bluuebunny/crossref_metadata_2025 huggingface dataset:
Assessing the impact of abiotic and biotic factors on seedling survival in an African montane forest
Authors: Abiem Iveren , Kenfack David , Chapman Hazel M.
Published: February 2023

Tree seedling dynamics underpin subsequent forest structure and diversity as different species/guilds respond variously to abiotic and biotic stresses. Thus, understanding differential seedling responses to stresses helps us to predict forest trajectories. Because forests vary in both environment and species composition, generalisations across tropical forests are difficult. Afromontane forests are important carbon stores, harbour high diversity and provide critical ecosystem services, yet they are vulnerable to climate change. Here, we investigate the importance of key abiotic and biotic factors on survival of seedling guilds along spatial and temporal scales in a montane forest in south-eastern Nigeria. We use data from 318 seedling plots censused every 3 months from 2017 to 2020 to identify seven key abiotic and four biotic factors influencing seedling survival. We used the Kaplan–Meier method to estimate the persistence time of 1,145 seedlings at community and guild levels. At the community level, newly recruited seedlings had a median survival time of 15 months and about 37% of the seedlings sampled where still alive after 24 months. Understory tree species survived significantly longer than the other growth form guilds and seedling survival did not differ across shade tolerance guilds. Conspecific adult density and steeper, more north facing slopes had a negative effect on tree seedlings survival. In addition, tree seedlings that recruited in October (end of wet season/beginning of dry) had lower survival probabilities compared to those that recruited in the other months. Except for initial height, seedling survival in lianas was not impacted by any of the abiotic and biotic variables tested. Our results suggest that under the current environment forest structure and diversity is changing, most noticeably lianas are increasing in abundance relative to trees.
Comparative transcriptome responses of leaf and root tissues to salt stress in wheat strains with different salinity tolerances
Authors: Li Jianfeng , Gao Xin , Chen Xunji , Fan Zheru , Zhang Yueqiang , Wang Zhong , Shi Jia , Wang Chunsheng , Zhang Hongzhi , Wang Lihong , Zhao Qi
Published: February 2023

Background: Salinity stress is a major adverse environmental factor that can limit crop yield and restrict normal land use. The selection of salt-tolerant strains and elucidation of the underlying mechanisms by plant breeding scientists are urgently needed to increase agricultural production in arid and semi-arid regions.

Results: In this study, we selected the salt-tolerant wheat (Triticum aestivum) strain ST9644 as a model to study differences in expression patterns between salt-tolerant and salt-sensitive strains. High-throughput RNA sequencing resulted in more than 359.10 Gb of clean data from 54 samples, with an average of 6.65 Gb per sample. Compared to the IWGSC reference annotation, we identified 50,096 new genes, 32,923 of which have functional annotations. Comparisons of abundances between salt-tolerant and salt-sensitive strains revealed 3,755, 5,504, and 4,344 genes that were differentially expressed at 0, 6, and 24 h, respectively, in root tissue under salt stress. KEGG pathway analysis of these genes showed that they were enriched for phenylpropanoid biosynthesis (ko00940), cysteine and methionine metabolism (ko00270), and glutathione metabolism (ko00480). We also applied weighted gene co-expression network analysis (WGCNA) analysis to determine the time course of root tissue response to salt stress and found that the acute response lasts >6 h and ends before 12 h. We also identified key alternative splicing factors showing different splicing patterns in salt-sensitive and salt-tolerant strains; however, only few of them were differentially expressed in the two groups.

Conclusion: Our results offer a better understanding of wheat salt tolerance and improve wheat breeding.
Engineered antibody cytokine chimera synergizes with DNA-launched nanoparticle vaccines to potentiate melanoma suppression in vivo
Authors: Tursi Nicholas J. , Xu Ziyang , Helble Michaela , Walker Susanne , Liaw Kevin , Chokkalingam Neethu , Kannan Toshitha , Wu Yuanhan , Tello-Ruiz Edgar , Park Daniel H. , Zhu Xizhou , Wise Megan C. , Smith Trevor R. F. , Majumdar Sonali , Kossenkov Andrew , Kulp Daniel W. , Weiner David B.
Published: February 2023

Cancer immunotherapy has demonstrated great promise with several checkpoint inhibitors being approved as the first-line therapy for some types of cancer, and new engineered cytokines such as Neo2/15 now being evaluated in many studies. In this work, we designed antibody-cytokine chimera (ACC) scaffolding cytokine mimetics on a full-length tumor-specific antibody. We characterized the pharmacokinetic (PK) and pharmacodynamic (PD) properties of first-generation ACC TA99-Neo2/15, which synergized with DLnano-vaccines to suppress in vivo melanoma proliferation and induced significant systemic cytokine activation. A novel second-generation ACC TA99-HL2-KOA1, with retained IL-2Rβ/γ binding and attenuated but preserved IL-2Rα binding, induced lower systemic cytokine activation with non-inferior protection in murine tumor studies. Transcriptomic analyses demonstrated an upregulation of Type I interferon responsive genes, particularly ISG15, in dendritic cells, macrophages and monocytes following TA99-HL2-KOA1 treatment. Characterization of additional ACCs in combination with cancer vaccines will likely be an important area of research for treating melanoma and other types of cancer.
Alpha fetoprotein promotes polarization of macrophages towards M2-like phenotype and inhibits macrophages to phagocytize hepatoma cells
Authors: Zhang Minni , Liu Kun , Zhang Qiuyue , Xu Junnv , Liu Jinchen , Lin Haifeng , Lin Bo , Zhu Mingyue , Li Mengsen
Published: February 2023

Alpha-fetoprotein(AFP) is a cancer biomarker for the diagnosis of hepatocellular carcinoma(HCC); however, its role in macrophage polarization and phagocytosis remains unclear. In the present study, we explored the correlation between AFP regulation of macrophage function and the possible regulatory mechanisms. Human mononuclear leukemia cells (THP-1) and monocytes from healthy donors were used to analyze the effect of AFP on the macrophages’ phenotype and phagocytosis. THP-1 cells and healthy human donor-derived monocytes were polarized into M0 macrophages induced by phorbol ester (PMA), and M0 macrophages were polarized into M1 macrophages induced by lipopolysaccharide(LPS) and interferon-γ(IFN-γ). Interleukin-4(IL-4) and interleukin-13(IL-13) were used to induce M0 macrophage polarization into M2 macrophages. Tumor-derived AFP(tAFP) stimulated M0 macrophage polarization into M2 macrophages and inhibited M1 macrophages to phagocytize HCC cells. The role of AFP in promoting macrophage polarization into M2 macrophages and inhibiting the M1 macrophages to phagocytize HCC cells may be involved in activating the PI3K/Akt signaling pathway. AFP could also enhanced the migration ability of macrophages and inhibited the apoptosis of HCC cells when co-cultured with M1-like macrophages. AFP is a pivotal cytokine that inhibits macrophages to phagocytize HCC cells.
Case report: Fecal microbiota transplantation in refractory ankylosing spondylitis
Authors: Wang Lei , Wei Zhimin , Pan Fei , Song Chuan , Peng Lihua , Yang Yunsheng , Huang Feng
Published: February 2023

Ankylosing spondylitis (AS) is the prototype of a group of systemic inflammatory diseases referred to as spondyloarthritis. Comorbid inflammatory bowel disease and changed gut microbiota in AS have attracted attention to the influence of gut–joint axis and encouraged treating AS by targeting gut microbiota. Here we first reported a patient with refractory AS and comorbid ulcerative colitis (UC) who underwent three fecal microbiota transplantations (FMTs). Inadequate response to conventional treatments including tumor necrosis factor inhibitors impelled FMT as alternative therapy. Notable improvements in AS and UC accompanied with changed fecal microbiota were recorded at 1 week post-FMT1. Further recovery was found after the other two FMTs, and a roughly stable status was maintained in the follow-up period. More studies are needed to validate the effectiveness of FMT in AS and its mechanisms.
The adenosinergic machinery in cancer: In-tandem insights from basic mechanisms to therapy
Authors: Kang Chifei , Liu Luyu , Wu Chengyu , Li Lingyun , Jia Xiao , Xie Wendi , Chen Siyu , Wu Xinying , Zheng Huaxiao , Liu Jingxin , Li Rongsong , Zeng Bin
Published: February 2023

Extracellular adenosine (eADO) signaling has emerged as an increasingly important regulator of immune responses, including tumor immunity. eADO is mainly produced from extracellular ATP (eATP) hydrolysis. eATP is rapidly accumulated in the extracellular space following cell death or cellular stress triggered by hypoxia, nutrient starvation, or inflammation. eATP plays a pro-inflammatory role by binding and activating the P2 purinergic receptors (P2X and P2Y), while eADO has been reported in many studies to mediate immunosuppression by activating the P1 purinergic receptors (A1, A2A, A2B, and A3) in diverse immune cells. Consequently, the hydrolysis of eATP to eADO alters the immunosurveillance in the tumor microenvironment (TME) not only by reducing eATP levels but also by enhancing adenosine receptor signaling. The effects of both P1 and P2 purinergic receptors are not restricted to immune cells. Here we review the most up-to-date understanding of the tumor adenosinergic system in all cell types, including immune cells, tumor cells, and stromal cells in TME. The potential novel directions of future adenosinergic therapies in immuno-oncology will be discussed.
Canine peripheral blood TCRαβ T cell atlas: Identification of diverse subsets including CD8A+ MAIT-like cells by combined single-cell transcriptome and V(D)J repertoire analysis
Authors: Eschke Maria , Moore Peter F. , Chang Haiyang , Alber Gottfried , Keller Stefan M.
Published: February 2023

The dog is valued as a companion animal and increasingly recognized as a model for human disorders. Given the importance of T cells in health and disease, comprehensive knowledge of canine T cells can contribute to our understanding of pathogenesis mechanisms and inform the development of new treatment strategies. However, the diversity of canine T cells is still poorly understood mainly due to the lack of species-reactive antibodies for use in flow cytometry. The aim of this study was to generate a detailed atlas of peripheral blood TCRαβ+ T cells of healthy dogs using single-cell RNA-sequencing (scRNAseq) combined with immune repertoire sequencing. A total of 22 TCRαβ+ T cell clusters were identified, which were classified into three major groups: CD4-dominant (11 clusters), CD8A-dominant (8 clusters), and CD4/CD8A-mixed (3 clusters). Based on differential gene expression, distinct differentiation states (naïve, effector, memory, exhausted) and lineages (e.g. CD4 T helper and regulatory T cells) could be distinguished. Importantly, several T cell populations were identified, which have not been described in dogs before. Of particular note, our data provide first evidence for the existence of canine mucosa-associated invariant T cell (MAIT)-like cells, representing one of three newly identified FCER1G+ innate-like CD8A+ T cell populations in the peripheral blood of healthy dogs. In conclusion, using scRNAseq combined with immune repertoire sequencing we were able to resolve canine TCRαβ+ T cell populations at unprecedented resolution. The peripheral blood TCRαβ+ T cell atlas of healthy dogs generated here represents an important reference data set for future studies and is of relevance for identifying new targets for T cell-specific therapies.
MAIT cells and the microbiome
Authors: Jabeen Maisha F. , Hinks Timothy S. C.
Published: February 2023

Mucosal associated invariant T (MAIT) cells are innate-like T lymphocytes, strikingly enriched at mucosal surfaces and characterized by a semi-invariant αβ T cell receptor (TCR) recognizing microbial derived intermediates of riboflavin synthesis presented by the MHC-Ib molecule MR1. At barrier sites MAIT cells occupy a prime position for interaction with commensal microorganisms, comprising the microbiota. The microbiota is a rich source of riboflavin derived antigens required in early life to promote intra-thymic MAIT cell development and sustain a life-long population of tissue resident cells. A symbiotic relationship is thought to be maintained in health whereby microbes promote maturation and homeostasis, and in turn MAIT cells can engage a TCR-dependent “tissue repair” program in the presence of commensal organisms conducive to sustaining barrier function and integrity of the microbial community. MAIT cell activation can be induced in a MR1-TCR dependent manner or through MR1-TCR independent mechanisms via pro-inflammatory cytokines interleukin (IL)-12/-15/-18 and type I interferon. MAIT cells provide immunity against bacterial, fungal and viral pathogens. However, MAIT cells may have deleterious effects through insufficient or exacerbated effector activity and have been implicated in autoimmune, inflammatory and allergic conditions in which microbial dysbiosis is a shared feature. In this review we summarize the current knowledge on the role of the microbiota in the development and maintenance of circulating and tissue resident MAIT cells. We also explore how microbial dysbiosis, alongside changes in intestinal permeability and imbalance between pro- and anti-inflammatory components of the immune response are together involved in the potential pathogenicity of MAIT cells. Whilst there have been significant improvements in our understanding of how the microbiota shapes MAIT cell function, human data are relatively lacking, and it remains unknown if MAIT cells can conversely influence the composition of the microbiota. We speculate whether, in a human population, differences in microbiomes might account for the heterogeneity observed in MAIT cell frequency across mucosal sites or between individuals, and response to therapies targeting T cells. Moreover, we speculate whether manipulation of the microbiota, or harnessing MAIT cell ligands within the gut or disease-specific sites could offer novel therapeutic strategies.
Artificial intelligence for fish behavior recognition may unlock fishing gear selectivity
Authors: Abangan Alexa Sugpatan , Kopp Dorothée , Faillettaz Robin
Published: February 2023

Through the advancement of observation systems, our vision has far extended its reach into the world of fishes, and how they interact with fishing gears—breaking through physical boundaries and visually adapting to challenging conditions in marine environments. As marine sciences step into the era of artificial intelligence (AI), deep learning models now provide tools for researchers to process a large amount of imagery data (i.e., image sequence, video) on fish behavior in a more time-efficient and cost-effective manner. The latest AI models to detect fish and categorize species are now reaching human-like accuracy. Nevertheless, robust tools to track fish movements in situ are under development and primarily focused on tropical species. Data to accurately interpret fish interactions with fishing gears is still lacking, especially for temperate fishes. At the same time, this is an essential step for selectivity studies to advance and integrate AI methods in assessing the effectiveness of modified gears. We here conduct a bibliometric analysis to review the recent advances and applications of AI in automated tools for fish tracking, classification, and behavior recognition, highlighting how they may ultimately help improve gear selectivity. We further show how transforming external stimuli that influence fish behavior, such as sensory cues and gears as background, into interpretable features that models learn to distinguish remains challenging. By presenting the recent advances in AI on fish behavior applied to fishing gear improvements (e.g., Long Short-Term Memory (LSTM), Generative Adversarial Network (GAN), coupled networks), we discuss the advances, potential and limits of AI to help meet the demands of fishing policies and sustainable goals, as scientists and developers continue to collaborate in building the database needed to train deep learning models.
Impact of satellite and regional in-situ profile data assimilation on a high-resolution ocean prediction system in the Northwest Pacific
Authors: Chang Inseong , Kim Young Ho , Jin Hyunkeun , Park Young-Gyu , Pak Gyundo , Chang You-Soon
Published: February 2023

The impacts of observation data sets on the high-resolution (1/24°) Northwest Pacific prediction system were investigated with the model sensitivity tests. We compared the model experiments assimilating the different combinations of the observation data sets, such as the sea surface height derived from satellite altimetry, sea surface temperature, and in-situ profiles, based on the Ensemble Optimal Interpolation. Pseudo-profiles constructed by the method of Cooper and Haines (1996, CH96) were assimilated into the model to assimilate sea surface height data. CH96 applied a conservation principle to derive pseudo-profiles by rearranging preexisting profiles. The comparison of the model experiments suggests that each observation data set enhances the model performance. Especially, the assimilation of the sea surface height reduces the model error by more than 9.81% and 6.44%, respectively, in terms of the root-mean-square error of the ocean temperature and salinity in the subsurface layer. It is interesting that the assimilation of the in-situ temperature profiles in the Korean marginal seas contributes to improving the reproducibility of the subsurface temperature and salinity in the East/Japan Sea (EJS) as well as Kuroshio-Kuroshio Extension (K-KE) regions. The improvement in the K-KE region seems to be related to the reproducibility of the Kuroshio axis. As the water mass in the EJS flows into the Pacific Ocean through the Tsugaru Strait, it affects the front of the Sanriku confluence, and it seems to eventually control the Oyashio Current and Kuroshio axis. In conclusion, this study evaluated the contribution of each observation component to ocean analysis in the KOOS-OPEM and confirmed the role of the existing observation networks. This study also suggests that greater attention should be paid to the role of regional ocean observation networks to improve the forecast skill of the ocean prediction system not only in the region but also in the open ocean, such as the Pacific Ocean.
Ocean turbulent boundary-layer influence on ice crystal behaviour beneath fast ice in an Antarctic ice shelf water plume: The “dirty ice”
Authors: Stevens Craig , Robinson Natalie , O’Connor Gabby , Grant Brett
Published: February 2023

The oceanic connection between ice shelf cavities and sea ice influences sea ice development and persistence. One unique feature in regions near ice shelves is the potential for sea ice growth due to crystal accretion on its underside. Here we present observations of ocean boundary-layer processes and ice crystal behaviour in an Ice Shelf Water outflow region from the Ross/McMurdo Ice Shelves. From a fast ice field camp during the Spring of 2015, we captured the kinematics of free-floating relatively large (in some cases 10s of mm in scale) ice crystals that were advecting and then settling upwards in a depositional layer on the sea ice underside (SIPL, sub-ice platelet layer). Simultaneously, we measured the background oceanic temperature, salinity, currents and turbulence structure. At the camp location the total water depth was 536 m, with the uppermost 50 m of the water column being in-situ super-cooled. Tidal flow speeds had an amplitude of around 0.1 m s-1 with dissipation rates in the under-ice boundary layer measured to be up to ε=10-6 W kg-1. Acoustic sampling (200 kHz) identified backscatter from large, individually identifiable suspended crystals associated with crystal sizes larger than normally described as frazil. Measurement of crystals in the SIPL found dimensions of the range 5-200 mm with an average of 93-101 mm depending on the year. The existence and settlement of crystals has implications for understanding SIPL evolution, the structure of sea ice, as well as the fate of Ice Shelf Water.
Estimating the shrimp farm’s production and their future growth prediction by remote sensing: Case study Gulf of California
Authors: González-Rivas David Alejandro , Tapia-Silva Felipe Omar
Published: February 2023

Shrimp farms are within the main aquaculture activities and In the last 30 years, shrimp farms have expanded along the Gulf of California. Because the shrimp farm’s production is related to the pond area and the extended location of shrimp farms, we employed a multi-disciplinary approach to study the process of annual shrimp farm expansion, in addition to predicting shrimp production in the short term. Our study hypothesizes that semi-intensive shrimp farm production is dependent on the pond area which can be accurately quantified by using remote sensing image classification combined with the historical production data of shrimp aquaculture. We could calculate the long-term expansion of the total pond area and forecast the total annual shrimp production in the short-term. Our results highlight the development over the last 28 years. The total surface area of the shrimp ponds grew by more than 1100%. The linear regression model between the shrimp farms area, calculated using remote sensing, and statistical data on shrimp production, was strongly positive and significant (r2 = 0.874, p =2.209e-11). Likewise, the linear regression model for the total pond area as a function of time resulted strong positive and statistically significant (r2 = 0.936, p =2.917e-15). We demonstrated that the shrimp production could be assessed based on the total pond area by year, obtained by remote sensing. We estimated the past long-term shrimp farm expansion in the study zone using remote sensing data. This methodology is valuable for monitoring food security, aquaculture management decisions, and coastal ecology.
Plasma hormone levels in the green turtle Chelonia mydas reared under captivity as a tool to predict mating and oviposition
Authors: Rubin Olga , Soffer Osher , Levy Yaniv , Aizen Joseph
Published: February 2023

Circulating estradiol (E2), testosterone (T) and progesterone (P4) concentrations, and blood chemistry were monitored in the female green turtle Chelonia mydas over continuous seasons at the Israel sea turtle breeding facility. The tested factors were analyzed with regard to the female`s nesting activity in the subsequent nesting season: Future nesters (FN) and Non-nesters (NN). Our analysis showed significant changes in all three sex steroids, E2, T, P4, and in 13 blood biochemical parameters between the two females` groups. All females presented consistent E2 profiles from year to year, with a single elevation in September in FN females. P4 concentrations in nesting females were high in April (mating) and higher towards the beginning of June due to oviposition, females that presented concentrations above 1ng/ml had successful oviposition (8 females: 1 female in 2018, 5 in 2019 and 2 in 2020). T profiles were high at the onset of vitellogenesis towards November and again high during April. We were able to predict which females would undergo oviposition with a specific profile seen only in FN females - elevated P4 concentrations from February to June and the elevation of metabolites electrolytes and Gamma-Glutamyl Transferase (GGT) concentrations toward November. This will facilitate selectively choice mating pairs to ensure that the Mediterranean population genetic variability is maintained. Clutches per female were between 2 and 6, with 25 in total. Females laid an average of 91 ± 7 eggs (range 39-139 eggs) per nest with emergence rate of ~10% (0-58%). Overall, the same trend in circulating steroid concentrations was revealed over the years in the females reaching oviposition only when a certain threshold was achieved. In this study all the factors mentioned above can indicate an upcoming oviposition at least 6 months prior to nesting as seen in the PCA analysis. This information can contribute to the success of green sea turtle breeding programs in captivity and will hopefully help the Israeli Rescue Center predict and prepare for nesting activities in the years ahead.
Numerical study of the water-sediment regulation scheme (WSRS) impact on suspended sediment transport in the Yellow River Estuary
Authors: Jia Wenfei , Yi Yujun
Published: February 2023

Introduction

The transport of suspended sediment plays an important role in regulating erosion-accretion in estuaries. The Yellow River, the second longest river in China, which has a large amount of sediment and contributes sediment to the Yellow River Estuary (YRE) every year. The water and sediment discharge patterns in the lower reaches of the Yellow River have experienced significant changes over recent decades. In particular, the water-sediment regulation scheme (WSRS) of the Xiaolangdi Reservoir transports large amounts of water and sediment to the YRE within a very short time, causing dramatic changes in the spatiotemporal estuarine sediment dynamics.

Methods

In this study, we presented a coupled numerical model based on FVCOM-SWAVE-SED that considered the highly dynamic sediment variations in the YRE. The sediment distribution and erosion-accretion patterns in the YRE during the WSRS in 2013 were analyzed by the high-resolution model.

Results

The sediment entering the YRE spread with freshwater, forming a high sediment concentration zone near the river mouth, where most of the sediments were deposited. The sediment dispersal distance was limited by the tidal shear frontal (TSF), and the southeast outspread length of the sediment was slightly larger than the northwest spread. Outside of the YRE, the areas with high flow currents exhibited high erosion. We examined the effects of the main external driving forces (such as waves, tides, and runoff) on the sediment distribution and showed that runoff, tides, and waves were the key factors affecting the sediment distribution of the YRE.

Results

This study shows that WSRS effectively changes the sediment distribution and erosion condition in the YRE and provides a data for researches on changes in estuarine ecosystems.
Seakeeping criteria of a moored and articulated multibody floating platform in head seas
Authors: Jiang Changqing , el Moctar Ould , Zhang Guiyong
Published: February 2023

Within the Space@Sea project, a multi-use floating concept was proposed by following the analogy of standardization to enlarge a floating platform using a multitude of smaller structures. An operability analysis must be performed to identify its seakeeping criteria and how the criteria limit its functionality. A two-step strategy is proposed to calculate the responses of the target floating concept in head waves, where nonlinearities of the mooring lines and mechanical joints are taken into account. The weakly nonlinear time-domain procedure relies on a diffraction-radiation model in the frequency domain. The motions of floating bodies are solved in the time domain, in which nonlinear Froude-Krylov and hydrostatic forces are estimated under instantaneous incident wave surface. Multibody interactions are resolved under consideration of catenary mooring lines and hinged joints. Wave-induced motions and loads are expressed in terms of transfer function for determining the limiting criteria, including the translational and rotational motions velocities and accelerations; relative motions, velocities and accelerations between module floaters; mooring tensions; as well as hinge forces. Assessments are carried out for various sea conditions against the prescribed values, for the chosen criteria, to address safety issues due to sever platform responses. Different operational requirements for trained workers and untrained passengers of motions and accelerations are taken into consideration. Results show that rotational motions have a significant influence on the platform’s seakeeping performance. Nevertheless, the root mean square (RMS) value of vertical acceleration dominates the comfort of persons onboard, defining the final limiting criterion of the entire platform.
Differentiating methicillin resistant and susceptible Staphylococcus aureus from ocular infections using photoacoustic labeling
Authors: Edgar Robert H. , Samson Anie-Pier , Kowalski Regis P. , Kellum John A. , Hempel John , Viator John A. , Jhanji Vishal
Published: February 2023

Introduction

Antibiotic resistance in bacterial species constitutes a growing problem in the clinical management of infections. Not only does it limit therapeutic options, but application of ineffective antibiotics allows resistant species to progress prior to prescribing more effective treatment to patients. Methicillin resistance in Staphylococcus aureus is a major problem in clinical infections as it is the most common hospital acquired infection.

Methods

We developed a photoacoustic flow cytometer using engineered bacteriophage as probes for rapid determination of methicillin resistance in Staphylococcus aureus with thirteen clinical samples obtained from keratitis patients. This method irradiates cells under flow with 532 nm laser light and selectively generates acoustic waves in labeled bacterial cells, thus enabling detection and enumeration of them. Staphylococcus aureus isolates were classified from culture isolation as either methicillin resistant or susceptible using cefoxitin disk diffusion testing. The photoacoustic method enumerates bacterial cells before and after treatment with antibiotics. Decreasing counts of bacteria after treatment indicate susceptible strains. We quantified the bacterial cells in the treated and untreated samples.

Results

Using k-means clustering on the data, we achieved 100% concordance with the classification of Staphylococcus aureus resistance using culture.

Discussion

Photoacoustics can be used to differentiate methicillin resistant and susceptible strains of bacteria from ocular infections. This method may be generalized to other bacterial species using appropriate bacteriophages and testing for resistance using other antibiotics.
External validation of a convolutional neural network for the automatic segmentation of intraprostatic tumor lesions on 68Ga-PSMA PET images
Authors: Ghezzo Samuele , Mongardi Sofia , Bezzi Carolina , Samanes Gajate Ana Maria , Preza Erik , Gotuzzo Irene , Baldassi Francesco , Jonghi-Lavarini Lorenzo , Neri Ilaria , Russo Tommaso , Brembilla Giorgio , De Cobelli Francesco , Scifo Paola , Mapelli Paola , Picchio Maria
Published: February 2023

Introduction

State of the art artificial intelligence (AI) models have the potential to become a “one-stop shop” to improve diagnosis and prognosis in several oncological settings. The external validation of AI models on independent cohorts is essential to evaluate their generalization ability, hence their potential utility in clinical practice. In this study we tested on a large, separate cohort a recently proposed state-of-the-art convolutional neural network for the automatic segmentation of intraprostatic cancer lesions on PSMA PET images.

Methods

Eighty-five biopsy proven prostate cancer patients who underwent 68Ga PSMA PET for staging purposes were enrolled in this study. Images were acquired with either fully hybrid PET/MRI (N = 46) or PET/CT (N = 39); all participants showed at least one intraprostatic pathological finding on PET images that was independently segmented by two Nuclear Medicine physicians. The trained model was available at https://gitlab.com/dejankostyszyn/prostate-gtv-segmentation and data processing has been done in agreement with the reference work.

Results

When compared to the manual contouring, the AI model yielded a median dice score = 0.74, therefore showing a moderately good performance. Results were robust to the modality used to acquire images (PET/CT or PET/MRI) and to the ground truth labels (no significant difference between the model’s performance when compared to reader 1 or reader 2 manual contouring).

Discussion

In conclusion, this AI model could be used to automatically segment intraprostatic cancer lesions for research purposes, as instance to define the volume of interest for radiomics or deep learning analysis. However, more robust performance is needed for the generation of AI-based decision support technologies to be proposed in clinical practice.
Changing liver utilization and discard rates in clinical transplantation in the ex-vivo machine preservation era
Authors: Azizieh Yara , Westhaver Lauren P. , Badrudin David , Boudreau Jeanette E. , Gala-Lopez Boris L.
Published: February 2023

Liver transplantation is a well-established treatment for many with end-stage liver disease. Unfortunately, the increasing organ demand has surpassed the donor supply, and approximately 30% of patients die while waiting for a suitable liver. Clinicians are often forced to consider livers of inferior quality to increase organ donation rates, but ultimately, many of those organs end up being discarded. Extensive testing in experimental animals and humans has shown that ex-vivo machine preservation allows for a more objective characterization of the graft outside the body, with particular benefit for suboptimal organs. This review focuses on the history of the implementation of ex-vivo liver machine preservation and how its enactment may modify our current concept of organ acceptability. We provide a brief overview of the major drivers of organ discard (age, ischemia time, steatosis, etc.) and how this technology may ultimately revert such a trend. We also discuss future directions for this technology, including the identification of new markers of injury and repair and the opportunity for other ex-vivo regenerative therapies. Finally, we discuss the value of this technology, considering current and future donor characteristics in the North American population that may result in a significant organ discard.
A workflow for viewing biomedical computational fluid dynamics results and corresponding data within virtual and augmented reality environments
Authors: Venn John , Larkee Christopher E. , Garcia Guilherme J. M. , Rayz Vitaliy L. , LaDisa John F.
Published: February 2023

Researchers conducting computational fluid dynamics (CFD) modeling can spend weeks obtaining imaging data, determining boundary conditions, running simulations and post-processing files. However, results are typically viewed on a 2D display and often at one point in time thus reducing the dynamic and inherently three-dimensional data to a static image. Results from different pathologic states or cases are rarely compared in real-time, and supplementary data are seldom included. Therefore, only a fraction of CFD results are typically studied in detail, and associations between mechanical stimuli and biological response may be overlooked. Virtual and augmented reality facilitate stereoscopic viewing that may foster extraction of more information from CFD results by taking advantage of improved depth cues, as well as custom content development and interactivity, all within an immersive approach. Our objective was to develop a straightforward, semi-automated workflow for enhanced viewing of CFD results and associated data in an immersive virtual environment (IVE). The workflow supports common CFD software and has been successfully completed by novice users in about an hour, demonstrating its ease of use. Moreover, its utility is demonstrated across clinical research areas and IVE platforms spanning a range of cost and development considerations. We are optimistic that this advancement, which decreases and simplifies the steps to facilitate more widespread use of immersive CFD viewing, will foster more efficient collaboration between engineers and clinicians. Initial clinical feedback is presented, and instructional videos, manuals, templates and sample data are provided online to facilitate adoption by the community.
Rickettsia association with two Macrolophus (Heteroptera: Miridae) species: A comparative study of phylogenies and within-host localization patterns
Authors: Dally Maria , Izraeli Yehuda , Belausov Eduard , Mozes-Daube Netta , Coll Moshe , Zchori-Fein Einat
Published: February 2023

Many arthropods host bacterial symbionts, some of which are known to influence host nutrition and diet breadth. Omnivorous bugs of the genus Macrolophus (Heteroptera: Miridae) are mainly predatory, but may also feed on plants. The species M. pygmaeus and M. melanotoma (=M. caliginosus) are key natural enemies of various economically important agricultural pests, and are known to harbor two Rickettsia species, R. bellii and R. limoniae. To test for possible involvement of symbiotic bacteria in the nutritional ecology of these biocontrol agents, the abundance, phylogeny, and distribution patterns of the two Rickettsia species in M. pygmaeus and M. melanotoma were studied. Both of the Rickettsia species were found in 100 and 84% of all tested individuals of M. pygmaeus and M. melanotoma, respectively. Phylogenetic analysis showed that a co-evolutionary process between Macrolophus species and their Rickettsia is infrequent. Localization of R. bellii and R. limoniae has been detected in both female and male of M. pygmaeus and M. melanotoma. FISH analysis of female gonads revealed the presence of both Rickettsia species in the germarium of both bug species. Each of the two Rickettsia species displayed a unique distribution pattern along the digestive system of the bugs, mostly occupying separate epithelial cells, unknown caeca-like organs, the Malpighian tubules and the salivary glands. This pattern differed between the two Macrolophus species: in M. pygmaeus, R. limoniae was distributed more broadly along the host digestive system and R. bellii was located primarily in the foregut and midgut. In contrast, in M. melanotoma, R. bellii was more broadly distributed along the digestive system than the clustered R. limoniae. Taken together, these results suggest that Rickettsia may have a role in the nutritional ecology of their plant-and prey-consuming hosts.
Crop rotations increased soil ecosystem multifunctionality by improving keystone taxa and soil properties in potatoes
Authors: Li Qing-mei , Zhang Dai , Zhang Ji-zong , Zhou Zhi-jun , Pan Yang , Yang Zhi-hui , Zhu Jie-hua , Liu Yu-hua , Zhang Li-feng
Published: February 2023

Continuous cropping of the same crop leads to soil degradation and a decline in crop production, and these impacts could be mitigated through rotation cropping. Although crop rotation enhances soil fertility, microbial community diversity, and potato yield, its effects on the soil ecosystem multifunctionality (EMF) remain unclear. In the present research, we comparatively examined the effects of potato continuous cropping (PP) and rotation cropping [potato–oat rotation (PO) and potato–forage maize rotation (PFM)] on the soil EMF as well as the roles of keystone taxa, microbes abundance, and chemical properties in EMF improvement. It was demonstrated that soil EMF is increased in rotation cropping (PO and PFM) than PP. Soil pH was higher in rotation cropping (PO and PFM) than in PP, while total phosphorus (TP) and available phosphorus (AP) were significantly decreased than that in PP. Rotation cropping (PO and PFM) markedly changed the bacterial and fungal community compositions, and improved the potential plant-beneficial fungi, e.g., Schizothecium and Chaetomium, while reducing the abundances of the potentially phytopathogenic fungi, e.g., Alternaria, Fusarium, Verticillium dahiae, Gibberella, Plectosphaerella, Colletotrichum, Phoma, and Lectera in comparison with PP. Also, co-occurrence patterns for bacteria and fungi were impacted by crop rotation, and keystone taxa, e.g., Nitrospira.1, Lysinibacillus, Microlunatus.1, Sphingomonas.3, Bryobacter.1, Micromonospora, and Schizothecium, were enriched in PO and PFM than PP. The structural equation model (SEM) further demonstrated that cropping systems increased soil ecosystem multifunctionality through regulating SOM and keystone taxa (Schizothecium1), and keystone taxa were mediated by soil pH. This study suggested that rotation cropping might contribute to the improvement of soil ecosystem multifunctionality as well as the development of disease-suppressive soils in comparison with potato continuous cropping.
Mitophagy in ototoxicity
Authors: Han Hezhou , Hu Sainan , Hu Yue , Liu Dongliang , Zhou Junbo , Liu Xiaofang , Ma Xiulan , Dong Yaodong
Published: February 2023

Mitochondrial dysfunction is associated with ototoxicity, which is caused by external factors. Mitophagy plays a key role in maintaining mitochondrial homeostasis and function and is regulated by a series of key mitophagy regulatory proteins and signaling pathways. The results of ototoxicity models indicate the importance of this process in the etiology of ototoxicity. A number of recent investigations of the control of cell fate by mitophagy have enhanced our understanding of the mechanisms by which mitophagy regulates ototoxicity and other hearing-related diseases, providing opportunities for targeting mitochondria to treat ototoxicity.
Clinical utility of paced finger tapping assessment in idiopathic normal pressure hydrocephalus
Authors: Shimizu Yoko , Tanikawa Motoki , Horiba Mitsuya , Sahashi Kento , Kawashima Shoji , Kandori Akihiko , Yamanaka Tomoyasu , Nishikawa Yusuke , Matsukawa Noriyuki , Ueki Yoshino , Mase Mitsuhito
Published: February 2023

Background

The Finger Tapping (F-T) test is useful for assessing motor function of the upper limbs in patients with idiopathic normal pressure hydrocephalus (iNPH). However, quantitative evaluation of F-T for iNPH has not yet been established. The purpose of this study was to investigate the usefulness of the quantitative F-T test and optimal measurement conditions as a motor evaluation and screening test for iNPH.

Methods

Sixteen age-matched healthy controls (mean age 73 ± 5 years; 7/16 male) and fifteen participants with a diagnosis of definitive iNPH (mean age 76 ± 5 years; 8/15 male) completed the study (mean ± standard deviation). F-T performance of the index finger and thumb was quantified using a magnetic sensing device. The performance of repetitive F-T by participants was recorded in both not timing-regulated and timing-regulated conditions. The mean value of the maximum amplitude of F-T was defined as M-Amplitude, and the mean value of the maximum velocity of closure of F-T was defined as cl-Velocity.

Results

Finger Tapping in the iNPH group, with or without timing control, showed a decrease in M-Amplitude and cl-Velocity compared to the control group. We found the only paced F-T with 2.0 Hz auditory stimuli was found to improve both M-Amplitude and cl-Velocity after shunt surgery.

Conclusion

The quantitative assessment of F-T with auditory stimuli at the rate of 2.0 Hz may be a useful and potentially supplemental screening method for motor assessment in patients with iNPH.
Altered glutamate–glutamine and amide proton transfer-weighted values in the hippocampus of patients with amnestic mild cognitive impairment: A novel combined imaging diagnostic marker
Authors: Chen Xin , Gong Tao , Chen Tong , Xu Changyuan , Li Yuchao , Song Qingxu , Lin Liangjie , Oeltzschner Georg , Edden Richard A. E. , Xia Zhangyong , Wang Guangbin
Published: February 2023

Background and purpose

Early diagnosis of amnestic mild cognitive impairment (aMCI) and timely management to delay the onset of Alzheimer's disease (AD) would benefit patients. Pathological metabolic changes of excitatory/inhibitory neurotransmitters and abnormal protein deposition in the hippocampus of aMCI may provide a new clue to imaging diagnosis. However, the diagnostic performance using these hippocampal metabolite measurements is still unclear. We aimed to quantify right hippocampal glutamate–glutamine (Glx) and gamma-aminobutyric acid (GABA) levels as well as protein-based amide proton transfer-weighted (APTw) signals of patients with aMCI and investigate the diagnostic performance of these metabolites.

Methods

In this cross-sectional study, 20 patients with aMCI and 20 age- and gender-matched healthy controls (HCs) underwent MEGA Point Resolved Spectroscopy (MEGA-PRESS) and APTw MR imaging at 3 T. GABA+, Glx, and APTw signals were measured in the right hippocampus. The GABA+ levels, Glx levels, Glx/GABA+ ratios, and APTw values were compared between the HCs and aMCI groups using the Mann–Whitney U test. Binary logistic regression and receiver operating characteristic (ROC) curve analyses were used to evaluate MEGA-PRESS and APTw parameters' diagnostic performance.

Results

Compared with HCs, patients with aMCI had significantly lower Glx levels in the right hippocampus (7.02 ± 1.41 i.u. vs. 5.81 ± 1.33 i.u., P = 0.018). No significant changes in the GABA+ levels were observed in patients with aMCI (HCs vs. aMCI: 2.54 ± 0.28 i.u. vs. 2.47 ± 0.36 i.u., P = 0.620). In addition, Glx/GABA+ ratios between the two groups (HCs vs. aMCI: 2.79 ± 0.60 vs. 2.37 ± 0.55, P = 0.035) were significantly different. Compared with HCs, patients with aMCI showed higher APTw values in the right hippocampus (0.99 ± 0.26% vs. 1.26% ± 0.28, P = 0.006). The ROC curve analysis showed that Glx, GABA+, Glx/GABA+, and APTw values had an area under the curve (AUC) of 0.72, 0.55, 0.70, and 0.75, respectively, for diagnosing aMCI. In the ROC curve analysis, the AUC of the combination of the parameters increased to 0.88, which is much higher than that observed in the univariate analysis (P < 0.05).

Conclusion

The combination of right hippocampal Glx levels and APTw values improved the diagnostic performance for aMCI, indicating it as a promising combined imaging diagnostic marker. Our study provided a potential imaging diagnostic strategy of aMCI, which may promote early detection of aMCI and facilitate timely intervention to delay the pathological progress toward AD.
Locus coeruleus and the defensive activation theory of rapid eye movement sleep: A mechanistic perspective
Authors: Knopper Rasmus West , Hansen Brian
Published: February 2023

The defensive activation theory (DAT) was recently proposed to explain the biological function of dreaming. Briefly, DAT states that dreams are primarily visual to prevent plastic take-over of an otherwise inactive visual cortex during sleep. Evidence to support the DAT revolve around the interplay between dream activity (REM%) and cortical plasticity found in evolutionary history, primate studies, and coinciding decline in human cortical plasticity and REM% with age. As the DAT may prove difficult to test experimentally, we investigate whether further support for the DAT can be found in the literature. Plasticity and REM sleep are closely linked to functions of the Locus Coeruleus (LC). We therefore review existing knowledge about the LC covering LC stability with age, and the role of the LC in the plasticity of the visual cortex. Recent studies show the LC to be more stable than previously believed and therefore, the LC likely supports the REM% and plasticity in the same manner throughout life. Based on this finding, we review the effect of aging on REM% and visual cortex plasticity. Here, we find that recent, weighty studies are not in complete agreement with the data originally provided as support for DAT. Results from these studies, however, are not in themselves irreconcilable with the DAT. Our findings therefore do not disprove the DAT. Importantly, we show that the LC is involved in all mechanisms central to the DAT. The LC may therefore provide an experimental window to further explore and test the DAT.