bluuebunny/crossref_metadata_2025_split huggingface dataset:
Occurrence of extrapulmonary tuberculosis is associated with geographical origin: spatial characteristics of the Frankfurt TB cohort 2013–2018
Authors: Wetzstein Nils , Drummer Alena-Pauline , Bockey Annabelle , Herrmann Eva , Küpper-Tetzel Claus Philippe , Graf Christiana , Koch Benjamin , Goetsch Udo , Vehreschild Maria J. G. T. , Guglielmetti Lorenzo , Lange Berit , Wichelhaus Thomas A. , Stephan Christoph 
Published: October 2022

Abstract
Introduction
Tuberculosis (TB) is caused by M. tuberculosis complex (MTB) and pulmonary tuberculosis (PTB) is its classical manifestation. However, in some regions of the world, extrapulmonary TB (EPTB) seems to be more frequent.

Methods
We performed a retrospective cohort study of all TB patients treated at University Hospital Frankfurt, Germany, for the time period 2013–2018. Patient charts were reviewed and demographic, clinical, and microbiological data recorded. Patients were subdivided according to their geographic origins.

Results
Of the 378 included patients, 309 were born outside Germany (81.7%). Three WHO regions were significantly associated with the occurrence of isolated EPTB: the South-East Asian Region (OR 3.37, CI 1.74–6.66, p < 0.001), the African Region (2.20, CI 1.25–3.90, p = 0.006), and the Eastern Mediterranean Region (OR 3.18, CI 1.78–5.76, p < 0.001). On a country level, seven countries of origin could be demonstrated to be significantly associated with the occurrence of isolated EPTB: India (OR 5.58, CI 2.30–14.20, p < 0.001), Nepal (OR 12.75, CI 1.73–259.28, p = 0.027), Afghanistan (OR 3.64, CI 1.14–11.98, p = 0.029), Pakistan (OR 3.64, CI 1.14–11.98, p = 0.029), Eritrea (OR 3.32, CI 1.52–7.47, p = 0.003), Somalia (OR 7.08, CI 2.77–19.43, p < 0.001), and Turkey (OR 9.56, CI 2.52–47.19, p = 0.002).

Conclusion
Geographical origin is a predictor for the occurrence of extrapulmonary TB. This might be linked to a delay in diagnosis in these patients, as well as specific responsible impairments of the host’s immune system, possible virulence factors of MTB, and relevant comorbidities.
Predictors of Worsening Erectile Function in Men with Functional Erections Early After Radical Prostatectomy
Authors: Salter Carolyn A. , Tin Amy L. , Bernie Helen L. , Nascimento Bruno , Katz Darren J. , Benfante Nicole E. , Carlsson Sigrid V. , Mulhall John P. 
Published: October 2022

AbstractBackgroundPrior studies suggest that men with good erectile function shortly after radical prostatectomy (RP) can subsequently have worsened erectile function.AimTo determine the prevalence and predictors of early erectile function recovery post-RP and of worsening erectile function after initial erectile function recovery.MethodsWe retrospectively queried our institutional database. Men who underwent RP during 2008–2017 and who completed the International Index of Erectile Function erectile function domain both pre-RP and serially post-RP, constituted the population. Functional erections were defined as International Index of Erectile Function (IIEF)-6 erectile function domain scores ≥24. We analyzed factors predicting functional erections at 3 months post-RP as well as factors predicting a decrease in functional erections between 3 and 6 months, defined as ≥2-point drop in the erectile function domain. Multivariable logistic regression models were used to identify predictors of early erectile function recovery and also of subsequent decline.OutcomesErectile function recovery rates at 3 months post-RP and predictive factors; rates of erectile function decline between 3-6 months and associated predictors.ResultsEligible patients comprised 1,655 men with median age of 62 (IQR 57, 67) years. Bilateral nerve-sparing (NS) surgery was performed in 71% of men, unilateral NS in 19%, and no NS in 10%. Of this population, 224 men (14%; 95% CI 12%, 15%) had functional erections at 3 months post-RP. On multivariable analysis, significant predictors of early erectile function recovery included: younger age (OR 0.93, P &lt; .001), higher baseline erectile function domain score (OR 1.14, P &lt; .001) and bilateral NS (OR 3.81, P = .002). The presence of diabetes (OR 0.43, P = .028) and a former smoking history (OR 0.63, P = .008; reference group: never smoker) was associated with the erectile dysfunction at 3 months post-RP. Of the men with early functional erections, 41% (95% CI 33%, 48%) had a ≥ 2-point decline in erectile function between 3 and 6 months. No factors were identified as predictors for this decline.Clinical ImplicationsOnly a small proportion of men have functional erections at 3 months post-RP and a notable number of them will experience a decline in erectile function between 3 and 6 months.Strengths and LimitationsStrengths: large patient population and the use of validated questionnaire. Limitations: single-center retrospective study.ConclusionA minority of men had functional erections 3 months post-RP, about half of whom had a decline in erectile function by month 6. We recommend appropriately counseling post-RP patients on the risk of such a decline in erectile function.
CRISPR-based kinome-screening revealed MINK1 as a druggable player to rewire 5FU-resistance in OSCC through AKT/MDM2/p53 axis
Authors: Mohanty Sibasish , Mohapatra Pallavi , Shriwas Omprakash , Ansari Shamima Azma , Priyadarshini Manashi , Priyadarsini Swatismita , Rath Rachna , Sultania Mahesh , Das Majumdar Saroj Kumar , Swain Rajeeb K. , Dash Rupesh 
Published: October 2022

AbstractCisplatin, 5FU and docetaxel (TPF) are the most common chemotherapy regimen used for advanced OSCC. However, many cancer patients experience relapse, continued tumor growth, and spread due to drug resistance, which leads to treatment failure and metastatic disease. Here, using a CRISPR/Cas9 based kinome knockout screening, Misshapen-like kinase 1 (MINK1) is identified as an important mediator of 5FU resistance in OSCC. Analysis of clinical samples demonstrated significantly higher MINK1 expression in the tumor tissues of chemotherapy non-responders as compared to chemotherapy responders. The nude mice and zebrafish xenograft experiments indicate that knocking out MINK1 restores 5FU mediated cell death in chemoresistant OSCC. An antibody based phosphorylation array screen revealed MINK1 as a negative regulator of p53. Mechanistically, MINK1 modulates AKT phosphorylation at Ser473, which enables p-MDM2 (Ser 166) mediated degradation of p53. We also identified lestaurtinib as a potent inhibitor of MINK1 kinase activity. The patient derived TPF resistant cell based xenograft data suggest that lestaurtinib restores 5FU sensitivity and facilitates a significant reduction of tumor burden. Overall, our study suggests that MINK1 is a major driver of 5FU resistance in OSCC. The novel combination of MINK1 inhibitor lestaurtinib and 5FU needs further clinical investigation in advanced OSCC.
Role of AI and digital pathology for colorectal immuno-oncology
Authors: Bilal Mohsin , Nimir Mohammed , Snead David , Taylor Graham S. , Rajpoot Nasir 
Published: October 2022

AbstractImmunotherapy deals with therapeutic interventions to arrest the progression of tumours using the immune system. These include checkpoint inhibitors, T-cell manipulation, cytokines, oncolytic viruses and tumour vaccines. In this paper, we present a survey of the latest developments on immunotherapy in colorectal cancer (CRC) and the role of artificial intelligence (AI) in this context. Among these, microsatellite instability (MSI) is perhaps the most popular IO biomarker globally. We first discuss the MSI status of tumours, its implications for patient management, and its relationship to immune response. In recent years, several aspiring studies have used AI to predict the MSI status of patients from digital whole-slide images (WSIs) of routine diagnostic slides. We present a survey of AI literature on the prediction of MSI and tumour mutation burden from digitised WSIs of haematoxylin and eosin-stained diagnostic slides. We discuss AI approaches in detail and elaborate their contributions, limitations and key takeaways to drive future research. We further expand this survey to other IO-related biomarkers like immune cell infiltrates and alternate data modalities like immunohistochemistry and gene expression. Finally, we underline possible future directions in immunotherapy for CRC and promise of AI to accelerate this exploration for patient benefits.
Hydrogen-substituted graphdiyne encapsulated cuprous oxide photocathode for efficient and stable photoelectrochemical water reduction
Authors: Zhou Xue , Fu Baihe , Li Linjuan , Tian Zheng , Xu Xiankui , Wu Zihao , Yang Jing , Zhang Zhonghai 
Published: October 2022

AbstractPhotoelectrochemical (PEC) water splitting is an appealing approach for “green” hydrogen generation. The natural p-type semiconductor of Cu2O is one of the most promising photocathode candidates for direct hydrogen generation. However, the Cu2O-based photocathodes still suffer severe self-photo-corrosion and fast surface electron-hole recombination issues. Herein, we propose a facile in-situ encapsulation strategy to protect Cu2O with hydrogen-substituted graphdiyne (HsGDY) and promote water reduction performance. The HsGDY encapsulated Cu2O nanowires (HsGDY@Cu2O NWs) photocathode demonstrates a high photocurrent density of −12.88 mA cm−2 at 0 V versus the reversible hydrogen electrode under 1 sun illumination, approaching to the theoretical value of Cu2O. The HsGDY@Cu2O NWs photocathode as well as presents excellent stability and contributes an impressive hydrogen generation rate of 218.2 ± 11.3 μmol h−1cm−2, which value has been further magnified to 861.1 ± 24.8 μmol h−1cm−2 under illumination of concentrated solar light. The in-situ encapsulation strategy opens an avenue for rational design photocathodes for efficient and stable PEC water reduction.
Wien effect in interfacial water dissociation through proton-permeable graphene electrodes
Authors: Cai J. , Griffin E. , Guarochico-Moreira V. H. , Barry D. , Xin B. , Yagmurcukardes M. , Zhang S. , Geim A. K. , Peeters F. M. , Lozada-Hidalgo M. 
Published: October 2022

AbstractStrong electric fields can accelerate molecular dissociation reactions. The phenomenon known as the Wien effect was previously observed using high-voltage electrolysis cells that produced fields of about 107 V m−1, sufficient to accelerate the dissociation of weakly bound molecules (e.g., organics and weak electrolytes). The observation of the Wien effect for the common case of water dissociation (H2O $$\leftrightarrows$$
⇆
H+ + OH−) has remained elusive. Here we study the dissociation of interfacial water adjacent to proton-permeable graphene electrodes and observe strong acceleration of the reaction in fields reaching above 108 V m−1. The use of graphene electrodes allows measuring the proton currents arising exclusively from the dissociation of interfacial water, while the electric field driving the reaction is monitored through the carrier density induced in graphene by the same field. The observed exponential increase in proton currents is in quantitative agreement with Onsager’s theory. Our results also demonstrate that graphene electrodes can be valuable for the investigation of various interfacial phenomena involving proton transport.
Energy landscape reshaped by strain-specific mutations underlies epistasis in NS1 evolution of influenza A virus
Authors: Kim Iktae , Dubrow Alyssa , Zuniga Bryan , Zhao Baoyu , Sherer Noah , Bastiray Abhishek , Li Pingwei , Cho Jae-Hyun 
Published: October 2022

AbstractElucidating how individual mutations affect the protein energy landscape is crucial for understanding how proteins evolve. However, predicting mutational effects remains challenging because of epistasis—the nonadditive interactions between mutations. Here, we investigate the biophysical mechanism of strain-specific epistasis in the nonstructural protein 1 (NS1) of influenza A viruses (IAVs). We integrate structural, kinetic, thermodynamic, and conformational dynamics analyses of four NS1s of influenza strains that emerged between 1918 and 2004. Although functionally near-neutral, strain-specific NS1 mutations exhibit long-range epistatic interactions with residues at the p85β-binding interface. We reveal that strain-specific mutations reshaped the NS1 energy landscape during evolution. Using NMR spin dynamics, we find that the strain-specific mutations altered the conformational dynamics of the hidden network of tightly packed residues, underlying the evolution of long-range epistasis. This work shows how near-neutral mutations silently alter the biophysical energy landscapes, resulting in diverse background effects during molecular evolution.
Fitness consequences of chronic exposure to different light pollution wavelengths in nocturnal and diurnal rodents
Authors: Vardi-Naim Hagar , Benjamin Ava , Sagiv Tali , Kronfeld-Schor Noga 
Published: October 2022

AbstractUse of artificial at night (ALAN) exposes the world to continuously increasing levels and distribution of light pollution. Our understanding of the adverse effects of ALAN is based mostly on observational or laboratory studies, and its effects are probably underestimated. Demonstration of direct experimental fitness consequences of ALAN on mammals is missing. We studied the effects of chronic light pollution at different wavelengths on fitness and glucocorticoid hormone levels under semi-natural conditions in two closely related species: the nocturnal common spiny mouse (Acomys cahirinus) and the diurnal golden spiny mouse (Acomys russatus). Our results clearly demonstrate the adverse effects of ALAN exposure on the fitness of both nocturnal and diurnal species, manifested by changes in cortisol levels and reproductive timing, reduced reproductive output and reduced survival, which differed between species and wavelengths. In A. russatus exposure to blue ALAN had the strongest effect on fitness, followed by white and yellow ALAN exposure. In A. cahirinus the results are more complex and suggest it suffered from the combined effects of ALAN and competition. Our research shows that light pollution presents a real threat to both nocturnal and diurnal species, affecting the species fitness directly and through interspecific interactions. Worryingly, these effects are probably not limited to spiny mice. The clear adverse effects we documented, as well as the differences between wave lengths, contribute to our ability to present science-based recommendations to decision makers regarding the use of artificial light at night. Such information and guidelines are highly important nowadays when lighting systems are being replaced to promote energy efficiency.
Single-shot off-axis digital holographic system with extended field-of-view by using multiplexing method
Authors: Kumar Manoj , Pensia Lavlesh , Kumar Raj 
Published: October 2022

AbstractWe propose a new configuration of single-shot off-axis digital holographic system to realize double the camera field-of-view (FOV) of the existing off-axis Mech-Zehnder type holographic setup. The double FOV is obtained by double spatial frequency multiplexing of two different areas of an object beam by inserting a Fresnel bi-prism in it, which divides the object beam into two, both carrying different object information. The image sensor is placed at the plane where these two different FOVs overlap so as to record simultaneously two parts of the wavefront of the object in a single-shot. The multiplexed hologram is carrying two interferometric images corresponding to two different FOVs of the object which are modulated with two different spatial carrier frequencies. The feasibility of the proposed digital holographic system is experimentally demonstrated by imaging two different areas of a resolution test target. The limitation of the proposed system and a method to overcome it, are also discussed. The proposed system is useful in a wide range of applications including microscopy and optical metrology.
Urtica dioica and Dodonaea viscosa leaf extracts as eco-friendly bioagents against Alternaria alternata isolate TAA-05 from tomato plant
Authors: Behiry Said I. , Philip Bassant , Salem Mohamed Z. M. , Amer Mostafa A. , El-Samra Ibrahim A. , Abdelkhalek Ahmed , Heflish Ahmed 
Published: October 2022

AbstractOne of the tomato’s acutely devastating diseases is Alternaria leaf spot, lowering worldwide tomato production. In this study, one fungal isolate was isolated from tomatoes and was assigned to Alternaria alternata TAA-05 upon morphological and molecular analysis of the ITS region and 18SrRNA, endoPG, Alt a1, and gapdh genes. Also, Urtica dioica and Dodonaea viscosa methanol leaf extracts (MLEs) were utilized as antifungal agents in vitro and compared to Ridomil, a reference chemical fungicide. The in vitro antifungal activity results revealed that Ridomil (2000 µg/mL) showed the highest fungal growth inhibition (FGI) against A. alternata (96.29%). Moderate activity was found against A. alternata by D. viscosa and U. dioica MLEs (2000 µg/mL), with an FGI value of 56.67 and 54.81%, respectively. The abundance of flavonoid and phenolic components were identified by HPLC analysis in the two plant extracts. The flavonoid compounds, including hesperidin, quercetin, and rutin were identified using HPLC in D. viscosa MLE with concentrations of 11.56, 10.04, and 5.14 µg/mL of extract and in U. dioica MLE with concentrations of 12.45, 9.21, and 5.23 µg/mL, respectively. α-Tocopherol and syringic acid, were also identified in D. viscosa MLE with concentrations of 26.13 and 13.69 µg/mL, and in U. dioica MLE, with values of 21.12 and 18.33 µg/mL, respectively. Finally, the bioactivity of plant extracts suggests that they play a crucial role as antifungal agents against A. alternata. Some phenolic chemicals, including coumaric acid, caffeic acid, ferulic acid, and α-tocopherol, have shown that they may be utilized as environmentally friendly fungicidal compounds.
Fractal features of soil grain-size distribution in a typical Tamarix cones in the Taklimakan Desert, China
Authors: Dong Zhengwu , Mao Donglei , Ye Mao , Li Shengyu , Ma Xiaodong , Liu Suiyunhao 
Published: October 2022

AbstractTamarix cones play key roles in preventing sand erosion and maintaining regional ecosystem stability. This study aimed to explore the characteristics of soil grain size distribution (GSD) in Tamarix cones across the Taklimakan Desert, verify the relationships between soil grain composition and the fractal dimension, and analyze the relationships between soil GSD and environmental factors. Soils of the Tamarix cones from 0 to 500 cm soil depth were sampled every 20 cm at four sites (Qiemo, Qira, Aral, and Tazhong) along the periphery to the hinterland of the Taklimakan Desert. A total of 300 soil samples were collected to measure soil grain sizes and soil properties. Soil grain size composition was dominated by silt and very fine sand, and the fraction of fine particles decreased and that of the coarse particles increased with soil depth, except for at Tazhong. This suggested that suspension-size particles are the main component of the soil GSD and decrease with the increasing depth in the profiles at the Tamarix cones. The soils were poorly and moderately poorly sorted. Kurtosis generally showed a mesokurtic peak, and the GSD was negatively skewed towards the coarser particles. The fractal dimensions of GSD decreased in the following order Qiemo (2.30) > Qira (2.07) > Aral (1.99) > Tazhong (1.96) because of the increase of coarse particles. The fractal dimension had a strong positive correlation with the clay and silt fractions, and a strong negative correlation with the sand fraction, indicating that the fractal dimension can reflect the characteristics of the soil GSD. The strong relationships between the fractal dimensions and selected soil properties indicate that the fractal dimension can not only quantify changes in soil properties, but also reflect the degree of desertification and degradation in the desert region. Considering the strong wind activities and different deposition sources in the Taklimakan Desert, this study provides a deep insight into the soil formation processes of Tamarix cones within extreme arid desert ecosystems.
Flapping and powering characteristics of a flexible piezoelectric nanogenerator at Reynolds number range simulating ocean current
Authors: Moon Joonkyeong , Kang Giho , Im Busi , Kim Jihoon , Cho Dae-Hyun , Byun Doyoung 
Published: October 2022

AbstractFor effective ocean energy harvesting, it is necessary to understand the coupled motion of the piezoelectric nanogenerator (PENG) and ocean currents. Herein, we experimentally investigate power performance of the PENG in the perspective of the fluid–structure interaction considering ocean conditions with the Reynolds number (Re) values ranging from 1 to 141,489. A piezoelectric polyvinylidene fluoride micromesh was constructed via electrohydrodynamic (EHD) jet printing technique to produce the β-phase dominantly that is desirable for powering performance. Water channel was set to generate water flow to vibrate the flexible PENG. By plotting theRevalues as a function of nondimensional bending rigidity (KB) and the structure-to-fluid mass ratio (M*), we could find neutral curves dividing the stable and flapping regimes. Analyzing the flow velocities between the vortex and surroundings via a particle image velocimetry, the larger displacement of the PENG in the chaotic flapping regime than that in the flapping regime was attributed to the sharp pressure gradient. By correlatingM*,Re,KB, and the PENG performance, we conclude that there is criticalKBthat generate chaotic flapping motion for effective powering. We believe this study contributes to the establishment of a design methodology for the flexible PENG harvesting of ocean currents.
Increased Type I interferon signaling and brain endothelial barrier dysfunction in an experimental model of Alzheimer’s disease
Authors: Jana Arundhati , Wang Xinge , Leasure Joseph W. , Magana Lissette , Wang Li , Kim Young-Mee , Dodiya Hemraj , Toth Peter T. , Sisodia Sangram S. , Rehman Jalees 
Published: October 2022

AbstractBlood–brain barrier (BBB) dysfunction is emerging as a key pathogenic factor in the progression of Alzheimer’s disease (AD), where increased microvascular endothelial permeability has been proposed to play an important role. However, the molecular mechanisms leading to increased brain microvascular permeability in AD are not fully understood. We studied brain endothelial permeability in female APPswe/PS1∆E9 (APP/PS1) mice which constitute a transgenic mouse model of amyloid-beta (Aβ) amyloidosis and found that permeability increases with aging in the areas showing the greatest amyloid plaque deposition. We performed an unbiased bulk RNA-sequencing analysis of brain endothelial cells (BECs) in female APP/PS1 transgenic mice. We observed that upregulation of interferon signaling gene expression pathways in BECs was among the most prominent transcriptomic signatures in the brain endothelium. Immunofluorescence analysis of isolated BECs from female APP/PS1 mice demonstrated higher levels of the Type I interferon-stimulated gene IFIT2. Immunoblotting of APP/PS1 BECs showed downregulation of the adherens junction protein VE-cadherin. Stimulation of human brain endothelial cells with interferon-β decreased the levels of the adherens junction protein VE-cadherin as well as tight junction proteins Occludin and Claudin-5 and increased barrier leakiness. Depletion of the Type I interferon receptor in human brain endothelial cells prevented interferon-β-induced VE-cadherin downregulation and restored endothelial barrier integrity. Our study suggests that Type I interferon signaling contributes to brain endothelial dysfunction in AD.