Miracle-dz/UniFAR-FTUs huggingface dataset:
A Yersinia T6SS Effector YezP Engages the Hemin Uptake Receptor HmuR and ZnuABC for Zn2+ Acquisition

Identifying the transporters involved in import of metal ions under normal physiological growth conditions in bacterial pathogens will clarify its pathogenic mechanism. Y. pseudotuberculosis YPIII, a common foodborne pathogen that infects animals and humans, uptake zinc via the T6SS4 effector YezP. However, the outer and inner transports involved in Zn2+ acquisition remain unknown. ABSTRACT Metal ions are essential nutrients for all life forms, and restriction of metal ion availability is an effective host defense against bacterial infection. Meanwhile, bacterial pathogens have developed equally effective means to secure their metal ion supply. The enteric pathogen Yersinia pseudotuberculosis was found to uptake zinc using the T6SS4 effector YezP, which is essential for Zn2+ acquisition and bacterial survival under oxidative stress. However, the mechanism of this zinc uptake pathway has not been fully elucidated. Here, we identified the hemin uptake receptor HmuR for YezP, which can mediate import of Zn2+ into the periplasm by the YezP-Zn2+ complex and demonstrated that YezP functions extracellularly. This study also confirmed that the ZnuCB transporter is the inner membrane transporter for Zn2+ from the periplasm to cytoplasm. Overall, our results reveal the complete T6SS/YezP/HmuR/ZnuABC pathway, wherein multiple systems are coupled to support zinc uptake by Y. pseudotuberculosis under oxidative stress. IMPORTANCE Identifying the transporters involved in import of metal ions under normal physiological growth conditions in bacterial pathogens will clarify its pathogenic mechanism. Y. pseudotuberculosis YPIII, a common foodborne pathogen that infects animals and humans, uptake zinc via the T6SS4 effector YezP. However, the outer and inner transports involved in Zn2+ acquisition remain unknown. The important outcomes of this study are the identification of the hemin uptake receptor HmuR and inner membrane transporter ZnuCB that import Zn2+ into the cytoplasm via the YezP-Zn2+ complex, and elucidation of the complete Zn2+ acquisition pathway consisting of T6SS, HmuRSTUV, and ZnuABC, thereby providing a comprehensive view of T6SS-mediated ion transport and its functions.
The Vacuum in Relativistic Quantum Field Theory

The status of the vacuum in relativistic quantum field theory is examined. A sharp distinction arises between the global vacuum and the local vacuum. The concept of local number density is critically assessed. The global vacuum state implies fluctuations for all local observables. Correlations between such fluctuations in space-like separated regions of space-time are discussed and the existence of correlations which are maximal in a certain sense is remarked on, independently of how far apart those regions may be. The analogy with the mirror-image correlations in the singlet state of two spin-1/2 particles is explained. The connection between these maximal correlations and the well-known violation of the Bell inequality in the vacuum state is discussed, together with the way in which the existence of these correlations might be exploited in developing a vacuum version of the Einstein-Podolsky-Rosen argument. The recent relativistic formulation of the Einstein-Podolsky-Rosen argument by Ghirardi and Grassi is critically assessed with particular reference to the vacuum case.
Previous Antibiotic Exposure Reshapes the Population Structure of Infecting Uropathogenic Escherichia coli Strains by Selecting for Antibiotic Resistance over Urovirulence

Urinary tract infections (UTIs) are one of the most common infections of dogs and humans. While antibiotic therapy is the standard of care for UTIs and other infections, antibiotic exposure may influence the pathogenic profile of subsequent infections. ABSTRACT Antibiotic therapy is the standard of care for urinary tract infections (UTIs) caused by uropathogenic Escherichia coli (UPEC). However, previous antibiotic therapy may impart a selective pressure that influences the population structure and pathogenic potential of infecting UPEC strains. Here, we conducted a 3-year study using whole-genome-sequencing analysis and retrospective medical record review to characterize how antibiotic exposure influenced the phenotypic antibiotic resistance, acquired resistome, virulome, and population structure of 88 UTI-causing E. coli strains from dogs. A majority of UTI-associated E. coli strains were from phylogroup B2 and clustered within sequence type 372. Previous antibiotic exposure was associated with a population shift toward UPEC from phylogroups other than the typical urovirulent phylogroup B2. The specific virulence profiles within the accessory virulome that were associated with antibiotic use were elicited by the effect of antibiotics on UPEC phylogenetic structure. Among phylogroup B2, antibiotic exposure increased the quantity of genes within the resistome and the odds of developing reduced susceptibility to at least one antibiotic. Non-B2 UPEC strains harbored a more diverse and greater resistome that conferred reduced susceptibility to multiple antibiotic classes following antibiotic exposure. Collectively, these data suggest that previous antibiotic exposure establishes an environment that provides a selective edge to non-B2 UPEC strains through their diverse and abundant antibiotic resistance genes, despite their lack of urovirulence genes. Our findings highlight the necessity for judicious use of antibiotics as we uncover another mechanism by which antibiotic exposure and resistance can influence the dynamics of bacterial infectious disease. IMPORTANCE Urinary tract infections (UTIs) are one of the most common infections of dogs and humans. While antibiotic therapy is the standard of care for UTIs and other infections, antibiotic exposure may influence the pathogenic profile of subsequent infections. We used whole-genome sequencing and retrospective medical record review to characterize the effect of systemic antibiotic therapy on the resistance, virulence, and population structure of 88 UTI-causing UPEC strains isolated from dogs. Our results indicate that antibiotic exposure alters the population structure of infecting UPEC strains, providing a selective edge for non-B2 phylogroups that harbor diverse and abundant resistance gene catalogues but fewer urovirulence genes. These findings highlight how antibiotic resistance can influence pathogen infection dynamics and have clinical implications for the judicious use of antibiotics for bacterial infections.
Diagnostic value of intraoperative fine‐needle aspiration cytologic diagnosis versus frozen section‐based histopathologic diagnosis in thoracic malignancies: A single institution's experience

Primary lung cancer is the leading cause of cancer death in the United States. Most lung cancers are diagnosed in an outpatient setting, but a subset requires intraoperative diagnosis. Two intraoperative diagnostic methods are available, frozen section (FS) and fine needle aspiration (FNA) cytology. This study compares intraoperative FNA cytology and FS based diagnosis in thoracic malignancies within the same clinical practice.
Systemic pharmacological treatment of digital ulcers in systemic sclerosis: a systematic literature review

Abstract Objective To evaluate the evidence concerning systemic pharmacological treatments for SSc digital ulcers (DUs) to inform the development of evidence-based treatment guidelines. Methods A systematic literature review of seven databases was performed to identify all original research studies of adult patients with SSc DUs. Randomized controlled trials (RCTs) and prospective longitudinal observational studies (OBSs) were eligible for inclusion. Data were extracted, applying the patient, intervention, comparison, outcome framework, and risk of bias (RoB) was assessed. Due to study heterogeneity, narrative summaries were used to present data. Results Forty-seven studies that evaluated the treatment efficacy or safety of pharmacological therapies were identified among 4250 references. Data from 18 RCTs of 1927 patients and 29 OBSs of 661 patients, at various RoB (total 2588 patients) showed that i.v. iloprost, phosphodiesterase-5 inhibitors and atorvastatin are effective for the treatment of active DUs. Bosentan reduced the rate of future DUs in two RCTs (moderate RoB) and eight OBSs at low to high RoB. Two small studies (moderate RoB) indicate that Janus kinase inhibitors may be effective for the treatment of active DUs, otherwise there are no data to support the use of immunosuppression or anti-platelet agents in the management of DUs. Conclusion There are several systemic treatments, across four medication classes, that are effective therapies for the management of SSc DUs. However, a lack of robust data means it is not possible to define the optimal treatment regimen for SSc DUs. The relatively low quality of evidence available has highlighted further areas of research need.
Optimization of mRNA extraction from human nasal mucosa biopsies for gene expression profile analysis by qRT‐PCR

Quantitative real‐time reverse transcriptase polymerase chain reaction (qRT‐PCR) is the gold‐standard method for analyzing modifications in gene expression in cells and tissues. However, large quantities of high‐quality RNA samples are needed for analyzing the expression of multiple genes from one human tissue sample. Here, we provide an optimized protocol for extracting large amounts of RNA from human nasal mucosal biopsies. The quality and quantity of samples were sufficient for qRT‐PCR analyses of the expressions of various genes, in duplicate. In contrast to other protocols, we optimized RNA isolation to increase the amount from nasal biopsy samples for analyses of multiple genes. In most previous publications, expressions of only one or a few genes, including housekeeping genes, were analyzed because the amount of biological material was small. We were able to improve our protocol with respect to the yield and quality of RNA. This is likely to produce better results from molecular analyses of very small biopsy samples of human nasal mucosa.
RANDOM HEMISPHERE METHOD FOR RADIATION RAY TRACING COMPUTATIONS

In the field of radiative heat transfer, the challen ge is to compute the radiative exchanges of energy between the surfaces which compose a geometrical 3D model. To quantify the interactions between the surfaces, we use an adimensional number called view factor, which represents the fraction of the diffusely emitted energy from a patch Pi which reaches a patch Pj directly. The calculation of the view factors is a difficult problem because we have to take into account possible masks between the surfaces. The second difficulty is the total number of view factors, which is equal to p 2 , where p is the number of patches which compose the model. Except in the case of simple configurations, no analytical expression is available. A numerical approach is necessary. In this paper, we present a new method that we have named hemisphere, where the geometrical model is projected onto the discretized unit sphere centred at the local origin. This projection is based on the Nusselt’s Analogy. Because the surface of projection is the hemisphere, this method is simpler and more natural than most existing methods, like the hemi cube and the singular plane. We present a tessellation of the hemisphere into cells characterized by an equal elementary view factor. This allows us to prevent over sampling and to waste computation time. In each cell, a random ray is shot. It is shown that this statistical hemisphere is the combination of two methods used to decrease the variance of random processes, which are stratified sampling and importance sampling. This method is expected to yield better results than a classical Monte Carlo ray tracing. The accuracy of the solution can be defined with two parameters, the maximum relative error e and the confidence interval α. It will be possible to design an algorithm able to compute automatically – and a priori – the number of rays necessary to achieve the desired accuracy. The first results related to this control are presented in this paper.
Recommendations for endotracheal tube insertion depths in children

Background Endotracheal tube (ETT) malposition is frequent in paediatric intubation. The current recommendations for ETT insertion depths are based on formulae that hold various limitations. This study aimed to develop age-based, weight-based and height-based curve charts and tables for ETT insertion depth recommendations in children. Methods In this retrospective single-centre study, we determined the individual optimal ETT insertion depths in paediatric patients by evaluating postintubation radiographic images. Age-based, weight-based and height-based ETT insertion depth recommendations were developed using regression analysis. We compared the insertion depths predicted by the models with previously published formulae. Results Intubations of 167 children (0–17.9 years) were analysed. Best-fit curves generated with logistic regression analysis revealed R2 values between 0.784 and 0.880. The insertion depths predicted by the models corresponded well with published age-based and height-based formulae. However, they demonstrated the unsuitability of weight-related linear formulae to predict ETT depth in children. Conclusion The recommendations developed in this study facilitate a fast and accurate determination of recommended ETT insertion depths in children. Our recommendations provide greater accuracy than previously published formulae and demonstrate that weight-related linear formulae are unsuitable for predicting ETT depth in children.
Probabilistic Aspects of Scramjet Design

Scramjet design is characterized by a multitude of design variables influencing a highly nonlinear and complex system. Methods such as mean line calculations, high fidelity computational fluid dynamics, and empirical studies are generally used to derive aircraft engine performance. Because of the high complexity and the incomplete knowledge of hypersonic flow regimes, the question of robust design arises in the given context and leads to the need of probabilistic methodology. In this paper a probabilistic approach to scramjet engine design assessing both inflow and model uncertainty is presented. The two different types of uncertainty are quantified with respect to their different nature by use of a two-step bootstrap methodology. A descriptive sampling Monte Carlo method is employed to propagate the quantified uncertainties through the engine model to exemplify the high sensitivity of net thrust vector to present uncertainties and to analyze the correlation between the parameters variations.
Development and validation of a rurality index for healthcare research in Japan: a modified Delphi study

Objectives Rural–urban healthcare disparities exist globally. Various countries have used a rurality index for evaluating the disparities. Although Japan has many remote islands and rural areas, no rurality index exists. This study aimed to develop and validate a Rurality Index for Japan (RIJ) for healthcare research. Design We employed a modified Delphi method to determine the factors of the RIJ and assessed the validity. The study developed an Expert Panel including healthcare professionals and a patient who had expertise in rural healthcare. Setting The panel members were recruited from across Japan including remote islands, mountain areas and heavy snow areas. The panel recruited survey participants whom the panel considered to have expertise. Participants The initial survey recruited 100 people, including rural healthcare providers, local government staff and residents. Primary outcome measures Factors to include in the RIJ were identified by the Expert Panel and survey participants. We also conducted an exploratory factor analysis on the selected factors to determine the factor structure. Convergent validity was examined by calculating the correlation between the index for physician distribution and the RIJ. Criterion-related validity was assessed by calculating the correlation with average life expectancy. Results The response rate of the final survey round was 84.8%. From the Delphi surveys, four factors were selected for the RIJ: population density, direct distance to the nearest hospital, remote islands and whether weather influences access to the nearest hospital. We employed the factor loadings as the weight of each factor. The average RIJ of every zip code was 50.5. The correlation coefficient with the index for physician distribution was −0.45 (p<0.001), and the correlation coefficients with the life expectancies of men and women were −0.35 (p<0.001) and −0.12 (p<0.001), respectively. Conclusion This study developed the RIJ using a modified Delphi method. The index showed good validity.
NoNliNEAR EffECTs iN oPTiCAl fibERs

Nonlinear optical effects are remarkable physical phenomena that can occur when a high-intensity light beam propagates through an optical medium [1]. if the pump beam is intense enough and the medium exhibits suitable nonlinear behavior, the typical properties of the medium (absorption, refractive index) can alter because of the input beam. Unlike the linear propagation of light where the spectral and spatial components of light do not affect each other in a medium, the nonlinear interaction of light with matter gives rise to complex coupling between the light components through the medium [2]. These effects have been very often regarded as detrimental to fiberbased optical communication systems [3]. However, they also offer new and exciting potential applications, such as devices in which light can be controlled by light [4]. Due to their strong light confinement capabilities, optical fibers have been long recognized as an ideal medium to exploit the nonlinear effects for all-optical processing applications in telecommunication and fiber laser industries [5]. This research field has recently been dramatically stimulated by the development of a new generation of highly nonlinear optical fibers which has an array of tiny holes running through the whole length of the fiber (see Chap. 7 for a complete description). These so-called photonic crystal or microstructured fibers allow conversion of a single-color laser beam into a white light supercontinuum spanning two octaves in frequency [6] (i.e., a laser rainbow extending from the ultraviolet well into the infrared, as shown in fig. 5.1). This new light source has revolutionized optical metrology, making absolute measurements of optical frequencies with unprecedented accuracy, and optical coherence tomography (oCT) with enhanced resolution. This topic will be described in more detail in Chapter 8. This Chapter is intended to provide an overview of nonlinear fiber optics in a way that is simultaneously accessible and technically comprehensive. first, we will describe some basic concepts of nonlinear propagation in dielectrics, so as to understand the origin of the main third-order nonlinear effects in fused silica, namely the optical Kerr effect and stimulated Raman scattering (sRs). The former, which arises from distortion of the electronic structure of silica molecules, gives
Finite time blowup for the fourth-order NLS

We consider the fourth-order Schrodinger equation with fo- cusing inhomogeneous nonlinearity (−|x| −2 |u| 4 n u) in high space dimen- sions. Extending Glassey's virial argument, we show the finite time blow- up of solutions when the energy is negative.
Risk factors for surgical site infection in patients with gastric cancer: A meta‐analysis

Surgical Site Infection (SSI) is one of the common postoperative complications after gastric cancer surgery. Previous studies have explored the risk factors (such as age, diabetes, anaemia and ASA score) for SSI in patients with gastric cancer. However, there are large differences in the research results, and the correlation coefficients of different research results are quite different. We aim to investigate the risk factors of surgical site infection in patients with gastric cancer. We queried four English databases (PubMed, Embase, Web of Science and the Cochrane Library) and four Chinese databases (China National Knowledge Infrastructure, Chinese Biological Medicine Database, Wanfang Database and Chinese Scientific Journal Database (VIP Database)) to identify published literature related to risk factors for surgical site infection in patients with gastric cancer. Rev Man 5.4 and Stata 15.0 were used in this meta‐analysis. A total of 15 articles (n = 6206) were included in this analysis. The following risk factors were found to be significantly associated with surgical site infection in gastric cancer: male (OR = 1.28, 95% CI [1.06, 1.55]), age >60 (OR = 2.75, 95% CI [1.65, 4.57]), smoking (OR = 1.99, 95% CI [1.46, 2.73]), diabetes (OR = 2.03, 95% CI [1.59, 2.61]), anaemia (OR = 4.72, 95% CI [1.66, 13.40]), preoperative obstruction (OR = 3.07, 95% CI [1.80, 5.23]), TNM ≥ III (OR = 2.05, 95% CI [1.56, 2.70]), hypoproteinemia (OR = 3.05, 95% CI [2.08, 4.49]), operation time ≥3 h (OR = 8.33, 95% CI [3.81, 18.20]), laparotomy (OR = 2.18, 95% CI [1.61, 2.94]) and blood transfusion (OR = 1.44, 95% CI [1.01, 2.06]). This meta‐analysis showed that male, age >60, smoking, diabetes, anaemia, preoperative obstruction, TNM ≥ III, hypoproteinemia, operation time ≥3 h, open surgery and blood transfusion were the risk factors for SSI in patients with gastric cancer.
Postpartum contraception: A matter of guidelines

The postpartum period is the perfect time to access family planning services. WHO guidelines contraindicate combined hormonal contraceptives postpartum in breastfeeding patients between 6 weeks and 6 months after delivery (Medical Eligibility Criteria category 3). On the contrary, the Faculty of Sexual and Reproductive Healthcare and the Centers for Disease Control and Prevention guidelines do not contraindicate their use in women who breastfeed from 6 weeks to 6 months postpartum. New combined hormonal contraceptives with natural estrogens have never been studied in this setting. Guidelines agree on the prescription of the progestin‐only pill postpartum in non‐breastfeeding women (category 1). Differences are found in women who breastfeed. In non‐breastfeeding women, an implant is considered safe (category 1) by all guidelines, without any distinction in time. Regarding postpartum breastfeeding women, the guidelines for implants give quite different indications but are still permissive. Intrauterine devices are viable options for postpartum contraception but guidelines give different indications about the timing of insertion. Postplacental intrauterine device placement can reduce the subsequent unintended pregnancy rate, particularly in settings at greatest risk of not having recommended postpartum controls. However, it has yet to be understood whether this approach can really have an advantage in high‐income countries. Postpartum contraception is not a ‘matter of guidelines’: it is the best customization for each woman, as early as possible but at the ideal timing.