bluuebunny/crossref_metadata_2025 huggingface dataset:
Remote sensing monitoring of total nitrogen and total phosphorus concentrations in the water around Chaohu Lake based on geographical division
Authors: Li Jiang , Wang Jie , Wu Yanlan , Cui Yuhuan , Yan Shijiang
Published: October 2022

Remote sensing is useful for quantifying water-quality parameters for managing inland water systems. However, the single water-quality retrieval model usually has poor applicability in large regions. To solve the issue of low retrieval accuracy of water-quality parameters in inland water, the study area herein is geographically divided into rural water and urban water according to the proportion of land-use types in the riparian zones. Furthermore, the machine-learning regression algorithms are used to construct the retrieval models suitable for the total nitrogen (TN) and total phosphorus (TP) concentrations based on the measured water-quality data and the simultaneous Sentinel-2 Multispectral Imager (MSI) images. Additionally, the optical retrieval models are applied to the MSI images acquired on different dates to analyze the variations of TN and TP concentrations in the water around Chaohu Lake of China. The results show that the three accuracy indices of determination coefficient (R2), mean square error (MSE), and mean absolute percentage error (MAPE) of the TN concentration retrieval models for rural water and urban water were 0.67, 0.37 mg/L, and 36.81%, and 0.78, 0.34 mg/L, and 8.34%, respectively, while those of the TP concentration retrieval model for rural water and urban water reached 0.46, 0.0034 mg/L, and 38.60%, and 0.58, 0.018 mg/L, and 37.57%, respectively. The accuracy of the TN and TP concentration retrieval model constructed using geographical division is significantly better than that which does not use geographical division. According to the retrieval results from MSI images, the TN and TP concentrations in urban water are higher than those in rural water. TN and TP concentrations in urban water are stable throughout the year and peak in December, while those of rural water are highest in March and lowest in November. The method proposed in this study can provide a new idea for improving the retrieval accuracy of water-quality parameters in different water bodies in a large-scale region, and the relevant conclusion can provide a theoretical basis for water pollution control and prevention strategies in agricultural basins.
Study on the deterioration trend of the rock mass on the reservoir banks under dry-wet cycles
Authors: Gao Xuecheng , Wang Luqi , Xiang Yuzhou , Jiang Xiang , Yang Yang , Ran Bo
Published: October 2022

The deterioration of rock mass under dynamic mechanical state is difficult to determine, especially when evolution trends of micro-fractures are considered. Taking the limestone from Wuxia section of the Three Gorges Reservoir area as studying case, cross-scale tests and theoretical analysis were adopted to study the influence of dry-wet cycles on rock deterioration. The weakly acidic condition (pH = 6) and the dry environment at 105°C were together constituted the two extreme mechanical states of the dry-wet cycles. Meanwhile, the number of dry-wet cycles and soaking time were used as the main variables to analyze the deterioration trend. After introducing the damage mechanics, the quantitative relationship between the mechanical parameters and changing mechanical states was obtained. Combined with the microstructure obtained by scanning electron microscope (SEM), it can be found that with the increase of dry-wet cycles and soaking time, the morphology of mineral particles changed, the number of secondary pores gradually increased, the surface structure became looser, and the microcracks gradually increased, causing the decrease of macro strength. The related method proposed in this paper could provide significant references to determine the mechanical parameters of rocky reservoir bank.
Analysis of the formation mechanism of debris flows after earthquakes – A case study of the Legugou debris flow
Authors: He Na , Fu Qixuan , Zhong Wei , Yang Zhiquan , Cai XianQing , Xu Linjuan
Published: October 2022

By means of the Graphic Method, Gray Correlation Method and Frequency Method, the total amount of loose solid materials, the amount of loose solid materials per unit area in the source area, and the risk degree and critical rainfall of the study area are determined, respectively. On the basis of the calculation results, the total amount of loose solid materials is 57.2 × 104 m3, the amount of loose solid materials per unit area is 0.13 m3/m2 (greater than 0.1 m3/m2), which better meets the initiation conditions for dilute debris flow. The Hazard Evaluation Model of Debris Flow in earthquake areas is established by the gray correlation method and the hazard index H = 0.725 is determined. According to the hazard classification standards for debris flows in earthquake areas, the debris flow in Lecugou was moderate after the earthquake. The critical rainfall value of 1H, calculated by the frequency method, ranged from 17.45 to 22.21 mm (Re = 25 mm) and 8.17 to 13.01 mm (Re = 50 mm). The critical rainfall value at 10 min ranged from 6.23 to 8.44 mm (Re = 25 mm) and 2.92 to 5.13 mm (Re = 50 mm), respectively. The maximum rainfall intensity of 45.5 mm/h was reached between 10:00 and 11:00 on July 29, 2019 and the cumulative rainfall reached 144 mm, far exceeding the critical rainfall of Legugou. Under the influence of earthquakes and human activities, the loose solid source amount and loose solid source amount per unit area increased greatly, and the critical rainfall for debris flow after earthquakes decreased sharply, which induced debris flows under the influence of heavy rainfall. This research will be helpful for the establishment of monitoring and early warning systems based on artificial intelligence methods, and can greatly improve the effectiveness of disaster prevention and mitigation.
The dental microwear texture of wild boars from Japan reflects inter- and intra-populational feeding preferences
Authors: Miyamoto Kohga , Kubo Mugino O. , Yokohata Yasushi
Published: October 2022

Dental microwear texture analysis (DMTA) is rapidly expanding for the dietary estimation of extinct animals. There has been an extensive accumulation of microwear texture data from herbivorous mammals, especially for ruminant artiodactyls, but suids are still underrepresented. Microwear varies depending on the diet, and suids are naturally more flexible than other artiodactyls. Thus, their microwear is prone to greater variability. In this study, we examine the tooth microwear texture of wild boars from Toyama Prefecture, Japan, for which detailed ecological and dietary information by stomach content analysis is available. We first investigated 205 individuals of wild-shot Toyama boars with known sex, age class, localities (the eastern high latitude region vs. the western low latitude region), and season of collection. The tooth surfaces of boarlets were rougher than those of juvenile and adult animals. The decrease in surface roughness with age implied that the frequency of tooth-tooth contact, which seemed to result in cracking of enamels and thus rough surfaces, decreased after the boars started feeding on solid foods (food-tooth contact), with progressive involvement of rooting behavior in mature adults. We further found that surface roughness showed significant differences between localities, with the western Toyama boars having flatter surfaces, possibly because they were involved in more rooting and feeding on soil-contaminated rhizomes than the eastern ones, as implied by the available stomach content data. The frequency of rooting was also evident in the broader comparison among Japanese boar populations with different habitat environments. The mainland boars inhabiting deciduous broad-leaved forests had a flatter and less rough tooth surfaces than those in the subtropical evergreen broad-leaved forests of the southern islands. This corresponds to the fact that above-ground dietary resources were more abundant in the habitat of the southern island boars, where crops like succulent vegetables and fruits, as well as naturally fallen acorns, were abundant, whereas underground plant parts were the dominant diet component for the mainland boars. This study proved that DMTA can identify the difference in foraging modes in suids and make it possible to estimate the frequency of rooting, which is informative for inferring breeding methods of boars/pigs from archaeological sites.
Application of next-generation sequencing for the high-resolution typing of MHC-B in Korean native chicken
Authors: Ediriweera Thisarani Kalhari , Manjula Prabuddha , Cho Eunjin , Kim Minjun , Lee Jun Heon
Published: October 2022

The major histocompatibility complex-B (MHC-B) region of chicken is crucially important in their immunogenesis and highly diverse among different breeds, lines, and even populations. Because it determines the resistance/susceptibility to numerous infectious diseases, it is important to analyze this genomic region, particularly classical class I and II genes, to determine the variation and diversity that ultimately affect antigen presentation. This study investigated five lines of indigenous Korean native chicken (KNC) and the Ogye breed using next-generation sequencing (NGS) data with Geneious Prime-based assembly and variant calling with the Genome Analysis Toolkit (GATK) best practices pipeline. The consensus sequences of MHC-B (BG1-BF2) were obtained for each chicken line/breed and their variants were analyzed. All of the Korean native chicken lines possessed an excessive number of variants, including an ample amount of high-impact variants that provided useful information regarding modified major histocompatibility complex molecules. The study confirmed that next-generation sequencing techniques can effectively be used to detect MHC variabilities and the KNC lines are highly diverse for the MHC-B region, suggesting a substantial divergence from red junglefowl.
Role of noncoding RNA in the pathophysiology and treatment of intrauterine adhesion
Authors: Liu Hui-Dong , Wang Shao-Wei
Published: October 2022

Intrauterine adhesion (IUA) is one of the most common diseases of the reproductive system in women. It is often accompanied by serious clinical problems that damage reproductive function, such as menstrual disorder, infertility, or recurrent abortion. The clinical effect of routine treatment is not ideal, and the postoperative recurrence rate is still very high. Therefore, exploring the pathological mechanism of IUA and finding new strategies for the effective prevention and treatment of IUA are needed. The main pathological mechanism of IUA is endometrial fibrosis and scar formation. Noncoding RNA (ncRNA) plays an important role in the fibrosis process, which is one of the latest research advances in the pathophysiology of IUA. Moreover, the exosomal miRNAs derived from mesenchymal stem cells can be used to improve IUA. This paper reviewed the role of ncRNAs in IUA pathogenesis, summarized the core pathways of endometrial fibrosis regulated by ncRNAs, and finally introduced the potential of ncRNAs as a therapeutic target.
Interim efficacy and safety of PD-1 inhibitors in preventing recurrence of hepatocellular carcinoma after interventional therapy
Authors: Qiao Wenying , Wang Qi , Hu Caixia , Zhang Yinghua , Li Jianjun , Sun Yu , Yuan Chunwang , Wang Wen , Liu Biyu , Zhang Yonghong
Published: October 2022

Introduction

Locoregional interventional therapy including transcatheter arterial chemoembolization (TACE) and ablation are the current standard of treatment for early-to-mid-stage hepatocellular carcinoma (HCC). However, questions remain unanswered regarding the management of recurrence after locoregional treatment. PD-1 inhibitors can block inhibitory signals of T-cell activation and proliferation to reduce the recurrence. We conducted a single-arm phase 2 trial to evaluate the efficacy and safety of PD-1 inhibitors following locoregional interventional therapy in HCC patients with high recurrence risk guided by our novel scoring system.

Methods

Patients enrolled initially treated by TACE combined with ablation, then willingly joined the experimental group. One month later, they received the anti-PD-1 adjuvant therapy (intravenous injection of 200 mg), which was repeated every 3 weeks for a total of 4 or 8 cycles. Within this same period, other patients were screened into the control group to match the experimental group by 1:1 based on the propensity score matching method (PSM). The primary endpoint was relapse-free survival (RFS). Secondary endpoints included overall survival (OS) recurrence modality, safety, and quality of life.

Result

At the time of data cutoff, the median RFS of the control group was 7.0 months while the experimental group had not reached it. Moreover, the 1-year RFS rate was 73.3% in the experimental group and 46.7% in the control group, showing a significant difference (P =0.02). The rate of local tumor progression in the experimental group was clearly lower than that in the control group (P = 0.027). Benefits associated with anti-PD-1 adjuvant therapy were observed in patients with multiple tumors and tumor size ≤2cm. Univariate and multivariate analyses demonstrated that anti-PD-1 adjuvant therapy was an independent favorable prognostic factor for RFS in HCC patients. The most frequent AE observed in this study was RCCEP, and other AEs included diarrhea, hepatotoxicity, rash, pruritus, and fatigue. The incidence of GRADE ≥3 AE and withdrawal in this study was low with no deaths recorded.

Conclusions

Interim analysis from the study suggest the addition of anti-PD-1 adjuvant therapy after TACE combined with ablation could significantly prolong RFS with controllable safety for early-to-mid-stage HCC patients with high recurrence risk.
Local cellular immune response plays a key role in protecting chickens against hepatitis-hydropericardium syndrome (HHS) by vaccination with a recombinant fowl adenovirus (FAdV) chimeric fiber protein
Authors: De Luca Carlotta , Schachner Anna , Heidl Sarah , Hess Michael , Liebhart Dieter , Mitra Taniya
Published: October 2022

Fowl adenovirus (FAdV)-induced diseases hepatitis-hydropericardium syndrome (HHS) and inclusion body hepatitis (IBH) have been affecting the poultry industry with increasing severity in the last two decades. Recently, a subunit vaccine based on a chimeric fiber protein with epitopes from different fowl adenovirus serotypes (named crecFib-4/11) has been shown to confer simultaneous protection against both HHS and IBH. However, the underlying immune mechanisms in chickens are still enigmatic, especially because of frequently absent neutralizing response despite high levels of protection. In this study, we investigated the kinetics of the humoral and cellular immune responses in specific pathogen-free chickens after vaccination with crecFib-4/11 and/or challenge with a HHS-causing strain, on a systemic level, as well as locally in target and lymphoid organs. The humoral response was assessed via enzyme-linked immunosorbent assay (ELISA) and virus neutralization test in serum, while the cellular immune response was determined by phenotyping using flow cytometry. Although vaccination induced serum antibodies, as confirmed by ELISA, such antibodies exhibited no pre-challenge neutralizing activity against FAdV-4. Nevertheless, immunized birds experienced a significant B cell increase in the liver upon challenge, remaining high throughout the experiment. Furthermore, vaccination stimulated the proliferation of cytotoxic T lymphocytes, with earlier circulation in the blood compared to the challenge control and subsequent increase in liver and spleen. Overall, these findings imply that protection of chickens from HHS after crecFib-4/11 vaccination relies on a prominent local immune response in the target organs, instead of circulating neutralizing antibodies.
Pan-neutralizing, germline-encoded antibodies against SARS-CoV-2: Addressing the long-term problem of escape variants
Authors: Lunderberg Justin Mark , Dutta Sanjucta , Collier Ai-Ris Y. , Lee Jeng-Shin , Hsu Yen-Ming , Wang Qiao , Zheng Weina , Hao Shushun , Zhang Haohai , Feng Lili , Robson Simon C. , Gao Wenda , Riedel Stefan
Published: October 2022

Despite the initially reported high efficacy of vaccines directed against ancestral SARS-CoV-2, repeated infections in both unvaccinated and vaccinated populations remain a major global health challenge. Because of mutation-mediated immune escape by variants-of-concern (VOC), approved neutralizing antibodies (neutAbs) effective against the original strains have been rendered non-protective. Identification and characterization of mutation-independent pan-neutralizing antibody responses are therefore essential for controlling the pandemic. Here, we characterize and discuss the origins of SARS-CoV-2 neutAbs, arising from either natural infection or following vaccination. In our study, neutAbs in COVID-19 patients were detected using the combination of two lateral flow immunoassay (LFIA) tests, corroborated by plaque reduction neutralization testing (PRNT). A point-of-care neutAb LFIA, NeutraXpress™, was validated using serum samples from historical pre-COVID-19 negative controls, patients infected with other respiratory pathogens, and PCR-confirmed COVID-19 patients. Surprisingly, potent neutAb activity was mainly noted in patients generating both IgM and IgG against the Spike receptor-binding domain (RBD), in contrast to samples possessing anti-RBD IgG alone. We propose that low-affinity, high-avidity, germline-encoded natural IgM and subsequent generation of class-switched IgG may have an underappreciated role in cross-protection, potentially offsetting immune escape by SARS-CoV-2 variants. We suggest Reverse Vaccinology 3.0 to further exploit this innate-like defense mechanism. Our proposition has potential implications for immunogen design, and provides strategies to elicit pan-neutAbs from natural B1-like cells. Refinements in future immunization protocols might further boost long-term cross-protection, even at the mucosal level, against clinical manifestations of COVID-19.
Current landscape and future directions of bispecific antibodies in cancer immunotherapy
Authors: Wei Jing , Yang Yueyao , Wang Gang , Liu Ming
Published: October 2022

Recent advances in cancer immunotherapy using monoclonal antibodies have dramatically revolutionized the therapeutic strategy against advanced malignancies, inspiring the exploration of various types of therapeutic antibodies. Bispecific antibodies (BsAbs) are recombinant molecules containing two different antigens or epitopes identifying binding domains. Bispecific antibody-based tumor immunotherapy has gained broad potential in preclinical and clinical investigations in a variety of tumor types following regulatory approval of newly developed technologies involving bispecific and multispecific antibodies. Meanwhile, a series of challenges such as antibody immunogenicity, tumor heterogeneity, low response rate, treatment resistance, and systemic adverse effects hinder the application of BsAbs. In this review, we provide insights into the various architecture of BsAbs, focus on BsAbs’ alternative different mechanisms of action and clinical progression, and discuss relevant approaches to overcome existing challenges in BsAbs clinical application.
MatchTope: A tool to predict the cross reactivity of peptides complexed with Major Histocompatibility Complex I
Authors: Mendes Marcus Fabiano de Almeida , de Souza Bragatte Marcelo , Vianna Priscila , de Freitas Martiela Vaz , Pöhner Ina , Richter Stefan , Wade Rebecca C. , Salzano Francisco Mauro , Vieira Gustavo Fioravanti
Published: October 2022

The therapeutic targeting of the immune system, for example in vaccinology and cancer treatment, is a challenging task and the subject of active research. Several in silico tools used for predicting immunogenicity are based on the analysis of peptide sequences binding to the Major Histocompatibility Complex (pMHC). However, few of these bioinformatics tools take into account the pMHC three-dimensional structure. Here, we describe a new bioinformatics tool, MatchTope, developed for predicting peptide similarity, which can trigger cross-reactivity events, by computing and analyzing the electrostatic potentials of pMHC complexes. We validated MatchTope by using previously published data from in vitro assays. We thereby demonstrate the strength of MatchTope for similarity prediction between targets derived from several pathogens as well as for indicating possible cross responses between self and tumor peptides. Our results suggest that MatchTope can enhance and speed up future studies in the fields of vaccinology and cancer immunotherapy.
Exploiting the role of T cells in the pathogenesis of Sjögren’s syndrome for therapeutic treatment
Authors: An Qi , Zhao Jingwen , Zhu Xueqing , Yang Baoqi , Wu Zewen , Su Yazhen , Zhang Liyun , Xu Ke , Ma Dan
Published: October 2022

Sjögrens syndrome (SS) is caused by autoantibodies that attack proprioceptive salivary and lacrimal gland tissues. Damage to the glands leads to dry mouth and eyes and affects multiple systems and organs. In severe cases, SS is life-threatening because it can lead to interstitial lung disease, renal insufficiency, and lymphoma. Histological examination of the labial minor salivary glands of patients with SS reveals focal lymphocyte aggregation of T and B cells. More studies have been conducted on the role of B cells in the pathogenesis of SS, whereas the role of T cells has only recently attracted the attention of researchers. This review focusses on the role of various populations of T cells in the pathogenesis of SS and the progress made in research to therapeutically targeting T cells for the treatment of patients with SS.
A catch limitation device to avoid excessive catches in the blue whiting (Micromesistius poutassou) Northeast Atlantic pelagic trawl fishery
Authors: Ingólfsson Ólafur Arnar , Breen Michael , Rosen Shale , Sistiaga Manu , Jørgensen Terje , Lilleng Dagfinn , Saltskår Jostein , Kvalvik Liz , Hannaas Sigurd , Pettersen Hermann
Published: October 2022

Blue whiting (Micromesistius poutassou) is harvested in the Northeast Atlantic by a multinational fleet of pelagic trawlers. Occasionally, vessels take catches which exceed their remaining holding capacity and in extreme cases large catches cause codends to burst, resulting in spill of catch. To control catch quantity, a catch limitation system was developed and tested. The system consists of three components: 1) escape opening(s) in front of the codend to release excess fish, 2) a fish lock to prevent loss of fish through the escape opening(s) during haulback and at the surface, and 3) a choking unit to match codend capacity to the desired size of catch. Blue whiting escaped through both longitudinal slots and large (≥ 2 m) meshes in front of the codend. However, video observations showed that with large meshes in the upper panel, large amounts of blue whiting escaped long before the codend was full. Therefore, a design with large openings in the bottom was combined with longitudinal slots in the side and top panels. Two fish locks were tested: an oblique netting panel designed to seal off the codend when vessel speed reduce during haulback, and a cylinder of netting with a choking rope that closed it after the codend was filled. Both fish lock designs inhibited release of fish during haulback and at the surface, but the attachment of the constricting rope in the cylinder frequently broke. The choking unit consisted of a depth triggered releaser connected to a strap of rope wrapped around the codend. Mechanical releasers with factory-set depth trigger and electronic versions were tested. Both freed the choke point as intended, but occasionally at unpredictable depth. A reliable relationship (r2 = 0.94) was attained between codend choking position and catch amount, demonstrating that codend capacity could be adjusted to achieve target catch quantities. Our work shows that controlling catch quantity in the blue whiting pelagic trawl fishery can be achieved effectively through relatively simple modifications to the codend section Future work is needed to optimize the fish lock design and ensure the codend choking rope releasers trigger reliably and at the proper depth.
Regional patterns in demersal fish assemblages among subsea pipelines and natural habitats across north-west Australia
Authors: Galaiduk Ronen , Radford Ben , Case Mark , Bond Todd , Taylor Michael , Cooper Tim , Smith Luke , McLean Dianne
Published: October 2022

Regional patterns of fish diversity, abundance, distribution, and assemblage composition are driven by a combination of biotic and abiotic conditions in the marine environment, but these conditions can be altered through anthropogenic activities, such as those associated with oil and gas extraction. The present study utilises data on fish relative abundance and diversity obtained from 1546 baited remote underwater video deployments conducted between 2004 – 2019 in depths of 9 – 170 m across 2000 km of coastline in north-west Australia on natural habitats and subsea pipelines to understand the influence of oil and gas infrastructure on fish assemblages. A total of 450 fish taxa from 56 families was observed, with populations dominated by generalist and invertebrate carnivore taxa. At the regional scale, subsea pipelines had lower diversity (lower taxonomic richness) than natural environments, but possessed a higher abundance of piscivorous and herbivorous fish taxa. Clear patterns in fish assemblage composition were observed in multivariate analyses, reflecting the proximity of oceanic shoals and banks, depth, and to a lesser extent, oil and gas infrastructure. Shallow-water and close to shoals assemblages were characterised by a diversity of site-attached (e.g., wrasses, tuskfish), reef-associated taxa (e.g., emperors). Mesophotic fish assemblages were characterised by commercially important (e.g., goldband snapper), wide-ranging (e.g., sharks) and sand-affiliated (e.g., toadfish, threadfin bream) taxa. Proximity to pipelines and platforms ranked low as predictors in the multivariate analyses suggesting a negligible regional influence of these structures on fish communities in comparison to depth and shoal habitats. Local-scale influences of subsea infrastructure, however, may be important for some fish species (infrastructure vs. immediate surrounds). Our study highlights the influence of abiotic factors on regional-scale patterns in fish assemblage structure across north-west Australia.
Prediction of early graft function after living donor kidney transplantation by quantifying the “nephron mass” using CT-volumetric software
Authors: Takahashi Kazuhiro , Furuya Kinji , Gosho Masahiko , Usui Joichi , Kimura Tomokazu , Hoshi Akio , Hashimoto Shinji , Nishiyama Hiroyuki , Oda Tatsuya , Yuzawa Kenji , Yamagata Kunihiro
Published: October 2022

Early renal function after living-donor kidney transplantation (LDKT) depends on the “nephron mass” in the renal graft. In this study, as a possible donor-recipient size mismatch parameter that directly reflects the “nephron mass,” the cortex to recipient weight ratio (CRWR) was calculated by CT-volumetric software, and its ability to predict early graft function was examined. One hundred patients who underwent LDKT were enrolled. Patients were classified into a developmental cohort (n = 79) and a validation cohort (n = 21). Using the developmental cohort, the correlation coefficients between size mismatch parameters, including CRWR, and the posttransplantation estimated glomerular filtration rate (eGFR) were calculated. Multiple regression analysis was conducted to define a formula to predict eGFR 1-month posttransplantation. Using the validation cohort, the validity of the formula was examined. The correlation coefficient was the highest for CRWR (1-month r = 0.66, p < 0.001). By multiple regression analysis, eGFR at 1-month was predicted using the linear model: 0.23 × donor preoperative eGFR + 17.03 × CRWR + 8.96 × preemptive transplantation + 5.10 (adjusted coefficient of determination = 0.54). In most patients in the validation cohort, the observed eGFR was within a 10 ml/min/1.73 m2 margin of the predicted eGFR. CRWR was the strongest parameter to predict early graft function. Predicting renal function using this formula could be useful in clinical application to select proper donors and to avoid unnecessary postoperative medical interventions.
Determination of phage load and administration time in simulated occurrences of antibacterial treatments
Authors: Plunder Steffen , Burkard Markus , Lauer Ulrich M. , Venturelli Sascha , Marongiu Luigi
Published: October 2022

The use of phages as antibacterials is becoming more and more common in Western countries. However, a successful phage-derived antibacterial treatment needs to account for additional features such as the loss of infective virions and the multiplication of the hosts. The parameters critical inoculation size (VF) and failure threshold time (TF) have been introduced to assure that the viral dose (Vϕ) and administration time (Tϕ) would lead to the extinction of the targeted bacteria. The problem with the definition of VF and TF is that they are non-linear equations with two unknowns; thus, obtaining their explicit values is cumbersome and not unique. The current study used machine learning to determine VF and TF for an effective antibacterial treatment. Within these ranges, a Pareto optimal solution of a multi-criterial optimization problem (MCOP) provided a pair of Vϕ and Tϕ to facilitate the user’s work. The algorithm was tested on a series of in silico microbial consortia that described the outgrowth of a species at high cell density by another species initially present at low concentration. The results demonstrated that the MCOP-derived pairs of Vϕ and Tϕ could effectively wipe out the bacterial target within the context of the simulation. The present study also introduced the concept of mediated phage therapy, where targeting booster bacteria might decrease the virulence of a pathogen immune to phagial infection and highlighted the importance of microbial competition in attaining a successful antibacterial treatment. In summary, the present work developed a novel method for investigating phage/bacteria interactions that can help increase the effectiveness of the application of phages as antibacterials and ease the work of microbiologists.
Resources of Iranian agarics (Basidiomycota) with an outlook on their antioxidant potential
Authors: Ghobad-Nejhad Masoomeh , Antonín Vladimír , Moghaddam Mohaddeseh , Langer Ewald
Published: October 2022

Agaric fungi are an important group of macromycetes with diverse ecological and functional properties, yet are poorly studied in many parts of the world. Here, we comprehensively analyzed 558 agaric species in Iran to reveal their resources of edible and poisonous species as well as their ecological guilds and luminescence potential. We also made a thorough survey of the antioxidant activity of the species. Phylogenetic relationships were reconstructed based on nuclear ribosomal LSU and ITS sequences. Our results reveal that agarics of Iran comprise about 189 edible, 128 poisonous, 254 soil saprotrophic, 172 ectomycorrhizal, 146 wood-inhabiting, 18 leaf/litter-inhabiting, 9 parasitic, and 19 luminescent species. Twenty percent of the Iranian agaric species possess antioxidant activity, phylogenetically distributed in four orders and 21 agaric families. About 5% of the antioxidant species can be considered strong antioxidants, many of which are also edible and could be utilized to develop functional foods. This is the first study combining phylogeny and antioxidant potential of agaric mushrooms in a large scale, and the obtained results would guide the selection of agaric taxa to be examined in the future for taxonomic revisions, biotechnological applications, and applied phylogeny studies.
Effect of short-term warming and drought on the methanogenic communities in degraded peatlands in Zoige Plateau
Authors: Li Wei , Shi Rui , Yuan Lingchen , Lan Xianli , Feng Defeng , Chen Huai
Published: October 2022

Peatlands in Qinghai-Tibetan are degrading with climate change and human activities. Peatland degradation and climate change affect methane emissions. Methanogens are key functional microbes during methane production; however, knowledge of methanogens in degraded peatlands is lacking. Here, we investigated the effects of short-term (1 year) warming (OTC), drought (20%), and their combination on methanogens in the degraded peatlands on the Zoige Plateau of China via qPCR and clone library analysis. The results showed thatMethanomicrobialesandMethanobacterialeswere predominant in all the treatments. Non-metric multidimensional scaling (NMDS) and PERMANOVA analyses showed that the methanogenic community structure among the climate change treatments was not significantly different. The relative abundance of methanogen communities showed insignificant variation among the climate change treatments. The copy number and Shannon diversity of methanogens were significantly different within the climate change treatments, and drought significantly decreased the copy number of methanogens when compared to the control. The Redundancy analysis (RDA) results and correlation analysis showed that the environmental variables measured had no significant effect on methanogenic community structure and Shannon diversity. These results indicate that methanogens are insensitive to short-term climate change in degraded peatlands. This study provides insight into methane emissions from the Zoige Plateau peatlands by focusing on the possible responses of the methanogens to climate-driven changes.
Olive agroforestry shapes rhizosphere microbiome networks associated with annual crops and impacts the biomass production under low-rainfed conditions
Authors: Ben zineb Ameni , Barkaoui Karim , Karray Fatma , Mhiri Najla , Sayadi Sami , Mliki Ahmed , Gargouri Mahmoud
Published: October 2022

Agroforestry (AF) is a promising land-use system to mitigate water deficiency, particularly in semi-arid areas. However, the belowground microbes associated with crops below trees remain seldom addressed. This study aimed at elucidating the effects of olive AF system intercropped with durum wheat (Dw), barely (Ba), chickpea (Cp), or faba bean (Fb) on crops biomass and their soil-rhizosphere microbial networks as compared to conventional full sun cropping (SC) under rainfed conditions. To test the hypothesis, we compared the prokaryotic and the fungal communities inhabiting the rhizosphere of two cereals and legumes grown either in AF or SC. We determined the most suitable annual crop species in AF under low-rainfed conditions. Moreover, to deepen our understanding of the rhizosphere network dynamics of annual crops under AF and SC systems, we characterized the microbial hubs that are most likely responsible for modifying the microbial community structure and the variability of crop biomass of each species. Herein, we found that cereals produced significantly more above-ground biomass than legumes following in descending order: Ba > Dw > Cp > Fb, suggesting that crop species play a significant role in improving soil water use and that cereals are well-suited to rainfed conditions within both types of agrosystems. The type of agrosystem shapes crop microbiomes with the only marginal influence of host selection. However, more relevant was to unveil those crops recruits specific bacterial and fungal taxa from the olive-belowground communities. Of the selected soil physicochemical properties, organic matter was the principal driver in shaping the soil microbial structure in the AF system. The co-occurrence network analyses indicated that the AF system generates higher ecological stability than the SC system under stressful climate conditions. Furthermore, legumes’ rhizosphere microbiome possessed a higher resilient capacity than cereals. We also identified different fungal keystones involved in litter decomposition and drought tolerance within AF systems facing the water-scarce condition and promoting crop production within the SC system. Overall, we showed that AF reduces cereal and legume rhizosphere microbial diversity, enhances network complexity, and leads to more stable beneficial microbial communities, especially in severe drought, thus providing more accurate predictions to preserve soil diversity under unfavorable environmental conditions.
Identification of salmoniformes aquaculture conditions to increase creatine and anserine levels using multiomics dataset and nonnumerical information
Authors: Shima Hideaki , Murata Izumi , Feifei Wei , Sakata Kenji , Yokoyama Daiki , Kikuchi Jun
Published: October 2022

Aquaculture is attracting attention as a sustainable protein source. Salmoniformes, which are generally called salmon, are consumed in large quantities worldwide and are popularly used for aquaculture. In this study, the relationship between muscle metabolites, intestinal microbiota, and nonnumerical information about the ecology of salmoniformes was investigated to improve the efficiency of aquaculture using nuclear magnetic resonance and next-generation sequencing with bioinformatics approach. It was revealed that salmoniformes are rich in anserine and creatine, which are useful for human health care, along with collagen and lipids. The important factors in increasing these useful substances and manage the environment of salmoniformes aquaculture should be noted.
Effect of aging on audiovisual integration: Comparison of high- and low-intensity conditions in a speech discrimination task
Authors: Yang Weiping , Guo Ao , Yao Hanyun , Yang Xiangfu , Li Zimo , Li Shengnan , Chen Jianxin , Ren Yanna , Yang Jiajia , Wu Jinglong , Zhang Zhilin
Published: October 2022

Audiovisual integration is an essential process that influences speech perception in conversation. However, it is still debated whether older individuals benefit more from audiovisual integration than younger individuals. This ambiguity is likely due to stimulus features, such as stimulus intensity. The purpose of the current study was to explore the effect of aging on audiovisual integration, using event-related potentials (ERPs) at different stimulus intensities. The results showed greater audiovisual integration in older adults at 320–360 ms. Conversely, at 460–500 ms, older adults displayed attenuated audiovisual integration in the frontal, fronto-central, central, and centro-parietal regions compared to younger adults. In addition, we found older adults had greater audiovisual integration at 200–230 ms under the low-intensity condition compared to the high-intensity condition, suggesting inverse effectiveness occurred. However, inverse effectiveness was not found in younger adults. Taken together, the results suggested that there was age-related dissociation in audiovisual integration and inverse effectiveness, indicating that the neural mechanisms underlying audiovisual integration differed between older adults and younger adults.
Brain structural network to investigate the mechanism of cognitive impairment in patients with acoustic neuroma
Authors: Deng Xueyun , Liu Lihua , Li Jiuhong , Yao Hui , He Shuai , Guo Zhiwei , Sun Jiayu , Liu Wenke , Hui Xuhui
Published: October 2022

Objective

Acoustic neuroma (AN) is a common benign tumor. Little is known of neuropsychological studies in patients with acoustic neuroma, especially cognitive neuropsychology, and the neuropsychological abnormalities of patients affect their life quality. The purpose of this study was to explore the changes in the cognitive function of patients with acoustic neuroma, and the possible mechanism of these changes by structural magnetic resonance imaging.

Materials and methods

We used a neuropsychological assessment battery to assess cognitive function in 69 patients with acoustic neuroma and 70 healthy controls. Then, we used diffusion tensor imaging data to construct the structural brain network and calculate topological properties based on graph theory, and we studied the relation between the structural brain network and cognitive function. Moreover, three different subnetworks (short-range subnetwork, middle-range subnetwork, and long-range subnetwork) were constructed by the length of nerve fibers obtained from deterministic tracking. We studied the global and local efficiency of various subnetworks and analyzed the correlation between network metrics and cognitive function. Furthermore, connectome edge analysis directly assessed whether there were differences in the number of fibers in the different brain regions. We analyzed the relation between the differences and cognitive function.

Results

Compared with the healthy controls, the general cognitive function, memory, executive function, attention, visual space executive ability, visual perception ability, movement speed, and information processing speed decreased significantly in patients with acoustic neuroma. A unilateral hearing loss due to a left acoustic neuroma had a greater impact on cognitive function. The results showed that changes in the global and local metrics, the efficiency of subnetworks, and cognitively-related fiber connections were associated with cognitive impairments in patients with acoustic neuroma.

Conclusion

Patients exhibit cognitive impairments caused by the decline of the structure and function in some brain regions, and they also develop partial compensation after cognitive decline. Cognitive problems are frequent in patients with acoustic neuroma. Including neuropsychological aspects in the routine clinical evaluation and appropriate treatments may enhance the clinical management and improve their life quality.
Enhanced recruitment of glutamate receptors underlies excitotoxicity of mitral cells in acute hyperammonemia
Authors: Li Mingxian , Liu Zhenqi , Lai Ke , Liu Hanwei , Gong Lina , Shi Haosong , Zhang Weitian , Wang Hui , Shi Haibo
Published: October 2022

Hepatic encephalopathy (HE)–a major complication of liver disease–has been found to increase the risk of olfactory dysfunction, which may be attributed to elevated levels of ammonia/ammonium in the blood and cerebrospinal fluid. However, the cellular mechanisms underlying hyperammonemia-induced olfactory dysfunction remain unclear. By performing patch-clamp recordings of mitral cells (MCs) in the mouse olfactory bulb (OB), we found that 3 mM ammonium (NH4+) increased the spontaneous firing frequency and attenuated the amplitude, but synaptic blockers could prevent the changes, suggesting the important role of glutamate receptors in NH4+-induced hyperexcitability of MCs. We also found NH4+ reduced the currents of voltage-gated K+ channel (Kv), which may lead to the attenuation of spontaneous firing amplitude by NH4+. Further studies demonstrated NH4+ enhanced the amplitude and integral area of long-lasting spontaneous excitatory post-synaptic currents (sEPSCs) in acute OB slices. This enhancement of excitatory neurotransmission in MCs occurred independently of pre-synaptic glutamate release and re-uptake, and was prevented by the exocytosis inhibitor TAT-NSF700. In addition, an NH4+-induced increasement in expression of NR1 and GluR1 was detected on cytoplasmic membrane, indicating that increased trafficking of glutamate receptors on membrane surface in MCs is the core mechanism. Moreover, NH4+-induced enhanced activity of glutamate receptors in acute OB slices caused cell death, which was prevented by antagonizing glutamate receptors or chelating intracellular calcium levels. Our study demonstrates that the enhancement of the activity and recruitment of glutamate receptor directly induces neuronal excitotoxicity, and contributes to the vulnerability of OB to acute hyperammonemia, thus providing a potential pathological mechanism of olfactory defects in patients with hyperammonemia and HE.
Computational models of neurotransmission at cerebellar synapses unveil the impact on network computation
Authors: Masoli Stefano , Rizza Martina Francesca , Tognolina Marialuisa , Prestori Francesca , D’Angelo Egidio
Published: October 2022

The neuroscientific field benefits from the conjoint evolution of experimental and computational techniques, allowing for the reconstruction and simulation of complex models of neurons and synapses. Chemical synapses are characterized by presynaptic vesicle cycling, neurotransmitter diffusion, and postsynaptic receptor activation, which eventually lead to postsynaptic currents and subsequent membrane potential changes. These mechanisms have been accurately modeled for different synapses and receptor types (AMPA, NMDA, and GABA) of the cerebellar cortical network, allowing simulation of their impact on computation. Of special relevance is short-term synaptic plasticity, which generates spatiotemporal filtering in local microcircuits and controls burst transmission and information flow through the network. Here, we present how data-driven computational models recapitulate the properties of neurotransmission at cerebellar synapses. The simulation of microcircuit models is starting to reveal how diverse synaptic mechanisms shape the spatiotemporal profiles of circuit activity and computation.
Physical therapy interventions for the correction of equinus foot deformity in post-stroke patients with triceps spasticity: A scoping review
Authors: Campanini Isabella , Bò Maria Chiara , Salsi Francesca , Bassi Maria Chiara , Damiano Benedetta , Scaltriti Sara , Lusuardi Mirco , Merlo Andrea
Published: October 2022

Objective

Equinus foot deformity (EFD) is the most common deformity following a stroke. Several approaches have been suggested for its correction, including pharmacological, surgical, and physical therapy (PT) interventions. This scoping review aims to map and synthesize the available evidence focusing on physical therapy treatments for EFD caused by triceps surae (TS) spasticity.

Methods

Scoping review methodological frameworks have been used. Pubmed, Cinahl, and Cochrane databases were searched for primary literature. Studies focusing on the treatment of EFD in adult stroke patients were included only when the intervention involved PT treatments and presented at least one outcome measure for the functional and/or structural condition of the TS. Data were systematically collected and reported in tables inclusive of type of intervention, sample characteristics, dosage, comparators, outcomes, follow-up timeline, and treatment efficacy. A narrative synthesis was also added.

Results

Of the 642 experimental or observational screened studies, 53 were included, focusing on stretching exercises, shock waves, electrical stimulation, dry needling, TENS, vibration therapy, ultrasounds, cryotherapy, and active physiotherapy. Patients with EFD benefited from specific physical therapy treatments. These usually resulted in Modified Ashworth Scale reduction, typically by 1 point, and an increase in ROM. Interventions consisting of shock waves, dry needling, and electrostimulation showed the best results in reducing EFD. Heterogeneous dosage and delivery mode generally limited conclusions.

Conclusions

This scoping review summarized available primary literature based on PT treatments for the correction of EFD. By highlighting the remaining gaps in knowledge, it provides a reference for future studies on this pathology. Further investigations are necessary to pinpoint the best dosage and delivery methods. Future studies should investigate whether early rehabilitation programs started during the acute phase might help prevent or limit the development of secondary deformities.