Miracle-dz/UniFAR-FTUs huggingface dataset:
Indirect effects of African megaherbivore conservation on bat diversity in the world's oldest desert

In extreme environments, temperature and precipitation are often the main forces responsible for structuring ecological communities and species distributions. The role of biotic interactions is typically thought to be minimal. By clustering around rare and isolated features, like surface water, however, effects of herbivory by desert‐dwelling wildlife can be amplified. Understanding how species interact in these environments is critical to safeguarding vulnerable or data‐deficient species. We examined whether African elephants (Loxodonta africana), black rhinoceros (Diceros bicornis), and southern giraffe (Giraffa giraffa) modulate insectivorous bat communities around permanent waterholes in the Namib Desert. We estimated megaherbivore use of sites based on dung transects, summarized vegetation productivity from satellite measurements of the normalized difference vegetation index, and surveyed local bat communities acoustically. We used structural equation models to identify relationships among megaherbivores and bat species richness and dry‐ (November 2016–January 2017) and wet‐ (February–May 2017) season bat activity. Site‐level megaherbivore use in the dry season was positively associated with bat activity—particularly that of open‐air foragers—and species richness through indirect pathways. When resources were more abundant (wet season), however, these relationships were weakened. Our results indicate that biotic interactions contribute to species distributions in desert areas and suggest the conservation of megaherbivores in this ecosystem may indirectly benefit insectivorous bat abundance and diversity. Given that how misunderstood and understudied most bats are relative to other mammals, such findings suggest that managers pursue short‐term solutions (e.g., community game guard programs, water‐point protection near human settlements, and ecotourism) to indirectly promote bat conservation and that research includes megaherbivores’ effects on biodiversity at other trophic levels.
Persistent Submicroscopic Plasmodium falciparum Parasitemia 72 Hours after Treatment with Artemether-Lumefantrine Predicts 42-Day Treatment Failure in Mali and Burkina Faso

A recent randomized controlled trial, the WANECAM (West African Network for Clinical Trials of Antimalarial Drugs) trial, conducted at seven centers in West Africa, found that artemether-lumefantrine, artesunate-amodiaquine, pyronaridine-artesunate, and dihydroartemisinin-piperaquine all displayed good efficacy. However, artemether-lumefantrine was associated with a shorter interval between clinical episodes than the other regimens. ABSTRACT A recent randomized controlled trial, the WANECAM (West African Network for Clinical Trials of Antimalarial Drugs) trial, conducted at seven centers in West Africa, found that artemether-lumefantrine, artesunate-amodiaquine, pyronaridine-artesunate, and dihydroartemisinin-piperaquine all displayed good efficacy. However, artemether-lumefantrine was associated with a shorter interval between clinical episodes than the other regimens. In a further comparison of these therapies, we identified cases of persisting submicroscopic parasitemia by quantitative PCR (qPCR) at 72 h posttreatment among WANECAM participants from 5 sites in Mali and Burkina Faso, and we compared treatment outcomes for this group to those with complete parasite clearance by 72 h. Among 552 evaluable patients, 17.7% had qPCR-detectable parasitemia at 72 h during their first treatment episode. This proportion varied among sites, reflecting differences in malaria transmission intensity, but did not differ among pooled drug treatment groups. However, patients who received artemether-lumefantrine and were qPCR positive at 72 h were significantly more likely to have microscopically detectable recurrent Plasmodium falciparum parasitemia by day 42 than those receiving other regimens and experienced, on average, a shorter interval before the next clinical episode. Haplotypes of pfcrt and pfmdr1 were also evaluated in persisting parasites. These data identify a possible threat to the parasitological efficacy of artemether-lumefantrine in West Africa, over a decade since it was first introduced on a large scale.
Multiword units lead to errors of commission in children's spontaneous production: “What corpus data can tell us?*”

Abstract Psycholinguistic research over the past decade has suggested that children's linguistic knowledge includes dedicated representations for frequently‐encountered multiword sequences. Important evidence for this comes from studies of children's production: it has been repeatedly demonstrated that children's rate of speech errors is greater for word sequences that are infrequent and thus unfamiliar to them than for those that are frequent. In this study, we investigate whether children's knowledge of multiword sequences can explain a phenomenon that has long represented a key theoretical fault line in the study of language development: errors of subject‐auxiliary non‐inversion in question production (e.g., “why we can't go outside? *”). In doing so we consider a type of error that has been ignored in discussion of multiword sequences to date. Previous work has focused on errors of omission – an absence of accurate productions for infrequent phrases. However, if children make use of dedicated representations for frequent sequences of words in their productions, we might also expect to see errors of commission – the appearance of frequent phrases in children's speech even when such phrases are not appropriate. Through a series of corpus analyses, we provide the first evidence that the global input frequency of multiword sequences (e.g., “she is going” as it appears in declarative utterances) is a valuable predictor of their errorful appearance (e.g., the uninverted question “what she is going to do? *”) in naturalistic speech. This finding, we argue, constitutes powerful evidence that multiword sequences can be represented as linguistic units in their own right.
Physicochemical characterization and in vitro antioxidant activity of hyaluronic acid produced by Streptococcus zooepidemicus CCT 7546

Abstract Hyaluronic acid (HA) is a biopolymer with applications in different areas such as medicine and cosmetics. HA is currently either isolated from animal sources or produced by microbial fermentation. Animal HA presents some disadvantages such as high cost and risk of viral cross-species or another infectious agent. In the present study, we evaluated the physicochemical characteristics and in vitro antioxidant capacity of HA produced by Streptococcus zooepidemicus CCT 7546. In addition, commercial sodium hyaluronate (SH) from an animal source was used as control. The microbial HA yield after purification was 69.8 mg/L. According to Fourier transform infrared spectroscopy, it was seen that bacterial and animal HA spectra are overlapped. The thermogravimetric analysis revealed that microbial HA was more stable than its equivalent from the animal source. However, scanning electron microscopy indicates that the purification method used in the animal product was more effective. Microbial HA showed activity in total antioxidant capacity (14.02 ± 0.38%), reducing power (18.18 ± 6.43%), DPPH radical-scavenging (5.57 ± 0.23 kmol TE/g), and hydroxyl radical-scavenging (28.39 ± 2.40%) tests. Therefore, in vitro antioxidant tests demonstrated that the antioxidant action mechanism occurs through scavenging reactive oxygen species (ROS) and donating electrons/hydrogen atoms. Graphical Abstract
MiR-379-5p aggravates experimental autoimmune uveitis in mice via the regulation of SEMA3A

Abstract Uveitis is a disease resulting in the inflammation of uveal tracts, but the factors resulting in uveitis is still obscure. Previous studies have shown that miR-379-5p was involved in the pathogenesis of several diseases, however, the role and regulatory mechanism of miR-379-5p in uveitis were unclear. In our study, we established experimental autoimmune uveitis (EAU) mouse models to explore the role of miR-379-5p in uveitis. RT-qPCR identified that miR-379-5p level was increased in serum of EAU mice. In mechanism, SEMA3A 3’UTR was proven to be directly targeted by miR-379-5p and SEMA3A expression was negatively regulated by miR-379-5p in CD4+ T cells. Moreover, ELISA analysis revealed that knockdown of miR-379-5p suppressed the production of inflammation cytokines including IL-17, TNF-α and IL-β in vitro. These results were reversed by SEMA3A overexpression. In addition, the reduction of Th17 cells under miR-379-5p inhibitor was neutralised by SEMA3A knockdown in vitro. Furthermore, we demonstrated that knockdown of miR-379-5p significantly reversed the increased clinical scores and inflammatory response resulting from EAU treatment and this effect was further countervailed by SEMA3A silencing. Our study suggested that miR-379-5p aggravated uveitis in EAU mice via the regulation of SEMA3A, which may provide a novel insight for uveitis treatment.
Frequency of Binge Drinking and Perception of Peer Alcohol Use

Abstract Objectives College and university student binge drinking is a critical health issue, and studies demonstrate students perceive high rates of drinking among their peers. High alcohol consumption and binge drinking are normalized throughout college and university, and there are gross misperceptions of perceived alcohol use among peers. The purpose of our study was to examine differences in perceptions of peer alcohol use after grouping students based on their frequency of binge drinking over a 2-week period. Methods A one-way analysis of variance test was used to compare the differences in the perception of peer alcohol use after grouping students by their frequency of binge drinking. Results Students who binge drink have significantly higher perceptions of peer alcohol use than their non-binge-drinking and abstaining peers. Conclusions These findings provide direction toward the feasibility of using perceptions of peer alcohol use to identify at-risk students to curtail dangerous drinking behavior.
Loss of Fis1 impairs proteostasis during skeletal muscle aging in Drosophila

Increased levels of dysfunctional mitochondria within skeletal muscle are correlated with numerous age‐related physiopathological conditions. Improving our understanding of the links between mitochondrial function and muscle proteostasis, and the role played by individual genes and regulatory networks, is essential to develop treatments for these conditions. One potential player is the mitochondrial outer membrane protein Fis1, a crucial fission factor heavily involved in mitochondrial dynamics in yeast but with an unknown role in higher‐order organisms. By using Drosophila melanogaster as a model, we explored the effect of Fis1 mutations generated by transposon Minos‐mediated integration. Mutants exhibited a higher ratio of damaged mitochondria with age as well as elevated reactive oxygen species levels compared with controls. This caused an increase in oxidative stress, resulting in large accumulations of ubiquitinated proteins, accelerated muscle function decline, and mitochondrial myopathies in young mutant flies. Ectopic expression of Fis1 isoforms was sufficient to suppress this phenotype. Loss of Fis1 led to unbalanced mitochondrial proteostasis within fly muscle, decreasing both flight capabilities and lifespan. Fis1 thus clearly plays a role in fly mitochondrial dynamics. Further investigations into the detailed function of Fis1 are necessary for exploring how mitochondrial function correlates with muscle health during aging.
A case of distal limb arterial tortuosity and dilation: observations and potential clinical significance.

Arterial tortuosity describes variation via bending of the arterial wall and has been noted in several arteries throughout the body. Tortuous blood vessels can cause nerve compression, as well as present difficulties to surgeons and radiologists. Here we present an unusual case of multi-vessel arterial tortuosity discovered in 78-year-old Hispanic male cadaver, independent of systemic pathology. The left ulnar and right tibial arteries were dissected, and using calibrated digital calipers, their external and internal diameters were measured both at the origin site and at the site of greatest dilation. Both wall thickness and the number of inflection points were also measured. Six bends were noticed in the ulnar artery and its diameter measured 8.11 mm at its widest, with a wall thickness of 0.88mm. On the lower extremity, the right tibial artery had three bends and its diameter measured 4.86 mm at its widest, with a wall thickness of 1.32 mm. This uncommon tortuosity is not only more prone to laceration during surgery, but the bending and thickening can be mistaken for tumors. Finally, fluid dynamics can be altered, resulting in an impact on blood pressure in the extremities. Thus, raising awareness is crucial to prevent both symptoms and iatrogenic complications.
Vascularization strategies in tissue engineering approaches for soft tissue repair

Insufficient vascularization during tissue repair is often associated with poor clinical outcomes. This is a concern especially when patients have critical‐sized injuries, where the size of the defect restricts vascularity, or even in small defects that have to be treated under special conditions, such as after radiation therapy (relevant to tumor resection) that hinders vascularity. In fact, poor vascularization is one of the major obstacles for clinical application of tissue engineering methods in soft tissue repair. As a key issue, lack of graft integration, caused by inadequate vascularization after implantation, can lead to graft failure. Moreover, poor vascularization compromises the viability of cells seeded in deep portions of scaffolds/graft materials, due to hypoxia and insufficient nutrient supply. In this article we aim to review vascularization strategies employed in tissue engineering techniques to repair soft tissues. For this purpose, we start by providing a brief overview of the main events during the physiological wound healing process in soft tissues. Then, we discuss how tissue repair can be achieved through tissue engineering, and considerations with regards to the choice of scaffold materials, culture conditions, and vascularization techniques. Next, we highlight the importance of vascularization, along with strategies and methods of prevascularization of soft tissue equivalents, particularly cell‐based prevascularization. Lastly, we present a summary of commonly used in vitro methods during the vascularization of tissue‐engineered soft tissue constructs.
Genetic code expansion enables visualization of Salmonella type three secretion system components and secreted effectors

Type three secretion systems enable bacterial pathogens to inject effectors into the cytosol of eukaryotic hosts to reprogram cellular functions. It is technically challenging to label effectors and the secretion machinery without disrupting their structure/function. Herein, we present a new approach for labeling and visualization of previously intractable targets. Using genetic code expansion, we site-specifically labeled SsaP, the substrate specificity switch, and SifA, a here-to-fore unlabeled secreted effector. SsaP was secreted at later infection times; SsaP labeling demonstrated the stochasticity of injectisome and effector expression. SifA was labeled after secretion into host cells via fluorescent unnatural amino acids or non-fluorescent labels and a subsequent click reaction. We demonstrate the superiority of imaging after genetic code expansion compared to small molecule tags. It provides an alternative for labeling proteins that do not tolerate N- or C-terminal tags or fluorophores and thus is widely applicable to other secreted effectors and small proteins.
Chitin Deacetylases are Required for Epichloë festucae Endophytic Cell Wall Remodelling During Establishment of a Mutualistic Symbiotic Interaction with Lolium perenne.

Epichloë festucae forms a mutualistic symbiotic association with Lolium perenne. This biotrophic fungus systemically colonizes the intercellular spaces of aerial tissues to form an endophytic hyphal network, and also grows as an epiphyte. However, little is known about the cell wall remodelling mechanisms required to avoid host defence and maintain intercalary growth within the host. Here we use a suite of molecular probes to show that the E. festucae cell wall is remodelled by conversion of chitin to chitosan during infection of L. perenne seedlings as the hyphae switch from free-living to endophytic growth. When hyphae transition from endophytic to epiphytic growth the cell wall is remodelled from predominantly chitosan to chitin. This conversion from chitin to chitosan is catalysed by chitin deacetylase. The genome of E. festucae encodes three putative chitin deacetylases, two of which (cdaA and cdaB) are expressed in planta. Deletion of either of these genes results in disruption of fungal intercalary growth in the intercellular spaces of plants infected with these mutants. These results establish that these two genes are required for maintenance of the mutualistic symbiotic interaction between E. festucae and L. perenne.
Effects of Combined and Alone Transcranial Motor Cortex Stimulation and Mirror Therapy in Phantom Limb Pain: A Randomized Factorial Trial

Phantom limb pain (PLP) is a frequent complication in amputees, which is often refractory to treatments. We aim to assess in a factorial trial the effects of transcranial direct current stimulation (tDCS) and mirror therapy (MT) in patients with traumatic lower limb amputation; and whether the motor cortex plasticity changes drive these results. In this large randomized, blinded, 2-site, sham-controlled, 2 × 2 factorial trial, 112 participants with traumatic lower limb amputation were randomized into treatment groups. The interventions were active or covered MT for 4 weeks (20 sessions, 15 minutes each) combined with 2 weeks of either active or sham tDCS (10 sessions, 20 minutes each) applied to the contralateral primary motor cortex. The primary outcome was PLP changes on the visual analogue scale at the end of interventions (4 weeks). Motor cortex excitability and cortical mapping were assessed by transcranial magnetic stimulation (TMS). We found no interaction between tDCS and MT groups (F = 1.90, P = .13). In the adjusted models, there was a main effect of active tDCS compared to sham tDCS (beta coefficient = −0.99, P = .04) on phantom pain. The overall effect size was 1.19 (95% confidence interval: 0.90, 1.47). No changes in depression and anxiety were found. TDCS intervention was associated with increased intracortical inhibition (coefficient = 0.96, P = .02) and facilitation (coefficient = 2.03, P = .03) as well as a posterolateral shift of the center of gravity in the affected hemisphere. MT induced no motor cortex plasticity changes assessed by TMS. These findings indicate that transcranial motor cortex stimulation might be an affordable and beneficial PLP treatment modality.
Surveillance for SARS‐CoV‐2 variants of concern in the Australian context

Genomic sequencing of the severe acute respiratory syndrome coronavirus 2 (SARSCoV2) has been rapidly implemented and scaledup in Australia and globally during the first 12 months of the coronavirus disease 2019 (COVID19) pandemic. This has allowed an unprecedented view of viral evolution in near realtime. As with all microbes, the natural evolutionary process introduces changes in the SARSCoV2 genome, with some changes providing new variants with improved fitness. This may manifest as changes in viral behaviour, such as transmission, disease severity, immune evasion or vaccine efficacy, and may also affect diagnostic sensitivity.1 The COVID19 pandemic has seen pathogen genomics integrated into daytoday public health responses in many countries, including in Australia.25 Moreover, a global collective sequencing effort has generated more than 1 000 000 publicly available sequences on the Global Initiative for Sharing Avian Influenza Data (GISAID; www.gisaid. org) platform. In Australia, SARSCoV2 genomic data have become a vital tool routinely used to support outbreak investigations and to trace international incursions.2 These data are now an expected element of government briefings to mainstream media. While the mutation rate of SARSCoV2 is relatively low at one to two substitutions per month, the natural selective pressure occurring during sustained transmission among the high global case numbers, and long term infections in immunocompromised individuals, provides opportunities for SARSCoV2 to adapt. Genomic sequencing data are now vital in the global surveillance efforts of variant detection and for linking defined variants to viral behaviour of particular concern for the control and management of the pandemic.
Control of the Serine Integrase Reaction: Roles of the Coiled-Coil and Helix E Regions in DNA Site Synapsis and Recombination

The robust and exquisitely regulated site-specific recombination reactions promoted by serine integrases are integral to the life cycle of temperate bacteriophage and, in the case of the A118 prophage, are an important virulence factor of Listeria monocytogenes. The properties of these recombinases have led to their repurposing into tools for genetic engineering and synthetic biology. ABSTRACT Bacteriophage serine integrases catalyze highly specific recombination reactions between defined DNA segments called att sites. These reactions are reversible depending upon the presence of a second phage-encoded directionality factor. The bipartite C-terminal DNA-binding region of integrases includes a recombinase domain (RD) connected to a zinc-binding domain (ZD), which contains a long flexible coiled-coil (CC) motif that extends away from the bound DNA. We directly show that the identities of the phage A118 integrase att sites are specified by the DNA spacing between the RD and ZD DNA recognition determinants, which in turn directs the relative trajectories of the CC motifs on each subunit of the att-bound integrase dimer. Recombination between compatible dimer-bound att sites requires minimal-length CC motifs and 14 residues surrounding the tip where the pairing of CC motifs between synapsing dimers occurs. Our alanine-scanning data suggest that molecular interactions between CC motif tips may differ in integrative (attP × attB) and excisive (attL × attR) recombination reactions. We identify mutations in 5 residues within the integrase oligomerization helix that control the remodeling of dimers into tetramers during synaptic complex formation. Whereas most of these gain-of-function mutants still require the CC motifs for synapsis, one mutant efficiently, but indiscriminately, forms synaptic complexes without the CC motifs. However, the CC motifs are still required for recombination, suggesting a function for the CC motifs after the initial assembly of the integrase synaptic tetramer. IMPORTANCE The robust and exquisitely regulated site-specific recombination reactions promoted by serine integrases are integral to the life cycle of temperate bacteriophage and, in the case of the A118 prophage, are an important virulence factor of Listeria monocytogenes. The properties of these recombinases have led to their repurposing into tools for genetic engineering and synthetic biology. In this report, we identify determinants regulating synaptic complex formation between correct DNA sites, including the DNA architecture responsible for specifying the identity of recombination sites, features of the unique coiled-coil structure on the integrase that are required to initiate synapsis, and amino acid residues on the integrase oligomerization helix that control the remodeling of synapsing dimers into a tetramer active for DNA strand exchange.