Miracle-dz/UniFAR-FTUs huggingface dataset:
Corrigendum: Escape of TLR5 recognition by Leptospira spp.: A rationale for atypical endoflagella

Leptospira interrogans are invasive bacteria responsible for leptospirosis, a worldwide zoonosis. They possess two periplasmic endoflagella that allow their motility. L. interrogans are stealth pathogens that escape the innate immune responses of the NOD-like receptors NOD1/2, and the human Toll-like receptor (TLR)4, sensing peptidoglycan and lipopolysaccharide (LPS), respectively. TLR5 is another receptor of bacterial cell wall components, recognizing flagellin subunits. To study the contribution of TLR5 in the host defense against leptospires, we infected WT and TLR5 deficient mice with pathogenic L. interrogans and tracked the infection by in vivo live imaging of bioluminescent bacteria or by q-PCR. We did not identify any protective or inflammatory role of murine TLR5 to control pathogenic Leptospira. Likewise, subsequent in vitro experiments showed that infections with different live strains of L. interrogans and L. biflexa did not trigger TLR5. However, unexpectedly, heat-killed bacteria stimulated human and bovine TLR5, although barely mouse TLR5. Abolition of TLR5 recognition required extensive boiling time of the bacteria or proteinase K treatment, showing an unusual high stability of the leptospiral flagellins. Interestingly, using antimicrobial peptides to destabilize live leptospires, we detected some TLR5 activity, suggesting that TLR5 could participate in the fight against leptospires in humans or cattle. Using different Leptospira strains with mutations in flagellin proteins, we further showed that neither FlaAs nor Fcps participated in the recognition by TLR5, suggesting a role for the FlaBs. These have structural homology to Salmonella FliC, and conserved residues important for TLR5 activation, as shown by in silico analyses. Accordingly, we found that leptospires regulate the expression of FlaB mRNA according to the growth phase in vitro, and that infection with L. interrogans in hamsters and in mice downregulated the expression of the FlaBs but not the FlaAs subunits. Altogether, in contrast to different bacteria that modify their flagellin sequences to escape TLR5 recognition, our study suggests that the peculiar central localization and stability of the FlaB monomers in the periplasmic endoflagella, associated with the downregulation of FlaB subunits in hosts, constitute an efficient strategy of leptospires to escape TLR5 recognition and the immune response.
Word surprisal predicts N400 amplitude during reading

We investigated the effect of word surprisal on the EEG signal during sentence reading. On each word of 205 experimental sentences, surprisal was estimated by three types of language model: Markov models, probabilistic phrasestructure grammars, and recurrent neural networks. Four event-related potential components were extracted from the EEG of 24 readers of the same sentences. Surprisal estimates under each model type formed a significant predictor of the amplitude of the N400 component only, with more surprising words resulting in more negative N400s. This effect was mostly due to content words. These findings provide support for surprisal as a generally applicable measure of processing difficulty during language comprehension.
Isolation and Characterization of Oligotrophic Bacteria Possessing Induced Systemic Disease Resistance against Plant Pathogens

Biocontrol microbes have mainly been screened among large collections of microorganisms via. nutrient-rich in vitro assays to identify novel and effective isolates. However, thus far, isolates from only a few genera, mainly spore-forming bacilli, have been commercially developed. In order to isolate field-effective biocontrol microbes, we screened for more than 200 oligotrophic bacterial strains, isolated from rhizospheres of various soil samples in Korea, which induced systemic resistance against the soft-rot disease caused by Pectobacterium carotovorum SCC1; we subsequently conducted in planta bioassay screening. Two oligotrophic bacterial strains were selected for induced systemic disease resistance against the Tobacco Mosaic Virus and the gray mold disease caused by Botrytis cinerea. The oligotrophic bacterial strains were identified as Pseudomonas manteilii B001 and Bacillus cereus C003 by biochemical analysis and the phylogenetic analysis of the 16S rRNA sequence. These bacterial strains did not exhibit any antifungal activities against plant pathogenic fungi but evidenced several other beneficial biocontrol traits, including phosphate solubilization and gelatin utilization. Collectively, our results indicate that the isolated oligotrophic bacterial strains possessing induced systemic disease resistance could provide useful tools as effective biopesticides and might be successfully used as cost-effective and preventive biocontrol agents in the field.
Eye structure and foraging in King Penguins Aptenodytes patagonicus

Anterior eye structure and retinal visual fields were determined in King Penguins Aptenodytes patagonicus using keratometry and an ophthalmoscopic reflex technique. The cornea is relatively flat (radius 32.9 mm) and hence of low refractive power (10.2 dioptres in air) and this may be correlated with the amphibious nature of penguin vision. The large size of the eye and of the fully dilated pupil may be correlated with activity at low light levels. In air, the binocular field is long (vertical extent 180d) and narrow (maximum width 29d), with the bill placed approximately centrally—a topography found in a range of bird species which employ visual guidance of bill position when foraging. Upon immersion in water, the optical power of the cornea is abolished, with the effect that the monocular fields decrease and binocularity is lost. King Penguins have a pupil type which has not hitherto been recorded in birds. In daylight it contracts to a square-shaped pinhole but dilates to a large circular aperture in darkness. This change alters retinal illumination by 300-fold (2.5 log10 units). When diving, this permits the retina to be pre-adapted to the low ambient light levels that the birds encounter upon reaching mesopelagic depths. These penguins also forage at depths where ambient light levels, even during the day, can fall below the equivalent of terrestrial starlight. Under these conditions, the birds must rely upon the detection of light from the photophores of their prey. In this they are aided by their absolutely large pupil size and broad cyclopean visual field.
Mapping social reward and punishment processing in the human brain: A voxel-based meta-analysis of neuroimaging findings using the social incentive delay task

Social incentives (rewards or punishments) motivate human learning and behaviour, and alterations in the brain circuits involved in the processing social incentives have been linked with several neuropsychiatric disorders. However, questions still remain about the exact neural substrates implicated in social incentive processing. Here, we conducted four Anisotropic Effect Size Signed Differential Mapping voxel-based meta-analyses of fMRI studies investigating the neural correlates of the anticipation and receipt of social rewards and punishments using the Social Incentive Delay task. We map the regions involved in each of these four processes in the human brain, identify decreases in the BOLD signal during the anticipation of both social reward and punishment avoidance that were missed in individual studies due to a lack of power, and characterise the effect size and direction of changes in the BOLD signal for each brain area. Our results provide a better understanding of the brain circuitry involved in social incentive processing and can inform hypotheses about potentially disrupted brain areas linked with dysfunctional social incentive processing during disease. Highlights Voxel-based meta-analysis of the neural underpinnings of social incentive processing We map the brain regions involved in the processing of social incentives in humans We identify new regions missed in individual studies as a result of lack of power Our work can inform research on pathological brain processing of social incentives
Patterns of speciation are similar across mountainous and lowland regions for a Neotropical plant radiation (Costaceae: Costus)

High species richness and endemism in tropical mountains are recognized as major contributors to the latitudinal diversity gradient. The processes underlying mountain speciation, however, are largely untested. The prevalence of steep ecogeographic gradients and the geographic isolation of populations by topographic features are predicted to promote speciation in mountains. We evaluate these processes in a species-rich Neotropical genus of understory herbs that range from the lowlands to montane forests and have higher species richness in topographically complex regions. We ask whether climatic niche divergence, geographic isolation, and pollination shifts differ between mountain-influenced and lowland Amazonian sister pairs inferred from a 756-gene phylogeny. Neotropical Costus ancestors diverged in Central America during a period of mountain formation in the last 3 My with later colonization of Amazonia. Although climatic divergence, geographic isolation, and pollination shifts are prevalent in general, these factors don’t differ between mountain-influenced and Amazonian sister pairs. Despite higher climatic niche and species diversity in the mountains, speciation modes in Costus appear similar across regions. Thus, greater species richness in tropical mountains may reflect differences in colonization history, diversification rates, or the prevalence of rapidly evolving plant life forms, rather than differences in speciation mode.
Pembelajaran Berbasis Edmodo dan Motivasi Belajar Peserta Didik di SMKN 2 Palopo

Edmodo learning is a social media platform, such as Facebook that was developed specifically for students and teachers, which can function to carry out learning. This study aims to determine the effect of Edmodo learning on learning motivation of students. This research is a field research with quantitative research design with an associative approach. Data collection techniques used were observation, questionnaires, and documentation. The results of the data analysis showed that there was a significant influence on Edmodo learning on student motivation in SMK Negeri 1 Palopo.
Motivational enhancement therapy versus cognitive behavioral therapy in a cohort of men and women with alcohol use disorder

The clinical manifestations of alcohol dependence are not homogeneous. Many studies described both cognitive impairments and psychiatric disorders among people with Alcohol use disorder (AUD). However, AUD can be present without comorbid psychiatric disorders or severe cognitive deficits, namely, “pure alcoholics”. Until now, knowledge about effective treatments for this typology of AUD patients remains unknown. The aim of the present study was to assess two psychological methods of intervention: Cognitive-behavioral treatment (CBT) in the short format and the Motivational enhancement therapy (MET). We then opted to compare the efficacy of methods in treating AUD in both men and women pure alcoholics. We performed a controlled and randomized study consisting of 325 people affected by AUD (244 men, 81 women). 72.3% (n=235; 181 men 54 women) were excluded according to selection criteria. The major percentage of exclusion (38.7%; n=91; 63 men 28 women) regarded patients with comorbid psychiatric disorders. Only the 90 remaining test subjects (27.7% of the sample population; 63 men and 27 women) classified as pure alcoholics were eligible for this study. The test subjects were divided into two groups. One group underwent MET (n=47; 35 men and 12 women) and the other underwent CBT (n=43; 28 men and 15 women). We found a significant adherence to the treatment in the CBT group (19 men and 9 women) compared to the MET group (3 men and 1 woman). At the end of treatment, the dropout rates for the CBT and MET therapy groups were 34.9% and 91.5%, respectively. Moreover, we found no differences in the percentage of abstinent days between CBT and MET groups at three months (CBT: n=36; mean 91.40±15.34; MET: n=18; mean 93.90±11.95; t(52)= 0.605, p=0.550), at six months (CBT: N=30; mean 85.00±30.71; MET: n=9; mean 87.78±33.08; t(37)=-0.234, p=0.820) and at twelve months from the beginning of treatment (CBT: n=28; mean 90.14±22.06; MET: n=4; mean 100±0; t(30)=-0.881, p=0.838). In conclusion, we disclose that CBT in the short format could be an effective treatment strategy for pure alcoholics without psychiatric disorders or severe cognitive deficits.
Control of denitrification enzyme activity in a streamside soil

Abstract Progress curve analysis of NO 3 − and NO 2 − reduction in surface soil samples from a streamside soil gave K m values of 4.24 and 6.33 μM, and V max values of 2.16 and 1.83 μmol l −1 min −1 , respectively. Recoveries of reduced NO 3 − and NO 2 − as gaseous N averaged 82 and 108%. The unrecovered NO 3 − -N was presumably dissimilated to NH 4 + -N. The idenitification enzyme activity (DEA) was examined throughout a year and showed seasonal and spatial variabilities of only 10% to 26%, suggesting a high persistency of denitrifying enzymes. Soil moisture and DEA correlated significantly ( r = 0.7671; P 3 − rarely enhanced the acctivity more than two-fold at either depth. Addition of glucose increased the activity 2.3 and 2.5 times in the surface soil and suboil respectively, indicating a moderate carbon limitation of denitrification. The activation energy of DEA was found to be 64.9 kJ mol −1 and Q 10 values for the 2–12°C and 12–22°C temperature ranges were 2.71 and 2.53, respectively. Extrapolation suggested there would be a 4.4-fold increase in DEA if the temperature was changed from 0 to 15°C. Substrate diffusion limited the denitrification 10 to 25 fold. Thus, under anaerobic moist conditions it appears that changes in denitrification might primarily be due to varying diffusion of substrates into the anaerobic soil centers. Over a year, fluctuations in DEA, temperature changes and fluctuations of electron-acceptor and -donor supply will only have a minor effect on natural denitrification activity.
Winter hardening in first-year black spruce (Picea mariana) seedlings

Winter hardening of first-year black spruce [Picea mariana (Mill.) B.S.P.] seedlings was studied by assessing a number of morphological and physiological changes under three hardening regimes: 1) early removal (ER), in which seedlings were exposed to natural daylengths and low ambient temperatures outside. 2) extended greenhouse culture (EG), in which seedlings were exposed to natural daylengths and warm temperatures, and 3) short day (SD), in which seedlings were exposed to short daylengths and low ambient temperatures outside. Measurements included needle primordia initiation, embryonic shoot volume, terminal bud mitotic index, embryonic shoot average cell volume, and shoot tip frost hardiness. EG seedlings formed buds containing 4 times as many needle primordia as ER stock. Embryonic shoot volume increased with number of needle primordia initiated, until late in the hardening period, when significant reductions in meristem volumes of SD and EG stock were observed. Frost hardiness increased sooner in seedlings which set bud in response to short days, but SD treatment did not result in significantly greater frost hardiness at the end of the trial. Frost hardiness was correlated with mitotic index of the embryonic shoot. Cell size in the embryonic shoot declined in seedlings of all treatments during hardening, however, EG seedlings had significantly lower cell volumes by the end of the trial in comparison to ER and SD seedlings.
Potentiometric titration of poly‐L‐lysine: the coil‐to‐β transition

We have performed potentiometric titrations of poly‐L‐lysine. From these data we have calculated the free energy and enthalpy changes for the folding of the random coil to the α‐helix in 10% ethanol (−120 and −120 cal/mole) and from the random coil to the β‐structure in water (−140 and 870 cal/mole) and in 10% ethanol (−180 and 980 cal mole). Comparison of these values with each other and with values for the coil → α‐ helix transition in water (−78 and −880 cal/mole) led to the following conclusions. The stabilization by ethanol of ethanol of the α‐helix with respect to the coil is that predicted from the known free energy of transfer of the peptide group from water to 10% ethanol. Similar data to explain the enthalpy difference are not available. The thermodynamic functions for the transition from α‐helix to β‐structure, obtained by subtracting those for the coil → α‐helix and coil → β‐structure transitions, are explained from a consideration of the structural differences: non bonded interactions of the polypeptide backbone are less favorable in the β‐structure than in the α‐helix, causing an increase in the energy, while hydrophobic contacts between side chains raise the entropy of the β‐structure as compared with the α‐helix, so that the free energy difference between the two structures is small, but enthalpy and entropy differences are large. The observation of only small differences in the free energy and enthalpy changes for the transition from coil β‐structure upon going from water to 10% ethanol is expected by considering both the free energy of transfer of the peptide group (as for the α‐helix) and the free energy and enthalpy of transfer of the apolar part of the side chain involved in hydrophobic bond formation.
EFFECT OF GRAIN COMPOSITION ON WATER UPTAKE BY MALTING BARLEY: A GENETIC AND ENVIRONMENTAL STUDY

Water uptake into the grain is a critical aspect off malting quality. Contrasting environments have been used to examine the role of protein and cell wall components in water uptake. A model based on a threshold value for protein content, the ratio of B to C hordeins and the composition and solubility of β-glucans has been formulated. Better malting performance is associated with lower levels of insoluble β-glucans and higher levels of C-Hordein.
Chromosomes of Pacific hydrothermal vent invertebrates: towards a greater understanding of the relationship between chromosome and molecular evolution

Karyotypes for several East Pacific Rise hydrothermal vent invertebrates are described here for the first time: the vestimentiferans Riftia pachyptila and Oasisia alvinae, the alvinellid polychaetes Alvinella pompejana, A. caudata and Paralvinella grasslei, the polynoid polychaetes Branchinotogluma grasslei and Branchipolynoe symmytilida, the serpulid Laminatubus alvini and the mytilid bivalve Bathymodiolus thermophilus. For comparative purposes, the karyotype of the Atlantic vent mussel Bathymodiolus azoricus is also described here for the first time. Each species has its own unique chromosomal characteristics which can be interpreted both in terms of group characteristics and species divergence. From comparisons with published results on other vent species and closely-related coastal species, we identified a positive correlation between chromosome number variation and molecular divergence at two ribosomal ribonucleic acid gene loci (the 18S and 28S rRNA). Whilst the patterns of chromosome divergence we found were generally within the ranges previously reported for these taxonomic groupings, there was an apparent inconsistency in the case of Branchipolynoe symmytilida (EPR) and Branchipolynoe seepensis (MAR), which show a greater degree of divergence at the chromosome level compared with other members of the same genus. Moreover, polychaetes as a whole showed greater variation in the number and structural divergence of chromosomes compared to Mytilids (structural information only). Our findings highlight the great potential for chromosome analysis in future taxonomic and evolutionary studies of the deep-sea vent fauna.
Does Home Range of the Black-Tailed Tree Rat (Thallomys nigricauda Thomas 1882) Change with Season Along an Aridity Gradient?

Home-range size may reflect the physiological state and energetic requirements of an individual. In the black-tailed tree rat (Thallomys nigricauda) we expected differences in the home-range size of populations in habitats of differing productivity, as measured along an aridity gradient, and between seasons. We studied the variations in home-range size of black-tailed tree rats by radiotracking in winter 2006, 2007 and summer 2007 at three study sites along an aridity gradient in southern Africa. Home ranges were estimated using 100% and 95% minimum convex polygons (MCP) and 95% and 50% fixed kernels. Home ranges varied widely, from 166 to 80 199 m2 for males and from 46 to 8810 m2 for females. Males had larger home ranges than females, which supports a promiscuous mating system reported for the species. Although range size was reduced in both sexes in winter, this was not significant. We found no significant difference in home-range size along the aridity gradient. It is suggested that a combination of habitat productivity, season and breeding system influences the size of home range and that this species displays phenotypic flexibility in terms of its behavioural responses to these factors.
Alfalfa growth following release from drought stress

Compensatory growth (increased growth relative to normal) of alfalfa (Medicago sativa L.) when released from periods of drought stress has been observed or suggested. The objective of this research was to determine whether such compensatory growth does occur. Alfalfa was subjected to drought stress (plant water potential < − 1.5 MPa) for 2 and 4 wk in a greenhouse study and 2, 4, and 6 wk in a field (Palouse silt loam soil, fine-silty, mixed, mesic Pachic Ultic Haploxerolls) study near Moscow, ID. Following harvest and removal of the drought stress, plant growth measurements were made after 30 d of growth in the greenhouse and biweekly during 5 wk of growth in the field [. ]