Miracle-dz/UniFAR-FTUs huggingface dataset:
The precise measurement of the attenuation coefficients of various IR optical materials applicable to immersion grating

Immersion grating is a next-generation diffraction grating which has the immersed the diffraction surface in an optical material with high refractive index of n > 2, and can provide higher spectral resolution than a classical reflective grating. Our group is developing various immersion gratings from the near- to mid-infrared region (Ikeda et al.1, 2, 3, 4, Sarugaku et al.5, and Sukegawa et al.6). The internal attenuation αatt of the candidate materials is especially very important to achieve the high efficiency immersion gratings used for astronomical applications. Nevertheless, because there are few available data as αatt < 0.01cm-1 in the infrared region, except for measurements of CVD-ZnSe, CVD-ZnS, and single-crystal Si in the short near-infrared region reported by Ikeda et al.7, we cannot select suitable materials as an immersion grating in an aimed wavelength range. Therefore, we measure the attenuation coefficients of CdTe, CdZnTe, Ge, Si, ZnSe, and ZnS that could be applicable to immersion gratings. We used an originally developed optical unit attached to a commercial FTIR which covers the wide wavelength range from 1.3μm to 28μm. This measurement system achieves the high accuracy of (triangle)αatt ~ 0.01cm-1. As a result, high-resistivity single-crystal CdZnTe, single-crystal Ge, single-crystal Si, CVD-ZnSe, and CVD-ZnS show αatt < 0.01cm-1 at the wavelength range of 5.5 - 19. 0μm, 2.0 - 10. 5μm, 1.3 - 5. 4μm, 1.7 - 13. 2μm, and 1.9 - 9. 2μm, respectively. This indicates that these materials are good candidates for high efficiency immersion grating covering those wavelength ranges. We plan to make similar measurement under the cryogenic condition as T ≤ 10K for the infrared, especially mid-infrared applications.
A comparative genomics approach for identifying genetic factors in Escherichia coli isolates associated with bovine diseases

E. coli are ubiquitously present bacterial pathogens that cause septicaemia, diarrhoea and other clinical illness in farm animals. Many pathogen factors can be associated with disease conditions. Currently, studies inferring E. coli genetic factors associated with infection in bovines are limited. Hence, the present study envisaged to determine the pathogen genetic factors associated with bovine disease conditions.
An Overlooked and Underrated Endemic Mycosis—Talaromycosis and the Pathogenic Fungus Talaromyces marneffei

Talaromycosis is an invasive mycosis endemic in tropical and subtropical Asia and is caused by the pathogenic fungus Talaromyces marneffei. Approximately 17,300 cases of T. marneffei infection are diagnosed annually, and the reported mortality rate is extremely high (~1/3). SUMMARY Talaromycosis is an invasive mycosis endemic in tropical and subtropical Asia and is caused by the pathogenic fungus Talaromyces marneffei. Approximately 17,300 cases of T. marneffei infection are diagnosed annually, and the reported mortality rate is extremely high (~1/3). Despite the devastating impact of talaromycosis on immunocompromised individuals, particularly HIV-positive persons, and the increase in reported occurrences in HIV-uninfected persons, diagnostic and therapeutic approaches for talaromycosis have received far too little attention worldwide. In 2021, scientists living in countries where talaromycosis is endemic raised a global demand for it to be recognized as a neglected tropical disease. Therefore, T. marneffei and the infectious disease induced by this fungus must be treated with concern. T. marneffei is a thermally dimorphic saprophytic fungus with a complicated mycological growth process that may produce various cell types in its life cycle, including conidia, hyphae, and yeast, all of which are associated with its pathogenicity. However, understanding of the pathogenic mechanism of T. marneffei has been limited until recently. To achieve a holistic view of T. marneffei and talaromycosis, the current knowledge about talaromycosis and research breakthroughs regarding T. marneffei growth biology are discussed in this review, along with the interaction of the fungus with environmental stimuli and the host immune response to fungal infection. Importantly, the future research directions required for understanding this serious infection and its causative pathogenic fungus are also emphasized to identify solutions that will alleviate the suffering of susceptible individuals worldwide.
The Bradyrhizobium japonicum fsrB gene is essential for utilization of structurally diverse ferric siderophores to fulfill its nutritional iron requirement

In Bradyrhizobium japonicum, iron uptake from ferric siderophores involves selective outer membrane proteins and non‐selective periplasmic and cytoplasmic membrane components that accommodate numerous structurally diverse siderophores. Free iron traverses the cytoplasmic membrane through the ferrous (Fe2+) transporter system FeoAB, but the other non‐selective components have not been described. Here, we identify fsrB as an iron‐regulated gene required for growth on iron chelates of catecholate‐ and hydroxymate‐type siderophores, but not on inorganic iron. Utilization of the non‐physiological iron chelator EDDHA as an iron source was also dependent on fsrB. Uptake activities of 55Fe3+ bound to ferrioxamine B, ferrichrome or enterobactin were severely diminished in the fsrB mutant compared with the wild type. Growth of the fsrB or feoB strains on ferrichrome were rescued with plasmid‐borne E. coli fhuCDB ferrichrome transport genes, suggesting that FsrB activity occurs in the periplasm rather than the cytoplasm. Whole cells of an fsrB mutant are defective in ferric reductase activity. Both whole cells and spheroplasts catalyzed the demetallation of ferric siderophores that were defective in an fsrB mutant. Collectively, the data support a model whereby FsrB is required for reduction of iron and its dissociation from the siderophore in the periplasm, followed by transport of the ferrous ion into the cytoplasm by FeoAB.
Gender differences in dry eye disease symptoms associated with psychological health indicators among adults using mobile mental health apps

Purpose We aimed to investigate the association between dry eye disease (DED) symptoms and mental health among Korean adults in the community. Methods A cross-sectional study analyzed the data of 152 participants using mobile-phone applications for recording mental health. We defined individuals with DED symptoms as those who experienced a sense of irritation or dryness of the eye (either constantly or often). Mental health (perceived stress, depression, and anxiety) was assessed using the Perceived Stress Scale, Patient Health Questionnaire-9, and General Anxiety Disorder-7, in this order. Multiple logistic regression analysis was conducted to examine the association between DED symptoms and mental health. We also adjusted for possible covariates. We investigated sex differences in mental health status in relation to DED. Results We found that 41.4% of the participants (48.4% female and 30.5% male) showed DED symptoms, and its prevalence was higher in female than in male. The average perceived stress and anxiety symptoms in the female with DED (24.69±4.73 and 6.56±5.09, respectively) were significantly higher than those without DED (21.38±4.68 and 4.54±4.03) (p = 0.020 and 0.038, respectively). Even after adjusting for possible covariates, female who had DED showed higher risks of perceived stress (OR = 1.28), depression (OR = 2.64), and anxiety (OR = 5.81). Conclusions Clinicians and nurses should therefore be aware of the possibility of mental health problems among female with DED.
Anti-diabetic effect of cotreatment with resveratrol and pioglitazone in diabetic rats.

OBJECTIVE Limitations and side effects associated with current anti-diabetic treatments have necessitated the search for new therapeutic alternatives. This study aimed to explore the combined use of resveratrol (RVT) and established anti-diabetic drug pioglitazone (PGZ) against streptozotocin (STZ)-induced diabetes mellitus (DM). MATERIALS AND METHODS STZ was supplemented daily to Sprague-Dawley rats to induce DM. The synergistic effect of the RVT (20 mg/kg) and PGZ (0.65 mg/kg) on DM complications was evaluated after 8 weeks of treatment. Biochemical analyses were performed to evaluate the effectiveness of our treatment on glucose level, insulin sensitivity, lipid disturbances, oxidative mediators and inflammatory markers. RESULTS STZ induced DM onset that is accompanied with elevated diabetic markers, lipid disturbances, remarkable oxidative damage and hyper-inflammation. The PGZ+RVT combination has the best effect as illustrated by significant (p < 0.05) decreases in fasting blood glucose, insulin, HbA1c and HOMA-IR levels. This combination attenuated (p < 0.05) lipid disturbances and their associated elevated atherogenic biomarkers. At the same time, treatments with PGZ+RVT exhibited an anti-inflammatory effect as it attenuated the increase in inflammatory parameters (CRP, TNF-α, IL-6). Also, it restored total antioxidant capacity and peroxisome proliferator-activated receptor (PPARg) levels that decreased by STZ-DM induction. CONCLUSIONS This study provides PGZ+RVT as promising DM therapeutic alternative. This synergistic combination alleviates most of DM-related complications and insulin resistance.
Treatment selection in multi-arm multi-stage designs: With application to a postpartum haemorrhage trial

Background: Multi-arm multi-stage trials are an efficient, adaptive approach for testing many treatments simultaneously within one protocol. In settings where numbers of patients available to be entered into trials and resources might be limited, such as primary postpartum haemorrhage, it may be necessary to select a pre-specified subset of arms at interim stages even if they are all showing some promise against the control arm. This will put a limit on the maximum number of patients required and reduce the associated costs. Motivated by the World Health Organization Refractory HaEmorrhage Devices trial in postpartum haemorrhage, we explored the properties of such a selection design in a randomised phase III setting and compared it with other alternatives. The objectives are: (1) to investigate how the timing of treatment selection affects the operating characteristics; (2) to explore the use of an information-rich (continuous) intermediate outcome to select the best-performing arm, out of four treatment arms, compared with using the primary (binary) outcome for selection at the interim stage; and (3) to identify factors that can affect the efficiency of the design. Methods: We conducted simulations based on the refractory haemorrhage devices multi-arm multi-stage selection trial to investigate the impact of the timing of treatment selection and applying an adaptive allocation ratio on the probability of correct selection, overall power and familywise type I error rate. Simulations were also conducted to explore how other design parameters will affect both the maximum sample size and trial timelines. Results: The results indicate that the overall power of the trial is bounded by the probability of ‘correct’ selection at the selection stage. The results showed that good operating characteristics are achieved if the treatment selection is conducted at around 17% of information time. Our results also showed that although randomising more patients to research arms before selection will increase the probability of selecting correctly, this will not increase the overall efficiency of the (selection) design compared with the fixed allocation ratio of 1:1 to all arms throughout. Conclusions: Multi-arm multi-stage selection designs are efficient and flexible with desirable operating characteristics. We give guidance on many aspects of these designs including selecting the intermediate outcome measure, the timing of treatment selection, and choosing the operating characteristics.
Association between nasal colonization of Staphylococcus aureus and surgical site infections in spinal surgery patients: a systematic review and meta-analysis.

OBJECTIVE The study aimed at examining the relationship between nasal colonization of Staphylococcus aureus (SA) or methicillin-resistant Staphylococcus aureus (MRSA) and the risk of SSI after spinal surgeries MATERIALS AND METHODS: PubMed, CENTRAL, Scopus, Web of Science, and Embase databases up to 24th September 2022 for articles on nasal colonization of SA/MRSA and spine surgeries. RESULTS Ten studies were included. Meta-analysis revealed that the incidence of SSI was not significantly different between SA-positive and SA-negative patients (RR: 0.75, 95% CI: 0.47, 1.18 I2=2% p=0.21). It was noted that when no decolonization was done, there was no statistically significant difference in the risk of SSI between MRSA positive and MRSA negative patients, but a tendency of higher SSI in MRSA carriers (RR: 2.40, 95% CI: 0.91, 6.32, I2=37% p=0.08). However, in the subgroup analysis with decolonization, the risk of SSI was significantly higher in the MRSA-positive group (RR: 2.99, 95% CI: 1.27, 7.03, I2=24% p=0.01). Specifically, the risk of MRSA-SSI was significantly higher in MRSA carriers with (RR: 6.05, 95% CI: 1.14, 31.99, I2=43% p=0.03) and without decolonization (RR: 7.54, 95% CI: 1.43, 39.85, I2=38% p=0.02). CONCLUSIONS Evidence from observational studies indicates that only MRSA nasal colonization increases the risk of SSIs in spinal surgery patients. Nasal decolonization was unable to reduce the risk of overall or MRSA-specific SSIs in MRSA carriers. Evidence was biased due to the extremely small number of MRSA-positive patients in the studies and the lack of adjustment of confounding factors.
Effect of Surface Steps on the Plastic Threshold in Nanoindentation

Using interfacial force microscopy and passivated Au surfaces, we have investigated the effect of surface steps on the initiation of plastic yield by performing nanoindentations as a function of separation between the probe and neighboring steps. The mean stress at yield was 30{percent} {endash}45{percent} lower at a step than in regions free of surface defects. In addition, the spatial extent of the step{close_quote}s influence was found to be approximately 3 times the contact radius at the yield threshold, suggesting that yield processes are not limited to the region in contact with the indenter. {copyright} {ital 1998} {ital The American Physical Society}
Clinical value of the renal pathologic scoring system in complement-mediated thrombotic microangiopathy

Abstract Objectives This study was initiated to establish a renal thrombotic microangiopathy (TMA) scoring system based on clinical needs and investigate its predictive value for patients’ long-term outcomes. Methods Kidney biopsy-proven Complement-mediated TMA (C-TMA) patients from January 2000 to December 2017 in Peking University First Hospital were retrospectively studied. Both acute and chronic TMA-related lesions, including 15 pathologic indices, were semiquantitatively scored. The interobserver and intraobserver reproducibility and correlation between the pathologic indices and clinical parameters were analyzed. Furthermore, the patients were divided into 2 groups by dialysis use at baseline, and the association of these pathologic indices with their prognostic outcomes was assessed between the two groups. Results Ninety-two patients with renal biopsy-proven C-TMA were enrolled. All fifteen included pathology indices showed good or moderate interobserver and intraobserver reproducibility and correlated well with several clinical parameters. Several clinicopathological indices were worse in the dialysis group than in the nondialysis group, such as serum creatinine, hemoglobin, platelet count, and estimated glomerular filtration rate. Moreover, morphologic features in the dialysis group presented with more severe vascular lesions. Interstitial fibrosis and chronic tubulointerstitial lesions were related to a trend of high risk of continuous dialysis in the dialysis group. Based on univariate and multivariable Cox regression analysis, more severe glomerular lesions, including glomerular mesangiolysis, glomerular basement membrane double contours and glomerular mesangial proliferation, were identified as risk factors predicting worse prognosis. Conclusions Our renal C-TMA semiquantitative scoring system is reliable with good reproducibility and prognostic value in clinical practice, which needs further validation.
COVID-19’s immuno-pathology and cardiovascular diseases

The pandemic of COVID-19 in worldwide causes recent millions of morbidity and mortality in all countries and is the most important challenge in the world in recent years. Coronavirus is a single-stranded RNA virus and infection with COVID-19 leads to acute respiratory distress syndrome, lung inflammation, cytokine storm, and death. The other complications include endothelial dysfunction, activation of coagulation, thromboembolic events, and vascular disease. Cardiovascular complications such as myocardial and stroke ischemia, pulmonary thromboembolism, systemic arterial, and deep vein thrombosis were reported. In this review, we presented immuno-pathological mechanisms and the effects of COVID-19 on the cardiovascular system, heart, vessels, coagulation system, and molecular glance of immuno-inflammation to the COVID-19’s pathology on the cardiovascular system.
Mapping Circulation in the Kuroshio Extension with an Array of Current and Pressure Recording Inverted Echo Sounders

Abstract The Kuroshio Extension System Study (KESS) aimed to quantify processes governing the variability of and the interaction between the Kuroshio Extension and the recirculation gyre. To meet this goal, a suite of instrumentation, including 43 inverted echo sounders equipped with bottom pressure gauges and current meters [current and pressure recording inverted echo sounders (CPIES)], was deployed. The array was centered on the first quasi-stationary meander crest and trough east of Japan, which is also the region of highest eddy kinetic energy. KESS was the first experiment to deploy a large quantity of these new CPIES instruments, and it was unique in that the instruments were deployed in water depths (5300–6400 m) close to their limit of operation. A comprehensive narrative of the methodology to produce mesoscale-resolving four-dimensional circulation fields of temperature, specific volume anomaly, and velocity from the KESS CPIES array is provided. In addition, an improved technique for removing p.
An Architectural Technical Debt Index Based on Machine Learning and Architectural Smells

A key aspect of technical debt (TD) management is the ability to measure the amount of principal accumulated in a system. The current literature contains an array of approaches to estimate TD principal, however, only a few of them focus specifically on architectural TD, but none of them satisfies all three of the following criteria: being fully automated, freely available, and thoroughly validated. Moreover, a recent study has shown that many of the current approaches suffer from certain shortcomings, such as relying on hand-picked thresholds. In this article, we propose a novel approach to estimate architectural technical debt principal based on machine learning and architectural smells to address such shortcomings. Our approach can estimate the amount of technical debt principal generated by a single architectural smell instance. To do so, we adopt novel techniques from Information Retrieval to train a learning-to-rank machine learning model (more specifically, a gradient boosting machine) that estimates the severity of an architectural smell and ensure the transparency of the predictions. Then, for each instance, we statically analyse the source code to calculate the exact number of lines of code creating the smell. Finally, we combine these two values to calculate the technical debt principal. To validate the approach, we conducted a case study and interviewed 16 practitioners, from both open source and industry, and asked them about their opinions on the TD principal estimations for several smells detected in their projects. The results show that for 71% of instances, practitioners agreed that the estimations provided were representative of the effort necessary to refactor the smell.
Density functional modeling of the binding energies between aluminosilicate oligomers and different metal cations

Interactions between negatively charged aluminosilicate species and positively charged metal cations are critical to many important engineering processes and applications, including sustainable cements and aluminosilicate glasses. In an effort to probe these interactions, here we have calculated the pair-wise interaction energies (i.e., binding energies) between aluminosilicate dimer/trimer and 17 different metal cations Mn+ (Mn+ = Li+, Na+, K+, Cu+, Cu2+, Co2+, Zn2+, Ni2+, Mg2+, Ca2+, Ti2+, Fe2+, Fe3+, Co3+, Cr3+, Ti4+ and Cr6+) using a density functional theory (DFT) approach. Analysis of the DFT-optimized structural representations for the clusters (dimer/trimer + Mn+) shows that their structural attributes (e.g., interatomic distances) are generally consistent with literature observations on aluminosilicate glasses. The DFT-derived binding energies are seen to vary considerably depending on the type of cations (i.e., charge and ionic radii) and aluminosilicate species (i.e., dimer or trimer). A survey of the literature reveals that the difference in the calculated binding energies between different Mn+ can be used to explain many literature observations associated with the impact of metal cations on materials properties (e.g., glass corrosion, mineral dissolution, and ionic transport). Analysis of all the DFT-derived binding energies reveals that the correlation between these energy values and the ionic potential and field strength of the metal cations are well captured by 2nd order polynomial functions (R 2 values of 0.99–1.00 are achieved for regressions). Given that the ionic potential and field strength of a given metal cation can be readily estimated using well-tabulated ionic radii available in the literature, these simple polynomial functions would enable rapid estimation of the binding energies of a much wider range of cations with the aluminosilicate dimer/trimer, providing guidance on the design and optimization of sustainable cements and aluminosilicate glasses and their associated applications. Finally, the limitations associated with using these simple model systems to model complex interactions are also discussed.