bluuebunny/crossref_metadata_2025 huggingface dataset:
The Cryo-EM structures of two amphibian antimicrobial cross-β amyloid fibrils
Authors: Bücker Robert , Seuring Carolin , Cazey Cornelia , Veith Katharina , García-Alai Maria , Grünewald Kay , Landau Meytal
Published: July 2022

The amyloid-antimicrobial link hypothesis is based on antimicrobial properties found in human amyloids involved in neurodegenerative and systemic diseases, along with amyloidal structural properties found in antimicrobial peptides (AMPs). Supporting this hypothesis, we here determined the fibril structure of two AMPs from amphibians, uperin 3.5 and aurein 3.3, by cryogenic electron microscopy (cryo-EM), revealing amyloid cross-β fibrils of mated β-sheets at atomic resolution. Uperin 3.5 formed a 3-blade symmetrical propeller of nine peptides per fibril layer including tight β-sheet interfaces. This cross-β cryo-EM structure complements the cross-α fibril conformation previously determined by crystallography, substantiating a secondary structure switch mechanism of uperin 3.5. The aurein 3.3 arrangement consisted of six peptides per fibril layer, all showing kinked β-sheets allowing a rounded compactness of the fibril. The kinked β-sheets are similar to LARKS (Low-complexity, Amyloid-like, Reversible, Kinked Segments) found in human functional amyloids.
Ports’ criticality in international trade and global supply-chains
Authors: Verschuur J. , Koks E. E. , Hall J. W.
Published: July 2022

We quantify the criticality of the world’s 1300 most important ports for global supply chains by predicting the allocation of trade flows on the global maritime transport network, which we link to a global supply-chain database to evaluate the importance of ports for the economy. We find that 50% of global trade in value terms is maritime, with low-income countries and small islands being 1.5 and 2.0 times more reliant on their ports compared to the global average. The five largest ports globally handle goods that embody >1.4% of global output, while 40 ports add >10% of domestic output of the economies they serve, predominantly small islands. We identify critical cross-border infrastructure dependencies for some landlocked and island countries that rely on specific ports outside their jurisdiction. Our results pave the way for developing new strategies to enhance the resilience and sustainability of port infrastructure and maritime trade.
Contextuality in infinite one-dimensional translation-invariant local Hamiltonians
Authors: Yang Kaiyan , Zeng Xiao , Luo Yujing , Yang Guowu , Shu Lan , Navascués Miguel , Wang Zizhu
Published: July 2022

In recent years there has been a growing interest in treating many-body systems as Bell scenarios, where lattice sites play the role of distant parties and only near-neighbor statistics are accessible. We investigate contextuality arising from three Bell scenarios in infinite, translation-invariant 1D models: nearest-neighbor with two dichotomic observables per site; nearest- and next-to-nearest neighbor with two dichotomic observables per site, and nearest-neighbor with three dichotomic observables per site. For the first scenario, we give strong evidence that it cannot exhibit contextuality, not even in non-signaling physical theories beyond quantum mechanics. For the second one, we identify several low-dimensional models that reach the ultimate quantum limits, paving the way for self-testing ground states of quantum many-body systems. For the last scenario, which generalizes the Heisenberg model, we give strong evidence that, in order to exhibit contextuality, the dimension of the local quantum system must be at least 3.
Akkermansia muciniphila phospholipid induces homeostatic immune responses
Authors: Bae Munhyung , Cassilly Chelsi D. , Liu Xiaoxi , Park Sung-Moo , Tusi Betsabeh Khoramian , Chen Xiangjun , Kwon Jaeyoung , Filipčík Pavel , Bolze Andrew S. , Liu Zehua , Vlamakis Hera , Graham Daniel B. , Buhrlage Sara J. , Xavier Ramnik J. , Clardy Jon
Published: July 2022

Multiple studies have established associations between human gut bacteria and host physiology, but determining the molecular mechanisms underlying these associations has been challenging1–3. Akkermansia muciniphila has been robustly associated with positive systemic effects on host metabolism, favourable outcomes to checkpoint blockade in cancer immunotherapy and homeostatic immunity4–7. Here we report the identification of a lipid from A. muciniphila’s cell membrane that recapitulates the immunomodulatory activity of A. muciniphila in cell-based assays8. The isolated immunogen, a diacyl phosphatidylethanolamine with two branched chains (a15:0-i15:0 PE), was characterized through both spectroscopic analysis and chemical synthesis. The immunogenic activity of a15:0-i15:0 PE has a highly restricted structure–activity relationship, and its immune signalling requires an unexpected toll-like receptor TLR2–TLR1 heterodimer9,10. Certain features of the phospholipid’s activity are worth noting: it is significantly less potent than known natural and synthetic TLR2 agonists; it preferentially induces some inflammatory cytokines but not others; and, at low doses (1% of EC50) it resets activation thresholds and responses for immune signalling. Identifying both the molecule and an equipotent synthetic analogue, its non-canonical TLR2–TLR1 signalling pathway, its immunomodulatory selectivity and its low-dose immunoregulatory effects provide a molecular mechanism for a model of A. muciniphila’s ability to set immunological tone and its varied roles in health and disease.
Cortical feedback loops bind distributed representations of working memory
Authors: Voitov Ivan , Mrsic-Flogel Thomas D.
Published: July 2022

Working memory—the brain’s ability to internalize information and use it flexibly to guide behaviour—is an essential component of cognition. Although activity related to working memory has been observed in several brain regions1–3, how neural populations actually represent working memory4–7 and the mechanisms by which this activity is maintained8–12 remain unclear13–15. Here we describe the neural implementation of visual working memory in mice alternating between a delayed non-match-to-sample task and a simple discrimination task that does not require working memory but has identical stimulus, movement and reward statistics. Transient optogenetic inactivations revealed that distributed areas of the neocortex were required selectively for the maintenance of working memory. Population activity in visual area AM and premotor area M2 during the delay period was dominated by orderly low-dimensional dynamics16,17 that were, however, independent of working memory. Instead, working memory representations were embedded in high-dimensional population activity, present in both cortical areas, persisted throughout the inter-stimulus delay period, and predicted behavioural responses during the working memory task. To test whether the distributed nature of working memory was dependent on reciprocal interactions between cortical regions18–20, we silenced one cortical area (AM or M2) while recording the feedback it received from the other. Transient inactivation of either area led to the selective disruption of inter-areal communication of working memory. Therefore, reciprocally interconnected cortical areas maintain bound high-dimensional representations of working memory.
Community established best practice recommendations for tephra studies—from collection through analysis
Authors: Wallace Kristi L. , Bursik Marcus I. , Kuehn Stephen , Kurbatov Andrei V. , Abbott Peter , Bonadonna Costanza , Cashman Katharine , Davies Siwan M. , Jensen Britta , Lane Christine , Plunkett Gill , Smith Victoria C. , Tomlinson Emma , Thordarsson Thor , Walker J. Douglas
Published: July 2022

Tephra is a unique volcanic product with an unparalleled role in understanding past eruptions, long-term behavior of volcanoes, and the effects of volcanism on climate and the environment. Tephra deposits also provide spatially widespread, high-resolution time-stratigraphic markers across a range of sedimentary settings and thus are used in numerous disciplines (e.g., volcanology, climate science, archaeology). Nonetheless, the study of tephra deposits is challenged by a lack of standardization that inhibits data integration across geographic regions and disciplines. We present comprehensive recommendations for tephra data gathering and reporting that were developed by the tephra science community to guide future investigators and to ensure that sufficient data are gathered for interoperability. Recommendations include standardized field and laboratory data collection, reporting and correlation guidance. These are organized as tabulated lists of key metadata with their definition and purpose. They are system independent and usable for template, tool, and database development. This standardized framework promotes consistent documentation and archiving, fosters interdisciplinary communication, and improves effectiveness of data sharing among diverse communities of researchers.
Standard metadata for 3D microscopy
Authors: Ropelewski Alexander J. , Rizzo Megan A. , Swedlow Jason R. , Huisken Jan , Osten Pavel , Khanjani Neda , Weiss Kurt , Bakalov Vesselina , Engle Michelle , Gridley Lauren , Krzyzanowski Michelle , Madden Tom , Maiese Deborah , Mandal Meisha , Waterfield Justin , Williams David , Hamilton Carol M. , Huggins Wayne
Published: July 2022

Recent advances in fluorescence microscopy techniques and tissue clearing, labeling, and staining provide unprecedented opportunities to investigate brain structure and function. These experiments’ images make it possible to catalog brain cell types and define their location, morphology, and connectivity in a native context, leading to a better understanding of normal development and disease etiology. Consistent annotation of metadata is needed to provide the context necessary to understand, reuse, and integrate these data. This report describes an effort to establish metadata standards for three-dimensional (3D) microscopy datasets for use by the Brain Research through Advancing Innovative Neurotechnologies® (BRAIN) Initiative and the neuroscience research community. These standards were built on existing efforts and developed with input from the brain microscopy community to promote adoption. The resulting 3D Microscopy Metadata Standards (3D-MMS) includes 91 fields organized into seven categories: Contributors, Funders, Publication, Instrument, Dataset, Specimen, and Image. Adoption of these metadata standards will ensure that investigators receive credit for their work, promote data reuse, facilitate downstream analysis of shared data, and encourage collaboration.
Factors associated with stroke associated pneumonia among adult stroke patients admitted to university of Gondar hospital, Northwest Ethiopia
Authors: Assefa Messay , Tadesse Abilo , Adane Aynishet , Yimer Mekonnen , Tadesse Melaku
Published: July 2022

Stroke is the major cause of disability and death in sub-Saharan African countries. The presence and severity of complications play a major role in the outcome of stroke. Stroke associated pneumonia is often noticed post stroke infection that has been linked to an increased risk of hospital mortality, a longer hospital stay and higher healthcare expenses. Report on details of stroke-associated pneumonia has never been documented in countries of sub-Saharan Africa. This study aimed to determine the incidence and risk factors of stroke-associated pneumonia among adult stroke patients in hospital settings, Northwest Ethiopia. The study was undertaken at a stroke care unit, University of Gondar hospital between January 1, 2020 and December 31, 2020. A convenience sampling method was used to recruit study subjects. Relevant clinical history was taken, focused physical examination was done, and brain imaging (CT scan or MRI) was performed to settle the diagnosis of stroke. A modified Centre for Disease Control and Prevention (CDC) criteria was used to diagnose stroke-associated pneumonia. All patients with stroke-associated pneumonia were treated according to the 2016 Infectious Diseases Society of America/American Thoracic Society Clinical Practice Guidelines. The Data were cleaned in Epi Info version 4.6.0.2, and analyzed using SPSS version 26. Variables associated with stroke-associated pneumonia were computed using logistic regression analysis. P value < 0.05 was considered to declare statistical significance. The study comprised a total of 325 adult stroke patients. The mean age of study subjects was 65.2 years (SD ± 15.7). The most prevalent type of stroke was ischemic stroke, which accounted for 68% of all cases. Hemiparesis (94%), facial palsy (87%), and swallowing disturbance (51%) were the frequently noticed neurological findings. Stroke-associated pneumonia complicated 116/325 (36%) of stroke patients. Multi-variate regression analysis revealed that patients who were elderly (age > 75 years) (AOR = 3.910, CI 1.181–12.936, P = 0.026), had swallowing disturbance (AOR = 4.656, CI 2.356–9.202, P-value < 0.001), epileptic seizures (AOR = 2.678, 95% CI 1.253–5.721, P-value < 0.001) and moderate to severe stroke (NIHSS score = 16–21) (AOR = 5.994, 95% CI 2.043–17.585, P-value < 0.001) were at risk of developing stroke-associated pneumonia. SAP was a substantial medical complication among stroke patients. Early identification and prompt intervention measures for the identified risk factors might address the burden of SAP.
Structural, electrical, and magnetic properties of nano Sr1−XLaXFe12O19 (X = 0.2–0.8)
Authors: Baba Basha D. , Suresh Kumar N. , Chandra Babu Naidu K. , Ranjith Kumar G.
Published: July 2022

The current work is mainly devoted to the synthesis, structural, electrical, and magnetic characterization of Sr1−XLaXFe12O19 (X = 0.2–0.8) (SLFO) nanoparticles synthesized via the hydrothermal technique. The hexagonal peaks were determined using X-ray diffraction analysis. The obtained results indicated that the lattice constants were noted to be increasing from 0.58801 to 0.58825 nm (a = b), and 2.30309 to 2.30341 nm (c) with increase of in ‘X’. The morphological studies ensured that the grains as well as nanoparticles of SLFO acquired almost spherical shape. The optical properties were investigated using FTIR and UV–Visible spectra. The optical bandgap (Eg) of SLFO was found to be increasing from 1.866 to 2.118 eV with increase of dopant content. The electrical properties of SLFO were studied in detail as a function of temperature, and frequency. In addition, the dielectric modulus, and impedance spectroscopy analysis was carried out to describe the space charge polarization, and electric conduction mechanism, respectively. The hysteresis loop (M–H curves) of SLFO revealed the decrease of magnetization from 36.34 to 7.17 emu/g with increase in ‘X’.
Pupal size as a proxy for fat content in laboratory-reared and field-collected Drosophila species
Authors: Enriquez Thomas , Lievens Victoria , Nieberding Caroline M. , Visser Bertanne
Published: July 2022

In arthropods, larger individuals tend to have more fat reserves, but data for many taxa are still missing. For the vinegar fly Drosophila melanogaster, only few studies have provided experimental data linking body size to fat content. This is rather surprising considering the widespread use of D. melanogaster as a model system in biology. Here, we hypothesized that fat content in D. melanogaster is positively correlated with body size. To test this, we manipulated the developmental environment of D. melanogaster by decreasing food availability. We then measured pupal size and quantified fat content of laboratory-reared D. melanogaster. We subsequently measured pupal size and fat content of several field-caught Drosophila species. Starvation, crowding, and reduced nutrient content led to smaller laboratory-reared pupae that contained less fat. Pupal size was indeed found to be positively correlated with fat content. The same correlation was found for field-caught Drosophila pupae belonging to different species. As fat reserves are often strongly linked to fitness in insects, further knowledge on the relationship between body size and fat content can provide important information for studies on insect ecology and physiology.
Left ventricular active strain energy density is a promising new measure of systolic function
Authors: MacIver David H. , Agger Peter , Rodrigues Jonathan C. L. , Zhang Henggui
Published: July 2022

The left ventricular ejection fraction does not accurately predict exercise capacity or symptom severity and has a limited role in predicting prognosis in heart failure. A better method of assessing ventricular performance is needed to aid understanding of the pathophysiological mechanisms and guide management in conditions such as heart failure. In this study, we propose two novel measures to quantify myocardial performance, the global longitudinal active strain energy (GLASE) and its density (GLASED) and compare them to existing measures in normal and diseased left ventricles. GLASED calculates the work done per unit volume of muscle (energy density) by combining information from myocardial strain and wall stress (contractile force per unit cross sectional area). Magnetic resonance images were obtained from 183 individuals forming four cohorts (normal, hypertension, dilated cardiomyopathy, and cardiac amyloidosis). GLASE and GLASED were compared with the standard ejection fraction, the corrected ejection fraction, myocardial strains, stroke work and myocardial forces. Myocardial shortening was decreased in all disease cohorts. Longitudinal stress was normal in hypertension, increased in dilated cardiomyopathy and severely decreased in amyloid heart disease. GLASE was increased in hypertension. GLASED was mildly reduced in hypertension (1.39 ± 0.65 kJ/m3), moderately reduced in dilated cardiomyopathy (0.86 ± 0.45 kJ/m3) and severely reduced in amyloid heart disease (0.42 ± 0.28 kJ/m3) compared to the control cohort (1.94 ± 0.49 kJ/m3). GLASED progressively decreased in the hypertension, dilated cardiomyopathy and cardiac amyloid cohorts indicating that mechanical work done and systolic performance is severely reduced in cardiac amyloid despite the relatively preserved ejection fraction. GLASED provides a new technique for assessing left ventricular myocardial health and contractile function.
Applying machine learning and predictive modeling to retention and viral suppression in South African HIV treatment cohorts
Authors: Maskew Mhairi , Sharpey-Schafer Kieran , De Voux Lucien , Crompton Thomas , Bor Jacob , Rennick Marcus , Chirowodza Admire , Miot Jacqui , Molefi Seithati , Onaga Chuka , Majuba Pappie , Sanne Ian , Pisa Pedro
Published: July 2022

HIV treatment programs face challenges in identifying patients at risk for loss-to-follow-up and uncontrolled viremia. We applied predictive machine learning algorithms to anonymised, patient-level HIV programmatic data from two districts in South Africa, 2016–2018. We developed patient risk scores for two outcomes: (1) visit attendance ≤ 28 days of the next scheduled clinic visit and (2) suppression of the next HIV viral load (VL). Demographic, clinical, behavioral and laboratory data were investigated in multiple models as predictor variables of attending the next scheduled visit and VL results at the next test. Three classification algorithms (logistical regression, random forest and AdaBoost) were evaluated for building predictive models. Data were randomly sampled on a 70/30 split into a training and test set. The training set included a balanced set of positive and negative examples from which the classification algorithm could learn. The predictor variable data from the unseen test set were given to the model, and each predicted outcome was scored against known outcomes. Finally, we estimated performance metrics for each model in terms of sensitivity, specificity, positive and negative predictive value and area under the curve (AUC). In total, 445,636 patients were included in the retention model and 363,977 in the VL model. The predictive metric (AUC) ranged from 0.69 for attendance at the next scheduled visit to 0.76 for VL suppression, suggesting that the model correctly classified whether a scheduled visit would be attended in 2 of 3 patients and whether the VL result at the next test would be suppressed in approximately 3 of 4 patients. Variables that were important predictors of both outcomes included prior late visits, number of prior VL tests, time since their last visit, number of visits on their current regimen, age, and treatment duration. For retention, the number of visits at the current facility and the details of the next appointment date were also predictors, while for VL suppression, other predictors included the range of the previous VL value. Machine learning can identify HIV patients at risk for disengagement and unsuppressed VL. Predictive modeling can improve the targeting of interventions through differentiated models of care before patients disengage from treatment programmes, increasing cost-effectiveness and improving patient outcomes.
Therapeutic effects of isosteviol sodium on non-alcoholic fatty liver disease by regulating autophagy via Sirt1/AMPK pathway
Authors: Mei Ying , Hu Hui , Deng Liangjun , Sun Xiaoou , Tan Wen
Published: July 2022

Isosteviol sodium (STVNa) is a beyerane diterpene synthesized via acid hydrolysis of stevioside, which can improve glucose and lipid metabolism in animals with diabetes. However, it remains unknown whether STVNa can exhibit a therapeutic effect on nonalcoholic fatty liver disease (NAFLD) and its underlying mechanism. We hypothesize that autophagic initiation may play a key role in mediating the development of NAFLD. Herein, we assessed the effects of STVNa on NAFLD and its underlying mechanisms. The results demonstrated that STVNa treatment effectively ameliorated NAFLD in rats fed high-fat diet (HFD). Moreover, STVNa decreased the expression of inflammation-related genes and maintained a balance of pro-inflammatory cytokines in NAFLD rats. STVNa also reduced lipid accumulation in free fatty acid (FFA)-exposed LO2 cells. In addition, STVNa attenuated hepatic oxidative stress and fibrosis in NAFLD rats. Furthermore, STVNa enhanced autophagy and activated Sirtuin 1/adenosine monophosphate-activated protein kinase (Sirt1/AMPK) pathway both in vivo and in vitro, thus attenuating intracellular lipid accumulation. In summary, STVNa could improve lipid metabolism in NAFLD by initiating autophagy via Sirt1/AMPK pathway. Therefore, STVNa may be an alternative therapeutic agent for treatment of NAFLD.
Williamson magneto nanofluid flow over partially slip and convective cylinder with thermal radiation and variable conductivity
Authors: Bilal M. , Siddique Imran , Borawski Andrzej , Raza A. , Nadeem M. , Sallah Mohammed
Published: July 2022

This article is concerned with the study of MHD non-Newtonian nanofluid flow over a stretching/shrinking cylinder along with thermal radiation effects. Two-component slip mechanism models, namely Brownian motion and thermophoresis of nanofluid for the mass and energy transportation, developed by Buongiorno, are used. Convective heat transfer and nonuniform magnetic field are retained for the expanding/contracting cylinder. Variable thermal conductivity and heat generation effects along with slip boundary conditions are utilized over the cylinder surface. By utilizing the similarity transformation, these governing partial differential equations are converted into nonlinear ordinary differential equations (ODEs). To obtain numerical results, these ODE’S are solved by the shooting method using MATLAB software. The impact of different parameters like variable thermal conductivity, radiation parameter, magnetic parameter, Prandtl number, Brownian motion parameter, the magnetic parameter, Weissenberg number, the viscosity ratio parameter and mass transfer parameter, on the velocity, temperature and concentration is discussed graphically. Further, the Sherwood number, Nusselt number, the skin friction coefficient are also discussed through figures. It is noted through analysis that the speed of the nanofluid reduces for the higher Weissenberg number and expanding cylinder. For the contracting cylinder, i.e., for the negative unsteadiness parameter, the velocity increases.
The impact of inter-observer variation in delineation on robustness of radiomics features in non-small cell lung cancer
Authors: Kothari Gargi , Woon Beverley , Patrick Cameron J. , Korte James , Wee Leonard , Hanna Gerard G. , Kron Tomas , Hardcastle Nicholas , Siva Shankar
Published: July 2022

Artificial intelligence and radiomics have the potential to revolutionise cancer prognostication and personalised treatment. Manual outlining of the tumour volume for extraction of radiomics features (RF) is a subjective process. This study investigates robustness of RF to inter-observer variation (IOV) in contouring in lung cancer. We utilised two public imaging datasets: ‘NSCLC-Radiomics’ and ‘NSCLC-Radiomics-Interobserver1’ (‘Interobserver’). For ‘NSCLC-Radiomics’, we created an additional set of manual contours for 92 patients, and for ‘Interobserver’, there were five manual and five semi-automated contours available for 20 patients. Dice coefficients (DC) were calculated for contours. 1113 RF were extracted including shape, first order and texture features. Intraclass correlation coefficient (ICC) was computed to assess robustness of RF to IOV. Cox regression analysis for overall survival (OS) was performed with a previously published radiomics signature. The median DC ranged from 0.81 (‘NSCLC-Radiomics’) to 0.85 (‘Interobserver’—semi-automated). The median ICC for the ‘NSCLC-Radiomics’, ‘Interobserver’ (manual) and ‘Interobserver’ (semi-automated) were 0.90, 0.88 and 0.93 respectively. The ICC varied by feature type and was lower for first order and gray level co-occurrence matrix (GLCM) features. Shape features had a lower median ICC in the ‘NSCLC-Radiomics’ dataset compared to the ‘Interobserver’ dataset. Survival analysis showed similar separation of curves for three of four RF apart from ‘original_shape_Compactness2’, a feature with low ICC (0.61). The majority of RF are robust to IOV, with first order, GLCM and shape features being the least robust. Semi-automated contouring improves feature stability. Decreased robustness of a feature is significant as it may impact upon the features’ prognostic capability.
A comparative study of a rabbit spinal tuberculosis model constructed by local direct infection via the posterior lateral approach
Authors: Yue Xuefeng , Zhu Xi , Wu Longyun , Shi Jiandang
Published: July 2022

The present study aims to establish a method of constructing a New Zealand rabbit spinal tuberculosis model by direct local infusion of M. tuberculosis H37Rv strain into the intervertebral disc space through the posterior lateral approach. Sixty-six New Zealand rabbits were pretreated with complete Freund's adjuvant and randomly divided into 4 group: the posterolateral approach model group (Group A, 25), ventral transverse process approach model group (Group B, 25), control group (Group C, 10), and blank group (Group D, 6). In Groups A and B, the bone holes were filled with gelatin sponge after drilling, and the local area was directly infused with 0.1 ml of M. tuberculosis H37Rv strain suspension. In Group C, the gelatin sponge was filled through the posterolateral approach and the local area was infused with 0.1 ml of normal saline suspension. In Group D, No specific treatment was performed. The general conditions of the experimental rabbits in each group were compared to those of a control group; the degree of vertebral body exposure, incision length, and complications of the two methods were compared; and the tuberculosis models were evaluated by imaging, histopathology, and bacterial culture. In Group A, the lateral side of the vertebral body was well exposed, the damage was mild, and no peritoneal rupture or gastrointestinal complications were observed. In Group B, the ventral side of the vertebral body and the intervertebral disc were exposed, and abdominal complications were more likely to occur. The survival rates of the experimental rabbits at 8 weeks after surgery were 92.0% in Group A, 88.00% in Group B, 90.0% in Group C, and 100% in Group D. MRI examinations showed that in Group A, the positive rate of radiographic bone findings was 86.9% at 4 weeks after surgery and 100% at 8 weeks after surgery; in Group B, the positive rate of radiographic bone findings was 78.2% at 4 weeks after surgery and 95.4% at 8 weeks after surgery. There was no significant difference between Groups A and B in the radiographic bone findings rate detected by the same imaging method at the same time point (P > 0.05). Eight weeks after surgery, bone destruction, paravertebral abscess, and caseous necrosis occurred in the vertebral bodies of surviving rabbits in Groups A and B. The BacT/ALERT 3D rapid culture system was used to culture the pus in the lesion, and the results showed that the positive rate of tuberculosis was 52.17% in Group A and 54.54% in Group B, and the difference was not statistically significant (P > 0.05). After pretreatment with complete Freund's adjuvant, direct infusion of the H37Rv strain of M. tuberculosis into the intervertebral disc space of New Zealand rabbits via the posterolateral approach and the ventral transverse process approach can successfully establish rabbit spinal tuberculosis models.
Eicosapentaenoic acid (EPA)-induced inhibitory effects on porcine coronary and cerebral arteries involve inhibition of prostanoid TP receptors
Authors: Yoshioka Kento , Obara Keisuke , Oikawa Shunya , Uemura Kohei , Yamaguchi Akina , Fujisawa Kazuki , Hanazawa Hitomi , Fujiwara Miki , Endoh Taison , Suzuki Taichi , De Dios Regadera Montserrat , Ito Daichi , Saitoh Noboru , Nakagome Yutaka , Yamashita Toma , Kiguchi Mayu , Saito Yuka , Nakao Yuri , Miyaji Hinako , Ou Guanghan , Xu Keyue , Tanaka Yoshio
Published: July 2022

This study was performed to elucidate whether eicosapentaenoic acid (EPA) suppresses spasm-prone blood vessel contractions induced by a thromboxane mimetic (U46619) and prostaglandin F2α (PGF2α) and determine whether the primary target of EPA is the prostanoid TP receptor. Accordingly, we assessed: (1) the tension changes in porcine basilar and coronary arteries, and (2) changes in the Fura-2 (an intracellular Ca2+ indicator) fluorescence intensity ratio at 510 nm elicited by 340/380 nm excitation (F340/380) in 293T cells expressing the human TP receptor (TP-293T cells) and those expressing the human prostanoid FP receptor (FP-293T cells). EPA inhibited both porcine basilar and coronary artery contractions induced by U46619 and PGF2α in a concentration-dependent manner, but it did not affect the contractions induced by 80 mM KCl. EPA also inhibited the increase in F340/380 induced by U46619 and PGF2α in TP-293T cells. In contrast, EPA showed only a marginal effect on the increase in F340/380 induced by PGF2α in FP-293T cells. These findings indicate that EPA strongly suppresses the porcine basilar and coronary artery contractions mediated by TP receptor and that inhibition of TP receptors partly underlies the EPA-induced inhibitory effects on these arterial contractions.
Ribosome selectivity and nascent chain context in modulating the incorporation of fluorescent non-canonical amino acid into proteins
Authors: Thommen Michael , Draycheva Albena , Rodnina Marina V.
Published: July 2022

Fluorescence reporter groups are important tools to study the structure and dynamics of proteins. Genetic code reprogramming allows for cotranslational incorporation of non-canonical amino acids at any desired position. However, cotranslational incorporation of bulky fluorescence reporter groups is technically challenging and usually inefficient. Here we analyze the bottlenecks for the cotranslational incorporation of NBD-, BodipyFL- and Atto520-labeled Cys-tRNACys into a model protein using a reconstituted in-vitro translation system. We show that the modified Cys-tRNACys can be rejected during decoding due to the reduced ribosome selectivity for the modified aa-tRNA and the competition with native near-cognate aminoacyl-tRNAs. Accommodation of the modified Cys-tRNACys in the A site of the ribosome is also impaired, but can be rescued by one or several Gly residues at the positions −1 to −4 upstream of the incorporation site. The incorporation yield depends on the steric properties of the downstream residue and decreases with the distance from the protein N-terminus to the incorporation site. In addition to the full-length translation product, we find protein fragments corresponding to the truncated N-terminal peptide and the C-terminal fragment starting with a fluorescence-labeled Cys arising from a StopGo-like event due to a defect in peptide bond formation. The results are important for understanding the reasons for inefficient cotranslational protein labeling with bulky reporter groups and for designing new approaches to improve the yield of fluorescence-labeled protein.
Hepatokine Fetuin B expression is regulated by leptin-STAT3 signalling and associated with leptin in obesity
Authors: Wang Dongmei , Wu Menghua , Zhang Xiaofang , Li Long , Lin Mingzhu , Shi Xiulin , Zhao Yan , Huang Caoxin , Li Xuejun
Published: July 2022

Obesity is an expanding global public health problem and a leading cause of metabolic disorders. The hepatokine Fetuin B participates in regulating insulin resistance, glucose metabolism and liver steatosis. However, the mechanism underlying Fetuin B activation remains unclear. Our previous population-based study demonstrated a significant association between serum Fetuin B and body fat mass in an obese population, which indicates its potential in mediating obesity-related metabolic disorders. In the present study, we further revealed a significant correlation between Fetuin B and leptin, the classic adipokine released by expanding adipose tissue, in this obese population. Consistently, elevated Fetuin B and leptin levels were confirmed in diet-induced obese mice. Furthermore, an in vitro study demonstrated that the leptin signalling pathway directly activated the transcription and expression of Fetuin B in primary hepatocytes and AML12 cells in a STAT3-dependent manner. STAT3 binds to the response elements on FetuB promoter to directly activate FetuB transcription. Finally, the mediating effect of Fetuin B in insulin resistance induced by leptin was confirmed according to mediation analysis in this obese population. Therefore, our study identifies leptin-STAT3 as an upstream signalling pathway that activates Fetuin B and provides new insights into the pathogenic mechanisms of obesity-related metabolic disorders.
Infusion of etoposide in the CA1 disrupts hippocampal immediate early gene expression and hippocampus-dependent learning
Authors: Boutros Sydney Weber , Kessler Kat , Unni Vivek K. , Raber Jacob
Published: July 2022

Tight regulation of immediate early gene (IEG) expression is important for synaptic plasticity, learning, and memory. Recent work has suggested that DNA double strand breaks (DSBs) may have an adaptive role in post-mitotic cells to induce IEG expression. Physiological activity in cultured neurons as well as behavioral training leads to increased DSBs and subsequent IEG expression. Additionally, infusion of etoposide—a common cancer treatment that induces DSBs—impairs trace fear memory. Here, we assessed the effects of hippocampal infusion of 60 ng of etoposide on IEG expression, learning, and memory in 3–4 month-old C57Bl/6J mice. Etoposide altered expression of the immediate early genes cFos and Arc in the hippocampus and impaired hippocampus-dependent contextual fear memory. These data add to the growing evidence that DSBs play an important role in IEG expression, learning, and memory, opening avenues for developing novel treatment strategies for memory-related disorders.
Physical activity and gender buffer the association of retirement with functional impairment in Ghana
Authors: Gyasi Razak M. , Amoah Padmore Adusei , Agyemang Seth , Siaw Lawrencia Pokua , Frempong Foster , Rani Ritu , Phillips David R.
Published: July 2022

Females on average live longer but with higher rates of functional impairment and lower physical and economic activities than men. However, research linking retirement to functional impairment and the modifying role of gender and physical activity (PA) is limited especially in low- and middle-income countries. This paper examines the association between retirement and functional impairment in Ghana and evaluates the effect modification of the association by gender and PA. The sample included 1201 adults aged ≥ 50 years from a population-based study. Functional impairment was assessed with the activities of daily living scale. Ordinary least squares regression models adjusted for confounding variables and estimated gender-wise and PA heterogeneity effect of retirement on functional impairment. Regressions showed that retirement predicted an increase in functional impairment score in the full sample (β = .76, p < .001) and in men (β = 1.96, p < .001), but not in women. Interestingly, retirement significantly increased functional impairment in ≥ 65 age cohort (full sample: β = .71, p < .005; men: β = 1.86, p < .001) although not in women. However, the effect was significantly moderated by PA such that retirement × PA predicted a decrease in functional impairment in the full sample (β = −.81, p < .005) and the ≥ 65 age group (β = −.43, p < .005). Functional impairment risk of retirement is gender-specific, but PA buffers the relationship. Retirement is generally commonplace, but these findings imply that promoting PA may hold promise for addressing functional impairment in old age. Attending to the physical health needs of men during retirement should be a social policy priority.
Molecular characterization of polyphenol oxidase between small and large leaf tea cultivars
Authors: Chen Chung‑Tse , Yang Chin-Ying , Tzen Jason T. C.
Published: July 2022

Tea is a widely consumed beverage prepared using the fresh leaves of Camellia sinensis L. Tea plants are classified into small- and large-leaf varieties. Polyphenol oxidase (PPO), a crucial enzyme in tea manufacturing, catalyzes essential phenolic metabolites into different derivatives. To compare the molecular characteristics of CsPPO between cultivars, we cloned the full-length sequence of CsPPO cDNA from four representative tea cultivars in Taiwan. Amino acid sequence alignment analyses indicated that CsPPO is highly conserved. PPO exhibited similar enzymatic activity in different tea cultivars. Quantitative real-time polymerase chain reaction revealed no significant differences in the CsPPO transcript level between the small- and large-leaf varieties. However, tea harvested in summer and from low-altitude areas had a higher CsPPO transcript level than that harvested in winter and from high-altitude areas. Regulation of CsPPO by temperature was more significant in the small-leaf variety than in the large-leaf variety. The content of flavonoids and the expression of chalcone synthase, anthocyanidin synthase, and anthocyanidin reductase genes involved in the tea flavonoid biosynthesis pathway were higher in the large-leaf than in the small-leaf varieties, suggesting that the large-leaf variety had a higher antioxidative capacity than did the small-leaf variety. Our study compared the molecular properties of CsPPO between two tea varieties and clarified the physiological role of PPO in tea.
Spin-flip-driven reversal of the angle-dependent magnetic torque in layered antiferromagnetic Ca0.9Sr0.1Co2As2
Authors: Kim Jong Hyuk , Kim Mi Kyung , Jeong Ki Won , Shin Hyun Jun , Hong Jae Min , Kim Jin Seok , Moon Kyungsun , Lee Nara , Choi Young Jai
Published: July 2022

Spin-flip transition can occur in antiferromagnets with strong magnetocrystalline anisotropy, inducing a significant modification of the anisotropic magnetic properties through phase conversion. In contrast to ferromagnets, antiferromagnets have not been thoroughly examined in terms of their anisotropic characteristics. We investigated the magnetic-field and angle-dependent magnetic properties of Ising-type antiferromagnetic Ca0.9Sr0.1Co2As2using magnetic torque measurements. An A-type antiferromagnetic order emerges belowTN = 97 K aligned along the magnetically easyc-axis. The reversal of the angle-dependent torque across the spin-flip transition was observed, revealing the strong influence of the magnetocrystalline anisotropy on the magnetic properties. Based on the easy-axis anisotropic spin model, we theoretically generated torque data and identified specific spin configurations associated with the magnetic torque variation in the presence of a rotating magnetic field. Our results enrich fundamental and applied research on diverse antiferromagnetic compounds by shedding new light on the distinct magnetic features of the Ising-type antiferromagnet.
A new approach to broaden the range of eye colour identifiable by IrisPlex in DNA phenotyping
Authors: Paparazzo Ersilia , Gozalishvili Anzor , Lagani Vincenzo , Geracitano Silvana , Bauleo Alessia , Falcone Elena , Passarino Giuseppe , Montesanto Alberto
Published: July 2022

IrisPlex system represents the most popular model for eye colour prediction. Based on six polymorphisms this model provides very accurate predictions that strongly depend on the definition of eye colour phenotypes. The aim of the present study was to introduce a new approach to improve eye colour prediction using the well-validated IrisPlex system. A sample of 238 individuals from a Southern Italian population was collected and for each of them a high-resolution image of eye was obtained. By quantifying eye colour variation into CIELAB space several clustering algorithms were applied for eye colour classification. Predictions with the IrisPlex model were obtained using eye colour categories defined by both visual inspection and clustering algorithms. IrisPlex system predicted blue and brown eye colour with high accuracy while it was inefficient in the prediction of intermediate eye colour. Clustering-based eye colour resulted in a significantly increased accuracy of the model especially for brown eyes. Our results confirm the validity of the IrisPlex system for forensic purposes. Although the quantitative approach here proposed for eye colour definition slightly improves its prediction accuracy, further research is still required to improve the model particularly for the intermediate eye colour prediction.
Reliability model of the security subsystem countering to the impact of typed cyber-physical attacks
Authors: Kovtun Viacheslav , Izonin Ivan , Gregus Michal
Published: July 2022

The article's main contribution is the description of the process of the security subsystem countering the impact of typed cyber-physical attacks as a model of end states in continuous time. The input parameters of the model are the flow intensities of typed cyber-physical attacks, the flow intensities of possible cyber-immune reactions, and the set of probabilities of neutralization of cyber-physical attacks. The set of admissible states of the info-communication system is described taking into account possible variants of the development of the modeled process. The initial parameters of the model are the probabilities of the studied system in the appropriate states at a particular moment. The dynamics of the info-communication system's life cycle are embodied in the form of a matrix of transient probabilities. The mentioned matrix connects the initial parameters in the form of a system of Chapman's equations. The article presents a computationally efficient concept based on Gershgorin's theorems to solve such a system of equations with given initiating values. Based on the presented scientific results, the article proposes the concept of calculating the time to failure as an indicator of the reliability of the info-communication system operating under the probable impact of typical cyber-physical attacks. The adequacy of the model and concepts presented in the article is proved by comparing a statically representative amount of empirical and simulated data. We emphasize that the main contribution of the research is the description of the process of the security subsystem countering the impact of typed cyber-physical attacks as a model of end states in continuous time. Based on the created model, the concept of computationally efficient solution of Chapman's equation system based on Gershgorin's theorems and calculating time to failure as an indicator of the reliability of the info-communication system operating under the probable impact of typed cyber-physical attacks are formalized. These models and concepts are the highlights of the research.
Protocol for quantifying inactive lithium in anode-free lithium batteries by mass spectrometry titration
Authors: Tao Mingming , Xiang Yuxuan , Zhao Danhui , Shan Peizhao , Yang Yong
Published: July 2022

Quantifying inactive lithium during cycling is essential for understanding the failure mechanisms of lithium-metal batteries. Although many quantitative studies of lithium-metal failure have been reported, insufficient attention has focused on the reproducibility of the data or the reliability of the analysis. Here, we propose a complete mass spectrometry titration protocol and show how to accurately quantify inactive lithium, showing that quantitative results with high repeatability can be achieved. We believe that this protocol can be extended to other alkali-metal battery systems, facilitating more reliable and accurate battery research.
A quantum radio frequency signal analyzer based on nitrogen vacancy centers in diamond
Authors: Magaletti Simone , Mayer Ludovic , Roch Jean-François , Debuisschert Thierry
Published: July 2022

The rapid development of radio-frequency (RF) technologies requires tools which can efficiently monitor the electromagnetic landscape. Broadband real-time RF spectral analyzers need to operate at room temperature, with low power consumption and have a compact design for on-board device integration. Here we describe a Quantum Diamond Signal Analyzer (Q-DiSA) which detects RF signals over a tunable frequency range of 25 GHz with frequency resolution down to 1 MHz, a millisecond temporal resolution and a large dynamic range (40 dB). This approach exploits the room temperature spin properties of an ensemble of nitrogen-vacancy (NV) centers in diamond. Performance is enabled via our analyzer architecture which combines a specific diamond crystallographic cut with a simplified magnetic arrangement. This allows us to maintain the alignment of the magnetic field along the nitrogen-vacancy center axis whilst frequency tuning. These results demonstrate the potential of the Q-DiSA method for real-time broadband spectral analysis.
Effects of oligosaccharides on the markers of glycemic control: a systematic review and meta-analysis of randomized controlled trials
Authors: An Ran , Zong Aizhen , Chen Shanbin , Xu Rui , Zhang Ruixin , Jiang Wen , Liu Lina , Du Fangling , Zhang Hongyan , Xu Tongcheng
Published: July 2022

This study is by far the most extensive systematic review to evaluate the role of oligosaccharides on markers of glycemic control. Meta-analysis revealed that oligosaccharide interventions can exert beneficial effects on FBG, FBI, HbA1c and HOMA-IR.
State-of-the-art advancements of atomically thin two-dimensional photocatalysts for energy conversion
Authors: Gao Wa , Li Zhengdao , Han Qiutong , Shen Yan , Jiang Chunhai , Zhang Yongcai , Xiong Yujie , Ye Jinhua , Zou Zhigang , Zhou Yong
Published: July 2022

This Feature article provides a concise overview of the preparation, strategies for boosting the photoconversion performance, various photocatalytic applications, and challenges and opportunities of atomically thin 2D photocatalysts.
Temporal control of protein labeling by a photo-caged benzaldehyde motif and discovery of host cell factors of avian influenza virus infection
Authors: Asiimwe Nicholas , Lee Jung Hoon , Hong Kyung Tae , Murale Dhiraj P. , Haque Md. Mamunul , Kim Dong-Hoon , Lee Jun-Seok
Published: July 2022

Photo-caged benzaldehyde probes using o-nitrophenylethylene glycol were designed for photo-activated electrophile generation.