Miracle-dz/UniFAR-FTUs huggingface dataset:
Elevated ozone and carbon dioxide affects the composition of volatile organic compounds emitted by Vicia faba (L.) and visitation by European orchard bee (Osmia cornuta)

Recent studies link increased ozone (O3) and carbon dioxide (CO2) levels to alteration of plant performance and plant-herbivore interactions, but their interactive effects on plant-pollinator interactions are little understood. Extra floral nectaries (EFNs) are essential organs used by some plants for stimulating defense against herbivory and for the attraction of insect pollinators, e.g., bees. The factors driving the interactions between bees and plants regarding the visitation of bees to EFNs are poorly understood, especially in the face of global change driven by greenhouse gases. Here, we experimentally tested whether elevated levels of O3 and CO2 individually and interactively alter the emission of Volatile Organic Compound (VOC) profiles in the field bean plant (Vicia faba, L., Fabaceae), EFN nectar production and EFN visitation by the European orchard bee (Osmia cornuta, Latreille, Megachilidae). Our results showed that O3 alone had significant negative effects on the blends of VOCs emitted while the treatment with elevated CO2 alone did not differ from the control. Furthermore, as with O3 alone, the mixture of O3 and CO2 also had a significant difference in the VOCs’ profile. O3 exposure was also linked to reduced nectar volume and had a negative impact on EFN visitation by bees. Increased CO2 level, on the other hand, had a positive impact on bee visits. Our results add to the knowledge of the interactive effects of O3 and CO2 on plant volatiles emitted by Vicia faba and bee responses. As greenhouse gas levels continue to rise globally, it is important to take these findings into consideration to better prepare for changes in plant-insect interactions.
Diagnostic performance of the GenoType MTBDRplus VER 2.0 line probe assay for the detection of isoniazid resistant Mycobacterium tuberculosis in Ethiopia

Background Isoniazid (INH) resistant Mycobacterium tuberculosis (Hr-TB) is the most common type of drug resistant TB, and is defined as M tuberculosis complex (MTBC) strains resistant to INH but susceptible to rifampicin (RIF). Resistance to INH precedes RIF resistance in almost all multidrug resistant TB (MDR-TB) cases, across all MTBC lineages and in all settings. Therefore, early detection of Hr-TB is critical to ensure rapid initiation of appropriate treatment, and to prevent progression to MDR-TB. We assessed the performance of the GenoType MTBDRplus VER 2.0 line probe assay (LPA) in detecting isoniazid resistance among MTBC clinical isolates. Methods A retrospective study was conducted among M. tuberculosis complex (MTBC) clinical isolates obtained from the third-round Ethiopian national drug resistance survey (DRS) conducted between August 2017 and December 2019. The sensitivity, specificity, positive predictive value, and negative predictive value of the GenoType MTBDRplus VER 2.0 LPA in detecting INH resistance were assessed and compared to phenotypic drug susceptibility testing (DST) using the Mycobacteria Growth Indicator Tube (MGIT) system. Fisher’s exact test was performed to compare the performance of LPA between Hr-TB and MDR-TB isolates. Results A total of 137 MTBC isolates were included, of those 62 were Hr-TB, 35 were MDR-TB and 40 were INH susceptible. The sensitivity of the GenoType MTBDRplus VER 2.0 for detecting INH resistance was 77.4% (95% CI: 65.5–86.2) among Hr-TB isolates and 94.3% (95% CI: 80.4–99.4) among MDR-TB isolates (P = 0.04). The specificity of the GenoType MTBDRplus VER 2.0 for detecting INH resistance was 100% (95% CI: 89.6–100). The katG 315 mutation was observed in 71% (n = 44) of Hr-TB phenotypes and 94.3% (n = 33) of MDR-TB phenotypes. Mutation at position-15 of the inhA promoter region alone was detected in four (6.5%) Hr-TB isolates, and concomitantly with katG 315 mutation in one (2.9%) MDR-TB isolate. Conclusions GenoType MTBDRplus VER 2.0 LPA demonstrated improved performance in detecting INH resistance among MDR-TB cases compared to Hr-TB cases. The katG315 mutation is the most common INH resistance conferring gene among Hr-TB and MDR-TB isolates. Additional INH resistance conferring mutations should be evaluated to improve the sensitivity of the GenoType MTBDRplus VER 2.0 for the detection of INH resistance among Hr-TB cases.
Nature of Driving Force on an Isolated Moving Vortex in Dirty Superconductors

We reconsider the force-balance relation on an isolated vortex in the flux flow state within the scheme of the time-dependent Ginzburg–Landau (TDGL) equation. We define the force on a vortex by the total force on superconducting electrons in the region S surrounding the vortex. We derive the local momentum balance relation of superconducting electrons and then find the force-balance relation on an isolated vortex while taking account of the fact that the transport current in charged superconductors is inherently spatially varying with the scale of the penetration depth λ. We also find that the nature of the driving force is hydrodynamic when S is a disk with radius R satisfying ξ ≪ R ≪ λ (ξ is the coherence length) while the hydrodynamic and magnetic parts contribute equally to the driving force for \(\lambda \lesssim R\).
Automated High‐Throughput Fatigue Testing of Freestanding Thin Films

Mechanical testing at small length scales has traditionally been resource‐intensive due to difficulties with meticulous sample preparation, exacting load alignments, and precision measurements. Microscale fatigue testing can be particularly challenging due to the time‐intensive, tedious repetition of single fatigue experiments. To mitigate these challenges, this work presents a new methodology for the high‐throughput fatigue testing of thin films at the microscale. This methodology features a microelectromechanical systems‐based Si carrier that can support the simultaneous and independent fatigue testing of an array of samples. To demonstrate this new technique, the microscale fatigue behavior of nanocrystalline Al is efficiently characterized via this Si carrier and automated fatigue testing with in situ scanning electron microscopy. This methodology reduces the total testing time by an order of magnitude, and the high‐throughput fatigue results highlight the stochastic nature of the microscale fatigue response. This manuscript also discusses how this initial capability can be adapted to accommodate more samples, different materials, new geometries, and other loading modes.
Chemotherapeutic drugs induced female reproductive toxicity and treatment strategies

Increase in success of cancer treatment with advancement in the screening, prognosis and diagnosis protocols have significantly improved the rate of cancer survivorship. With the declining cancer mortality, however, the cancer survivors are also subjected to the adverse consequences of chemotherapy, particularly in the female reproductive system. Recent studies have shown the sensitivity of the ovarian tissue to the chemotherapeutic drugs‐induced toxicity. Several in vitro and in vivo studies have assessed the toxic effects of chemotherapeutic drugs. The most frequently used chemotherapeutic drugs such as doxorubicin, cyclophosphamide, cisplatin and paclitaxel have been reported to cause ovarian damage, diminution of follicular pool reserve, premature ovarian failure and early menopause, resulting into declining fertility potential among females. The chemotherapy often employs combination of drug regimen to increase the efficacy of the treatment. However, the literature mostly consists of clinical data regarding the gonadotoxicity caused by anticancer drugs but there lacks the understanding of toxicity mechanism. Therefore, understanding of the different toxicity mechanisms will be helpful in development of possible therapeutic interventions for preservation of declining female fertility among cancer survivors. The current review comprehends the underlying mechanisms of female reproductive toxicity induced by the most commonly used chemotherapeutic drugs. In addition, the review also summarizes the recent findings related to the use of various protectants to diminish or at least in managing the toxicity induced by different chemotherapeutic drugs in females.
Insight into the Antibacterial Action of Iodinated Imine, an Analogue of Rafoxanide: a Comprehensive Study of Its Antistaphylococcal Activity

Antibiotic resistance is among the largest threats to global health, with a potentially serious socioeconomic impact. One of the strategies to deal with the predicted catastrophic future scenarios associated with the rapid emergence of resistant infectious agents lies in the discovery and research of new anti-infectives. ABSTRACT In this study, we have focused on a multiparametric microbiological analysis of the antistaphylococcal action of the iodinated imine BH77, designed as an analogue of rafoxanide. Its antibacterial activity against five reference strains and eight clinical isolates of Gram-positive cocci of the genera Staphylococcus and Enterococcus was evaluated. The most clinically significant multidrug-resistant strains, such as methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant S. aureus (VRSA), and vancomycin-resistant Enterococcus faecium, were also included. The bactericidal and bacteriostatic actions, the dynamics leading to a loss of bacterial viability, antibiofilm activity, BH77 activity in combination with selected conventional antibiotics, the mechanism of action, in vitro cytotoxicity, and in vivo toxicity in an alternative animal model, Galleria mellonella, were analyzed. The antistaphylococcal activity (MIC) ranged from 15.625 to 62.5 μM, and the antienterococcal activity ranged from 62.5 to 125 μM. Its bactericidal action; promising antibiofilm activity; interference with nucleic acid, protein, and peptidoglycan synthesis pathways; and nontoxicity/low toxicity in vitro and in vivo in the Galleria mellonella model were found to be activity attributes of this newly synthesized compound. In conclusion, BH77 could be rightfully minimally considered at least as the structural pattern for future adjuvants for selected antibiotic drugs. IMPORTANCE Antibiotic resistance is among the largest threats to global health, with a potentially serious socioeconomic impact. One of the strategies to deal with the predicted catastrophic future scenarios associated with the rapid emergence of resistant infectious agents lies in the discovery and research of new anti-infectives. In our study, we have introduced a rafoxanide analogue, a newly synthesized and described polyhalogenated 3,5-diiodosalicylaldehyde-based imine, that effectively acts against Gram-positive cocci of the genera Staphylococcus and Enterococcus. The inclusion of an extensive and comprehensive analysis for providing a detailed description of candidate compound-microbe interactions allows the valorization of the beneficial attributes linked to anti-infective action conclusively. In addition, this study can help with making rational decisions about the possible involvement of this molecule in advanced studies or may merit the support of studies focused on related or derived chemical structures to discover more effective new anti-infective drug candidates.
Dynamics and stage-specificity of between-population gene expression divergence in the Drosophila melanogaster larval fat body

Gene expression variation is pervasive across all levels of organismal organization, including development. Few studies, however, have examined variation in developmental transcriptional dynamics among populations, or how it contributes to phenotypic divergence. Indeed, the evolution of gene expression dynamics when both the evolutionary and temporal timescale are comparatively short remains relatively uncharacterized. Here, we examined coding and non-coding gene expression in the fat body of an ancestral African and a derived European Drosophila melanogaster population across three developmental stages spanning ten hours of larval development. Between populations, expression divergence was largely stage-specific. We detected higher expression variation during the late wandering stage, which may be a general feature of this stage. During this stage, we also detected higher and more extensive lncRNA expression in Europe, suggesting that lncRNA expression may be more important in derived populations. Interestingly, the temporal breadth of protein-coding and lncRNA expression became more restricted in the derived population. Taken together with the signatures of potential local adaptation that we detected at the sequence level in 9–25% of candidate genes (those showing evidence of expression divergence between populations), this finding suggests that gene expression becomes more developmental stage-specific during adaptation to new environments. We further used RNAi to identify several candidate genes that likely contribute to known phenotypic divergence between these populations. Our results shed light on the evolution and dynamics of expression variation over short developmental and evolutionary timescales, and how this variation contributes to population and phenotypic divergence.
Tumor Microenvironment CD8 T and Treg Cells–related Genes Signature Distinguishes Distinct Prognosis and Targeted Therapies Response in Endometrial Cancer

Although most endometrial cancer (EC) patients have a favorable prognosis, the overall survival (OS) of metastatic and recurrent EC could hardly be improved by the current chemoradiotherapy. We aimed to reveal the tumor microenvironment immune infiltration characteristics to elucidate the underlying mechanism of EC progression and guide clinical decisions. In the Cancer Genome Atlas (TCGA) cohort, Kaplan-Meier survival curves confirmed Tregs and CD8 T cells were prognosis-protective factors in OS of EC (P<0.05). Weighted gene coexpression network analysis identified 2 gene modules closely correlated with Tregs and CD8 T-cell infiltration. We randomly split the TCGA EC cohort into the training and testing cohorts at a ratio of 7:3. An immune-related prognosis risk index (IRPRI), including NR3C1, E2F1, OTOG, TTK, PPP1R16B, and FOXP3, was established by univariate, Least Absolute Shrinkage and Selection Operator, and multivariate Cox regression with area under the curve >0.67. Distinct clinical, immune, and mutation characteristics existed between IRPRI groups by multiomics analysis. Cell proliferation and DNA damage repair-related pathways were activated, and immune-related pathways were inactivated in the IRPRI-high group. Furthermore, patients in the IRPRI-high group had lower tumor mutation burden, programmed death-ligand 1 expression, and Tumor Immune Dysfunction and Exclusion scores, indicating a poor response to immune checkpoint inhibitors therapy (P<0.05), which was also validated in the TCGA testing cohort and independent cohorts, GSE78200, GSE115821, and GSE168204. Also, the higher mutation frequencies of BRCA1, BRCA2, and genes enrolled in homologous recombination repair in the IRPRI-low group predicted a good response to PARP inhibitors. Finally, a nomogram integrating the IRPRI group and prognosis significant clinicopathological factors for EC OS prediction was developed and validated with good discrimination and calibration.
Complete Genome of “Candidatus Phytoplasma rubi” RS, a Phytopathogenic Bacterium Associated with Rubus Stunt Disease

The phytoplasma “Candidatus Phytoplasma rubi” is associated with Rubus stunt disease. The complete genome was determined by assembling Oxford Nanopore Technologies system-derived long reads, with short-read polishing with Illumina reads. The genome of strain RS, from Germany, is organized in one circular chromosome with a length of 762 kb. ABSTRACT The phytoplasma “Candidatus Phytoplasma rubi” is associated with Rubus stunt disease. The complete genome was determined by assembling Oxford Nanopore Technologies system-derived long reads, with short-read polishing with Illumina reads. The genome of strain RS, from Germany, is organized in one circular chromosome with a length of 762 kb.
Adaptive Sliding Mode Controller Design for Fault Tolerant Flight Control System

In this study, a fault tolerant flight control system based on adaptive and sliding mode control scheme is proposed. The merits of adaptive and sliding mode control scheme are that (i) the magnitude of sliding mode controller gain can be reduced and (ii) the fault detection and isolation process is not required. Using the timescale separation principle, the aircraft system can be decomposed into fast inner-loop dynamics and slow outer-loop dynamics. Angular velocity components are used as virtual inputs for the slow dynamics, which are angular variables in the outer-loop control system. The inner-loop controller is designed to make the fast states, that is, angular velocities, follow the outer-loop control input trajectories using the aileron, elevator, and rudder to complete the maneuver. The stability analysis of the proposed control law is performed using Lyapunov theory and LaSalleYoshizawa theorem. To verify the effectiveness of the proposed control scheme, numerical simulation is performed for a high performance six degree of freedom nonlinear aircraft model. Simulation results demonstrate that the closed-loop system has good performance in spite of the actuator fault and the nonlinearity of aircraft system.
The Denoising of Ultrasonic Signal Based on Asymptotic Semi-soft Thresholding Function

Asymptotic semi-soft function has been proposed to overcome the discontinuous shortcoming of the hard-threshold function and the dispersion between the estimated wavelet coefficients and the decomposed wavelet coefficients of the soft-threshold function,as well as the problem how to select the parameter in the threshold function.It was testified that the estimated wavelet coefficients gradually approached the authentic wavelet coefficients as the threshold function using the asymptotic adjustment factor.Simulation results showed that the asymptotic semi-soft function could obtain higher signal-to-noise ratio(SNR) and smaller mean squared error(MSE) in ultrasonic signal denosing.A better denoising effect had been obtained in comparison with the hard-threshold function.
Endoscopic submucosal dissection of rectal lesion recurrence at the anastomosis site: when the staples lead the way

A 75-year-old man underwent an anterior rectum resection due to an early neoplastic rectal lesion. On surveillance endoscopy 4 years later, the surgical anastomosis was identified at 8 cm from the anal margin and was associated with a 35-mm lateral spreading tumor (LST), compatible with neoplastic recurrence. The LST reached the anastomosis as well as an adjacent pseudodiverticular recess (▶Fig. 1). White-light and narrow-band imaging evaluation looking for signs of invasive disease were unremarkable, so endoscopic submucosal dissection (ESD) was decided upon. The procedure was performed using a Flush Knife BT (1.5mm; Fujifilm Co., Tokyo, Japan) (▶Video 1). Submucosal injection of a solution made of polygeline (Gelafundin), indigo carmine, and epinephrine showed the nonlifting sign in the lesion area over the surgical anastomosis. After dissection of the submucosa without fibrosis, an extensive line of 2-cm surgical staples was reached. At this point, the ESD became technically challenging not only due to the presence of the staples, which often hindered passage of the electric current, but also because of the severe associated fibrosis (▶Fig. 2). During the dissection, two adjacent 2-mm microperforations were noted (▶Fig. 3); after a failed attempt at closure with through-the-scope clips, these were effectively closed with two over-the-scope clips. En bloc resection was achieved (▶Fig. 4) and histopathology analysis showed R0 resection of a tubular adenoma with low and focally high grade dysplasia. Six-month endoscopic follow-up showed the ESD scar without any residual lesion. Patients who have undergone colorectal surgery for either cancer or benign lesions continue to be at risk of developing recurrent, residual, or metachronous lesions in the remaining colon, including at the anastomosis site [1]. Surgical resection of a recurrent rectal lesion involves radical en bloc resection of the lesion together with all involved structures followed by major reconstructive procedures; morbidity can be high [2]. ESD is a minimally invasive therapy for superficial neoplastic neoplasms [3] and, in expert hands, is a feasible strategy for lesions at the anastomosis site [1].
Linear response analysis of supersonic turbulent channel flows with a large parameter space

Abstract In this work, the linear responses of turbulent mean flow to both harmonic and stochastic forcing are investigated for supersonic channel flow. Well-established universal relations are utilized to obtain efficiently the mean profiles with a large parameter space, with the bulk Mach number up to 5 and the friction Reynolds number up to $10^4$, so a systematic parameter study is feasible. The most amplified structure takes the form of streamwise velocity and temperature streaks forced optimally by the streamwise vortices. The outer peak of the pre-multiplied energy amplification corresponds to the large-scale motion, whose spanwise wavelength ($\lambda _z^+$) is very insensitive to compressibility effects. In contrast, the classic inner peak representing small-scale near-wall motions disappears for the stochastic response with increasing Mach number. Meanwhile, the small-scale motions become much less coherent. A decomposition of the forcing identifies different effects of the incompressible counterpart and the thermodynamic components. Wall-cooling effects, arising with high Mach number, increase the spacing of the most amplified near-wall streaks; the spacing becomes nearly invariant with Mach number if expressed in semi-local units. Meanwhile, the coherence of stochastic response with $\lambda _z^+>90$ is enhanced, but on the other hand, with $\lambda _z^+<90$ it is decreased. The geometrical self-similarity of the response in the mid-$\lambda _z$ range is still roughly satisfied, insensitive to Mach number. Finally, theoretical analyses of the perturbation equations are presented to help with understanding the scaling of energy amplification.
Review of the state-of-the-art of in-line holographic microscopy

In-line Digital Holographic Microscopy (DHM) is an imaging technique that creates 3D images from holographic data. We categorize DHM reconstruction methods into direct, iterative, and machine learning based algorithms. Direct methods can be fast but often suffer from noise and low contrast due to the inherent twin-image aberration present in holographic reconstruction. Iterative methods improve accuracy and reduce noise but are generally more time consuming and computationally complex. Finally, machine learning methods can be extremely fast at inference but require large amounts of resources and training data. We provide a literary and illustrative summary of these methods (Figure 1), allowing for easy comparison.