jimnoneill/paper-to-field-training huggingface dataset:
Transcriptomics: A Step behind the Comprehension of the Polygenic Influence on Oxidative Stress, Immune Deregulation, and Mitochondrial Dysfunction in Chronic Kidney Disease

Chronic kidney disease (CKD) is an increasing and global health problem with a great economic burden for healthcare system. Therefore to slow down the progression of this condition is a main objective in nephrology. It has been extensively reported that microinflammation, immune system deregulation, and oxidative stress contribute to CKD progression. Additionally, dialysis worsens this clinical condition because of the contact of blood with bioincompatible dialytic devices. Numerous studies have shown the close link between immune system impairment and CKD but most have been performed using classical biomolecular strategies. These methodologies are limited in their ability to discover new elements and enable measuring the simultaneous influence of multiple factors. The “omics” techniques could overcome these gaps. For example, transcriptomics has revealed that mitochondria and inflammasome have a role in pathogenesis of CKD and are pivotal elements in the cellular alterations leading to systemic complications. We believe that a larger employment of this technique, together with other “omics” methodologies, could help clinicians to obtain new pathogenetic insights, novel diagnostic biomarkers, and therapeutic targets. Finally, transcriptomics could allow clinicians to personalize therapeutic strategies according to individual genetic background (nutrigenomic and pharmacogenomic). In this review, we analyzed the available transcriptomic studies involving CKD patients.

Topic: Dialysis and Renal Disease Management
Subfield: Nephrology
Field: Medicine
Domain: Health Sciences
From blindsight to sight: Cognitive rehabilitation of visual field defects

Purpose: Traditionally, post-chiasmatic lesions were believed to result in complete and permanent visual loss in the topographically related areas of the visual field. However, a number of studies with monkeys, and later with humans, have demonstrated spared implicit visual functioning, referred to as 'blindsight'. The present study assessed whether training this phenomenon would induce an objective restoration of conscious vision in the blind field of hemianopic patients. Methods: For a period of 22 weeks nine patients with unilateral occipital damage participated in several forced-choice visual tasks known to elicit blindsight: pointing to visual targets, letter recognition, visual comparison between the two hemifields, target localization, and letter identification. Before and after rehabilitation, patients were submitted to a behavioral pre- and post-test, including visual detection and letter identification as well as to automated perimetry visual field testing (Humphrey Automated 24-2 Full Threshold). Results: An objective improvement was found in the behavioral tasks for all patients at the post-test stage as well as an objective enlargement of the contralesional visual field for all except one of the nine patients. An overall decrease is seen in the number of undetected points (out of 30) on automated perimetry visual field testing after rehabilitation (F (1, 16) = 22.57; p &lt; 0.001) for both eyes (Right Eye, RE: T = 0; z = 2.52; p &lt; 0.05; Left Eye, LE: T = 0, z = 2.37; p &lt; 0.05) regardless of lesion side. Conclusions: The results suggest that explicit (conscious) visual detection can be restored in the blind visual field by using implicit (unconscious) visual capacities. Results are discussed regarding visual field defect rehabilitation, blindsight, attention, and brain plasticity hypotheses.

Topic: Visual perception and processing mechanisms
Subfield: Cognitive Neuroscience
Field: Neuroscience
Domain: Life Sciences
Using the Uniform and Gaussian Distribution of Frequencies for the Analysis of Broadband Dielectric Relaxation Spectra

Dielectric spectroscopy is an important method for studying many materials using in electronic technology. This method allows study physical processes, which determine certain properties of materials, what is needed when developing new electronics components. In many cases experiments show that the spectrum of dielectric dispersion is broadened, because these dielectrics have polar complexes characterized by different relaxation times. To describe such spectra, in this work, we use the distribution of relaxing complexes not in time but in the frequency band, and we use not usual empirical but model description of broadband dielectric spectra.

Topic: Solid-state spectroscopy and crystallography
Subfield: Materials Chemistry
Field: Materials Science
Domain: Physical Sciences
Integrating Pathologic Stage and Perioperative Circulating Tumor Cell Variations: Early Relapse Prediction Model for Resectable Non–Small Cell Lung Cancer

PURPOSE The primary therapeutic objective for patients with resectable non–small cell lung cancer (NSCLC) is the prevention of disease relapse. This study aimed to examine the correlation between perioperative circulating tumor cell (CTC) variations and disease relapse. MATERIALS AND METHODS Ninety-nine patients with resectable NSCLC were enrolled and classified into cohort 0-1a and cohort 1b-4 on the basis of the presence of lymph node metastasis. CTC levels were measured, and their correlation with disease-free survival was analyzed. RESULTS In cohort 0-1a, patients with a CTC count difference between postoperative day 3 and postoperation of &lt;2.75, and a difference between postoperative day 3 and postoperation day 1 of &lt;–0.25, showed no disease relapse. In cohort 1b-4, patients with a CTC count difference between postoperative day 3 and postoperation ≥6.25 had the highest risk of relapse, with all patients experiencing relapse within 2 years. For those with a difference &lt;6.25, most relapses were identified within 2 years postoperation. CONCLUSION The proposed relapse prediction model effectively identified patients with no risk for disease relapse in cohort 0-1a and those with the highest risk for relapse in cohort 1b-4. These results may assist physicians in focusing on and prescribing adjuvant treatment for patients with a higher relapse risk.

Topic: Lung Cancer Diagnosis and Treatment
Subfield: Pulmonary and Respiratory Medicine
Field: Medicine
Domain: Health Sciences
Evaluating of the Synergistic Effect of three Essential Oils on the Virulence Factors (resistance gene) of Pseudomonas aeruginosa and Serratia fonticola Isolated from Wounds

Depending on the high resistance to antibiotics, five isolates of Pseudomonas aeruginosa and 7 isolates of Serratia fonticola were selected out of 150 bacterial isolates from burn wards in Baghdad hospitals, which were later identified by VITEK2. A susceptibility test was done by using 15 antibiotics. The results showed that all the selected isolates were resistant to antibiotics: AMP, CTX, CAZ, GEN, PIP, TIC and TMP especially, while they were sensitive to IPE. The essential oils of Aloysia citrodora (Family: Verbenaceae), Rosmarinus officinalis (Family: Lamiaceae) and Thymus vulgaris (Family: Lamiaceae) were extracted by the Clevenger. The synergistic effect of essential oils of these plants on bacterial growth were studied by determining the MIC of essential oils for P. aeruginosa and S. fonticola. The MIC concentration of P. aeruginosa was: 2500 ppm of A. citrodora, 2500 ppm of R. officinalis, 2500 ppm of T. vulgaris, whilst the synergistic effect of each two plants was:1250 ppm of A. citrodora with 2500 ppm of R. officinalis, 1250 ppm of A. citrodora with 312.5 ppm of T. vulgaris, 1250 ppm of R. officinalis with 156.25 ppm of T. vulgaris, whereas the synergistic effect of three plants was: 156.25 ppm of A. citrodora with 156.25 ppm of R. officinalis and 39.0625 ppm T. vulgaris. While the MIC concentration of S. fonticola was: 1250 ppm of A. citrodora, 5000 ppm of R. officinalis, 1250 ppm of T. vulgaris, whilst the synergistic effect of each two plants was: 1250 ppm of A. citrodora with 2500 ppm of R. officinalis, 1250 ppm of A. citrodora with 312.5 ppm of T. vulgaris, 1250 ppm of R. officinalis with 156.25 ppm of T. vulgaris, whereas the synergistic effect of three plants was: 312.5 ppm of A. citrodora with 312.5 ppm of R. officinalis and 78.125 ppm T. vulgaris. The results of bacterial gene expression showed that three isolates of P. aeruginosa had a mexB gene expression that ranged between 2.5 - 0.4 (concentration 1) and 2.8 to 0.6 (concentration 2). It increased in two isolates and decreased in one isolate. The melting point ranged between 90.91 - 91.280C compared with 89.89 to 90.330C for fbp gene. Whereas S. fonticola did not have blaKPc gene, instead it had blaTEM gene with the gene expression ranging between 2.4 - 0.1 (concentration 1) and 4.5 - 0.2 (concentration 2). The gene expression increased in two isolates and decreased in five isolates. The melting point ranged between 83.63 - 84.200C compared with 75.82 - 85.560C for gyrB gene.

Topic: Essential Oils and Antimicrobial Activity
Subfield: Food Science
Field: Agricultural and Biological Sciences
Domain: Life Sciences
Flow-cytometry-enhanced fine-needle aspiration biopsy of the spleen.

Flow-cytometry-enhanced fine-needle aspiration of the spleen is a safe and useful tool for the interventional radiologist. In our institution, it evolved as the result of effective teamwork between diagnostic radiologists and pathologists. Flow cytometry promises to be increasingly useful in the diagnosis and management of lymphoproliferative diseases.

Topic: Abdominal Trauma and Injuries
Subfield: Surgery
Field: Medicine
Domain: Health Sciences
Child language brokering in Swedish welfare institutions

Abstract This chapter investigates the asymmetries associated to child language brokering in Swedish welfare institutions. Group interviews with (a) people who have experiences of language brokering as children and (b) public service professionals who have used children as brokers in encounters with non-Swedish speaking service users are analyzed. Results show that both groups consider that resorting to child language brokering is wrong but at the same time they reproduce this social practice and see benefits in it. This ambiguity leads interviewees to lay responsibility on several levels: the parents who place unreasonable demands on their children; the public service professionals who allow children to take on responsibility in precarious situations, and society at large that may be accomplice to structural discrimination of non-Swedish speaking service users. The responsibilities identified by interviewees in their narratives are critically discussed in relation to the concept of “structural complicity” showing how power relations and social structures create situations where individuals act with complicity even when they do something that they consider to be a good solution for an imperative problem and for which they do not see any alternatives.

Topic: Migration, Refugees, and Integration
Subfield: Sociology and Political Science
Field: Social Sciences
Domain: Social Sciences
The Life Attitudes Schedule: A Scale to Assess Adolescent Life‐Enhancing and Life‐Threatening Behaviors

The purpose of this study was to develop a questionnaire to measure suicidal and other risk‐taking behaviors, the Life Attitudes Schedule (LAS), and to test a theoretical model that postulates a single domain of behaviors to which all life‐threatening and life‐enhancing behaviors belong. The LAS was developed and piloted on 1539 high school students and young adults. The schedule measures four different content categories: death related, health related, injury related, and self‐related. Each content category includes an equal number of items designed to assess actions, thoughts, and feelings. Consistent with the theoretical model, the LAS includes positive (life‐enhancing) and negative (life‐threatening) behaviors. In this paper we present psychometric information for the LAS. The results are interpreted as providing support for a broad, bipolar conceptualization of suicidal and other risk‐taking behavior that encompasses life‐threatening and life‐enhancing behaviors.

Topic: Suicide and Self-Harm Studies
Subfield: Clinical Psychology
Field: Psychology
Domain: Social Sciences
Exploring Parkinson’s disease: A question and answer-based approach

Parkinson’s disease (PD) is the second most common neurodegenerative disorder after Alzheimer’s disease, affecting 1%–2% people over the age of 65 years and up to 4% population over 85 years of age. Herein, we present four separate case-based scenarios commonly encountered in the neurology practice and provide the current evidence-based answers to commonly asked questions by patients, caregivers, and primary care physicians regarding the diagnosis and management of patients with PD, separating issues pertaining to early- versus late-onset PD, and management throughout various stages of disease. The discussion points within each case may apply across all cases.

Topic: Parkinson's Disease Mechanisms and Treatments
Subfield: Neurology
Field: Medicine
Domain: Health Sciences
Condoms On and Off: A Review of Prophylactic Barrier Use and Youth Sexual Well-Being

AMSTARs: Adolescent Contraception: Basics and Beyond highlights the fundamental aspects of contraception with an overview of contraceptive methods and epidemiology, provides up-to-date guidance on medical eligibility criteria, and reviews critical policy advances supporting contraceptive access.https://shop.aap.org/amstarsadolescent-contraception-basics-and-beyond-paperback/

Topic: Adolescent Sexual and Reproductive Health
Subfield: General Health Professions
Field: Health Professions
Domain: Health Sciences
A robust approach for analyzing and mapping hierarchical brain connectome towards laminar-specific neural networks

Abstract Probing neuronal activity and functional connectivity at cortical layer and sub-cortical nucleus level provides opportunities for mapping local and remote neural circuits and resting-state networks (RSN) critical for understanding cognition and behaviors. However, conventional resting-state fMRI (rs-fMRI) has been applied predominantly at relatively low spatial resolution and macroscopic level, unable to obtain laminar-specific information and neural circuits across the cortex at mesoscopic level. In addition, it is lack of sophisticated processing pipeline to deal with small laminar structures in rodent brains. To fill this gap, we conducted a high-resolution rs-fMRI study of mouse brain at ultra-high field and developed an fMRI preprocessing pipeline that features in random matrix theory-based principal component analysis to remove thermal noise, non-rigid image registration strategy to improve head motion estimation, one-time image voxel shift correction to minimize multi-interpolation-induced spatial blur, and improve subject-level alignment to facilitate group analysis. By applying this pipeline to the high-resolution mouse rs-fMRI with atlas-based connectivity analysis, we achieved high-quality hierarchical connectomes covering from large brain regions to cortical layers, and between white matter bundle fibers and cortices in mice. We demonstrate the hierarchical connectomes connecting to three representative brain regions: somatosensory areas, hippocampal regions, and lateral forebrain white matter bundles, showing previously undetected networks. The distinct laminar-specific networks evidence that the spontaneous neuronal activity is not uniform across the cortical layers in the resting brain, consistent with the layer-specific neuronal projection patterns that were observed in AAV viral tracer projections. Additionally, we also observed extended functional connections in areas with sparse viral tracer projections. The feasibility of achieving laminar-specific connectomes with distinct RSNs provides opportunities to study neural circuits and brain functions at multiple scales, though achieving high fidelity and specificity in mapping laminar-specific connectomes may require even higher spatial resolution.

Topic: Functional Brain Connectivity Studies
Subfield: Cognitive Neuroscience
Field: Neuroscience
Domain: Life Sciences
Effect of Humidity and Temperature on Composite Plates With Different Fiber Orientations

In this study, the effect of humidity and temperature on glass fiber reinforced epoxy composite plates with different fiber reinforcement angles and different widths were experimentally investigated. For this purpose, composite plates with fiber reinforcement angles of [0°]8 and [45°/-45°/0°/90°]s were prepared in 25 mm and 30 mm dimensions and kept in hot water at 40 °C, 60 °C and 80 °C for 15, 30 and 45 days. At the end of the duration, the moisture absorption rates and strengths of the specimens were obtained. The obtained data were compared among themselves and with that of dry specimens. In addition, the morphologies of the specimens were visualized with the help of Scanning Electron Microscope (SEM) and the effects of humidity and temperature on failure behavior were examined. It was determined that the strength of the [45°/-45°/0°/90°]s fiber orientations specimens was lower than the strength values obtained from the [0°]8 fiber orientations specimens. It has been determined that when the waiting time and temperature increase, the matrix/fiber structure of the specimens deteriorates and the strength values decrease accordingly.

Topic: Natural Fiber Reinforced Composites
Subfield: Polymers and Plastics
Field: Materials Science
Domain: Physical Sciences
Detection of Bartonella DNA in Cat Blood with Nested-PCR

Three different nested-PCR assays were evaluated in terms of their ability to detect Bartonella DNA in catblood samples. The primer pairs used were parts of the citrate synthase (gltA) gene, heat shock protein (htrA) gene and 16S-23S rRNA intergenic region (ITS) gene, respectively. Of the 29 culture-positive cats-blood samples, Bartonella DNA was detected in 20 (68.9%) by the gltA nested-PCR and htrA nested-PCR. The ITS nested- PCR detected Bartonella DNA in 26 of 29 (89.7%). In two of 29 specimens, none of the gene examined was detected. These results indicate that the nested-PCR is a useful tool for the detection of Bartonella DNA in cat-blood samples.

Topic: Bartonella species infections research
Subfield: Parasitology
Field: Immunology and Microbiology
Domain: Life Sciences
Food additive emulsifiers and cancer risk: results from the French prospective NutriNet-Santé cohort

Abstract Background Food additive emulsifiers are found in thousands of industrial foods and may exert deleterious effects on gut microbiota and carcinogenesis according to experimental studies. However, their associations with cancer risk has not been investigated yet. This study aimed to investigate these associations in a large population-based prospective cohort. Methods This study included 102,485 French adults from the NutriNet-Santé cohort (42.1y [14.5], 78.8% female, 2009-2021). Food additive emulsifier intakes were estimated using repeated 24h dietary records linked to brand-specific food composition databases on food additives. Associations with incident cancer risk were assessed using Multivariable Cox models. Results 3,511 incident cancer cases were diagnosed during follow-up (1,026 breast, 431 prostate, and 279 colorectal cancers). Intakes of sodium citrate (E331, HR = 1.12 [1.02-1.23], p-trend=0.009), xanthan gum (E415, HR = 1.11 [1.02-1.21], p-trend=0.02), and mono- and diglycerides of fatty acids (E471, HR = 1.17 [1.06-1.28], p-trend=0.001 and total: E471, E472a-b-c-e, HR = 1.11, [1.02-1.22], p-trend=0.02) were associated with increased overall cancer risk. Higher intakes of E331 (p-trend = 0.046), sodium stearoyl-2-lactylate (E481, p-trend=0.01), total lactylates (E481-482, p-trend=0.01), total celluloses (E460-468, p-trend=0.03), carob bean gum (E410, p-trend=0.01), and E471 (p-trend=0.006) were associated with increased overall breast cancer risk. Higher intakes of carrageenan (E407, p-trend=0.04), E415 (p-trend=0.02), and triphosphates (E451, p-trend=0.03) were associated with increased post-menopausal breast cancer risk. Conclusions These results are the first to investigate and report direct associations between cancer risk and exposures to seven individual and three groups of food additive emulsifiers. If replicated, they may have an important public health impact, considering the omnipresence of these additives in industrial foods globally. Key messages • This study is the first to precisely assess exposures to food additive emulsifiers in a population-based study. • Intakes of food additive emulsifiers were associated with increased risk of cancer.

Topic: Nutritional Studies and Diet
Subfield: Public Health, Environmental and Occupational Health
Field: Medicine
Domain: Health Sciences
Oryza sativa Linnaeus IRGC 114690

Plant Genetic Resource.<br>Taxonomy: Oryza sativa Linnaeus<br>Common name(s): Rice<br>Other names: YELICANG<br>Conserved by: International Rice Research Institute (IRRI), Philippines<br>Local sample unique identifier: IRGC 114690<br>Method of creation: Acquisition<br>Date: 1998-12-01<br>Other identifiers: n/a,1821776<br>Historical: No<br>MLS status: Art. 15 collection

Topic: Immune responses and vaccinations
Subfield: Immunology
Field: Immunology and Microbiology
Domain: Life Sciences
Efficient CO2 Electroreduction on Tin Modified Cuprous Oxide Synthesized via a One-Pot Microwave-Assisted Route

Bimetallic copper-tin catalysts are considered cost-effective and suitable for large-scale electrochemical conversion of CO2 to valuable products. In this work, a class of tin (Sn) modified cuprous oxide (Cu2O) is simply synthesized through a one-pot microwave-assisted solvothermal method and thoroughly characterized by various techniques. Sn is uniformly distributed on the Cu2O crystals showing a cube-within-cube structure, and CuSn alloy phase emerges at high Sn contents. The atomic ratio of Cu to Sn is found to be crucially important for the selectivity of the CO2 reduction reaction, and a ratio of 11.6 leads to the optimal selectivity for CO. This electrode shows a high current density of 47.2 mA cm−2 for CO formation at −1.0 V vs. the reversible hydrogen electrode and also displays good CO selectivity of 80–90% in a wide potential range. In particular, considerable CO selectivity of 72–81% is achieved at relatively low overpotentials from 240 mV to 340 mV. During the long-term tests, satisfactory stability is observed for the optimal electrode in terms of both electrode activity and CO selectivity. The relatively low price, the fast and scalable synthesis, and the encouraging performance of the proposed material implies its good potential to be implemented in large-scale CO2 electrolyzers.

Topic: CO2 Reduction Techniques and Catalysts
Subfield: Renewable Energy, Sustainability and the Environment
Field: Energy
Domain: Physical Sciences