Miracle-dz/UniFAR-FTUs huggingface dataset:
Bacterial cytological profiling reveals interactions between jumbo phage φKZ infection and cell wall active antibiotics in Pseudomonas aeruginosa

The emergence of antibiotic resistance in bacteria has led to the investigation of alternative treatments, such as phage therapy. In this study, we examined the interactions between the nucleus-forming jumbo phage ФKZ and antibiotic treatment against Pseudomonas aeruginosa. Using the fluorescence microscopy technique of bacterial cytological profiling, we identified mechanism-of-action-specific interactions between antibiotics that target different biosynthetic pathways and ФKZ infection. We found that certain classes of antibiotics strongly inhibited phage replication, while others had no effect or only mildly affected progression through the lytic cycle. Antibiotics that caused an increase in host cell length, such as the cell wall active antibiotic ceftazidime, prevented proper centering of the ФKZ nucleus via the PhuZ spindle at midcell, leading us to hypothesize that the kinetic parameters of the PhuZ spindle evolved to match the average length of the host cell. To test this, we developed a computational model explaining how the dynamic properties of the PhuZ spindle contribute to phage nucleus centering and why some antibiotics affect nucleus positioning while others do not. These findings provide an understanding of the molecular mechanisms underlying the interactions between antibiotics and jumbo phage replication.
Downregulation of VEGFR2 signaling by cedrol abrogates VEGF‑driven angiogenesis and proliferation of glioblastoma cells through AKT/P70S6K and MAPK/ERK1/2 pathways

Cedrol is a sesquiterpene alcohol isolated from Cedrus atlantica, which has been traditionally used in aromatherapy and has anticancer, antibacterial and antihyperalgesic effects. One characteristic of glioblastoma (GB) is the overexpression of vascular endothelial growth factor (VEGF), which induces a high degree of angiogenesis. Although previous studies have reported that cedrol inhibits GB growth by inducing DNA damage, cell cycle arrest and apoptosis, its role in angiogenesis remains unclear. The aim of the present study was to investigate the effects of cedrol on VEGF-induced angiogenesis of human umbilical vein endothelial cells (HUVECs). HUVECs were treated with 0–112 µM cedrol and 20 ng/ml VEGF for 0–24 h, and then anti-angiogenic activation of cedrol was determined by MTT assay, wound healing assay, Boyden chamber assay, tube formation assay, semi-quantitative reverse transcription-PCR and western blotting. These results demonstrated that cedrol treatment inhibited VEGF-induced cell proliferation, migration and invasion in HUVECs. Furthermore, cedrol prevented VEGF and DBTRG-05MG GB cells from inducing capillary-like tube formation in HUVECs and decreased the number of branch points formed. Moreover, cedrol downregulated the phosphorylation of VEGF receptor 2 (VEGFR2) and the expression levels of its downstream mediators AKT, ERK, VCAM-1, ICAM-1 and MMP-9 in HUVECs and DBTRG-05MG cells. Taken together, these results demonstrated that cedrol exerts anti-angiogenic effects by blocking VEGFR2 signaling, and thus could be developed into health products or therapeutic agents for the prevention or treatment of cancer and angiogenesis-related diseases in the future.
The influences of surface effect and elastic strain energy on structure and mechanical properties of dislocations in several diamond- and sphalerite-structured materials

The fundamental properties of dislocations in diamond-structured Si and sphalerite-structured GaAs, InP and CdTe are investigated based on lattice theory of dislocation, hoping to provide some theoretical references in improving the properties of related materials. The influences of the surface effect(SE) and elastic strain energy on the structure and mechanical property of dislocation are discussed systematically. After considering the SE, the core width of dislocation becomes wider due to the elastic interaction between atoms becomes stronger. Compared to glide partial dislocation, the correction of SE to shuffle dislocation is more obvious. Both the SE and the elastic strain energy affect the energy barrier and Peierls stress of dislocation. The influence of SE on energy barrier and Peierls stress mainly results from the misfit energy and elastic strain energy become lower when the core of dislocation becomes wider. While the influence of elastic strain energy on energy barrier and Peierls stress mainly results from the cancellation between misfit energy and elastic strain energy for they possess comparable amplitudes but opposite phases. In addition, it is deduced that for the studied crystals, the shuffle dislocations control the deformation at medium and low temperatures, while glide partial dislocations are responsible for high temperature plasticity.
Infektiologie in der stationären Versorgung in Deutschland: Positionspapier der Deutschen Gesellschaft für Infektiologie (DGI)

Spezifische infektiologische Kompetenz verbessert die stationäre Versorgung von Patienten mit Infektionskrankrankheiten. Mit der neuen Facharztbezeichnung Innere Medizin und Infektiologie wird diese Expertise auch in Deutschland zugänglich. Die strukturelle Einbindung der Infektiologie und die Definition einer Leistungsgruppe in Kliniken der Level 2 und 3 werden dargestellt.
A Rare Case of Antinuclear Antibody (ANA)-Negative Lupus Nephritis

Because most patients with lupus nephritis have a positive antinuclear antibody (ANA), ANA-negative lupus nephritis is a rare complication of systemic lupus erythematosus (SLE). In the 2019 European Alliance of Associations for Rheumatology/American College of Rheumatology (EULAR/ACR) classification criteria for SLE, a negative ANA precludes further work-up of SLE. The following case discusses a patient with multiple negative ANA titers but was diagnosed with SLE based on the findings of the kidney biopsy showing lupus nephritis. Though ANA was negative, anti-double-stranded DNA (anti-dsDNA) and anti-Sjogren's syndrome-A (anti-SS-A) antibodies were high. This case highlights the nuances of SLE and further illustrates the challenges in making a diagnosis of SLE when serology alone is relied on for screening.
Elder fish means more microplastics? Alaska pollock microplastic story in the Bering Sea

Marine microplastics are an increasingly big concern. We analyze the occurrence of microplastics in Alaska pollock (Gadus chalcogrammus) across 2+ to 12+ ages sampled from the Bering Sea. Results show that 85% of the fish have ingested microplastics and elder fish ingest more with over a third of microplastics in the 100- to 500-micrometer size range, indicating the prevalence of microplastics in Alaska pollock distributed in the Bering Sea. A positive linear relationship is obtained between fish age and microplastic size. Meanwhile, the number of polymer types increases in elder fish. The link between microplastic characteristics in Alaska pollock and the surrounding seawater suggests an extended spatial impact of microplastics. The impact of age-related microplastic ingestion on the population quality of Alaska pollock is still unknown. Therefore, we need to further investigate the potential impact of microplastics on marine organisms and the marine ecosystem, taking age as an important factor.
A Brief Measure of Fidelity for Mindfulness Programs: Development and Evaluation of the Concise Fidelity for Mindfulness-Based Interventions Tool

Background Mindfulness research and clinical programs are widespread, and it is important that mindfulness-based interventions are delivered with fidelity, or as intended, across settings. The MBI:TAC is a comprehensive system for assessing teacher competence, yet it can be complex to implement. A standardized, simple fidelity/engagement tool to address treatment delivery is needed. Objective We describe the development, evaluation, and outcomes of a brief, practical tool for assessing fidelity and engagement in online mindfulness-based programs. The tool contains questions about session elements such as meditation guidance and group discussion, and questions about participant engagement and technology-based barriers to engagement. Methods The fidelity rating tool was developed and tested in OPTIMUM, Optimizing Pain Treatment in Medical settings Using Mindfulness. The OPTIMUM study is a 3-site pragmatic randomized trial of group medical visits and adapted mindfulness-based stress reduction for primary care patients with chronic low back pain, delivered online. Two trained study personnel independently rated 26 recorded OPTIMUM sessions to determine inter-rater reliability of the Concise Fidelity for Mindfulness-Based Interventions (CoFi-MBI) tool. Trained raters also completed the CoFi-MBI for 105 sessions. Raters provided qualitative data via optional open text fields within the tool. Results Inter-rater agreement was 77-100% for presence of key session components, and 69-88% for Likert ratings of participant engagement and challenges related to technology, with discrepancies only occurring within 2 categories: ‘very much’ and ‘quite a bit’. Key session components occurred as intended in 94-100% of the 105 sessions, and participant engagement was rated as ‘very much’ or ‘quite a bit’ in 95% of the sessions. Qualitative analysis of rater comments revealed themes related to engagement challenges and technology failures. Conclusion The CoFi-MBI provides a practical way to assess basic adherence to online delivery of mindfulness session elements, participant engagement, and extent of technology obstacles. Optional text can guide strategies to improve engagement and reduce technology barriers.
Association between fall-related serious injury and activity during fall in an acute care hospital

Objectives Few studies have evaluated the mechanism of serious injury in acute hospitalization. Thus, the association between fall-related serious injury and activity during falls in acute care hospital remains unclear. Herein, we investigated the relationship between serious injury caused by fall and activity at the time of the fall in an acute care hospital. Methods This retrospective cohort study was conducted at Asa Citizens Hospital. All inpatients aged 65 years and older were eligible for the study, which was conducted from April 1, 2021, through March 31, 2022. The magnitude of the association between injury severity and activity during the fall was quantified using odds ratio. Results Among the 318 patients with reported falls, 268 (84.3%) had no related injury, 40 (12.6%) experienced minor injury, 3 (0.9%) experienced moderate injury, 7 (2.2%) experienced major injury. Moderate or major injuries caused by a fall was associated with the activity during the fall (odds ratio: 5.20; confidence intervals: 1.43–18.9, p = 0.013). Conclusion This study recognizes that falling during ambulation caused moderate or major injuries in an acute care hospital. Our study suggests that falls while ambulating in an acute care hospital were associated not only with fractures, but also with lacerations requiring sutures and brain injuries. Among the patients with moderate or major injuries, more falls occurred outside the patient’s bedroom as compared with patients with minor or no injuries. Therefore, it is important to prevent moderate or major injuries related to falls that occur while the patient is walking outside their bedroom in an acute care hospital.
Can portable glucose and lactate meters be a useful tool in quantifying stress of juvenile Chinook salmon?

Abstract Blood plasma analyses can provide researchers, aquaculture facilities and fisheries managers with valuable insights into the physiological state and welfare of fish. For example, glucose and lactate are part of the secondary stress response system, and elevated concentrations are indicators of stress. However, analysing blood plasma in the field can be logistically difficult and typically involves sample storage and transport to quantify concentrations in a laboratory setting. Portable glucose and lactate meters offer an alternative to laboratory assays and have shown to be relatively accurate in fish, but these tools have only been validated for a few fish species. The objective of this study was to investigate if portable meters could be reliably used in Chinook salmon (Oncorhynchus tshawytscha). As part of a larger stress response study, juvenile Chinook salmon (157 ± 17 mm fork length [mean ± standard deviation; SD]) were exposed to stress-inducing treatments and sampled for blood. Laboratory reference glucose concentrations (milligrams per deciliter; mg/dl; n = 70) were positively correlated with the Accu-Check Aviva meter (Roche Diagnostics, Indianapolis, IN) measurements (R2 = 0.79), although glucose values were 1.21 ± 0.21 (mean ± SD) times higher in the laboratory than with the portable meter. Lactate concentrations (milliMolar; mM; n = 52) of the laboratory reference were also positively correlated (R2 = 0.76) with the Lactate Plus meter (Nova Biomedical, Waltham, MA) and were 2.55 ± 0.50 times higher than portable meter. Our results indicate both meters could be used to measure relative glucose and lactate concentrations in Chinook salmon and provide fisheries professionals with a valuable tool, particularly in remote field settings.
Five-year follow-up after stereotactic body radiotherapy for medically inoperable early-stage non-small cell lung cancer: a multicenter study

Background Stereotactic body radiotherapy (SBRT) has proven to provide high rates of tumor control for patients with early-stage non-small cell lung cancer (NSCLC). We are reporting a multicenter experience of long-term clinical outcomes and adverse effect profiles of patients with medically inoperable early-stage NSCLC treated with SBRT. Methods A total of 145 early-stage NSCLC patients underwent SBRT at the Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Shandong Cancer Hospital and Institute, and Shanghai Pulmonary Hospital between October 2012 and March 2019. Four-dimensional computed tomography (4D-CT) simulation was used for all patients. All received a biologically effective dose (BED; α/β=10) of 96–120 Gy with the prescribed isodose line covering >95% of the planning target volume (PTV). Survival was analyzed by the Kaplan-Meier method. Survival was estimated using the Kaplan-Meier method. Results The median tumor diameter was 2.2 (range, 0.5–5.2) cm. The median follow-up was of 65.6 months. Thirty-five patients (24.1%) developed disease recurrence. The rates of local, regional, and distant disease recurrence were, respectively, 5.1%, 7.4%, and 13.2% at 3 years; and 9.6%, 9.8%, and 15.8% at 5 years. Progression-free survival (PFS) rates at 3 and 5 years were 69.2% and 60.5% respectively; the overall survival (OS) rates were 78.1% and 70.1%, respectively. Five patients (3.4%) experienced grade 3 treatment-related adverse events (AEs). No patient experienced grade 4 or 5 toxicity. Conclusions From our retrospective analysis with long-term follow-up in Chinese population, SBRT achieved high rate of local control (LC) and low toxicity in patients with early-stage NSCLC. This study offered robust long-term outcome data of SBRT in the Chinese population, which was very rarely reported in China before.
DPAGT1‐CDG: Recurrent fetal death

Congenital disorders of glycosylation (CDG) are a series of relatively uncommon genetic disorders, and variants in the dolichyl‐phosphate N‐acetylglucosamine‐1‐phosphotransferase (DPAGT1) gene can cause DPAGT1‐CDG, which is characterized by multisystem abnormalities: failure to thrive, psychomotor retardation, seizures, etc.
BIAS SKALA DATA DALAM PENDUGAAN KOEFISIEN KORELASI

Penelitian ini ditujukan untuk mengetahui besar dan perilaku bias dalam pendugaan koefisien korelasi dua variabel berskala ordinal (kategori) dengan berbagai jumlah kategori dan sample. Informasi ini sangat penting mengingat sebagian besar penelitian sosial yang berbasis survey lazim mengumpulkan data berskala ordinal dengan berbagai jumlah kategori. Ini dilakukan dengan alasan kemudahan dalam pengukuran karakteristik objek amatan. Masalah muncul manakala data dianalisis dengan pendekatan parametrik yang mensyaratkan datanya berskala ratio atau kontinu, akibatnya timbul bias dugaan. Korelasi Pearson digunakan sebagai basis analisis untuk mengetahui besar bias dugaan yang dihitung dengan kaidah Mean Absolut Percentage Error (MAPE). Disimpulkan bahwa, semakin banyak jumlah kategori maupun sample data, maka besarmya bias akan semakin mengecil. Penurunan bias akan semakin cepat bila jumlah kategori semakin membesar. Manfaat dari hasil ini adalah, data dengan 5 kategori merupakan pilihan ideal untuk digunakan dalam mengukur karakteristik amatan berskala ordinal, karena besarnya bias dugaan yang timbul masih dapat ditolerir. Dalam penerapannya 5 pilihan jawaban masih relatif mudah bagi responden dalam memilihnya.
Diagnostic Value of Inflammation-Related Indicators in Distinguishing Early Colon Cancer and Adenomatous Polyps

Background There are few clinical symptoms in early colorectal cancer, so it is necessary to find a simple and economical tumor detection index for auxiliary diagnosis. This study aims to explore the diagnostic value of preoperative inflammation-related indicators, such as neutrophil, lymphocyte, platelet count, platelet to lymphocyte ratio (PLA), neutrophil to lymphocyte ratio (NLR), and systemic immune-inflammation index (SII), for early colorectal cancer, and determine whether inflammation-related indicators can provide more accurate diagnostic judgment for patients. Methods This study was a retrospective study. Patients who were first diagnosed with colorectal cancer or colorectal adenomatous polyp at Beijing Friendship Hospital from October 2016 to October 2017 were retrospectively collected. According to inclusion and exclusion criteria, a total of 342 patients were included, including 216 patients with colorectal cancer and 126 patients with colorectal adenomatous polyp. Fasting venous blood and other clinical features were collected to compare the differences between colorectal cancer and colorectal adenoma. Results There were statistically significant differences in age, carcinoembryonic antigen, albumin, hemoglobin, mean platelet volume, lymphocyte, monocyte, NLR, PLA, SII, and mean platelet volume to platelet count ratio between colorectal cancer group and colorectal adenoma group (P < .05), and a Nomogram model was established. Using inflammatory markers to differentiate colorectal and colorectal polyps produced greater AUC than using tumor markers alone (.846 vs .695). Conclusion Inflammation-related indicators, such as lymphocyte, monocyte, and mean platelet volume, may serve as potential indicators to assist in the diagnosis of early colorectal cancer.
Bayesian Computation for High-Dimensional Continuous & Sparse Count Data

Bayesian Computation for High-Dimensional Continuous & Sparse Count Data by Ye Wang Department of Statistical Science Duke University Date: Approved: David B. Dunson, Supervisor Colin Rundel Rebecca C. Steorts Rong Ge An abstract of a dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Department of Statistical Science in the Graduate School of Duke University 2018 Copyright c © 2018 by Ye Wang All rights reserved except the rights granted by the Creative Commons Attribution-Noncommercial Licence
Simulations et méthodes de Monte Carlo

Les methodes de Monte Carlo sont indispensables dans des domaines aussi varies que la finance, les telecommunications, la biologie ou encore les sciences sociales. Elles permettent de resoudre des problemes centres sur un calcul a l’aide du hasard. Cet article effectue une presentation de ces methodes, au travers dans un premier temps des principes de base (calcul de sommes et integrales, simulation a evenements discrets, etc.). Dans un second temps, une analyse de la precision de ces methodes est proposee : elle aborde notamment les intervalles de confiance, les replications independantes, les estimations par blocs, etc.
A two-phase method for control constrained elliptic optimal control problem

Elliptic optimal control problems with pointwise box constraints on the control (EOCP) are considered. To solve EOCP, the primal-dual active set (PDAS) method, which is a special semismooth Newton (SSN) method, used to be a priority in consideration of their locally superlinear convergence. However, in general solving the Newton equations is expensive, especially when the discretization is in a fine level. Motivated by the success of applying alternating direction method of multipliers (ADMM) for solving large scale convex minimization problem in finite dimension, it is reasonable to extend the ADMM to solve EOCP. To numerically solve EOCP, the finite element (FE) method is used for discretization. Then, a two-phase strategy is presented to solve discretized problems. In Phase-I, an inexact heterogeneous ADMM (ihADMM) is proposed with the aim of solving discretized problems to moderate accuracy or using it to generate a reasonably good initial point to warm-start Phase-II. Different from the classical ADMM, our ihADMM adopts two different weighted inner product to define the augmented Lagrangian function in two subproblems, respectively. Benefiting from such different weighted techniques, two subproblems of ihADMM can be efficiently implemented. Furthermore, theoretical results on the global convergence as well as the iteration complexity results $o(1/k)$ for ihADMM are given. In Phase-II, in order to obtain more accurate solution, the primal-dual active set (PDAS) method is used as a postprocessor of the ihADMM. Numerical results show that the ihADMM and the two-phase strategy are highly efficient.
UV lidar measurement of stratospheric aerosol layer observational results at Fukuoka (33.6°N) during October 1982 through May 1983

After the volcanic eruptions of Mt. El Chichon in Mexico, increase of stratospheric aerosols has been measured by a UV lidar at a wavelength of 340.5nm at Fukuoka (33.65*N, 130.35*E) since October 1982. The altitude of the maximum backscattering ratio (Rmax* 3.5) was 24km in October 1982, and it decreased to 20km in January 1983. The value of Rmax-1 decreased by a factor of 2.4, but large changes of aerosol backscattering coefficient integrated over an altitude range of 15-30km were not recognized during this period. A brief consideration is given on this lowering of the aerosol layer.
Online multimodal dictionary learning through Tucker decomposition

We propose a new online approach for multimodal dictionary learning. The method developed in this work addresses the great challenges posed by the computational resource constraints in dynamic environment when dealing with large scale tensor sequences. Given a sequence of tensors, i.e. a set composed of equal-size tensors, the approach proposed in this paper allows to infer a basis of latent factors that generate these tensors by sequentially processing a small number of data samples instead of using the whole sequence at once. Our technique is based on block coordinate descent, gradient descent and recursive computations of the gradient. A theoretical result is provided and numerical experiments on both real and synthetic data sets are performed.