bluuebunny/crossref_metadata_2025 huggingface dataset:
The first issue of InJAST available in print and online
Authors: Priatna Dolly , A. Monk Kathryn
Published: October 2021

It is our great pleasure to announce that the very first issue of the Indonesian Journal of Applied Environmental Studies (InJAST) is now be  available   in  both  print  and  online.  This journal has evolved from the Journal of Environmental Education which started in 2015, and was managed  by the Study Programme of Population and Environmental Education, Graduate Programme of Pakuan University. Because this study programme has now become the Study Programme of Environmental Management,  we have decided to establish this new journal to publish scientific articles covering broader environmental issues that are written by the  Indonesian  students  of  graduate programmes either in Pakuan and other universities or researchers. Meanwhile, the publication and management  of the Journal of Environmental Education will be transferred to another relevant faculty or study programme within Pakuan University.We intend the new InJAST to be  published in English (with abstracts  both in English and Bahasa) so that it can reach a wider readership internationally, and we hope encourage international  environmental  students  and scientists working  in Indonesia or on topics of specific relevance to Indonesia,   to disseminate their research results and findings through  this journal.We are pleased to also announce that it has been agreed  in principle that  this new journal will be published collaboratively between the Graduate School of Pakuan University and PERWAKU (Perhimpunan Cendikiawan Pemerhati  Lingkungan  Indonesia,  the Indonesian Association of Environmentalist Scholars). A formal Memorandum of Understanding   between  both  parties  will  be signed in the near future.In this occasion, we, as the chief editors of this new journal, would like to express our gratitude  to various parties and individuals who have supported this initiative,  especially to Prof. Dr. H. Bibin Rubini, M.Pd. (Chancellor of Pakuan University), Prof. Dr. Ing. H. Soewarto Hardhienata (Dean of Graduate School Pakuan University), and Prof. Jatna Supriatna, Ph.D. (Chairman   of   PERWAKU  Indonesia).     We would also like to express special thanks to our national and international  colleagues at Pakuan University  and     elsewhere, who have so generously offered their time as members of the editorial board of the journal.Last but not least, we hope that the Indonesian Journal  of  Applied Environmental Studies  (InJAST) will  provide new  colour and perspectives the scientific journals published by Pakuan Univeristy,  and become the vehicle of choice for environmental  science students  and scientists to disseminate of their work.
Natural resources management to deliver Sustainable Development Goals (SDGs)
Authors: Widiyono Wahyu
Published: October 2021

Indonesia is known as a rich natural resources country, but at the same time has a problem of water shortage, soil degradation, pollution, agriculture and forest production, biodiversity conservation, and mineral and energy sustainability. The national natural resources management planning alignment with SDGs programme, particularly the water resources management,  afforestation programme,  a guide for sustainable management of Indonesia’s biodiversity, government and non-government organizations participant in conservation practice, exploring alternative energy sources to reduce dependence on oil, mainstreaming of SDGs into National Development agenda, National Action Plan, and  SDGs program for Sub-national level. This program was participated by all stakeholders included government, civil society organizations, philanthropy and business society, academics as well as experts. This literature review paper will discuss about the natural resources management to deliver sustainable development goals programme in Indonesian, with specific and focus topics for water and pollution, soil, land product  (agriculture, forest and biological resources), mineral and energy. The objective of this paper was to describe  the alignment of the natural resources management planning and SDGs programme as evaluation to improve their implementation in Indonesia. Though the government has already implemented SDGs program but innovative strategic need to be developed.Indonesia dikenal sebagai negara yang kaya sumberdaya alam, tetapi pada saat yang sama menghadapi masalah kelangkaan air, degradasi lahan, polusi, produksi pertanian dan kehutanan, konservasi keanekaragaman hayati, keberlangsungan mineral dan energi. Rencana pengelolaan sumberdaya alam nasional sejalan dengan program SDGs,  khususnya terkait pengelolaan air, program perhutanian, pengelolaan keanekaragaman hayati secara berkelanjutan, pemerintah dan para pihak yang berpartisipasi dalam praktek konservasi, eksplorasi energi alternatif untuk mengurangi ketergantungan pada minyak bumi, dan pengarus-utamakaan program SDGs ke dalam agenda pembangunan nasional, rencana aksi nasional, dan program di tingkat wilayah. Program ini diikuti oleh seluruh para pihak, termasuk pemerintah, organisasi masyarakat sipil, masyarakat bisnis dan filantropi, kaum akademisi dan para ahli. Studi Pustaka ini akan membahas tentang pengelolaan sumberdaya alam untuk mencapai program pembangunan berkelanjutan di Indonesia, khususnya tentang masalah air, polusi, produsi lahan (meliputi pertanian, hutan, sumberdaya biologi), mineral dan energi. Tujuan penulisan naskah adalah untuk memberikan gambaran keterkaitan antara rencana pengelolaan sumberdaya alam dan pelaksanaan program pembangunan berkelanjutan, sebagai evaluasi untuk meningkatkan implementasinya di Indonesia. Meskipun pemerintah telah melaksanakan program SDGs, tetapi strategi yang inovatif perlu dikembangkan.
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Published: October 2021

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STUDY OF GEOLOGICAL SECTIONS OF THE ORDOVIK AGE OF GORNY ALTAI
Authors: Ilyin Danil A. , Kokorina Irina P.
Published: October 2021

The article deals with the study of geological sections of the Ordovic age in Gorny Altai. On the territory of the Altai Mountains, outcrops of rocks of the Ordovic age were found. As a result of the work on the sections, the lithological composition was analyzed and the fauna was collected, the taxonomic composition of which was then determined in the Paleozoic laboratory of the Institute of Geological and Geological Development of the Siberian Branch of the Russian Academy of Sciences. On the basis of the data of geological survey, mapping of the territory, the results of the study of geological sections, their lithology and faunistic composition, it is planned to create an interactive cartographic service in the future.
MODERN PROBLEMS OF RECLAMATION AND ASSESSMENT OF TERRITORIES ALLOCATED FOR THE TURNOVER OF WASTE PRODUCTS
Authors: Kopkina Anastasia A. , Tatarenko Valery I.
Published: October 2021

The object of the study is the territories allocated for the disposal of industrial waste and municipal solid waste. One of the main modern problems of mankind is the accumulation of large amounts of waste, which is an indispensable by-product of the modern production and consumption. Among the efficient solutions to the problem is the organization of an optimized system of waste management and utilization, which minimizes their disposal in specially designated landfills. Another, no less significant problem for the Russian Federation, is the return to circulation of huge territories previously allocated for waste disposal and the use of which as landfills was discontinued.
JUSTIFICATION OF THE NEED TO ENSURE INFORMATION SECURITY OF AN ENTERPRISE IN THE ERA OF DIGITALIZATION
Authors: Obidenko Anton V. , Shaburova Aelita V.
Published: October 2021

The relevance of information security research aimed at reducing information risks and optimizing enterprise costs for information protection. The results make it possible to increase the degree of information protection at enterprises by using methods, algorithms and practical procedures in the formation of an information security system aimed at reducing information risks.
DEVELOPMENT AND ANALYSIS OF A CONCEPTUAL MODEL OF BIOMETRIC INFORMATION FROM THE POINT OF VIEW OF THE EXISTING LEGISLATIVE AND REGULATORY FRAMEWORKS
Authors: Shurugin Sergei V. , Matveev Arif U. , Gritskevich Evgeny V.
Published: October 2021

The proposed work is devoted to the classification of biometric systems for recognizing subjects, which play an important role in modern information security systems, since they are currently one of the main means of identification and authentication of an individual. The classification schemes presented in this paper allow us to apply a systematic approach to the development of new methods of biometrics.
TESTING INFORMATION SYSTEM OF AN ENTERPRISE FOR VULNERABILITY USING VIRTUAL ENVIRONMENT
Authors: Gorohov Roman S. , Karmanov Igor N.
Published: October 2021

The paper focused on options for examining the organization's local area network for external sources of access. The approaches to finding the points of interaction of a potential attacker with the system are described. A variant of solving the problem of the impossibility of using the existing information system by using a virtual environment is also proposed. Thus, it becomes possible to test the information system for the presence of security threats, on a model that is as close to reality as possible.
DOMINASI GENERA KARANG KERAS (HARD CORAL) DI PERAIRAN DESA TANJUNG TIRAM, KAB. KONAWE SELATAN
Authors: Massar Mundzir , Sadarun Baru , Subhan .
Published: October 2021

Ekosistem terumbu karang di Desa Tanjung Tiram memiliki sumberdaya yang beranekaragam dan berlimpah. Namun dalam beberapa dekade terakhir, keberadaannya terancam oleh kegiatan penangkapan ikan yang tidak ramah lingkungan. Penelitian ini bertujuan untuk mengetahui dominasi genera karang keras dan persentase tutupan karang hidup serta hubungan faktor lingkungan dengan sebaran kondisi terumbu karang di perairan Desa Tanjung Tiram. Penelitian ini dilaksanakan pada bulan September 2020. Hasil penelitian ini ditemukan 3 genera dominasi yaitu Porites, Fungia dan Favites dimana Porites merupakan genus karang yang paling dominan ditemukan di area reef slope dan reef flat. Secara keseluruhan persentase tutupan karang hidup Perairan Tanjung Tiram berada di bawah 60%. Semakin dalam perairan presentase tutupan karang hidup makin rendah dan patahan mendominasi.Kata kunci: Dominasi, Karang Keras, Tanjung Tiram.
Obtaining Damages for Corporate Human Rights Violations in Investment Arbitration Through a Procedural Lens
Authors: S Yasmin
Published: October 2021

Over the past decades, transnational corporations have come under increasing public scrutiny for their involvement in human rights abuses, particularly in developing countries. One may think of violent acts against local communities, slave labor, and grand scale environmental pollution. International investment law protects and safeguards the rights of foreign investors but falls short of holding them accountable to societies where they operate. Recently, a few arbitral tribunals have grappled with the question of whether corporations can be held accountable for illegalities that constitute human rights violations inflicted upon the host state or its people. This article discusses the arbitral treatment of corporate human rights violations by investment tribunals in three treaty-based cases: Copper Mesa v. Ecuador, Burlington v. Ecuador and Urbaser v. Argentina and draws on recent scholarly work on causation in investor-state arbitration to evaluate their approaches.
The Properly Improper: Making Sense of Humanity through Derrida, Butler and Rosaldo
Authors: Arora Manali
Published: October 2021

That which is proper to humans or which makes a human proper- of which hundreds have been conceptualized- consists of ethics, moral values, expression, responsibilities at the nexus of society, culture, individual differences. As these conceptualizations are closely scrutinized, the universality of a proper being begins to disintegrate, binaries emerge along with the ethical questions to which the answers are not easily found. In this paper, beginning with the religious theorization of what is a proper human, making sense of it through Kafka’s Metamorphosis and elucidating on the aspects of humans like Gaze, Animality, and Rage that puts propriety into question, ethical questions are raised which are suggestive of human ignorance towards the obvious. Abstracting from the works of Jacques Derrida, Renato Rosaldo, and Judith Butler, this paper attempts to answer the question of what is being a proper human by examining the culture, contexts, and contemporary intersectionality.
Application of Modified Grey Forecasting Model to Predict the Municipal Solid Waste Generation using MLP and MLE
Authors: Anjum Mohd , Shahab Sana , Umar Mohammad Sarosh
Published: October 2021

Grey forecasting theory is an approach to build a prediction model with limited data to produce better forecasting results. This forecasting theory has an elementary model, represented as the GM(1,1) model , characterized by the first-order differential equation of one variable. It has the potential for accurate and reliable forecasting without any statistical assumption. The research proposes a methodology to derive the modified GM(1,1) model with improved forecasting precision. The residual series is forecasted by the GM(1,1) model to modify the actual forecasted values. The study primarily addresses two fundamental issues: sign prediction of forecasted residual and the procedure for formulating the grey model. Accurate sign prediction is very complex, especially when the model lacks in data. The signs of forecasted residuals are determined using a multilayer perceptron to overcome this drawback. Generally, the elementary model is formulated conventionally, containing the parameters that cannot be calculated straightforward. Therefore, maximum likelihood estimation is incorporated in the modified model to resolve this drawback. Three statistical indicators, relative residual, posterior variance test, and absolute degree of grey indices, are evaluated to determine the model fitness and validation. Finally, an empirical study is performed using actual municipal solid waste generation data in Saudi Arabia, and forecasting accuracies are compared with the linear regression and original GM(1,1). The MAPEs of all models are rigorously examined and compared, and then it is obtained that the forecasting precision of GM(1,1) model , modified GM(1,1) model, and linear regression is 15.97%, 8.90%, and 27.90%, respectively. The experimental outcomes substantiate that the modified grey model is a more suitable forecasting approach than the other compared models.
Numerical Solution of the Time-Depending Flow of Immiscible Fluids with Fuzzy Boundary Conditions
Authors: Chandrawat Rajesh Kumar , Joshi Varun
Published: October 2021

Fluid flow modeling using fuzzy boundary conditions is one of the viable areas in biofluid mechanics, drug suspension in pharmacology, as well as in the cytology and electrohydrodynamic analysis of cerebrospinal fluid data. In this article, a fuzzy solution for the two immiscible fluid flow problems is developed, which is motivated by biomechanical flow engineering. Two immiscible fluids, namely micropolar and Newtonian fluid, are considered with fuzzy boundary conditions in the horizontal channel. The flow is considered unsteady and carried out by applying a constant pressure gradient in the X-direction of the channel. The coupled partial differential equations are modeled for fuzzy profiles of velocity and micro-rotation vectors then the numerical results are obtained by the modified cubic B - spline differential quadrature method. The evolution of membership grades for velocity and microrotation profiles has been depicted with the fuzzy boundaries at the channel wall. It is observed that Micropolar fluid has a higher velocity change than Newtonian fluid, and both profiles indicate a declining nature toward the interface.
Some New Solutions of Non Linear Evolution Equations With Mutable Coefficients
Authors: Virdi Jasvinder Singh
Published: October 2021

We construct the traveling wave solutions of some NonLinear Evolution Equations (NLEEs) with mutable coefficients arising in different branches of physics and mathematics. we apply a novel (G′G)-formalism to construct more general solitary traveling wave solutions of NLEEs such as Sharma-Tasso-Olver with mutable coefficients and Zakharov Kuznetsov equation. Interesting solutions of NLEEs are investigated by traveling wave solutions which are in form of trigonometric, rational, and hyperbolic functions. This may build more unified new solutions for different kinds of such NLEEs with mutable coefficients arising in mathematics and physics. Wolfram Mathematica 11 is used to perform the computation work and their corresponding plots and counter graphs are plotted. This method is found to be more useful and efficient for searching the exact solutions of NLEEs.
Four Global Catastrophic Risks – A Personal View
Authors: Blong Russell
Published: October 2021

Global catastrophic risks (GCRs) affect a larger than hemispheric area and produce death tolls of many millions and/or economic losses greater than several trillion USD. Here I explore the biophysical, social-economic, demographic and cultural strands of four global catastrophic risks – sea level rise, a VEI 7 eruption, a pandemic, and a geomagnetic storm – one human-exacerbated at the least, one geological, one biological in large part, and one from space. Durations of these biophysical events range from a day or two to more than 100 years and the hazards associated range from none to numerous. Each of the risks has an average return period of no more than a few hundred years and lie within a range where many regulators ordinarily demand efforts in the case of less extreme events at enhancing resilience. Losses produced by GCRs and other natural hazards are usually assessed in terms of human mortality or dollars but many less tangible losses are at least as significant. Despite the varying durations, biophysical characteristics, and the wide array of potential consequences, the aftermath at global (and at more granular scales) can be summarised by one of four potential futures. While this assessment considers the present and the near future (the Anthropocene), much of this appraisal applies also to global catastrophic risks in the Early Holocene.
Strong Genetic Structure Observed in Primulina danxiaensis, a Small Herb Endemic to Mount Danxia With Extremely Small Populations
Authors: Chen Sufang , Guo Wei , Chen Zaixiong , Liao Wenbo , Fan Qiang
Published: October 2021

Danxia landform occurring sporadically in southern China is a unique type of petrographic geomorphology. It has nurtured about 400 rare or threatened plant and animal species, whose diversity, endemism, and conservation have called increasing scientific and public attentions. Among them, Primulina danxiaensis (W. B. Liao, S. S. Lin, and R. J. Shen) W. B. Liao and K. F. Chung is a tiny perennial grass species recorded only in Mount Danxia, a natural World Heritage Site as part of China’s Danxia. In this study, restriction site-associated DNA sequencing (RAD-seq) was performed to investigate genetic diversity among these 12 populations of P. danxiaensis. A total of 432,041 variant sites were detected in 84,779 loci across 94 samples. The expected heterozygosity (HE) ranged from 0.017 to 0.139. Bottleneck signals were detected in most populations, Tajima’s D tests showed that most loci could be under recent positive selection, and one of the six positively selected loci identified by BayeScan was annotated as tRNAGlu, which may contribute to the species’ adaptation to shady environment. STRUCTURE analysis and phylogenetic tree showed that the 12 populations of P. danxiaensis could be divided into four gene pools (clades) corresponding to their geographic locations, and significant correlation was observed between genetic and geographic distances. Our study demonstrated that P. danxiaensis maintained a middle level of genetic diversity and strong population structure; geographic distance could be an important factor limiting gene flow among populations of P. danxiaensis, which were only sporadically recorded in Mount Danxia.
Predator-Prey Dynamics of Intra-Host Simian Immunodeficiency Virus Evolution Within the Untreated Host
Authors: Rife Magalis Brittany , Autissier Patrick , Williams Kenneth C. , Chen Xinguang , Browne Cameron , Salemi Marco
Published: October 2021

The dynamic nature of the SIV population during disease progression in the SIV/macaque model of AIDS and the factors responsible for its behavior have not been documented, largely owing to the lack of sufficient spatial and temporal sampling of both viral and host data from SIV-infected animals. In this study, we detail Bayesian coalescent inference of the changing collective intra-host viral effective population size (Ne) from various tissues over the course of infection and its relationship with what we demonstrate is a continuously changing immune cell repertoire within the blood. Although the relative contribution of these factors varied among hosts and time points, the adaptive immune response best explained the overall periodic dynamic behavior of the effective virus population. Data exposing the nature of the relationship between the virus and immune cell populations revealed the plausibility of an eco-evolutionary mathematical model, which was able to mimic the large-scale oscillations in Ne through virus escape from relatively few, early immunodominant responses, followed by slower escape from several subdominant and weakened immune populations. The results of this study suggest that SIV diversity within the untreated host is governed by a predator-prey relationship, wherein differing phases of infection are the result of adaptation in response to varying immune responses. Previous investigations into viral population dynamics using sequence data have focused on single estimates of the effective viral population size (Ne) or point estimates over sparse sampling data to provide insight into the precise impact of immune selection on virus adaptive behavior. Herein, we describe the use of the coalescent phylogenetic frame- work to estimate the relative changes in Ne over time in order to quantify the relationship with empirical data on the dynamic immune composition of the host. This relationship has allowed us to expand on earlier simulations to build a predator-prey model that explains the deterministic behavior of the virus over the course of disease progression. We show that sequential viral adaptation can occur in response to phases of varying immune pressure, providing a broader picture of the viral response throughout the entire course of progression to AIDS.
Activation of iNKT Cells Facilitates Liver Repair After Hepatic Ischemia Reperfusion Injury Through Acceleration of Macrophage Polarization
Authors: Goto Takuya , Ito Yoshiya , Satoh Masashi , Nakamoto Shuji , Nishizawa Nobuyuki , Hosono Kanako , Naitoh Takeshi , Eshima Koji , Iwabuchi Kazuya , Hiki Naoki , Amano Hideki
Published: October 2021

Macrophage polarization is critical for liver tissue repair following acute liver injury. However, the underlying mechanisms of macrophage phenotype switching are not well defined. Invariant natural killer T (iNKT) cells orchestrate tissue inflammation and tissue repair by regulating cytokine production. Herein, we examined whether iNKT cells played an important role in liver repair after hepatic ischemia-reperfusion (I/R) injury by affecting macrophage polarization. To this end, we subjected male C57BL/6 mice to hepatic I/R injury, and mice received an intraperitoneal (ip) injection of α-galactosylceramide (α-GalCer) or vehicle. Compared with that of the vehicle, α-GalCer administration resulted in the promotion of liver repair accompanied by acceleration of macrophage differentiation and by increases in the numbers of Ly6Chigh pro-inflammatory macrophages and Ly6Clow reparative macrophages. iNKT cells activated with α-GalCer produced interleukin (IL)-4 and interferon (IFN)-γ. Treatment with anti-IL-4 antibodies delayed liver repair, which was associated with an increased number of Ly6Chigh macrophages and a decreased number of Ly6Clow macrophages. Treatment with anti-IFN-γ antibodies promoted liver repair, associated with reduced the number of Ly6Chigh macrophages, but did not change the number of Ly6Clow macrophages. Bone marrow-derived macrophages up-regulated the expression of genes related to both a pro-inflammatory and a reparative phenotype when co-cultured with activated iNKT cells. Anti-IL-4 antibodies increased the levels of pro-inflammatory macrophage-related genes and decreased those of reparative macrophage-related genes in cultured macrophages, while anti-IFN-γ antibodies reversed the polarization of macrophages. Cd1d-deficient mice showed delayed liver repair and suppressed macrophage switching, compared with that in wild-type mice. These results suggest that the activation of iNKT cells by α-GalCer facilitated liver repair after hepatic I/R injury by both IL-4-and IFN-γ-mediated acceleration of macrophage polarization. Therefore, the activation of iNKT cells may represent a therapeutic tool for liver repair after hepatic I/R injury.
TNF-α Carried by Plasma Extracellular Vesicles Predicts Knee Osteoarthritis Progression
Authors: Zhang Xin , Hsueh Ming-Feng , Huebner Janet L. , Kraus Virginia B.
Published: October 2021

Objectives

To identify plasma extracellular vesicles (EVs) associated with radiographic knee osteoarthritis (OA) progression.

Methods

EVs of small (SEV), medium (MEV) and large (LEV) sizes from plasma of OA participants (n=30) and healthy controls (HCs, n=22) were profiled for surface markers and cytokine cargo by high-resolution flow cytometry. The concentrations of cytokines within (endo-) and outside (exo-) EVs were quantified by multiplex ELISA. EV associations with knee radiographic OA (rOA) progression were assessed by multivariable linear regression (adjusted for baseline clinical variables of age, gender, BMI and OA severity) and receiver operating characteristic (ROC) curve analysis.

Results

Based on integrated mean fluorescence intensity (iMFI), baseline plasma MEVs carrying CD56 (corresponding to natural killer cells) predicted rOA progression with highest area under the ROC curve (AUC) 0.714 among surface markers. Baseline iMFI of TNF-α in LEVs, MEVs and SEVs, and the total endo-EV TNF-α concentration, predicted rOA progression with AUCs 0.688, 0.821, 0.821, 0.665, respectively. In contrast, baseline plasma exo-EV TNF-α (the concentration in the same unit of plasma after EV depletion) did not predict rOA progression (AUC 0.478). Baseline endo-EV IFN-γ and exo-EV IL-6 concentrations were also associated with rOA progression, but had low discriminant capacity (AUCs 0.558 and 0.518, respectively).

Conclusions

Plasma EVs carry pro-inflammatory cargo that predict risk of knee rOA progression. These findings suggest that EV-associated TNF-α may be pathogenic in OA. The sequestration of pathogenic TNF-α within EVs may provide an explanation for the lack of success of systemic TNF-α inhibitors in OA trials to date.
Genetic Elucidation of Quorum Sensing and Cobamide Biosynthesis in Divergent Bacterial-Fungal Associations Across the Soil-Mangrove Root Interface
Authors: Zhou Zhengyuan , Hu Ruiwen , Ni Yanmei , Zhuang Wei , Luo Zhiwen , Huang Weiming , Yan Qingyun , He Zhili , Zhong Qiuping , Wang Cheng
Published: October 2021

Plant roots in soil host a repertoire of bacteria and fungi, whose ecological interactions could improve their functions and plant performance. However, the potential microbial interactions and underlying mechanisms remain largely unknown across the soil-mangrove root interface. We herein analyzed microbial intra- and inter-domain network topologies, keystone taxa, and interaction-related genes across four compartments (non-rhizosphere, rhizosphere, episphere, and endosphere) from a soil-mangrove root continuum, using amplicon and metagenome sequencing technologies. We found that both intra- and inter-domain networks displayed notable differences in the structure and topology across four compartments. Compared to three peripheral compartments, the endosphere was a distinctive compartment harboring more dense co-occurrences with a higher average connectivity in bacterial-fungal network (2.986) than in bacterial (2.628) or fungal network (2.419), which could be related to three bacterial keystone taxa (Vibrio, Anaerolineae, and Desulfarculaceae) detected in the endosphere as they are known to intensify inter-domain associations with fungi and stimulate biofilm formation. In support of this finding, we also found that the genes involved in cell-cell communications by quorum sensing (rhlI, lasI, pqsH, and lasR) and aerobic cobamide biosynthesis (cobG, cobF, and cobA) were highly enriched in the endosphere, whereas anaerobic cobamide biosynthesis (encoded by cbiT and cbiE) was dominant in three peripheral compartments. Our results provide genetic evidence for the intensified bacterial-fungal associations of root endophytes, highlighting the critical role of the soil-root interface in structuring the microbial inter-domain associations.
Nlrp3 Increases the Host’s Susceptibility to Tularemia
Authors: Suresh Ragavan V. , Bradley Elizabeth W. , Higgs Matthew , Russo Vincenzo C. , Alqahtani Maha , Huang Wiehua , Bakshi Chandra Shekhar , Malik Meenakshi
Published: October 2021

Francisella tularensis(F. tularensis) is a Gram-negative, intracellular bacterium and the causative agent of a fatal human disease known as tularemia. The CDC has classifiedF. tularensisas a Tier 1 Category A select agent based on its ease of aerosolization, low infectious dose, past use as a bioweapon, and the potential to be used as a bioterror agent.Francisellahas a unique replication cycle. Upon its uptake,Francisellaremains in the phagosomes for a short period and then escapes into the cytosol, where the replication occurs.Francisellais recognized by cytosolic pattern recognition receptors, Absent In Melanoma 2 (Aim2) andNachtLRR andPYD domains containing Protein3(Nlrp3). The recognition ofFrancisellaligands by Aim2 and Nlrp3 triggers the assembly and activation of the inflammasome. The mechanism of activation of Aim2 is well established; however, how Nlrp3 inflammasome is activated in response toF. tularensisinfection is not known. Unlike Aim2, the protective role of Nlrp3 againstFrancisellainfection is not fully established. This study investigated the role of Nlrp3 and the potential mechanisms through which Nlrp3 exerts its detrimental effects on the host in response toF. tularensisinfection. The results fromin vitrostudies demonstrate that Nlrp3 dampens NF-κB and MAPK signaling, and pro-inflammatory cytokine production, which allows replication ofF. tularensisin infected macrophages.In vivo, Nlrp3 deficiency results in differential expression of several genes required to induce a protective immune response against respiratory tularemia. Nlrp3-deficient mice mount a stronger innate immune response, clear bacteria efficiently with minimal organ damage, and are more resistant toFrancisellainfection than their wild-type counterparts. Together, these results demonstrate that Nlrp3 enhances the host’s susceptibility toF. tularensisby modulating the protective innate immune responses. Collectively, this study advances our understanding of the detrimental role of Nlrp3 in tularemia pathogenesis.
Free DNA and Metagenomics Analyses: Evaluation of Free DNA Inactivation Protocols for Shotgun Metagenomics Analysis of Human Biological Matrices
Authors: Mancabelli Leonardo , Milani Christian , Anzalone Rosaria , Alessandri Giulia , Lugli Gabriele Andrea , Tarracchini Chiara , Fontana Federico , Turroni Francesca , Ventura Marco
Published: October 2021

Culture-independent approaches now represent the gold standard for the investigation of both environmental and host-associated complex microbial communities. Nevertheless, despite the great advantages offered by these novel methodologies based on the use of next-generation DNA sequencing approaches, a number of bias sources have been identified. Among the latter, free DNA contained in biological matrices is one of the main sources of inaccuracy in reconstructing the resident microbial population of viable cells. For this reason, the photoreactive DNA-binding dye propidium monoazide (PMAxx™) has been developed by improving standard PMA. This compound binds and inactivates free DNA, thus preventing its amplification and sequencing. While the performances of PMA have been previously investigated, the efficiency with PMAxx™ has been tested mainly for amplicon-based profiling approaches on a limited number of biological matrices. In this study, we validated the performance of PMAxx™ for shotgun metagenomics approaches employing various human-associated matrices. Notably, results revealed that the effectiveness of PMAxx™ in inactivating free DNA of prokaryotes and eukaryotes tends to vary significantly based on the biological matrices analyzed.
Expanding Characterized Diversity and the Pool of Complete Genome Sequences of Methylococcus Species, the Bacteria of High Environmental and Biotechnological Relevance
Authors: Oshkin Igor Y. , Danilova Olga V. , But Sergey Y. , Miroshnikov Kirill K. , Suleimanov Ruslan Z. , Belova Svetlana E. , Tikhonova Ekaterina N. , Kuznetsov Nikolai N. , Khmelenina Valentina N. , Pimenov Nikolai V. , Dedysh Svetlana N.
Published: October 2021

The bacterial genus Methylococcus, which comprises aerobic thermotolerant methanotrophic cocci, was described half-a-century ago. Over the years, a member of this genus, Methylococcus capsulatus Bath, has become a major model organism to study genomic and metabolic basis of obligate methanotrophy. High biotechnological potential of fast-growing Methylococcus species, mainly as a promising source of feed protein, has also been recognized. Despite this big research attention, the currently cultured Methylococcus diversity is represented by members of the two species, M. capsulatus and M. geothermalis, while finished genome sequences are available only for two strains of these methanotrophs. This study extends the pool of phenotypically characterized Methylococcus strains with good-quality genome sequences by contributing four novel isolates of these bacteria from activated sludge, landfill cover soil, and freshwater sediments. The determined genome sizes of novel isolates varied between 3.2 and 4.0Mb. As revealed by the phylogenomic analysis, strains IO1, BH, and KN2 affiliate with M. capsulatus, while strain Mc7 may potentially represent a novel species. Highest temperature optima (45–50°C) and highest growth rates in bioreactor cultures (up to 0.3h−1) were recorded for strains obtained from activated sludge. The comparative analysis of all complete genomes of Methylococcus species revealed 4,485 gene clusters. Of these, pan-genome core comprised 2,331 genes (on average 51.9% of each genome), with the accessory genome containing 846 and 1,308 genes in the shell and the cloud, respectively. Independently of the isolation source, all strains of M. capsulatus displayed surprisingly high genome synteny and a striking similarity in gene content. Strain Mc7 from a landfill cover soil differed from other isolates by the high content of mobile genetic elements in the genome and a number of genome-encoded features missing in M. capsulatus, such as sucrose biosynthesis and the ability to scavenge phosphorus and sulfur from the environment.
Pyrophosphate and Irreversibility in Evolution, or why PPi Is Not an Energy Currency and why Nature Chose Triphosphates
Authors: Wimmer Jessica L. E. , Kleinermanns Karl , Martin William F.
Published: October 2021

The possible evolutionary significance of pyrophosphate (PPi) has been discussed since the early 1960s. Lipmann suggested that PPi could have been an ancient currency or a possible environmental source of metabolic energy at origins, while Kornberg proposed that PPi vectorializes metabolism because ubiquitous pyrophosphatases render PPi forming reactions kinetically irreversible. To test those ideas, we investigated the reactions that consume phosphoanhydride bonds among the 402 reactions of the universal biosynthetic core that generates amino acids, nucleotides, and cofactors from H2, CO2, and NH3. We find that 36% of the core’s phosphoanhydride hydrolyzing reactions generate PPi, while no reactions use PPi as an energy currency. The polymerization reactions that generate ~80% of cell mass – protein, RNA, and DNA synthesis – all generate PPi, while none use PPi as an energy source. In typical prokaryotic cells, aminoacyl tRNA synthetases (AARS) underlie ~80% of PPi production. We show that the irreversibility of the AARS reaction is a kinetic, not a thermodynamic effect. The data indicate that PPi is not an ancient energy currency and probably never was. Instead, PPi hydrolysis is an ancient mechanism that imparts irreversibility, as Kornberg suggested, functioning like a ratchet’s pawl to vectorialize the life process toward growth. The two anhydride bonds in nucleoside triphosphates offer ATP-cleaving enzymes an option to impart either thermodynamic control (Pi formation) or kinetic control (PPi formation) upon reactions. This dual capacity explains why nature chose the triphosphate moiety of ATP as biochemistry’s universal energy currency.
The Acquisition of Culturally Patterned Attention Styles Under Active Inference
Authors: Constant Axel , Tschantz Alexander Daniel Dunsmoir , Millidge Beren , Criado-Boado Felipe , Martinez Luis M , Müeller Johannes , Clark Andy
Published: October 2021

This paper presents an active inference based simulation study of visual foraging. The goal of the simulation is to show the effect of the acquisition of culturally patterned attention styles on cognitive task performance, under active inference. We show how cultural artefacts like antique vase decorations drive cognitive functions such as perception, action and learning, as well as task performance in a simple visual discrimination task. We thus describe a new active inference based research pipeline that future work may employ to inquire on deep guiding principles determining the manner in which material culture drives human thought, by building and rebuilding our patterns of attention.
Investigating Data Cleaning Methods to Improve Performance of Brain–Computer Interfaces Based on Stereo-Electroencephalography
Authors: Liu Shengjie , Li Guangye , Jiang Shize , Wu Xiaolong , Hu Jie , Zhang Dingguo , Chen Liang
Published: October 2021

Stereo-electroencephalography (SEEG) utilizes localized and penetrating depth electrodes to directly measure electrophysiological brain activity. The implanted electrodes generally provide a sparse sampling of multiple brain regions, including both cortical and subcortical structures, making the SEEG neural recordings a potential source for the brain–computer interface (BCI) purpose in recent years. For SEEG signals, data cleaning is an essential preprocessing step in removing excessive noises for further analysis. However, little is known about what kinds of effect that different data cleaning methods may exert on BCI decoding performance and, moreover, what are the reasons causing the differentiated effects. To address these questions, we adopted five different data cleaning methods, including common average reference, gray–white matter reference, electrode shaft reference, bipolar reference, and Laplacian reference, to process the SEEG data and evaluated the effect of these methods on improving BCI decoding performance. Additionally, we also comparatively investigated the changes of SEEG signals induced by these different methods from multiple-domain (e.g., spatial, spectral, and temporal domain). The results showed that data cleaning methods could improve the accuracy of gesture decoding, where the Laplacian reference produced the best performance. Further analysis revealed that the superiority of the data cleaning method with excellent performance might be attributed to the increased distinguishability in the low-frequency band. The findings of this work highlighted the importance of applying proper data clean methods for SEEG signals and proposed the application of Laplacian reference for SEEG-based BCI.
Case Report: Reduced CSF Orexin Levels in a Patient With Sepsis
Authors: Ogawa Yasuhiro , Ezaki Seioh , Shimojo Nobutake , Kawano Satoru
Published: October 2021

Sepsis is a potentially lethal condition characterized by systemic inflammation and multiple organ failure, and sepsis-associated encephalopathy (SAE) is an independent risk factor for mortality in patients with sepsis. We previously reported that orexin improved survival in an animal model of sepsis by acting in the brain. Peripherally administered orexin entered the brain under the conditions of systemic inflammation because of BBB dysfunction and produced survival-related effects. As a therapeutic concept, we hypothesized that orexin treatment enhances recovery from sepsis by restoring reduced orexin levels in cerebrospinal fluid (CSF). Here, we report that CSF orexin levels were reduced in a 63-year-old woman with sepsis. The patient presented with coma, fever, headache, vomiting, and seizures upon arrival at the emergency room. She had a history of subarachnoid hemorrhage which led to the development of hydrocephalus, and as a consequence, a ventriculoperitoneal shunt (VP shunt) tube had been installed to ameliorate the complication. Physical examinations showed dehydration and abnormality of circulation, arterial blood gas analysis showed insufficient oxygenation, blood tests showed an inflammatory response, liver injury, kidney injury, hyperkalemia, and hyperglycemia, and radio graphical examinations showed mild hydrocephalus and several old microinfarctions. She was diagnosed with sepsis because her Sequential Organ Failure Assessment (SOFA) score was 13 and Enterococcus faecalis was isolated form her blood and CSF. Status epilepticus, hyperglycemia, and sepsis-associated encephalopathy were considered possible causes of coma. Her CSF could be safely sampled because she had a VP shunt, although it is ethically difficult to sample CSF routinely from patients with sepsis. Reduced CSF orexin levels gradually recovered as she recovered from sepsis. Unexpectedly, orexin was detected in the blood, which is unusual in healthy humans. Blood orexin was not detected after recovery from sepsis. This result may imply that orexin leaks into the blood because of BBB dysfunction. To the best of our knowledge, this is the first report investigating orexin levels in the CSF and blood of a patient with sepsis, and the data obtained from this case may provide a new understanding of the pathophysiology of SAE.
Transcriptomic Correlates of Immunologic Activation in Head and Neck and Cervical Cancer
Authors: Saiz-Ladera Cristina , Baliu-Piqué Mariona , Cimas Francisco J. , Manzano Aránzazu , García-Barberán Vanesa , Camarero Santiago Cabezas , Hinojal Gonzalo Fernández , Pandiella Atanasio , Győrffy Balázs , Stewart David , Cruz-Hernández Juan J. , Pérez-Segura Pedro , Ocana Alberto
Published: October 2021

Targeting the immune system has emerged as an effective therapeutic strategy for the treatment of various tumor types, including Head and Neck Squamous Cell Carcinoma (HNSCC) and Non-small-Cell Lung Cancer (NSCLC), and checkpoint inhibitors have shown to improve patient survival in these tumor types. Unfortunately, not all cancers respond to these agents, making it necessary to identify responsive tumors. Several biomarkers of response have been described and clinically tested. As of yet what seems to be clear is that a pre-activation state of the immune system is necessary for these agents to be efficient. In this study, using established transcriptomic signatures, we identified a group of gene combination associated with favorable outcome in HNSCC linked to a higher presence of immune effector cells. CD2, CD3D, CD3E, and CXCR6 combined gene expression is associated with improved outcome of HNSCC patients and an increase of infiltrating immune effector cells. This new signature also identifies a subset of cervical squamous cell carcinoma (CSCC) patients with favorable prognosis, who show an increased presence of immune effector cells in the tumor, which outcome shows similarities with the HP-positive HNSCC cohort of patients. In addition, CD2, CD3D, CD3E, and CXCR6 signature is able to predict the best favorable prognosis in terms of overall survival of CSSC patients. Of note, these findings were not reproduced in other squamous cell carcinomas like esophageal SCC or lung SCC. Prospective confirmatory studies should be employed to validate these findings.
Case Report: Intestinal Nodular Lymphoid Hyperplasia as First Manifestation of Activated PI3Kδ Syndrome Due to a Novel PIK3CD Variant
Authors: Marzollo Antonio , Bresolin Silvia , Colavito Davide , Cani Alice , Gaio Paola , Bosa Luca , Mescoli Claudia , Rossini Linda , Barzaghi Federica , Perilongo Giorgio , Leon Alberta , Biffi Alessandra , Cananzi Mara
Published: October 2021

Nodular lymphoid hyperplasia (NLH) is a lymphoproliferative disease caused by non-clonal expansion of lymphoid cells in the gut mucosa. Little is known about the pathogenesis of NLH, which is often disregarded as an insignificant or para-physiologic phenomenon. We present the case of a girl with isolated diffuse NLH (extending from the stomach to the rectum) caused by activated PI3Kδ syndrome (APDS) due to the novel p.Glu525Gly variant in PIK3CD. The gain-of-function effect of the variant was confirmed by demonstration of over activation of the Akt/mTOR pathway in the patient's cells. APDS diagnosis led to treatment with sirolimus, which resulted in the complete remission of NLH and in the prevention of extra intestinal complications. In conclusion, we identify APDS as a novel cause of isolated NLH and suggest that patients with severe pan-enteric NLH should be screened for this disorder that may not be apparent on first-line immunological testing.
Conservative Treatment Without Any Intervention Compared With Other Therapeutic Strategies for Symptomatic Patent Ductus Arteriosus in Extremely Preterm Infants: A Nationwide Cohort Study in Korea
Authors: Shin Jeonghee , Lee Jin A , Oh Sohee , Lee Eun Hee , Choi Byung Min
Published: October 2021

Objective: Although symptomatic treatment is the most preferred treatment strategy for proven symptomatic patent ductus arteriosus (PDA), a considerable number of infants only received conservative treatment without any pharmacological or surgical interventions in the lower gestational age and lower birth weight group in Korea. We compared in-hospital outcomes of infants treated conservatively without any intervention and those of infants managed by other therapeutic strategies in extremely preterm infants with symptomatic PDA.

Methods: A prospectively collected cohort study for 2,303 infants with gestational ages <28 weeks from the Korean Neonatal Network database. These infants were classified into four groups according to the presence of PDA-related symptoms and therapeutic treatment strategy: prophylactic treatment group, pre-symptomatic treatment (PST) group, symptomatic treatment (ST) group, and conservative treatment (CT) without any intervention group.

Results: In multivariable logistic regression analysis, the risk of death was significantly decreased in the PST group (adjusted odds ratio [aOR] = 0.507; 95% confidence interval [CI] 0.311–0.826) and ST group (aOR = 0.349; 95% CI: 0.230–0.529) compared with the CT group. However, the risk of composite outcome of severe bronchopulmonary dysplasia or death had not increased in the PST group and ST group. Neonatal death due to pulmonary hemorrhage or neurological disease was significantly higher in the CT group than in the PST group or ST group.

Conclusion: In extremely preterm infants, who are at highest risk of PDA-related morbidities and mortality, even less interventional approach for PDA can be allowed; the rescued pharmacological or surgical interventions are necessary if they met the criteria for hemodynamically significant PDA.