Miracle-dz/UniFAR-FTUs huggingface dataset:
Reproduction of a Rare New Zealand Reptile, the Tuatara Sphenodon punctatus, on Rat‐Free and Rat‐Inhabited Islands

We compared evidence for successful reproduction of tuatara (Sphenodon punctatus punctatus) in the presence or absence of introduced Pacific rats (kiore, Rattus exulans) for islands in the Mercury Group and Hen and Chickens Group, New Zealand Tuatara were captured more frequently on the two kiore-free islands than on the six kiore-inhabited islands, suggesting reduced density in the presence of kiore. On the two kiore-free islands, 22.2–30.8% of all tuatara captured were juveniles or small adults (<200 mm snout-vent length). In contrast, juvenile tuatara were not seen on five of the six kiore-inhabited islands and small adults were absent from three. These data support an earlier study suggesting that kiore inhibit recruitment of tuatara. Both sexes of adult tuatara were present on kiore-inhabited islands, and plasma concentrations of sex hormones suggest that at least some adults remain reproductively active on most islands. Throughout their range, tuatara have become extinct this century on four islands inhabited by kiore, they are on the verge of extinction on two kiore-inhabited islands sampled in this study and two kiore-inhabited islands not sampled, and they are absent from at least six other kiore-inhabited islands on which on biogeographic grounds they would be expected to be present. Although the data remain circumstantial, the most plausible explanation of these observations is that kiore can cause extinction of tuatara through competition for food and/or predation on eggs and juveniles. In the absence of kiore eradication the four worst-case populations of tuatara would probably be extinct within 10–20 years and populations on three other islands would probably be relictual or extinct within 30–50 years. Kiore eradication is being carried out on most of these islands, in part to help ensure tuatara survival Well-monitored eradication programs will enable an experimental test of the hypothesis that tuatara densities and recruitment rates are enhanced in the absence of kiore.
Slot Length Limits for Largemouth Bass in Small Private Impoundments

Abstract Fourteen small private impoundments were studied from 1976 to 1979 to determine if a slot length limit of 12.0–15.0 in for largemouth bass Micropterus salmoides would result in proportional stock densities (PSDs) of 40–60 for largemouth bass and 20–40 for bluegills Lepomis macrochirus. Impoundments meeting the PSD objectives increased from three to six for largemouth bass, from two to five for bluegills, and from one to three for both species. Relative abundance of largemouth bass 12.0 in and longer increased in most ponds with initially low PSDs of largemouth bass; relative abundance of bluegills 3.0–5.9 in long also increased in those ponds. Anglers released about 45% of their catch of largemouth bass shorter than 12.0 in. Anglers kept few largemouth bass shorter than 9.0 in, and only the 11.0–11.9-in fish were kept more than 50% of the time. The data suggest that high recruitment of largemouth bass causes low PSD and surplus numbers of 8.0–11.9-in largemouth bass. Predation by stock-length lar.
Trait-convergence and divergence assembly patterns in a temperate forest herbaceous layer along the gradient of canopy closure

Gradients of physical conditions and biological interactions of species may generate assembly patterns of trait-convergence and trait-divergence in the structure of plant communities. Here we report evidence on the effect of canopy closure on non-random patterns in the functional structure of herbaceous plant communities in temperate forest. We evaluated SLA (specific leaf area), leaf area and shape, dry matter content, presence of rhizomes, and plant height and inclination. In one of the three sites surveyed we found clear patterns of both trait-convergence and trait-divergence. Along the canopy closure gradient we observed communities formed by species with large SLA and long and narrow leaves being replaced by communities formed by species with smaller SLA and rounded leaves, which we interpret as environmental filtering producing such a trait-convergence. Further, communities located in more open sites contained more distinct species in terms of SLA, leaf area and leaf shape, i.e., indicating a divergence pattern along the canopy closure gradient. The other study sites showed no significant patterns when analyzed alone. When the three sites were analyzed jointly, a significant pattern of convergence for plant inclination was found. Although subjected to local variation and historical agents, our study presents consistent patterns of both trait-convergence and divergence and evidence of assembly rules and non-random patterns in communities of herbaceous plants along a canopy closure gradient.
Peroxisome proliferator-activated receptor α and γ ligands inhibit the growth of human ovarian cancer

In this study, we investigated the inhibitory effect of clofibric acid (CA), a ligand for peroxisome proliferator-activated receptor (PPAR)alpha, and pioglitazone, a ligand for PPARgamma, on ovarian cancer in in vivo experiments using human ovarian cancer cell lines, and we aimed to elucidate the molecular mechanism of their anticancer effect. The antitumor effects of CA (3,000 ppm in the daily diet), pioglitazone (240 ppm in the daily diet) or the combination were studied in female nu/nu mice, xenografted with subcutaneous OVCAR-3 tumors or with intraperitoneal DISS tumors. The tumor tissues were quantified for expression levels of AP-1, cyclooxygenase-2 (COX-2) and vascular endothelial growth factor (VEGF) using Western blot analysis or immunohistochemistry. CD-31-stained microvessel density (MVD) was measured in the tumors. The induction of apoptosis was quantified by the TUNEL method. Treatment with CA or pioglitazone significantly suppressed the growth of subcutaneously xenotransplanted OVCAR-3 tumors and prolonged the survival of mice with malignant ascites derived from DISS cells as compared to the control. Combination of both agents enhanced the anticancer effect. Increase of apoptosis and necrosis as well as decrease of VEGF expression and MVD were found in solid OVCAR-3 tumors treated with CA, pioglitazone or the combination. The combination significantly induced apoptotic cells, compared to CA or pioglitazone alone. The combination significantly reduced expression of AP-1, which is a transcriptional regulator of COX-2, and also significantly decreased COX-2 expression in OVCAR-3 tumors compared to the control, CA or pioglitazone alone, although CA or pioglitazone alone decreased them with a marginal significance compared to the control. These findings indicate that the combination of CA and pioglitazone produces a potent antitumor effect on ovarian cancer through reduction of AP-1 expression.
Evaluation of polysaccharides content in fruit bodies and their antimicrobial activity of four Ganoderma lucidum (W Curt.: Fr.) P. Karst. strains cultivated on different wood type substrates

Quantitative determination of polysaccharides in Ganoderma lucidum fruit bodies from different sawdust cultivation substrates and their antibacterial activity was done. Thirty six samples were analyzed. Four strains of Ganoderma lucidum (GL01, GL02, GL03 and GL04) were cultivated on the growth substrates of three different sawdust types: birch (Bo), maple (Kl) or alder (Ol) amended with wheat bran in three different concentrations: 10, 20 and 30% (w/w). Even though the richest in polysaccharides was GL01 strain, the highest yields of the polysaccharides were determined in GL04Kl3 sample and was 112.82 mg/g of dry weight. The antibacterial activity of polysaccharides was determined in vitro using micro-dilution broth method. The panel of eight reference bacterial strains was used. All the polysaccharide samples tested showed the broad spectrum and the moderate antibacterial activity. Micrococcus luteus ATCC 10240 strain was the most sensitive with MIC (minimal inhibitory concentration) = 0.63 − 1.25 mg/mL.
Effect of specific mechanical energy on protein bodies and α-zeins in corn flour extrudates

ABSTRACT Zeins, the storage proteins of corn, are located in spherical entities called protein bodies. The disruption of protein bodies and zein release during extrusion may influence the texture of corn-based extruded foods. In this work, chemical and microscopic studies were conducted on corn flour that had been extruded under mild to extreme conditions to determine the specific mechanical energy (SME) required to break apart protein bodies and release α-zein, and to assess changes in protein-protein interactions. Transmission electron microscopy with immunolocalization of α-zein revealed that starch granules and protein bodies remained intact under mild processing conditions (SME 35–40 kJ/kg), but under harsher conditions, protein bodies were disrupted and α-zein was released. At SME ≈100 kJ/kg, protein bodies appeared highly deformed and fused together with the α-zein released, whereas at higher SME, protein bodies were completely disrupted and α-zein was dispersed and may have formed protein fibrils.
Tumor-free elongation of mammalian nephrogenesis by excess fetal GDNF

Due to poor regenerative capacity of adult kidneys, nephron endowment defined by the nephrogenic program during the fetal period dictates renal and related cardiovascular health throughout life. We show that the neurotropic factor GDNF, which is in clinical trials for Parkinson’s disease, is capable of prolonging the nephrogenic program beyond its normal cessation without increasing the risk of kidney tumors. Our data demonstrates that excess GDNF expands the nephrogenic program by maintaining nephron progenitors and nephrogenesis in postnatal mouse kidneys. GDNF, through its transcriptional targets excreted from the adjacent epithelium, has a major effect on nephron progenitor self-renewal and maintenance; abnormally high GDNF inhibits nephron progenitor proliferation, but lowering its level normalizes the nephrogenic program to that permissive for nephron progenitor self-renewal and differentiation. Based on our results, we propose that the lifespan of nephron progenitors is determined by mechanisms related to perception of GDNF and other signaling levels.
Heterogeneous somatostatin-expressing neuron population in mouse ventral tegmental area

The cellular architecture of the ventral tegmental area (VTA), the main hub of the brain reward system, remains only partially characterized. To extend the characterization to inhibitory neurons, we have identified three distinct subtypes of somatostatin (Sst)-expressing neurons in the mouse VTA. These neurons differ in their electrophysiological and morphological properties, anatomical localization, as well as mRNA expression profiles. Importantly, similar to cortical Sst-containing interneurons, most VTA Sst neurons express GABAergic inhibitory markers, but some of them also express glutamatergic excitatory markers and a subpopulation even express dopaminergic markers. Furthermore, only some of the proposed marker genes for cortical Sst neurons were expressed in the VTA Sst neurons. Physiologically, one of the VTA Sst neuron subtypes locally inhibited neighboring dopamine neurons. Overall, our results demonstrate the remarkable complexity and heterogeneity of VTA Sst neurons and suggest that these cells are multifunctional players in the midbrain reward circuitry.
Toxin-like neuropeptides in the sea anemone Nematostella unravel recruitment from the nervous system to venom

Significance Although venom has evolved independently numerous times in animals, the origin of many proteins composing venom remains poorly characterized. We report a case of protein recruitment from the nervous to venom system in the sea anemone Nematostella. We discovered a toxin packaged in the stinging cells and with lethal activity against fish. Surprisingly, it is similar to a peptide from the nervous system (neuropeptide) regulating Nematostella development. Comparisons with other sea anemones showed that these two functionally different peptides originated due to a duplication of a neuropeptide gene followed by recruitment of one of the copies into venom. Additionally, we characterized four other toxin-like neuropeptides, suggesting a recurring pattern of venom recruitment from neuropeptides in sea anemones. The sea anemone Nematostella vectensis (Anthozoa, Cnidaria) is a powerful model for characterizing the evolution of genes functioning in venom and nervous systems. Although venom has evolved independently numerous times in animals, the evolutionary origin of many toxins remains unknown. In this work, we pinpoint an ancestral gene giving rise to a new toxin and functionally characterize both genes in the same species. Thus, we report a case of protein recruitment from the cnidarian nervous to venom system. The ShK-like1 peptide has a ShKT cysteine motif, is lethal for fish larvae and packaged into nematocysts, the cnidarian venom-producing stinging capsules. Thus, ShK-like1 is a toxic venom component. Its paralog, ShK-like2, is a neuropeptide localized to neurons and is involved in development. Both peptides exhibit similarities in their functional activities: They provoke contraction in Nematostella polyps and are toxic to fish. Because ShK-like2 but not ShK-like1 is conserved throughout sea anemone phylogeny, we conclude that the two paralogs originated due to a Nematostella-specific duplication of a ShK-like2 ancestor, a neuropeptide-encoding gene, followed by diversification and partial functional specialization. ShK-like2 is represented by two gene isoforms controlled by alternative promoters conferring regulatory flexibility throughout development. Additionally, we characterized the expression patterns of four other peptides with structural similarities to studied venom components and revealed their unexpected neuronal localization. Thus, we employed genomics, transcriptomics, and functional approaches to reveal one venom component, five neuropeptides with two different cysteine motifs, and an evolutionary pathway from nervous to venom system in Cnidaria.
THE USE OF LOGARITHMS IN THE INTERPRETATION OF CERTAIN ENTOMOLOGICAL PROBLEMS

SUMMARY Evidence is brought forward that in comparing the numbers of insects caught under varying conditions, with particular reference to captures in a light trap, more consistent results are obtained if the geometric means are compared than by the use of arithmetic means. This is most conveniently done by summing the logarithms of the numbers instead of the numbers themselves. If any of the numbers in the series is zero it has been found practical to add one unit to all the captures in the series and so deal with log (n+1) instead of log n. The use of the logarithms prevents the swamping of the results in a series of observations by very high numbers on a single night. It also gives a more normal distribution of departures from a mean. As a result of the latter it is possible to apply the statistical formulae for standard deviation etc. which are not applicable to the skew curve obtained by the use of the departures of the numbers themselves from an arithmetic mean.
Significant functional differences despite morphological and molecular similarity in fully differentiated matched Conditionally Reprogrammed (CRC) and Feeder free dual SMAD inhibited expanded human nasal epithelial cells

Background Patient-derived airway cells differentiated at Air Liquid Interface (ALI) are valuable models for Cystic fibrosis (CF) precision therapy. Advances in culture techniques have improved expansion capacity of airway basal cells, while retaining functional airway epithelium physiology. However, considerable variation in response to CFTR modulators is observed even when using similar ALI culture techniques. We aimed to address if variation in response reflects true biological differences between patients or technical differences as a consequence of different culture expansion methods. Methods Nasal epithelial brushings from 14 individuals (CF=9; non-CF=5) were collected, then equally divided and expanded under conditional reprogramming culture (CRC) and feeder-serum-free “dual-SMAD inhibition” (SMADi) methods. Expanded cells from each culture were differentiated with proprietary PneumaCult™-ALI media. Morphology (Immunofluorescence), global proteomics (LC-MS/MS) and function (barrier integrity, cilia motility, and ion transport) were compared in CRCALI and SMADiALI under basal and CFTR corrector treated (VX-809) conditions. Results No significant difference in the structural morphology or global proteomics profile were observed. Barrier integrity and cilia motility were significantly different, despite no difference in cell junction morphology or cilia abundance. Epithelial Sodium Channels and Calcium-activated Chloride Channel activity did not differ but CFTR mediated chloride currents were significantly reduced in SMADiALI compare to their CRCALI counterparts. Conclusion Alteration of cellular physiological function in vitro occurs were more prominent than structural and differentiation potential in airway ALI. Since culture conditions significantly influence CFTR activity, this could lead to false conclusions if data from different labs are compared against each other without specific reference ranges.
A giant leap in sequence space reveals the intracellular complexities of evolving a new function

Selection for a promiscuous enzyme activity provides substantial opportunity for competition between endogenous and new substrates to influence the evolutionary trajectory, an aspect that has generally been overlooked in laboratory directed evolution studies. We evolved the Escherichia coli nitro/quinone reductase NfsA to detoxify chloramphenicol by randomising eight active site residues simultaneously and interrogating ∼250,000,000 reconfigured NfsA variants. Analysis of every possible evolutionary intermediate of the two best chloramphenicol reductases revealed complex epistatic interactions that restrict each hypothetical trajectory. In both cases, improved chloramphenicol detoxification was only possible after one essential substitution had eliminated activity with endogenous quinone substrates. Unlike the predominantly weak trade-offs seen in previous experimental studies, this substrate incompatibility suggests endogenous metabolites have considerable potential to shape evolutionary outcomes. Unselected prodrug-converting activities were mostly unaffected, which emphasises the importance of negative selection to effect enzyme specialisation, and offers an application for the evolved genes as dual-purpose selectable/counter-selectable markers.
Representational Connectivity Analysis: Identifying Networks of Shared Changes in Representational Strength through Jackknife Resampling

The structure of information in the brain is crucial to cognitive function. The representational space of a brain region can be identified through Representational Similarity Analysis (RSA) applied to functional magnetic resonance imaging (fMRI) data. In its classic form, RSA collapses the time-series of each condition, eliminating fluctuations in similarity over time. We propose a method for identifying representational connectivity (RC) networks, which share fluctuations in representational strength, in an analogous manner to functional connectivity (FC), which tracks fluctuations in BOLD signal, and informational connectivity, which tracks fluctuations in pattern discriminability. We utilize jackknife resampling, a statistical technique in which observations are removed in turn to determine their influence. We applied the jackknife technique to an existing fMRI dataset collected as participants viewed videos of animals (Nastase et al., 2017). We used ventral temporal cortex (VT) as a seed region, and compared the resulting network to a second-order RSA, in which brain regions’ representational spaces are compared, and to the network identified through FC. The novel representational connectivity analysis identified a network comprising regions associated with lower-level visual processing, spatial cognition, perceptual-motor integration, and visual attention, indicating that these regions shared fluctuations in representational similarity strength with VT. RC, second-order RSA and FC identified areas unique to each method, indicating that analyzing shared fluctuations in the strength of representational similarity reveals previously undetectable networks of regions. The RC analysis thus offers a new way to understand representational similarity at the network level.
From babble to words: Infants’ early productions match words and objects in their environment

Infants' early babbling allows them to engage in proto-conversations with caretakers, well before clearly articulated, meaningful words are part of their productive lexicon. Moreover, the well-rehearsed sounds from babble serve as a perceptual 'filter', drawing infants' attention towards words that match the sounds they can reliably produce. Using naturalistic home recordings of 44 10-11-month-olds (an age with high variability in early speech sound production), this study tests whether infants' early consonant productions match words and objects in their environment. We find that infants' babble matches the consonants produced in their caregivers' speech. Infants with a well-established consonant repertoire also match their babble to objects in their environment. Our findings show that infants' early consonant productions are shaped by their input: by 10 months, the sounds of babble match what infants see and hear.
Automatic Analysis of Flaws in Pre-Trained NLP Models

Most tools for natural language processing today are based on machine learning and come with pre-trained models. In addition, third-parties provide pre-trained models for popular NLP tools. The predictive power and accuracy of these tools depends on the quality of these models. Downstream researchers often base their results on pre-trained models instead of training their own. Consequently, pre-trained models are an essential resource to our community. However, to be best of our knowledge, no systematic study of pre-trained models has been conducted so far. This paper reports on the analysis of 274 pre-models for six NLP tools and four potential causes of problems: encoding, tokenization, normalization and change over time. The analysis is implemented in the open source tool Model Investigator. Our work 1) allows model consumers to better assess whether a model is suitable for their task, 2) enables tool and model creators to sanity-check their models before distributing them, and 3) enables improvements in tool interoperability by performing automatic adjustments of normalization or other pre-processing based on the models used.