Miracle-dz/UniFAR-FTUs huggingface dataset:
Elevation and the Morphology, Flight Energetics, and Foraging Ecology of Tropical Hummingbirds

The power that a hummingbird must expend to hover increases with decreasing air density and therefore with increasing elevation. Equations are available for estimating this power output requirement and for computing the easily obtained parameter of wing disc loading (ratio of body weight to area of disc whose diameter is wing span), to which power output is directly related. We test four related predictions based on these equations and on empirical patterns of exploitation versus interference competition among hummingbirds. (1) Species having the same morphology over broad elevational range are expected to engage in more interference competition at high elevations. (2) The allowable extremes of power output for hovering should be relatively constant with elevation. (3) Mean wing disc loading of hummingbird assemblages should decrease with increasing elevation. (4) The mean power output among hummingbird assemblages should not vary with elevation. Tests with field data verify the last three predictions; although independent data for testing the first prediction directly are not yet available, its validity is confirmed by a clearcut corollary. These results imply a precise interrelationship between hummingbird behavior, morphology, energetics, and competition.
Developmental eye disease — a genome era paradigm

Charles Darwin described eyes as ‘organs of extreme perfection and complication’, aware that their diversity across different phyla posed a strong challenge to his theory of evolution by gradual change through fully functional intermediate forms. Eye design vanes enormously through evolution from simple eye spots through compound eyes to single lens and photoreceptor array eyes (1, 2). It now seems that eyes evolved repeatedly, perhaps as many as 40 times, each time utilising a series of pre-determined building blocks: genes already co-adapted to work together in sensorineural development (2). PAX6 brought home this concept for eye development when mutant vertebrate and fly homologues were shown cause eyeless phenotypes (3-5). Evidence for involvement of conserved interacting ‘gene cassettes’ emerged as molecular analysis of visual function in several species from Drosophila to man became feasible (6, 7). Conserved gene usage is also seen in many other developmental systems (8, 9). The vertebrate eye is a complex organ whose development, with contributions from surface ectoderm, neural ectoderm, neural crest and mesodermal mesenchyme, is well documented (10, 11). The retina is frequently used as an accessible model system to study neural differentiation (12, 13). The
Attractiveness of color traps to Strobilomyia spp. (Diptera: Anthomyiidae)

We field-tested two sticky traps used to monitor populations of Strobilomyia spp. developing in the French Alps: a bright yellow horizontal trap and a bright yellow vertical trap with purple stripes. Fluorescent yellow traps captured significantly more flies than nonfluorescent yellow traps. Males of Strobilomyia melania Ackland were trapped significantly more often than females of other Strobilomyia species regardless of sex. Significantly more males were trapped per week when males were removed daily rather than weekly. Spectral patterns of the colors used in this experiment changed only slightly after 1 wk of exposure to sunlight and did not affect the daily captures of flies.
Effects of quercetin on the gastrointestinal tract in rats and mice

Intraperitoneal administration of quercetin (6.25–50 mg/kg) significantly (p<0.5‐0.01) reduced intestinal transit in mice and this effect was antagonized by yohimbine and phentolamine but not by atropine or naloxone. Quercetin (12.5–50 mg/kg) reduced also (p<0.05‐0.01) intraluminal accumulation of fluid and diarrhoea induced by castor oil and these effects were antagonized by yohimbine. Finally quercetin (12.5–50 mg/kg) reduced the area of gastric ulcer but not the number. It is suggested that α2‐adrenergic receptors mediate the effect of quercetin on intestinal motility and secretion.
Divergent Evolution of Mutation Rates and Biases in the Long-Term Evolution Experiment with Escherichia coli

All organisms encode enzymes that replicate, maintain, pack, recombine, and repair their genetic material. For this reason, mutation rates and biases also evolve by mutation, variation, and natural selection. By examining metagenomic time series of the Lenski long-term evolution experiment (LTEE) with Escherichia coli (Good, et al. 2017), we find that local mutation rate variation has evolved during the LTEE. Each LTEE population has evolved idiosyncratic differences in their rates of point mutations, indels, and mobile element insertions, due to the fixation of various hypermutator and antimutator alleles. One LTEE population, called Ara+3, shows a strong, symmetric wave pattern in its density of point mutations, radiating from the origin of replication. This pattern is largely missing from the other LTEE populations, most of which evolved missense, indel, or structural mutations in topA, fis, and dusB— loci that all affect DNA topology. The distribution of mutations in those genes over time suggests epistasis and historical contingency in the evolution of DNA topology, which may have in turn affected local mutation rates. Overall, the replicate populations of the LTEE have largely diverged in their mutation rates and biases, even though they have adapted to identical abiotic conditions.
The coupling of global brain activity and cerebrospinal fluid inflow is correlated with Alzheimer’s disease related pathology

The glymphatic system plays an important role in clearing the amyloid-β and tau proteins that are closely linked to Alzheimer’s disease (AD) pathology. Glymphatic clearance, as well as amyloid-β accumulation, is highly dependent on sleep, but the sleep-dependent driving forces behind cerebrospinal fluid (CSF) movements essential to the glymphatic flux remain largely unclear. Recent studies have reported that widespread, high-amplitude spontaneous brain activations in the drowsy state and during sleep, which are shown as large global signal peaks in resting-state fMRI, is coupled with the CSF movements, suggesting their potential link to the glymphatic flux and metabolite clearance. By analyzing multimodal data from the Alzheimer’s Disease Neuroimaging Initiative project, here we showed that the coupling between the global fMRI signal and CSF influx is correlated with AD-related pathology, including various risk factors for AD, the severity of AD-related diseases, the cortical amyloid-β level, and the cognitive decline over a two-year follow-up. These results provide critical initial evidence for involvement of sleep-dependent global brain activity, as well as the associated physiological modulations, in the clearance of AD-related brain waste.
A phylogenetic supertree of oscine passerine birds (Aves: Passeri)

Oscine passerine birds make up almost half of all avian diversity. Relationships within the group, and its classification, have long been controversial. Over the last 10 years numerous molecular phylogenies have been published. We compiled source phylogenies from 99 published studies to construct an oscine supertree. We aimed to illustrate weak and strong parts of the phylogeny and set targets for future phylogenetic work and therefore preferred a heuristic approach where we judged the adequacy of taxon sampling and molecular method of each source tree instead of using matrices and automated tree‐building programs. We present an estimate of the phylogenetic relationships of 1723 extant and one extinct species of oscine passerine birds (Aves: Passeri) — more than 37% of the total. We included 34/35 (97%) families, 38/39 (97%) subfamilies and 40/43 (93%) tribes. Overall resolution is 83% of a fully bifurcating tree. The basal lineages are all distributed in the Australo‐Papuan region, but several more distal lineages dispersed out of this region and radiated in other parts of the world. However, taxa of the Australian region suffer from larger evolutionary gaps and the deep branches of the Sylvioidea and nine South American primaried oscines are still poorly resolved.
Hunting rates and hunting success in the spotted hyena (Crocuta crocuta)

Hunting group size, hunting rates and hunting success were monitored over a seven-year period among members of one large clan of spotted hyenas (Crocuta crocuta) inhabiting the Masai Mara National Reserve, in south-west Kenya. Prey availability varied seasonally in this study area, and hyenas tended to hunt whichever prey species were most abundant during each month of the year. Over 75% of 272 hunting attempts were made by lone hyenas, even when they hunted antelope three times their own body mass, such as wildebeest and topi. Of all prey that were commonly hunted, only zebra were usually hunted in groups. Approximately one-third of all hunting attempts resulted in prey capture. Although no significant sex differences were observed in juvenile or adult hunting rates, low-ranking adult females hunted at significantly higher hourly rates than did higher-ranking females. Hunting success was not influenced by the social rank of hunters, but hunting group size and hunter's age strongly influenced success. Young hyenas were poor hunters, and did not achieve adult competency levels until they were 5–6 years old.
Skipping and sliding to optimize target search on protein-bound DNA and RNA

Rapidly finding a specific nucleic-acid sequences in a large pool of competing off-targets is a fundamental challenge overcome by all living systems. To optimize the search and beat the diffusion limit, it is known that searchers should spend time sliding along the nucleic-acid substrate. Still, such sliding generally has to contend with high levels of molecular crowding on the substrate, and it remains unclear what effect this has on optimal search strategies. Using mechanistic modelling informed by single-molecule data, we show how sliding combined with correlated short-ranged skips allow searchers to maintain search speed on densely crowded substrates. We determine the conditions of optimal search, which show that an optimized searchers always spend more than half its time skipping and sliding along the substrate. Applying our theory to single-molecule data, we determine that both human and bacterial Argonaute proteins alternate between sliding 10 nt and skipping 30 nt along the substrate. We show that this combination of skipping and sliding lengths allows the searcher to maintain search speeds largely unaffected by molecular roadblocks covering up to 70% of the substrate. Our novel combination of experimental and theoretical approach could also help elucidate how other systems ensure rapid search in crowded environments.
Chemical Composition and Antifungal Activity of Essential Oils from Various Bulgarian Mentha x piperita L. Cultivars Against Clinical Isolates of Candida albicans

Abstract The antifungal activities of peppermint essential oils obtained from standard cul-tivar, two newly selected Mentha x piperita L. and allopolyploid hybrid of Mentha x piperita L. x Mentha arvensis, growing in Bulgaria, were investigated against 15 clinical isolates of Candida albicans (5 oropharyngeal, 5 vaginal and 5 skin damaging strains) and C. albicans ATCC 10231. Furthermore, the Chemical composition of these peppermint oils was evaluated by GC and GC-MS. The strains isolated from oropharyngeal infections were more resistible to peppermint oils, while C. albicans ATCC 10231 was more susceptible. Antifungal activity of peppermint oils depended mainly on menthol content and strain specific susceptibility. The newly selected and introduced allopolyp-loid hybrid Mentha x piperita L. x Mentha arvensis, characterized with an increased content of menthol, resulted in especially low MIC (4,5μg/mL) and MFC (4,5 μg/mL) against C.albicans ATCC 10231.
Neuralized regulates a travelling wave of Epithelium-to-Neural Stem Cell morphogenesis in Drosophila

Many tissues are produced during development by specialized progenitor cells emanating from epithelia via an Epithelial-to-Mesenchymal Transition (EMT). Most studies have so far focused on cases involving single or isolated groups of cells. Here we describe an EMT-like process that requires tissue level coordination. This EMT-like process occurs along a continuous front in the Drosophila optic lobe neuroepithelium to produce neural stem cells (NSCs). We find that emerging NSCs remain epithelial and apically constrict before dividing asymmetrically to produce neurons. Apical constriction is associated with contractile myosin pulses and requires the E3 ubiquitin ligase Neuralized and RhoGEF3. Neuralized down-regulates the apical protein Crumbs via its interaction with Stardust. Disrupting the regulation of Crumbs by Neuralized led to defects in apical constriction and junctional myosin accumulation, and to imprecision in the integration of emerging NSCs into the transition front. Neuralized therefore appears to mechanically couple NSC fate acquisition with cell-cell rearrangement to promote smooth progression of the differentiation front.
Fitting phenological curves with Generalized Linear Mixed Models (GLMMs)

Understanding organismal phenology has been an emerging interest in ecology, in part because phenological shifts are one of the most conspicuous signs of climate change. While we are seeing increased collection of phenological data and creative use of historical data sets, existing statistical tools to measure phenology are generally either limited (e.g., first day of observation, which has problematic biases) or are challenging to implement (often requiring custom coding, or enough data to fit many parameters). We present a method to fit phenological data with Gaussian curves using linear models, and show how robust phenological metrics can be obtained using standard linear regression tools. We then apply this method to eight years of Baltimore checkerspot data using generalized linear mixed models (GLMMs). This case study illustrates the ability of years with extensive data to inform years with less data and shows that butterfly flight activity is somewhat earlier in warmer years. We believe our new method fills a convenient midpoint between ad hoc measures and custom-coded models.
Equations governing dynamics of excitation and inhibition in the mouse corticothalamic network

Although cortical circuits are complex and interconnected with the rest of the brain, their macroscopic dynamics are often approximated by modeling the averaged activities of excitatory and inhibitory cortical neurons, without interactions with other brain circuits. To verify the validity of such mean-field models, we optogenetically stimulated populations of excitatory and parvalbumin-expressing inhibitory neurons in awake mouse visual cortex, while recording population activity in cortex and in its thalamic correspondent, the lateral geniculate nucleus. The cortical responses to brief test pulses could not be explained by a mean-field model including only cortical excitatory and inhibitory populations. However, these responses could be predicted by extending the model to include thalamic interactions that cause net cortical suppression following activation of cortical excitatory neurons. We conclude that mean-field models can accurately summarize cortical dynamics, but only when the cortex is considered as part of a dynamic corticothalamic network.
Production ecology of Thuja occidentalis

Equations to predict branch and tree leaf area, foliar mass, and stemwood volume were developed from 25 destructively sampled northern white-cedar (Thuja occidentalis L.) trees, a species whose production ecology has not been studied. Resulting models were applied to a large sample of 296 cored trees from 60 sites stratified across a soil gradient throughout northern Maine. Nonlinear regression analysis was used to assess alternative forms of the relationship between volume increment (VINC) and projected leaf area (PLA); analysis of covariance was used compare stemwood growth efficiency (GE) among soil-site classes, light exposure classes, and the presence of decay. Stem volume was estimated with Honer’s equation (T.G. Honer. 1967. Forest Management Research and Services Institute) with refitted parameters. PLA was best predicted with Maguire and Bennett’s nonlinear model (D.A. Maguire and W.S. Bennett. 1996. Can. J. For. Res. 26: 1991–2005) using sapwood area or crown length and the ratio of tree height .
Distinct gene expression profiles in leukocortical demyelinated white and grey matter areas of Multiple Sclerosis patients

Demyelination of the CNS is a prominent pathological hallmark of Multiple Sclerosis (MS) and affects both white (WM) and grey matter (GM). However, demyelinated WM and GM areas exhibit clear pathological differences, most notably the presence or absence of inflammation and activated glial cells in WM and GM, respectively. In order to gain more insight into the differential pathology of demyelinated WM and GM areas, we micro-dissected neighbouring WM and GM demyelinated areas as well as normal appearing matter from leukocortical lesions of human post-mortem material and used these samples for RNA-sequencing. Our data show that even neighbouring WM and GM demyelinated areas share only 10% overlap in gene expression, implying a distinct gene expression profile, which is extending to a specific glial cell related signature. We propose that, based on their distinct expression profile, pathological processes in neighbouring WM and GM are likely different which could have implications for the efficacy of current MS treatments.
Evaluation of in vitro activity of manogepix against multidrug-resistant and pan-resistant Candida auris from the New York Outbreak

An ongoing Candida auris outbreak in the New York metropolitan area is the largest recorded to date in North America. Laboratory surveillance revealed NY C. auris isolates are resistant to fluconazole, with variable resistance to other currently used broad-spectrum antifungal drugs, and that several isolates are pan-resistant. Thus, there is an urgent need for new drugs with a novel mechanism of action to combat the resistance challenge. Manogepix (MGX) is a first-in-class agent that targets the fungal Gwt1 enzyme. The prodrug, fosmanogepix, is currently in Phase 2 clinical development for the treatment of fungal infections. We evaluated the susceptibility of 200 New York C. auris isolates to MGX and 10 comparator drugs using CLSI methodology. MGX demonstrated lower MICs than comparators (MIC50 and MIC90 0.03 mg/L; range 0.004-0.06 mg/L). The MGX epidemiological cutoff value (ECV, 99% cutoff) for the tested C. auris isolates was 0.06 mg/L. MGX was 8-32-fold more active than the echinocandins, 16-64-fold more active than the azoles, and 64-fold more active than amphotericin B. No differences were found in the MGX or comparators’ MIC50, MIC90, or GEOMEAN values when subsets of clinical, surveillance, and environmental isolates were evaluated. The range of MGX MIC values for six C. auris pan-resistant isolates was 0.008-0.015 mg/L, and the median and mode MIC values were 0.015 mg/L, demonstrating that MGX retains activity against these isolates. These data support further clinical evaluation of fosmanogepix for the treatment of C. auris infections, including highly resistant isolates.
Detection of Envelope Glycoprotein Assembly from Old World Hantaviruses in the Golgi Apparatus of Living Cells

In this work, we investigate protein-protein interactions that drive the assembly of the hantavirus envelope. These emerging pathogens have the potential to cause deadly outbreaks in the human population. ABSTRACT Hantaviruses are emerging pathogens that occasionally cause deadly outbreaks in the human population. While the structure of the viral envelope has been characterized with high precision, protein-protein interactions leading to the formation of new virions in infected cells are not fully understood. We used quantitative fluorescence microscopy (i.e., number and brightness analysis and fluorescence fluctuation spectroscopy) to monitor the interactions that lead to oligomeric spike complex formation in the physiological context of living cells. To this aim, we quantified protein-protein interactions for the glycoproteins Gn and Gc from Puumala and Hantaan orthohantaviruses in several cellular models. The oligomerization of each protein was analyzed in relation to subcellular localization, concentration, and the concentration of its interaction partner. Our results indicate that, when expressed separately, Gn and Gc form, respectively, homo-tetrameric and homo-dimeric complexes, in a concentration-dependent manner. Site-directed mutations or deletion mutants showed the specificity of their homotypic interactions. When both glycoproteins were coexpressed, we observed in the Golgi apparatus clear indication of Gn-Gc interactions and the formation of Gn-Gc multimeric protein complexes of different sizes, while using various labeling schemes to minimize the influence of the fluorescent tags. Such large glycoprotein multimers may be identified as multiple Gn viral spikes interconnected via Gc-Gc contacts. This observation provides the possible first evidence for the initial assembly steps of the viral envelope within this organelle, and does so directly in living cells. IMPORTANCE In this work, we investigate protein-protein interactions that drive the assembly of the hantavirus envelope. These emerging pathogens have the potential to cause deadly outbreaks in the human population. Therefore, it is important to improve our quantitative understanding of the viral assembly process in infected cells, from a molecular point of view. By applying advanced fluorescence microscopy methods, we monitored the formation of viral spike complexes in different cell types. Our data support a model for hantavirus assembly according to which viral spikes are formed via the clustering of hetero-dimers of the two viral glycoproteins Gn and Gc. Furthermore, the observation of large Gn-Gc hetero-multimers provide the possible first evidence for the initial assembly steps of the viral envelope, directly in the Golgi apparatus of living cells.