Miracle-dz/UniFAR-FTUs huggingface dataset:
Transient MutS-Based Hypermutation System for Adaptive Evolution of Lactobacillus casei to Low pH

ABSTRACT This study explored transient inactivation of the gene encoding the DNA mismatch repair enzyme MutS as a tool for adaptive evolution of Lactobacillus casei. MutS deletion derivatives of L. casei 12A and ATCC 334 were constructed and subjected to a 100-day adaptive evolution process to increase lactic acid resistance at low pH. Wild-type parental strains were also subjected to this treatment. At the end of the process, the ΔmutS lesion was repaired in representative L. casei 12A and ATCC 334 ΔmutS mutant isolates. Growth studies in broth at pH 4.0 (titrated with lactic acid) showed that all four adapted strains grew more rapidly, to higher cell densities, and produced significantly more lactic acid than untreated wild-type cells. However, the adapted ΔmutS derivative mutants showed the greatest increases in growth and lactic acid production. Further characterization of the L. casei 12A-adapted ΔmutS derivative revealed that it had a significantly smaller cell volume, a rougher cell surface, and significantly better survival at pH 2.5 than parental L. casei 12A. Genome sequence analysis confirmed that transient mutS inactivation decreased DNA replication fidelity in both L. casei strains, and it identified genetic changes that might contribute to the lactic acid-resistant phenotypes of adapted cells. Targeted inactivation of three genes that had acquired nonsense mutations in the adapted L. casei 12A ΔmutS mutant derivative showed that NADH dehydrogenase (ndh), phosphate transport ATP-binding protein PstB (pstB), and two-component signal transduction system (TCS) quorum-sensing histidine protein kinase (hpk) genes act in combination to increase lactic acid resistance in L. casei 12A. IMPORTANCE Adaptive evolution has been applied to microorganisms to increase industrially desirable phenotypes, including acid resistance. We developed a method to increase the adaptability of Lactobacillus casei 12A and ATCC 334 through transient inactivation of the DNA mismatch repair enzyme MutS. Here, we show this method was effective in increasing the resistance of L. casei to lactic acid at low pH. Additionally, we identified three genes that contribute to increased acid resistance in L. casei 12A. These results provide valuable insight on methods to enhance an organism's fitness to complex phenotypes through adaptive evolution and targeted gene inactivation.
A NOVEL NORMAL INCLUSION MODELING STRATEGY FOR VORTEX PINNING IN TWO-BAND, HIGH-TEMPERATURE SUPERCONDUCTORS

New high-temperature superconductors give great promise to a new generation of superconducting electronics, free of electrical resistance, which is made feasible by higher critical temperature values. Modeling and simulating a process known as vortex pinning is crucial in preserving the resistance free properties of these materials. Unfortunately, many of these materials are what is known as two-band superconductors making the conventional modeling strategy for vortex pinning unsuitable. In this paper, a novel strategy to model vortex pinning in two-band superconductors is presented and simulations of the material magnesium diboride are shown to validate this strategy.
Estimated Prevalence of the Target Population for Brain-Computer Interface Neurotechnology in the Netherlands

Background. People who suffer from paralysis have difficulties participating in society. Particularly burdensome is the locked-in syndrome (LIS). LIS patients are not able to move and speak but are cognitively healthy. They rely on assistive technology to interact with the world and may benefit from neurotechnological advances. Optimal research and design of such aids requires a well-defined target population. However, the LIS population is poorly characterized and the number of patients in this condition is unknown. Objective. Here we estimated and described the LIS patient population in the Netherlands to define the target population for assistive (neuro)technology. Methods. We asked physicians in the Netherlands if they had patients suffering from severe paralysis and communication problems in their files. Physicians responding affirmatively were asked to fill out a questionnaire on the patients’ status. Results. We sent out 9570 letters to general practitioners (GPs), who reported 83 patients. After first screening, the GPs of 46 patients received the questionnaire. Based on the responses, 26 patients were classified as having LIS. Extrapolation of these numbers resulted in a prevalence of 0.73 patients per 100 000 inhabitants. Notable results from the questionnaire were the percentage of patients with neuromuscular disease (>50%) and living at home (>70%). Conclusions. We revealed an etiologically diverse group of LIS patients. The functioning and needs of these patients were, however, similar and many relied on assistive technology. By characterizing the LIS population, our study may contribute to optimal development of assistive (neuro)technology.
Natural Language Description of Video Streams Using Task-Specific Feature Encoding

In recent years, deep learning approaches have gained great attention due to their superior performance and the availability of high speed computing resources. These approaches are also extended towards the real time processing of multimedia content exploiting its spatial and temporal structure. In this paper, we propose a deep learning-based video description framework which first extracts visual features from video frames using deep convolutional neural networks (CNN) and then pass the derived representations into a long-short term memory-based language model. In order to capture accurate information for human presence, a fine-tuned multi-task CNN is presented. The proposed pipeline is end-to-end, trainable, and capable of learning dense visual features along with an accurate framework for the generation of natural language descriptions of video streams. The evaluation is done by calculating Metric for Evaluation of Translation with Explicit ORdering and Recall-Oriented Understudy for Gisting Evaluation (ROUGE) scores between system generated and human annotated video descriptions for a carefully designed data set. The video descriptions generated by the traditional feature learning and proposed deep learning frameworks are also compared through the ROUGE scores.
Predictors of abnormal brain computed tomography findings in patients with acute altered mental status in the emergency department

Objective Brain computed tomography (CT) is commonly performed to diagnose acute altered mental status (AMS), a critically important symptom in many serious diseases. However, negative CT results are common, which result in unnecessary CT use. Therefore, this study aimed to determine the clinical factors associated with positive CT findings. Methods Patients with acute AMS selected from an emergency department-based registry were retrospectively evaluated. Patients with non-traumatic and noncommunicable diseases on initial presentation and with Glasgow Comal Scale scores of <15 were included in the study. Results Among the 367 brain CT results of patients with AMS during the study period, 146 (39.8%) were positive. In a multivariate analysis, the presence of focal neurologic deficit (odds ratio [OR], 132.6; 95% confidence interval [CI], 37.8 to 464.6), C-reactive protein level <2 mg/dL (OR, 3.9; 95% CI, 1.4 to 10.6), and Glasgow Comal Scale score <9 (OR, 2.4; 95% CI, 1.2 to 4.8) were significantly associated with positive brain CT results. Conclusion The presence of focal neurologic deficit, initial Glasgow Comal Scale score of <9, and initial C-reactive protein levels of <2 mg/dL can facilitate the selection of brain CT to diagnose patients with acute AMS in the emergency department.
PDCA: An eHealth service for the management of drug interactions with complementary and alternative medicines

The new era in medicine focuses on the development of tools and applications that empower citizens towards advanced health care practices and personalized approaches. Despite the vast achievements in pharmaceutical industry with innovative drugs of high specificity regarding their pharmacological mechanism of action, the use of complementary and alternative medicine (CAM) products worldwide, is on the rise. CAM products, which are usually of plant origin (herbal medicines), are generally advertised as natural and thus harmless with minimum side effects and frequently used by citizens as part of their self-medication lifestyle. However, several studies have shown that herbal medicines, as well as other CAM products, can potentially modulate biological mechanisms that are related with the pharmacological action of drugs and thus lead to what is called drug-herb interactions. In this respect, availability of relevant eHealth services and applications providing user-friendly information to patients regarding potential interactions of CAM products that they plan to use with their concurrent administered therapy, is of paramount importance. Such services could be used by both the healthcare providers (doctors, pharmacists, nurses etc.) for advanced and personalized approaches, and by the citizens themselves for minimization of self-medication errors. In this work we present an eHealth web application that utilizes drug-herb interaction databases and provides potential notifications of interactions in a simplified and secure way, facilitating the exchange of information between the user and healthcare provider.
A Phenotype Classification of Internet Use Disorder in a Large-Scale High-School Study

Internet Use Disorder (IUD) affects numerous adolescents worldwide, and (Internet) Gaming Disorder, a specific subtype of IUD, has recently been included in DSM-5 and ICD-11. Epidemiological studies have identified prevalence rates up to 5.7% among adolescents in Germany. However, little is known about the risk development during adolescence and its association to education. The aim of this study was to: (a) identify a clinically relevant latent profile in a large-scale high-school sample; (b) estimate prevalence rates of IUD for distinct age groups and (c) investigate associations to gender and education. N = 5387 adolescents out of 41 schools in Germany aged 11–21 were assessed using the Compulsive Internet Use Scale (CIUS). Latent profile analyses showed five profile groups with differences in CIUS response pattern, age and school type. IUD was found in 6.1% and high-risk Internet use in 13.9% of the total sample. Two peaks were found in prevalence rates indicating the highest risk of IUD in age groups 15–16 and 19–21. Prevalence did not differ significantly between boys and girls. High-level education schools showed the lowest (4.9%) and vocational secondary schools the highest prevalence rate (7.8%). The differences between school types could not be explained by academic level.
The Utility of the Memorable Messages Framework as an Intermediary Evaluation Tool for Fruit and Vegetable Consumption in a Nutrition Education Program

Additional strategies to evaluate the impact of community nutrition education programs on low-income individuals are needed. The objective of this qualitative study was to examine the use of the Memorable Messages Framework as an intermediary nutrition education program evaluation tool to determine what fruit and vegetable messages were reported as memorable and the characteristics of those memorable messages. A convenience sample of low-income, primarily African American adults (N = 58) who previously completed a series of community nutrition education lessons within an urban area of Indiana participated in a focus group (N = 8 focus groups). A lead moderator using a semistructured script conducted the focus groups to determine what information about fruits and vegetables was most memorable from the participants’ nutrition lessons and why this information was memorable. All focus group audiotapes were transcribed verbatim and ATLAS.ti software was used to code and identify themes within the data. Participants cited quantity, variety, and the positive nutritional impact of eating fruits and vegetables as most memorable. Information given in the form of recipes was also cited as most memorable. For example, participants referred to the recipe demonstrations as not only fun but also key components of the program that helped with message retention and memorability. Key characteristics of memorable messages included personal relevance and message vividness. These findings indicated that the Memorable Messages Framework may serve as an intermediary program evaluation tool to identify what information and messages are most influential to participants in community nutrition education programs.
A Robust Image Watermarking Technique Based on DWT, APDCBT, and SVD

Copyright protection for digital multimedia has become a research hotspot in recent years. As an efficient solution, the digital watermarking scheme has emerged at the right moment. In this article, a highly robust and hybrid watermarking method is proposed. The discrete wavelet transform (DWT) and all phase discrete cosine biorthogonal transform (APDCBT) presented in recent years as well as the singular value decomposition (SVD) are adopted in this method to insert and recover the watermark. To enhance the watermark imperceptibility, the direct current (DC) coefficients after block-based APDCBT in high frequency sub-bands (LH and HL) are modified by using the watermark. Compared with the conventional SVD-based watermarking method and another watermarking technique, the watermarked images obtained by the proposed method have higher image quality. In addition, the proposed method achieves high robustness in resisting various image processing attacks.
Magnetite–polypyrrole core–shell structured microspheres and their dual stimuli-response under electric and magnetic fields

Polypyrrole (PPy)–coated magnetite (Fe3O4) hybrid particles were synthesized under sonication. PPy was coated on the surface of Fe3O4 microspheres, whereas pyrrole monomers filled the interior of the Fe3O4 particles and were then polymerized. The structure of the Fe3O4–PPy microspheres was confirmed by transmission electron microscopy. The electric and magnetic properties were confirmed by optical microscopy and vibrating sample magnetometry, respectively. The suspension of the Fe3O4–PPy composite microspheres dispersed in silicone oil exhibited both electrorheological and magnetorheological properties when measured using a rotational rheometer under an applied electric and magnetic field, respectively.
Neuropeptides Modulate Female Chemosensory Processing upon Mating in Drosophila

A female’s reproductive state influences her perception of odors and tastes along with her changed behavioral state and physiological needs. The mechanism that modulates chemosensory processing, however, remains largely elusive. Using Drosophila, we have identified a behavioral, neuronal, and genetic mechanism that adapts the senses of smell and taste, the major modalities for food quality perception, to the physiological needs of a gravid female. Pungent smelling polyamines, such as putrescine and spermidine, are essential for cell proliferation, reproduction, and embryonic development in all animals. A polyamine-rich diet increases reproductive success in many species, including flies. Using a combination of behavioral analysis and in vivo physiology, we show that polyamine attraction is modulated in gravid females through a G-protein coupled receptor, the sex peptide receptor (SPR), and its neuropeptide ligands, MIPs (myoinhibitory peptides), which act directly in the polyamine-detecting olfactory and taste neurons. This modulation is triggered by an increase of SPR expression in chemosensory neurons, which is sufficient to convert virgin to mated female olfactory choice behavior. Together, our data show that neuropeptide-mediated modulation of peripheral chemosensory neurons increases a gravid female’s preference for important nutrients, thereby ensuring optimal conditions for her growing progeny.
Laboratory Diagnosis of Mycobacterium tuberculosis Infection and Disease in Children

ABSTRACT Diagnosis of tuberculosis in children is challenging; even with advanced technologies, the diagnosis is often difficult to confirm microbiologically in part due to the paucibacillary nature of the disease. Clinical diagnosis lacks standardization, and traditional and molecular microbiologic methods lack sensitivity, particularly in children. Immunodiagnostic tests may improve sensitivity, but these tests cannot distinguish tuberculosis disease from latent infection and some lack specificity. While molecular tools like Xpert MTB/RIF have advanced our ability to detect Mycobacterium tuberculosis and to determine antimicrobial resistance, decades old technologies remain the standard in most locales. Today, the battle against this ancient disease still poses one of the primary diagnostic challenges in pediatric laboratory medicine.
Two-photon oxygen nanosensors based on a conjugated fluorescent polymer doped with platinum porphyrins

Ratiometric fluorescent nanoparticles (NPs) under two-photon excitation are successfully developed for sensing dissolved oxygen. The NPs comprise the oxygen probe Pt(II)-porphyrins (PtTFPP) and fluorescent organic semiconducting polymer (PFO). PFO polymer acts as both a two-photon antenna and a reference dye, while PtTFPP absorbs the photonic energy transferred by the PFO under two-photon excitation at 740 nm to sense oxygen. The red fluorescence of PtTFPP is sensitive to oxygen with a quenching response of 88% from nitrogen saturation to oxygen saturation, and PFO gives oxygen-insensitive referenced blue fluorescence. The fluorescence quenching of the NPs against oxygen at two-photon excitation follows a linear Stern–Volmer behavior. The nanosensors exhibit low cytotoxic effects as well as effortless cellular uptake. When incorporated into cells, the ratio of the signals increases up to about 500% from oxygen-saturated to oxygen-free environment.
Angiotensin-Converting Enzyme 2 Inhibits Angiotensin II-Induced Abdominal Aortic Aneurysms in Mice.

Recent studies have demonstrated that angiotensin-converting enzyme 2 (ACE2) plays an important role in the pathogenesis of abdominal aortic aneurysms (AAAs). However, few studies have reported the direct effect of ACE2 overexpression on the aneurysm. This study hypothesized that the overexpression of ACE2 may prevent the pathogenesis of aneurysms by decreasing RAS activation. Thirty-nine mice were randomly assigned to three groups (n = 13 in each group): the Ad.ACE2 group, the Ad.EGFP group, and a control group. After 8 weeks of treatment, abdominal aortas with AAAs were obtained for hematoxylin and eosin staining, Verhoeff Van Gieson staining, immunohistochemistry, and Western blotting. The incidence and severity of AAAs, macrophage infiltration, and MMP protein expression were all recorded. The results showed that ACE2 gene transfer significantly decreased the occurrence of AAAs and inhibited AAA formation in ApoE-/- mice by inhibiting the inflammatory response and MMP activation, and the mechanisms may involve decreased ERK and Ang II-nuclear factor kappa B signaling pathways.
Are Proteins Dynamically Heterogeneous? Neutron Scattering Analysis of Hydrogen Displacement Distributions

Dynamic neutron scattering is a technique to record time resolved the molecular displacements of hydrogen atoms in biomolecules. With spectrometers, measuring the energy exchange, ħω, and momentum exchange, ħQ, of neutrons with the hydrogen atoms of the sample, one determines the scattering function S (Q, ω). The central physical quantity of interest, which can be derived from the scattering function by a double Fourier transform, is the displacement distribution Gs(r, t) . In this article we explain by three theoretical methods, how to determine the displacement distribution of hydrogen atoms in proteins from experimental data: (1) a moment expansion, (2) a numerical transform of the scattering function and (3) an analytical model of two principal dynamic components. The expansion yields a temperature dependent second moment of the displacement distribution and a Gauss-deviation, suggesting asymmetric motions. The numerical transform reveals a temperature dependent bimodal distribution function of small scale diffusive displacements and of rotational jumps on a larger scale. The principal components of the analytical model are thus rotational transitions of side chains and local diffusion of residues in a quasi-harmonic potential. The local diffusion is modelled by an over-damped Brownian oscillator derived from the Smoluchowski equation. The rotational transitions are treated by a three equivalent site model of the methyl group. Comparison of the model predictions with experimental data in the time domain show a remarkable agreement within a wide range of time scales, momentum exchange and temperature. The microscopic dynamics are compared with functional kinetic studies of ligand binding to myoglobin on a longer time scale. Dynamical heterogeneity is reduced to a bimodal distribution of molecular processes. Multiple scattering calculations provide an alternative explanation to heterogeneous quasi-elastic neutron scattering spectra and energy landscapes.
Effect of a participatory organizational-level occupational health intervention on short-term sickness absence: a cluster randomized controlled trial.

OBJECTIVES The aim of this study was to examine whether employees in pre-schools that implemented a participatory organizational-level intervention focusing on the core task at work had a lower incidence of short-term sickness absence compared to employees in the control group. METHODS The cluster randomized controlled trial (RCT) comprised 78 pre-schools that were allocated to the intervention (44 pre-schools with 1760 employees) or control (34 pre-schools with 1279 employees) group. The intervention lasted 25 months and followed a stepwise and structured approach, consisting of seminars, workshops, and workplace-directed intervention activities focusing on the core task at work. Using Poisson regression, we tested differences in incidence rates in short-term sickness absence between the intervention and control groups during a 29-months follow-up. RESULTS Estimated short-term sickness absence days per person-year during follow-up were 8.68 and 9.17 in the intervention and control groups, respectively. The rate ratio (RR) for comparing incident sickness absence in the intervention to control groups during follow-up was 0.93 [95% confidence interval (95% CI) 0.86-1.00] in the crude analysis and 0.89 (95% CI 0.83-0.96) when adjusting for age, sex, job group, type and size of workplace, and workplace average level of previous short-term sickness absence. A supplementary analysis showed that the intervention also was associated with a reduced risk of long-term sickness absence with a crude RR of 0.83 (95% CI 0.69-0.99) and an adjusted RR of 0.84 (95% CI 0.69-1.01). CONCLUSIONS Pre-school employees participating in an organizational-level occupational health intervention focusing on the core task at work had a lower incidence of short-term sickness absence during a 29-month follow-up compared with control group employees.