bluuebunny/crossref_metadata_2025 huggingface dataset:
Essential oils as natural additives in dry-fermented sausages
Authors: Sojic B , Tomovic V , Jokanovic M , Pavlic B
Published: November 2021

The usage of food additives is one of the key methods for inhibiting microorganisms’ growth and delaying oxidative changes in dry-fermented sausages (DFS). However, they have numerous negative health effects, so the novel meat industry is oriented towards different natural alternatives while focusing on plant extracts, including essential oils (EOs). EOs are interesting since they are generally recognized as safe (marked as GRAS) and have a broad acceptance from the consumers. Their activity depends on numerous parameters including the method of extraction, concentrations and possible synergistic effects of their bioactive compounds. Various conventional (hydrodistillation and organic solvent extraction) and novel (microwave-assisted, ultrasound-assisted and supercritical fluid extraction) extraction techniques are being applied for EO recovery, and optimization of these process is an essential step towards cost-effective production of high-quality extracts. Generally, it can be concluded that EOs are added into DFS to delay or prevent lipid oxidation, retard microorganisms’ growth, improve colour stability and extend the shelf-life.
Polish meat products - tradition and modernity
Authors: Szafrańska J O , Sołowiej B G
Published: November 2021

The production and promotion of high-quality traditional food are playing an important role in the European Union. One of the main indications of the production quality is the awarding of signs confirming the quality of the traditional products. Meat and meat products play an important role in preserving the tradition. They are produced according to traditional recipes, passed down from generation to generation, and their preparation uses products typical of the region, from local crops and breeding. Thanks to this, they gain specific taste values, unheard of in other parts of the country.
Artificial neural network prediction of microbiological quality of beef minced meat processed for fast-food meals
Authors: Ranitovic Aleksandra , Pezo Lato , Sovljanski Olja , Tomic Ana , Cvetkovic Dragoljub , Markov Sinisa
Published: November 2021

In this study, the microbiological quality of 72 minced beef meat samples collected during six months from a local butcher was defined after laboratory analysis and developing advanced mathematical models. This new simultaneous approach provided adequate precision for the prediction of the microbiological profile of minced beef meat as one of the easily spoiled products with a short shelf life. For the first time, an artificial network model was developed to predict the microbiological profile of beef minced meat in a fast-food restaurant according to meat and storage temperatures, butcher identification, and work shift. A concurrent statistical study of practical analysis and the developing mathematical models provided adequate precision for the prediction of the microbiological profile of minced beef meat. The developed ANN provided a good prediction of the microbiological profile of beef minced meat with an overall R2 of 0.867 during the training cycle.
Culinary preparation and processing of meat with wooden breast myopathy
Authors: Starcevic M , Boskovic S , Vujadinovic D , Rajcic A , Branković Lazic I , Baltic B , Baltic M Z
Published: November 2021

Recently, poultry meat production and consumption has become increased worldwide. Decades of intensive selection in poultry breeding resulted in fast-growing broilers, improved food conversion, low production costs, and high yield of breast meat, as the most valuable part of the carcass. Some side-effects of intensive production and rapid growth of broilers include the appearance of myopathies in breast muscle. Increasing attention has been paid to the defect known as "wooden breast" (WB) due its incidence and severity of anomaly. WB is characterized by the hardness and pale colour of the fillet. These changes lower the consumer acceptance of the meat, and a pronounced WB is unsuitable for culinary and industrial processing. Different procedures can be used to tenderize the meat and include physical and chemical procedures, often combined in industry. Physical procedures comprise the application of heating, mechanical force, ultrasound, electric stimulation, hydrodynamic shock wave-pressure technology, high pressure processing, and pulsed electric field. Chemical procedures include marinating, exposure to the endogenous enzymes, and the use of exoenzymes. In the future, it is necessary to develop optimal tenderizing techniques or combinations of different tenderizing techniques to achieve better sensory quality and improved nutritional value of WB.
Development and validation of modified QuEChERS methods for the analysis of fipronil and its metabolites in chicken meat
Authors: Tasic Aleksandra , Nesic Ksenija , Pavlovic Marija , Radojicic Djordje
Published: November 2021

A sensitive method for the precisely and accurate determining the presents of fipronil and its metabolites in chicken meat was developed and validated using a modified quick, easy, cheap, effective, rugged and safe approach coupled with gas chromatography-mass spectrometry analysis. The solvent acetonitrile was used for the extraction of the samples with the salt phases composed of sodium chloride and magnesium sulphate, and then in the second phase used C18 and anhydrous magnesium sulphate. The linearity of the analytical response across the studied range of concentrations (0.005-0.050 mg kg-1) was excellent, obtaining correlation coefficients higher than 0.99. The average recoveries of the pesticide ranged from 75 to 106% for fortification levels of 0.005, 0.01 and 0.05 mg kg-1. The precision values associated with the analytical method, expressed as RSD values, were less than 11.15%. Matrix-matched solutions were also prepared by serially diluting the intermediate solution with blank chicken meat sample extracts containing none of the tested analytes to perform matrix-matched calibration with the same concentrations as in the solvent. The validated method was used to analyse the target compounds in 30 real samples imported from European countries. The present of fipronil-desulfinyl metabolite was confirmed in four samples.
Attitudes and beliefs of Eastern European meat consumers–a review
Authors: Tomasevic I , Solowiej BG , Djordjevic V , Vujadinovic D , Djekic I
Published: November 2021

Eastern European consumers are traditional meat eaters who are still not looking forward in order to substitute their traditional meat-based dishes with meat analogues or their substitutes. In general, vegetarianism is in its infancy if we do not take into account Lenten fasting, the period of the year when in Orthodox countries of Eastern Europe one can find food not containing meat, dairy and eggs, widely available. Chicken meat is the most frequently consumed type of meat, and it is preferred because it is easy to prepare. Eastern European meat consumers believe that meat from castrated pigs is of better quality, and one third of them is indifferent towards animal welfare issues. The highest proportion of Eastern European consumers (42.9%) believes that game meat has many health benefits, is rich in proteins and is more organic than other types of meat. However, two thirds of Eastern European consumers eat game meat less than once a year. Differences in attitudes and beliefs of Eastern European meat consumers compared to their Western European equivalents are evident.
Mercury in female cattle livers and kidneys from Vojvodina, northern Serbia
Authors: Tomovic V , Jokanovic M , Tomovic M , Sojic B , Lazovic M , Vasiljevic I , Skaljac S , Martinovic A , Vujadinovic D , Vukic M
Published: November 2021

Concentrations of mercury (Hg) were analysed in livers (n = 26) and kidneys (n = 26) of female cattle (412–2502 days old) from farms for milk production in the area of Vojvodina. Concentration of Hg was analysed by ICP-OES, after digestion by microwave. The Hg concentrations in the livers and kidneys ranged from below detection limits (LOD < 0.006 mg/kg) to 0.206 mg/kg wet weight and from below detection limits (LOD < 0.006 mg/kg) to 0.018 mg/kg wet weight, respectively.
Organic agriculture – importance and development
Authors: Veskovic Moracanin Slavica , Djukic Dragutin , Saponjić Milinko , Ostojic Zoran
Published: November 2021

Agriculture, as the most important strategic industry, is tasked with providing sufficient quantities of quality and safe food. Intensive and often excessive, uncontrolled, and unskilled use of the means for protection and nutrition of plants, as well as means for the prevention or treatment of animals, are carried out to increase yields in conventional production. This approach in food production has contributed to the increasingly common endangerment of the health of plants, animals and humans, as well as significant environmental endangerment. Unlike conventional production, organic food production is now increasingly attracting interest from modern consumers. However, organic agriculture involves not only producing without artificial fertilizers and other agrochemicals, but without antibiotics and hormones too. It is more of a holistic production system that functions as a sustainable unit, and unites interconnected and conditioned actors: plants, animals, microorganisms, insects, organic and mineral soil matter, and humans. In Serbia, organic agriculture has been developing for the last thirty years. However, the intensive development of organic agriculture has only happened in the last decade, with plant organic production being more developed than animal organic production.
Effects of using chia (Salvia hispanica L.) mucilage and different cooking procedures on quality parameters of beef patties
Authors: Yüncü Ö , Kavuşan H S , Serdaroğlu M
Published: November 2021

This study was carried out to investigate the effects of chia (Salvia hispanica L.) mucilage (CM) as a fat replacer in grilled or pan-fried beef patties. For this purpose, beef fat was replaced by CM at levels of 0, 25, 50, and 75%. The use of CM and cooking method affected cooking-related parameters. Cooking yield was lower in pan-fried patties, while the addition CM increased the cooking yields. Moisture retention, shrinkage, changes in diameter, and thickness of grilled patties were improved compared to the pan-fried samples. The addition of CM increased moisture retention, while shrinkage values decreased. Results of our investigation revealed that CM retarded oxidative changes in pan-fried patties. Textural parameters and sensory properties of samples were not negatively affected by the addition of CM.
Experimental investigation on cladding with metal cored wire using GMAW process and parametric optimization
Authors: Kaushik Ashish , Singh Vivek , Choudhury Bishub , Ashutosh Som , Chandrasekaran M
Published: November 2021

Cladding is widely used in manufacturing industries for the production of pressure vessel by depositing thick layer of filler material for providing corrosion resistant-surface. The use of metal cored wire in gas metal arc welding (GMAW) process is popular due to its higher deposition rate and productivity. This work investigates the effect of process parameters on the deposition of cladding layer with ER 309L metal core wire (as filler material) on a corrosion resistant material (IS 2062). The welding parameters viz., wire feed rate (WFR), voltage (V), welding speed (S) and nozzle to plate distance (NTD) are employed as process parameters while penetration (P), bead width (W), reinforcement (R), weld penetration shape factor (WPSF) and weld reinforcement form factor (WRFF) as welding responses. The predictive model developed for P, W, R, WPSF, and WRFF using the response surface methodology (RSM) approach is found adequate at 95% confidence interval. The validation results for the developed model results in a model accuracy (MA) of 92.82%, 96.34%, 91.47% 88.98% and 87.75% for model P, W, R, WPSF, and WRFF respectively and it shows higher predictability and accuracy. The process parameters are optimized simultaneously with integrated optimization approach using RSM with Jaya algorithm and obtain optimal solution in less than 20 number of iterations. The minimum fitness value obtained as 1.3008 at an optimal parameter setting of WFR = 12 m min−1, V = 26 V, S = 280 mm min−1, NTD = 10 mm. The validation result at the optimal parameter setting results in an improvement of 6.45%, 11.29%, 13.58%, 16.07%, 15.38% is noted for P, W, R, WPSF, and WRFF respectively.
Optimization of photovoltaic conversion performance of a TiO2 based dye sensitized solar cells (DSSCs)
Authors: Kumar Deepak , Kuchhal Piyush , Parmar Kanakpal Singh
Published: November 2021

Combined theoretical and experimental investigations are carried out to achieve an optimum photovoltaic (PV) conversion performance (η) of a DSSC. All theoretical studies are done in tiberCAD software, wherein simulated parameters are calibrated and correlated with the measured experimental parameters of a DSSC fabricated using nearly spherical shape nanosize TiO2 working electrode. For two types of dye molecules, theoretically optimized electrode’s thicknesses were 6 μm (η ∼ 6.45%) and 18 μm (η ∼ 7.51%) for DB and LEG4 dyes, respectively. Relatively a better short-circuit photocurrent density (JSC) was found for a LEG4 dye although it had a lower light absorbance compared to a DB dye. The theoretical investigation revealed that charge recombination of a DB dye is 7 times higher than that of a LEG4 dye, and this high recombination becomes one of the most critical factors affecting the overall incident photon to current conversion efficiency.
Computational behavioral models in public goods games with migration between groups
Authors: Tomassini Marco , Antonioni Alberto
Published: November 2021

In this study we have simulated numerically two models of linear public goods games where players are equally distributed among a given number of groups. Agents play in their group by using two simple sets of rules, called ‘blind’ and ‘rational’ model, respectively, that are inspired by the observed behavior of human participants in laboratory experiments. In addition, unsatisfied agents have the option of leaving their group and migrating to a new random one through probabilistic choices. Stochasticity, and the introduction of two types of players in the blind model, help simulate the heterogeneous behavior that is often observed in experimental work. Our numerical simulations of the corresponding dynamical systems show that being able to leave a group when unsatisfied favors contribution and avoids free-riding to a good extent in a range of the enhancement factor where defection would prevail without migration. Our numerical simulation presents results that are qualitatively in line with known experimental data when human agents are given the same kind of information about themselves and the other players in the group. This is usually not the case with customary mathematical models based on replicator dynamics or stochastic approaches. As a consequence, models like the ones described here may be useful for understanding experimental results and also for designing new experiments by first running cheap computational simulations instead of doing costly preliminary laboratory work. The downside is that models and their simulation tend to be less general than standard mathematical approaches.
Complex systems are always correlated but rarely information processing
Authors: Wiesner Karoline , Ladyman James
Published: November 2021

‘Complex systems are information processors’ is a statement that is frequently made. Here we argue for the distinction between information processing—in the sense of encoding and transmitting a symbolic representation—and the formation of correlations (pattern formation/self-organisation). The study of both uses tools from information theory, but the purpose is very different in each case: explaining the mechanisms and understanding the purpose or function in the first case, versus data analysis and correlation extraction in the latter. We give examples of both and discuss some open questions. The distinction helps focus research efforts on the relevant questions in each case.
Calf circumference refines sarcopenia in correlating with mortality risk
Authors: Wu Shou-En , Chen Wei-Liang
Published: November 2021

Background

Recommendations in current guidelines on the use of calf circumference (CC) as a diagnostic measure in sarcopenia is conflicting. In this study, we incorporated CC into conventional models of sarcopenia and compared their predictive scores on mortality.

Objective

To clarify the predictive capacity of CC-added models of sarcopenia on and establish the correlation of CC with mortality risk.

Design, Setting and Subjects

From the National Health and Nutrition Examination Survey 1999–2002, 2,532 participants aged 50–85 and comprising 51.7% male were included.

Methods

Our definitions contained four sarcopenic components, low CC (C), low muscle strength (S), low muscle mass (M) and low gait speed (G). Cox proportional hazard models and the receiver-operator characteristic curves for all-cause, cardiovascular (CV) and cancer mortality were conducted to compare the different sarcopenia definitions.

Results

For all-cause mortality, the hazard ratio (HR) of C + S + M + G was 15.062, which was substantially higher than the conventional definition S + M + G (HR = 6.433). Other CC-added definitions such as C + M (HR = 2.260), C + G (HR = 4.978), C + S + M (HR = 5.761) also revealed higher HR than their without-CC counterparts. Similar patterns were observed in CV mortality, for instance, HR of C + S + M + G was 31.812 comparing to the conventional definition S + M + G (HR = 18.434). Concerning accuracy in predicting mortality, the area under the curve (AUC) of CC + S + G + M (AUC = 0.702) and C + S + G (AUC = 0.708) were higher than the conventional definition S + G + M (AUC = 0.697). A significant correlation was found between CC and each of the three conventional components of sarcopenia.

Conclusions

CC-added definitions of sarcopenia correlated with higher all-cause and CV mortality risks. CC is potentially a simple but valuable screening tool for sarcopenia that could improve diagnostic accuracy when used with other parameters.
Accurate protein function prediction via graph attention networks with predicted structure information
Authors: Lai Boqiao , Xu Jinbo
Published: November 2021

Experimental protein function annotation does not scale with the fast-growing sequence databases. Only a tiny fraction (<0.1%) of protein sequences has experimentally determined functional annotations. Computational methods may predict protein function very quickly, but their accuracy is not very satisfactory. Based upon recent breakthroughs in protein structure prediction and protein language models, we develop GAT-GO, a graph attention network (GAT) method that may substantially improve protein function prediction by leveraging predicted structure information and protein sequence embedding. Our experimental results show that GAT-GO greatly outperforms the latest sequence- and structure-based deep learning methods. On the PDB-mmseqs testset where the train and test proteins share <15% sequence identity, our GAT-GO yields Fmax (maximum F-score) 0.508, 0.416, 0.501, and area under the precision-recall curve (AUPRC) 0.427, 0.253, 0.411 for the MFO, BPO, CCO ontology domains, respectively, much better than the homology-based method BLAST (Fmax 0.117, 0.121, 0.207 and AUPRC 0.120, 0.120, 0.163) that does not use any structure information. On the PDB-cdhit testset where the training and test proteins are more similar, although using predicted structure information, our GAT-GO obtains Fmax 0.637, 0.501, 0.542 for the MFO, BPO, CCO ontology domains, respectively, and AUPRC 0.662, 0.384, 0.481, significantly exceeding the just-published method DeepFRI that uses experimental structures, which has Fmax 0.542, 0.425, 0.424 and AUPRC only 0.313, 0.159, 0.193.
HiC1Dmetrics: framework to extract various one-dimensional features from chromosome structure data
Authors: Wang Jiankang , Nakato Ryuichiro
Published: November 2021

Eukaryotic genomes are organized in a three-dimensional spatial structure. In this regard, the development of chromosome conformation capture methods has enabled studies of chromosome organization on a genomic scale. Hi-C, the high-throughput chromosome conformation capture method, can reveal a population-averaged, hierarchical chromatin structure. The typical Hi-C analysis uses a two-dimensional (2D) contact matrix that indicates contact frequencies between all possible genomic position pairs. Oftentimes, however, such a 2D matrix is not amenable to handling quantitative comparisons, visualizations and integrations across multiple datasets. Although several one-dimensional (1D) metrics have been proposed to depict structural information in Hi-C data, their effectiveness is still underappreciated. Here, we first review the currently available 1D metrics for individual Hi-C samples or two-sample comparisons and then discuss their validity and suitable analysis scenarios. We also propose several new 1D metrics to identify additional unique features of chromosome structures. We highlight that the 1D metrics are reproducible and robust for comparing and visualizing multiple Hi-C samples. Moreover, we show that 1D metrics can be easily combined with epigenome tracks to annotate chromatin states in greater details. We develop a new framework, called HiC1Dmetrics, to summarize all 1D metrics discussed in this study. HiC1Dmetrics is open-source (github.com/wangjk321/HiC1Dmetrics) and can be accessed from both command-line and web-based interfaces. Our tool constitutes a useful resource for the community of chromosome-organization researchers.
Deep graph learning of inter-protein contacts
Authors: Xie Ziwei , Xu Jinbo
Published: November 2021

Motivation

Inter-protein (interfacial) contact prediction is very useful for in silico structural characterization of protein–protein interactions. Although deep learning has been applied to this problem, its accuracy is not as good as intra-protein contact prediction.

Results

We propose a new deep learning method GLINTER (Graph Learning of INTER-protein contacts) for interfacial contact prediction of dimers, leveraging a rotational invariant representation of protein tertiary structures and a pretrained language model of multiple sequence alignments. Tested on the 13th and 14th CASP-CAPRI datasets, the average top L/10 precision achieved by GLINTER is 54% on the homodimers and 52% on all the dimers, much higher than 30% obtained by the latest deep learning method DeepHomo on the homodimers and 15% obtained by BIPSPI on all the dimers. Our experiments show that GLINTER-predicted contacts help improve selection of docking decoys.

Availability and implementation

The software is available at https://github.com/zw2x/glinter. The datasets are available at https://github.com/zw2x/glinter/data.

Supplementary information

Supplementary data are available at Bioinformatics online.
Climate-Friendly Seafood: The Potential for Emissions Reduction and Carbon Capture in Marine Aquaculture
Authors: Jones Alice R , Alleway Heidi K , McAfee Dominic , Reis-Santos Patrick , Theuerkauf Seth J , Jones Robert C
Published: November 2021

Aquaculture is a critical food source for the world's growing population, producing 52% of the aquatic animal products consumed. Marine aquaculture (mariculture) generates 37.5% of this production and 97% of the world's seaweed harvest. Mariculture products may offer a climate-friendly, high-protein food source, because they often have lower greenhouse gas (GHG) emission footprints than do the equivalent products farmed on land. However, sustainable intensification of low-emissions mariculture is key to maintaining a low GHG footprint as production scales up to meet future demand. We examine the major GHG sources and carbon sinks associated with fed finfish, macroalgae and bivalve mariculture, and the factors influencing variability across sectors. We highlight knowledge gaps and provide recommendations for GHG emissions reductions and carbon storage, including accounting for interactions between mariculture operations and surrounding marine ecosystems. By linking the provision of maricultured products to GHG abatement opportunities, we can advance climate-friendly practices that generate sustainable environmental, social, and economic outcomes.
A novel stroke lesion network mapping approach: improved accuracy yet still low deficit prediction
Authors: Pini Lorenzo , Salvalaggio Alessandro , De Filippo De Grazia Michele , Zorzi Marco , Thiebaut de Schotten Michel , Corbetta Maurizio
Published: November 2021

Lesion network mapping estimates functional network abnormalities caused by a focal brain lesion. The method requires embedding the volume of the lesion into a normative functional connectome and using the average functional magnetic resonance imaging signal from that volume to compute the temporal correlation with all other brain locations. Lesion network mapping yields a map of potentially functionally disconnected regions. Although promising, this approach does not predict behavioural deficits well. We modified lesion network mapping by using the first principal component of the functional magnetic resonance imaging signal computed from the voxels within the lesioned area for temporal correlation. We measured potential improvements in connectivity strength, anatomical specificity of the lesioned network and behavioural prediction in a large cohort of first-time stroke patients at 2-weeks post-injury (n = 123). This principal component functional disconnection approach localized mainly cortical voxels of high signal-to-noise; and it yielded networks with higher anatomical specificity, and stronger behavioural correlation than the standard method. However, when examined with a rigorous leave-one-out machine learning approach, principal component functional disconnection approach did not perform better than the standard lesion network mapping in predicting neurological deficits. In summary, even though our novel method improves the specificity of disconnected networks and correlates with behavioural deficits post-stroke, it does not improve clinical prediction. Further work is needed to capture the complex adjustment of functional networks produced by focal damage in relation to behaviour.
Multiplex connectome changes across the alzheimer’s disease spectrum using gray matter and amyloid data
Authors: Canal-Garcia Anna , Gómez-Ruiz Emiliano , Mijalkov Mite , Chang Yu-Wei , Volpe Giovanni , Pereira Joana B ,   Alzheimer’s Disease Neuroimaging Initiative
Published: November 2021

The organization of the Alzheimer’s disease (AD) connectome has been studied using graph theory using single neuroimaging modalities such as positron emission tomography (PET) or structural magnetic resonance imaging (MRI). Although these modalities measure distinct pathological processes that occur in different stages in AD, there is evidence that they are not independent from each other. Therefore, to capture their interaction, in this study we integrated amyloid PET and gray matter MRI data into a multiplex connectome and assessed the changes across different AD stages. We included 135 cognitively normal (CN) individuals without amyloid-β pathology (Aβ−) in addition to 67 CN, 179 patients with mild cognitive impairment (MCI) and 132 patients with AD dementia who all had Aβ pathology (Aβ+) from the Alzheimer’s Disease Neuroimaging Initiative. We found widespread changes in the overlapping connectivity strength and the overlapping connections across Aβ-positive groups. Moreover, there was a reorganization of the multiplex communities in MCI Aβ + patients and changes in multiplex brain hubs in both MCI Aβ + and AD Aβ + groups. These findings offer a new insight into the interplay between amyloid-β pathology and brain atrophy over the course of AD that moves beyond traditional graph theory analyses based on single brain networks.
Frontopolar tDCS induces frequency-dependent changes of spontaneous low-frequency fluctuations: a resting-state fMRI study
Authors: Ren Ping , Ma Manxiu , Wu Donghui , Ma Yuanye
Published: November 2021

Transcranial direct current stimulation (tDCS) is a noninvasive neuromodulation technique that can modulate cortical excitability and behavioral performance. However, its effects on spontaneous low-frequency fluctuations of brain activity are still poorly understood. Here, we systematically investigated the frontopolar tDCS effects on resting-state brain activity and connectivity. Twelve healthy participants were recruited and received anode, cathode, and sham stimulation in a randomized order. Resting-state functional magnetic resonance imaging was performed before and after stimulation. Functional connectivity was calculated to examine tDCS effects within and beyond the frontopolar network. To assess the frequency-dependent changes of brain activity, fractional amplitude of low-frequency fluctuations (fALFF) was computed in the slow-4 (0.027–0.073 Hz) and slow-5 (0.01–0.027 Hz) bands. The results showed anodal tDCS-induced widespread connectivity reduction within and beyond the frontopolar network. Regardless of tDCS polarity, stimulation effect on fALFF was significantly larger in slow-5 band compared with the slow-4. Notably, anodal tDCS-induced connectivity changes were associated with pre-tDCS fALFF in slow-4 band, showing positive correlations in the frontal regions and negative correlations in the temporal regions. Our findings imply that tDCS-induced brain alterations may be frequency-dependent, and pre-tDCS regional brain activity could be used to predict post-tDCS connectivity changes.
Constitutional Theories of International Organisations: Beyond the West
Authors: Peters Anne
Published: November 2021

The Joint Statement by the Foreign Ministers of China and Russia on Certain Aspects of Global Governance in Modern Conditions of 23 March 2021 calls for “the establishment of a fairer, more democratic and rational multipolar world order.” The paper inquires how constitutional theories of international organisations have in the past and present sought to contribute to world order. It identifies three waves of such theory since the 1960s. Looking in more detail at the ongoing third wave, it identifies and seeks to pull out further a constitutional model which upscales the proto-democratic practices in international organisations by strengthening forums for participation and contestation, which rectifies to the north-south imbalance inter alia rooted in the colonial heritage by involving more actors from the global south, and which tackles the global social question upfront.
Identification and Functional Characterization of Antifreeze Protein and Its Mutants in Dendroctonus armandi (Coleoptera: Curculionidae: Scolytinae) Larvae Under Cold Stress
Authors: Fu Danyang , Sun Yaya , Gao Haiming , Liu Bin , Kang Xiaotong , Chen Hui
Published: November 2021

Dendroctonus armandi (Tsai and Li) (Coleoptera: Curculionidae: Scolytinae) is considered to be the most destructive forest pest in the Qinling and Bashan Mountains of China. Low winter temperatures limit insect’s populations, distribution, activity, and development. Insects have developed different strategies such as freeze-tolerance and freeze-avoidance to survive in low temperature conditions. In the present study, we used gene cloning, real-time polymerase chain reaction (PCR), RNA interference (RNAi), and heterologous expression to study the function of the D. armandi antifreeze protein gene (DaAFP). We cloned the 800 bp full-length cDNA encoding 228 amino acids of DaAFP and analyzed its structure using bioinformatics analysis. The DaAFP amino acid sequence exhibited 24–86% similarity with other insect species. The expression of DaAFP was high in January and in the larvae, head, and midgut of D. armandi. In addition, the expression of DaAFP increased with decreasing temperature and increasing exposure time. RNAi analysis also demonstrated that AFP plays an important role in the cold tolerance of overwintering larvae. The thermal hysteresis and antifreeze activity assay of DaAFP and its mutants indicated that the more regular the DaAFP threonine-cystine-threonine (TXT) motif, the stronger the antifreeze activity. These results suggest that DaAFP plays an essential role as a biological cryoprotectant in overwintering D. armandi larvae and provides a theoretical basis for new pest control methods.
Impact of ascending aortic prosthetic grafts on early postoperative descending aortic biomechanics on cardiac magnetic resonance imaging
Authors: Palumbo Maria C , Redaelli Alberto , Wingo Matthew , Tak Katherine A , Leonard Jeremy R , Kim Jiwon , Rong Lisa Q , Park Christine , Mitlak Hannah W , Devereux Richard B , Roman Mary J , RoyChoudury Arindam , Lau Christopher , Gaudino Mario F L , Girardi Leonard N , Weinsaft Jonathan W
Published: November 2021

OBJECTIVES

Among patients with ascending thoracic aortic aneurysms, prosthetic graft replacement yields major benefits but risk for recurrent aortic events persists for which mechanism is poorly understood. This pilot study employed cardiac magnetic resonance to test the impact of proximal prosthetic grafts on downstream aortic flow and vascular biomechanics.

METHODS

Cardiac magnetic resonance imaging was prospectively performed in patients with thoracic aortic aneurysms undergoing surgical (Dacron) prosthetic graft implantation. Imaging included time resolved (4-dimensional) phase velocity encoded cardiac magnetic resonance for flow quantification and cine-cardiac magnetic resonance for aortic wall distensibility/strain.

RESULTS

Twenty-nine patients with thoracic aortic aneurysms undergoing proximal aortic graft replacement were studied; cardiac magnetic resonance was performed pre- [12 (4, 21) days] and postoperatively [6.4 (6.2, 7.2) months]. Postoperatively, flow velocity and wall shear stress increased in the arch and descending aorta (P < 0.05); increases were greatest in hereditary aneurysm patients. Global circumferential strain correlated with wall shear stress (r = 0.60–0.72, P < 0.001); strain increased postoperatively in the native descending and thoraco-abdominal aorta (P < 0.001). Graft-induced changes in biomechanical properties of the distal native ascending aorta were associated with post-surgical changes in descending aortic wall shear stress, as evidenced by correlations (r = −0.39–0.52; P ≤ 0.05) between graft-induced reduction of ascending aortic distensibility and increased distal native aortic wall shear stress following grafting.

CONCLUSIONS

Prosthetic graft replacement of the ascending aorta increases downstream aortic wall shear stress and strain. Postoperative increments in descending aortic wall shear stress correlate with reduced ascending aortic distensibility, suggesting that grafts provide a nidus for high energy flow and adverse distal aortic remodelling.
Contesting Homogeneity: Stereotypes and Heteronormativity in Aruni Kashyap’s His Father’s Disease
Authors: Biswas Debajyoti
Published: November 2021

This article analyses Aruni Kashyap’s short story collection His Father’s Disease. Kashyap challenges hegemonic structures through an emerging writing area tentatively classified as ‘Anglophone fiction from Northeast India’. By engaging with Foucault’s reading of Power/Knowledge this article examines the disciplining of literary regionalism (Anglophone literature from Northeast India), territory and sexuality encapsulated in Kashyap’s exposition of heteronormative societies across cultures. Through the stories Kashyap weaves a dialogic space within the narrative world that challenges various forms of stereotypes relating to regional representation in literary works as well as regional identity and sexuality prevailing in the contemporary world’s existing social and literaryscape. Therefore, it becomes pertinent to observe how Kashyap’s text becomes a site of contention where on one hand the stereotype is accommodated within the power structure, hence controlled and regulated by various agencies, and on the other hand the same knowledge is appropriated by the author as a counter-narrative/reverse-discourse.
The Cardiology Society of India-Kerala Acute Heart Failure Registry: poor adherence to guideline-directed medical therapy
Authors: Joseph Stigi , Panniyammakal Jeemon , Abdullakutty Jabir , S Sujithkumar , Vaikathuseril L Jayaprakash , Joseph Johny , Mattummal Shaffeq , Punnose Eapen , Unni Govindan , Natesan Syam , Sivadasanpillai Harikrishnan
Published: November 2021

Aims

Data on the burden of acute heart failure (AHF) admissions, practice patterns, and outcomes are rare from India and other low- and middle-income countries. We aimed to describe the baseline characteristics, guideline-directed medical therapy (GDMT) prescribing patterns and 90-day mortality rates in patients admitted with AHF in Kerala, India.

Methods and results

The Cardiology Society of India-Kerala Acute Heart Failure Registry (CSI-KHFR) is an observational registry from 50 hospitals in Kerala, India, with prospective follow-up. Consecutive patients with AHF, who consented to participate, were enrolled. The 2016 European Society of Cardiology criteria were used for the diagnosis of AHF. Kaplan–Meier survival analysis and Cox-proportional hazard models were used for data analysis. The variables in the MAGGIC risk score were used in the multivariable model. A total of 7507 patients with AHF (37% female) participated in the CSI-KHFR. The mean age was 64.3 (12.9) years. More than two-third had reduced ejection fraction (EF) (67.5%). Nearly one-fourth (28%) of patients with heart failure (HF) with reduced EF received GDMT. Overall, in-hospital and 90-day mortality rates were 7% and 11.6%, respectively. Prescriptions of different components of GDMT were independently associated with 90-day mortality.

Conclusion

The CSI-KHFR recorded an in-hospital and 90-day mortality of 7% and 11.6%, respectively. Only one of four patients received GDMT. AHF mortality was independently associated with GDMT initiation. Quality improvement initiatives that focus on increasing GDMT prescription may improve the survival of HF patients in India.
Barriers to care for perinatal patients with opioid use disorder: family physician perspectives
Authors: St. Louis Joshua , Barreto Tyler , Taylor Melina , Kane Claire , Worringer Emma , Eden Aimee R
Published: November 2021

Background

While barriers to care for pregnant patients with opioid use disorder (OUD) have been described, the experiences and challenges of the physicians providing care to these patients are poorly understood.

Objectives

To describe the experiences of family physicians providing comprehensive care to pregnant people with OUD and the challenges they face in providing such care.

Methods

Qualitative thematic analysis of 17 semistructured interviews conducted from July 2019 to September 2020 with family physicians who possess a Drug Enforcement Administration “X” waiver and provide care to pregnant patients.

Results

Seventeen family physicians practicing in the United States who care for pregnant people with OUD were interviewed. They described physician-, patient-, and systems-level barriers to providing and accessing care for this patient population. Of the 12 interrelated themes regarding challenges to delivering and accessing this care, 3 were particularly salient: the pervasive effects of social determinants of health, a lack of adequately trained providers, and social stigma associated with pregnant people with OUD.

Conclusion

A comprehensive, multilevel, and multidisciplinary approach is necessary to address these barriers and move towards health equity for this vulnerable patient population.
The spread of the plasmid RP4 in a synthetic bacterial community is dependent on the particular donor strain
Authors: Heß Stefanie , Kneis David , Virta Marko , Hiltunen Teppo
Published: November 2021

The rapid spread of antibiotic resistance challenges modern medicine. So far, mechanistic and quantitative knowledge concerning the spread of resistance genes mainly relies on laboratory experiments with simplified setups, e.g. two strain communities. Thus, the transferability of the obtained process rates might be limited. To investigate the role of a diverse community concerning the dissemination of the multidrug resistance plasmid RP4, an Escherichia coli harboring RP4 invaded a microbial community consisting of 21 species. Changes in the community composition as well as plasmid uptake by community members were monitored for 22 days. Special focus was laid on the question of whether the observed changes were dependent on the actual invading donor isolate and the ambient antibiotic concentration. In our microcosm experiment, the community composition was primarily influenced by the given environmental variables and only secondarily by the particular invader E. coli. The establishment of resistance within the community, however, was directly dependent on the donor identity. The extent to which ambient conditions influence the spread of RP4 depended on the E. coli donor strain. These results emphasize that even within one species there are great differences in the ability to conquer an ecological niche and to spread antibiotic resistance.
High Temperature Requirement A (HtrA) protease ofListeria monocytogenesand its interaction with extracellular matrix molecules
Authors: Radhakrishnan Deepthi , M C Amrutha , Hutterer Evelyn , Wessler Silja , Ponnuraj Karthe
Published: November 2021

High Temperature Requirement A (HtrA) was identified as a secreted virulence factor in many pathogenic bacteria, including Listeria monocytogenes. Recently, it was discovered that Helicobacter pylori and Campylobacter jejuni HtrAs can directly cleave the human cell-adhesion molecule E-cadherin, which facilitates bacterial transmigration. HtrAs also interact with extracellular matrix (ECM) molecules. However, only a limited number of studies have been carried out in this regard. In the present study, the protease and ECM binding properties of L. monocytogenes HtrA (LmHtrA) were studied using native rLmHtrA, catalytically inactive rLmHtrA(S343A) and rLmHtrA lacking the PDZ domain (∆PDZ) to gain more insights into HtrA–ECM molecule interaction. The results show that (1) native rLmHtrA cleaves fibrinogen, fibronectin, plasminogen and casein in a time and temperature dependent manner, (2) interaction of rLmHtrA with various host proteins was found in the micromolar to nanomolar range, (3) in the absence of PDZ domain, rLmHtrA exhibits no drastic change in binding affinity toward the host molecules when compared with native rLmHtrA and (4) the PDZ domain plays an important role in the substrate cleavage as rLmHtrA1-394∆PDZ cleaves the substrates only under certain conditions. The proteolysis of various ECM molecules by rLmHtrA possibly highlights the role of HtrA in L. monocytogenes pathogenesis involving ECM degradation.
Assessing Rapid Relaxed-Clock Methods for Phylogenomic Dating
Authors: Barba-Montoya Jose , Tao Qiqing , Kumar Sudhir
Published: November 2021

Rapid relaxed-clock dating methods are frequently applied to analyze phylogenomic data sets containing hundreds to thousands of sequences because of their accuracy and computational efficiency. However, the relative performance of different rapid dating methods is yet to be compared on the same data sets, and, thus, the power and pitfalls of selecting among these approaches remain unclear. We compared the accuracy, bias, and coverage probabilities of RelTime, treePL, and least-squares dating time estimates by applying them to analyze computer-simulated data sets in which evolutionary rates varied extensively among branches in the phylogeny. RelTime estimates were consistently more accurate than the other two, particularly when evolutionary rates were autocorrelated or shifted convergently among lineages. The 95% confidence intervals (CIs) around RelTime dates showed appropriate coverage probabilities (95% on average), but other methods produced rather low coverage probabilities because of overly narrow CIs of time estimates. Overall, RelTime appears to be a more efficient method for estimating divergence times for large phylogenies.
A method for assaying peptide:N-glycanase/N-glycanase 1 activities in crude extracts using anN-glycosylated cyclopeptide
Authors: Hirayama Hiroto , Tachida Yuriko , Seino Junichi , Suzuki Tadashi
Published: November 2021

Cytosolic peptide: N-glycanase (PNGase; NGLY1), an enzyme responsible for de-glycosylation of N-glycans on glycoproteins, is known to play pivotal roles in a variety of biological processes. In 2012, NGLY1 deficiency, a rare genetic disorder, was reported and since then, more than 100 patients have now been identified worldwide. Patients with this disease exhibit several common symptoms that are caused by the dysfunction of NGLY1. However, correlation between the severity of patient symptoms and the extent of the reduction in NGLY1 activity in these patients remains to be clarified, mainly due to the absence of a facile quantitative assay system for this enzyme, especially in a crude extract as an enzyme source. In this study, a quantitative, non-radioisotope (RI)-based assay method for measuring recombinant NGLY1 activity was established using a BODIPY-labeled asialoglycopeptide (BODIPY-ASGP) derived from hen eggs. With this assay, the activities of 27 recombinant NGLY1 mutants that are associated with the deficiency were examined. It was found that the activities of three (R469X, R458fs and H494fs) out of the 27 recombinant mutant proteins were 30–70% of the activities of wild-type NGLY1. We further developed a method for measuring endogenous NGLY1 activity in crude extracts derived from cultured cells, patients’ fibroblasts, iPS cells or peripheral blood mononuclear cells (PBMCs), using a glycosylated cyclopeptide (GCP) that exhibited resistance to the endogenous proteases in the extract. Our methods will not only provide new insights into the molecular mechanism responsible for this disease but also promises to be applicable for its diagnosis.
Small RNAs encoded by human endogenous retrovirus K overexpressed in PBMCs may contribute to the diagnosis and evaluation of systemic lupus erythematosus as novel biomarkers
Authors: Liu Xinyi , Ding Yanjun , Zheng Xiaoqiu , Huang He , Shi Liyu , Yang Xiaolan , Wei Jing , Li Yang , Kao Wenping , Zhang Fengmin , Qian Jun
Published: November 2021

This study aimed to identify the genes and small RNAs (sRNAs) expressed by the human endogenous retrovirus K (HERV-K) HML2 and their associations with the immune process of systemic lupus erythematosus (SLE). RNA-Seq data including 99 SLE patients and 18 controls (GSE72420) was obtained from the Gene Expression Omnibus. Differentially expressed genes (DEGs) as well as HML2-DEGs between SLE patients and normal controls were identified. Five HML2-DEGs involved in immune-regulating function were identified using weighted gene co-expression network analysis. The associations between these genes and the proportions of immune cells were determined by CIBERSORT. Ten candidate HML2-encoded sRNAs were identified based on specific criteria, and three of them were further validated in SLE patients by qRT-PCR. The diagnostic values of these three sRNAs were evaluated in SLE and lupus nephritis (LN). This study suggested that HML2 genes and their encoded sRNAs might be involved in the immune regulation and progress of SLE. These potential sRNAs might function as regulatory molecules and diagnostic biomarkers of SLE and LN.