Miracle-dz/UniFAR-FTUs huggingface dataset:
Modulation of miR-29a and miR-29b Expression and Their Target Genes Related to Inflammation and Renal Fibrosis by an Oral Nutritional Supplement with Probiotics in Malnourished Hemodialysis Patients

Malnutrition is prevalent in patients with chronic kidney disease (CKD), especially those on hemodialysis. Recently, our group described that a new oral nutritional supplement (ONS), specifically designed for malnourished (or at risk) hemodialysis patients with a “similar to the Mediterranean diet” pattern, improved caloric-protein intake, nutritional status and biomarkers of inflammation and oxidation. Our aim in this study was to evaluate whether the new ONS, associated with probiotics or not, may produce changes in miRNA’s expression and its target genes in malnourished hemodialysis patients, compared to individualized diet recommendations. We performed a randomized, multicenter, parallel-group trial in malnourished hemodialysis patients with three groups (1: control (C) individualized diet (n = 11); 2: oral nutritional supplement (ONS) + placebo (ONS-PL) (n = 10); and 3: ONS + probiotics (ONS-PR) (n = 10)); the trial was open regarding the intake of ONS or individualized diet recommendations but double-blinded for the intake of probiotics. MiRNAs and gene expression levels were analyzed by RT-qPCR at baseline and after 3 and 6 months. We observed that the expression of miR-29a and miR-29b increased significantly in patients with ONS-PR at 3 months in comparison with baseline, stabilizing at the sixth month. Moreover, we observed differences between studied groups, where miR-29b expression levels were elevated in patients receiving ONS-PR compared to the control group in the third month. Regarding the gene expression levels, we observed a decrease in the ONS-PR group compared to the control group in the third month for RUNX2 and TNFα. TGFB1 expression was decreased in the ONS-PR group compared to baseline in the third month. PTEN gene expression was significantly elevated in the ONS-PR group at 3 months in comparison with baseline. LEPTIN expression was significantly increased in the ONS-PL group at the 3-month intervention compared to baseline. The new oral nutritional supplement associated with probiotics increases the expression levels of miR-29a and miR-29b after 3 months of intervention, modifying the expression of target genes with anti-inflammatory and anti-fibrotic actions. This study highlights the potential benefit of this oral nutritional supplement, especially associated with probiotics, in malnourished patients with chronic renal disease on hemodialysis.
Effects of Extended Light/Dark Cycles on Solanaceae Plants

The absence of an externally-imposed 24 h light/dark cycle in closed plant production systems allows setting the light environmental parameters in unconventional ways. Innovative lighting modes for energy-saving, high-quality, and yield production are widely discussed. This study aimed to evaluate the effects of the light/dark cycles of 16/8 h (control) and 24/12 h, 48/24 h, 96/48 h, 120/60 h (unconventional cycles) based on the same total light amount, and continuous lighting (360/0 h) on plant performance of some Solanaceae species. Responses of eggplant (Solanum melongena L.), sweet pepper (Capsicum annuum L.), tobacco (Nicotiana tabacum L.), and tomato (Solanum lycopersicum L.) plants to extended light/dark cycles and continuous lighting were studied under controlled climate conditions. Plants with two true leaves were exposed to different light/dark cycles for 15 days. Light intensity was 250 µmol m−2 s−1 PPFD, provided by light-emitting diodes (LEDs). After the experiment, tomato, sweet pepper, and eggplant transplants were planted in a greenhouse and grown under identical conditions of natural photoperiod for the estimation of the after-effect of light treatments on fruit yield. Extended light/dark cycles of 24/12 h, 48/24 h, 96/48 h, 120/60 h, and 360/0 h affected growth, development, photosynthetic pigment content, anthocyanin and flavonoid content, and redox state of plants. Effects varied with plant species and length of light/dark cycles. In some cases, measured parameters improved with increasing light/dark periods despite the same total sum of illumination received by plants. Treatments of tomato and pepper transplants with 48/24 h, 96/48 h, and 120/60 h resulted in higher fruit yield compared to conventional 16/8 h photoperiod. The conclusion was made that extended light/dark cycles can result in increased light use efficiency compared to conventional photoperiod and, therefore, reduced product cost, but for practical application, the effects need to be further explored for individual plant species or even cultivars.
Fish, Wildlife, and Bombs: The Struggle to Clean Up Vieques

I n may 2003, after hundreds of arrests, marches, and constant pickets, mass protest forced the U.S. Navy off Vieques, Puerto Rico. Since World War II, the navy had maintained one of its key military installations in the Western Hemisphere on this 51-squaremile island, located six miles off the southeast coast of Puerto Rico. Yet Vieques was also home to 10,000 U.S. citizens who lived sandwiched between an ammunition depot and a military training area. The navy test-fired both landbased and naval artillery, as well as small arms. It rehearsed amphibious landing exercises, parachute drops, and submarine maneuvers. The navy bombed Vieques from air, land, and sea. In the 1980s and 1990s, the navy trained an average of 180 days per year and dropped or fired an average of 1,464 tons of bombs and explosives annually on Vieques. In 1998, the last year before protest interrupted maneuvers, the navy dropped 23,000 bombs on the island, most of which contained live explosives. After six decades of intensive military training, residents are preoccupied with cleaning up the island. Dangerous levels of cadmium and lead appear in the island’s crabs. Lead is concentrated in pasture grass grazed by horses and cattle. Ordnance occasionally washes ashore. Such contamination from heavy metals, and other toxins poses major environmental and health concerns. For example, the island’s cancer rate is 27% higher than the rest of Puerto Rico, raising troubling questions about the military’s toxic legacy and its shortand long-term impact on islanders’ health. Cleanup, however, has been stymied. When the navy left Vieques, the majority of its 18,000acre landholding was transferred to the U.S. 35 Fish, Wildlife, and Bombs: The Struggle to Clean Up Vieques
An Overview of Advances in Rare Cancer Diagnosis and Treatment

Cancer stands as the leading global cause of mortality, with rare cancer comprising 230 distinct subtypes characterized by infrequent incidence. Despite the inherent challenges in addressing the diagnosis and treatment of rare cancers due to their low occurrence rates, several biomedical breakthroughs have led to significant advancement in both areas. This review provides a comprehensive overview of state-of-the-art diagnostic techniques that encompass new-generation sequencing and multi-omics, coupled with the integration of artificial intelligence and machine learning, that have revolutionized rare cancer diagnosis. In addition, this review highlights the latest innovations in rare cancer therapeutic options, comprising immunotherapy, targeted therapy, transplantation, and drug combination therapy, that have undergone clinical trials and significantly contribute to the tumor remission and overall survival of rare cancer patients. In this review, we summarize recent breakthroughs and insights in the understanding of rare cancer pathophysiology, diagnosis, and therapeutic modalities, as well as the challenges faced in the development of rare cancer diagnosis data interpretation and drug development.
Evaluation of the Feasibility of In Vitro Metabolic Interruption of Trimethylamine with Resveratrol Butyrate Esters and Its Purified Monomers

Resveratrol (RSV), obtained from dietary sources, has been shown to reduce trimethylamine oxide (TMAO) levels in humans, and much research indicates that TMAO is recognized as a risk factor for cardiovascular disease. Therefore, this study investigated the effects of RSV and RSV-butyrate esters (RBE) on the proliferation of co-cultured bacteria and HepG2 cell lines, respectively, and also investigated the changes in trimethylamine (TMA) and TMOA content in the medium and flavin-containing monooxygenase-3 (FMO3) gene expression. This study revealed that 50 µg/mL of RBE could increase the population percentage of Bifidobacterium longum at a rate of 53%, while the rate was 48% for Clostridium asparagiforme. In contrast, co-cultivation of the two bacterial strains effectively reduced TMA levels from 561 ppm to 449 ppm. In addition, regarding TMA-induced HepG2 cell lines, treatment with 50 μM each of RBE, 3,4′-di-O-butanoylresveratrol (ED2), and 3-O-butanoylresveratrol (ED4) significantly reduced FMO3 gene expression from 2.13 to 0.40–1.40, which would also contribute to the reduction of TMAO content. This study demonstrated the potential of RBE, ED2, and ED4 for regulating TMA metabolism in microbial co-cultures and cell line cultures, which also suggests that the resveratrol derivative might be a daily dietary supplement that will be beneficial for health promotion in the future.
Dkk1 as a Prognostic Marker for Neoadjuvant Chemotherapy Response in Breast Cancer Patients

Simple Summary The identification of prognostic markers in neoadjuvant therapy patients is critical for treatment optimisation. The purpose of our retrospective study was to determine the role of Dkk1 as a predictor of NACT response in BC patients. Dkk1 levels were found to be lower in treated BC tumours than in untreated tumours. The results of 68 matched pre- and post-therapy tissues showed that advanced G status and TNBC subtype were associated with a higher percentage of Dkk1 expression reduction. In addition, decreased Dkk1-IRS in core needle biopsy tissues independently predicted regression grade (R4), according to Sinn. Dkk1 could then be identified as a biomarker for personalised neoadjuvant therapy. Abstract Purpose: To investigate the role of Dkk1 as a predictor of response to NACT in BC patients. Methods: This retrospective monocentric study included 145 women who had undergone NACT followed by breast surgery. Dkk1 protein expression was assessed using immunohistochemistry staining in core needle biopsies and mammary carcinoma specimens. Results: Dkk1 levels were lower in treated BC tumours than in untreated tumours. The outcomes of 68 matched pre- and post-therapy tissues showed that Dkk1 levels in mammary carcinoma tissues were significantly predicted by levels in core needle biopsies and that Dkk1 expression was reduced in 83% of cases. Smaller cT stage, positive Her2 expression, and decreased Dkk1-IRS in core needle biopsy tissues were all independent predictors of regression grade (R4), according to Sinn. However, the percentage of Dkk1 expression differences prior to and following NACT had no effect on PFS or OS. Conclusions: In this study, we demonstrated for the first time that Dkk1 could be identified as an independent predictor of NACT response in BC patients, particularly those with TNBC. Further research with a multicentric expanded (pre-/post-therapy) sample set and better-defined populations in terms of molecular subtypes, therapy modality, and long-term follow-up is recommended to obtain more solid evidence.
Implementing a Food Prescription Program during COVID-19: Benefits and Barriers

Food prescription programs (Food Rx) have the potential to improve management of diet-related chronic diseases or underlying conditions such as type 2 diabetes (T2D), hypertension, and high body mass index (BMI) among food-insecure patients. The purpose of this study was to examine the effectiveness of a Food Rx program implemented in two community-based clinics in Florida. Data were collected through researcher-administered surveys (food insecurity, demographics, and socio-economic variables) and biometric data (HbA1c, blood pressure, and BMI). Key results include the following: (1) Hispanic patients are more likely to utilize the program than their Black and White counterparts (p < 0.001); (2) older patients (≥50 years) have a higher food redemption rate when compared to younger patients (36–49.9 years); (3) food redemption rate is negatively associated with food security scores indicating improvements in food security status over time (r2 = −0.184, p = 0.036); (4) diabetic patients with higher baseline HbA1c (>9%) have significant reductions in glycated hemoglobin (p = 0.011) over time as compared to patients with lower baseline values (<7%); and (5) patients enrolled in the program for at least 6 months have a significant reduction in systolic blood pressure (p = 0.051). Changes in BMI were not significantly associated with redemption rates. This study is significant as it offers insights into the potential benefits and challenges of implementing Food Rx programs to address diet-related chronic diseases among underserved populations.
Welded Carbon Nanotube–Graphene Hybrids with Tunable Strain Sensing Behavior for Wide-Range Bio-Signal Monitoring

Carbon nanotubes (CNTs) and graphene have commonly been applied as the sensitive layer of strain sensors. However, the buckling deformation of CNTs and the crack generation of graphene usually leads to an unsatisfactory strain sensing performance. In this work, we developed a universal strategy to prepare welded CNT–graphene hybrids with tunable compositions and a tunable bonding strength between components by the in situ reduction of CNT–graphene oxide (GO) hybrid by thermal annealing. The stiffness of the hybrid film could be tailored by both initial CNT/GO dosage and annealing temperature, through which its electromechanical behaviors could also be defined. The strain sensor based on the CNT–graphene hybrid could be applied to collect epidermal bio-signals by both capturing the faint skin deformation from wrist pulse and recording the large deformations from joint bending, which has great potential in health monitoring, motion sensing and human–machine interfacing.
Upregulation of Wheat Heat Shock Transcription Factor TaHsfC3-4 by ABA Contributes to Drought Tolerance

Drought stress can seriously affect the yield and quality of wheat (Triticum aestivum). So far, although few wheat heat shock transcription factors (Hsfs) have been found to be involved in the stress response, the biological functions of them, especially the members of the HsfC (heat shock transcription factor C) subclass, remain largely unknown. Here, we identified a class C encoding gene, TaHsfC3-4, based on our previous omics data and analyzed its biological function in transgenic plants. TaHsfC3-4 encodes a protein containing 274 amino acids and shows the basic characteristics of the HsfC class. Gene expression profiles revealed that TaHsfC3-4 was constitutively expressed in many tissues of wheat and was induced during seed maturation. TaHsfC3-4 could be upregulated by PEG and abscisic acid (ABA), suggesting that this Hsf may be involved in the regulation pathway depending on ABA in drought resistance. Further results represented that TaHsfC3-4 was localized in the nucleus but had no transcriptional activation activity. Notably, overexpression of TaHsfC3-4 in Arabidopsis thaliana pyr1pyl1pyl2pyl4 (pyr1pyl124) quadruple mutant plants complemented the ABA-hyposensitive phenotypes of the quadruple mutant including cotyledon greening, root elongation, seedling growth, and increased tolerance to drought, indicating positive roles of TaHsfC3-4 in the ABA signaling pathway and drought tolerance. Furthermore, we identified TaHsfA2-11 as a TaHsfC3-4-interacting protein by yeast two-hybrid (Y2H) screening. The experimental data show that TaHsfC3-4 can indeed interact with TaHsfA2-11 in vitro and in vivo. Moreover, transgenic Arabidopsis TaHsfA2-11 overexpression lines exhibited enhanced drought tolerance, too. In summary, our study confirmed the role of TaHsfC3-4 in response to drought stress and provided a target locus for marker-assisted selection breeding to improve drought tolerance in wheat.
Comparison of Experimental Methodologies Based on Bulk-Metagenome and Virus-like Particle Enrichment: Pros and Cons for Representativeness and Reproducibility in the Study of the Fecal Human Virome

Studies on the human virome based on the application of metagenomic approaches involve overcoming a series of challenges and limitations inherent not only to the biological features of viruses, but also to methodological pitfalls which different approaches have tried to minimize. These approaches fall into two main categories: bulk-metagenomes and virus-like particle (VLP) enrichment. In order to address issues associated with commonly used experimental procedures to assess the degree of reliability, representativeness, and reproducibility, we designed a comparative analysis applied to three experimental protocols, one based on bulk-metagenomes and two based on VLP enrichment. These protocols were applied to stool samples from 10 adult participants, including two replicas per protocol and subject. We evaluated the performances of the three methods, not only through the analysis of the resulting composition, abundance, and diversity of the virome via taxonomical classification and type of molecule (DNA versus RNA, single stranded vs. double stranded), but also according to how the a priori identical replicas differed from each other according to the extraction methods used. Our results highlight the strengths and weaknesses of each approach, offering valuable insights and tailored recommendations for drawing reliable conclusions based on specific research goals.
An Archaeomagnetic Study of Hangi Stones in New Zealand

Burnt or fired archaeological artefacts often retain a record of the magnetic field in which they were last heated and cooled. Over the past four years we have collected oriented hangi stones from 10 archaeological sites spread across the North and South Islands of New Zealand. The stones vary in lithology from andesites, originating from the central North Island volcanoes, favoured by Maori for their durability and with remanent magnetization up to 30 A/m, to sandstones and schists from the main axial ranges, with magnetizations as weak as 10-4 A/m. Radiocarbon dating of charcoal fragments retrieved from amongst the stones indicates that the sites span from ca. 1400 AD to the present. In all cases, we have independently oriented and retrieved several stones, and we have made several samples from each stone, either by drilling (standard cylindrical samples) or sawing (pseudo-cubes) in the laboratory. We have calculated site mean palaeomagnetic directions (Dec between 1.5o and 19.6o and Inc between -52.2o and -68.3o) from principal component analysis of thermal demagnetization and alternating field demagnetization data, discarding the data of stones that show evidence of disturbance after cooling. The directions are in good agreement with recently published palaeosecular variation records from lake sediments. We have carried out palaeointensity experiments using the Coe/Thellier method with pTRM and tail checks, and with selection criteria modified to the situation. Palaeointensities range from 50μT to 77μT. Rock magnetic experiments contribute to our understanding of the mineralogy, domain state and blocking temperature spectra. We compare our data with predictions of the global field models ARCH3k and gufm1, and suggest that the addition of our new data will improve these models for the SW Pacific region for the most recent time period. Archaeomagnetic measurements are also used to date hangi sites by matching the palaeo-direction to an established archaeomagnetic dating model, NZPSV1k. Archaeomagnetic dating is used to resolve ambiguities in the calibration of radiocarbon dates, and shows up inconsistencies due to unreliable source material for radiocarbon dating. Archaeomagnetic dating and radiocarbon dating results are combined to give the best estimates of the best age of the hangi sites.
A short note on methods of ranking fuzzy numbers in risk analysis problems

The numerous studies on comparing and ranking fuzzy numbers clear that this task is still young. However, the observation that many papers do not hesitate to use some incorrect ranking methods in risk analysis problems, encouraged the author to point out the shortcoming of some of these methods. In this note, we review briefly the methods for ranking fuzzy
Translation and Cultural Adaptation into Arabic of Patient-Reported Outcome Measurement Information System® Item Banks: Cognitive Function Abilities and Physical Function for Samples with Mobility Aid Users

Purpose: This study aimed to provide Arabic-speaking individuals with tools to assess their cognitive abilities and physical function and to contribute to a better understanding of these capabilities in this population. Thus, the specific objective was to translate into Arabic and culturally adapt two Patient-Reported Outcome Measurement Information System (PROMIS) item banks: the Adult Cognitive Function Abilities and the Physical Function for Samples with Mobility Aid Users item banks. This study employed the Functional Assessment of Chronic Illness Therapy (FACIT) multilingual translation methodology to ensure cultural and linguistic relevance. The translation process included forward and back translations, expert reviews, and finalisation by a language coordinator. Cognitive debriefing interviews were conducted with 30 native healthy Arabic speakers to assess the clarity and comprehension of translated items. Most items were well understood, but two items related to cognitive ability and four related to physical functions required revision to address participant confusion. The translations were refined based on the participants’ feedback and expert recommendations. This study followed a rigorous translation process and included cognitive debriefing interviews to ensure linguistic and cultural equivalence. The availability of these tools in Arabic enhances cross-cultural research and practice in healthcare and contributes to a global understanding of cognitive and physical functions.
Physicochemical Characterization of Pectic Polysaccharides from Rose Essential Oil Industry By-Products

The rose essential oil industry generates large quantities of solid byproducts yearly. These by-products, usually discarded, could yield valuable substances, such as pectic polysaccharides, widely used in the food industry as jelling agents. Seven industrial by-products were investigated as a source of pectic polysaccharides: four samples resulted from the treatment of Rosa damascena, two from Rosa alba, and one from Rosa centifolia. Three by-products were from steam-water distillation, two from CO2-supercritical extraction, and two after extraction with hexane and 1,1,1,2-tetrafluoroethane. The by-products were pretreated with 70% ethanol and extracted with 0.1 M HCl. The highest polysaccharide yield was observed for 1,1,1,2-tetrafluoroethane-extracted (RD_F) Rosa damascena by-products (13.98 ± 0.14%), followed by hexane (RD_X) and CO2-extracted (RD_CO2) Rosa damascena (12.68 ± 0.11 and 12.66 ± 0.10%, respectively). The polysaccharides were middle-methoxylated pectins, except RD_F and RD_X, having 26.68 ± 1.14 and 31.39 ± 1.39 mol % degree of methoxylation (low-methoxyl pectins). The polysaccharides had molecular masses in the 2.3–2.6 × 104 Da range. The rheological studies suggested RD_F formed a strong high-sucrose gel, while the others yielded weak gels. RD_F and RD_X formed strong Ca2+-mediated gels, comparable with commercial low-methoxylated citrus pectin. This study suggests that rose oil industry by-products could be successfully valorized and yield pectic polysaccharides with gelling properties, comparable with commercial citrus pectins.