bluuebunny/crossref_metadata_2025 huggingface dataset:
Varicella-zoster plaque assay and plaque reduction neutralization test by the immunoperoxidase technique
Authors: Gerna G , Chambers R W
Published: June 2021

A new plaque assay for the quantitation of varicella-zoster virus and a plaque reduction neutralization test for the determination of neutralizing antibody titer have been developed using the indirect immunoperoxidase technique. As compared with the classical plaque assay using a solid overlay, the test gives earlier results since plaque counting can be performed on day 3 after the inoculation of cell cultures. In six patients with zoster infection, neutralizing antibody titers ranged from 1:20 to 1:40 before the onset of infection and reached high levels (1:320 to 1:5,120) during the convalescent phase of the disease. Complement-fixing (CF) titers were all negative (less than 1:8) in prezoster serum samples from the same patients and ranged from 1:128 to 1:2,048 in the convalescent-phase sera. In the two cases in which late serum samples were available, neutralizing antibody titers matched the preillness levels, whereas CF titers dropped to undetectable levels. Neither neutralizing nor CF antibody was detected in two sera from individuals with no history of varicella-zoster infection. No differences in virus titers or neutralizing antibody titers were observed between the immunoperoxidase and the classical plaque assays. The appropriate characterization of reagent specificity is required before routine application of the test.
Hemolysis-in-gel test for demonstration of Chlamydia antibodies
Authors: Lycke E , Peterson M
Published: June 2021

Sheep erythrocytes were coated with antigens of a strain of Chlamydia trachomatis serotype D. Chlamydial antibodies in sera from patients with salpingitis or pneumonia were demonstrated by passive hemolysis in agarose gel.
Vesicular stomatitis virus plaque production in monolayer cultures with liquid overlay medium: description and adaptation to a one-day, human interferon-plaque
Authors: Green J A , Stanton G J , Goode J , Baron S
Published: June 2021

Vesicular stomatitis virus forms discrete, microscopic plaques in stationary cultures of the WISH amnion cell line. Microplaque formation is rapid, reproducible, and easily quantitated, occurs at temperatures ranging from 33 to 40 degrees C, and does not require a semisolid overlay. WISH cells, however, are less sensitive to vesicular stomatitis virus than are chicken embryo, 3T6, or Vero cells. WISH amnion cells also are highly sensitive to the antiviral effects of human interferon, and a quantitative human interferon assay, based on vesicular stomatitis virus plaque reduction in WISH cells, is described. This interferon assay can be performed within 1 day, uses a liquid overlay medium, does not require a vital stain, is as sensitive as other methods that use diploid cell strains, and is performed in a microtiter system.
RNA editing in kinetoplastid protozoa
Authors: Stuart K , Allen T E , Heidmann S , Seiwert S D
Published: June 2021

Mitochondrial transcripts in kinetoplastids undergo remarkable posttranscriptional editing by uridylate insertion and deletion. The often dramatic remodeling of pre-mRNA sequences is directed by small guide RNAs (gRNAs) to produce mature mRNAs. In vitro analyses of editing have been used to determine the mechanism of editing and show that editing occurs by a series of enzyme-catalyzed steps. They also show that chimeric gRNA/mRNA molecules are not editing intermediates as proposed but are aberrant end products of editing. The complexes and molecules that catalyze editing are now being identified and characterized. The origin of editing, its developmental regulation which helps control the switching between terminal respiratory systems during the life cycle of trypanosomes, and other areas for future study are discussed.
Genetic regulation of nitrogen metabolism in the fungi
Authors: Marzluf G A
Published: June 2021

In the fungi, nitrogen metabolism is controlled by a complex genetic regulatory circuit which ensures the preferential use of primary nitrogen sources and also confers the ability to use many different secondary nitrogen sources when appropriate. Most structural genes encoding nitrogen catabolic enzymes are subject to nitrogen catabolite repression, mediated by positive-acting transcription factors of the GATA family of proteins. However, certain GATA family members, such as the yeast DAL80 factor, act negatively to repress gene expression. Selective expression of the genes which encode enzymes for the metabolism of secondary nitrogen sources is often achieved by induction, mediated by pathway-specific factors, many of which have a GAL4-like C6/Zn2 DNA binding domain. Regulation within the nitrogen circuit also involves specific protein-protein interactions, as exemplified by the specific binding of the negative-acting NMR protein with the positive-acting NIT2 protein of Neurospora crassa. Nitrogen metabolic regulation appears to play a significant role in the pathogenicity of certain animal and plant fungal pathogens.
Kinase cascades regulating entry into apoptosis
Authors: Anderson P
Published: June 2021

All cells are constantly exposed to conflicting environment cues that signal cell survival or cell death. Survival signals are delivered by autocrine or paracrine factors that actively suppress a default death pathway. In addition to survival factor withdrawal, cell death can be triggered by environmental stresses such as heat, UV light, and hyperosmolarity or by dedicated death receptors (e.g., FAS/APO-1 and tumor necrosis factor [TNF] receptors) that are counterparts of growth factor or survival receptors at the cell surface. One of the ways that cells integrate conflicting exogenous stimuli is by phosphorylation (or dephosphorylation) of cellular constituents by interacting cascades of serine/threonine and tyrosine protein kinases (and phosphatases). Survival factors (e.g., growth factors and mitogens) activate receptor tyrosine kinases and selected mitogen-activated, cyclin-dependent, lipid-activated, nucleic acid-dependent, and cyclic AMP-dependent kinases to promote cell survival and proliferation, whereas environmental stress (or death factors such as FAS/APO-1 ligand and TNF-alpha) activates different members of these kinase families to inhibit cell growth and, under some circumstances, promote apoptotic cell death. Because individual kinase cascades can interact with one another, they are able to integrate conflicting exogenous stimuli and provide a link between cell surface receptors and the biochemical pathways leading to cell proliferation or cell death.
Evolutionary divergence and salinity-mediated selection in halophilic archaea
Authors: Dennis P P , Shimmin L C
Published: June 2021

Halophilic (literally salt-loving) archaea are a highly evolved group of organisms that are uniquely able to survive in and exploit hypersaline environments. In this review, we examine the potential interplay between fluctuations in environmental salinity and the primary sequence and tertiary structure of halophilic proteins. The proteins of halophilic archaea are highly adapted and magnificently engineered to function in an intracellular milieu that is in ionic balance with an external environment containing between 2 and 5 M inorganic salt. To understand the nature of halophilic adaptation and to visualize this interplay, the sequences of genes encoding the L11, L1, L10, and L12 proteins of the large ribosome subunit and Mn/Fe superoxide dismutase proteins from three genera of halophilic archaea have been aligned and analyzed for the presence of synonymous and nonsynonymous nucleotide substitutions. Compared to homologous eubacterial genes, these halophilic genes exhibit an inordinately high proportion of nonsynonymous nucleotide substitutions that result in amino acid replacement in the encoded proteins. More than one-third of the replacements involve acidic amino acid residues. We suggest that fluctuations in environmental salinity provide the driving force for fixation of the excessive number of nonsynonymous substitutions. Tinkering with the number, location, and arrangement of acidic and other amino acid residues influences the fitness (i.e., hydrophobicity, surface hydration, and structural stability) of the halophilic protein. Tinkering is also evident at halophilic protein positions monomorphic or polymorphic for serine; more than one-third of these positions use both the TCN and the AGY serine codons, indicating that there have been multiple nonsynonymous substitutions at these positions. Our model suggests that fluctuating environmental salinity prevents optimization of fitness for many halophilic proteins and helps to explain the unusual evolutionary divergence of their encoding genes.
The first living systems: a bioenergetic perspective
Authors: Deamer D W
Published: June 2021

The first systems of molecules having the properties of the living state presumably self-assembled from a mixture of organic compounds available on the prebiotic Earth. To carry out the polymer synthesis characteristic of all forms of life, such systems would require one or more sources of energy to activate monomers to be incorporated into polymers. Possible sources of energy for this process include heat, light energy, chemical energy, and ionic potentials across membranes. These energy sources are explored here, with a particular focus on mechanisms by which self-assembled molecular aggregates could capture the energy and use it to form chemical bonds in polymers. Based on available evidence, a reasonable conjecture is that membranous vesicles were present on the prebiotic Earth and that systems of replicating and catalytic macromolecules could become encapsulated in the vesicles. In the laboratory, this can be modeled by encapsulated polymerases prepared as liposomes. By an appropriate choice of lipids, the permeability properties of the liposomes can be adjusted so that ionic substrates permeate at a sufficient rate to provide a source of monomers for the enzymes, with the result that nucleic acids accumulate in the vesicles. Despite this progress, there is still no clear mechanism by which the free energy of light, ion gradients, or redox potential can be coupled to polymer bond formation in a protocellular structure.
Cyclopropane ring formation in membrane lipids of bacteria
Authors: Grogan D W , Cronan J E
Published: June 2021

It has been known for several decades that cyclopropane fatty acids (CFAs) occur in the phospholipids of many species of bacteria. CFAs are formed by the addition of a methylene group, derived from the methyl group of S-adenosylmethionine, across the carbon-carbon double bond of unsaturated fatty acids (UFAs). The C1 transfer does not involve free fatty acids or intermediates of phospholipid biosynthesis but, rather, mature phospholipid molecules already incorporated into membrane bilayers. Furthermore, CFAs are typically produced at the onset of the stationary phase in bacterial cultures. CFA formation can thus be considered a conditional, postsynthetic modification of bacterial membrane lipid bilayers. This modification is noteworthy in several respects. It is catalyzed by a soluble enzyme, although one of the substrates, the UFA double bond, is normally sequestered deep within the hydrophobic interior of the phospholipid bilayer. The enzyme, CFA synthase, discriminates between phospholipid vesicles containing only saturated fatty acids and those containing UFAs; it exhibits no affinity for vesicles of the former composition. These and other properties imply that topologically novel protein-lipid interactions occur in the biosynthesis of CFAs. The timing and extent of the UFA-to-CFA conversion in batch cultures and the widespread distribution of CFA synthesis among bacteria would seem to suggest an important physiological role for this phenomenon, yet its rationale remains unclear despite experimental tests of a variety of hypotheses. Manipulation of the CFA synthase of Escherichia coli by genetic methods has nevertheless provided valuable insight into the physiology of CFA formation. It has identified the CFA synthase gene as one of several rpoS-regulated genes of E. coli and has provided for the construction of strains in which proposed cellular functions of CFAs can be properly evaluated. Cloning and manipulation of the CFA synthase structural gene have also enabled this novel but extremely unstable enzyme to be purified and analyzed in molecular terms and have led to the identification of mechanistically related enzymes in clinically important bacterial pathogens.
Cell biology and molecular basis of denitrification
Authors: Zumft W G
Published: June 2021

Denitrification is a distinct means of energy conservation, making use of N oxides as terminal electron acceptors for cellular bioenergetics under anaerobic, microaerophilic, and occasionally aerobic conditions. The process is an essential branch of the global N cycle, reversing dinitrogen fixation, and is associated with chemolithotrophic, phototrophic, diazotrophic, or organotrophic metabolism but generally not with obligately anaerobic life. Discovered more than a century ago and believed to be exclusively a bacterial trait, denitrification has now been found in halophilic and hyperthermophilic archaea and in the mitochondria of fungi, raising evolutionarily intriguing vistas. Important advances in the biochemical characterization of denitrification and the underlying genetics have been achieved with Pseudomonas stutzeri, Pseudomonas aeruginosa, Paracoccus denitrificans, Ralstonia eutropha, and Rhodobacter sphaeroides. Pseudomonads represent one of the largest assemblies of the denitrifying bacteria within a single genus, favoring their use as model organisms. Around 50 genes are required within a single bacterium to encode the core structures of the denitrification apparatus. Much of the denitrification process of gram-negative bacteria has been found confined to the periplasm, whereas the topology and enzymology of the gram-positive bacteria are less well established. The activation and enzymatic transformation of N oxides is based on the redox chemistry of Fe, Cu, and Mo. Biochemical breakthroughs have included the X-ray structures of the two types of respiratory nitrite reductases and the isolation of the novel enzymes nitric oxide reductase and nitrous oxide reductase, as well as their structural characterization by indirect spectroscopic means. This revealed unexpected relationships among denitrification enzymes and respiratory oxygen reductases. Denitrification is intimately related to fundamental cellular processes that include primary and secondary transport, protein translocation, cytochrome c biogenesis, anaerobic gene regulation, metalloprotein assembly, and the biosynthesis of the cofactors molybdopterin and heme D1. An important class of regulators for the anaerobic expression of the denitrification apparatus are transcription factors of the greater FNR family. Nitrate and nitric oxide, in addition to being respiratory substrates, have been identified as signaling molecules for the induction of distinct N oxide-metabolizing enzymes.
Low-temperature thermochronology constraints on the evolution of the Eastern Kunlun Range, northern Tibetan Plateau
Authors: Wu Chen , Li Jie , Ding Lin
Published: June 2021

Signals of uplift and deformation across the Tibetan Plateau associated with the Cenozoic India-Asia collision can be used to test debated deformation mechanism(s) and the growth history of the plateau. The spatio-temporal evolution of the Eastern Kunlun Range in northern Tibet provides a window for understanding the intracontinental tectonic evolution of the region. The Eastern Kunlun Range exposes the Cenozoic Kunlun left-slip fault and kinematically linked thrust belts. In this contribution, integrated field observations and apatite fission-track thermochronology were conducted to constrain the initiation ages of localized thrust faults and the exhumation history of the Eastern Kunlun Range. Our analyses reveal four stages of cooling of the Eastern Kunlun Range. We relate these four stages to the following interpreted tectonic evolution: (1) an initial period of early Cretaceous cooling and slow exhumation over the early Cenozoic, which is associated with the formation of a regional unconformity observed between Cretaceous strata and early Cenozoic sediments; (2) rapid Oligocene cooling that occurred at the eastern domain of the Eastern Kunlun Range related to the southern Qaidam thrusts; (3) extensive rapid cooling since the early-middle Miocene in most of the eastern-central domains and significant uplift of the entire range; and (4) a final pulse of rapid late Miocene-to-present cooling associated with the initiation of the Kunlun left-slip fault and dip-slip shortening at the western and eastern termination of the left-slip fault. Early Cenozoic deformation was distributed along the northern extent of the Tibetan Plateau, and overprinting out-of-sequence deformation migrated back to the south with the initiation of Miocene-to-present deformation in the Eastern Kunlun Range.
Interaction of Peptides Containing CRAC Motifs with Lipids in Membranes of Various Composition
Authors: Volynsky P. E. , Galimzyanov T. R. , Akimov S. A.
Published: June 2021

The lateral distribution of integral and peripheral proteins, as well as lipids in the plasma membranes of mammalian cells is extremely heterogeneous. It is believed that various lipid-protein domains are formed in membranes. Domains enriched in sphingomyelin and cholesterol are called rafts. It is assumed that the distribution of proteins into rafts is largely related to the presence in their primary sequence of a specific amino acid region called the CRAC motif, which is responsible for cholesterol binding. In this work, the interaction of two peptides containing CRAC motifs in their structure with membranes of different compositions was studied by means of molecular dynamics. It has been shown that the average number of lipid molecules in contact with each peptide is proportional to the mole fraction of lipid in the membrane. The predominant interaction of peptides with cholesterol was not observed. In addition, cholesterol did not form long-lived contacts with any amino acid or amino acid sequence. We suppose that in some cases the predominant lateral distribution of peptides and proteins containing CRAC motifs into rafts may be due to amphipathicity of the CRAC motif rather than due to specific strong binding of cholesterol.
JAK 2 positive myeloproliferative neoplasm presenting as stroke, recurrent TIA and isolated third nerve palsy
Authors: Bolaji Paul , Das Saugata , Ahmad Nasar
Published: June 2021

A man in his early 40s with no significant vascular risk factors was managed within a period of 6 months for recurrent vascular events: ischaemic stroke, transient ischaemic attack and isolated third nerve palsy. He was extensively investigated throughout the course of illness. The only potential aetiological factor identified was a positive janus kinase 2 (JAK 2) mutation after screening on account of mildly elevated platelet count noted during his most recent admission. Bone marrow aspiration confirmed essential thrombocythaemia. He was started on hydroxycarbamide and has remained relatively symptom free since then.

This case reiterates the known associations between thrombosis and JAK 2 mutation even without overt myeloproliferative neoplasms. It also highlights the need for specialists in stroke to consider screening for JAK 2 mutation in a young patient with cryptogenic stroke with or without polycythemia or thrombocytosis.
Traditional Chinese Medicine Decoctions Significantly Reduce the Mortality in Severe and Critically Ill Patients with COVID-19: A Retrospective Cohort Study
Authors: Sun Qin-Guo , An Xue-Dong , Xie Ping , Jiang Bo , Tian Jia-Xing , Yang Qian , Li Xiu-Yang , Luo Meng , Liu Ping , Zhao Sheng-Hui , Duan Li-Yun , Lang Su-Ping , Fan An , Luo Peng-Cheng , Lian Feng-Mei , Huang Xiao-Dong , Tong Xiao-Lin
Published: June 2021

Coronavirus disease (COVID-19) is a new infectious disease associated with high mortality, and traditional Chinese medicine decoctions (TCMDs) have been widely used for the treatment of patients with COVID-19 in China; however, the impact of these decoctions on severe and critical COVID-19-related mortality has not been evaluated. Therefore, we aimed to address this gap. In this retrospective cohort study, we included inpatients diagnosed with severe/critical COVID-19 at the Tongren Hospital of Wuhan University and grouped them depending on the recipience of TCMDs (TCMD and non-TCMD groups). We conducted a propensity score-matched analysis to adjust the imbalanced variables and treatments and used logistic regression methods to explore the risk factors associated with in-hospital death. Among 282 patients with COVID-19 who were discharged or died, 186 patients (66.0%) received TCMD treatment (TCMD cohort) and 96 (34.0%) did not (non-TCMD cohort). After propensity score matching at a 1:1 ratio, 94 TCMD users were matched to 94 non-users, and there were no significant differences in baseline clinical variables between the two groups of patients. The all-cause mortality was significantly lower in the TCMD group than in the non-TCMD group, and this trend remained valid even after matching (21.3% [20/94] vs. 39.4% [37/94]). Multivariable logistic regression model showed that disease severity (odds ratio: 0.010; 95% CI: 0.003, 0.037; [Formula: see text]¡ 0.001) was associated with increased odds of death and that TCMD treatment significantly decreased the odds of in-hospital death (odds ratio: 0.115; 95% CI: 0.035, 0.383; [Formula: see text]¡ 0.001), which was related to the duration of TCMD treatment. Our findings show that TCMD treatment may reduce the mortality in patients with severe/critical COVID-19.
Gut Microbiota and Urine Metabonomics Alterations in Constitution after Chinese Medicine and Lifestyle Intervention
Authors: Jing Yuan , Han Shuangshuang , Chen Jieyu , Lai Yigui , Cheng Jingru , Li Fei , Xiao Ya , Jiang Pingping , Sun Xiaomin , Luo Ren , Zhao Xiaoshan , Liu Yanyan
Published: June 2021

Traditional Chinese Medicine Constitution (TCMC) divides human beings into balanced (ping-he) constitution (PH) and unbalanced constitution. Yang-deficiency (yang-xu) constitution (YAX) is one of the most common unbalanced constitutions in Chinese general population, and it causes susceptibility to particular diseases. However, unbalanced constitutions can be regulated by Chinese medicine and lifestyle intervention in clinical practice. Gui-fu-di-huang-wan (GFDHW) is a well-known Chinese medicine with yang-invigorating activity and is regarded as improving YAX. In this study, 60 healthy YAX students selected from a prospective population of 5185 were enrolled in a randomized clinical trial and completed the study. We compared the gut microbiota and urinary metabolome between individuals with PH and those with YAX before and after one-month-intervention. Compared with the control group, the health status of the intervention group improved significantly, the YAX symptom score was reduced, and the efficacy remained high at the one-year follow-up. The gut microbiota of the healthy PH exhibited greater diversity, and significantly higher species were identified. Compared to PH group, YAX individuals showed increased abundance of Bacteroidetes and Bacteroides, also had higher levels of gut microbial-derived urinary metabolites. After one-month-intervention, both GFDHW treatment and lifestyle intervention enriched the diversity and modulated the structure in YAX. The intervention group also partially restored the microbiome and metabolome to healthy PH-like levels. Further, a microbiota co-occurrence network analysis showed that the metabolites enriched in YAX were correlated with microbial community structure. Taken together, our results suggest that Chinese medicine combined with lifestyle intervention benefits YAX individuals. Gut microbiota/metabolite crosstalk might be involved in the Chinese medicine-mediated effects.
The gravitational energy density of the Universe
Authors: Formiga J. B. , Gonçalves V. R.
Published: June 2021

The teleparallel gravitational energy–momentum tensor density of the Friedmann–Lemaître–Robertson–Walker spacetime is calculated and analyzed: it is decomposed into density, isotropic pressure, non-isotropic pressures, and the heat-flux 4-vector; the antisymmetric part is decomposed into “electric” and “magnetic” components. It is found that the gravitational field obeys a radiation-like equation of state, the antisymmetric part does not contribute to the gravitational energy–momentum; and the total energy density, the non-isotropic pressures and the heat-flux 4-vector vanish for spatially flat universes. Finally, it is verified that the field equations have a well-defined vacuum.
Average Edge-Connectivity of Cubic Graphs
Authors: Zhuo Miaomiao , Li Qinqin , Wu Baoyindureng , An Xinhui
Published: June 2021

In this paper, we consider the concept of the average edge-connectivity [Formula: see text] of a graph [Formula: see text], defined to be the average, over all pairs of vertices, of the maximum number of edge-disjoint paths connecting these vertices. Kim and O previously proved that [Formula: see text] for any connected cubic graph on [Formula: see text] vertices. We refine their result by showing that [Formula: see text] We also characterize the graphs where equality holds.
Clustering Heterogeneous Information Network by Joint Graph Embedding and Nonnegative Matrix Factorization
Authors: Zhang Benhui , Gong Maoguo , Huang Jianbin , Ma Xiaoke
Published: June 2021

Many complex systems derived from nature and society consist of multiple types of entities and heterogeneous interactions, which can be effectively modeled as heterogeneous information network (HIN). Structural analysis of heterogeneous networks is of great significance by leveraging the rich semantic information of objects and links in the heterogeneous networks. And, clustering heterogeneous networks aims to group vertices into classes, which sheds light on revealing the structure–function relations of the underlying systems. The current algorithms independently perform the feature extraction and clustering, which are criticized for not fully characterizing the structure of clusters. In this study, we propose a learning model by joint Graph Embedding and Nonnegative Matrix Factorization (aka
GEjNMF
), where feature extraction and clustering are simultaneously learned by exploiting the graph embedding and latent structure of networks. We formulate the objective function of GEjNMF and transform the heterogeneous network clustering problem into a constrained optimization problem, which is effectively solved by
l
0
-norm optimization. The advantage of GEjNMF is that features are selected under the guidance of clustering, which improves the performance and saves the running time of algorithms at the same time. The experimental results on three benchmark heterogeneous networks demonstrate that GEjNMF achieves the best performance with the least running time compared with the best state-of-the-art methods. Furthermore, the proposed algorithm is robust across heterogeneous networks from various fields. The proposed model and method provide an effective alternative for heterogeneous network clustering.
Adverse Effects of Medications on Micronutrient Status: From Evidence to Guidelines
Authors: Daniels Michael S. , Park Brian I. , McKay Diane L.
Published: June 2021

Recent dietary reference intake workshops focusing on nutrient requirements in chronic disease populations have called attention to the potential adverse effects of chronic medication use on micronutrient status. Although this topic is mostly ill defined in the literature, several noteworthy drug–nutrient interactions (DNIs) are of clinical and public health significance. The purpose of this narrative review is to showcase classic examples of DNIs and their impact on micronutrient status, including those related to antidiabetic, anticoagulant, antihypertensive, antirheumatic, and gastric acid–suppressing medications. Purported DNIs related to other drug families, while relevant and worthy of discussion, are not included. Unlike previous publications, this review is primarily focused on DNIs that have sufficient evidence supporting their inclusion in US Food and Drug Administration labeling materials and/or professional guidelines. While the evidence is compelling, more high-quality research is needed to establish clear and quantitative relationships between chronic medication use and micronutrient status.
Model Study of Penetration of Cl− Ions from Solution into Organic Self-Assembled-Monolayer on Metal Substrate: Trends and Modeling Aspects
Authors: Kokalj Anton , Costa Dominique
Published: June 2021

Organic molecules that form self-assembled-monolayers on metal substrates may provide efficient corrosion protection. Herein we study how such self-assembled-monolayers hinder the penetration of

Cl

−

ions from aqueous solution toward the metal substrate. We first elucidate some aspects that are relevant for modeling charged ions near surfaces with slab models that utilize periodic-boundary-conditions, in particular: (i) solvation effects, (ii) inter-ion electrostatics, (iii) depolarization effects, and (iv) effects of periodic-boundary-conditions along lateral directions and, for multi-slab models, also along the surface normal direction. The last two effects are artifacts hence they can be avoided or at least minimized by proper modeling. We further present a simple scheme that describes the activation barrier for

Cl

−

penetration into self-assembled-monolayer as a function of the electrode potential and show that the activation barrier decreases as the electrode potential increases, as would be intuitively expected, however, for thick self-assembled-monolayers the barrier remains sizable even at rather positive potentials, which may be one of the reasons why dense and sufficiently thick self-assembled-monolayers can efficiently inhibit corrosion. By utilizing a simple model where metal substrate, organic layer, and aqueous solvent are described implicitly by dielectric continuum slabs, we analyze two important effects by which self-assembled-monolayers hinder the penetration of

Cl

−

ions toward the metal substrate. The first effect is due to inferior solvation of ions in organic layer compared to that in aqueous solvent and the estimated difference is larger than 1 eV. This effect is independent of the thickness of the organic layer, provided that the layer is sufficiently thick (≳10 Å). The second effect is due to electric field at the electrochemical interface and the extent by which it affects the penetration of

Cl

−

depends on the electrode potential and on the thickness of the organic layer. Other effects, such as local deformation of organic layer during

Cl

−

penetration, cannot be described by current simple models and will be considered in our next publication. Finally, calculations indicate that due to stronger solvation of Na+ counter-ions their penetration into organic layer is inferior to that of

Cl

−

. Energetically the most favorable way for Na+ to penetrate is in the form of Na+/

Cl

−

ion-pairs, but it is inferior to penetration of

Cl

−

alone.
Comprehensive Analysis of Regulatory Network for LINC00472 in Clear Cell Renal Cell Carcinoma
Authors: Gao Shuoze , Wang Zhiping
Published: June 2021

Renal cell carcinoma (RCC) accounts for about 2% to 3% of adult malignancies, and clear cell renal cell carcinoma (ccRCC) is the most common and aggressive type of kidney cancer. It accounts for 75% of all kidney tumors. Although new targeted drugs continue to appear, they are still not suitable for all patients. Therefore, an in-depth study of the molecular mechanism of the development of ccRCC and exploration of new targets for the treatment of ccRCC will help to achieve precise treatment for ccRCC. With the development of molecular research, the study of long noncoding RNA (LncRNA) has given us a new understanding of tumors. Although LncRNA does not encode proteins, it directly interacts with proteins in various signaling pathways and affects cell functions. Therefore, it is of great significance to study the mechanism of LncRNA in ccRCC. The expression level of Linc00472 in ccRCC tissues is significantly lower than adjacent normal tissues, and its low expression is closely related to Furman’s high grade. The low expression of Linc00472 is associated with poor prognosis in patients with ccRCC. The results of protein interaction and functional enrichment analysis indicate that genes upregulated in renal clear cell carcinoma may play a major role. Analysis of target gene prediction results showed that Linc00472 may be used as ceRNA in the miR-24-3p-HLA-DPB1 pathway, miR-24-3p-CXCL9 pathway, miR-221-3p-C3aR1-VEGFR2 pathway, miR-17-5p-HLA-DQA1/HLA-DQB1 pathway, and miR-17-5p-C3aR1/C5aR1-VEGFR2 pathway which play important functions. In addition, the regulatory relationship between miR-24-3p and TNFR2 (TNFRSF1B), CD36, and COL4A1 should also be noted. The value of Linc00472 in the diagnosis and treatment of ccRCC is worthy of further study.
miRNA-146a and miRNA-202-3p Attenuate Inflammatory Response by Inhibiting TLR4, IRAK1, and TRAF6 Expressions in Rats following Spinal Cord Injury
Authors: Sun Feng , Zhang Haiwei , Shi Jianhui , Huang Tianwen , Wang Yansong
Published: June 2021

Spinal cord injury (SCI) is a catastrophic disease that induces a complex cascade of cellular reactions at the local lesion area, including secondary cell death and inflammatory reactions. Accumulating evidence has showed pro- and anti-inflammatory roles of microRNAs (miRNAs), a class of small RNAs, in SCI. The present study is aimed at investigating the effects of two miRNAs, miRNA-146a and miRNA-202-3p, on inflammatory response after SCI. Initially, we found that the expression levels of miRNA-146a and miRNA-202-3p were increased in the plasma samples of 32 SCI patients at days 3 and 7 after admission and the rat spinal cord at days 3 and 7 after SCI modeling compared with healthy controls and sham-operated rats, respectively. The expression levels of TLR4, IRAK1, and TRAF6 were declined in the rat spinal cord at days 1, 3, and 7 after SCI modeling compared with sham-operated rats. Injection of miRNA-146a mimic or miRNA-202-3p mimic decreased TLR4, IRAK1, and TRAF6 expressions in the rat spinal cord at days 1, 3, and 7 after SCI modeling, while injection of miRNA-146a antagomir or miRNA-202-3p antagomir produced opposed results. Subsequent results showed that the expression levels of tumor necrosis factor-α (TNF-α), IL-1β, IL-6, and IL-8 were upregulated in the rat serum at days 1, 3, and 7 after SCI modeling compared with sham-operated rats. Injection of miRNA-146a mimic or miRNA-202-3p mimic decreased TNF-α, IL-1β, IL-6, and IL-8 expression levels in the rat serum at days 1, 3, and 7 after SCI modeling, while injection of miRNA-146a antagomir or miRNA-202-3p antagomir yielded opposed results. The expression levels of TNF-α, IL-1β, IL-6, and IL-8 were higher in the supernatants of PC12 cells transfected with anti-miRNA-146a or anti-miRNA-202-3p than in those transfected with si-TLR4, si-IRAK1, or si-TRAF6. These findings support the notion that miRNA-146a/miRNA-202-3p exerts anti-inflammatory functions after SCI.
[Retracted] College English Teaching Quality Evaluation System Based on Information Fusion and Optimized RBF Neural Network Decision Algorithm
Authors: Chen Yajun
Published: June 2021

In the process of deepening and developing the current higher education reform, people pay more and more attention to the research of college English education. The key to improve the college English education is to improve the quality of education, and learning evaluation is the key measure to improve the quality of education and training. This paper mainly studies the college English teaching quality evaluation system based on information fusion and optimized RBF neural network decision algorithm. This paper analyzes the main problems and complexity of creating an ideal learning quality evaluation system. On the basis of analyzing the advantages and disadvantages of the previous learning quality evaluation methods, this paper summarizes the existing learning quality evaluation methods and puts forward some suggestions according to the existing evaluation methods. A learning quality evaluation model based on RBF algorithm of neural network is proposed. RBF regularization network method, RBF neural network decision algorithm, and experimental investigation method are used to study the college English teaching quality evaluation system based on information fusion and optimization of RBF neural network decision algorithm. By innovating teaching methods and enriching teaching means, college students’ thirst for English knowledge can be aroused, and teachers’ teaching level can be improved. The results show that 50% of college students think that the level of college English teaching is average and needs to be improved. In the performance evaluation system of college English teaching quality based on information fusion and optimized RBF neural network decision algorithm, it is necessary to establish a learning evaluation system, monitor the learning quality in real time, find problems and improve them in time, and recognize the current situation of education.
R2AU-Net: Attention Recurrent Residual Convolutional Neural Network for Multimodal Medical Image Segmentation
Authors: Zuo Qiang , Chen Songyu , Wang Zhifang
Published: June 2021

In recent years, semantic segmentation method based on deep learning provides advanced performance in medical image segmentation. As one of the typical segmentation networks, U-Net is successfully applied to multimodal medical image segmentation. A recurrent residual convolutional neural network with attention gate connection (R2AU-Net) based on U-Net is proposed in this paper. It enhances the capability of integrating contextual information by replacing basic convolutional units in U-Net by recurrent residual convolutional units. Furthermore, R2AU-Net adopts attention gates instead of the original skip connection. In this paper, the experiments are performed on three multimodal datasets: ISIC 2018, DRIVE, and public dataset used in LUNA and the Kaggle Data Science Bowl 2017. Experimental results show that R2AU-Net achieves much better performance than other improved U-Net algorithms for multimodal medical image segmentation.
Improving Indoor Air Quality in Classrooms via Wind-Induced Natural Ventilation
Authors: Bayoumi Mohannad
Published: June 2021

Student performance in classrooms is related to the indoor environmental quality. High air change rates are necessary to secure an acceptable level of indoor air quality and provide fresh air, which require large amounts of energy and technical installations. Mostly, mechanically supplied air is partially mixed with the return air. In warm climates, the capacity for natural ventilation is not fully exploited in modern buildings. During periods of acceptable outdoor temperatures, buildings need to adapt and employ available free renewable resources, such as wind. In this context, the building form, orientation, and envelope openings are crucial to enable an increased air change rate, user satisfaction, and energy savings. Owing to the difficulty of providing cross-ventilation in buildings with double-loaded corridors, single-sided ventilation is the most common approach. This study investigates the methods to improve the wind-driven air exchange of classrooms in warm climates, where naturally ventilated corridors help increase air movement. This study examines the potential of a set of alternatives within the context of a generic model regarding the pressure distribution, thermal sensation, air velocity, and air change rate. The study suggests that no single opening scenario can be applied to all façades at any time. Each façade requires special treatment. Decisions on natural ventilation need to be made during the early design stages for each façade. It was found that with the aid of low-tech modifications, remarkable increases in air change rates, in some cases up to 14.5 times that of the typical single-sided ventilation case, could be achieved.
Evaluation of Drinking Water Quality in Rural Area of Amhara Region, Ethiopia: The Case of Mecha District
Authors: Lewoyehu Mekuanint
Published: June 2021

This study was conducted to assess the drinking water quality of north Mecha district, Amhara Region, Ethiopia. 26 drinking water samples were collected from the water points of the dweller community in the dry seasons of 2020 and subjected to the analysis of physicochemical parameters, bacteriological parameters, and the level of trace metals. The analysis of physicochemical parameters and the trace metals was carried out following the standard procedures of the laboratory, and the bacteriological water qualities were measured using the membrane filtration method. The F−, NO3−, SO42−, and Cu levels of the water samples were within the permissible limits of the WHO and compulsory Ethiopian standard (CES). Depending on turbidity, 61.54% of the tested water samples crossed the WHO limit of drinking water quality, and 100% of the samples surpassed the limits of EPA. Based on iron and ammonia levels, 38.46%, and 100% of the studied water samples violated the environmental protection agency (EPA) guidelines; 23.07%, and 3.84%, of the samples surpassed the WHO and CES drinking water quality standards. In view of pH, 23.07% of the tested water samples were not within the safe limit of the WHO and CES. 92.31% of the studied water samples were not potable as coliform bacterium (thermo tolerant indicator bacterium) growth was detected. The study revealed that the water sources of the study area are not safe for drinking unless appropriate treatment measurements are taken. Higher values of water quality parameters for the water samples from Koga irrigation site than the values for the water samples from the study sites found out of the irrigation site indicated the pollution load of Koga irrigation on the water quality of the area.
Experimental and Numerical Investigation on Hydraulic Fracture Propagation Law of Composite Rock Materials considering the Disturbing Stress Effect
Authors: Zhang Xin , Zhang Yuqi , Zhang Tao
Published: June 2021

The stress disturbance effect will significantly affect the propagation path of hydraulic fractures in the composite rock reservoir. To reveal the influence mechanism of stress disturbance effect on the hydraulic fracture propagation, several groups of laboratory tests and simulation tests were carried out. The test results showed that the hydraulic fracture tip formed a disturbing stress field because of the pore water pressure. Before the hydraulic fracture was extended to the bedding plane, the bedding plane had been damaged under stress disturbance, and the disturbed fracture zone was formed. The propagation mode of hydraulic fracture at the bedding plane was highly sensitive to the formation of the disturbed fracture zone. The sensitivity is mainly reflected from two aspects. (1) Under the action of the hydraulic fracture tip disturbance stress, many microfractures are generated and penetrated into the disturbance fracture zone on the bedding plane. This behavior is accompanied by energy dissipation causing the bedding plane material to be significantly softened, and the energy required for hydraulic fracture propagation is reduced dramatically. (2) The formation of the disturbed fracture zone improves the degree of fragmentation of the bedding plane, and the permeability of the local area increases significantly, forming the dominant circulation path. The higher the development of the disturbed fracture zone, the greater the hydraulic fracture propagation tendency along the bedding plane. According to the formation characteristics of the bedding plane disturbed fracture zone, the author proposed a nonlinear fracture model of the bedding plane disturbed fracture zone and established the hydraulic fracture propagation path criterion. This paper further analyzed the influencing factors of the disturbed fracture zone’s formation conditions and found that the bedding plane’s cementation strength was the main factor affecting the development degree of the disturbed fracture zone.
Scaling Human‐Object Interaction Recognition in the Video through Zero‐Shot Learning
Authors: Maraghi Vali Ollah , Faez Karim
Published: June 2021

Recognition of human activities is an essential field in computer vision. The most human activity consists of the interaction between humans and objects. Many successful works have been done on human‐object interaction (HOI) recognition and achieved acceptable results in recent years. Still, they are fully supervised and need to train labeled data for all HOIs. Due to the enormous space of human‐object interactions, listing and providing the training data for all possible categories is costly and impractical. We propose an approach for scaling human‐object interaction recognition in video data through the zero‐shot learning technique to solve this problem. Our method recognizes a verb and an object from the video and makes an HOI class. Recognition of the verbs and objects instead of HOIs allows identifying a new combination of verbs and objects. So, a new HOI class can be identified, which is not seen by the recognizer system. We introduce a neural network architecture that can understand and represent the video data. The proposed system learns verbs and objects from available training data at the training phase and can identify the verb‐object pairs in a video at test time. So, the system can identify the HOI class with different combinations of objects and verbs. Also, we propose to use lateral information for combining the verbs and the objects to make valid verb‐object pairs. It helps to prevent the detection of rare and probably wrong HOIs. The lateral information comes from word embedding techniques. Furthermore, we propose a new feature aggregation method for aggregating extracted high‐level features from video frames before feeding them to the classifier. We illustrate that this feature aggregation method is more effective for actions that include multiple subactions. We evaluated our system by recently introduced Charades challengeable dataset, which has lots of HOI categories in videos. We show that our proposed system can detect unseen HOI classes in addition to the acceptable recognition of seen types. Therefore, the number of classes identifiable by the system is greater than the number of classes used for training.
Assessment of Untreated Coffee Wastes for the Removal of Chromium (VI) from Aqueous Medium
Authors: Loulidi Ilyasse , Boukhlifi Fatima , Ouchabi Mbarka , Amar Abdelouahed , Jabri Maria , Kali Abderahim , Hadey Chaimaa
Published: June 2021

Industrial discharges loaded with heavy metals present several problems for aquatic ecosystems and human health. In this context, the present study aims to evaluate the potential of raw spent coffee grounds to remove chromium from an aqueous medium. A structural and textural study of coffee grounds was carried out by FTIR, XRD, and TGA analysis. The optimum conditions for the removal of Cr(VI), for a solution with an initial concentration of 100 mg/l, were adsorbent dose 2.5 g/l, pH 4.0, and contact time 90 min. The adsorption equilibrium results show that the Langmuir isotherm best describes the process with an adsorption capacity of 42.9 mg/g and that the adsorption kinetics follows the pseudosecond-order model. The calculated thermodynamic parameters showed that the adsorption is exothermic and spontaneous. The activation energy value (Ea) indicated that the retention is physisorptive in nature. The regeneration of the adsorbent was carried out by three eluents, among which HCl was the best. Finally, a brief cost estimation showed the great potential of coffee grounds as a low-cost adsorbent.