, which may be related to agricultural intensification and land abandonment. Land-use changes were positive for some forest bird species that were mainly associated with mixed and deciduous forests, generalist diets and tree-nesting strategies. Yet cavity-nesting birds have suffered substantial reductions in their distributions, suggesting that cumulative effects of intensive logging and wildfires on mature forests pose a threat for forest-specialist species. Habitat suitability changes predicted by our coarse-scale species distribution models partially agreed with the long-term trends reported by the North American Breeding Bird Survey. Our findings confirm land-use change as a key driving force for shaping bird communities in southern Quebec, together with the need to explicitly incorporate it into global change scenarios that better inform decision-makers on conservation and management.
Strongman Log Push Press: The Effect Log Diameter has on Force-Time Characteristics

Abstract Renals, L, Lake, J, Keogh, J, and Austin, K. Strongman log push press: The effect log diameter has on force-time characteristics. J Strength Cond Res 32(10): 2693–2700, 2018—Strongman training is becoming more common in strength and conditioning practices, particularly the log press. The existing literature analyzes force characteristics of the log clean and jerk or press compared with the weightlifting clean and jerk exercise. This investigation aims to explore the braking and propulsive phase performance characteristics of the push press with a barbell and strongman logs of different sizes. Ten experienced athletes volunteered to perform the push press exercise using 65% of their 1 repetition maximum using a small-diameter log, a large-diameter log, and a barbell. Analysis of variance showed a significant difference in all mean braking and propulsive characteristics (force, velocity, power, impulse, and displacement) between the barbell and both logs but there was no difference in lift duration. Comparison between both logs showed that the small log had significantly greater power (6%, p = 0.01), velocity (2%, p = 0.01), impulse (5%, p = 0.03), and force (3%, p = 0.01) but no difference in center of mass displacement or lift duration. In addition, propulsive phase when using the barbell was 4.4 times greater in force, 2.2 times in impulse, 1.8 times in velocity, and 2.3 times in power, and this was greater when compared with the larger diameter log. The athletes achieved larger propulsive outputs with a barbell over a log in the push press exercise in addition to showing a higher mechanical demand with a log that increases the larger log diameter, which may mean that the athlete needs to adapt loads when looking to optimize training parameters.
Editorial: Cognitive and Neuroimaging Effects of Chemotherapy: Evidence Across Cancer Types and Treatment Regimens.

Over the past 40years, increasing evidence has been found of cognitive effects of treatments for non–central nervous system (CNS) cancers and of effects prior to systemic treatment sugges-tive of contributions of host or disease factors. The most consistent finding has been cognitive sequelae of systemic chemotherapy. A growing neuroimaging literature has sought to elucidate the neural basis of these changes, largely focusing on breast cancer patients. Findings have included decreased gray matter density and volume, decreased white matter integrity, and altered structural and functional connectivity, which have been shown to correlate with objective neuropsychological performance and subjective cognitive complaints (1–5). Similar effects have recently been found in lung (6) and ovarian (7) cancers. The paper by Amidi et al. (8) in this issue of the Journal adds to this growing literature. Amidi cancer structural
Two new species of Phyllonema (Rivulariaceae, Cyanobacteria) with an emendation of the genus

Two untapered, heterocytous species were observed and collected from the intertidal and supratidal zones of the Mexican coastline of the Pacific Ocean near Oaxaca and from the Gulf of Mexico. These populations were highly similar in morphology to the freshwater taxon Petalonema incrustans in the Scytonemataceae. However, 16S rRNA sequence data and phylogenetic analysis indicated that they were sister taxa to the epiphyllic, Brazilian species Phyllonema aveceniicola in the Rivulariaceae, described from culture material. While genetic identity between the two new species was high, they differed significantly in morphology, 16S rRNA gene sequence identity, and sequence and structure of the 16S–23S ITS region. Their morphology differed markedly from the generitype of the previously monotypic Phyllonema, which has tapered, heteropolar, single‐false branched trichomes with very thin or absent sheath. The two new species, Phyllonema ansata and Phyllonema tangolundensis, described from both culture and environmental material, have untapered, isopolar, geminately false branched trichomes with thick, lamellated sheaths, differences so significant that the species would not be placed in Phyllonema without molecular corroboration. The morphological differences are so significant that a formal emendation of the genus is required. These taxa provide a challenge to algal taxonomy because the morphological differences are such that one would logically conclude that they represent different genera, but the phylogenetic evidence for including them all in the same genus is conclusive. This conclusion is counter to the current trend in algal taxonomy in which taxa with minor morphological differences have been repeatedly placed in separate genera based primarily upon DNA sequence evidence.
Clinically diagnosed urticaria and risk of systemic lupus erythematosus in children: A nationwide population‐based case‐control study

Urticaria is one of the most common diseases seen in clinical practice, whereas several reports have proposed that urticaria may have a link with autoimmune disorders. Few studies have examined the clinical association between urticaria with systemic lupus erythematosus (SLE). By conducting a nationwide population‐based case‐control study in Taiwan, we evaluated the risk of SLE in children with a prior clinical diagnosis of urticaria.
IGF1R Variants in Patients With Growth Impairment: Four Novel Variants and Genotype-Phenotype Correlations

Objective IGF1R gene mutations have been associated with varying degrees of intrauterine and postnatal growth retardation, as well as microcephaly. Both autosomal-dominant and autosomal-recessive inheritance patterns have been reported. This study aimed to analyze the IGF1R gene in children with growth impairment using whole-exome sequencing (WES) and assess the clinical features with the autosomal-dominant and autosomal-recessive models. Methods We performed WES in 28 unrelated patients and found three children harboring IGF1R gene variants. We compared the clinical findings in our cases carrying IGF1R mutations to those in patients reported in the Human Gene Mutation Database (HGMD). Results We identified four IGF1R gene variations by WES in three unrelated patients, including one missense variant [c.3740T>C (p.M1247T)] (patient 1) inherited from an affected mother, one missense variant [c.744T>G (p.C248W)] (patient 2) inherited from an affected father, and two compound heterozygous variations [c.2305G>C (p.E769Q) and c.2684G>A (p.R895Q)] (patient 3). To date, 22 patients have been described as harboring pathogenic variations in IGF1R in the HGMD. We found that patients with compound heterozygous or homozygous variations displayed more severe phenotypes that were mainly characterized by developmental and speech delays, as well as mental retardation. Conclusion We identified four pathogenic variations in the IGF1R gene, which expanded the known mutation spectrum. Through a comparison among patients with reported IGF1R pathogenic variations, this study determined that an autosomal-recessive inheritance model of the IGF1R gene may result in a more severe phenotype with developmental and speech delays, as well as mental retardation.
Assessment of cold sink effect in postulated renal cryoablation by analyzing radiographic ice ball on computed tomography.

OBJECTIVE We analyzed CT characteristics of radiographic ice ball according to anatomical location and freezing number in renal cryoablation. METHODS 30 patients who underwent percutaneous cryoablation for renal lesions. Computed tomography (CT) was conducted at 9 min during every freezing in order to evaluate a radiographic ice ball. Software was used to reconstruct CT images of the radiographic ice ball perpendicular to cryoprobes. For each radiographic ice ball, two types of radius were measured: (a) lateral radius from epicenter to perirenal direction and (b) medial radius from epicenter to renal sinus direction. Lateral and medial radius or diameters (lateral radius plus medial radius) during the first and second freezing were compared using paired t-test, respectively. RESULTS Medial radius of radiographic ice ball was significantly shorter than lateral radius (first freezing, 13.8 vs 17.0 mm, p < 0.001; second freezing, 16.0 vs 19.3 mm, p < 0.001). The diameter during the second freezing was significantly longer than that during the first freezing (35.3 vs 30.8 mm, p < 0.001). CONCLUSION In renal cryoablation, evaluating radiographic ice ball helps identify potential postulated cold sink effect in the central portion of kidney. Advances in knowledge: Radiologic information of postulated cold sink effect in the kidney may help secure sufficient safety margins.
Evolution of Sex-Biased Gene Expression and Dosage Compensation in the Eye and Brain of Heliconius Butterflies.

Differences in behavior and life history traits between females and males are the basis of divergent selective pressures between sexes. It has been suggested that a way for the two sexes to deal with different life history requirements is through sex-biased gene expression. In this study, we performed a comparative sex-biased gene expression analysis of the combined eye and brain transcriptome from ﬁve Heliconius species, H. charithonia , H. sara , H. erato , H. melpomene and H. doris , representing ﬁve of the main clades from the Heliconius phylogeny. We found that the degree of sexual dimorphism in gene expression is not conserved across Heliconius . Most of the sex-biased genes identiﬁed in each species are not sex-biased in any other, suggesting that sexual selection might have driven sexually dimorphic gene expression. Only three genes shared sex-biased expression across multiple species: ultraviolet opsin UVRh1 and orthologs of Drosophila Kru¨ppel-homolog 1 and CG9492 . We also observed that in some species female-biased genes have higher evolutionary rates, but in others, male-biased genes show the fastest rates when compared with unbiased genes, suggesting that selective forces driving sex-biased gene evolution in Heliconius act in a sex- and species-speciﬁc manner. Furthermore, we found dosage compensation in all the Heliconius tested, providing additional evidence for the conservation of dosage compensation across Lepidoptera. Finally, sex-biased genes are signiﬁcantly enriched on the Z, a pattern that could be a result of sexually antagonistic selection.
[FeFe]-Hydrogenase Mimetic Metallopolymers with Enhanced Catalytic Activity for Hydrogen Production in Water.

Electrocatalytic [FeFe]-hydrogenase mimics for the hydrogen evolution reaction (HER) generally suffer from low activity, high overpotential, aggregation, oxygen sensitivity, and low solubility in water. By using atom-transfer radical polymerization (ATRP), a new class of [FeFe]-metallopolymers with precise molar mass, defined composition, and low polydispersity, has been prepared. The synthetic methodology introduced here allows facile variation of polymer composition to optimize the [FeFe] solubility, activity, and long-term chemical and aerobic stability. Water soluble functional metallopolymers facilitate electrocatalytic hydrogen production in neutral water with loadings as low as 2 ppm and operate at rates an order of magnitude faster than hydrogenases (2.5×105 s-1 ), and with low overpotential requirement. Furthermore, unlike the hydrogenases, these systems are insensitive to oxygen during catalysis, with turnover numbers on the order of 40 000 under both anaerobic and aerobic conditions.
Generating a high-confidence reference genome map of the Greater Duckweed by integration of cytogenomic, optical mapping, and Oxford Nanopore technologies.

Duckweeds are the fastest growing angiosperms and have the potential to become a new generation of sustainable crops. Although a seed plant, Spirodela polyrhiza clones rarely flower and multiply mainly through vegetative propagation. Whole-genome sequencing using different approaches and clones yielded two reference maps. One for clone 9509, supported in its assembly by optical mapping of single DNA molecules, and one for clone 7498, supported by cytogenetic assignment of 96 fingerprinted bacterial artificial chromosomes (BACs) to its 20 chromosomes. However, these maps differ in the composition of several individual chromosome models. We validated both maps further to resolve these differences and addressed whether they could be due to chromosome rearrangements in different clones. For this purpose, we applied sequential multicolor fluorescence in situ hybridization (mcFISH) to seven S. polyrhiza clones, using 106 BACs that were mapped onto the 39 pseudomolecules for clone 7498. Furthermore we integrated high-depth Oxford Nanopore (ON) sequence data for clone 9509 to validate and revise the previously assembled chromosome models. We found no major structural rearrangements between these seven clones, identified seven chimeric pseudomolecules and Illumina assembly errors in the previous maps, respectively. A new S. polyrhiza genome map with high contiguity was produced with the ON sequence data and genome-wide synteny analysis supported the occurrence of two Whole Genome Duplication events during its evolution. This work generated a high confidence genome map for S. polyrhiza at the chromosome scale, and illustrates the complementarity of independent approaches to produce whole-genome assemblies in the absence of a genetic map.
Patient iPSC‐derived neural stem cells exhibit phenotypes in concordance with the clinical severity of mucopolysaccharidosis I

Abstract Mucopolysaccharidosis type I (MPS I) is caused by deficiency of &agr;‐l‐iduronidase (IDUA), a lysosomal enzyme involved in the breakdown and recycling of glycosaminoglycans (GAGs). Although enzyme replacement therapy is available, the efficacy of the treatment for neuropathic manifestations is limited. To facilitate drug discovery and model disease pathophysiology, we generated neural stem cells (NSCs) from MPS I patient‐derived induced pluripotent stem cells (iPSCs). The NSCs exhibited characteristic disease phenotypes with deficiency of IDUA, accumulation of GAGs and enlargement of lysosomes, in agreement with the severity of clinical subgroups of MPS I. Transcriptome profiling of NSCs revealed 429 genes that demonstrated a more extensive change in expression in the most severe Hurler syndrome subgroup compared to the intermediate Hurler‐Scheie or the least severe Scheie syndrome subgroups. Clustering and pathway analysis revealed high concordance of the severity of neurological defects with marked dysregulation of GAG biosynthesis, GAG degradation, lysosomal function and autophagy. Gene ontology (GO) analysis identified a dramatic upregulation of the autophagy pathway, especially in the Hurler syndrome subgroup. We conclude that GAG accumulation in the patient‐derived cells disrupts lysosomal homeostasis, affecting multiple related cellular pathways in response to IDUA deficiency. These dysregulated processes likely lead to enhanced autophagy and progressively severe disease states. Our study provides potentially useful targets for clinical biomarker development, disease diagnosis and prognosis, and drug discovery.
Are physical fitness outcomes in patients attending cardiac rehabilitation determined by the mode of delivery?

Background Cardiac rehabilitation (CR) is a well-evidenced and effective secondary intervention proven to reduce mortality and readmission in patients with cardiovascular disease. Improving physical fitness outcomes is a key target for CR programmes, with supervised group-based exercise dominating the mode of the delivery. However, the method of traditional supervised CR fails to attract many patients and may not be the only way of improving physical fitness. Methods Using real-world routine clinical data from the National Audit of Cardiac Rehabilitation across a 5-year period, this study evaluates the extent of association between physical fitness outcomes, incremental shuttle walk and 6 min walk test, and mode of delivery, delivered as traditional supervised versus facilitated self-delivered. Results The proportion of patients receiving each mode were 80.6% supervised with 19.4% to self-delivered. The study analysis comprised of 10 142 patients who were included in the two models. The self-delivered group contained a greater proportion of females and older patients. The regression model showed no clinical or statistical significance between mode of delivery and post-CR physical fitness outcomes. Conclusions This study is unique as it has identified through a routine clinical population that regardless of the mode of delivery of rehabilitation, patients improve their physical fitness outcomes at meaningful levels. This study provides a strong evidence base for patients to be offered greater choice in the mode of CR delivery as improvements in physical fitness are comparable.
Anthrax protective antigen is a calcium-dependent serine protease

ABSTRACT Bacillus anthracis secretes a three component exotoxin-complex, which contributes to anthrax pathogenesis. Formation of this complex starts with the binding of protective antigen (PA) to its cellular receptor. In this study, we report that PA is a calcium-dependent serine protease and that the protein potentially uses this proteolytic activity for receptor binding. Additionally our findings shed new light on previous research describing the inhibition of anthrax toxins and exotoxin formation. Importantly, inhibition of the proteolytic activity of protective antigen could be a novel therapeutic strategy in fighting B. anthracis-related infections.
Secondary metabolite production and the safety of industrially important members of the Bacillus subtilis group

Abstract Members of the ‘Bacillus subtilis group’ include some of the most commercially important bacteria, used for the production of a wide range of industrial enzymes and fine biochemicals. Increasingly, group members have been developed for use as animal feed enhancers and antifungal biocontrol agents. The group has long been recognised to produce a range of secondary metabolites and, despite their long history of safe usage, this has resulted in an increased focus on their safety. Traditional methods used to detect the production of secondary metabolites and other potentially harmful compounds have relied on phenotypic tests. Such approaches are time consuming and, in some cases, lack specificity. Nowadays, accessibility to genome data and associated bioinformatical tools provides a powerful means for identifying gene clusters associated with the synthesis of secondary metabolites. This review focuses primarily on well-characterised strains of B. subtilis and B. licheniformis and their synthesis of non-ribosomally synthesised peptides and polyketides. Where known, the activities and toxicities of their secondary metabolites are discussed, together with the limitations of assays currently used to assess their toxicity. Finally, the regulatory framework under which such strains are authorised for use in the production of food and feed enzymes is also reviewed.
Phrenic neuropathy and diaphragm dysfunction in neuralgic amyotrophy

Objective To describe the clinical phenotype and recovery of diaphragm dysfunction caused by neuralgic amyotrophy in a large cohort of patients, to improve accurate awareness of this entity, and to encourage adoption of a standardized approach for diagnosis and treatment. Methods This observational cohort study recruited adult patients with neuralgic amyotrophy and symptoms of idiopathic phrenic neuropathy from the database of the Dutch expert center for neuralgic amyotrophy and the Dutch centers for home mechanical ventilation. Demographic and clinical information on diagnosis, symptoms, and recovery was obtained from chart review. We attempted to contact all patients for a follow-up interview. Results Phrenic neuropathy occurs in 7.6% of patients with neuralgic amyotrophy. Unilateral diaphragmatic dysfunction and bilateral diaphragmatic dysfunction are frequently symptomatic, causing exertional dyspnea, orthopnea, disturbed sleep, and excessive fatigue. Diagnostic practices varied widely and were often not optimally targeted. The majority of patients experienced at least moderate recovery within 2 years. Conclusion We recommend screening every patient with neuralgic amyotrophy for diaphragm dysfunction by asking about orthopnea and by performing upright and supine vital capacity screening and diaphragm ultrasound in cases of suspected phrenic neuropathy to optimize diagnosis and care.
Transcription and mRNA export machineries SAGA and TREX-2 maintain monoubiquitinated H2B balance required for DNA repair

DNA repair is critical to maintaining genome integrity, and its dysfunction can cause accumulation of unresolved damage that leads to genomic instability. The Spt–Ada–Gcn5 acetyltransferase (SAGA) coactivator complex and the nuclear pore–associated transcription and export complex 2 (TREX-2) couple transcription with mRNA export. In this study, we identify a novel interplay between human TREX-2 and the deubiquitination module (DUBm) of SAGA required for genome stability. We find that the scaffold subunit of TREX-2, GANP, positively regulates DNA repair through homologous recombination (HR). In contrast, DUBm adaptor subunits ENY2 and ATXNL3 are required to limit unscheduled HR. These opposite roles are achieved through monoubiquitinated histone H2B (H2Bub1). Interestingly, the activity of the DUBm of SAGA on H2Bub1 is dependent on the integrity of the TREX-2 complex. Thus, we describe the existence of a functional interaction between human TREX-2 and SAGA DUBm that is key to maintaining the H2B/HB2ub1 balance needed for efficient repair and HR.