Miracle-dz/UniFAR-FTUs huggingface dataset:
Discovery of Novel Resistance Mechanisms of Vibrio parahaemolyticus Biofilm against Aminoglycoside Antibiotics

Inappropriate use of antibiotics eventually leads to the emergence of antibiotic-resistant strains and invalidates the treatment of infectious diseases. Aminoglycoside antibiotics (AGAs) are a class of broad-spectrum cationic antibiotics widely used for the treatment of Gram-negative bacterial infections. Understanding the AGA resistance mechanism of bacteria would increase the efficacy of treating these infections. This study demonstrates a significant correlation between AGA resistance and the adaptation of biofilms by Vibrio parahaemolyticus (VP). These adaptations were the result of challenges against the aminoglycosides (amikacin and gentamicin). Confocal laser scanning microscope (CLSM) analysis revealed an enclosure type mechanism where the biological volume (BV) and average thickness (AT) of V. parahaemolyticus biofilm were significantly positively correlated with amikacin resistance (BIC) (p < 0.01). A neutralization type mechanism was mediated by anionic extracellular polymeric substances (EPSs). The biofilm minimum inhibitory concentrations of amikacin and gentamicin were reduced from 32 µg/mL to 16 µg/mL and from 16 µg/mL to 4 µg/mL, respectively, after anionic EPS treatment with DNase I and proteinase K. Here, anionic EPSs bind cationic AGAs to develop antibiotic resistance. Transcriptomic sequencing revealed a regulatory type mechanism, where antibiotic resistance associated genes were significantly upregulated in biofilm producing V. parahaemolyticus when compared with planktonic cells. The three mechanistic strategies of developing resistance demonstrate that selective and judicious use of new antibiotics are needed to win the battle against infectious disease.
Multi-band Monopole Antennas Loaded with Metamaterial TL

Abstract A novel metamaterial transmission line (TL) by loading complementary single Archimedean spiral resonator pair (CSASRP) is investigated and used to design a set of multi-frequency monopole antennas. The particularity is that the CSASRP which features dual-shunt branches in the equivalent circuit model is directly etched in the signal strip. By smartly controlling the element parameters, three antennas are designed and one of them covering UMTS and Bluetooth bands is fabricated and measured. The antenna exhibits impedance matching better than –10 dB and normal monopolar radiation patterns at working bands of 1.9–2.22 and 2.38–2.5 GHz. Moreover, the loaded element also contributes to the radiation, which is the major advantage of this prescription over previous lumped-element loadings. The proposed antenna is also more compact over previous designs.
Engaging health sciences librarians on data ethics: case study on a pilot curriculum

Background: Ethical decision-making regarding data collection, visualization and communication is of growing importance to librarians. Data ethics training opportunities for librarians, however, are uncommon. To fill this gap, librarians at an academic medical center developed a pilot data ethics curriculum for librarians across the US and Canada. Case Presentation: Three data librarians in a health sciences library developed a pilot curriculum to address perceived gaps in librarian training for data ethics. One of the team members had additional academic training in bioethics, which helped to provide an intellectual foundation for this project. The three-module class provided students with an overview of ethical frameworks, skills to apply those frameworks to data issues, and an exploration of data ethics challenges in libraries. Participants from library schools and professional organizations were invited to apply. Twenty-four participants attended the Zoom-based classes and shared feedback through surveys taken after each session and in a focus group after the course's conclusion. Discussion: Responses to the focus group and surveys indicated a high level of student engagement and interest in data ethics. Students also expressed a desire for more time and ways to apply what was learned to their own work. Specifically, participants indicated an interest in dedicating time for networking with other members of their cohort, as well as more extensive discussion of class topics. Several students also suggested creating concrete outputs of their thoughts (e.g., a reflective paper or final project). Finally, student responses expressed a strong interest in mapping ethical frameworks directly to challenges and issues librarians face in the workplace.
Consumption of Solnul™ Resistant Potato Starch Produces a Prebiotic Effect in a Randomized, Placebo-Controlled Clinical Trial

The effects of resistant starch at high doses have been well-characterized, but the potential prebiotic effects of resistant starch at doses comparable to oligosaccharide prebiotics have not been evaluated. A three-arm randomized, double-blind, placebo-controlled clinical trial was conducted to evaluate the effect of 3.5 g and 7 g daily doses of Solnul™ resistant potato starch (RPS) on beneficial populations of gut bacteria and stool consistency after a 4-week period. The relative abundance of Bifidobacterium and Akkermansia was determined by employing 16Sv4 sequencing of stool samples. To assess the effect of RPS on laxation and bowel movements, stools were recorded and scored using the Bristol Stool Form Scale. Participants consuming 3.5 g/day of RPS experienced significantly greater changes in Bifidobacterium and Akkermansia compared to the placebo after 4 weeks. The number of diarrhea- and constipation-associated bowel movements were both significantly lower in the 3.5 g RPS arm compared to the placebo group. Participants consuming 7 g of RPS responded similarly to those in the 3.5 g arm. Our analyses demonstrate that Solnul™ RPS has a prebiotic effect when consumed for 4 weeks at the 3.5 g per day dose, stimulating increases in beneficial health-associated bacteria and reducing diarrhea- and constipation-associated bowel movements when compared to the placebo group.
The prognostic role and metabolic function of GGPS1 in oral squamous cell carcinoma

Background: GGPS1(geranylgeranyl diphosphate synthase 1) is a member of the prenyltransferase family. Abnormal expression of GGPS1 can disrupt the balance between protein farnesylation and geranylgeranylation, thereby affecting a variety of cellular physiologic and pathological processes. However, it is still unknown how this gene could contribute to the prognosis of oral squamous cell carcinoma (OSCC). This study aimed to explore the prognostic role of GGPS1 in OSCC and its relationship with clinical features. Methods: The RNA-seq data and clinical data were obtained from TCGA. The survival analyses, Cox regression analyses, ROC curves, nomograms, calibration curves, and gene function enrichments were established by R software. Results: The results showed that the high expression of GGPS1 in OSCC is related to poor prognosis. At the same time, multivariate Cox regression analyses showed that GGPS1 could be an independent prognostic biomarker, and its gene expression level is closely related to the histological stage of cancer. GGPS1 may promote tumorigenesis because of its metabolic function. Conclusion: This study came to a conclusion that GGPS1, whose high expression has a significantly unfavorable meaning toward the prognosis of OSCC, can act as a novel independent biomarker for OSCC.
A Lightweight Authentication and Key Exchange Protocol With Anonymity for IoT

The number of IoT devices is growing rapidly, and the interaction between devices and servers is also more frequent. However, IoT devices are often at the edge of the network, which leads their communications with the server to be completely exposed, making it more vulnerable to attacks. Moreover, IoT devices have limited energy and computational resources. Therefore, we propose in this paper a lightweight authentication and key exchange protocol with anonymity for IoT devices. The proposed scheme supports mutual authentication between IoT devices and the server. We verify the security of the protocol through formal and informal analyses. Finally, we compare security and performance with other protocols, which shows that our protocol has the advantages of being lightweight and secure.
Development and Characterization of Bio-Composites from the Plant Wastes of Water Hyacinth and Sugarcane Bagasse: Effect of Water Repellent and Gamma Radiation

Plant waste is a huge source of natural fibers and has great potential in the field of reinforced polymer composites to replace the environmentally harmful synthetic composites. In this study, fibers were extracted from water hyacinth (WH) petiole and sugarcane bagasse (SB) to make nonwovens by wet-laid web formation, and reinforced on the polyester (P) and epoxy (E) resins to make four types of composites namely, water hyacinth nonwoven reinforced epoxy (WH + E), water hyacinth nonwoven reinforced polyester (WH + P), sugarcane bagasse nonwoven reinforced epoxy (SB + E) and sugarcane bagasse nonwoven reinforced polyester (SB + P) composites. Water repellent (WR) on the nonwovens and gamma radiation (GR) on the composites were applied to improve the hydrophobicity and mechanical properties, such as tensile strength (TS), elongation at break and tensile modulus (TM) of the composites. The morphological structure of the fiber surfaces and tensile fractures were analyzed by SEM. FTIR spectra showed changes in functional groups before and after treatment. XRD analysis exhibited an increase in crystallinity for gamma-irradiated composites and a decrease in crystallinity for WR-treated composites compared to untreated composites. The SB composites (SB + E, SB + P) and polyester composites (WH + P, SB + P) showed higher water absorbency and lower mechanical properties than the WH composites (WH + E, WH + P) and epoxy composites (WH + E, SB + E), respectively. Hydrophobicity improved significantly by approximately 57% (average) at a concentration of 10% WR. However, TS and TM were reduced by approximately 24% at the same concentration. Thus, 5% WR is considered an optimum concentration due to the very low deterioration of TS and TM (<10%) but significant improvement in hydrophobicity (~39%) at this dose. On the other hand, GR treatment significantly improved TS, TM and hydrophobicity by 41, 32 and 25%, respectively, and decreased Eb% by 11% at a dose of 200 krd. However, mechanical properties and hydrophobicity deteriorated with further increase in dose at 300 krd. Thus, 200 krd is considered the optimum dose of GR.
Frequency response of cantilever beams immersed in viscous fluids with applications to the atomic force microscope: Arbitrary mode order

The frequency response of a cantilever beam is well known to depend strongly on the fluid in which it is immersed. In this article, we present a theoretical model for the frequency response of a rectangular cantilever beam immersed in a viscous fluid that enables the flexural and torsional modes of arbitrary order to be calculated. This extends the previous models of Sader and Green [J. Appl. Phys. 84, 64 (1998); 92, 6262 (2002)], which were formulated primarily for the fundamental mode and the next few harmonics, to the general case of arbitrary mode order by accounting for the three-dimensional nature of the flow field around the cantilever beam. Due to its importance in atomic force microscope applications, results for the thermal noise spectrum are presented and the influence of mode order on the frequency response investigated.
Crystallization of Amorphous Nimesulide: The Relationship between Crystal Growth Kinetics and Liquid Dynamics

Understanding crystallization and its correlations with liquid dynamics is relevant for developing robust amorphous pharmaceutical solids. Herein, nimesulide, a classical anti-inflammatory agent, was used as a model system for studying the correlations between crystallization kinetics and molecular dynamics. Kinetic parts of crystal growth (ukin) of nimesulide exhibited a power law dependence upon the liquid viscosity (η) as ukin~η−0.61. Bulk molecular diffusivities (DBulk) of nimesulide were predicted by a force-level statistical–mechanical model from the α-relaxation times, which revealed the relationship as ukin~Dbulk0.65. Bulk crystal growth kinetics of nimesulide in deeply supercooled liquid exhibited a fragility-dependent decoupling from τα. The correlations between growth kinetics and α-relaxation times predicted by the Adam–Gibbs–Vogel equation in a glassy state were also explored, for both the freshly made and fully equilibrated glass. These findings are relevant for the in-depth understanding and prediction of the physical stability of amorphous pharmaceutical solids.
Spatiotemporal Patterns and Road Mortality Hotspots of Herpetofauna on a Mediterranean Island

Traffic intensification, often in conjunction with habitat fragmentation, has caused frequent roadkill incidents, particularly among reptiles, amphibians, and other taxa. Herpetofauna species, which are slow moving and habitat dependent, are particularly susceptible to these incidents because they often use roads during thermoregulation. Lesvos, the eighth-largest Mediterranean island, boasts a biodiversity that surpasses most other Mediterranean islands of similar or larger size, with a plethora of herpetofauna species inhabiting its terrain. In recent years, new roads were constructed on Lesvos, which are considered to be one of the most important factors that negatively affect the island’s wildlife as they increase the non-natural mortality of animals, are obstacles to their mobility, and reduce the connectivity of populations by limiting their dynamics. In the present study, we examined the road mortality of amphibians and reptiles by analyzing (a) the temporal and seasonal patterns of such incidents, (b) the relationship between roadside habitats and road network characteristics with the roadkilled herpetofauna species, and (c) their spatial distribution on Lesvos during the years 2009–2012 and 2016–2019. To identify significant clusters of reptile and amphibian roadkills, we performed hotspot analysis by utilizing kernel density estimation and Getis Ord Gi* statistics. We recorded a total of 330 roadkills among 20 species, with the highest rates emerging among the European green toad (Bufotes viridis), the European glass lizard (Pseudopus apodus), the Rhodos green lizard (Lacerta diplochondrodes), and the snake-eyed lizard (Ophisops elegans). Spatial statistical analysis revealed that roads close to herpetofauna habitats exhibit statistically significant clusters of roadkills that intensify during the spring season. Regular monitoring and mapping of herpetofauna road mortality will enable the implementation of management strategies to mitigate the negative impact of this phenomenon.
Stochastic Simulation of Cell Cycle

Dynamic model of cell cycle from G1 to S stage is described by a system of six ordinary differential equations. These equations display the rate of changes in concentrations of proteins, cyclin E, CycE, cyclin dependent kinase, CDK2 and protein phosphatase, CDC25. We have developed a stochastic model of G1iÂ®S transition of cell cycle on the basis of the above mentioned dynamic model. The model is realized by the Gillespie algorithm of stochastic simulation using the Matlab 7.0 and FORTRAN 95. Scaling factor converts the normalized concentration of the dynamic model to the number of molecules of the stochastic model. The increase of scaling factor is related to the increasing number of the molecules of CycE, inactive CycE/CDK2 complex, active CycE/CDK2 complex, and mono and dephosphorylated CDC25. Solutions of this model show limit cycle depending on the time. When scaling factor is small the solution shows drastic random fluctuations. The solutions of the stochastic model is approached to the solutions of dynamic model, especially, when the scaling factor is more than two hundred (âÂ¦=200). In this case, fluctuations of periods of limit cycle are stabilized.
CALIPSO Lidar Description and Performance Assessment

Abstract This paper provides background material for a collection of Cloud–Aerosol Lidar with Orthogonal Polarization (CALIOP) algorithm papers that are to be published in the Journal of Atmospheric and Oceanic Technology. It provides a brief description of the design and performance of CALIOP, a three-channel elastic backscatter lidar on the Cloud–Aerosol Lidar and Infrared Pathfinder Satellite Observation (CALIPSO) satellite. After more than 2 yr of on-orbit operation, CALIOP performance continues to be excellent in the key areas of laser energy, signal-to-noise ratio, polarization sensitivity, and overall long-term stability, and the instrument continues to produce high-quality data products. There are, however, some areas where performance has been less than ideal. These include short-term changes in the calibration coefficients at both wavelengths as the satellite passes between dark and sunlight, some radiation-induced effects on both the detectors and the laser when passing through the South Atlant.
BROADBAND, TIME-DEPENDENT, SPECTROSCOPY OF THE BRIGHTEST BURSTS OBSERVED BY BATSE LAD AND EGRET TASC

The Energetic Gamma Ray Experiment Telescope (EGRET) calorimeter, Total Absorption Shower Counter (TASC), was triggered by the Burst And Transient Source Experiment (BATSE) and thus observed several bursts in the energy range of 1–200 MeV. The analysis of combined BATSE Large Area Detector and EGRET TASC data have been developed and discussed previously. Spectroscopy of GRB941017 based on this analysis uncovered an MeV component that would be hidden in the brightness of the synchrotron component in a time-integrated spectrum of the whole burst, while separation into shorter time intervals allowed a unique identification of a new component different from the synchrotron component. In this paper the spectral temporal evolution of the 68 brightest long BATSE bursts, in the broadest energy range yet reported, is studied using the analysis used for GRB941017. We consider the Band function to describe the spectra from keV to MeV energies. Only 21 of the 68 bursts showed MeV emission detectable by TASC. We observed three bursts that contained spectra with peak energy Epeak>2 MeV.
Diagnostic Accuracy of 18F-Fluorodeoxyglucose Positron Emission Tomography/Computed Tomography in Preoperative Mediastinal/Extramediastinal Nodal Staging of Non–Small-Cell Lung Carcinoma

Introduction: Lung cancer has the highest incidence and mortality among malignancies in many countries. 18 F-Fluorodeoxyglucose ( 18 F-FDG) positron emission tomography/computed tomography (PET/CT) is commonly indicated for the preoperative nodal staging of non–small-cell lung carcinoma. While maximum standardised uptake value (SUV max ), visual scoring systems and nodal diameter have been proposed to distinguish benign from malignant nodes, studies comparing the different measurements have been limited. Correct nodal staging is crucial in determining if treatment intent is curative or palliative. This study aimed to evaluate the accuracies of nodal staging in 18 F-FDG PET/CT based on different methods. Methods: A total of 467 mediastinal/extramediastinal lymph nodes from 97 patients, who underwent staging 18 F-FDG PET/CT at our centre for non–small-cell lung carcinoma, were retrospectively reviewed. The nodes were evaluated based on SUV max , five-point visual interpretation score, and diameter. Their sensitivities, specificities and accuracies were compared with histology using receiver operating characteristics curves and areas under the curves (AUCs). Subgroup analyses based on T staging, histology, epidermal growth factor receptor (EGFR) status, lymph node locations, and tumour SUV max were also investigated. Results: The diagnostic performance of visual score (at optimal cut-off of 3) yielded the highest specificity (0.932), accuracy (0.916), positive predictive value (0.623), and negative predictive value (0.972), results of which were similar to SUV max of 2.5 and better than nodal diameter of 10 mm. Subgroup analyses showed that visual interpretation achieved satisfactory AUCs in different T stages, histologies, EGFR statuses, locations of lymph nodes, and tumour SUVs max . Conclusion: The five-point visual interpretation is a convenient diagnostic tool with performance better than nodal diameter, and similar to that of SUV max .
Circulating miRNAs in Women with Polycystic Ovary Syndrome: A Longitudinal Cohort Study

Background: Women with polycystic ovary syndrome (PCOS) often change their metabolic profile over time to decrease levels of androgens while often gaining a propensity for the development of the metabolic syndrome. Recent discoveries indicate that microRNAs (miRNAs) play a role in the development of PCOS and constitute potential biomarkers for PCOS. We aimed to identify miRNAs associated with the development of an impaired metabolic profile in women with PCOS, in a follow-up study, compared with women without PCOS. Methods and materials: Clinical measurements of PCOS status and metabolic disease were obtained twice 6 years apart in a cohort of 46 women with PCOS and nine controls. All participants were evaluated for degree of metabolic disease (hypertension, dyslipidemia, central obesity, and impaired glucose tolerance). MiRNA levels were measured using Taqman® Array cards of 96 pre-selected miRNAs associated with PCOS and/or metabolic disease. Results: Women with PCOS decreased their levels of androgens during follow-up. Twenty-six of the miRNAs were significantly changed in circulation in women with PCOS during the follow-up, and twenty-four of them had decreased, while levels did not change in the control group. Four miRNAs were significantly different at baseline between healthy controls and women with PCOS; miR-103-3p, miR-139-5p, miR-28-3p, and miR-376a-3p, which were decreased in PCOS. After follow-up, miR-28-3p, miR-139-5p, and miR-376a-3p increased in PCOS women to the levels observed in healthy controls. Of these, miR-139-5p correlated with total testosterone levels (rho = 0.50, padj = 0.013), while miR-376-3p correlated significantly with the waist-hip ratio at follow-up (rho = 0.43, padj = 0.01). Predicted targets of miR-103-3p, miR-139-5p, miR-28-3p, and miR-376a-3p were enriched in pathways associated with Insulin/IGF signaling, interleukin signaling, the GNRH receptor pathways, and other signaling pathways. MiRNAs altered during follow-up in PCOS patients were enriched in pathways related to immune regulation, gonadotropin-releasing hormone signaling, tyrosine kinase signaling, and WNT signaling. Conclusions: These studies indicate that miRNAs associated with PCOS and androgen metabolism overall decrease during a 6-year follow-up, reflecting the phenotypic change in PCOS individuals towards a less hyperandrogenic profile.
A magnetically- and electrically-tunable microwave phase shifter using yttrium iron garnet/gadolinium gallium garnet thin film

A new type of tunable microwave phase shifter that combines ferromagnetic resonance (FMR)-based magnetic tuning in a yttrium iron garnet-thin-film and DC electrical tuning in a varactor-loaded composite band-pass filter is reported. For the frequency range of 10.37 to 10.87 GHz, a phase shift of 147.5 to 280° was first obtained by applying a reversed bias voltage from 6 to 18 V, and the total phase shift was subsequently increased to 406.5° by varying the bias magnetic field from 2700 to 3450 Oe. The corresponding insertion loss variation measured ±1.5 dB. Similar performance figures could also be obtained for other frequency ranges by varying the bias magnetic field and the corresponding FMR frequency. Thus, the composite phase shifter has clearly demonstrated its capability for a large and continuously tunable phase shift with a moderate insertion loss variation over a wide range of operating frequencies.