Miracle-dz/UniFAR-FTUs huggingface dataset:
Miniaturized variable-focus objective employing a liquid-filled tunable aspherical lens

Abstract. We discuss the design, realization, and characterization of a miniaturized focus-tunable camera objective featuring a gravity-neutral, liquid-tunable aspherical lens and compare its performance to an equivalent system optimized for a conventional tunable lens. In addition to the innovative component, the objective design features three fixed elements and an aperture, which are all assembled to form a 5×5×13 mm system. With an image sensor size of 3 mm, the objective provides a viewing angle of 40 deg. By tuning the lens in its gravity-neutral range, the object distance can be shifted from 5 mm to infinity, with image-side cutoff frequency remaining above 84 lp/mm across the entire range. Through ray-tracing simulations and experimental results, we demonstrate that for optical trains of identical complexity, tunable aspherical lenses provide substantially better imaging quality over the object distance range of interest, compared to conventional, spherical tunable lenses.
Scorpionfish BPI is highly active against multiple drug-resistant Pseudomonas aeruginosa isolates from people with cystic fibrosis

Chronic pulmonary infection is a hallmark of cystic fibrosis (CF) and requires continuous antibiotic treatment. In this context, Pseudomonas aeruginosa (Pa) is of special concern since colonizing strains frequently acquire multiple drug resistance (MDR). Bactericidal/permeability-increasing protein (BPI) is a neutrophil-derived, endogenous protein with high bactericidal potency against Gram-negative bacteria. However, a significant range of people with CF (PwCF) produce anti-neutrophil cytoplasmic antibodies against BPI (BPI-ANCA), thereby neutralizing its bactericidal function. In accordance with literature, we describe that 51.0% of a total of 39 PwCF expressed BPI-ANCA. Importantly, an orthologous protein to human BPI (huBPI) derived from the scorpionfish Sebastes schlegelii (scoBPI) completely escaped recognition by these autoantibodies. Moreover, scoBPI exhibited high anti-inflammatory potency towards Pa LPS and was bactericidal against MDR Pa derived from PwCF at nanomolar concentrations. In conclusion, our results highlight the potential of highly active orthologous proteins of huBPI in treatment of MDR Pa infections, especially in the presence of BPI-ANCA.
A Machine Learning Framework Identifies Plastid-Encoded Proteins Harboring C3 and C4 Distinguishing Sequence Information

Abstract C4 photosynthesis is known to have at least 61 independent origins across plant lineages making it one of the most notable examples of convergent evolution. Of the >60 independent origins, a predicted 22–24 origins, encompassing greater than 50% of all known C4 species, exist within the Panicoideae, Arundinoideae, Chloridoideae, Micrairoideae, Aristidoideae, and Danthonioideae (PACMAD) clade of the Poaceae family. This clade is therefore primed with species ideal for the study of genomic changes associated with the acquisition of the C4 photosynthetic trait. In this study, we take advantage of the growing availability of sequenced plastid genomes and employ a machine learning (ML) approach to screen for plastid genes harboring C3 and C4 distinguishing information in PACMAD species. We demonstrate that certain plastid-encoded protein sequences possess distinguishing and informative sequence information that allows them to train accurate ML C3/C4 classification models. Our RbcL-trained model, for example, informs a C3/C4 classifier with greater than 99% accuracy. Accurate prediction of photosynthetic type from individual sequences suggests biologically relevant, and potentially differing roles of these sequence products in C3 versus C4 metabolism. With this ML framework, we have identified several key sequences and sites that are most predictive of C3/C4 status, including RbcL, subunits of the NAD(P)H dehydrogenase complex, and specific residues within, further highlighting their potential significance in the evolution and/or maintenance of C4 photosynthetic machinery. This general approach can be applied to uncover intricate associations between other similar genotype-phenotype relationships.
The prevalence of burnout among pulmonologists or respiratory therapists pre- and post-COVID-19: a systematic review and meta-analysis

Abstract Objectives The coronavirus disease-19 (COVID-19) increased the already heavy workload in the pulmonary and respiratory departments, which therefore possibly increased the prevalence of burnout among pulmonologists or respiratory therapists. We aimed to compare the differences in burnout among pulmonologists or respiratory therapists pre- and post-COVID-19 by doing a systematic review with meta-analysis. Methods We searched pulmonologist, or pulmonary, or respiratory, and burnout up to 29 January 2023 in six databases. We included studies investigating pulmonologists or respiratory therapists and reporting the prevalence of burnout among them. The risk of bias was assessed by a tool for prevalence studies. The overall prevalence of burnout was pooled. Results A total of 2859 records were identified and 16 studies were included in the final analysis. The included studies reported 3610 responding individuals and 2336 burnouts. The pooled prevalence of burnout was 61.7% (95% confidence interval (CI), 48.6–73.2%; I2 = 96.3%). The pooled prevalence of burnout during COVID-19 was significantly higher than it was prior to the outbreak (68.4% vs. 41.6%, p = .01). The result of the meta-regression revealed that COVID-19 coverage was significantly associated with the prevalence of burnout (p = .04). Conclusions Burnout was widely prevalent among pulmonologists or respiratory therapists and increasingly perceived during COVID-19. Therefore, interventions were needed to reduce burnout in this specialty. KEY MESSASGES The coronavirus disease-19 increased the already heavy workload in the pulmonary and respiratory departments. Burnout was widely prevalent among pulmonologists or respiratory therapists and increasingly perceived during COVID-19.
A change-point model for survival data with long-term survivors

Change-point hazard models have been extensively investigated by many authors, but the literature on change-point problems with survival data subject to censoring is rather small. In an earlier example provided by Matthews and Farewell (1982), a set of nonlymphoblastic leukemia data were fitted by using a change-point model. But for that data set, the Kaplan-Meier estimator of the distribution function levels off well below 1, which indicates the presence of “longterm survivors” in the data. In this paper, we propose a new change-point model for survival data that accounts for long-term survivors. Estimation methods for the proposed model are investigated, and large-sample properties of the estimators are established. A simulation study is carried out to evaluate the performance of the estimating methods. As an application, the nonlymphoblastic leukemia data are re-analyzed using the new model.
Generation of field‐aligned current (FAC) and convection through the formation of pressure regimes: Correction for the concept of Dungey's convection

In this paper, we try to elucidate the generation mechanism of the field‐aligned current (FAC) and coexisting convection. From the comparison between the theoretical prediction and the state of numerical solution from the high‐resolution global simulation, we obtain the following conclusions about the distribution of dynamo, the magnetic field structure along the flow path that diverges Poynting flux, and energy conversion promoting the generation of electromagnetic energy. The dynamo for the region 1 FAC, which is in the high‐latitude‐side cusp‐mantle region, has a structure in which magnetic field is compressed along the convection path by the slow mode motion. The dynamo for the region 2 FAC is in the ring current region at the inner edge of the plasma sheet, and has a structure in which magnetic field is curved outward along the convection path. Under these structures, electromagnetic energy is generated from the work done by pressure gradient force, in both dynamos for the region 1 and region 2 FACs. In these generation processes of the FACs, the excitation of convection and the formation of pressure regimes occur as interdependent processes. This structure leads to a modification in the way of understanding the Dungey's convection. Generation of the FAC through the formation of pressure regimes is essential even for the case of substorm onset.
Comparative expression of TRPS1, GATA3, SOX10, mammaglobin, and GCDFP‐15 in effusion specimens with breast carcinoma

Traditional immunohistochemistry (IHC) for breast carcinomas has shown low detection rates of metastatic breast carcinoma (MBC) in effusions. Although GATA3 has enhanced diagnostic accuracy in this realm, its limited utility in detecting triple‐negative breast carcinoma (TNBC) has been highlighted. TRPS1 has been introduced as a potentially sensitive and specific marker in detecting MBC on histologic samples. We investigate the utility of TRPS1 as a marker for MBC in effusion specimens and compare its performance to SOX10, GATA3, mammaglobin (MG), and GCDFP‐15.
Loss of aquaporin-1 expression is associated with worse clinical outcomes in clear cell renal cell carcinoma: an immunohistochemical study

Background Aquaporin (AQP) expression has been investigated in various malignant neoplasms, and the overexpression of AQP is related to poor prognosis in some malignancies. However, the expression of AQP protein in clear cell renal cell carcinoma (ccRCC) has not been extensively investigated by immunohistochemistry with large sample size. Methods We evaluated the AQP expression in 827 ccRCC with immunohistochemical staining in tissue microarray blocks and classified the cases into two categories, high and low expression. Results High expression of aquaporin-1 (AQP1) was found in 320 cases (38.7%), but aquaporin-3 was not expressed in ccRCC. High AQP1 expression was significantly related to younger age, low TNM stage, low World Health Organization/International Society of Urologic Pathology nuclear grade, and absence of distant metastasis. Furthermore, high AQP1 expression was also significantly associated with longer overall survival (OS; p<.001) and progression-specific survival (PFS; p<.001) and was an independent predictor of OS and PFS in ccRCC. Conclusions Our study revealed the prognostic significance of AQP1 protein expression in ccRCC. These findings could be applied to predict the prognosis of ccRCC.
Exponential synchronisation of complex networks with delays and perturbations via impulsive and adaptive control

This study considers exponential synchronisation of complex networks (CNs) with time-varying delays and non-identical perturbations by using hybrid control schemes. Quantised adaptive control and quantised impulsive control are combined, and 1-norm-based analytical techniques are wielded. By using hybrid quantised controller, applying 1-norm-based analytical methods, and designing new Lyapunov function, sufficient conditions on exponential synchronisation are derived. These synchronisation criteria can guarantee that the considered CNs synchronise with given goal dynamics. Compared with some existing results, the authors results are more general and practical. Numerical simulations are exploited to validate the theoretical results.
CircTLK1 alleviates oxygen-glucose deprivation/reperfusion induced apoptosis in HK-2 cells through miR-136-5p/Bcl2 signal axis

Abstract The biological functions of circTLK1 in acute kidney injury (AKI), which mainly results from renal ischemia-reperfusion (IR), remain largely unknown. HK-2 cell treatment with oxygen and glucose deprivation, reoxygenation, and glucose (OGD/R) was used to simulate an AKI model that was mainly caused by renal IR. Then, the circTLK1 expression level in HK-2 cells treated with OGD/R was assessed by quantitative reverse transcription polymerase chain reaction (RT-qPCR). Functional experiments were performed with circTLK1 knockdown of HK-2 cells via Cell Counting Kit-8 (CCK8), flow cytometry (FCM), RT-qPCR, and western blotting. The circTLK1-miRNAs-mRNAs network was constructed following the ceRNA mechanism and visualized by Cytoscape software to investigate the mechanism of circTLK1 in AKI. RT-qPCR was performed to verify the relationship between circTLK1, miR-136-5p, and Bcl2. The level of miR-136-5p was knocked down to ensure its function in OGD/R-triggered apoptosis through experiments, including CCK8, FCM, RT-qPCR, and western blotting. CircTLK1 was downregulated in HK-2 cells subjected to OGD/R treatment and in mouse kidney tissues after renal IR, but the expression of miR-136-5p was the opposite. Interference with circTLK1 expression accelerated HK-2 cell apoptosis, which was overturned by miR-136-5p inhibitors. CircTLK1 targets miR-136-5p to upregulate Bcl2 expression and attenuate apoptosis in HK-2 cells. These data revealed the possible role of circTLK1 as a new biomarker for diagnosis as well as a target in AKI through the miR-136-5p/Bcl2 signaling axis.
A systematic review to summarize treatment patterns, guidelines, and characteristics of patients with renal cell carcinoma in the Asia-Pacific region

ABSTRACT Introduction This systematic review evaluated treatment patterns and guidelines in advanced/metastatic and adjuvant renal cell carcinoma (RCC) in the Asia-Pacific region. Areas covered Embase, PubMed, and congresses were searched for observational studies and guidelines in accordance with PRISMA. Records published during 2016–2021 (2019–2021 for congresses) were included. Expert opinion Nine studies and three guidelines were identified overall. In advanced/metastatic RCC, the most common treatments were tyrosine kinase inhibitors (TKIs) (notably sunitinib: 33–100%) for first-line, and everolimus (13–85%) or axitinib (2–89%) for second-line therapy. In adjuvant RCC, sunitinib was most used (54%), followed by mammalian target of rapamycin inhibitors (mTORis, 27%) with immunotherapy being less common (16%). The guidelines provided varying recommendations for advanced/metastatic RCC. For first-line in advanced/metastatic clear cell RCC (the most common subtype), guidelines recommended mTORis (everolimus for poor-risk patients) (India, 2016); clinical study enrollment for high-risk patients or TKIs for low- to medium-risk patients (China, 2019); or immunotherapy based on survival benefits over sunitinib; dose adjustment was also recommended to manage TKI toxicities (Hong Kong, 2019). The landscape remained more static in the adjuvant setting, but best practice was uncertain. No clear trends were identified in patient characteristics.
Single-center study on clinicopathological and typical molecular pathologic features of metastatic brain tumor

Background The metastatic brain tumor is the most common brain tumor. The aim of this study was to demonstrate the clinicopathological and molecular pathologic features of brain metastases (BM). Methods A total of 269 patients were diagnosed with BM through surgical resection at Seoul St. Mary’s Hospital from January 2010 to March 2020. We reviewed the clinicopathological features and molecular status of primary and metastatic brain tissues using immunohistochemistry and molecular pathology results. Results Among 269 patients, 139 males and 130 females were included. The median age of primary tumor was 58 years (range, 13 to 87 years) and 86 patients (32.0%) had BM at initial presentation. Median BM free interval was 28.0 months (range, 1 to 286 months). The most frequent primary site was lung 46.5% (125/269), and followed by breast 15.6% (42/269), colorectum 10.0% (27/269). Epidermal growth factor receptor (EGFR) mutation was found in 50.8% (32/63) and 58.0% (40/69) of lung primary and BM, respectively. In both breast primary and breast cancer with BM, luminal B was the most frequent subtype at 37.9% (11/29) and 42.9% (18/42), respectively, followed by human epidermal growth factor receptor 2 with 31.0% (9/29) and 33.3% (14/42). Triple-negative was 20.7% (6/29) and 16.7% (7/42), and luminal A was 10.3% (3/29) and 7.1% (3/42) of breast primary and BM, respectively. In colorectal primary and colorectal cancer with BM, KRAS mutation was found in 76.9% (10/13) and 66.7% (2/3), respectively. Conclusions We report the clinicopathological and molecular pathologic features of BM that can provide useful information for understanding the pathogenesis of metastasis and for clinical trials based on the tumor’s molecular pathology.
Correlates of Rates and Treatment Readiness for Depressive Symptoms, Pain, and Fatigue in Hemodialysis Patients: Results from the TĀCcare Study

Key Points Lower neighborhood walkability was associated with higher depressive symptoms and fatigue and younger age with depressive symptoms. Depressive symptoms, pain, and fatigue were frequently reported, often occurred together, and were often not all already treated. Patients with a higher symptom burden and men may be more likely to be ready to seek treatment for depressive symptoms, pain, or fatigue. Background Patients on hemodialysis (HD) often experience clinically significant levels of pain, fatigue, and depressive symptoms. We explored potential sociodemographic differences in symptom burden, current treatment, and readiness to seek treatment for these symptoms in patients screened for the TĀCcare trial. Methods In-center HD patients from Pennsylvania and New Mexico were screened for fatigue (≥5 on 0–10-point Likert scale), pain (Likert scale ≥4), depressive symptoms (≥10 Patient Health Questionnaire-9), and readiness to seek treatment (5–item Stages of Behavior Change questionnaire). Symptom burden and treatment status by sociodemographic factors were evaluated using chi square, Fisher exact tests, and logistic regression models. Results From March 2018 to December 2021, 506 of 896 (57%) patients screened met eligibility criteria and completed the symptom screening (mean age 60±13.9 years, 44% female, 17% Black, 25% American Indian, and 25% Hispanics). Of them, 77% screened positive for ≥1 symptom and 35% of those were receiving treatment for ≥1 of these symptoms. Pain, fatigue, and depressive symptom rates were 52%, 64%, and 24%, respectively. Age younger than 65 years was associated with a higher burden of depressive symptoms, pain, and reporting ≥1 symptom (P<0.05). The percentage of patients ready to seek treatment increased with symptom burden. More men reported readiness to seek treatment (85% versus 68% of women, P<0.001). Among those with symptoms and treatment readiness, income was inversely associated with pain (>$60,000/yr: odds ratio [OR]=0.16, confidence interval [CI]=0.03 to 0.76) and living in less walkable neighborhoods with more depressive symptoms (OR= 5.34, CI=1.19 to 24.05) and fatigue (OR= 5.29, CI=1.38 to 20.33). Conclusions Pain, fatigue, and depressive symptoms often occurred together, and younger age, less neighborhood walkability, and lower income were associated with a higher burden of symptoms in HD patients. Male patients were less likely to be receiving treatment for symptoms. These findings could inform priority HD patient symptom identification and treatment targets.
Growth and characterization of few unit-cell NbN superconducting films on 3C-SiC/Si substrate

Superconducting δ-NbN ultrathin film has become a key element in extremely sensitive detector applications in recent decades because of its excellent electronic properties. We have realized the epitaxial growth of ultrathin δ-NbN films on (100)-oriented 3C-SiC/Si substrates by dc reactive magnetron sputtering at 760 °C with a deposition rate of 0.054 nm s−1. High-resolution transmission electron microscope images confirm the excellent epitaxy of these films. Even with a thickness of 1.3 nm (∼3 unit cells), the δ-NbN film shows a superconducting transition above 8 K. Furthermore, our ultrathin δ-NbN films demonstrate a long Ginzburg–Landau superconducting coherent length ( ξ G L ( 0 ) > 5 nm ) with a critical current density of about 2.2 MA cm−2, and good stability in an ambient environment.
An interchangeable prion-like domain is required for Ty1 retrotransposition

Significance Retrovirus-like retrotransposons help shape the genome evolution of their hosts and replicate within cytoplasmic particles. How their building blocks associate and assemble within the cell is poorly understood. Here, we report a prion-like domain (PrLD) in the budding yeast retrotransposon Ty1 Gag protein that builds virus-like particles. The PrLD has similar sequence properties to prions and disordered protein domains that can drive the formation of assemblies that range from liquid to solid. We demonstrate that the Ty1 PrLD can function as a prion and that certain prion sequences can replace the PrLD and support Ty1 transposition. This interchangeable system is a useful platform to study disordered sequences in living cells.
Insights into the pathological basis of dementia from population‐based neuropathology studies

The epidemiological neuropathology perspective of population and community‐based studies allows unbiased assessment of the prevalence of various pathologies and their relationships to late‐life dementia. In addition, this approach provides complementary insights to conventional case–control studies, which tend to be more representative of a younger clinical cohort. The Cognitive Function and Ageing Study (CFAS) is a longitudinal study of cognitive impairment and frailty in the general United Kingdom population. In this review, we provide an overview of the major findings from CFAS, alongside other studies, which have demonstrated a high prevalence of pathology in the ageing brain, particularly Alzheimer's disease neuropathological change and vascular pathology. Increasing burdens of these pathologies are the major correlates of dementia, especially neurofibrillary tangles, but there is substantial overlap in pathology between those with and without dementia, particularly at intermediate burdens of pathology and also at the oldest ages. Furthermore, additional pathologies such as limbic‐predominant age‐related TDP‐43 encephalopathy, ageing‐related tau astrogliopathy and primary age‐related tauopathies contribute to late‐life dementia. Findings from ageing population‐representative studies have implications for the understanding of dementia pathology in the community. The high prevalence of pathology and variable relationship to dementia status has implications for disease definition and indicate a role for modulating factors on cognitive outcome. The complexity of late‐life dementia, with mixed pathologies, indicates a need for a better understanding of these processes across the life‐course to direct the best research for reducing risk in later life of avoidable clinical dementia syndromes.
Fine Computability of Probability Distribution Functions and Computability of Probability Distributions on the Real Line

We continue our work in [9] on an effective relationship between the sequence of probability distributions and the corresponding sequence of probability distribution functions. In order to deal with discontinuous distribution functions, we define the notion of Fine topology on the whole real line, and show that, when a probability distribution is associated with a Fine continuous distribution function, the computability of the former and the sequential computability of the latter can be effectively mutually translatable under a certain condition. The effectivity of the translations is secured by the treatment of the sequences of the objects in concern. The equivalences of effective convergences will also be proved.