Miracle-dz/UniFAR-FTUs huggingface dataset:
Temporal trends in stream-fish distributions, and species traits as invasiveness drivers in New River (USA) tributaries

Biological invasions represent both an urgent conservation problem and an opportunity to advance ecological theory. Development of pertinent research questions and proactive management strategies require knowledge of which introduced species are present and of spatiotemporal trends in the distribution of natives and invaders. In Chapter 2 we developed a quantitative framework to identify spreaders and decliners and estimate invasion chronologies based on a historical fish presence data set for upper and middle New River (UMNR) tributaries. Our framework accounts for spatiotemporal variability in sampling effort by aggregating presences by watershed and expressing range size as a function of the number of watersheds sampled per time period. The majority (55%) of fish species present in the study area were introduced, 51% of which were spreaders. Most spreaders (84%) appeared to be spreading exponentially. The rate of new introductions detected in the study area has slowed since the mid20 th century. Two natives, the mound-spawning bluehead chub Nocomis leptocephalus and its strong nest associate (reproductive mutualist), mountain redbelly dace Chrosomus oreas, were among the most rapid spreaders. Four natives showed evidence of decline. Our framework leverages historical presence data to reconstruct temporal trends in species distributions. It sets the stage for further study of factors driving stream fish invasions and declines in the Appalachian region, and is transferable to diverse taxonomic groups and geographic regions. Species traits and human activities mediating stream-fish invasions remain poorly understood. In Chapter 3 we modeled the contribution of species traits to invasion success of UMNR tributary fishes during the colonization and spread stages. Biological traits accurately explained colonization and spread success, whereas ecological traits resulted in less accurate models. Colonization success was positively related to time since introduction, benthic feeding, an equilibrium life history, and nest spawning. Successful spread was positively related to winter air temperature in the native range and an equilibrium life history. Variables estimating human use and propagule pressure were non-informative. Traits that influenced invasion success were consistent with the hypothesis that human land-use practices have increased the invasibility of highland watersheds by creating novel conditions suited to lowland and equilibrium invaders.
Persistent broken chromosome inheritance drives genome instability

Persistent DNA damage arising from unrepaired broken chromosomes or telomere loss can promote DNA damage checkpoint adaptation, and cell cycle progression, thereby increasing cell survival but also genome instability. However, the nature and extent of such instability is unclear. We show, using Schizosaccharomyces pombe, that inherited broken chromosomes, arising from failed homologous recombination repair, are subject to cycles of segregation, DNA replication and extensive end-processing, termed here SERPent cycles, by daughter cells, over multiple generations. Following Chk1 loss these post-adaptive cycles continue until extensive processing through inverted repeats promotes annealing, fold-back inversion and a spectrum of chromosomal rearrangements, typically isochromosomes, or chromosome loss, in the resultant population. These findings explain how persistent DNA damage drives widespread genome instability, with implications for punctuated evolution, genetic disease and tumorigenesis. One Sentence Summary Replication and processing of inherited broken chromosomes drives chromosomal instability.
Tetanus neurotoxin sensitive SNARE-mediated glial signaling limits motoneuronal excitability

Peripheral nerves contain motoneuron axons coated by glial cells, which essentially contribute to function but cellular reactions remain poorly understood. We here identify non-neuronal Synaptobrevin (Syb) as the essential vesicular SNARE in glia to insulate and metabolically supply Drosophila motoneurons. Interfering with Syb-functionality by glial knockdown, or glial expression of tetanus neurotoxin light chain (TeNT-LC) caused motonerve disintegration, blocked axonal transport, induced tetanic muscle hyperactivity and caused lethal paralysis. Surprisingly, not the established TeNT-LC-target, neuronal Synaptobrevin (nSyb), is the relevant SNARE, but non-neuronal Synaptobrevin (Syb): Knockdown of Syb- (but not nSyb-) phenocopied glial TeNT-LC expression whose effects were reverted by a TeNT-LC-insensitive Syb mutant. We link Syb-necessity to two distinct glia: to establish nerve insulating septate junctions in subperineurial glia and to integrate monocarboxylate transporters along the nerve in wrapping glia for motoneuronal metabolic supply. Our study identifies crucial roles of Syb in glial subtypes for nerve function and pathology, animal motility and survival.
Enzyme Variability and Modes of Evolution in Bommeria (Pteridaceae)

As is true of other plants inhabiting xeric environments, desert ferns may be mor- phologically similar because of convergent evolution. Since phylogenetically important reproduc- tive features in these plants may be affected by vegetative modifications, electrophoretically de- tectable variability in 11 enzymes coding for 13 loci has been analyzed to provide an expanded, comparative data base for defining systematic relationships and population structure in the four species of Bommeria. Contrary to the ad hoc assumption that because Bommeria species have relatively high chromosome numbers they should be polyploid, enzyme studies suggest that all species are genetic diploids. These studies also demonstrate that genetic variability is partitioned among the individuals within populations and that the sexual species are outcrossing. Analyses of allelic frequencies indicate that the four species are genetically more distinct from one another than are angiosperm congeners. Bommeria subpaleacea and B. ehrenbergiana emerge as the most similar taxa with B. pedata and B. hispida being more distant. The enzyme data, combined with other characters, support the hypotheses that the mountains of west-central Mexico are the center of origin of Bommeria and that the triploid apomict B. pedata was not derived through hybridization among extant sexual species. Although the corroborative morphological, biogeographical, and enzymatic data present a reasonable phylogenetic hypothesis, the extraordinary genetic distance among these congeners suggests that Bommeria may be polyphyletic, composed of species that are grouped together because of superficial resemblance. Evolution in plants of warm deserts has been characterized by considerable vegetative and physiological convergence (Orians and Solbrig 1977). In assessing characters for phylogenetic analysis of these plants, it is necessary to con- sider carefully the role that the environment may have played in directing morphological modifications. Among angiosperms, xero- morphic, perennial members of the Cactaceae, Euphorbiaceae, and Asclepiadaceae share many vegetative features but may be unambiguously separated into distinct evolutionary lines based on floral characters. Since flowers are relatively ephemeral, their features are less affected by environmental pressures and can be used as reasonably accurate indicators of phylogenetic relationships. Among the ferns, there is a suite of genera commonly associated with xeric habitats. These share many of the features considered to be adaptations for survival in environments hav- ing frequent droughts, low humidity, and high insolation. Plants in genera such as Cheilanthes, Notholaena, Pellaea, and Bommeria are small, have highly dissected leaves, and are often clothed
SARS-CoV-2 lineage B.6 is the major contributor to transmission in Malaysia

Background As of June 30, 2020, Malaysia had confirmed 8,639 cases of COVID-19. About 39% of these were associated with a religious mass gathering event held in Kuala Lumpur between February 27 and March 1, 2020, which drove community transmission during Malaysia’s main wave. We analysed genome sequences of SARS-CoV-2 from Malaysia to understand the molecular epidemiology. Methods We obtained whole genome sequences of SARS-CoV-2 from 58 COVID-19 patients in Kuala Lumpur, Malaysia, and performed phylogenetic analyses on these and a further 50 Malaysian sequences available in the GISAID database. Malaysian lineage B.6 sequences were further analysed with all available worldwide lineage B.6 sequences. Results Nine different SARS-CoV-2 lineages (A, B, B.1, B.1.1, B.1.1.1, B.1.36, B.2, B.3 and B.6) were detected in Malaysia. The B.6 lineage was first reported a week after the mass gathering and became predominant (63%) despite being relatively rare (1.4%) among available global sequences. Increases in reported cases and community-acquired B.6 lineage strains were temporally linked. Non-B.6 lineages were mainly associated with travel and showed limited onward transmission. There were also temporally-correlated increases in B.6 sequences in other Southeast Asian countries, India and Australia, linked to participants returning from this event. We also report the presence of a nsp3-C6310A substitution found in 40.5% of global B.6 sequences which has associated with reduced sensitivity in a commercial assay. Conclusion Lineage B.6 became the predominant cause of community transmission in Malaysia after likely introduction during a religious mass gathering. This event also contributed to spikes of lineage B.6 in other countries in the region. Author Summary The COVID-19 pandemic in Malaysia was driven mainly by transmission following a religious mass gathering held in Kuala Lumpur at the end of February. To study the genetic epidemiology of SARS-CoV-2 in Malaysia, we analysed 50 available and 58 newly-generated Malaysian whole genome virus sequences. We found that lineage B.6, rare (1.4%) globally, first appeared after the mass gathering and became the most predominant (62.9%) in Malaysia. Increases in COVID-19 cases and locally-acquired B.6 strains were temporally linked. Non-B.6 viruses were mainly associated with travel and showed limited spread. Increases in B.6 viruses in Southeast Asian countries, India and Australia were linked to participants returning from this mass gathering. Altogether, 95.3% of global B.6 sequences originated in Asia or Australia. We also report a mutation in the virus nsP3 gene found in 40.5% of global B.6 sequences and associated with reduced detection by a commercial diagnostic test. In conclusion, the religious mass gathering in Kuala Lumpur was associated with the main wave of COVID-19 cases of predominantly B.6 lineage in Malaysia, and subsequent spread of B.6 viruses regionally. Genome sequence data provides valuable insight into virus spread and is important for monitoring continued accuracy of diagnostic kits.
Network Asynchrony Underlying Increased Broadband Gamma Power

Synchronous activity of cortical inhibitory interneurons expressing parvalbumin (PV) underlies expression of cortical γ rhythms. Paradoxically, deficient PV inhibition is associated with increased broadband γ power in the local field potential. Increased baseline broadband γ is also a prominent characteristic in schizophrenia and a hallmark of network alterations induced by NMDAR antagonists, such as ketamine. Whether enhanced broadband γ is a true rhythm, and if so, whether rhythmic PV inhibition is involved or not, is debated. Asynchronous and increased firing activities are thought to contribute to broadband power increases spanning the γ band. Using male and female mice lacking NMDAR activity specifically in PV neurons to model deficient PV inhibition, we here show that neuronal activity with decreased synchronicity is associated with increased prefrontal broadband γ power. Specifically, reduced spike time precision and spectral leakage of spiking activity because of higher firing rates (spike “contamination”) affect the broadband γ band. Desynchronization was evident at multiple time scales, with reduced spike entrainment to the local field potential, reduced cross-frequency coupling, and fragmentation of brain states. Local application of S(+)-ketamine in (control) mice with intact NMDAR activity in PV neurons triggered network desynchronization and enhanced broadband γ power. However, our investigations suggest that disparate mechanisms underlie increased broadband γ power caused by genetic alteration of PV interneurons and ketamine-induced power increases in broadband γ. Our study confirms that enhanced broadband γ power can arise from asynchronous activities and demonstrates that long-term deficiency of PV inhibition can be a contributor. SIGNIFICANCE STATEMENT Brain oscillations are fundamental to the coordination of neuronal activity across neurons and structures. γ oscillations (30-80 Hz) have received particular attention through their association with perceptual and cognitive processes. Synchronous activity of inhibitory parvalbumin (PV) interneurons generates cortical γ oscillation, but, paradoxically, PV neuron deficiency is associated with increases in γ oscillations. We here reconcile this conundrum and show how deficient PV inhibition can lead to increased and asynchronous excitatory firing, contaminating the local field potential and manifesting as increased γ power. Thus, increased γ power does not always reflect a genuine rhythm. Further, we show that ketamine-induced γ increases are caused by separate network mechanisms.
Will an outbreak exceed available resources for control? Estimating the risk from invading pathogens using practical definitions of a severe epidemic

Forecasting whether or not initial reports of disease will be followed by a severe epidemic is an important component of disease management. Standard epidemic risk estimates involve assuming that infections occur according to a branching process and correspond to the probability that the outbreak persists beyond the initial stochastic phase. However, an alternative assessment is to predict whether or not initial cases will lead to a severe epidemic in which available control resources are exceeded. We show how this risk can be estimated by considering three practically relevant potential definitions of a severe epidemic; namely, an outbreak in which: (i) a large number of hosts are infected simultaneously; (ii) a large total number of infections occur; and (iii) the pathogen remains in the population for a long period. We show that the probability of a severe epidemic under these definitions often coincides with the standard branching process estimate for the major epidemic probability. However, these practically relevant risk assessments can also be different from the major epidemic probability, as well as from each other. This holds in different epidemiological systems, highlighting that careful consideration of how to classify a severe epidemic is vital for accurate epidemic risk quantification.
Trait-based responses to forestry and reindeer husbandry modify long-term changes in forest understories Running title: Trait-based responses to forestry and reindeer husbandry

Aim:​ Land use is the foremost cause of global biodiversity decline, but species do not respond equally to land-use practices. Instead, it is suggested that responses vary with species traits, but long-term data on the trait-mediated effects of land-use on communities is scarce. Here we study how forest understory communities have been affected by common land-use practices during 4–5 decades, and whether changes in plant diversity are related to changes in functional composition. Location:​ Finland Time period:​ 1968–2019 Major taxa studied:​ Vascular plants Methods:​ We resurveyed 245 vegetation plots in boreal herb-rich forest understories, and used hierarchical Bayesian linear models to relate changes in diversity, species composition, average plant size, and leaf economic traits to reindeer abundance, forest management intensity, and changes in climate, canopy cover and composition. Results:​ Forestry decreased species richness and increased turnover, but did not affect functional composition. Increased reindeer densities corresponded with decreased height and specific leaf area, and increased leaf dry matter content, evenness and diversity. Successional changes in the canopy were associated with increased specific leaf area and decreased leaf dry matter content and height over the study period. Effects of reindeer abundance and canopy density on diversity were partially mediated by vegetation height, which had a negative relationship with evenness. Climate change had no discernible effect on any variable. Main conclusions:​ Functional traits are useful in connecting vegetation changes to the mechanisms that drive them, and provide unique information compared to turnover and diversity metrics. These trait-dependent selection effects could inform whether species benefit or suffer from land use changes and explain observed vegetation shifts under global change.
A ±5A Integrated Current-Sensing System With ±0.3% Gain Error and 16μA Offset From -55°C +85°C

−This paper presents an integrated current-sensing system (CSS) that is intended for use in battery-powered devices. It consists of a 10-mΩ on-chip metal shunt resistor, a switchedcapacitor ΔΣ ADC, and a dynamic bandgap reference (BGR) that provides the ADC’s reference voltage and also senses the shunt’s temperature. The CSS is realized in a standard 0.13-μm CMOS process, occupies 1.15 mm and draws 55 μA from a 1.5-V supply. Extensive measurements were made on 24 devices, 12 of which were directly bonded to a printed-circuitboard (PCB) and 12 of which were packaged in a standard HVQFN plastic package. For currents ranging from –5 A to +5 A and over a temperature range of –55°C to +85°C, they exhibit a maximum offset of 16 μA and a maximum gain error of ±0.3%. This level of accuracy represents a significant improvement on the state-of-the-art, and was achieved by the use of an accurate shunt temperature compensation scheme, a low-leakage sampling scheme and several dynamic error correction techniques. Index Terms−Coulomb counter, current-sensing system, metal shunt resistor, dynamic bandgap reference, temperature sensor, temperature compensation. This is the author's version of an article that has been published in this journal. Changes were made to this version by the publisher prior to publication. The final version of record is available at http://dx.doi. org/10.1109/JSSC.2015. 2511168 (c) 2018 European Union Copyright. Personal use is permitted. For any other purposes, permission must be obtained from the IEEE by emailing pubs-permissions@ieee.org.
Competing Risks Models for an Enterprises Duration on the Market

Abstract Research background: Enterprises are an important element of the economy, which explains that the analysis of their duration on the market is an important and willingly undertaken research topic. In the case of complex problems like this, considering only one type of event, which ends the duration, is often insufficient for full understanding. Purpose: In this paper there is an analysis of the duration of enterprises on the market, taking into account various reasons for the termination of their business activity as well as their characteristics. Research methodology: A survival analysis can be used to study duration on the market. However, the possibility of considering the waiting time for only one type of event is its important limitation. One solution is to use competing risks. Various competing risks models (naive Kaplan-Meier estimator, subdistribution model, subhazard and cause-specific hazard) are presented and compared with an indication of their advantages and weakness. Results: The competing risks models are estimated to investigate the impact of the causes of an enterprises liquidation on duration distribution. The greatest risk concerns enterprises with a natural person as the owner (regardless of the reason of failure). For each of the competing risks, it is also indicated that there is a section of activity which adversely affects the ability of firms to survive on the market. Novelty: A valuable result is considering the reasons for activity termination in the duration analysis for enterprises from the Mazowieckie Voivodeship.
Determinants of audit fees: Evidence from Poland

Abstract Unlike many studies concerning audit fees in Western Europe or the United States, literature concerning this kind of research is very limited in Central and Eastern Europe. This study aimed to show what factors shape audit fees in Poland. It was conducted based on data collected from the financial statements of 111 companies listed on the Warsaw Stock Exchange in 2018. The study used a linear regression model to verify the determinants of audit fees. The research results indicate a positive relationship between audit fees and company size, measures of complexity (in addition to the ratio of inventories and receivables to total assets) and the fact that a company is audited by the ‘Big Four’ accounting firms.
Immune Enhancing Effect by Orally-Administered Mixture of Saccharomyces cerevisiae and Fermented Rice Bran

The mixture (PM) of Saccharomyces cerevisiae and fermented rice bran on the activation of macrophage and bone marrow cell proliferation was studied in mice. PM stimulated not only the activation of macrophage (1.8-fold of saline) but also IL-6 production from macrophage (1.5-fold) at 2.0 g/kg/day during 7 days of oral administration. By the culture supernatant of Peyer's patch cells from C3H/HeJ mice fed PM at 2.0 g/kg/day for 7 days, the bone marrow cells significantly proliferated compared with that of mice receiving only saline (1.7-fold). In addition, the contents of GM-CSF and IL-6 in the culture supernatant of Peyer's patch cells from mice fed PM at 2.0 g/kg/day were increased in comparison with those from the control (1.8 and 1.4-fold, respectively). These results revealed that oral administration of PM may modulate IL-6 production to induce the activation of macrophage, and also enhance secretion of hematopoietic growth factors such as GM-CSF and IL-6 from Peyer's patch cells.
The Relationship Between the Financial Innovation and the Money Supply: Empirical Study on the Maghreb Countries

Abstract This article examines the relationship between money supply and financial innovation in the Maghreb countries over the period of 1980–2018 for a large annual data set on five Maghreb countries using the panel autoregressive distributed lag model (PANEL-ARDL). The results obtained from the cointegration technique of Pesaran and Shin (1999) confirm that a long-term relationship exists between M2 and its determinants: GDP, inflation, and the credit interest rate. Above all, the results of the research show that mobile money positively and significantly influences the money supply both in the strict sense and in the broad sense. Also, the number of ATMs positively but not significantly influences the supply of money in the broad sense. Failure to take into account the expansion of the number of ATMs can therefore lead to a poor specification of the money supply, and monetary authorities need to explicitly integrate the effect of financial innovation for effective policy action to stabilize economies.