Miracle-dz/UniFAR-FTUs huggingface dataset:
Increase of insular exotic arthropod diversity is a fundamental dimension of the current biodiversity crisis

A dramatic insect decline has been documented on the grasslands and forests of European or North American mainland. Yet, other parts of the world and other ecosystems remain much less studied with unknown patterns. Using a unique time‐series dataset, we investigate recent trends on abundance and richness of arthropods sampled in Azorean native forest over 6 years (2013–2018). We test the hypothesis that biodiversity erosion drivers are changing the diversity and relative species abundance structure (species abundance distribution, SAD) of endemics, native non‐endemics and exotic species over time. We also examine temporal trends in abundance for each individual species. In contrast with mainland studies, we observed no decline in overall arthropod diversity, but a clear increase in the diversity of exotic arthropods and some evidence of a tendency for decreasing abundance for some endemic species. We also document stronger species turnover for exotic species, but no specific changes in the SAD. We argue that many changes, particularly in unique systems such as islands, will be noticed not at the richness but mostly at compositional level. Special attention should be given to exotic species which are known to be one of the major drivers of biodiversity erosion on islands.
A population‐based, controlled study of the relation between HIV infection and cervical neoplasia

Objective To study a geographically defined population of women exposed to a drug‐related risk for human immunodeficiency virus (HIV), together with carefully matched neighbourhood controls, in order to examine (1) the proportion of different groups having cervical cytopathology screening; (2) the association between HIV infection and cervical intraepithelial neoplasia; (3) the independent effect of CD4+ lymphocyte count and duration of HIV infection; and (4) the correspondence between cervical cytopathology and colposcopically directed biopsy.
Root-nodule symbionts of Derris elliptica Benth. are members of three distinct genera Rhizobium, Sinorhizobium and Bradyrhizobium.

Eleven strains of root-nodule bacteria were isolated from the medicinal legume Derris elliptica Benth. grown in Thailand. A numerical analysis of phenotypic features including utilization of carbon and nitrogen sources, antibiotics resistance, vitamins requirement and growth under different conditions were performed. The partial 16S rDNA of these strains were sequenced and analyses of the sequences by BLASTN revealed that the strains were closely related to members of 3 distinct genera Rhizobium, Sinorhizobium and Bradyrhizobium. The partial nifH and nodC genes amplified from the representative strains of each genus also showed high homology with the nifH and nodC genes from their genera. The nifH and nodC gene trees indicate that different genera of D. elliptica Benth. symbionts represent variation among symbiotic genes.
Effect of dietary antioxidant on mercuric chloride induced lung toxicity and oxidative stress

Abstract This study was conducted to evaluate the effect of environmental contaminant mercuric chloride on levels of trace elements and oxidative parameters in rat lungs and to investigate the efficacy of possible protection by natural antioxidant diallylsulphide (DAS) against lung injury. Twenty-four healthy male rats were randomly divided into four groups: I – control, II – DAS (200 mg/kg), III – HgCl2 (50 mg/kg), and IV – DAS (200 mg/kg) + HgCl2 (50 mg/kg). Mercuric chloride induced oxidative stress was indicated by a significant decrease in levels of superoxide dismutase, catalase, and glutathione peroxidase as compared to the control group (p–<0.05). Also, hydroxyproline (HYP) content in lung tissues of mercuric chloride-treated group was significantly increased (p < 0.05). DAS markedly attenuated mercuric-induced biochemical alterations in lungs by upregulating the activities of antioxidant enzymes. These findings indicated that within the doses selected, DAS can provide significant protection against HgCl2-induced toxicity.
Prey consumption and survival of the predatory mite, Amblydromalus limonicus, on different prey and host plants

ABSTRACT Amblydromalus limonicus consumed fewer first instar Frankliniella occidentalis thrips than Bactericera cockerelli psyllids per day when on the same (1.7 thrips, 3.7 psyllids) or separate (2.9 thrips, 4.4 psyllids) capsicum leaf discs. Mites ate fewer psyllids per day on tomato (1.9) than on capsicum (3.1). Mite survival was similar on both prey and plants.
Fitness, population growth rate and flowering in Carex bigelowii, a clonal sedge

without daughter tillers, together with an increase in the proportion of tillers with more than one daughter tiller. At the third site the same phenomena were observed but, in addition, the proportion of tillers with one daughter tiller was slightly reduced as well. Tiller systems at this site also differed from the others by showing a positive correlation between fitness and variation in daughter tiller production. At no site was mean rhizome length of tiller systems correlated with fitness. At the population level, the tiller densities at the lower and intermediate sites appeared to have been stationary (no net trend) during the past 10-20 years. At the upper site, the number of tillers in the sampled quadrats had increased, either due to high mobility of the tiller systems or to an actual increase in overall population density. We also measured the flowering rates in the populations and found no major differences between the sites. No seedling establishment of C. bigelowii has been recorded in this area and the costs of sexual reproduction, in terms of decreased vegetative reproduction, are therefore expected to be low. This expectation was in accordance with an earlier study finding no such costs associated with flowering and seed set.
XANTHOPHYLLS AND CAROTENES OF DIATOMS, BROWN ALGAE, DINOFLAGELLATES, AND SEA-ANEMONES

Carotenoid pigments of several groups of algae have been obtained through utilization of the chromatographic adsorption method. The selectivity of this method and the relative positions of the pigments in the columns have been found to vary with the solvents and adsorbents that were employed.Xanthophylls of algae represent a large proportion of the carotenoid pigments produced in the world's vegetation. Most of the algal xanthophylls were readily convertible, reversibly, into one or more isomers that were separated on the adsorption columns. The principal xanthophylls were the more stable, presumably trans, isomers. Some of the labile isomers also appeared to be normal constituents of the cells. All the algal xanthophylls were unesterified.The following xanthophylls have been obtained from each of six species of diatoms: diatoxanthin, diadinoxanthin (both new xanthophylls), fucoxanthin, neofucoxanthin A, and neofucoxanthin B. From some eight species of brown algae there were obtained: diatoxanthin (occasi.
Efficacy and welfare assessment of an encapsulated para-aminopropiophenone (PAPP) formulation as a bait-delivered toxicant for feral cats (Felis catus)

Abstract Context Feral cats are invasive predators of small and medium-sized fauna throughout Australia. The only broad-scale population-management technique for feral cats currently available in Australia is poison baiting. As poison baits for feral cats must be surface-laid, this can lead to the unintended exposure of non-target species consuming the baits. Encapsulation of a toxin within a robust, controlled-release pellet implanted within the meat lure (the combination of which is termed the Curiosity® bait) substantially reduces the potential risk to non-target species. Para-aminopropiophenone (PAPP) has been shown to be an effective toxin to which cats are highly susceptible. Aims The present study aimed to measure the efficacy of encapsulating PAPP toxin in a controlled-release pellet on feral cats in a pen situation and to document the observed behaviours through the toxication process. Methods Pen trials with captive cats were undertaken to document efficacy of encapsulating PAPP toxin in a controlled-release pellet and to assess the behaviours during toxicosis. These behaviours inform an assessment of the humaneness associated with the Curiosity bait using a published relative humaneness model. Key results The trials demonstrated a 95% consumption of the toxic pellet and observed the pattern of behaviours exhibited during the intoxication process. There was a definitive delay in the onset of clinical signs and death followed at ∼185 min after the first definitive sign. The humaneness using the relative humaneness model was scored at ‘mild suffering’. Conclusions The encapsulating PAPP toxin in a controlled-release pellet for feral cats is effective. The feral cats display a range of behaviours through the toxication process, and these have been interpreted as mild suffering under the relative humaneness model. Implications The documented efficacy and behaviours of encapsulating PAPP toxin in a controlled-release pellet provides knowledge of how the PAPP toxin works on feral cats, which may assist in decision-making processes for conservation land managers controlling feral cats and whether to incorporate the use of the Curiosity® bait into existing management techniques.
Synthesis and Biological Activity of Some Novel Aryl‐Substituted 1,3,4‐Oxadiazole Mannich Bases Containing Pyrimidine Rings

A series of novel Mannich base derivatives (E1–E15) of 5-aryl-1,3,4-oxadiazole-2-thione with substituted pyrimidine were synthesized and characterized by elemental analysis, IR, 1H-NMR. The antifungal activities of these compounds were also originally studied. The results showed that most of the title compounds exhibited relatively good fungicidal activities. Especially compounds E8 and E13 showed better antifungal activity than comparison compound hymexazol. The relationship of structure and activity revealed that the presence of the methyl group at four and six positions of pyrimidine ring remarkably enhanced the antifungal activity of title compounds.
An evaluation of alternative measurement techniques for estimating the volume of logging residues.

Logging residue is currently one of the largest underutilized residues potentially available for biomass energy production. The cost of collection, processing, and transporting this material is high in proportion to its value; the result is that there are potentially small proﬁt margins. Therefore, managers must develop and execute efﬁcient supply chains. The ﬁrst step in developing an efﬁcient supply chain requires a reliable estimate of pile volume because this will allow the manager to deploy the appropriately sized transportation and processing operations. This article compares two methods used to measure logging residue piles to terrestrial light detection and ranging (LiDAR)-generated estimates; one uses a geometric base and the other uses a laser rangeﬁnder. The geometric method, which has been used since the 1980s, derives volume by ﬁrst ocularly estimating the simpliﬁed geometric shape of the pile. The second step measures the parameters to compute the volume of that shape. The other method uses a laser rangeﬁnder with an electronic compass that collects coordinates of the pile and then computes a volume. A LiDAR estimate was used as a control and both methods were compared to the LiDAR-generated results for 33 piles in western Oregon. The laser rangeﬁnder produced results that were closer to the LiDAR-generated estimates than the geometric shapes, which showed larger deviations from the LiDAR-generated estimate for larger piles. We believe that the consistency of the laser rangeﬁnder along with its improved reliability makes it the superior method for estimating volume of biomass stored in piles.
Computational prediction of telomerase RNAs in yeast genomes

by DONG ZHANG (Under the Direction of Liming Cai) ABSTRACT Telomerase RNA (TR) is a vital component of the telomerase enzyme which ensures the complete replication of chromosome ends. Experimental identification of TRs is expensive and lacks a general approach due to the divergent TR sequences across many eukaryotes. Computational prediction of TRs can help narrow down the number of plausible candidates for further experimental validations. The common core structure found in all known TRs may form the basis for a prediction. However, the structure contains a recently identified triple helix as well as structural elements divergent across many eukaryotes, beyond the capability of existing RNA structure profiling techniques. The structure-based prediction of TRs thus remains challenging. I introduce a pseudoknot-prediction-capable utility computer program, called TRFolder. Unlike existing general purpose structure prediction programs, TRFolder is effective in predicting core TR elements including pseudoknots, triple helices, template-boundary elements and core-closing stems that occur in yeast TRs.
Open Research Online

Low cost digital cameras in smartphones and wearable devices make it easy for people to automatically capture and share images as a visual lifelog. Having been inspired by a US campus based study that explored individual privacy behaviours of visual lifeloggers, we conducted a similar study on a UK campus, however we also focussed on the privacy behaviours of groups of lifeloggers. We argue for the importance of replicability and therefore we built a publicly available toolkit, which includes camera design, study guidelines and source code. Our results show some similar sharing behaviour to the US based study: people tried to preserve the privacy of strangers, but we found fewer bystander reactions despite using a more obvious camera. In contrast, we did not find a reluctance to share images of screens but we did find that images of vices were shared less. Regarding privacy behaviours in groups of lifeloggers, we found that people were more willing to share images of people they were interacting with than of strangers, that lifelogging in groups could change what defines a private space, and that lifelogging groups establish different rules to manage privacy for those inside and outside the group.
Modeling Effects of Length Limit Regulations on Riverine Populations of Channel Catfish

AbstractChannel Catfish Ictalurus punctatus is an important species among anglers in North America. Channel Catfish management strategies vary greatly in the United States and Canada, and there are few examples of regulations aimed at improving size structure in the literature. The goal of this study was to model the response of Channel Catfish to changes in regulations that meet specific management objectives. We modeled a suite of regulations to determine if minimum length limits or a protected slot limit could be used to improve size structure or avoid growth overfishing of Channel Catfish in a large river. We modeled three minimum length limits (304, 356, and 406 mm) and a 356–456-mm protected slot limit to assess the effectiveness of each at delaying or eliminating growth overfishing and increasing the number of quality-sized fish in the Missouri River, Nebraska. Our models indicated a 406-mm minimum length limit could be used to avoid growth overfishing until exploitation rates were greater than 45%.
Deriving Habitat Models for Northern Long-Eared Bats from Historical Detection Data: A Case Study Using the Fernow Experimental Forest

Abstract The listing of the northern long-eared bat (Myotis septentrionalis) as federally threatened under the Endangered Species Act following severe population declines from white-nose syndrome presents considerable challenges to natural resource managers. Because the northern long-eared bat is a forest habitat generalist, development of effective conservation measures will depend on appropriate understanding of its habitat relationships at individual locations. However, severely reduced population sizes make gathering data for such models difficult. As a result, historical data may be essential in development of habitat models. To date, there has been little evaluation of how effective historical bat presence data, such as data derived from mist-net captures, acoustic detection, and day-roost locations, may be in developing habitat models, nor is it clear how models created using different data sources may differ. We explored this issue by creating presence probability models for the northern long-eare.
Diurnal Changes in Tissue Glutathione and Protein Pools of Molting White-crowned Sparrows: The Influence of Photoperiod and Feeding Schedule

In molting birds keratin synthesis is intense and continuous through day and night. Keratins are much richer in cystine than are most tissue proteins. We hypothesized that glutathione (γ-glutamylcysteinylglycine) helps to sustain feather synthesis and spare bodyprotein during overnight fasting by serving as a cysteine reservoir. To test this hypothesis, we measured the responses of liver and muscle glutathione and protein pools to various feeding schedules (cysteine supply) andperiods of overnight fasting (cysteine demand) in molting white-crowned sparrows. Our main purpose was to ascertain whether these pools change passively or are instead regulated in relation to cysteine need in the postabsorptive state. During molt, significantly more liver glutathione and pectoralis protein were stored by day and utilized overnight than in postmolt. Liver glutathione and pectoralis protein were stored and utilized diurnally during molt in proportion to the duration of the overnight fast (12 h > 8 h > 4 h). Diurnal changes in these pools resulted from significantly larger evening pools, not from significantly smaller morning pools. Liver glutathione and pectoralis protein pools appeared to be specifically regulated to support the demands of overnight feather synthesis. In contrast, changes in liver protein pools during molt were smaller than in postmolt and were unrelated to the duration of the overnight fast. The sizes of liver protein pools in evening were nearly the same in molting and nonmolting birds. Similarly, the size of pectoralis glutathione pools in evening was nearly the same in molting and nonmolting birds, butpectoralis glutathione was utilized overnight in molt in relation to the duration of the overnight fast. Liver protein pools and possibly other tissue protein pools appeared to be spared by storage of glutathione in the liver. Pectoralis glutathione pools appeared to be passively emptied according to overnight cysteine demand. Overnight force-feeding of chick starter mash or serial injection of cysteine (im) attenuated overnight utilization of liver and muscle glutathione, indicating a specific role for GSH as a cysteine reservoir. The dynamics of tissue glutathione and protein pools during molt in relation to photoperiod may have important consequences for the energetic and amino acid costs of molt.
REVIEW

The mid-Piacenzian warm period (3.264 to 3.025 Ma) is the most recent geological period with a present-like atmospheric pCO2 exhibiting significant warming relative to present conditions. With the advanced understanding of the climate variability of this interval, a specific interglacial (marine isotope stage KM5c, MIS KM5c, 3.205 Ma) is selected for 15 Pliocene Model Intercomparison Project phase 2 (PlioMIP 2) and updated boundary conditions are provided. In this study, we carried out series of experiments according to the design of PlioMIP2 with two versions of the IPSL Atmosphere-Ocean Coupled General Circulation Model (AOGCM) (IPSL-CM5A and IPSL-CM5A2). By comparing with PlioMIP 1 experiment, run with IPSL-CM5A, our results show that the simulated MIS KM5c climate presents enhanced warming in mid-to-high latitudes, especially in ocean regions. This warming can be attributed to the largely enhanced Atlantic Meridional 20 Overturning Circulation caused by the high latitude seaway changes. The tier experiments, conducted with IPSL-CM5A2 (with faster computation scheme), show that besides the increased pCO2, both modified orography and reduced ice sheets contribute substantially in mid-to-high latitudes warming of MIS KM5c. When considering the pCO2 uncertainties, the warming pattern changes, our model response to the variation of pCO2 by +/-50ppmv is not symmetric in the surface air temperature, due to the non-linear response of the cryosphere (snow cover and sea ice extent). By analysing the Greenland 25 Ice Sheet surface mass balance, we also demonstrate its vulnerability under both MIS KM5c and modern warm climate.
Regulatory Divergence of Aspartate Transcarbamoylase from the Pseudomonads

Aspartate transcarbamoylase (ATCase) was purified from 16 selected bacterial species including existing Pseudomonas species and former species reassigned to new genera. An enormous diversity was seen among the 16 enzymes with each class of ATCase being represented. The smallest class, class C, with a catalytically active homotrimer, at 100 kDa, was found in Bacillus and other Gram positive bacteria. In this report, the ATCases from the Gram negatives, Shewanella putrefaciens and Stenotrophomonas maltophilia were added to class C membership. The enteric bacteria typify class B ATCases at 310 kDa, with a dodecameric structure composed of two catalytic trimers coupled to three regulatory dimers. A key feature of class B ATCases is the dissociability of the holoenzyme into regulatory and catalytic subunits which were enzymatically active. In this report, the ATCase from Pseudomonas indigofera was added to class B ATCases. The largest class, at 480 kDa, class A, contains the fluorescent Pseudomonas including most members of the 16S rRNA homology group I. Two polypeptides are produced from overlapping pyrBC' genes. The former, pyrB, encodes a 34 kDa catalytic polypeptide while pyrC' encodes a 45 kDa dihydroorotase-like polypeptide. Two non active trimers are made from six 34 kDa chains which are cemented by six 45 kDa chains to form the active dodecameric structure. Dissociation of the holoenyzme into its separate active subunits has not been possible. In this report, the ATCases from Comamonas acidovorans and C. testosteroni, were added to the class A enzymes. An even larger class of ATCase than class A at 600 kDa was discovered in Burkholderia cepacia. Stoichiometric measurements predict a dodecamer of six 39 kDa polypeptides and six 60 kDa polypeptides. Unlike other large pseudomonads ATCases, the enzyme from B. cepacia was dissociable into smaller active forms. Both the holoenzyme and its dissociated forms were regulated by nucleotide effectors. A new class of ATCase was proposed for B. cepacia type enzymes.
Molecular predictive testing in precision oncology: The Italian experience

In this review, we describe molecular pathology testing to predict response to targeted treatment of solid tumors, focusing on Italian routine clinical practice. The combination of the universal health care system organized at national, regional, and local levels has led a decentralized model, with a large number of local laboratories performing in‐house molecular testing following guidelines issued and external quality assessment organized by the Italian Society of Pathology and Cytopathology–Italian Division of the International Academy of Pathology. In this framework, in the early days of predictive testing, sponsored informatics platforms support to set up national programs that aimed to integrate the activity of oncologists and pathologists to test cancer patients for druggable alterations. More recently, reimbursement for molecular testing is being covered completely by the Italian National Health Service. In the near future, considering the development of complex technologies, we expect that outsourcing samples to next‐generation sequencing referral laboratories will take place.