bluuebunny/crossref_metadata_2025 huggingface dataset:
The beneficial effects of commensal E. coli for colon epithelial cell recovery are related with Formyl peptide receptor 2 (Fpr2) in epithelial cells
Authors: Chen Keqiang , McCulloch John , Das Neves Rodrigo , Rodrigues Gisele , Hsieh Wang-Ting , Gong Wanghua , Yoshimura Teizo , Huang Jiaqiang , O’hUigin Colm , Difilippantonio Simone , McCollum Matthew , Jones Georgette , Durum Scott K. , Trinchieri Giorgio , Wang Ji Ming
Published: June 2023

Background

Formyl peptide receptor 2 (Fpr2) plays a crucial role in colon homeostasis and microbiota balance. Commensal E. coli is known to promote the regeneration of damaged colon epithelial cells. The aim of the study was to investigate the connection between E. coli and Fpr2 in the recovery of colon epithelial cells.

Results

The deficiency of Fpr2 was associated with impaired integrity of the colon mucosa and an imbalance of microbiota, characterized by the enrichment of Proteobacteria in the colon. Two serotypes of E. coli, O22:H8 and O91:H21, were identified in the mouse colon through complete genome sequencing. E. coli O22:H8 was found to be prevalent in the gut of mice and exhibited lower virulence compared to O91:H21. Germ-free (GF) mice that were pre-orally inoculated with E. coli O22:H8 showed reduced susceptibility to chemically induced colitis, increased proliferation of epithelial cells, and improved mouse survival. Following infection with E. coli O22:H8, the expression of Fpr2 in colon epithelial cells was upregulated, and the products derived from E. coli O22:H8 induced migration and proliferation of colon epithelial cells through Fpr2. Fpr2 deficiency increased susceptibility to chemically induced colitis, delayed the repair of damaged colon epithelial cells, and heightened inflammatory responses. Additionally, the population of E. coli was observed to increase in the colons of Fpr2−/− mice with colitis.

Conclusion

Commensal E. coli O22:H8 stimulated the upregulation of Fpr2 expression in colon epithelial cells, and the products from E. coli induced migration and proliferation of colon epithelial cells through Fpr2. Fpr2 deficiency led to an increased E. coli population in the colon and delayed recovery of damaged colon epithelial cells in mice with colitis. Therefore, Fpr2 is essential for the effects of commensal E. coli on colon epithelial cell recovery.
Economics of Yak herding in the Kanchenjunga landscape of the Eastern Himalayas
Authors: Rai Rajesh K. , Joshi Srijana , Dorji Tashi , Pant Basant
Published: June 2023

Yak herding is one of the oldest market-based traditions, which is part of an integrated social-ecological system. But, it is at risk of extinction as yak herders are gradually shifting towards alternative occupations. The discontinuation of herding may have several implications such as loss of culture and degradation of the rangeland ecosystem. Though yak herding is not limited to the financial aspect of herding, this is considered a main cause of the discontinuation. Therefore, it is important to understand the economics of yak herding. A benefit–cost analysis of yak herding was carried out based on the interviews with 60 yak herders in the Kanchenjunga landscape, Nepal. The results indicate that yak herding is not financially attractive. High mortality of calves and adults is threatening this occupation, and degrading rangelands are increasing the costs. Yak herding generates substantial amount of social and ecological benefits in terms of preserving culture, maintaining rangeland ecosystems and curbing illegal activities. If these benefits are included, then the benefit–cost ratio and internal rate of return would be 1.32 and 10.44 respectively. Since yak herding generates low direct profits and requires herders to stay in remote areas, there is a high risk of discontinuation of this profession by successive generations of youth. This study suggests to improve rangeland management through prescribed burning and provisioning of health services, particularly in summer pastures and incentivize yak herders for generating positive externalities.
Treatment of critically ill patients with cefiderocol for infections caused by multidrug-resistant pathogens: review of the evidence
Authors: Viale Pierluigi , Sandrock Christian E. , Ramirez Paula , Rossolini Gian Maria , Lodise Thomas P.
Published: June 2023

Appropriate antibiotic treatment for critically ill patients with serious Gram-negative infections in the intensive care unit is crucial to minimize morbidity and mortality. Several new antibiotics have shown in vitro activity against carbapenem-resistant Enterobacterales (CRE) and difficult-to-treat resistant Pseudomonas aeruginosa. Cefiderocol is the first approved siderophore beta-lactam antibiotic with potent activity against multidrug-resistant, carbapenem-resistant, difficult-to-treat or extensively drug-resistant Gram-negative pathogens, which have limited treatment options. The spectrum of activity of cefiderocol includes drug-resistant strains of Acinetobacter baumannii, P. aeruginosa, Stenotrophomonas maltophilia, Achromobacter spp. and Burkholderia spp. and CRE that produce serine- and/or metallo-carbapenemases. Phase 1 studies established that cefiderocol achieves adequate concentration in the epithelial lining fluid in the lung and requires dosing adjustment for renal function, including patients with augmented renal clearance and continuous renal-replacement therapy (CRRT); no clinically significant drug–drug interactions are expected. The non-inferiority of cefiderocol versus high-dose, extended-infusion meropenem in all-cause mortality (ACM) rates at day 14 was demonstrated in the randomized, double-blind APEKS–NP Phase 3 clinical study in patients with nosocomial pneumonia caused by suspected or confirmed Gram-negative bacteria. Furthermore, the efficacy of cefiderocol was investigated in the randomized, open-label, pathogen-focused, descriptive CREDIBLE–CR Phase 3 clinical study in its target patient population with serious carbapenem-resistant Gram-negative infections, including hospitalized patients with nosocomial pneumonia, bloodstream infection/sepsis, or complicated urinary tract infections. However, a numerically greater ACM rate with cefiderocol compared with BAT led to the inclusion of a warning in US and European prescribing information. Cefiderocol susceptibility results obtained with commercial tests should be carefully evaluated due to current issues regarding their accuracy and reliability. Since its approval, real-world evidence in patients with multidrug-resistant and carbapenem-resistant Gram-negative bacterial infections suggests that cefiderocol can be efficacious in certain critically ill patient groups, such as those requiring mechanical ventilation for COVID-19 pneumonia with subsequently acquired Gram-negative bacterial superinfection, and patients with CRRT and/or extracorporeal membrane oxygenation. In this article, we review the microbiological spectrum, pharmacokinetics/pharmacodynamics, efficacy and safety profiles and real-world evidence for cefiderocol, and look at future considerations for its role in the treatment of critically ill patients with challenging Gram-negative bacterial infections.
Efficacy and safety of proxalutamide (GT0918) in severe or critically ill patients with COVID-19: study protocol for a prospective, open-label, single-arm, single-center exploratory trial
Authors: Yang Dawei , Ju Minjie , Wang Hao , Jia Yichen , Wang Xiaodan , Fang Hao , Fan Jia
Published: June 2023

Background

The rapid worldwide spread of COVID-19 has caused a global health challenge with high mortality of severe or critically ill patients with COVID-19. To date, there is no specific efficient therapeutics for severe or critically ill patients with COVID-19. It has been reported that androgen is related to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Proxalutamide as an androgen receptor antagonist has shown potential treatment effects on COVID-19 patients. Thus, this trial is designed to investigate the efficacy and safety of proxalutamide in severe or critically ill patients with COVID-19.

Methods

This single-arm, open-label, single-center prospective exploratory trial is planned to recruit 64 severe or critically ill patients with COVID-19 in China. Recruitment started on 16 May 2022 and is foreseen to end on 16 May 2023. Patients will be followed-up until 60 days or death, whichever comes first. The primary outcome is the 30-day all-cause mortality. Secondary endpoints included 60-day all-cause mortality, rate of clinical deterioration within 30 days after administration, time to sustain clinical recovery (determined using an 8-point ordinal scale), mean change in the Acute Physiology and Chronic Health Evaluation II scores, change in oxygenation index, changes in chest CT scan, percentage of patients confirmed negative for SARS-CoV-2 by nasopharyngeal swab, change in Ct values of SARS-CoV-2 and safety. Visits will be performed on days 1 (baseline), 15 or 30, 22, and 60.

Discussion

The trial is the first to investigate the efficacy and safety of proxalutamide in severe or critically ill patients with COVID-19. The findings of this study might lead to the development of better treatment for COVID-19 and provide convincing evidence regarding the efficacy and safety of proxalutamide.

Trial registration

This study was registered on 18 June 2022 at the Chinese Clinical Trial Registry (ChiCTR2200061250).
Strong-motion simulation for the 1944 Tonankai earthquake based on the statistical green’s function method and stochastic representation of complex source process
Authors: Ito Eri , Nakano Kenichi , Sekiguchi Haruko , Nagashima Fumiaki , Kawase Hiroshi
Published: June 2023

Precisely evaluating the source, path, and site terms in a broadband frequency range is indispensable for quantitatively predicting strong motions. We conducted a generalized spectral inversion of strong motion in Japan to delineate both the spectral amplitude and phase characteristics for statistical Green’s functions. To predict ground motion from future megathrust earthquakes, we also need to model a kinematic source with a stochastic representation of the slip and rupture velocities on the fault surface. In this fundamental study, we first reported the basic features of statistical Green’s functions used for summation. We then demonstrated the construction of a kinematic source with distinctive strong-motion-generation areas with spatially random slip and rupture velocity variations. After the summation of statistical Green’s functions following the constructed kinematic source, we found that the peak ground accelerations and peak ground velocities of synthetics for the Mw8.2 1944 Tonankai earthquake are in good agreement with those of the well-established empirical formula in Japan because the medians of the synthetic values are well within the average plus/minus one standard deviation of the formula. Based on the simulation results of conducted parametric studies, we observed relatively small but meaningful effects of random slip distribution, as well as relatively small effects of random rupture velocity perturbation. In conclusion, our implementation of the complex source model and the empirically obtained statistical Green’s function used as an element source can be a viable combination for broadband (0.1 to 20 Hz) strong-motion simulations, realistic in terms of the amplitude and duration, without any hybrid scheme.

Graphical Abstract
Association between D-dimer and long-term mortality in patients with acute severe hypertension visiting the emergency department
Authors: Kim Byung Sik , Shin Jeong-Hun
Published: June 2023

Objective

High levels of d-dimer, a marker of thrombotic events, are associated with poor outcomes in patients with various cardiovascular diseases. However, there has been no research on its prognostic implications in acute severe hypertension. This study investigated the association between d-dimer levels and long-term mortality in patients with severe acute hypertension who visited the emergency department.

Design and method

This observational study included patients with acute severe hypertension who visited the emergency department between 2016 and 2019. Acute severe hypertension was defined as a systolic blood pressure ≥ 180 mmHg or a diastolic blood pressure ≥ 100 mmHg. Among the 10,219 patients, 4,127 who underwent d-dimer assay were analyzed. The patients were categorized into tertiles based on their d-dimer levels at the time of emergency department admission.

Results

Among the 4,127 patients with acute severe hypertension, 3.1% in the first (lowest) tertile, 17.0% in the second tertile, and 43.2% in the third (highest) tertile died within 3 years. After the adjustment for confounding variables, the third tertile of the d-dimer group (hazard ratio, 6.440; 95% confidence interval, 4.628–8.961) and the second tertile of the d-dimer group (hazard ratio, 2.847; 95% confidence interval, 2.037–3.978) had a significantly higher risk of all-cause mortality over 3 years than the first tertile of the d-dimer group.

Conclusions

d-dimer may be a useful marker for identifying the risk of mortality among patients with acute severe hypertension who visit the emergency department.
Extending Technology Acceptance Model to higher-education students’ use of digital academic reading tools on computers
Authors: Lin Yupeng , Yu Zhonggen
Published: June 2023

Digital academic reading tools on computers bring multiple benefits to higher-education students. Through structural equation modeling methods, this study contributes to the following findings: (1) Perceived ease of use, perceived usefulness, and lecturers’ positive responses significantly predict students’ positive attitudes toward digital academic reading tools on computers; (2) perceived ease of use, lectures’ positive responses, and expectations of academic achievement are significantly positive predictors of students’ perceived usefulness of these tools; (3) attitudes and expectations of academic achievement significantly predict students’ positive intentions to use these tools; (4) academic experience significantly predicts students’ negative attitudes toward these tools; (5) perceived ease for collaborative learning and self-efficacy are significantly positive predictors of students’ perceived ease of using these tools. Findings in this study may contribute to understanding the external factors influencing students’ acceptance and use of digital academic reading tools on computers with a substantial explanatory power of the proposed model (R2 = 64.70–84.20%), which may benefit researchers, instructors, students, and technology designers.
Guideline “Motor neuron diseases” of the German Society of Neurology (Deutsche Gesellschaft für Neurologie)
Authors: Petri Susanne , Grehl Torsten , Grosskreutz Julian , Hecht Martin , Hermann Andreas , Jesse Sarah , Lingor Paul , Löscher Wolfgang , Maier André , Schoser Benedikt , Weber Marcus , Ludolph Albert C.
Published: June 2023

Introduction

In 2021, the Deutsche Gesellschaft für Neurology published a new guideline on diagnosis and therapy of motor neuron disorders. Motor neuron disorders affect upper motor neurons in the primary motor cortex and/or lower motor neurons in the brain stem and spinal cord. The most frequent motor neuron disease amyotrophic lateral sclerosis (ALS) is a rapidly progressive disease with an average life expectancy of 2–4 years with a yearly incidence of 3.1/100,000 in Central Europe (Rosenbohm et al. in J Neurol 264(4):749–757, 2017. https://doi.org/10.1007/s00415-017-8413-3). It is considered a rare disease mainly due to its low prevalence as a consequence of short disease duration.

Recommendations

These guidelines comprise recommendations regarding differential diagnosis, neuroprotective therapies and multidisciplinary palliative care including management of respiration and nutrition as well as provision of assistive devices and end-of-life situations.

Conclusion

Diagnostic and therapeutic guidelines are necessary due the comparatively high number of cases and the aggressive disease course. Given the low prevalence and the severe impairment of patients, it is often impossible to generate evidence-based data so that ALS guidelines are partially dependent on expert opinion.
Effective Long-term Pediatric Pegvisomant Monotherapy to Final Height in X-linked Acrogigantism
Authors: Burren Christine P , Williams Georgina , Coxson Edward , Korbonits Márta
Published: June 2023

X-linked acrogigantism (X-LAG) is characterized by extreme tall stature from early childhood resulting from duplication of the GPR101 gene, in turn resulting in GH excess. Most cases present with pituitary tumors secreting GH and prolactin. Diffuse pituitary hyperplasia is uncommon and normal prolactin is rare. We present a girl with tall stature from 3 years of age; her height was +4.25 SD score at 5 years, with no signs of syndromic disease. She had significant GH excess, serum IGF-1 4 times the upper limit of normal and normal circulating GHRH, with normal pituitary magnetic resonance imaging over 13 years. No abnormalities were found in either the AIP or MEN1 genes. Treatment with somatostatin analogues and dopamine agonists showed minimal therapeutic benefit, but significant side effects. She tested positive for duplication of GPR101 6 years after the initial diagnosis. She was then initiated on pegvisomant aged 12 years, achieving prompt IGF-1 normalization and growth cessation. Aged 16.5 years, she showed escape from IGF-1 control, and height velocity increased, but this responded well to a dose increase in pegvisomant, with reassuring long-term pediatric safety over 7 years. Her final height is +2.9 SD score. Currently, life-long pegvisomant treatment is planned with genetic counselling regarding future offspring.
Thyrotoxicosis and Impending Thyroid Storm: A Rare Paraneoplastic Syndrome in an Infant With Hepatoblastoma
Authors: Vyas Neha , Neto Arino , Carakushansky Mauri , Gurnurkar Shilpa
Published: June 2023

Graves’ disease is the most common cause of pediatric hyperthyroidism and thyrotoxicosis. Thyroid storm is a rare initial manifestation of Graves’ disease and represents an endocrine emergency. We report a case of transient hyperthyroidism, possibly a paraneoplastic syndrome presenting as impending thyroid storm in a patient with undiagnosed hepatoblastoma. To our knowledge, this is the first case of this association reported in children. A previously healthy 21-month-old male presented with abdominal pain and unremitting tachycardia. He was managed for thyrotoxicosis and impending thyroid storm. He subsequently was found to have hepatomegaly leading to a diagnosis of hepatoblastoma. Autoimmune markers for Graves’ disease were negative, along with a negative human chorionic gonadotropin. After initiation of neoadjuvant chemotherapy, he had complete resolution of thyrotoxicosis. Paraneoplastic syndromes may occur with any tumor. We present a unique case of a patient developing human chorionic gonadotropin-negative hyperthyroidism, possibly as a paraneoplastic syndrome from hepatoblastoma.
Trending Ability of End-Tidal Capnography Monitoring During Mechanical Ventilation to Track Changes in Arterial Partial Pressure of Carbon Dioxide in Critically Ill Patients With Acute Brain Injury: A Monocenter Retrospective Study
Authors: Coëffic Adrien , Joachim Jona , Manquat Elsa , Felliot Élodie , Vallée Fabrice , Mebazaa Alexandre , Gayat Étienne , Chousterman Benjamin Glenn , Barthélémy Romain
Published: June 2023

BACKGROUND:

Changes in arterial partial pressure of carbon dioxide (Paco
2) may alter cerebral perfusion in critically ill patients with acute brain injury. Consequently, international guidelines recommend normocapnia in mechanically ventilated patients with acute brain injury. The measurement of end-tidal capnography (Etco
2) allows its approximation. Our objective was to report the agreement between trends in Etco
2 and Paco
2 during mechanical ventilation in patients with acute brain injury.

METHODS:

Retrospective monocenter study was conducted for 2 years. Critically ill patients with acute brain injury who required mechanical ventilation with continuous Etco
2 monitoring and with 2 or more arterial gas were included. The agreement was evaluated according to the Bland and Altman analysis for repeated measurements with calculation of bias, and upper and lower limits of agreement. The directional concordance rate of changes between Etco
2 and Paco
2 was evaluated with a 4-quadrant plot. A polar plot analysis was performed using the Critchley methods.

RESULTS:

We analyzed the data of 255 patients with a total of 3923 paired ΔEtco
2 and ΔPaco
2 (9 values per patient in median). Mean bias by Bland and Altman analysis was −8.1 (95 CI, −7.9 to −8.3) mm Hg. The directional concordance rate between Etco
2 and Paco
2 was 55.8%. The mean radial bias by polar plot analysis was −4.4° (95% CI, −5.5 to −3.3) with radial limit of agreement (LOA) of ±62.8° with radial LOA 95% CI of ±1.9°.

CONCLUSIONS:

Our results question the performance of trending ability of Etco
2 to track changes in Paco
2 in a population of critically ill patients with acute brain injury. Changes in Etco
2 largely failed to follow changes in Paco
2 in both direction (ie, low concordance rate) and magnitude (ie, large radial LOA). These results need to be confirmed in prospective studies to minimize the risk of bias.
Relationships between environmental variables and abundance of Cnidaria and Echinodermata in Çardak Lagoon, Çanakkale Strait
Authors: Acar Seçil , Ateş Abdullah Suat , Dağlı Ertan , Doğan Alper
Published: June 2023

This study is on the relationships between the abundances, of cnidarians and echinoderms found in Çardak Lagoon and environmental variables. The benthos samples were collected in three replicates in October 2018, February, April, and June 2019, using a metal framed quadrat system of 100 x 100 cm and 393 cm3 sediment core by a SCUBA diver. Sediment material was collected at 7 sampling points of Çardak Lagoon in Çanakkale Strait. A total of 259 individuals belonging to phylum, Cnidaria and Echinodermata were found in the study area. Cnidarian, Actinia sp. and echinoderm, Asterina gibbosa were the most dominant species. The highest positive correlation value was between Cnidaria species number and organic matter (OM%) content in the sediment. The highest negative correlation value was between Echinodermata species number and NO2+NO3 in lagoon system.
Efficient Algorithms for Stochastic Ride-Pooling Assignment with Mixed Fleets
Authors: Luo Qi , Nagarajan Viswanath , Sundt Alexander , Yin Yafeng , Vincent John , Shahabi Mehrdad
Published: June 2023

Ride-pooling, which accommodates multiple passenger requests in a single trip, has the potential to substantially enhance the throughput of mobility-on-demand (MoD) systems. This paper investigates MoD systems that operate mixed fleets composed of “basic supply” and “augmented supply” vehicles. When the basic supply is insufficient to satisfy demand, augmented supply vehicles can be repositioned to serve rides at a higher operational cost. We formulate the joint vehicle repositioning and ride-pooling assignment problem as a two-stage stochastic integer program, where repositioning augmented supply vehicles precedes the realization of ride requests. Sequential ride-pooling assignments aim to maximize total utility or profit on a shareability graph: a hypergraph representing the matching compatibility between available vehicles and pending requests. Two approximation algorithms for midcapacity and high-capacity vehicles are proposed in this paper; the respective approximation ratios are [Formula: see text] and [Formula: see text], where p is the maximum vehicle capacity plus one. Our study evaluates the performance of these approximation algorithms using an MoD simulator, demonstrating that these algorithms can parallelize computations and achieve solutions with small optimality gaps (typically within 1%). These efficient algorithms pave the way for various multimodal and multiclass MoD applications.

History: This paper has been accepted for the Transportation Science Special Issue on Emerging Topics in Transportation Science and Logistics.

Funding: This work was supported by the National Science Foundation [Grants CCF-2006778 and FW-HTF-P 2222806], the Ford Motor Company, and the Division of Civil, Mechanical, and Manufacturing Innovation [Grants CMMI-1854684, CMMI-1904575, and CMMI-1940766].

Supplemental Material: The online appendix is available at https://doi.org/10.1287/trsc.2021.0349 .
entre corpos, danças e educações: uma experiência infantil
Authors: De barros Mayra Giovaneti , Leite César Donizetti pereira
Published: June 2023

This paper is the result of reflections inspired by observing and participating in dancing sessions with children. Our experience of the latter led to the production of images that provoked a variety of questions, and invited us to think about the relationships between bodies, dance, and various forms of education. Among these questions were: what clues about the experience of human embodiment are given through observing children’s dance? What can children teach us through participating with them in this performative medium, and what are its implications for education, most especially in light of our observations of children's inventiveness in this regard? Our impressions resonate and find expression in the oeuvre of Gilles Deleuze, Félix Guattari, Michel Foucault, Jan Masschelein and Manoel de Barros. Placing ourselves under their influence, we mobilized our thinking and opened ourselves to the emergent character of  their ideas, resulting in what might be called a form of “dancing-writing”  in which those two forms of expression interact. This dancing-writing is informed by and imbued with children’s lived experience: step by step, we walked the paths that they opened, recording as best we could their multisensorial approach to the world—gaze, taste, smell, sound, touch, movement. Ours was an experience of research on movement, with movement, in movement. As such, we harbor no intention to present final answers, but rather offer the reader an invitation to think philosophically and childishly. Ours is an invitation to dance with and among the questions which that very dance inspired.
COVID-19 em profissionais de enfermagem no Maranhão (2020-2021): características clínico-epidemiológicas dos casos e fatores associados aos óbitos
Authors: Silva Weslei Melo da , Sousa Giana Gislanne Da Silva de , Pascoal Lívia Maia , Rolim Isaura Leticia Tavares Palmeira , Santos Floriacy Stabnow , Neto Marcelino Santos
Published: June 2023

Objetivo: descrever características clínico-epidemiológicas dos casos de COVID-19 em profissionais de enfermagem e analisar fatores associados aos óbitos. Método: estudo transversal realizado com casos e óbitos por COVID-19 em profissionais de enfermagem registrados no período entre abril de 2020 e março de 2021 no estado do Maranhão. Utilizou-se a estatística descritiva e modelos de regressão logística. Resultados: verificaram-se 2.116 casos de COVID-19 em profissionais de enfermagem, a maioria eram técnicos (63,23%), sexo feminino (86,48%), raça/cor preta/parda (48,20%), na faixa etária de 31 a 40 anos (40,69%) e média de idade de 38,11 anos (DP=9,58). A hipertensão arterial sistêmica foi a principal comorbidade apresentada (62,03%). Os fatores de risco para o óbito foram: idade >60 anos, comorbidades como hipertensão arterial sistêmica, diabetes mellitus e obesidade. Conclusão: esses dados podem direcionar intervenções em saúde mais efetivas com intuito de minimizar os riscos de infecção e os danos à saúde desses trabalhadores.
OCT based corneal densitometry: the confounding effect of epithelial speckle
Authors: Miażdżyk Maria , Consejo Alejandra , Iskander D. Robert
Published: June 2023

Corneal densitometry is a clinically validated method for objectively assessing the transparency of stroma. The technique is currently dominated by Scheimpflug technology. Still, optical coherence tomography (OCT), in which examination of the statistical properties of corneal speckle is undertaken, has also been considered to assess corneal densitometry. In-vivo, the stroma is observed via the epithelium. However, the effect of this external layer on stromal densitometry has not been considered as yet. This study aims to quantify the influence of epithelium integrity on corneal OCT densitometry. OCT images from eleven freshly enucleated porcine eyes before and after epithelial debridement were used. OCT densitometry was investigated at different stromal depths using four metrics of speckle statistics. Results indicate that there exist statistically significant differences in speckle statistics for a given stromal depth depending on the presence or absence of the epithelium. The estimation error in speckle statistics can reach over 20% depending on the stromal depth. The anterior stroma densitometry values are the ones most affected by epithelial integrity. In conclusion, if OCT densitometry stromal parameters are to be considered in absolute terms, it is essential to consider the confounding effect of the epithelial layer in the analysis.
Serum-based Raman spectroscopic diagnosis of blast-induced brain injury in a rat model
Authors: Ge Meilan , Wang Yuye , Wu Tong , Li Haibin , Yang Chuanyan , Chen Tunan , Feng Hua , Xu Degang , Yao Jianquan
Published: June 2023

The diagnosis of blast-induced traumatic brain injury (bTBI) is of paramount importance for early care and clinical therapy. Therefore, the rapid diagnosis of bTBI is vital to the treatment and prognosis in clinic. In this paper, we reported a new strategy for label-free bTBI diagnosis through serum-based Raman spectroscopy. The Raman spectral characteristics of serum in rat were investigated at 3 h, 24 h, 48 h and 72 h after mild and moderate bTBIs. It has been demonstrated that both the position and intensity of Raman characteristic peaks exhibited apparent differences in the range of 800-3000cm−1 compared with control group. It could be inferred that the content, structure and interaction of biomolecules in the serum were changed after blast exposure, which might help to understand the neurological syndromes caused by bTBI. Furthermore, the control group, mild and moderate bTBIs at different times (a total of 9 groups) were automatically classified by combining principal component analysis and four machine learning algorithms (quadratic discriminant analysis, support vector machine, k-nearest neighbor, neural network). The highest classification accuracy, sensitivity and precision were up to 95.4%, 95.9% and 95.7%. It is suggested that this method has great potential for high-sensitive, rapid, and label-free diagnosis of bTBI.
Analysis of frequency chirping on the electron bunch acceleration during Laguerre–Gauss laser interaction
Authors: Firouzjaei Ali Shekari , Akou Hossein
Published: June 2023

We intend to examine the impact of frequency chirping on the efficient vacuum acceleration of an electron bunch using a chirped Laguerre–Gauss (LG) laser pulse. The study demonstrates that achieving high-energy electron acceleration relies not only on significant pulse asymmetry but also on ensuring phase synchronization in the LG laser interaction. The findings highlight the feasibility of generating outgoing electron bunches with high energy and low divergence through the selection of an optimal chirping value. Furthermore, we establish that chirping the LG laser pulse facilitates the acceleration of electrons to high energy using a lower laser intensity compared to the scenario without chirping.
Widely tunable room-temperature green-pumped continuous-wave optical parametric oscillator from the red to mid-infrared
Authors: Devi Kavita , Ebrahim-Zadeh M.
Published: June 2023

We report, to the best of our knowledge, the first realization of a room-temperature green-pumped continuous-wave (cw) optical parametric oscillator (OPO), providing wide and rapid tunability directly from the red to mid-infrared. The OPO, based on fanout MgO:sPPLT crystal and pumped at 532 nm, can provide a total signal and idler wavelength tuning range over 2554 nm, from 638 to 3192 nm. By deploying finite output coupling of the resonant wave at room temperature, also for the first time, to the best of our knowledge, we achieve enhanced output power and extraction efficiency, with the OPO delivering 4.6 W of total output power with pump depletion of 75% and total external efficiency as high as 50%. We believe 638 nm is the shortest signal wavelength generated from a cw green-pumped OPO in any fanout-grating nonlinear material to date. The passive power and frequency stability, linewidth, spatial beam profile, and beam pointing stability of the output-coupled signal, which are crucial for many applications, have been studied.
High sensitivity and stability probe-type refractive index sensor based on an optical fiber metasurface
Authors: Zhou Xue , Wang Yiming , Sun Yuanqi , Wang Fang , Yan Xin , Zhang Xuenan , Suzuki Takenobu , Ohishi Yasutake , Cheng Tonglei
Published: June 2023

A specific probe-type sensor based on an optical fiber metasurface was proposed and simulated for refractive index (RI) sensing. In this work, a metasurface has been integrated with an optical fiber platform, which has huge potential applications in imaging, sensing, and communications. The designed RI sensor consists of stacking layers of Au and ZnO in a 2D structure deposited on the end face of commercial multimode optical fiber. The parameters and performance of the sensor structure are designed and simulated. The results show that the designed sensor structure can generate mode resonance and realize RI sensing. Numerical simulations reveal that when the pair of Au/ZnO layers is 4, the width of the nanopillars is 300 nm, the thickness of the Au layer is 45 nm, the thickness of ZnO layer is 40 nm, and the RI sensitivity of the designed sensor reaches 1415 nm/RIU. In addition, the high RI of Au/ZnO, along with its compatibility with the fiber core (SiO2), makes it a perfect candidate to realize a multifunctional device. It also is a the biocompatible material that can be functionalized easily and used to realize biosensing.
Interferometric phase estimation and quantum resource dynamics in Bell coherent-state superpositions generated via a unitary beam splitter
Authors: Slaoui Abdallah , Amghar Brahim , Ahl Laamara Rachid
Published: June 2023

Beam splitters are optical elements widely used in modern technological applications to split the initial light beam into a required number of beams, and they play a very promising role for generating entangled optical states. Here, a potential scheme is proposed to generate Bell coherent-state superpositions through the action of a beam splitter when a Glauber coherent state is injected on one input mode and a vacuum state is incident on the other. Different quantifiers are used to measure the quantumness in the output state, such as concurrence entanglement, entropic quantum discord, quantum coherence, geometric measure of quantum discord, local quantum uncertainty (LQU), and local quantum Fisher information. Thereby, we derive their analytical formulas and focus more on the behavior and bounds of each measure. Besides, we have introduced the notion of “weak measurement-induced LQU” captured by weak measurements as the generalization of normal LQU defined for standard projective measurement, and we investigate the effect of the measurement strength on the estimated phase enhancement if the generated Bell cat states are the probe states in quantum metrology. Our results suggest that the sensitivity of the interferometric phase estimation depends on how strongly one perturbs the probe state and that a weak measurement does not necessarily capture more quantumness in the composite system.
Quantifying the coherent backscatter enhancement of non-spherical particles with discrete dipole approximation
Authors: Zhou Chen , Han Xue , Bi Lei
Published: June 2023

The prevailing backscattering peak associated with the scattering phase function of large non-absorptive particles can be interpreted with the coherent backscatter enhancement (CBE) theory, but has not been explicitly quantified with numerical simulations based on solving Maxwell’s equations. In this paper, representative numerical simulations performed with the discrete-dipole-approximation (DDA) model are used to quantify the effect of CBE on the single-scattering phase function. For each scattering case, the particle volume was divided into multiple thin slices parallel to the incident beam. The dipole polarizations in the j’th slice in response to the incident field of the i’th slice were computed, and then the corresponding contribution to the scattering phase function was calculated. Interference between conjugate terms representing reversible wave paths is constructive at the backscattering direction, which corresponds to the CBE. Subsequently, the contribution of CBE to the scattering phase function was quantified by comparing the electric fields calculated with and without the interference between conjugate terms. Results from these numerical simulations are consistent with conclusions obtained from the CBE theory. The simulations also quantitatively explain why it is difficult to identify a CBE-induced backscattering peak for the phase function of small particles and strong-absorptive particles.
Enhancing nonclassical properties of quantum states of light using linear optics
Authors: Mattos E. P. , Vidiella-Barranco A.
Published: June 2023

In this Letter, we present a simple and versatile scheme for enhancing the nonclassical properties of light states using only linear optics and photodetectors. By combining a coherent state |α〉 and an arbitrary pure state of light |ϕ〉 (excluding coherent states) at two beam splitters, we show that the amplitude α of the coherent state can be tuned to filter out specific Fock components and generate states of light with increased nonclassical features. We provide two examples of input states and demonstrate the effectiveness of our scheme in enhancing the sub-Poissonian statistics or the quadrature squeezing of the output states.
Plant virus movement proteins originated from jelly-roll capsid proteins
Authors: Butkovic Anamarija , Dolja Valerian V. , Koonin Eugene V. , Krupovic Mart
Published: June 2023

Numerous, diverse plant viruses encode movement proteins (MPs) that aid the virus movement through plasmodesmata, the plant intercellular channels. MPs are essential for virus spread and propagation in distal tissues, and several unrelated MPs have been identified. The 30K superfamily of MPs (named after the molecular mass of tobacco mosaic virus MP, the classical model of plant virology) is the largest and most diverse MP variety, represented in 16 virus families, but its evolutionary origin remained obscure. Here, we show that the core structural domain of the 30K MPs is homologous to the jelly-roll domain of the capsid proteins (CPs) of small RNA and DNA viruses, in particular, those infecting plants. The closest similarity was observed between the 30K MPs and the CPs of the viruses in the families Bromoviridae and Geminiviridae. We hypothesize that the MPs evolved via duplication or horizontal acquisition of the CP gene in a virus that infected an ancestor of vascular plants, followed by neofunctionalization of one of the paralogous CPs, potentially through the acquisition of unique N- and C-terminal regions. During the subsequent coevolution of viruses with diversifying vascular plants, the 30K MP genes underwent explosive horizontal spread among emergent RNA and DNA viruses, likely permitting viruses of insects and fungi that coinfected plants to expand their host ranges, molding the contemporary plant virome.
Bioschemas training profiles: A set of specifications for standardizing training information to facilitate the discovery of training programs and resources
Authors: Castro Leyla Jael , Palagi Patricia M. , Beard Niall , Attwood Teresa K. , Brazas Michelle D.
Published: June 2023

Stand-alone life science training events and e-learning solutions are among the most sought-after modes of training because they address both point-of-need learning and the limited timeframes available for “upskilling.” Yet, finding relevant life sciences training courses and materials is challenging because such resources are not marked up for internet searches in a consistent way. This absence of markup standards to facilitate discovery, re-use, and aggregation of training resources limits their usefulness and knowledge translation potential. Through a joint effort between the Global Organisation for Bioinformatics Learning, Education and Training (GOBLET), the Bioschemas Training community, and the ELIXIR FAIR Training Focus Group, a set of Bioschemas Training profiles has been developed, published, and implemented for life sciences training courses and materials. Here, we describe our development approach and methods, which were based on the Bioschemas model, and present the results for the 3 Bioschemas Training profiles: TrainingMaterial, Course, and CourseInstance. Several implementation challenges were encountered, which we discuss alongside potential solutions. Over time, continued implementation of these Bioschemas Training profiles by training providers will obviate the barriers to skill development, facilitating both the discovery of relevant training events to meet individuals’ learning needs, and the discovery and re-use of training and instructional materials.
Damage sensing mediated by serine proteases Hayan and Persephone for Toll pathway activation in apoptosis-deficient flies
Authors: Nakano Shotaro , Kashio Soshiro , Nishimura Kei , Takeishi Asuka , Kosakamoto Hina , Obata Fumiaki , Kuranaga Erina , Chihara Takahiro , Yamauchi Yoshio , Isobe Toshiaki , Miura Masayuki
Published: June 2023

The mechanisms by which the innate immune system senses damage have been extensively explored in multicellular organisms. In Drosophila, various types of tissue damage, including epidermal injury, tumor formation, cell competition, and apoptosis deficiency, induce sterile activation of the Toll pathway, a process that requires the use of extracellular serine protease (SP) cascades. Upon infection, the SP Spätzle (Spz)-processing enzyme (SPE) cleaves and activates the Toll ligand Spz downstream of two paralogous SPs, Hayan and Persephone (Psh). However, upon tissue damage, it is not fully understood which SPs establish Spz activation cascades nor what damage-associated molecules can activate SPs. In this study, using newly generated uncleavable spz mutant flies, we revealed that Spz cleavage is required for the sterile activation of the Toll pathway, which is induced by apoptosis-deficient damage of wing epidermal cells in adult Drosophila. Proteomic analysis of hemolymph, followed by experiments with Drosophila Schneider 2 (S2) cells, revealed that among hemolymph SPs, both SPE and Melanization Protease 1 (MP1) have high capacities to cleave Spz. Additionally, in S2 cells, MP1 acts downstream of Hayan and Psh in a similar manner to SPE. Using genetic analysis, we found that the upstream SPs Hayan and Psh contributes to the sterile activation of the Toll pathway. While SPE/MP1 double mutants show more impairment of Toll activation upon infection than SPE single mutants, Toll activation is not eliminated in these apoptosis-deficient flies. This suggests that Hayan and Psh sense necrotic damage, inducing Spz cleavage by SPs other than SPE and MP1. Furthermore, hydrogen peroxide, a representative damage-associated molecule, activates the Psh-Spz cascade in S2 cells overexpressing Psh. Considering that reactive oxygen species (ROS) were detected in apoptosis-deficient wings, our findings highlight the importance of ROS as signaling molecules that induce the activation of SPs such as Psh in response to damage.
Exploring the mechanism of BK polyomavirus-associated nephropathy through consensus gene network approach
Authors: Sato Noriaki , Mori Keita P. , Sakai Kaoru , Miyata Hitomi , Yamamoto Shinya , Kobayashi Takashi , Haga Hironori , Yanagita Motoko , Okuno Yasushi
Published: June 2023

BK polyomavirus-associated nephropathy occurs in kidney transplant recipients under immunosuppressive treatment. BK polyomavirus is implicated in cancer development and invasion, and case reports of renal cell carcinoma and urothelial carcinoma possibly associated with BK polyomavirus has been reported. Further, it has been suggested that the immune responses of KT-related diseases could play a role in the pathogenesis and progression of renal cell carcinoma. Thus, we thought to examine the relationship between BK polyomavirus-associated nephropathy and renal cell carcinoma in terms of gene expression. To identify the common and specific immune responses involved in kidney transplantation-related diseases with a specific focus on BK polyomavirus-associated nephropathy, we performed consensus weighted gene co-expression network analysis on gene profile datasets of renal biopsy samples from different institutions. After the identification of gene modules and validation of the obtained network by immunohistochemistry of the marker across kidney transplantation-related diseases, the relationship between prognosis of renal cell carcinoma and modules was assessed. We included the data from 248 patients and identified the 14 gene clusters across the datasets. We revealed that one cluster related to the translation regulating process and DNA damage response was specifically upregulated in BK polyomavirus-associated nephropathy. There was a significant association between the expression value of hub genes of the identified cluster including those related to cGAS-STING pathway and DNA damage response, and the prognosis of renal cell carcinoma. The study suggested the potential link between kidney transplantation-related diseases, especially specific transcriptomic signature of BK polyomavirus associated nephropathy and renal cell carcinoma.
Practice walking on a treadmill-mounted balance beam modifies beam walking sacral movement and alters performance in other balance tasks
Authors: Symeonidou Evangelia-Regkina , Esposito Nicole M. , Reyes Roehl-Dean , Ferris Daniel P.
Published: June 2023

The goals of this study were to determine if a single 30-minute session of practice walking on a treadmill mounted balance beam: 1) altered sacral marker movement kinematics during beam walking, and 2) affected measures of balance during treadmill walking and standing balance. Two groups of young, healthy human subjects practiced walking on a treadmill mounted balance beam for thirty minutes. One group trained with intermittent visual occlusions and the other group trained with unperturbed vision. We hypothesized that the subjects would show changes in sacrum movement kinematics after training and that there would be group differences due to larger improvements in beam walking performance by the visual occlusions group. We also investigated if there was any balance transfer from training on the beam to treadmill walking (margin of stability) and to standing static balance (center of pressure excursion). We found significant differences in sacral marker maximal velocity after training for both groups, but no significant differences between the two groups from training. There was limited evidence of balance transfer from beam-walking practice to gait margin of stability for treadmill walking and for single leg standing balance, but not for tandem stance balance. The number of step-offs while walking on a narrow beam had the largest change with training (partial η2 = 0.7), in accord with task specificity. Other balance metrics indicative of transfer had lower effect sizes (partial η2<0.5). Given the limited transfer across balance training tasks, future work should examine how intermittent visual occlusions during multi-task training improve real world functional outcomes.