Miracle-dz/UniFAR-FTUs huggingface dataset:
A Novel Phage Infecting the Marine Photoheterotrophic Bacterium Citromicrobium bathyomarinum

This study isolated and characterized a new phage infecting the marine photoheterotrophic bacterium Citromicrobium bathyomarinum, which fills the gap in research on phages targeting this ecologically important species. The phage vB_CbaS-RXM (RXM) has a dsDNA genome with a length of 104,206 bp and G+C content of 61.64%. The taxonomic analysis found a close evolutionary relationship between RXM, Erythrobacter phage vB_EliS-L02, and Sphingobium phage Lacusarx, and we propose that RXM represents a new species of the Lacusarxvirus genus. A one-step growth curve revealed a burst size of 75 plaque-forming units (PFUs) per cell in a 3-hour infection cycle. The lysis profile of RXM showed an intraspecific lethal rate of 26.3% against 38 citromicrobial strains. RXM contains 15 auxiliary metabolic genes (AMGs) related to diverse cellular processes, such as putative metabolic innovation and hijacking of host nucleotide metabolism to enhance its biosynthetic capacity. An in-depth analysis showed that phage functional genes strongly rely on the host for translation, while the translation of unique phage genes with less host dependency may be complemented by phage tRNA. Overall, our study investigated the infection kinetics, genetic traits, taxonomy, and predicted roles of AMGs and tRNA genes of this new phage, which contributes to a better understanding of phage diversity and phage–bacterium interactions.
SVseg: Stacked Sparse Autoencoder-Based Patch Classification Modeling for Vertebrae Segmentation

Precise vertebrae segmentation is essential for the image-related analysis of spine pathologies such as vertebral compression fractures and other abnormalities, as well as for clinical diagnostic treatment and surgical planning. An automatic and objective system for vertebra segmentation is required, but its development is likely to run into difficulties such as low segmentation accuracy and the requirement of prior knowledge or human intervention. Recently, vertebral segmentation methods have focused on deep learning-based techniques. To mitigate the challenges involved, we propose deep learning primitives and stacked Sparse autoencoder-based patch classification modeling for Vertebrae segmentation (SVseg) from Computed Tomography (CT) images. After data preprocessing, we extract overlapping patches from CT images as input to train the model. The stacked sparse autoencoder learns high-level features from unlabeled image patches in an unsupervised way. Furthermore, we employ supervised learning to refine the feature representation to improve the discriminability of learned features. These high-level features are fed into a logistic regression classifier to fine-tune the model. A sigmoid classifier is added to the network to discriminate the vertebrae patches from non-vertebrae patches by selecting the class with the highest probabilities. We validated our proposed SVseg model on the publicly available MICCAI Computational Spine Imaging (CSI) dataset. After configuration optimization, our proposed SVseg model achieved impressive performance, with 87.39% in Dice Similarity Coefficient (DSC), 77.60% in Jaccard Similarity Coefficient (JSC), 91.53% in precision (PRE), and 90.88% in sensitivity (SEN). The experimental results demonstrated the method’s efficiency and significant potential for diagnosing and treating clinical spinal diseases.
Experience of Vancomycin Therapeutic Drug Monitoring in Two Multidisciplinary Hospitals in Latvia

Background and Objectives: Management of infectious diseases is a huge burden to every healthcare system worldwide. Antimicrobial resistance, including antibacterial resistance, is an increasing problem worldwide; therefore, more new antibiotics are necessary to be discovered. Meanwhile, “old” antibacterial agents are still administered to fight infectious diseases caused by resistant bacteria. One of these antibacterial agents is vancomycin, which is effective in treating serious systemic infections caused by gram-positive bacteria. Thus, it is necessary to perform vancomycin concentration measurements in plasma due to its narrow therapeutic index. Various approaches are implemented for more precise therapy, including therapeutic drug monitoring (TDM) of vancomycin and with a supervision of a clinical pharmacist. The purpose of the study was to investigate if the TDM practice is improved with a local vancomycin TDM protocol applied in a hospital. The results of TDM in two multidisciplinary hospitals, one with a local TDM protocol implemented and applied and the other with no local TDM protocol implemented and applied, were compared. Materials and Methods: A retrospective study was performed in two multidisciplinary hospitals in Latvia. The data were collected for a time period of 4 years (2016–2020) in a hospital without a local TDM protocol and for a time period of 2 years (2018–2020) in a hospital with a local TDM protocol, starting with a period of time when the vancomycin TDM protocol was developed. The data about the patients included in the study were analyzed based on gender, age, body weight, and renal function. Vancomycin therapy was analyzed based on dosing schemes (vancomycin dose and dosing interval), data about loading and maintenance doses, vancomycin concentration, and details about vancomycin concentration (sampling time and concentration level). Results: Differences between the hospitals were found in terms of the initiation of vancomycin administration and concentration sampling. In the hospital with a TDM protocol compared with the hospital without a TDM protocol, more accurate initiation was found, alongside adaption of therapy (97.22% vs. 18.95%, p < 0.001), better performance of administration of a loading dose (22.73% vs. 1.29%, p < 0.01), and reaching of target concentration (55.56% vs. 35.29%, p < 0.01). Concentration sampling in the correct timeframe before the vancomycin dose and vancomycin administration did not show statistically better results in either of the hospitals (4.60% vs. 6.29%, p = 0.786). Conclusions: Better results of adequate adjustments of vancomycin therapy were achieved in the hospital with a TDM protocol. In the long term, sustainable results and regular medical professionals’ training is necessary.
The misperception of the environment: A critical evaluation of the work of Tim Ingold and an alternative guide to the use of the senses in anthropological theory

This article presents a critical evaluation of the work of Tim Ingold from the standpoint of social and sensory anthropology. It acknowledges the novelty of the emphasis on enskillment, movement, process, and growth in Ingold's work. However, it is critical of his abstraction of the senses, which are rendered ‘interchangeable’, and of persons, who are reduced to generic individuals. Ingold's anthropology is shown to be pre-cultural and post-social at once, with the result that it fails to address the sociality of sensation and cultural mediation of perception. Ingold's doctrine of ‘direct perception’ is exposed as particularly problematic. In place of his emphasis on ‘the life of lines’, this article foregrounds the life of the senses, and in lieu of his diminution of the social, it acknowledges the politics of perception that inform most every perceptual act. The article concludes with a series of reflections on how to go about sensualizing anthropological theory and practicing sensory ethnography (i.e. the methodology of participant sensation).
Quality Comparison of Analog and Digital X-Ray Equipment and Materials in a Dental Clinic

Many dental clinics are swapping analog x-ray equipment for digital systems to obtain medical images in the search for improvements such as reduced costs and better care of the images and fast response. However it is necessary to analyze if the digital images have quality requirements in order to provide the diagnosis in a similar or superior way to the analog films. The objective of this paper is to analyze the quality of the digitized x-ray diagnostic images in relation to the structures represented. The research was conducted in a dental clinic that was changing the analog x-ray equipment for one digital. The results by means of statistical analysis demonstrated that the digital system has better spatial resolution and better contrast. As a suggestion of future research an analysis by dentists to see if on the day of the clinic, these theoretical advantages are confirmed in better diagnostics.
The Impacts of Prepared Plasma-Activated Medium (PAM) Combined with Doxorubicin on the Viability of MCF-7 Breast Cancer Cells: A New Cancer Treatment Strategy.

Background For many years, the chemotherapeutic agent doxorubicin (DOX) has been used to treat various cancers; however, DOX initiates several critical adverse effects. Many studies have reported that non-thermal atmospheric pressure plasma can provide novel, but challenging, treatment strategies for cancer patients. To date, tissues and cells have been treated with plasma-activated medium (PAM) as a practical therapy. Consequently, due to the harmful adverse effects of DOX, we were motivated to elucidate the impact of PAM in the presence of DOX on MCF-7 cell proliferation. Methods MTT assay, N-acetyl-L-cysteine (NAC) assay, and flow cytometry analysis were utilized in this research. Results The results demonstrated that 0.45 µM DOX combined with 3-min PAM significantly induced apoptosis (p< 0.01) through intracellular ROS generation in MCF-7 when compared with 0.45 µM DOX alone or 3-min PAM alone. In contrast, after treatment with 0.45 µM DOX plus 4-min PAM, cell necrosis was increased. Hence, DOX combined with 4-min PAM has cytotoxic effects with different mechanisms than 4-min PAM alone, in which the number of apoptotic cells increases. Conclusion Although further investigations are crucial, low doses of DOX plus 3-min PAM could be a promising strategy for cancer therapy. The findings from this research may offer advantageous and innovative clinical strategies for cancer therapy using PAM.
Experimental Investigation of Significance Parameters in Surface Grinding – Quality Evaluation

The resurgence of the high quality and precision parts by manufacturing industries has enabled the development of ultraprecision machine tools. Surface roughness and tolerances are the most critical quality measures of any mating mechanical parts produced. The quality evaluation requirement of manufactured parts is becoming the prime factor as it determines not only the esthetics values, but also the lifespan and function of its purpose. Grinding is one the most popular methods of machining hard materials which widely known as random point cutting. The main aim of this experimental work is to investigate the significant parameter(s) in surface grinding which affect the machined surface roughness. Two work materials, namely, mild steel and carbon steel have been investigated with two variables; feed rate and depth of cut for the response of surface roughness totaling eight experiments with three replications. Statistical approach using Design of Experiment (DOE) has been carried out in this investigation. The ANOVA results of the analysis have been based to determine the significance and correlation of the input and output parameters.
Overlaps and accumulations: The anatomy of cultural non-participation in Finland, 2007 to 2018

There is a fervent belief that culture is, among other desirable ideals, “good for you. ” This has been the baseline of the cultural policies in many countries. Through cultural policies, some forms of cultural participation over others are subvented through public funding, which makes it yet more important to ask which groups intentionally withdraw—or are left out—from which forms of it. We address the debate on cultural non-participation by scrutinizing nationally representative and longitudinal survey data from Finland, a Nordic welfare country with allegedly low social and cultural hierarchies, for years 2007 and 2018. We explore the changes in cultural non-participation by asking whether the main frequencies of cultural non-participation have changed between 2007 and 2018, what forms of different cultural non-participation patterns can be distinguished, and which socioeconomic factors best predict which form of cultural non-participation most in both years. Finally, we ask whether certain everyday forms of participation would compensate or complement non-existing cultural participation. We find three main cultural non-participation patterns: highbrow avoidance, mainstream avoidance, and nightlife avoidance. While the changes in non-participation look small from the macro level, their internal dynamics face a steep change between 2007 and 2018. Especially higher education becomes a continuously more significant factor for any kind of cultural activity. We also show that cultural participation is not compensated by everyday activities as often claimed in the literature, but that cultural and everyday non-participation overlap. Our results indicate that the alleged egalitarianism in Finland does not reach cultural participation: avoiding most forms of participation is more and more related to socio-economic differences reflecting social and cultural hierarchies.
GWAS to Identify Novel QTNs for WSCs Accumulation in Wheat Peduncle Under Different Water Regimes

Water-soluble carbohydrates (WSCs) play a vital role in water stress avoidance and buffering wheat grain yield. However, the genetic architecture of stem WSCs’ accumulation is partially understood, and few candidate genes are known. This study utilizes the compressed mixed linear model-based genome wide association study (GWAS) and heuristic post GWAS analyses to identify causative quantitative trait nucleotides (QTNs) and candidate genes for stem WSCs’ content at 15 days after anthesis under different water regimes (irrigated, rainfed, and drought). Glucose, fructose, sucrose, fructans, total non-structural carbohydrates (the sum of individual sugars), total WSCs (anthrone based) quantified in the peduncle of 301 bread wheat genotypes under multiple environments (E01-E08) pertaining different water regimes, and 14,571 SNPs from “35K Axiom Wheat Breeders” Array were used for analysis. As a result, 570 significant nucleotide trait associations were identified on all chromosomes except for 4D, of which 163 were considered stable. A total of 112 quantitative trait nucleotide regions (QNRs) were identified of which 47 were presumable novel. QNRs qWSC-3B.2 and qWSC-7A.2 were identified as the hotspots. Post GWAS integration of multiple data resources prioritized 208 putative candidate genes delimited into 64 QNRs, which can be critical in understanding the genetic architecture of stem WSCs accumulation in wheat under optimum and water-stressed environments. At least 19 stable QTNs were found associated with 24 prioritized candidate genes. Clusters of fructans metabolic genes reported in the QNRs qWSC-4A.2 and qWSC-7A.2. These genes can be utilized to bring an optimum combination of various fructans metabolic genes to improve the accumulation and remobilization of stem WSCs and water stress tolerance. These results will further strengthen wheat breeding programs targeting sustainable wheat production under limited water conditions.
EFFECTS OF SMOOTH, MEDIUM SMOOTH AND MEDIUM RECONSTRUCTION KERNELS ON IMAGE QUALITY IN THREE-PHASE CT OF LIVER

Reconstruction kernel is one of the parameters that affects the computed tomography (CT) image quality. This study aimed to evaluate the effects of applying three different reconstruction kernels on image quality in 3-phased CT of the liver. A total of 63 CT liver images including normal liver (n = 43) and liver lesion (n = 20) were retrospectively reviewed. Smooth (B20f), medium smooth (B30f) and medium (B40f) reconstruction kernels were employed in the image reconstruction process. Mean attenuation, image noise, and signal-to-noise ratio (SNR) values from each kernel reconstruction were quantified and compared among those kernels using One Way Analysis of Variance (ANOVA) statistical analysis. Significant changes in image noise and SNR were observed in the normal liver (p < 0.001, respectively) following the application of those reconstruction kernels. However, no significant changes in mean attenuation, image noise, and SNR were demonstrated in the liver lesion (p > 0.05). Application of smooth (B20f), medium smooth (B30f), and medium (B40f) kernel reconstructions would significantly affect the image noise and SNR in the normal liver of CT images instead of liver lesions. Hence, proper selection of reconstruction kernel is important in CT images reconstruction to improve precision in diagnostic CT interpretation.
ContentsNew Zealand College of Midwives Journal

A Corresponding author: hoyneng. wongsoon@aut.ac. nz B Auckland University of Technology, Auckland, Aotearoa New Zealand Background: Healthy eating is crucial for optimal development during all stages of life and most particularly during pregnancy. According to Stats NZ, Pasefika people make up 8.1% of the total Aotearoa New Zealand population. Information from the Ministry of Health suggests that Pasefika people have the highest level of food insecurity and the highest level of obesity. Women are more likely than men to be involved with food preparation; therefore, it is important to know to what extent women are aware of what healthy eating means for themselves and their families. Aim: This study aimed to explore an understanding of the levels of food literacy among representatives of three generations of women in five Samoan families; how each of the three generations ensured that their dietary intake contributed to their quality of health; and whether the extent offood literacy was influenced both within and between/across generations. Method: The study used a combined Delphi-Talanoa approach to interview 15 Samoan women about the levels of their understanding of food literacy. Findings: Midwives played an important role in helping pregnant Samoan women understand about healthy eating during pregnancy. Women shared with other female relatives what they had learned about healthy eating from their midwives. Learnings taken from midwives included the importance of choosing healthy foods, portion control and physical activity. Conclusion: All study participants who had received antenatal care in Aotearoa New Zealand mentioned the important role of midwives in increasing their understanding of healthy lifestyle choices. What the women learned from their midwives also informed their wider family or aiga.
Size–Abundance Relationships of Freshwater Macroinvertebrates in Two Contrasting Floodplain Channels of Rhone River

Body size is perhaps the most fundamental property of an organism and its relationship with abundance is one of the most studied relationships in ecology. Although numerous studies have examined these relationships in local communities, few have investigated how they vary at different temporal and spatial scales. We investigated the relationship between body size and abundance of local macroinvertebrate communities in two floodplain channels of the French upper Rhone River. The two channels differ in their vegetation coverage (high vs. low vegetation) and hydrological regimes. The shapes of the size–abundance relationship were similar between channels on a yearly basis but differed when compared between months. The variation in local size–abundance relationships between months was related to variation in the functional diversity across time. Our findings suggest that local size–abundance relationships are able to quantitatively describe temporal changes in community structure, showing the importance of relating diversity with ecosystem function in a more realistic context.
ANP32 Family as Diagnostic, Prognostic, and Therapeutic Biomarker Related to Immune Infiltrates in Hepatocellular Carcinoma

Hepatocellular carcinoma (HCC) is one of the most common tumors worldwide, with high incidence and mortality rate. There is an urgent need to identify effective diagnostic and prognostic biomarkers for HCC. Members of the acidic leucine-rich nucleophosphoprotein 32 (ANP32) family, which mainly includes ANP32A, ANP32B, and ANP32E, are abnormally expressed and have prognostic value in certain cancers. However, the diagnostic, prognostic, and therapeutic value of ANP32 family members in HCC has not yet been fully studied. In this study, we identified the diagnostic and prognostic value of ANP32 family members in HCC. Transcriptome data from public databases, such as the Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) databases, suggested that ANP32A, ANP32B, and ANP32E were upregulated in HCC tissues, and high expression of ANP32 family members was associated with advanced pathologic stage and histologic grade. Our immunohistochemistry and western blot results further verified the differential expression of ANP32 family members. ANP32A, ANP32B, and ANP32E had an outstanding diagnostic potential. Survival analysis of HCC patients in TCGA databases demonstrated that ANP32A, ANP32B, and ANP32E were associated with poor overall survival (OS) and disease-specific survival (DSS). Univariate and multivariate Cox analyses suggested the capability of ANP32B and ANP32E to independently predict the OS and DSS of HCC patients. Gene set enrichment analysis (GSEA) showed that ANP32 family members were associated with immune response, epidermal cell differentiation, and stem cell proliferation. Expression of ANP32 family members was associated with immune cell infiltration and immune status in the tumor microenvironment of HCC, and patients with high ANP32 family expression had poor sensitivity to immunotherapy. Finally, we identified potential chemotherapy drugs for HCC patients with high ANP32 family expression by CellMiner database. This study suggested the diagnostic, prognostic, and therapeutic roles of the ANP32 family in HCC patients, providing potential therapeutic targets for HCC.
EFFECTS OF LIGHT ILLUMINATION AND SUBCULTURE FREQUENCY ON BIOMASS PRODUCTION IN CELL SUSPENSION CULTURES OF Clinacanthus nutans

Clinacanthus nutans (Burm. f.) Lindau is a medicinal plant rich in polyphenols and possesses multiple pharmacological properties. It is widely used as a side treatment for cancer and to prevent oxidative stress-related diseases. The present study aims to investigate the effects of light illumination and subculture frequency on the growth and proliferation of cells in the suspension culture of C. nutans. Friable callus induced from leaf explants C. nutans were cultured in liquid Murashige & Skoog medium supplemented with 0.25 mg/L 2, 4-dichlorophenoxyacetic acid, and 0.25 mg/L 6-benzylaminopurine to initiate the cell suspension culture. The suspension cultures were incubated under different conditions (16 hr photoperiod and continuous darkness). Subcultures were conducted every two weeks for ten subculture cycles. Results revealed that higher cell biomass was obtained under the exposure of 16 hr photoperiod with the highest biomass production at the fifth subculture cycle (growth index of 11.8) exhibiting stable growth from the eighth to the tenth subculture cycle. The suspension cells showed stable growth rates up to the 10th subculture cycle producing small aggregates and single cells. The present study indicated that light illumination significantly impacts the growth of suspension cultures for C. nutans in the production of valuable secondary metabolites.