Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluation of a commercial loop-mediated isothermal amplification assay, 3MTM Molecular Detection Assay 2 – Campylobacter, for the detection of Campylobacter from poultry matrices

ABSTRACT 1. The objective of this study was to evaluate performance of a commercial loop-mediated isothermal amplification (LAMP) method as an alternative method for the detection of Campylobacter spp. in primary production samples, poultry rinses and raw poultry products, as compared to the US Department of Agriculture Food Inspection Service Microbiology Laboratory Guide Book PCR reference method, MLG 41A. 2. The Campylobacter spp. LAMP was used in conjunction with a ready-to-use enrichment broth that does not require microaerophilic incubation. After enrichment, boot swabs from poultry farms, carcase rinses and raw poultry products were tested by the LAMP method and the MLG 41A PCR method. 3. The ready-to-use enrichment broth enabled the growth of Campylobacter spp. within 22 to 28 hours under aerobic incubation conditions. The LAMP method enabled Campylobacter detection in the enriched samples of various poultry matrices and had equivalent sensitivity and specificity to the MLG 41A PCR method. 4. No significant difference (95% confidence interval) was found between the alternative and the MLG 41A PCR method, as determined by probability of detection analysis, except for neutralising buffered peptone water post-chill rinsates. For the post-chill neutralising buffered peptone water rinsates, the LAMP method had significantly higher confirmed portions.
Fate of alachlor and atrazine in a riparian zone field site

A field site was established and instrumented in Amana, Iowa to investigate the fate and transport of the pesticides alachlor and atrazine in the unsaturated zone adjacent to a drainage lake. The pesticides were applied to a barren plot, a plot planted with corn, and a plot planted with deep-rooted poplar trees (Populus spp.) to study the characteristic behaviors of a typical agricultural environment (corn plot) and a novel pollutant interception technique (poplar plot) in comparison to unmanaged land (barren plot). A mass balance model was developed and solved for the pesticides on each of the three plots. While the majority of alachlor and atrazine adsorbed to the soil and eventually degraded or accumulated in the unsaturated zone, portions of the pesticides remained in the aqueous phase and subsequently were transported in the surface runoff and to the water table [. ]
Explicit and implicit measurement of nonsuicidal self-injury in the prediction of concurrent and prospective self-injury.

OBJECTIVE The relationship between explicit nonsuicidal self-injury (NSSI) behavior and implicit identification with NSSI is important to understand considering the under-reported nature of NSSI and the subsequent elevated risk of more severe NSSI. It was expected that implicit assessment of NSSI at baseline would be associated with past-year NSSI frequency assessed at baseline and that it would more strongly associate with NSSI frequency than self-reported future likelihood of NSSI at a 6-month follow-up. METHOD Data were collected from 420 young adults (mean age = 19; 83% women, 87% White) with recent NSSI at baseline, and 324 were assessed at 6-month follow-up. Participants completed self-report measures and the Self-Injury Implicit Association Task (SI-IAT) at each time point. RESULTS Baseline implicit NSSI scores significantly predicted NSSI frequency at baseline but not at 6-month follow-up. However, explicit ratings were strongly and significantly associated with future NSSI frequency. CONCLUSIONS These findings suggest that although implicit identification with oneself and NSSI is important to understand, there are limitations regarding the possible utility of the SI-IAT in predicting future NSSI engagement and further research is needed to fully understand why NSSI continues to be such a strong predictor of future NSSI behavior, and suicidal ideation and behavior.
Origin of the Characteristic Electron Energy Losses in Aluminum

The characteristic electron energy loss spectrum of aluminum has been measured by analyzing the energy distribution of 760-, 1000-, 1520-, and 2020-ev electrons scattered by an evaporated specimen through 90'. Twelve loss peaks were observed, made up of combinations of elementary 10.3- and 15.3-ev losses. The former, the low-lying loss, is identified with the lowered plasma loss proposed by Ritchie, and the latter with the plasma loss proposed by Bohm and Pines and previously observed by many other workers. In measurements made with very thin evaporated targets, it was found that the low-lying loss changed considerably in position, as well as in intensity relative to the 15.3-ev loss. These changes, which are interpreted in terms of Ritchie s theory, definitely indicate that the low-lying loss is inQuenced by the surface layers of the specimen. As targets of high surface and volume purity could be prepared, it is concluded that results obtained by the present reQection technique, when examining loss behavior affected by surface phenomena, are superior to measurements of the characteristic loss spectrum of electrons transmitted through thin 61ms. SUMMARY OF PREVIOUS %'ORE HE 6rst systematic measurements of characteristic electron energy losses were carried out by Rudberg' who analyzed the energy distribution of 50— 400 ev electrons scattered from the surfaces of a number of metals. In each energy distribution he found peaks which occurred at fixed energy displacements from the peak of elastically scattered electrons, irrespective of the primary bombarding energy or the scattering angle. These peaks therefore corresponded to electrons which had lost definite amounts of energy in the material. Rudberg and Slater' proposed that the energy losses were due to excitation of conduction electrons to higher allowed energy levels, and calculated the form of the characteristic loss spectrum of copper, in fair agreement with Rudberg's results. Ruthemann' was the first to extend the measurements to the energy analysis of electrons transmitted through thin films of various materials. Since then, nearly all of the published work has been concerned with the latter type of measurement, and in this paper the two techniques will be referred to as reQection and transmission experiments, respectively. A large number of workers4 " has investigated the * Work supported by the Research Grants Committee of the
Healthcare professionals' views of a new second-level nursing associate role: a qualitative study exploring early implementation in an acute setting.

AIM The study aimed to establish the views of a range of stakeholders about their experiences of the newly implemented nursing associate role in England and its potential to contribute to patient care. BACKGROUND Second-level nursing roles are increasingly used internationally within the healthcare workforce. In response to registered nurse workforce deficits, a new nursing associate role has been introduced in England to augment care provided by registered nurses and enable career progression of support workers. DESIGN Qualitative descriptive design. METHODS Semi-structured interviews and a focus group were conducted with a range of healthcare professionals in a large inner-city acute secondary care healthcare organisation in England. Interviews were guided by the Consolidated Framework for Implementation Research and analysed using Framework Analysis. The study was reported according to COREQ guidelines. RESULTS 33 healthcare professionals were interviewed - directors of nursing, ward managers, nursing associates and multidisciplinary team members. Participants perceived the role was broadly adaptable to different healthcare settings and provided a positive professional development mechanism for healthcare support workers. Managers felt training commitments made implementing the role complex and costly. Participants argued the role had limitations, particularly with intravenous medicine management. Implementation was impeded by rapid pace and consequent lack of clear communication and planning. CONCLUSIONS The nursing associate role was perceived as an inclusive pathway into nursing but with limitations when working with high-acuity patients. Further evaluation is needed to investigate how the role has embedded over time. RELEVANCE TO CLINICAL PRACTICE The role should be seen as both a stepping-stone into registered nursing positions and valued as part of the nursing workforce. Consideration must be given to how the role can be safely implemented in different settings. Findings have relevance to healthcare leaders internationally, who continue to work in a climate of economic pressure and staffing shortages.
Associations Between Brain Gray Matter Volumes and Adipose Tissue Metabolism in Healthy Adults

Gray matter (GM) volume in different brain loci has been shown to vary in obesity and diabetes, and elevated fasting plasma nonesterified fatty acid (NEFA) levels have been suggested as one potential mechanism. The hypothesis presented in this study is that brown adipose tissue (BAT) activity may correlate with GM volume in areas negatively associated with obesity and diabetes.
On the influence of electron-electron correlation on the current-voltage characteristics of a short molecular wire

It is demonstrated that detailed information can be gained on the inelastic mechanism of correlated electron transfer through a molecular wire if one analyses the current behavior in dependence on the strength of the external electric field. The approach is complementary to the derivation of the current-voltage characteristics, and the given analysis of the current-length effect observed at a fixed electric field-strength allows to specify the influence of the blocking transmission factor on incoherent electron transfer. It is found that at small external electric field-strength the current through a regular molecular wire exhibits an Ohmic behaviour while at strong fields electron-electron correlations lead to an exponential decrease of the current.
Beyond the Warburg Effect: Oxidative and Glycolytic Phenotypes Coexist within the Metabolic Heterogeneity of Glioblastoma

Glioblastoma (GBM) is the most aggressive primary brain tumor, with a median survival at diagnosis of 16–20 months. Metabolism represents a new attractive therapeutic target; however, due to high intratumoral heterogeneity, the application of metabolic drugs in GBM is challenging. We characterized the basal bioenergetic metabolism and antiproliferative potential of metformin (MF), dichloroacetate (DCA), sodium oxamate (SOD) and diazo-5-oxo-L-norleucine (DON) in three distinct glioma stem cells (GSCs) (GBM18, GBM27, GBM38), as well as U87MG. GBM27, a highly oxidative cell line, was the most resistant to all treatments, except DON. GBM18 and GBM38, Warburg-like GSCs, were sensitive to MF and DCA, respectively. Resistance to DON was not correlated with basal metabolic phenotypes. In combinatory experiments, radiomimetic bleomycin exhibited therapeutically relevant synergistic effects with MF, DCA and DON in GBM27 and DON in all other cell lines. MF and DCA shifted the metabolism of treated cells towards glycolysis or oxidation, respectively. DON consistently decreased total ATP production. Our study highlights the need for a better characterization of GBM from a metabolic perspective. Metabolic therapy should focus on both glycolytic and oxidative subpopulations of GSCs.
Phage-Encoded Endolysins

Due to the global emergence of antibiotic resistance, there has been an increase in research surrounding endolysins as an alternative therapeutic. Endolysins are phage-encoded enzymes, utilized by mature phage virions to hydrolyze the cell wall from within. There is significant evidence that proves the ability of endolysins to degrade the peptidoglycan externally without the assistance of phage. Thus, their incorporation in therapeutic strategies has opened new options for therapeutic application against bacterial infections in the human and veterinary sectors, as well as within the agricultural and biotechnology sectors. While endolysins show promising results within the laboratory, it is important to document their resistance, safety, and immunogenicity for in-vivo application. This review aims to provide new insights into the synergy between endolysins and antibiotics, as well as the formulation of endolysins. Thus, it provides crucial information for clinical trials involving endolysins.
Mercator: a pipeline for multi-method, unsupervised visualization and distance generation

Abstract Summary Unsupervised machine learning provides tools for researchers to uncover latent patterns in large-scale data, based on calculated distances between observations. Methods to visualize high-dimensional data based on these distances can elucidate subtypes and interactions within multi-dimensional and high-throughput data. However, researchers can select from a vast number of distance metrics and visualizations, each with their own strengths and weaknesses. The Mercator R package facilitates selection of a biologically meaningful distance from 10 metrics, together appropriate for binary, categorical and continuous data, and visualization with 5 standard and high-dimensional graphics tools. Mercator provides a user-friendly pipeline for informaticians or biologists to perform unsupervised analyses, from exploratory pattern recognition to production of publication-quality graphics. Availabilityand implementation Mercator is freely available at the Comprehensive R Archive Network (https://cran.r-project.org/web/packages/Mercator/index.html).
High-Content Analysis-Based Sensitivity Prediction and Novel Therapeutics Screening for c-Met-Addicted Glioblastoma

Simple Summary Real-time ex vivo drug testing tailors individual therapeutics based on predicted drug responses. Most technologies to date rely on conventional drug screening that provides low confidence data. Here, we present high-content analysis-based drug testing of glioblastoma patients to identify the right glioblastoma patients for a given drug. This generates multi-parameter biomarker and phenotype readouts providing a better reliability of the assay. Additionally, we showed a high-content drug repurposing screen and defined a new c-Met-inhibiting function of the CDK4/6 inhibitor Abemaciclib. Large-scale high throughput screening results demonstrate that Abemaciclib sensitivity in glioblastoma patients is highly correlated with the c-Met inhibitors sensitivity, further supporting the accuracy of the platform and important new clinical implications regarding multiple functions of Abemaciclib. Abstract (1) Background: Recent advances in precision oncology research rely on indicating specific genetic alterations associated with treatment sensitivity. Developing ex vivo systems to identify cancer patients who will respond to a specific drug remains important. (2) Methods: cells from 12 patients with glioblastoma were isolated, cultured, and subjected to high-content screening. Multi-parameter analyses assessed the c-Met level, cell viability, apoptosis, cell motility, and migration. A drug repurposing screen and large-scale drug sensitivity screening data across 59 cancer cell lines and patient-derived cells were obtained from 125 glioblastoma samples. (3) Results: High-content analysis of patient-derived cells provided robust and accurate drug responses to c-Met-targeted agents. Only the cells of one glioblastoma patient (PDC6) showed elevated c-Met level and high susceptibility to the c-Met inhibitors. Multi-parameter image analysis also reflected a decreased c-Met expression and reduced cell growth and motility by a c-Met-targeting antibody. In addition, a drug repurposing screen identified Abemaciclib as a distinct CDK4/6 inhibitor with a potent c-Met-inhibitory function. Consistent with this, we present large-scale drug sensitivity screening data showing that the Abemaciclib response correlates with the response to c-Met inhibitors. (4) Conclusions: Our study provides a new insight into high-content screening platforms supporting drug sensitivity prediction and novel therapeutics screening.
Recurrent implantation failure – an overview of current research

Abstract Background Recurrent implantation failure (RIF) can be defined as a failure to achieve a clinical pregnancy after transfer of at least four embryos of good quality in a minimum of three fresh or frozen cycles in women under the age of 40. RIF is often a complex problem with a wide variety of etiologies and mechanisms as well as treatment options. Summary Anatomical conditions of the uterus, thrombophilia, genetic abnormalities, or immunological factors are only a few examples which could be responsible for RIF. The recommendations for women with RIF vary depending on the source of their problem. There is not just one treatment option, but many depending on the etiology and the severity of the problem. Key message However, it would help to establish a set of standardized examinations and tests to use, in order to do a preliminary evaluation on each patient, which would then hopefully direct the approach of treatment for each individual couple.
Scalable fabrication of renal spheroids and nephron-like tubules by bioprinting and controlled self-assembly of epithelial cells

Scalable fabrication concepts of 3D kidney tissue models are required to enable their application in pharmaceutical high-throughput screenings. Yet the reconstruction of complex tissue structures remains technologically challenging. We present a novel concept reducing the fabrication demands, by using controlled cellular self-assembly to achieve higher tissue complexities from significantly simplified construct designs. We used drop-on-demand bioprinting to fabricate locally confined patterns of renal epithelial cells embedded in a hydrogel matrix. These patterns provide defined local cell densities (cell count variance <11%) with high viability (92 ± 2%). Based on these patterns, controlled self-assembly leads to the formation of renal spheroids and nephron-like tubules with a predefined size and spatial localization. With this, we fabricated scalable arrays of hollow epithelial spheroids. The spheroid sizes correlated with the initial cell count per unit and could be stepwise adjusted, ranging from Ø = 84, 104, 120–131 µm in diameter (size variance <9%). Furthermore, we fabricated scalable line-shaped patterns, which self-assembled to hollow cellular tubules (Ø = 105 ± 22 µm). These showed a continuous lumen with prescribed orientation, lined by an epithelial monolayer with tight junctions. Additionally, upregulated expression of kidney-specific functional genes compared to 2D cell monolayers indicated increased tissue functionality, as revealed by mRNA sequencing. Furthermore, our concept enabled the fabrication of hybrid tubules, which consisted of arranged subsections of different cell types, combining murine and human epithelial cells. Finally, we integrated the self-assembled fabrication into a microfluidic chip and achieved fluidic access to the lumen at the terminal sites of the tubules. With this, we realized flow conditions with a wall shear stress of 0.05 ± 0.02 dyne cm−2 driven by hydrostatic pressure for scalable dynamic culture towards a nephron-on-chip model.
Food allergy as an asthma comorbidity in children and adolescents: a practical approach through a real-world study.

INTRODUCTION Several studies have shown interactions between food allergy (FA) and asthma, but the influence of FA in asthma traits has been scarcely studied. METHODS A real-world retrospective observational study was conducted among patients between 3 and 18 years old referred to our Asthma Clinic from November 2014 to November 2017. Data were obtained from daily clinical practice. Only patients properly diagnosed with asthma and FA were included. RESULTS 815 patients were included: 483 asthmatics and 332 non-asthmatics and 180 FA and 635 no FA. Food allergy was statistically more prevalent among asthma patients (p = 0.014). In a high pollen exposure area, Madrid, among subjects with asthma (121 FA, 362 no-FA), sensitization to lipid transfer protein (LTP) (p = 0.016, OR: 3.064, RR: 2.512) and pollen (p = 0.016, OR: 3.064, RR: 2.512) are risk factors to have a concomitant FA diagnosis, whereas sensitization to profilin is not. Peripheral blood eosinophils were higher in subjects with asthma and FA (≥450 eos/µL) than in asthmatics without FA (≤300 eos/µL) (p = 0.031). Blood eosinophilia, using a cut-off >300 eos/µL, was only present in the FA group. Therefore, this trait should be considered when phenotyping a patient as eosinophilic asthma. Sex had an impact on several variables: height, weight, BMI, blood eosinophils count, sensitization profile, and early-onset asthma. CONCLUSIONS Asthma and FA are closely related and the presence of FA should be investigated in every asthma patient. This study shows an association between asthma with concomitant FA and sensitization to pollen and LTP, blood eosinophilia, and growth alterations. Differences between boys and girls were also described, so a sex-specific approach is recommended.
Research paperSalmonella contamination of broiler chicken carcasses at critical steps of the slaughter process and in the environment of two slaughter plants: Prevalence, genetic profiles and association with the final carcass status.

Salmonella is a foodborne pathogen commonly associated with poultry products. The aims of this work were to 1) estimate the impact of critical steps of the slaughter process on Salmonella detection from broiler chicken carcasses in two commercial poultry slaughter plants in Quebec, Canada, 2) investigate the presence of the pathogen in the slaughter plant environment, 3) describe, using a high resolution melting (HRM) approach, the HRM Salmonella profiles and serotypes present on carcasses and in the slaughter plant environment and 4) evaluate if the HRM flock status after chilling could be predicted by the flock status at previous steps of the slaughter process, or by the status of previous flocks, or by the status of the processing environment, for a same HRM profile. Eight visits were conducted in each slaughter plant over a 6-month period. A total of 379 carcass rinsates from 79 flocks were collected at 5 critical steps of the slaughter process. Environmental samples were also collected from seven critical sites in each slaughter plant. The bleeding step was the most contaminated with >92% of positive carcasses. A decrease of the contamination along the slaughtering process was noted, with carcasses sampled after dry-air chilling showing ≤2.5% Salmonella prevalence. The most frequently isolated serotypes were S. Heidelberg, S. Kentucky and S. Schwarzengrund. The detection of the S. Heidelberg 1-1-1 HRM profile on carcasses after chilling was significantly associated with its detection at previous steps of the slaughter process and in previously slaughtered flocks during a same sampling day. Results highlight the importance of the chilling step in the control of Salmonella on broiler chicken carcasses and the need to further describe and compare the competitive advantage of Salmonella serotypes to survive processing. The current study also illustrates the usefulness of HRM typing in investigating Salmonella contamination along the slaughter process.