bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reaction-based fluorogenic probes for selective detection of cysteinyl oxidation in living cells
Authors: Ferreira Renan , Fu Ling , Yang Jing , Carroll Kate 
Published: October 2021

Abstract
Measuring reactive oxygen, nitrogen and sulfur species in cells is established technology, but turn-on fluorescence tools for detecting the products of their reaction with protein cysteines remain essentially unknown. Toward this goal, here we describe fluorogenic probes for sulfenic acid, a redox modification of protein cysteines inextricably linked to signaling and oxidative stress. The probes, called CysOx1 and CysOx2, are reaction-based, exhibit excellent cell permeability, rapid reactivity, and high selectivity with minimal cytotoxicity. We applied CysOx2 in a cell-based 96-well plate assay to determine whether kinase inhibitors modulate protein S-sulfenylation as well as O-phosphorylation. Analysis of these data revealed an unexpected positive association of S-sulfenylation and inhibition of select kinases within the TK, AGC, and CMGC families including GSK3, a multitasking Ser/Thr kinase and emerging therapeutic target for neurodegenerative and mood disorders. Chemoproteomic mapping of sulfenic acid-modified cysteines in GSK3 inhibitor-treated cells shows that sites of S-oxidation localize to regulatory cysteines within key components of antioxidant defense systems. Our studies with CysOx probes offer up new insights into kinase-inhibitor dependent modulation of sulfenylome dynamics and should accelerate future efforts in the modern era of translational redox medicine.
Road Network Evolution in the Urban and Rural United States Since 1900
Authors: Burghardt Keith , Uhl Johannes , Lerman Kristina , Leyk Stefan 
Published: October 2021

Abstract
We examine a key component of human settlements mediating pollution and congestion, as well as economic development: roads and their expansion in cities, towns, and villages. Our analysis of road networks in more than 850 US cities and rural counties since 1900 reveals significant variations in the structure of roads both within cities and across the conterminous US. Despite differences in the evolution of these networks, there are commonalities: newer roads tend to become less grid-like. These results persist across the rural-urban continuum and are therefore not just a product of urban growth. These findings illuminate the need for policies for urban and rural planning including the critical assessment of new development trends.
Effect of Chemical Treatment on Silicon Manganese: Its Morphological, Elemental and Spectral Properties and Its Usage in Concrete
Authors: Yun Chin Mei , Bakri Muhammad Khusairy Bin , Rahman Md Rezaur , Kuok Kuok King , Khui Perry Law Nyuk 
Published: October 2021

Abstract
The effect of chemical treatment on silicon manganese slag and the effect of curing time on the compressive strength of completely replacement coarse aggregate silicon manganese concrete (SMC) relative to normal weight concrete (NWC) with gravel as coarse aggregate is the subject of this paper. Alkali and acidic base chemicals are used to alter the neat silicon manganese slag during chemical preparation. The mixture pattern proportions for Grade 30 and Grade 50, respectively, were used to create the concrete. Before the compressive strength tests, the samples were cast and cured for 7-, 14-, and 28-days. The properties of the silicon manganese slag and its concrete were studied using a scanning electron microscope (SEM), energy dispersive x-ray spectroscopy (EDS), and Fourier transform infrared spectroscopy (FTIR). The compressive pressure of SMC30 and SMC50 obtained were 37.3 MPa and 51.1 MPa, respectively, on the 28-day. The alkaline treatment smoothest the matrix, while the acid treatment roughens the composition of the silicon manganese slag, according to SEM. The functional group demonstrated a major improvement in FTIR, while EDS revealed a high content of both silicon (Si) and manganese (Mn) elements. As a result, it can be observed that the power of SMC increases as the curing time increases for samples with complete replacement of normal aggregates using silicon slag
Delivering CBT-E In an Online Group Format: A Pilot Study in a Child and Adolescent Eating Disorder Service
Authors: Hamadi Layla , Hilson Reece , Lunn Amy , Ralph Emily , Rodrigues Evangeline , Sohail Rabeeah 
Published: October 2021

Abstract
Background: The increased prevalence of eating disorders during the COVID-19 pandemic has placed services for children and adolescents under immense pressure. The high number of people at medical risk has led to longer waiting lists for psychological support for those who are physically stable. A pilot study was conducted to evaluate the feasibility and effectiveness of providing group enhanced cognitive behavioral therapy for eating disorders (CBT-E), in a virtual setting, as a way of increasing the provision of evidence-based treatment during the pandemic.Method: Clinicians in a child and adolescent eating disorder service were invited to refer patients to take part in a six-session course of therapy comprising the CBT-E Stage Three Body Image module. Primary outcomes were acceptance rates, completion rates, qualitative feedback and quantitative data from routine measures of eating disorder psychopathology and psychosocial impairment.Results: From 22 eligible referrals, 12 participants accepted and enrolled in therapy. Eight completed all six sessions. Qualitative feedback was positive. Both the content and group nature of the intervention were described as helpful. There was an improvement in all scores on the psychometric tests. Conclusions: This pilot study demonstrated that online group CBT-E was a feasible method of providing psychological therapy within the service. A larger trial is recommended to robustly test the effectiveness of the intervention compared to one-to-one in-person CBT-E, and to test whether other modules of the CBT-E protocol can be similarly delivered in this population.Trial registration: This study was pre-registered and approved as a clinical service evaluation by the Oxford Health NHS Foundation Trust, United Kingdom
Tempo and drivers of plant diversification in the European mountain system
Authors: Smycka Jan , Roquet Cristina , Boleda Martí , Alberti Adriana , Boyer Frédéric , Douzet Rolland , Perrier Christophe , Rome Maxime , Valay Jean-Gabriel , Denoeud France , Šemberová Kristýna , Zimmermann Niklaus , Thuiller Wilfried , Wincker Patrick , Alsos Inger , Coissac Eric , Lavergne Sebastien 
Published: October 2021

Abstract
There is still limited consensus on the evolutionary history of the species-rich temperate alpine floras due to a lack of comparable and high-quality phylogenetic data covering multiple plant lineages. Here we reconstructed when and how European alpine plant lineages diversified, i.e., the tempo and drivers of speciation events. We performed full-plastome phylogenomics and used multi-clade comparative models applied to six representative angiosperm lineages that have diversified in the European mountains. The diversification rates remained surprisingly steady for most clades, even during Pleistocene glaciations, with speciation events being mostly driven by geographic divergence and bedrock shifts. Interestingly, we inferred asymmetrical historical migration rates from siliceous to calcareous bedrocks, and from higher to lower elevations, likely due to repeated shrinkage and expansion of high elevation habitats during the Pleistocene. This may have buffered climate-related extinctions, but prevented plant speciation along elevation gradients as are often documented for tropical alpine floras.
Prognostic Value of Critical Laboratory Values in Burn Patients: a Retrospective Observational Study
Authors: Lin Jian-Chang , Su Jian-Sheng , Zheng Jian-Jun , Chen Xiao-Dong , Chen Zhao-Hong 
Published: October 2021

Abstract
Background: Information about the relative importance of critical laboratory values in burn patients has not yet been reported. The purpose of this study was to investigate the morbidity of analytes of critical laboratory values and their association with in-hospital mortality in burn patients.Methods: This was a retrospective observational study. The clinical data and critical laboratory values of burn patients admitted to the Fujian Province Burn Center from July 1, 2017, to May 1, 2021, were downloaded from the Big Data Center of Fujian Medical University Union Hospital. The morbidity of analytes of critical laboratory values and the impact of these critical laboratory results on in-hospital mortality were investigated. Logistic regression analysis was performed to analyse the independent association between analytes of critical laboratory values and in-hospital mortality in burn patients.Results: There were 18 common analytes of critical laboratory values in burn patients in a provincial burn centre, and their morbidity was as follows: hypertroponinemia, alkalemia, positive blood culture (PBC), acidaemia, hypocapnia, hypercapnia, hypocalcaemia, hypoxemia, hyperglycaemia, high activated partial thrombin time (APPT), hypokalaemia, hypernatremia, hypofibrinogenemia, hypohemoglobinemia, hyperkalaemia, hypoglycaemia, hypothrombosis and high prothrombin time (PT). Compared with patients without critical laboratory results, patients with critical laboratory results had a significantly higher in-hospital mortality rate (P < 0.001). The in-hospital mortality of patients with two or more analytes of critical laboratory values was significantly higher than that of patients with one analyte (P < 0.001). Multivariate logistic regression analysis showed that the critical results of hyperglycaemia (P = 0.005), hyperkalaemia (P = 0.030), hypofibrinogenemia (P = 0.015), hypertroponinemia (P = 0.023) and hypoxemia (P = 0.008) were all independently associated with in-hospital mortality.Conclusion: In a group of hospitalized burn patients at a provincial burn centre, the morbidity of analytes of critical laboratory values and their association with in-hospital mortality were investigated for the first time. The critical results of hyperglycaemia, hyperkalaemia, hypofibrinogenemia, hypertroponinemia and hypoxemia were all independent risk factors for in-hospital mortality in burn patients.
Aging and the risks of all-cause and cause-specific mortality among diabetics: a prospective cohort study
Authors: Chen Li , Zhao Ying , Chen Huimin , Tan Tianqi , Yao Ping , Tang Yuhan 
Published: October 2021

Abstract
BackgroundAging is an important driver for age-related diseases and death, but the evidence regarding the effects of aging on diabetics is limited. This study aims to evaluate the associations of aging with all-cause and cause-specific mortality among diabetics.MethodsA total of 5,278 diabetics from the National Health and Nutrition Examination Survey 1999-2014 were included. The aging status was measured from different perspectives, including Phenotypic Age, Biological Age, telomere length, and Klotho concentration. Cox proportional hazards models were used to examine the relationships between aging and all-cause, cardiovascular disease (CVD), and cancer mortality. Mediation analysis was performed to elucidate the role of aging in associations of metformin with mortality.Results Over median follow-up for 7.3 years, 1,355 diabetics died. There was a positive and linear association of mortality with Phenotypic Age (hazard ratio (HR)all-cause 1.05, 95% confidence interval (CI) 1.05-1.06; HRCVD 1.05, 95%CI 1.04-1.07; HRcancer 1.05, 95%CI 1.04-1.07; all P<0.001) and Biological Age (HRall-cause 1.07, 95%CI 1.05-1.08; HRCVD 1.08, 95%CI 1.05-1.10; HRcancer 1.05, 95%CI 1.03-1.08; all P<0.001). Telomere length was inversely associated with all-cause mortality (tertile (T)3 vs. T1: HR 0.67, 95%CI 0.45-0.98; Ptrend=0.036). The concentration of Klotho had a U-shaped relationship with mortality (T2 vs. T1: HRall-cause 0.62, 95%CI 0.43-0.88; HRCVD 0.48, 95%CI 0.26-0.86; HRcancer 0.47 95%CI 0.25-0.88). Additionally, metformin users had a lower HR for mortality compared to those without use (HRall-cause 0.64, 95%CI 0.56-0.73; HRCVD 0.51, 95%CI 0.37-0.70; HRcancer 0.65, 95%CI 0.44-0.95; all P<0.001), which was partly mediated by Phenotypic Age and Biological Age. ConclusionsThese findings suggested aging was a noteworthy risk factor of mortality for diabetics and therapies targeting anti-aging could be encouraged to halt the progression of diabetes.
Interferenceless Coded Aperture Correlation Holography with Point Spread Holograms of Isolated Chaotic Islands for 3D Imaging
Authors: Dubey Nitin , Rosen Joseph 
Published: October 2021

Abstract
Interferenceless coded aperture correlation holography (I-COACH) is an incoherent digital holographic technique with lateral and axial resolution similar to a regular lens-based imaging system. The properties of I-COACH are dictated by the shape of the system’s point response termed point spread hologram (PSH). As previously shown, chaotic PSHs which are continuous over some area on the image sensor enable the system to perform three-dimensional (3D) holographic imaging. We also showed that a PSH of an ensemble of sparse dots improves the system’s signal-to-noise ratio (SNR) but reduces the dimensionality of the imaging from three to two dimensions. In this study, we test the midway shape of PSH, an ensemble of sparse islands distributed over the sensor plane. A PSH of isolated chaotic islands improves the SNR of the system compared to continuous chaotic PSH without losing the capability to perform 3D imaging. Reconstructed images of this new system are compared with images of continuous PSH, dot-based PSH, and direct images of a lens-based system. Visibility, SNR, and the product of visibility with SNR are the parameters used in the study. We also demonstrate the imaging capability of a system with partial annular apertures. The reconstruction results have better SNR and visibility than lens-based imaging systems with the same annular apertures.
Catestatin Selects for the Colonization of Antimicrobial-Resistant Gut Bacterial Communities
Authors: González-Dávila Pamela , Schwalbe Markus , Danewalia Arpit , Dalila Boushra , Verbeke Kristin , Mahata Sushil , Aidy Sahar El 
Published: October 2021

Abstract
The gut microbiota is in continuous interaction with the innermost layer of the gut, namely the epithelium. Among the various functions of the gut epithelium, is to keep the microbes at bay to avoid overstimulation of the underlying mucosa immune cells. To do so, the gut epithelia secrete a variety of antimicrobial peptides, such as catestatin (CST). As a defense mechanism, gut microbes have evolved antimicrobial resistance mechanisms to counteract the killing effect of the secreted peptides. To this end, we treated wild-type mice and mice with a knockout in the CST coding region of the chromogranin-A gene (CST-KO) with CST for 15 consecutive days. CST treatment was associated with a shift in the diversity and composition of the microbiota in the CST-KO mice. This effect was less prominent in WT mice. Levels of the microbiota-produced short-chain fatty acids, in particular, butyrate and acetate were significantly increased in CST-treated CST-KO mice but not the WT group. Remarkably, both CST-treated CST-KO and WT mice showed a significant increase in microbiota-harboring phosphoethanolamine transferase-encoding genes, which facilitate their antimicrobial resistance. Finally, we show that CST was degraded by Escherichia coli via an omptin-protease and that the abundance of this gene was significantly higher in metagenomic datasets collected from patients with Crohn’s disease but not with ulcerative colitis. Overall, this study illustrates how the endogenous antimicrobial peptide, CST, shapes the microbiota composition in the gut and primes further research to uncover the role of bacterial resistance to CST in disease states such as inflammatory bowel disease.
Research On Water-Immersion Softening Mechanism of Coal Rock Mass Based on Split Hopkinson Pressure Bar Experiment
Authors: Liu Zhiyuan , Wang Gang , Li Jinzhou , Li Huaixing , Zhao Haifeng , Shi Hongwei , Lan Jianli 
Published: October 2021

Abstract
The coal mining process is affected by multiple sources of water such as groundwater and coal seam water injection. Understanding the dynamic mechanical parameters of water-immersed coal is helpful to the safe production of coal mines. The impact compression tests were performed on coal with different moisture contents by using the ϕ50 mm Split Hopkinson Pressure Bar (SHPB) experimental system, and the dynamic characteristics and energy loss laws of water-immersed coal with different compositions and water contents were analyzed. Through analysis and discussion, it is found that: (1) When the moisture content of the coal sample is 0%, 30%, 60%, the stress, strain rate and energy first increase and then decrease with time; (2) When the moisture content of the coal sample increases from 30% to 60%, the stress "plateau" of the coal sample disappears, resulting in an increase in the interval of the compressive stress and a decrease in the interval of the expansion stress. (3) The increase of the moisture content of the coal sample will affect its impact deformation and failure mode. When the moisture content is 60%, the incident rod end and the transmission rod end of the coal sample will have obvious compression failure, and the middle part of the coal sample will also experience expansion and deformation. (4) The coal composition ratio suitable for the impact experiment of coal immersion softening is optimized.
An intra-cytoplasmic route for SARS-CoV-2 transmission unveiled by Helium-ion microscopy
Authors: Merolli Antonio , Kasaei Leila , Ramsamy Santhamani , Kolloli Afsal , Kumar Ranjeet , Subbian Selvakumar , Feldman Leonard 
Published: October 2021

Abstract
SARS-CoV-2 virions enter the host cells by docking their spike glycoproteins to the membrane-bound Angiotensin Converting Enzyme 2. After intracellular assembly, the newly formed virions are released from the infected cells to propagate the infection, using the extra-cytoplasmic ACE2 docking mechanism. However, the molecular events underpinning SARS-CoV-2 transmission between host cells are not fully understood. Here, we report the findings of a scanning Helium-ion microscopy study performed on Vero E6 cells infected with mNeonGreen-expressing SARS-CoV-2. Our data reveal, with unprecedented resolution, the presence of: 1)-long tunneling nanotubes that connect two or more host cells over submillimeter distances; 2)-large scale multiple cell fusion events (syncytia); and 3)-abundant extracellular vesicles of various sizes. Taken together, these ultrastructural features describe a novel intra-cytoplasmic connection among SARS-CoV-2 infected cells that may act as an alternative route of viral transmission, disengaged from the well-known extra-cytoplasmic ACE2 docking mechanism. Our findings may explain the elusiveness of SARS-CoV-2 to survive from the immune surveillance of the infected host.
The Stay Strong App as a Self-Management Tool for First Nations People with Chronic Kidney Disease: A Qualitative Study
Authors: Nagel Tricia , Dingwall Kylie M. , Sweet Michelle , Kavanagh David , Majoni Sandawana W. , Sajiv Cherian , Cass Alan 
Published: October 2021

Abstract
Background: The high burden of chronic kidney disease and its substantial impact on quality of life demands innovative patient care strategies. Improved outcomes are linked with patient centred interventions which address psychosocial as well as physical needs. Given the high incidence of kidney disease among First Nations people, culturally responsive approaches are also needed. The Stay Strong app is a holistic wellbeing tool designed with Northern Territory First Nations people. This study explores the suitability of the Stay Strong app as a patient-centred self-management tool as shown by the readiness of participants to engage in goal setting. Data were collected during a clinical trial which showed efficacy of the tool in improving wellbeing for people with both End Stage Kidney Disease and symptoms of distress and depression. Methods: First Nations (i.e., Aboriginal and Torres Strait Islander) participants receiving haemodialysis in the Northern Territory (n = 156) entered a three-arm, waitlist, single-blind randomised controlled trial which provided collaborative goal setting using the Stay Strong app at baseline or at 3 months. Qualitative data gathered during delivery of the intervention were examined using both content and thematic analysis. Results: Almost all participants (147, 94%) received a Stay Strong session: of these, 135 (92%) attended at least two sessions, and 83 (56%) set more than one wellbeing goal. Using a deductive approach to manifest content, 13 categories of goals were identified. The three most common were to: ‘connect with family or other people’, ‘go bush/be outdoors’ and ‘go home/be on country’. Analysis of latent content identified three themes throughout the goals: ‘social and emotional wellbeing’, ‘physical health’ and ‘cultural connection’. Conclusion: This study provides evidence of the suitability of the Stay Strong app for use as a chronic condition self-management tool for First Nations people. Participants set goals that addressed physical as well as social and emotional wellbeing needs. The goal setting intervention aligns directly with self-management approaches that are holistic and prioritise individual empowerment. While biomedical models focus on the mechanics of illness, the findings share a strong message that healing also comes through family, country, and cultural identity. Implementation of self-management strategies into routine care remains a key challenge and further research is needed to establish drivers of success.
A Soil-Borne Mn(II)-Oxidizing Bacterium of Providencia sp. Exploits a Strategy of Superoxide Production Coupled To Hydrogen Peroxide Consumption To Generate Mn Oxides
Authors: Chen Sha , Ding Zhexu , Chen Jinyuan , Luo Jun , Ruan Xiaofang , Li Zongpei , Liao Fengfeng , He Jing , Li Ding 
Published: October 2021

Abstract
Bacterial non-enzymatic Mn(II) oxidation involving reactive oxygen species (ROS) (i.e. indirect oxidation), initially discovered from a marine alpha-proteobacterium, is believed to be of importance in controlling biogeochemical cycles. For soil-borne bacteria, however, evidence of indirect Mn(II) oxidation remains unclear. In this study, the indirect Mn(II) oxidation was evidenced in a soil-borne bacterium, Providencia sp. LLDRA6. First, with and without 50 mM of Mn(II) exposure for LLDRA6, 300 differentially expressed genes were found to be linked to Mn(II) exposure via transcriptome sequencing. Among them, an operon, responsible for phenylacetic acid catabolism, was sharply upregulated in transcription, drawing us a special attention since its transcriptional upregulation has recently shown to be important for withstanding ROS. Next, a fluorometric probe, 2′,7′-Dichlorofluorescin diacetate (DCFDA), was used to qualitatively detect ROS from cells, showing a distinct increase in fluorescence intensities of ROS during Mn(II) exposure. Further, concentrations of superoxide and hydrogen peroxide from cells were detected respectively with and without Mn(II) exposure, exhibiting that when Mn(II) oxidation occurred, superoxide concentration significantly increased but hydrogen peroxide concentration significantly decreased. Particularly, superoxide produced by LLDRA6 was proven to be the oxidant for Mn(II) in the formation of Mn oxides. Finally, we predicted links between phenylacetic acid metabolism pathway and ROS during Mn(II) exposure, proposing that the excessive ROS, generated in response to Mn(II) exposure, transcriptionally activate phenylacetic acid catabolism presumably by increasing concentrations of highly reactive oxepins.