Miracle-dz/UniFAR-FTUs huggingface dataset:
Belowground Interactions Impact the Soil Bacterial Community, Soil Fertility, and Crop Yield in Maize/Peanut Intercropping Systems

Intercropping has been widely used to control disease and improve yield in agriculture. In this study, maize and peanut were used for non-separation intercropping (NS), semi-separation intercropping (SS) using a nylon net, and complete separation intercropping (CS) using a plastic sheet. In field experiments, two-year land equivalent ratios (LERs) showed yield advantages due to belowground interactions when using NS and SS patterns as compared to monoculture. In contrast, intercropping without belowground interactions (CS) showed a yield disadvantage. Meanwhile, in pot experiments, belowground interactions (found in NS and SS) improved levels of soil-available nutrients (nitrogen (N) and phosphorus (P)) and enzymes (urease and acid phosphomonoesterase) as compared to intercropping without belowground interactions (CS). Soil bacterial community assay showed that soil bacterial communities in the NS and SS crops clustered together and were considerably different from the CS crops. The diversity of bacterial communities was significantly improved in soils with NS and SS. The abundance of beneficial bacteria, which have the functions of P-solubilization, pathogen suppression, and N-cycling, was improved in maize and peanut soils due to belowground interactions through intercropping. Among these bacteria, numbers of Bacillus, Brevibacillus brevis, and Paenibacillus were mainly increased in the maize rhizosphere. Burkholderia, Pseudomonas, and Rhizobium were mainly increased in the peanut rhizosphere. In conclusion, using maize and peanut intercropping, belowground interactions increased the numbers of beneficial bacteria in the soil and improved the diversity of the bacterial community, which was conducive to improving soil nutrient (N and P) supply capacity and soil microecosystem stability.
A Simulation Modeling Framework to Optimize Programs Using Financial Incentives to Motivate Health Behavior Change

Introduction. While increasingly popular among mid- to large-size employers, using financial incentives to induce health behavior change among employees has been controversial, in part due to poor quality and generalizability of studies to date. Thus, fundamental questions have been left unanswered: To generate positive economic returns on investment, what level of incentive should be offered for any given type of incentive program and among which employees? Methods. We constructed a novel modeling framework that systematically identifies how to optimize marginal return on investment from programs incentivizing behavior change by integrating commonly collected data on health behaviors and associated costs. We integrated “demand curves” capturing individual differences in response to any given incentive with employee demographic and risk factor data. We also estimated the degree of self-selection that could be tolerated: that is, the maximum percentage of already-healthy employees who could enroll in a wellness program while still maintaining positive absolute return on investment. In a demonstration analysis, the modeling framework was applied to data from 3000 worksite physical activity programs across the nation. Results. For physical activity programs, the incentive levels that would optimize marginal return on investment ($367/employee/year) were higher than average incentive levels currently offered ($143/employee/year). Yet a high degree of self-selection could undermine the economic benefits of the program; if more than 17% of participants came from the top 10% of the physical activity distribution, the cost of the program would be expected to always be greater than its benefits. Discussion. Our generalizable framework integrates individual differences in behavior and risk to systematically estimate the incentive level that optimizes marginal return on investment.
The MIC and MBC of Silver Nanoparticles against Enterococcus faecalis - A Facultative Anaerobe

Aim: To determine the Minimum Inhibitory Concentration (MIC) and Minimum Bactericidal Concentration (MBC) of silver nanoparticles against Enterococcus faecalis (E.faecalis). Methodology: The antimicrobial efficacy of the silver nanoparticles was determined by the standard methods of Clinical and Laboratory Standards Institute (CLSI). Different concentrations of silver nanoparticles were prepared, and MIC was calculated by tube macro dilution method. The MBC was determined by the lowest concentration that kills 99.9% of the initial bacterial population. The data was analyzed by non-parametric test of Kruskal-Wallis using SPSS software package (version 17). Results: The MIC and MBC of silver nanoparticles against E. faecalis was found to be optimum at 5 mg/ml. Conclusion: The result obtained from this study shows that silver nanoparticles have potential bactericidal effects against E. faecalis at a concentration of 5 mg/ml. Silver nanoparticles can be incorporated in the root canal medicaments, sealers and irrigants, as it possess potent antimicrobial efficacy against E. faecalis. Significance and impact of study: The antimicrobial property of silver nano particles against E.faecalis can be used clinically as an alternate to various other intra canal medicaments as irrigants.
An RNAi-Based Control of Fusarium graminearum Infections Through Spraying of Long dsRNAs Involves a Plant Passage and Is Controlled by the Fungal Silencing Machinery

Meeting the increasing food and energy demands of a growing population will require the development of ground-breaking strategies that promote sustainable plant production. Host-induced gene silencing has shown great potential for controlling pest and diseases in crop plants. However, while delivery of inhibitory noncoding double-stranded (ds)RNA by transgenic expression is a promising concept, it requires the generation of transgenic crop plants which may cause substantial delay for application strategies depending on the transformability and genetic stability of the crop plant species. Using the agronomically important barley—Fusarium graminearum pathosystem, we alternatively demonstrate that a spray application of a long noncoding dsRNA (791 nt CYP3-dsRNA), which targets the three fungal cytochrome P450 lanosterol C-14α-demethylases, required for biosynthesis of fungal ergosterol, inhibits fungal growth in the directly sprayed (local) as well as the non-sprayed (distal) parts of detached leaves. Unexpectedly, efficient spray-induced control of fungal infections in the distal tissue involved passage of CYP3-dsRNA via the plant vascular system and processing into small interfering (si)RNAs by fungal DICER-LIKE 1 (FgDCL-1) after uptake by the pathogen. We discuss important consequences of this new finding on future RNA-based disease control strategies. Given the ease of design, high specificity, and applicability to diverse pathogens, the use of target-specific dsRNA as an anti-fungal agent offers unprecedented potential as a new plant protection strategy.
Alzheimer’s Disease Assessment: A Review and Illustrations Focusing on Item Response Theory Techniques

Alzheimer’s disease (AD) affects neurological, cognitive, and behavioral processes. Thus, to accurately assess this disease, researchers and clinicians need to combine and incorporate data across these domains. This presents not only distinct methodological and statistical challenges but also unique opportunities for the development and advancement of psychometric techniques. In this article, we describe relatively recent research using item response theory (IRT) that has been used to make progress in assessing the disease across its various symptomatic and pathological manifestations. We focus on applications of IRT to improve scoring, test development (including cross-validation and adaptation), and linking and calibration. We conclude by describing potential future multidimensional applications of IRT techniques that may improve the precision with which AD is measured.
The virtual maze: A behavioural tool for measuring trust

Trusting another person may depend on our level of generalised trust in others, as well as perceptions of that specific person’s trustworthiness. However, many studies measuring trust outcomes have not discussed generalised versus specific trust. To measure specific trust in others, we developed a novel behavioural task. Participants navigate a virtual maze and make a series of decisions about how to proceed. Before each decision, they may ask for advice from two virtual characters they have briefly interviewed earlier. We manipulated the virtual characters’ trustworthiness during the interview phase and measured how often participants approached and followed advice from each character. We also measured trust through ratings and an investment game. Across three studies, we found participants followed advice from a trustworthy character significantly more than an untrustworthy character, demonstrating the validity of the maze task. Behaviour in the virtual maze reflected specific trust rather than generalised trust, whereas the investment game picked up on generalised trust as well as specific trust. Our data suggest the virtual maze task may provide an alternative behavioural approach to measuring specific trust in future research, and we demonstrate how the task may be used in traditional laboratories.
Cerebral microbleeds and CSF Alzheimer biomarkers in primary progressive aphasias

Objective To reveal the prevalence and localization of cerebral microbleeds (CMBs) in the 3 main variants of primary progressive aphasia (PPA) (logopenic, semantic, and nonfluent/agrammatic), to identify the relationship with underlying Alzheimer pathology, and to explore whether CMBs contribute to language breakdown. Methods We used a cross-sectional design in a multicenter cohort of 82 patients with PPA and 19 similarly aged healthy controls. MRI allowed for rating CMBs (2-dimensional gradient recalled echo T2*, susceptibility weighted imaging sequences) and white matter hyperintensities. CSF Alzheimer disease biomarker analyses available in 63 of the 82 patients provided the stratification of PPA into subgroups with patients who had or did not have probable underlying Alzheimer pathology. Results The prevalence of CMBs was higher in patients with PPA (28%) than in controls (16%). They were more prevalent in logopenic PPA (50%) than in semantic PPA (18%) and nonfluent/agrammatic PPA (17%). The localization of CMBs was mainly lobar (81%) with no difference between the PPA variants. CMBs were more frequent in PPA patients with positive than with negative CSF Alzheimer disease biomarkers (67% vs 20%). Patients with and without lobar CMBs had similar volumes of white matter hyperintensities. Language and general cognitive impairment in PPA was unrelated to CMB rates. Conclusions CMB prevalence in PPA is higher than in healthy controls. CMBs were most prevalent in the logopenic variant, were related to underlying Alzheimer pathology, and did not affect the language/cognitive impairment. Our findings also suggest that CMB detection with MRI contributes to PPA variant diagnosis, especially of logopenic PPA, and provides an estimator of the underlying neuropathology.
Mechanism of Intramembrane Cleavage of Alcadeins by γ-Secretase

Background Alcadein proteins (Alcs; Alcα, Alcβand Alcγ) are predominantly expressed in neurons, as is Alzheimer's β-amyloid (Aβ) precursor protein (APP). Both Alcs and APP are cleaved by primary α- or β-secretase to generate membrane-associated C-terminal fragments (CTFs). Alc CTFs are further cleaved by γ-secretase to secrete p3-Alc peptide along with the release of intracellular domain fragment (Alc ICD) from the membrane. In the case of APP, APP CTFβ is initially cleaved at the ε-site to release the intracellular domain fragment (AICD) and consequently the γ-site is determined, by which Aβ generates. The initial ε-site is thought to define the final γ-site position, which determines whether Aβ40/43 or Aβ42 is generated. However, initial intracellular ε-cleavage sites of Alc CTF to generate Alc ICD and the molecular mechanism that final γ-site position is determined remains unclear in Alcs. Methodology Using HEK293 cells expressing Alcs plus presenilin 1 (PS1, a catalytic unit of γ-secretase) and the membrane fractions of these cells, the generation of p3-Alc possessing C-terminal γ-cleavage site and Alc ICD possessing N-terminal ε-cleavage site were analysed with MALDI-TOF/MS. We determined the initial ε-site position of all Alcα, Alcβ and Alcγ, and analyzed the relationship between the initially determined ε-site position and the final γ-cleavage position. Conclusions The initial ε-site position does not always determine the final γ-cleavage position in Alcs, which differed from APP. No additional γ-cleavage sites are generated from artificial/non-physiological positions of ε-cleavage for Alcs, while the artificial ε-cleavage positions can influence in selection of physiological γ-site positions. Because alteration of γ-secretase activity is thought to be a pathogenesis of sporadic Alzheimer's disease, Alcs are useful and sensitive substrate to detect the altered cleavage of substrates by γ-secretase, which may be induced by malfunction of γ-secretase itself or changes of membrane environment for enzymatic reaction.
The influence of bleeding, extra water and superplasticizer on the SCC plastic shrinkage cracking: case of hot weather

Abstract Self-compacting concrete (SCC) is a new material able to be put in place without vibration. However, this advantage is offset by some drawbacks, such as plastic shrinkage, one of the causes of cracking in concrete. Furthermore, the presence of fines absorbs a large amount of water and therefore minimizes bleeding. This paper endeavours to provide a better understanding of the appearance of plastic shrinkage cracking, and to justify his relation with bleeding phenomena. Five SCC formulas with different W/C ratios were prepared and compared to the same range of ordinary concrete (OC) in terms of restrained shrinkage (cracking width). At the same time, a study of cracks’ propagation over time (cracking length) was conducted on the equivalent mortars (mOCe, mSCCe). Mixtures were placed in different hot environmental conditions. The results showed that bleeding significantly reduces cracking length and has no effect on cracking width. In the second part, extra water and superplasticizer was proposed as a solution to prevent SCC cracking and findings show the addition of 10% of water reduces cracking length and a slightly lower addition of superplasticizer reduces SCC’s crack width.
Blocked vs. interleaved presentation and proactive interference in episodic memory

ABSTRACT Although a number of theoretical accounts of proactive interference (PI) in episodic memory have been proposed, existing empirical evidence does not support conclusively a single view yet. In two experiments we tested the predictions of the temporal discrimination theory of PI against alternative accounts by manipulating the presentation schedule of study materials (lists blocked by category vs. interleaved). In line with the temporal discrimination theory, we observed a clear buildup of (and release from) PI in the blocked condition, in which all the lists of the same category were presented sequentially. In the interleaved condition, with alternating lists of different categories, a more gradual and smoother buildup of PI was observed. When participants were left free to choose their presentation schedule, they spontaneously adopted an interleaved schedule, resulting again in more gradual PI. After longer delays, we observed recency effects at the list level in overall recall and, in the blocked condition, PI-related effects. The overall pattern of findings agrees with the predictions of the temporal discrimination theory of PI, complemented with categorical processing of list items, but not with alternative accounts, shedding light on the dynamics and underpinnings of PI under diverse presentation schedules and over different time scales.
In Vitro Acid-Mediated Initial Dental Enamel Loss Is Associated with Genetic Variants Previously Linked to Caries Experience

We have previously shown that AQP5 and BTF3 genetic variation and expression in whole saliva are associated with caries experience suggesting that these genes may have a functional role in protecting against caries. To further explore these results, we tested ex vivo if variants in these genes are associated with subclinical dental enamel mineral loss. DNA and enamel samples were obtained from 53 individuals. Enamel samples were analyzed for Knoop hardness of sound enamel, integrated mineral loss after subclinical carious lesion creation, and change in integrated mineral loss after remineralization. DNA samples were genotyped for single nucleotide polymorphisms using TaqMan chemistry. Chi-square and Fisher's exact tests were used to compare individuals above and below the mean sound enamel microhardness of the cohort with alpha of 0.05. The A allele of BTF3 rs6862039 appears to be associated with harder enamel at baseline (p = 0.09), enamel more resistant to demineralization (p = 0.01), and enamel that more efficiently regain mineral and remineralize (p = 0.04). Similarly, the G allele of AQP5 marker rs3759129 and A allele of AQP5 marker rs296763 are associated with enamel more resistant to demineralization (p = 0.03 and 0.05, respectively). AQP5 and BTF3 genetic variations influence the initial subclinical stages of caries lesion formation in the subsurface of enamel.
The price of information: Increased inspection costs reduce the confirmation bias in visual search

In visual search, there is a confirmation bias such that attention is biased towards stimuli that match a target template, which has been attributed to covert costs of updating the templates that guide search [Rajsic, Wilson, & Pratt, 2015. Confirmation bias in visual search. Journal of Experimental Psychology: Human Perception and Performance. Advance online publication. doi:10.1037/xhp0000090]. In order to provide direct evidence for this speculation, the present study increased the cost of inspections in search by using gaze- and mouse-contingent searches, which restrict the manner in which information in search displays can be accrued, and incur additional motor costs (in the case of mouse-contingent searches). In a fourth experiment, we rhythmically mask elements in the search display to induce temporal inspection costs. Our results indicated that confirmation bias is indeed attenuated when inspection costs are increased. We conclude that confirmation bias results from the low-cost strategy of matching information to a single, concrete visual template, and that more sophisticated guidance strategies will be used when sufficiently beneficial. This demonstrates that search guidance itself comes at a cost, and that the form of guidance adopted in a given search depends on a comparison between guidance costs and the expected benefits of their implementation.
Single-Dose Pharmacokinetics and Safety of Meropenem-Vaborbactam in Subjects with Chronic Renal Impairment

ABSTRACT Vaborbactam is a member of a new class of β-lactamase inhibitors with inhibitory activity against serine carbapenemases (e.g., Klebsiella pneumoniae carbapenemase) that has been developed in combination with meropenem. The pharmacokinetics of the combination was evaluated in 41 subjects with chronic renal impairment in a phase 1, open-label, single-dose study. Subjects were assigned to one of five groups based on renal function: normal (creatinine clearance of ≥90 ml/min), mild (estimated glomerular filtration rate [eGFR] of 60 to 89 ml/min/1.73 m2), moderate (eGFR of 30 to <60), or severe (eGFR of <30) impairment plus end-stage renal disease (ESRD) patients on hemodialysis. Subjects received a single intravenous dose of 1 g of meropenem plus 1 g of vaborbactam by 3-h infusion. The ESRD group received two doses (on and off dialysis) separated by a washout. Pharmacokinetic parameters were estimated by standard noncompartmental methods. For both meropenem and vaborbactam, the area under the concentration-time curve was larger and the elimination half-life was longer with decreasing renal function. Meropenem and vaborbactam total plasma clearance (CLt) rates were similar and decreased with decreasing renal function. Slopes of the linear relationship between eGFR and CLt were similar, indicating a similar proportional reduction in CLt with decreasing renal function. Hemodialysis significantly increased drug clearance of meropenem (mean of 2.21-fold increase in CLt, P < 0.001) and vaborbactam (mean of 5.11-fold increase, P = 0.0235) relative to drug administration off dialysis, consistent with dose recovery rates of 38.3% and 52.9% for meropenem and vaborbactam, respectively, in dialysate. Plasma clearance of meropenem and vaborbactam is reduced with renal impairment, requiring dose adjustment. Hemodialysis removes both drugs. (This study has been registered at ClinicalTrials.gov under identifier NCT02020434.)
SUMOylation of human septins is critical for septin filament bundling and cytokinesis

Septins are cytoskeletal proteins that assemble into nonpolar filaments. They are critical in diverse cellular functions, acting as scaffolds for protein recruitment and as diffusion barriers for subcellular compartmentalization. Human septins are encoded by 13 different genes and are classified into four groups based on sequence homology (SEPT2, SEPT3, SEPT6, and SEPT7 groups). In yeast, septins were among the first proteins reported to be modified by SUMOylation, a ubiquitin-like posttranslational modification. However, whether human septins could be modified by small ubiquitin-like modifiers (SUMOs) and what roles this modification may have in septin function remains unknown. In this study, we first show that septins from all four human septin groups can be covalently modified by SUMOs. We show in particular that endogenous SEPT7 is constitutively SUMOylated during the cell cycle. We then map SUMOylation sites to the C-terminal domain of septins belonging to the SEPT6 and SEPT7 groups and to the N-terminal domain of septins from the SEPT3 group. We finally demonstrate that expression of non-SUMOylatable septin variants from the SEPT6 and SEPT7 groups leads to aberrant septin bundle formation and defects in cytokinesis after furrow ingression. Altogether, our results demonstrate a pivotal role for SUMOylation in septin filament bundling and cell division.
Xenotransplantation: past, present, and future

Purpose of review To review the progress in the field of xenotransplantation with special attention to most recent encouraging findings which will eventually bring xenotransplantation to the clinic in the near future. Recent findings Starting from early 2000, with the introduction of galactose-&agr;1,3-galactose (Gal)-knockout pigs, prolonged survival especially in heart and kidney xenotransplantation was recorded. However, remaining antibody barriers to non-Gal antigens continue to be the hurdle to overcome. The production of genetically engineered pigs was difficult requiring prolonged time. However, advances in gene editing, such as zinc finger nucleases, transcription activator-like effector nucleases, and most recently clustered regularly interspaced short palindromic repeats (CRISPR) technology made the production of genetically engineered pigs easier and available to more researchers. Today, the survival of pig-to-nonhuman primate heterotopic heart, kidney, and islet xenotransplantation reached more than 900, more than 400, and more than 600 days, respectively. The availability of multiple-gene pigs (five or six genetic modifications) and/or newer costimulation blockade agents significantly contributed to this success. Now, the field is getting ready for clinical trials with an international consensus. Summary Clinical trials in cellular or solid organ xenotransplantation are getting closer with convincing preclinical data from many centers. The next decade will show us new achievements and additional barriers in clinical xenotransplantation.