Miracle-dz/UniFAR-FTUs huggingface dataset:
Demography of Tuta absoluta (Meyrick) (Lepidoptera: Gelechiidae) reared on elicitor-treated tomato plants with an innovative comparison of projected population sizes and application of the multinomial theorem for population survival.

BACKGROUND Due to the considerable damage of tomato leafminer in tomato crop, the use of integrated methods is essentially recommended. In this study, the effect of three different elicitors, i.e., methyl jasmonate (MJ), salicylic acid (SA) and ascorbic acid (AA) on the life table parameters of Tuta absoluta were evaluated. The paired bootstrap test and the different bootstrap percentiles were used to compare the projected population sizes on specific date. The survival probabilities were calculated by innovatively linking of life table and multinomial theorem. RESULTS The preadult duration and mortality significantly increased, and the net reproductive rate (R0 ), intrinsic rate of increase (r), and finite rate of increase (λ) significantly decreased in all elicitor treatments. The lowest fecundity (F = 71.89 eggs/female) was observed in SA treatment, with R0 of 13.48 offspring/individual, r of 0.0932 d-1 , and λ of 1.0977 d-1 . The population projection revealed the stage structure of T. absoluta during population growth and the elicitor treatments significantly reduced the population growth of T. absoluta. The survival probability of bootstrap samples significantly lowered; whereas, the extinction probabilities increased in elicitor treatments than control when the survival criterion is set to two fertile pairs. CONCLUSION Our results demonstrated that the application of elicitors could reduce the risks of the T. absoluta damage. Furthermore, population projection based on life tables is applicable to obtain the frequency distribution of population size at different times. The joined application of life table and multinomial theorem can be used to calculate the risk of pest emergence. This article is protected by copyright. All rights reserved.
Muscle-specific ER-associated degradation maintains postnatal muscle hypertrophy and systemic energy metabolism

The growth of skeletal muscle relies on a delicate equilibrium between protein synthesis and degradation; however, how proteostasis is managed in the endoplasmic reticulum (ER) is largely unknown. Here, we report that the SEL1L-HRD1 ER-associated degradation (ERAD) complex, the primary molecular machinery that degrades misfolded proteins in the ER, is vital to maintain postnatal muscle growth and systemic energy balance. Myocyte-specific SEL1L deletion blunts the hypertrophic phase of muscle growth, resulting in a net zero gain of muscle mass during this developmental period and a 30% reduction in overall body growth. In addition, myocyte-specific SEL1L deletion triggered a systemic reprogramming of metabolism characterized by improved glucose sensitivity, enhanced beigeing of adipocytes, and resistance to diet-induced obesity. These effects were partially mediated by the upregulation of the myokine FGF21. These findings highlight the pivotal role of SEL1L-HRD1 ERAD activity in skeletal myocytes for postnatal muscle growth, and its physiological integration in maintaining whole-body energy balance.
The Experimentalist’s Guide to Machine Learning for Small Molecule Design

Initially part of the field of artificial intelligence, machine learning (ML) has become a booming research area since branching out into its own field in the 1990s. After three decades of refinement, ML algorithms have accelerated scientific developments across a variety of research topics. The field of small molecule design is no exception, and an increasing number of researchers are applying ML techniques in their pursuit of discovering, generating, and optimizing small molecule compounds. The goal of this review is to provide simple, yet descriptive, explanations of some of the most commonly utilized ML algorithms in the field of small molecule design along with those that are highly applicable to an experimentally focused audience. The algorithms discussed here span across three ML paradigms: supervised learning, unsupervised learning, and ensemble methods. Examples from the published literature will be provided for each algorithm. Some common pitfalls of applying ML to biological and chemical data sets will also be explained, alongside a brief summary of a few more advanced paradigms, including reinforcement learning and semi-supervised learning.
Genomic investigation of multi-species and multi-variant blaNDM outbreak reveals key role of horizontal IncN and IncX3 plasmid transfer

Objectives: New Delhi metallo-beta-lactamases (NDMs) are major contributors to the spread of carbapenem resistance globally. In Australia, NDMs were previously associated with international travel but from 2019 we noted increasing NDM episodes. We conducted an investigation to determine the clinical and genomic epidemiology of NDM-carriage at a tertiary Australian hospital from 2016-2021. Methods: We identified 49 patients with 84 NDM-carrying isolates in an institutional database and collected clinical data from electronic medical records. Short- and long-read whole genome sequencing was performed on all isolates. Completed genome assemblies were used to assess the genetic setting of blaNDM genes and compare NDM plasmids. Results: Of 49 patients, 38 (78%) were identified in 2019-2021 and only 11/38 (29%) reported prior travel compared with 9/11 (82%) in 2016-2018 (P=0.037). In patients with NDM infection, crude 7-day mortality was 0% and 30-day mortality was 14% (2/14 patients). NDMs were noted in 41 bacterial strains (i.e. species/sequence type combinations). Four NDM variants (blaNDM-1, blaNDM-4, blaNDM-5, blaNDM-7) were detected across 13 plasmid groups. We noted a change from a diverse NDM plasmid repertoire in 2016-2018 to the emergence of conserved blaNDM-1 IncN and blaNDM-7 IncX3 epidemic plasmids with inter-strain spread in 2019-2021. These plasmids were noted in 19/38 (50%) patients and 35/68 (51%) genomes in 2019-2021. Conclusions: Increased NDM case numbers were due to local circulation of two epidemic plasmids with extensive inter-strain transfer. Our study underscores the challenges of outbreak detection when horizontal transmission of plasmids is the primary mode of spread.
Association of Childhood and Midlife Neighborhood Socioeconomic Position With Cognitive Decline

Key Points Question Is neighborhood socioeconomic position (nSEP) associated with cognitive decline? Findings In this longitudinal cohort study of 5711 men and women, the rate of cognitive decline from midlife to older adulthood decreased by 9.2% with each 1-SD increase in childhood nSEP. No associations of midlife nSEP with cognitive decline were observed. Meaning This study suggests that early childhood experiences are associated with cognitive trajectories in adulthood.
A SEMANTIC ACCESS CONTROL MODEL FOR ONLINE SOCIAL NETWORKS

Online Social Networks (OSNs) are very popular and users share various information in these networks. To protect these resources from unauthorized accesses, these frameworks must support flexible access control mechanisms. Semantic technology provides new opportunities for this purpose. This paper proposes a Prioritized Ontology. Based Access Control (POBAC) model for protecting users' information in OSNs.
Inhibition by components of Glycyrrhiza uralensis of 3CLpro and HCoV-OC43 proliferation

Abstract Coronavirus disease 2019 (COVID-19) is an infectious disease caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). 3CLpro is a key enzyme in coronavirus proliferation and a treatment target for COVID-19. In vitro and in silico, compounds 1–3 from Glycyrrhiza uralensis had inhibitory activity and binding affinity for 3CLpro. These compounds decreased HCoV-OC43 cytotoxicity in RD cells. Moreover, they inhibited viral growth by reducing the amounts of the necessary proteins (M, N, and RDRP). Therefore, compounds 1–3 are inhibitors of 3CLpro and HCoV-OC43 proliferation.
Development of Lamotrigine Solid Dispersion for the Formulation and Evaluation of Fast Dissolving Tablets

Lamotrigine is an anticonvulsant drug used in the treatment of epilepsy and bipolar disorders. Its acts primarily by obstructing voltage dependent sodium channel hence a decreased level of excitatory neurotransmitter. Solid dispersion is a newer technique of enhancing the solubility of poorly soluble drugs using suitable polymer. Moreover, for obtaining better drug absorption, faster onset of action and safety regarding its administration fast dissolving tablets are becoming standards. These upon administration into mouth gets rapidly dissolve due to presence of saliva without any need of water. Lamotrigine solid dispersion was prepared using PEG 6000 as polymer in the ratio (1: 1). Fast dissolving tablet of lamotrigine was formulated using 3 different superdisintegrants (crosscarmellose, kollidon, sodium starch glycolate (SSG)) in different ratios. The formulated tablets were then evaluated for its different parameters. The result of invitro dissolution study showed that formulation F5 is most successful as it dissolved in a very short period containing combination of kollidon and SSG in the ratio (1: 3). An increased disintegration time was noted with combination of crosscarmellose and SSG (1: 1) ratio.
Development of canagliflozin nanocrystals sublingual tablets in the presence of sodium caprate permeability enhancer: formulation optimization, characterization, in-vitro, in silico, and in-vivo study

Abstract Canagliflozin (CFZ) is a sodium-glucose cotransporter-2 inhibitor (SGLT2) that lowers albuminuria in type-2 diabetic patients, cardiovascular, kidney, and liver disease. CFZ is classified as class IV in the Biopharmaceutical Classification System (BCS) and is characterized by low permeability, solubility, and bioavailability, most likely attributed to hepatic first-pass metabolism. Nanocrystal-based sublingual formulations were developed in the presence of sodium caprate, as a wetting agent, and as a permeability enhancer. This formulation is suitable for children and adults and could enhance solubility, permeability, and avoid enterohepatic circulation due to absorption through the sublingual mucosa. In the present study, formulations containing various surfactants (P237, P338, PVA, and PVP K30) were prepared by the Sono-homo-assisted precipitation ion technique. The optimized formula prepared with PVP-K30 showed the smallest particle size (157 ± 0.32 nm), Zeta-potential (−18 ± 0.01), and morphology by TEM analysis. The optimized formula was subsequently formulated into a sublingual tablet containing Pharma burst-V® with a shorter disintegration time (51s) for the in-vivo study. The selected sublingual tablet improved histological and biochemical markers (blood glucose, liver, and kidney function), AMP-activated protein kinase (AMPK), and protein kinase B (AKT) pathway compared to the market formula, increased CFZ’s antidiabetic potency in diabetic rabbits, boosted bioavailability by five-fold, and produced faster onset of action. These findings suggest successful treatment of diabetes with CFZ nanocrystal-sublingual tablets.
Pyrame 3, an online framework for Calice SiW-Ecal

Pyrame 3 is the new version of the Pyrame framework [1], with emphasize on the online data treatment and the complex tasks scripting. A new mechanism has been implemented to allow any module to treat and publish data in real time. Those data are made available to any requesting module. A circular buffer mechanism allows to break the real-time constraint and to serve the slower programs in a generic subsampling way. On the other side, a programming facility called event-loop has been provided in C/C++ language to ease the development of monitoring programs. On the SiW-Ecal prototype, the acquisition chain launches a bunch of online decoders that makes available raw data plus some basic reconstruction data (true coordinate, true time, data quality tags\ldots). With the event-loop, it is now really very easy to implement new online monitoring programs. On the other side, the scripting mechanism has been enhanced to provide complete control of the detector to the scripts. This way, we are able to script and monitor complex behaviours like position or energy scanning, calibrations or data driven reconfigurations.
TSLP Induces Epithelial–Mesenchymal Transition in Nasal Epithelial Cells From Allergic Rhinitis Patients Through TGF-β1/Smad2/3 Signaling

Background Airway remodeling is demonstrated in Asian patients with allergic rhinitis (AR). The epithelial–mesenchymal transition (EMT) is one of the key mechanisms underlying airway remodeling. Thymic stromal lymphopoietin (TSLP) is an important contributor to airway remodeling. Although increased TSLP is found in AR, little is known about whether TSLP is involved in airway remodeling through induction of the EMT. Objective We investigated the effect of TSLP on the EMT in human nasal epithelial cells (HNECs) from AR patients. Methods Human nasal epithelial cells from AR patients were stimulated with TSLP in the absence or presence of the preincubation with a selective inhibitor of transforming growth factor beta 1 (TGF-β1) receptor (SB431542). The expression of TGF-β1 in the cells was evaluated by using real-time polymerase chain reaction, Western blotting, and immunocytochemistry. Western blotting and immunocytochemistry were used to assay EMT markers including vimentin, fibroblast-specific protein 1 (FSP1) and E-cadherin, small mothers against decapentaplegic homolog2/3 (Smad2/3), and phosphorylated Smad2/3 in the cells. The levels of extracellular matrix components such as collagens I and III in supernatants were measured by enzyme-linked immunoassay. Morphological changes of the cells were observed under inverted phase-contrast microscope. Results A concentration-dependent increase of TGF-β1 mRNA and protein was observed following stimulation with TSLP. Furthermore, TSLP decreased the expression of E-cadherin protein, but upregulated the production of FSP1 and vimentin proteins along with increased levels of collagens I and III, and the morphology of the cells was transformed into fibroblast-like shape. Additionally, a significant increase was found in phosphorylation of Smad2/3 protein. However, these effects were reversed by SB431542 preincubation. Conclusion TSLP–induced HNECs to undergo the EMT process via TGF-β1-mediated Smad2/3 activation. TSLP is an activator of the EMT in HNECs and might be a potential target for inhibiting EMT and reducing airway remodeling in AR.
Computing Loops with at Most One External Support Rule for Basic Logic Programs with Arbitrary Constraint Atoms

The well-founded semantics of logic programs is not only an important semantics but also serves as an essential tool for program simplification in answer set computations. Recently, it has been shown that for normal and disjunctive programs, the well-founded models can be computed by unit propagation on program completion and loop formulas of loops with no external support. An attractive feature of this approach is that when loop formulas of loops with exactly one external support are added, consequences beyond the well-founded model can be computed, which sometimes can significantly speed up answer set computation. In this paper, we extend this approach to basic logic programs with abstract constraint atoms. We define program completion and loop formulas and show how to capture the well-founded semantics that approximate answer sets of basic logic programs. We show that by adding the loop formulas of loops with one external support, consequences beyond well-founded models can be computed. Our experiments show that for certain logic programs with constraints accepted by lparse, the consequences computed by our algorithms can speed up current ASP solvers smodels and clasp.
Bias Assessment and Reduction in Kernel Smoothing

When performing local polynomial regression (LPR) with kernel smoothing, the choice of the smoothing parameter, or bandwidth, is critical. The performance of the method is often evaluated using the Mean Square Error (MSE). Bias and variance are two components of MSE. Kernel methods are known to exhibit varying degrees of bias. Boundary effects and data sparsity issues are two potential problems to watch for. There is a need for a tool to visually assess the potential bias when applying kernel smooths to a given scatterplot of data. In this dissertation, we propose pointwise confidence intervals for bias and demonstrate a software tool to implement the confidence bands in practice. The effectiveness of the proposed bias assessment tool is demonstrated using simulated data and is illustrated by its application to classical data sets. To reduce the bias of LPR while keeping other good properties of it, as well as to mitigate the sparsity and boundary issues, this thesis extends the technique of double-smoothing from the local linear regression context to higher order local polynomial regression, with particular focus on local quadratic and local cubic regression. Double-smoothing is a technique that involves two levels of smoothing and is known to reduce bias in nonparametric regression while maintaining control over variance. What was not known is that the method is often sub-optimal when the bandwidths at both levels of smoothing are equal. In this thesis, we propose a simple method for obtaining the second-level smoothing bandwidth while using a cross-validation method for the first level. The proposed tools in this dissertation are employed to address real problems related to wildfire management: one is for modelling the time to initial attack using fire case records for the years from 1930 to 2012 in a Northeastern Ontario area. Another one is for the experimental results of burning debris as a randomized component in a firebrand spotting simulator.
SPECIES IN THE FECES: DNA METABARCODING TO DETECT POTENTIAL GASTROPOD HOSTS OF PARELAPHOSTRONGYLUS TENUIS CONSUMED BY MOOSE (ALCES ALCES)

Abstract: Our understanding of wildlife multihost pathogen transmission systems is often incomplete due to the difficulty of observing contact between hosts. Understanding these interactions can be critical for preventing disease-induced wildlife declines. The proliferation of high-throughput sequencing technologies provides new opportunities to better explore these cryptic interactions. Parelaphostrongylus tenuis, a multihost parasite, is a leading cause of death in some moose (Alces alces) populations threatened by local extinction in the midwestern and northeastern US and southeastern Canada. Moose contract P. tenuis by consuming infected gastropod intermediate hosts, but little is known about which gastropod species moose consume. To gain more insight, we used a genetic metabarcoding approach on 258 georeferenced and temporally stratified moose fecal samples collected May–October 2017–20 from a declining population in the north-central US. We detected moose consumption of three species of gastropods across five positive samples. Two of these (Punctum minutissimum and Helisoma sp.) have been minimally investigated for the ability to host P. tenuis, while one (Zonitoides arboreus) is a well-documented host. Moose consumption of gastropods documented herein occurred in June and September. Our findings prove that moose consume gastropod species known to become infected by P. tenuis and demonstrate that fecal metabarcoding can provide novel insight on interactions between hosts of a multispecies pathogen transmission system. After determining and improving test sensitivity, these methods may also be extended to document important interactions in other multihost disease systems.
Skeletal Muscle Adaptations to High-Load Resistance Training With Pre-Exercise Blood Flow Restriction

Abstract Hammert, WB, Moreno, EN, Martin, CC, Jessee, MB, and Buckner, SL. Skeletal muscle adaptations to high-load resistance training with pre-exercise blood flow restriction. J Strength Cond Res 37(12): 2381–2388, 2023—This study aimed to determine if blood flow restriction (BFR) could augment adaptations to a high-load training protocol that was inadequate for muscle growth. Forty nontrained individuals had each arm assigned to 1 of 3 elbow flexion protocols: (a) high-load resistance training [TRAD; 4 sets to muscular failure at 70% 1 repetition maximum (1RM)], (b) low repetition high-load resistance training with pre-exercise BFR (PreBFR; 4 sets of 3 repetitions at 70% 1RM + 3 min of pre-exercise BFR), and (c) low repetition high-load resistance training (LRTRAD); 4 sets of 3 repetitions at 70% 1RM). Muscle thickness (MT), 1RM strength, and local muscular endurance (LME) of the elbow flexors were measured before and after 8 weeks. An alpha level of 0.05 was used for all comparisons. For the 50% site, MT increased for TRAD (0.211 cm, 95% confidence interval [95% CI]: 0.143–0.280), PreBFR (0.105 cm, 95% CI: 0.034–0.175), and LRTRAD (0.073 cm, 95% CI: 0.000–0.146). The change for TRAD was greater than PreBFR and LRTRAD. For the 60% site, MT increased for TRAD (0.235 cm, 95% CI: 0.153–0.317), PreBFR (0.097 cm, 95% CI: 0.014–0.180), and LRTRAD (0.082 cm, 95% CI: 0.000–0.164). The change for TRAD was greater than PreBFR and LRTRAD. For the 70% site MT increased for TRAD (0.308 cm, 95% CI: 0.247–0.369), PreBFR (0.103 cm, 95% CI: 0.041–0.166), and LRTRAD (0.070 cm, 95% CI: 0.004–0.137). The change for TRAD was greater than PreBFR and LRTRAD. One repetition maximum and LME significantly increased for each condition, with no differences between conditions. Collapsed across conditions 1RM strength increased 2.094 kg (95% CI: 1.771–2.416) and LME increased 7.0 repetitions (95% CI: 5.7–8.3). In conclusion, the application of BFR to low-repetition, high-load training did not enhance the adaptative response.
Visual inspection with acetic acid as a feasible screening test for cervical neoplasia in Iran

The aim of this study was to estimate the sensitivity and specificity of visual inspection of the uterine cervix with acetic acid (VIA) as a screening test for cervical carcinoma and its precursors. One thousand and two hundred eligible women were screened by VIA and Papanicolaou smear. Those positive on one or both of these screening tests (n = 308) or those who had clinically suspicious lesions, even if the tests were negative [25% of remainders (n = 290)], were referred for colposcopy. Three hundred and fifty five of 598 women at colposcopy underwent biopsies or endocervical curettage. Those with cervical intraepithelial neoplasia I (CIN I) or worse lesions, diagnosed by histology, were considered true positive. VIA was positive in 191 women (16.1%). In 175 true-positive cases, VIA detected 130 cases, yielding a sensitivity of 74.3% and a specificity of 94%. By considering atypical squamous cell of undetermined significance or worse lesions on Papanicolaou smear as referring threshold for colposcopy, the sensitivity and specificity of cytology were 72 and 90.2%, respectively. In conclusion, the sensitivity and specificity of VIA is high and comparable with that of cytology. Hence, VIA can be undertaken as a feasible method of screening in cervical cancer in countries where access to cytopathology is limited.