Miracle-dz/UniFAR-FTUs huggingface dataset:
Insights into the effect of human civilization on Malus evolution and domestication

Abstract The evolutionary history of the Malus genus has not been well studied. In the current study, we presented genetic evidence on the origin of the Malus genus based on genome sequencing of 297 Malus accessions, revealing the genetic relationship between wild species and cultivated apples. Our results demonstrated that North American and East Asian wild species are closer to the outgroup (pear) than Central Asian species, and hybrid species including natural (separated before the Pleistocene, about 2.5 Mya) and artificial hybrids (including ornamental trees and rootstocks) are between East and Central Asian wild species. Introgressions from M. sylvestris in cultivated apples appeared to be more extensive than those from M. sieversii, whose genetic background flowed westward across Eurasia and eastward to wild species including M. prunifolia, M. × asiatica, M. × micromalus, and M. × robust. Our results suggested that the loss of ancestral gene flow from M. sieversii in cultivated apples accompanied the movement of European traders around the world since the Age of Discovery. Natural SNP variations showed that cultivated apples had higher nucleotide diversity than wild species and more unique SNPs than other apple groups. An apple ERECTA‐like gene that underwent selection during domestication on 15th chromosome was identified as a likely major determinant of fruit length and diameter, and an NB‐ARC domain‐containing gene was found to strongly affect anthocyanin accumulation using a genome‐wide association approach. Our results provide new insights into the origin and domestication of apples and will be useful in new breeding programmes and efforts to increase fruit crop productivity.
Dementia in Scottish military veterans: early evidence from a retrospective cohort study

Abstract Background Few studies have examined whether UK military veterans are at an increased risk of dementia. We explored the risk of dementia in Scottish military veterans aged up to 73 years in comparison with people who have never served. Methods Retrospective cohort study of 78 000 veterans and 253 000 people with no record of service, matched for age, sex and area of residence, with up to 37 years follow-up, using Cox proportional hazard analysis to compare risk of dementia in veterans and non-veterans, overall and by subgroup. Results Dementia was recorded in 0.2% of both veterans and non-veterans overall, Cox proportional hazard ratio 0.98, 95% confidence interval (CI) 0.82–1.19, p = 0.879 (landmark age: 50 years), with no difference for men but increased risk in veteran women and Early Service Leavers. Post-traumatic stress disorder (PTSD) was associated with a higher risk of dementia in both veterans and non-veterans, although possibly to a lesser degree in veterans. A history of mood disorder was strongly associated with developing dementia, greater in veterans than in non-veterans, odds ratio 1.54, 95% CI 1.01–2.35, p = 0.045. Conclusions There was no evidence to suggest that military service increased the risk of dementia, although this may change as the cohort ages. The well-documented association with PTSD shows no evidence of being stronger in veterans; by contrast, the association of mood disorder with dementia is much stronger in veterans. Healthcare providers should carefully assess the cognitive status of older veterans presenting with depressive illness in order to identify early dementia and ensure optimum management.
Dietary habits in patients with fibromyalgia: a cross-sectional study.

OBJECTIVES To the scarce information on dietary habits in fibromyalgia (FM), it is added that there are no comparative studies with other rheumatic diseases. The objective of this study was to characterise the dietary habits of patients with FM by comparing, for the first time, with healthy controls (HC) and rheumatoid arthritis (RA). METHODS This cross-sectional, observational study was based on data obtained from the Dietfibrom project for FM and from the IMID Consortium for RA and HC. All participants completed a food frequency questionnaire evaluating their weekly dietary intake of main food groups. The three cohorts were compared using a multiple logistic regression model adjusted for age, sex, and body mass index. RESULTS After quality control, n=287 FM, n=1,983 HC and n=1,942 RA patients were analysed. We found that FM had a profound impact in the diet compared to HC, reducing the consumption of dairy (OR=0.32, p<0.0001), bread and/or whole grain cereals (OR=0.59, p=0.0006), fresh fruit (OR=0.66, P=0.008), and fish (OR=0.64, p=0.002). These same four food groups were also significantly reduced in FM patients in comparison to RA patients (p<0.0005 in all cases). Additionally, a lower consumption of pasta, rice and/or potatoes was also observed in FM compared to RA (OR=0.72, p=0.028). CONCLUSIONS The present cross-sectional study shows that FM is associated to a significant change in the normal dietary patterns. These results underscore the importance of diet in this prevalent disease and are a warning of the potential long-range effects of a deficient nutritional status.
Exploring the Relationship Between Domestic Violence Perpetration and Suicidal Behavior in Male Prisoners

Abstract This study is the first to explore the relationship between domestic violence perpetration and suicidal behavior in prisoners in England and Wales. The nature of this relationship is unclear, however, understanding and reducing suicide in prisons is a critical issue for frontline staff and policy makers. Eight participants with a history of suicide attempts and domestic violence perpetration were interviewed. Five key themes were identified through thematic analysis; “Trauma, victimization and life struggles,” “Relationship ideals versus relationship reality”, “Explaining domestic violence”, “The impact of prison” and “Suicide as a coping strategy”. This study shows that the relationship between domestic violence and suicide risk in prisoners may be better understood through a pathway of experiences rather than individual risk factors. Further research is needed to test the replicability of this pathway in other samples.
An observational study on the relationship between zinc concentrations in bulk tank milk and in serum and farmer-reported zinc supplementation of dairy cattle for facial eczema prophylaxis

ABSTRACT Aims To describe the concentration of Zn in bulk tank milk (BTM) in a sample of New Zealand dairy farms, investigate the association between the method of Zn administration for facial eczema prophylaxis and Zn concentrations in BTM and investigate the relationship between the concentration of Zn in serum and that in BTM. Methods Multiple BTM samples (n = 3,330) collected during milk pick-up by the milk tanker driver were stored and tested for 121 farms, in Northland (n = 50), Waikato (n = 51) and Southland (n = 20) from February to May 2017. Enrolled farms provided retrospective information on the type of Zn supplementation (if any) used for the prevention of facial eczema and the timeframe over which supplementation occurred. In addition, the concentration of Zn in serum was measured in blood samples collected from ≥15 cattle per farm for 22 farms from Northland (n = 11) and Waikato (n = 11), and compared against the concentrations of Zn in BTM on the day of blood sampling. A linear mixed model was used to model log Zn concentrations in BTM using method of Zn supplementation, region, milk fat and protein percentage, volume of milk, and frequency of milk pick-up as risk factors. A mixed logistic regression model was used to assess the relationship between Zn concentrations in BTM and the presence of cows with a concentration of Zn in serum of ≥20 µmol/L. Results The median Zn concentration in BTM was 67.9 (min 38.9, max 146.6) µmol/L. The median range of Zn concentrations for repeated samples of BTM within farm was 22.6 µmol/L. In comparison to farms that did not use any form of Zn supplementation, farms that supplemented Zn through a slow-release capsule, oral drench, in feed or a combination of in-feed and water were associated with increased concentrations of Zn in BTM (p < 0.001). There was no difference in Zn concentrations in BTM between farms that administered Zn through the water only and farms that did not administer Zn (p = 0.22). Every 15.3 μmol/L increase in Zn concentration in BTM was associated with 2.2 times (95% CI=1.7–2.9) the odds of a cow having Zn concentration in serum ≥20 μmol/L. Conclusion and clinical relevance Zn concentration in BTM is highly variable between farms, days and Zn administration method. Zn concentration in BTM content has modest potential as a way to signal whether a herd has achieved the high Zn status considered to be protective against FE.
Isolation of exosomes from serum of patients with lung cancer: a comparison of the ultra-high speed centrifugation and precipitation methods

Background Extracellular vesicles (EVs) is a group of heterogeneous cell-derived membrane structures, which is composed of a large number of exosomes released by cells, microbubbles (MVs) and apoptotic bodies. The formation of exocrine body is a process of fine regulation, which includes four stages: initiation, endocytosis, polycystic body formation and exocrine body secretion. Ultracentrifugation is currently the gold standard for external body separation; it includes a series of centrifugation steps at a rotation speed of 100,000 rpm or more to purify exocrine bodies from protein contaminants. Thus far, some in vitro separation methods, such as ultracentrifugation, polymer-based exosome separation kits and immune affinity-based isolation using antibodies against exosome surface proteins, have been used for tumor exosome isolation. It is not very clear which method is more suitable for the separation of serum exosomes from lung cancer patients. Methods Two methods for the extraction of exosomes from serum samples of lung cancer patients, namely, ultra-high speed centrifugation (Ultra-Exo) and precipitation (Prekit-Exo), were analyzed and compared. The biological morphologies of the extracted exosomes were studied by negative staining matter with transmission electron microscopy and cryo-electron microscopy. The particle size and the distribution were detected using nanoparticle tracking analysis (NTA). Results Bio-transmission electron microscopy revealed that the morphologies of exosomes extracted by ultracentrifugation were superior to exosomes extracted with the Prekit-Exo kit. Ultracentrifugation was able to extract more exosomes compared to the Prekit-Exo kit. NTA showed that the exosomes obtained by ultra-high speed centrifugation had a smaller particle size compared to exosomes obtained by precipitation (30.4±26.8 vs. 150.3±6.8 nm, respectively). It is possible that the precipitant used in the precipitation kit was extracted with the exosomes, thereby causing the particle size to increase. Notably, the particle size of the exosomes extracted by the precipitation kit method showed a relatively narrow range in size. This could be due to the coating effect of the precipitation reagent, reducing the difference in the particle size of the exosomes. Conclusions Exosomes collected from the serum of lung cancer patients using the two extraction methods differed in morphology and numbers, with the ultracentrifugation method being superior to the precipitation method.
A novel, minimally invasive technique to establish the animal model of spinal cord injury

Background Spinal cord injury (SCI) is a traumatic disease that is associated with high morbidity, disability, and mortality worldwide. The animal spinal cord contusion model is similar to clinical SCI; therefore, this model is often used to study the pathophysiological changes and treatment strategies for humans after SCI. The present study aimed to introduce a novel, minimally invasive technique to establish an SCI model, and to evaluate its advantages compared with conventional methods. Methods Incision length, blood loss, length of time, and model success rate during the operation were recorded. Postoperative hematuria, incision hematoma, scoliosis [detected by micro computed tomography (Micro-CT)] and mortality were analyzed to evaluate surgical complications. The visual observation of the tissue was used to compare the effect of laminectomy by 2 methods on the scar hyperplasia at the injured site. Basso-Beattie-Bresnahan (BBB) score and catwalk automated quantitative gait analysis were conducted to measure behavioral function recovery. To evaluate the nerve function recovery of rats postoperatively, somatosensory evoked potential (SEP) and motor evoked potential (MEP) were studied by electrophysiological analyses. Results The results of operation-related parameters of the two models (conventional surgery group vs. minimally invasive surgery group) were as follows: surgical incision length: 23.58±1.58 versus 12.67±1.50 mm (P<0.05), blood loss: 3.96±1.05 versus 1.34±0.87 mL (P<0.05), and total operative time: 12.67±1.78 versus 10.33±1.92 min (P<0.05). In addition, the success rate of the 2 models was 100%. Surgical complications (conventional surgery group vs. minimally invasive surgery group) were as follows: hematuria: 25% versus 8.3%, kyphosis: 25% versus 0%, incision hematoma: 30% versus 9%, and mortality: 25% versus 8.3%. Micro-CT indicated severe scoliosis in the conventional surgery group. Gross tissue results showed that the conventional surgery group had more severe fibrous scar hyperplasia. The results of the BBB scores, catwalk automated quantitative gait analysis, and electrophysiology showed that the difference between the two groups was statistically significant in terms of behavioral recovery and neuroelectrophysiology. Conclusions The minimally invasive technique has the advantages of small incision and reduced tissue damage and surgical complications, and may be used as an alternative spinal cord contusion method.
Nanoscale analysis of historical paintings by means of O-PTIR spectroscopy: The identification of the organic particles in L'Arlésienne (portrait of Madame Ginoux) by Van Gogh.

Optical-photothermal infrared (O-PTIR) spectroscopy is a recently developed technique that provides spectra comparable to traditional transmission FTIR spectroscopy with nanometric spatial resolution. Hence, O-PTIR is a promising candidate for the analysis of historical paintings, as well as other cultural heritage objects, but its potential has not yet been evaluated.
Genetic diversity and structure of Musa balbisiana populations in Vietnam and its implications for the conservation of banana crop wild relatives

Crop wild relatives (CWR) are an indispensable source of alleles to improve desired traits in related crops. While knowledge on the genetic diversity of CWR can facilitate breeding and conservation strategies, it has poorly been assessed. Cultivated bananas are a major part of the diet and income of hundreds of millions of people and can be considered as one of the most important fruits worldwide. Here, we assessed the genetic diversity and structure of Musa balbisiana, an important CWR of plantains, dessert and cooking bananas. Musa balbisiana has its origin in subtropical and tropical broadleaf forests of northern Indo-Burma. This includes a large part of northern Vietnam where until now, no populations have been sampled. We screened the genetic variation and structure present within and between 17 Vietnamese populations and six from China using 18 polymorphic SSR markers. Relatively high variation was found in populations from China and central Vietnam. Populations from northern Vietnam showed varying levels of genetic variation, with low variation in populations near the Red River. Low genetic variation was found in populations of southern Vietnam. Analyses of population structure revealed that populations of northern Vietnam formed a distinct genetic cluster from populations sampled in China. Together with populations of central Vietnam, populations from northern Vietnam could be subdivided into five clusters, likely caused by mountain ranges and connected river systems. We propose that populations sampled in central Vietnam and on the western side of the Hoang Lien Son mountain range in northern Vietnam belong to the native distribution area and should be prioritised for conservation. Southern range edge populations in central Vietnam had especially high genetic diversity, with a high number of unique alleles and might be connected with core populations in northern Laos and southwest China. Southern Vietnamese populations are considered imported and not native.
Expanding the phenotypic spectrum of FINCA (fibrosis, neurodegeneration, and cerebral angiomatosis) syndrome beyond infancy

Fibrosis, neurodegeneration, and cerebral angiomatosis (FINCA, MIM#618278) is a rare clinical condition caused by bi‐allelic variants in NHL repeat containing protein 2 (NHLRC2, MIM*618277). Pulmonary disease may be the presenting sign and the few patients reported so far, all deceased in early infancy. Exome sequencing was performed on patients with childhood interstitial lung disease (chILD) and additional neurological features. The chILD‐EU register database and an in‐house database were searched for patients with NHLRC2 variants and clinical features overlapping FINCA syndrome. Six patients from three families were identified with bi‐allelic variants in NHLRC2. Two of these children died before the age of two while four others survived until childhood. Interstitial lung disease was pronounced in almost all patients during infancy and stabilized over the course of the disease with neurodevelopmental delay (NDD) evolving as the key clinical finding. We expand the phenotype of FINCA syndrome to a multisystem disorder with variable severity. FINCA syndrome should also be considered in patients beyond infancy with NDD and a history of distinct interstitial lung disease. Managing patients in registers for rare diseases helps identifying new diagnostic entities and advancing care for these patients.
Vulnerabilities of nurses in an intensive care unit: an integrative review.

OBJECTIVES to identify vulnerabilities of nurses who work in an intensive care unit. METHODS an integrative review was held from 2006 to 2019, with searches on the platforms/databases LILACS, BDENF, SciELO, MEDLINE, Scopus, CINAHL, and Web of Science. The theoretical framework of ergology, by Schwartz, was used and the guiding question "What are the main vulnerabilities of nurses who work in an intensive care unit"? RESULTS eleven articles were included. Five topics of vulnerabilities emerged: physical, emotional, communication process, care process, and organizational. We observed that the organizational vulnerability was kept as a common and intersection factor in developing the other four. CONCLUSIONS vulnerabilities found have a relationship to the physical, emotional, communication, care process, and institution organization elements. The organization aspect intersected with the others, configuring itself as the core in this context.
Anti–Double‐Stranded DNA Antibodies Recognize DNA Presented on HLA Class II Molecules of Systemic Lupus Erythematosus Risk Alleles

Specific HLA class II alleles are associated with susceptibility to systemic lupus erythematosus (SLE). The role of HLA class II molecules in SLE pathogenesis remains unclear, although anti‐DNA antibodies are specific to SLE and correlate with disease activity. We previously demonstrated that misfolded proteins bound to HLA class II molecules are specific targets for the autoantibodies produced in autoimmune diseases. This study was undertaken to validate our hypothesis that DNA binds to HLA class II molecules in a manner similar to that of misfolded proteins and that DNA bound to HLA class II molecules is involved in SLE pathogenesis.
Comparative Hepatic and Intestinal Efflux Transport of Statins

Previous studies have shown that lipid-lowering statins are transported by various ATP-binding cassette (ABC) transporters. However, because of varying methods, it is difficult to compare the transport profiles of statins. Therefore, we investigated the transport of 10 statins or statin metabolites by six ABC transporters using human embryonic kidney cell-derived membrane vesicles. The transporter protein expression levels in the vesicles were quantified with liquid chromatography–tandem mass spectrometry and used to scale the measured clearances to tissue levels. In our study, apically expressed breast cancer resistance protein (BCRP) and P-glycoprotein (P-gp) transported atorvastatin, fluvastatin, pitavastatin, and rosuvastatin. Multidrug resistance-associated protein 3 (MRP3) transported atorvastatin, fluvastatin, pitavastatin, and, to a smaller extent, pravastatin. MRP4 transported fluvastatin and rosuvastatin. The scaled clearances suggest that BCRP contributes to 87%–91% and 84% of the total active efflux of rosuvastatin in the small intestine and the liver, respectively. For atorvastatin, the corresponding values for P-gp–mediated efflux were 43%–79% and 66%, respectively. MRP3, on the other hand, may contribute to 23%–26% and 25%–37% of total active efflux of atorvastatin, fluvastatin, and pitavastatin in jejunal enterocytes and liver hepatocytes, respectively. These data indicate that BCRP may play an important role in limiting the intestinal absorption and facilitating the biliary excretion of rosuvastatin and that P-gp may restrict the intestinal absorption and mediate the biliary excretion of atorvastatin. Moreover, the basolateral MRP3 may enhance the intestinal absorption and sinusoidal hepatic efflux of several statins. Taken together, the data show that statins differ considerably in their efflux transport profiles. SIGNIFICANCE STATEMENT This study characterized and compared the transport of atorvastatin, fluvastatin, pitavastatin, pravastatin, rosuvastatin, and simvastatin acid and four atorvastatin metabolites by six ABC transporters (BCRP, MRP2, MRP3, MRP4, MRP8, P-gp). Based on in vitro findings and protein abundance data, the study concludes that BCRP, MRP3, and P-gp have a major impact in the efflux of various statins. Together with in vitro metabolism, uptake transport, and clinical data, our findings are applicable for use in comparative systems pharmacology modeling of statins.
Obtención de biodiesel por transesterificación de aceite

Resumen La evaluacion de diferentes aceites vegetales para la obten-cion de biocombustibles se ha convertido en una estrategia global en la produccion de biodiesel, con miras a reducir costos de produccion, aumentar el rendimiento de la reaccion, evitar el uso de materias primas consideradas como alimentos y disminuir la contaminacion ambiental. En el presente trabajo se evaluo la obtencion de biodiesel a partir de aceite de cocina usado, empleando la catalisis con hidroxido de sodio y potasio. Se evaluaron tres relaciones molares de metanol: aceite, 6:1, 9:1 y 12:1, dos catali-zadores KOH y NaOH y dos porcentajes de catalizador 1 % y 2 %; se realizo un diseno factorial por duplicado. La temperatura se mantuvo en 60 °C, y el tiempo de reaccion, en 2 horas. Se determino el contenido de metilesteres y de mono-, di- y trigliceridos mediante cromatografia de gases. Las mejores condiciones para NaOH y KOH como catalizadores se obtuvieron cuando el porcentaje de catalizador fue 1 % y la relacion molar alcohol:aceite fue 12:1. En estas condiciones se obtuvo una conversion del 64,1 %, un rendimiento de 98 % y un porcentaje de metilesteres de 99,1 % cuando el catalizador fue NaOH. Con KOH la conversion fue 63,2 %; el rendimiento, 88 %, y el porcentaje de metilesteres, 98,4 %. Los resultados de este estudio muestran un alto rendimiento de la reaccion al emplear aceite usado, por lo cual su implementacion in-dustrial dependera de la evaluacion economica.