Miracle-dz/UniFAR-FTUs huggingface dataset:
Prenatal diagnosis of abnormality of the umbilical portal DV complex: difficulty in universal classification due to various alternative routes in hepatic circulation for placental drainage

Abstract Objective To review our experience with fetal abnormality of the umbilical-portal-DV complex and to discuss the new classification system for umbilical portal systemic venous shunts (UPSVS) according to our cases. Methods This study was a retrospective analysis of fetuses with a prenatal diagnosis of abnormality of the umbilical-portal-DV complex. The integrity of the fetal umbilical-portal ductus venosus complex and the hepatic venous system were evaluated using two-dimensional color Doppler sonography. The origin of the shunt, the location of the drainage, and the presence or absence of intrahepatic portal venous system and DV were noted. Results 35 cases of abnormality of the umbilical-portal-DV complex were identified. Agenesis of ductus venous was detected in 33 of them. Based on the abnormality of the umbilical-portal-DV complex, we divided the cases into five groups. Group 1, ductus venosus agenesis with normal hepatic venous anatomy (n = 11); Group 2 downward displacement of the umbilical-portal-DV complex (n = 13); Group 3, umbilical-systemic shunt (n = 5); Group 4, intrahepatic portosystemic shunt (n = 4), Group 5, hepatic arteriovenous malformation (n = 2). Three different intrahepatic portosystemic shunt and one different downward displacement of the umbilical-portal-DV complex cases were detected. Conclusions Disruption of the normal anatomy of the umbilical-portal-DV complex causes various alternative pathway of the placental drainage. This illustrates highlights the challenge of creating a universal classification.
Edinburgh Research Explorer Draft genome sequence of Solanum aethiopicum provides insights into disease resistance, drought tolerance, and the evolution of the genome

Background: The African eggplant ( Solanum aethiopicum ) is a nutritious traditional vegetable used in many African countries, including Uganda and Nigeria. It is thought to have been domesticated in Africa from its wild relative, Solanum anguivi . S. aethiopicum has been routinely used as a source of disease resistance genes for several Solanaceae crops, including Solanum melongena . A lack of genomic resources has meant that breeding of S. aethiopicum has lagged behind other vegetable crops. Results: We assembled a 1.02-Gb draft genome of S. aethiopicum , which contained predominantly repetitive sequences (78.9%). We annotated 37,681 gene models, including 34,906 protein-coding genes. Expansion of disease resistance genes was observed via 2 rounds of amplification of long terminal repeat retrotransposons, which may have occurred ∼ 1.25 and 3.5 million years ago, respectively. By resequencing 65 S. aethiopicum and S. anguivi genotypes, 18,614,838 single-nucleotide polymorphisms were identified, of which 34,171 were located within disease resistance genes. Analysis of domestication and demographic history revealed active selection for genes involved in drought tolerance in both “Gilo” and “Shum” groups. A pan-genome of S. aethiopicum was assembled, containing 51,351 protein-coding genes; 7,069 of these genes were missing from the reference genome. Conclusions: The genome sequence of S. aethiopicum enhances our understanding of its biotic and abiotic resistance. The single-nucleotide polymorphisms identified are immediately available for use by breeders. The information provided here will accelerate selection and breeding of the African eggplant, as well as other crops within the Solanaceae family. KEGG: Kyoto Encyclo-pedia of Genes and Genomes; LTR: long terminal repeat; LD: linkage disequilibrium; LTR-R: long terminal repeat retrotrans-poson; Multiple Alignment using Fast Fourier Trans-form; nucleotide-binding, leucine-rich nucleotide-binding, leucine-rich repeat-related; principal component analysis;
The Evolving Role of Ophthalmology Clinics in Screening for Early Alzheimer’s Disease: A Review

Alzheimer’s disease (AD) is the leading cause of dementia, which is a growing public health concern. Although there is no curative treatment for established AD, early recognition and modification of the known risk factors can reduce both severity and the rate of progression. Currently, an early diagnosis of AD is rarely achieved, as there is no screening for AD. The cognitive decline in AD is gradual and often goes unnoticed by patients and caregivers, resulting in patients presenting at later stages of the disease. Primary care physicians (general practitioners in the UK) can administer a battery of tests for patients presenting with memory problems and cognitive impairment, however final diagnosis of AD is usually made by specialised tertiary level clinics. Recent studies suggest that in AD, visuospatial difficulties develop prior to the development of memory problems and screening for visuospatial difficulties may offer a tool to screen for early stage AD. AD and cataracts share common risk and predisposing factors, and the stage of cataract presentation for intervention has shifted dramatically with early cataract referral and surgical intervention becoming the norm. This presentation offers an ideal opportunity to administer a screening test for AD, and visuospatial tools can be administered at post-operative visits by eye clinics. Abnormal findings can be communicated to primary care physicians for further follow up and assessment, or possible interventions which modify risk factors such as diabetes, hypertension and obesity can be undertaken. We propose that eye clinics and ophthalmology facilities have a role to play in the early diagnosis of AD and reducing the burdens arising from severe dementia.
Data Reproducibility and Effectiveness of Bronchodilators for Improving Physical Activity in COPD Patients

Increasing physical activity (PA) in patients with chronic obstructive pulmonary disease (COPD) is an important issue, however, the effect of bronchodilators on PA is still controversial. The indicators of PA, as measured by an accelerometer, can easily fluctuate based on several factors, which might cause inconsistent results. In this review, we listed the indicators of PA and the factors influencing the reproducibility of indicators of PA, and reviewed reports in which the effects of bronchodilators on PA were evaluated by an accelerometer. Then, we investigated the association between the processing of influencing factors and the effectiveness of bronchodilators for improving the PA of COPD patients. Fifteen reports were extracted using the PubMed database. In all seven reports in which adjustment was performed for at least two of four influencing factors (non-wear time, data from days with special behavior, environmental factors, and number of valid days required to obtain reproducible data), bronchodilators showed beneficial effects on PA. No adjustment was made for any of these factors in any of the four bronchodilator-ineffective reports. This suggests that the processing of influencing factors to secure reproducibility might affect the results regarding the effectiveness of bronchodilators for improving PA in COPD patients.
Comparative Genomic Analysis of Dactylonectria torresensis Strains from Grapevine, Soil and Weed Highlights Potential Mechanisms in Pathogenicity and Endophytic Lifestyle

The soil-borne fungus Dactylonectria torresensis is the most common causal agent of black-foot disease in Europe. However, there is a lack of understanding on how this fungus can provoke plant symptoms. In this study, we sequenced, annotated and analyzed the genomes of three isolates of D. torresensis collected from asymptomatic vine, weed and soil. Sequenced genomes were further compared to those of 27 fungal species including root and aerial pathogens, white rot degraders, indoor biodeterioration agents, saprotrophs, dark septate endophytes and mycorrhiza. Strains of D. torresensis present genomes with between 64 and 65 Mbp and with up to 18,548 predicted genes for each strain. Average Nucleotide Identity (ANI) shows that strains are different according to genome contents. Clusters of orthologous groups were compared, and clusters of genes related to necroses were particularly detected in all strains of D. torresensis (necrosis inducing peptides and proteins, and ethylene inducing peptides) as well as several genes involved in resistance against fungicides frequently used in viticulture such as copper. Interestingly, an expanded high number of genes related to carbohydrate-active enzymes were detected in each Dactylonectria strain, especially those related to glycoside hydrolases that could be involved in penetration of plant tissues or pathogenicity. An increased number of candidate genes for CAZyme classes AA9 and AA3-1 supports the ability of strains to efficiently degrade plant material. High numbers of genes of D. torresensis related to secretome and small secreted proteins were further characterized. Moreover, the presence of several gene clusters such as fujikurin-like genes was detected and were normally found in Fusarium fujikuroi, that have been linked to fungal pathogenicity. The phenotypes of the three strains investigated showed further difference in light response. We found that Dactylonectria strains have an increased number of photoreceptor encoding genes and we showed sequence alterations. Altogether, the results highlight several gene clusters present in D. torresensis strains that could be linked to endophytic lifestyle, pathogenicity, plant maceration and degradation of plant tissues as well as adaptation to soil contaminated with metals and metalloids and light response.
Aberrant functional connectivity of neural circuits associated with thought-action fusion in patients with obsessive–compulsive disorder

Abstract Background Cognitive theories of obsessive–compulsive disorder (OCD) stress the importance of dysfunctional beliefs in the development and maintenance of the disorder. However, a neurobiological understanding of these cognitive models, including thought-action fusion (TAF), is surprisingly lacking. Thus, this functional magnetic resonance imaging study aimed to investigate whether altered functional connectivity (FC) is associated with the TAF paradigm in OCD patients. Methods Forty-one OCD patients and 47 healthy controls (HCs) participated in a functional magnetic resonance imaging study using a TAF task, in which they were asked to read the name of a close or a neutral person in association with positive and negative statements. Results The conventional TAF condition (negative statements/close person) induced significant FC between the regions of interest (ROIs) identified using multivoxel pattern analysis and the visual association areas, default mode network subregions, affective processing, and several subcortical regions in both groups. Notably, sparser FC was observed in OCD patients. Further analysis confined to the cortico-striato-thalamo-cortical (CSTC) and affective networks demonstrated that OCD patients exhibited reduced ROI FC with affective regions and greater ROI FC with CSTC components in the TAF condition compared to HCs. Within the OCD patients, middle cingulate cortex–insula FC was correlated with TAF and responsibility scores. Conclusions Our TAF paradigm revealed altered context-dependent engagement of the CSTC and affective networks in OCD patients. These findings suggest that the neurobiology of cognitive models corresponds to current neuroanatomical models of OCD. Further, they elucidate the underlying neurobiological mechanisms of OCD at the circuit-based level.
Single‐cell transcriptome analysis reveals thyrocyte diversity in the zebrafish thyroid gland

The thyroid gland regulates growth and metabolism via production of thyroid hormone in follicles composed of thyrocytes. So far, thyrocytes have been assumed to be a homogenous population. To uncover heterogeneity in the thyrocyte population and molecularly characterize the non‐thyrocyte cells surrounding the follicle, we developed a single‐cell transcriptome atlas of the region containing the zebrafish thyroid gland. The 6249‐cell atlas includes profiles of thyrocytes, blood vessels, lymphatic vessels, immune cells, and fibroblasts. Further, the thyrocytes show expression heterogeneity, including bimodal expression of the transcription factor pax2a. To validate thyrocyte heterogeneity, we generated a CRISPR/Cas9‐based pax2a knock‐in line that monitors pax2a expression in the thyrocytes. A population of pax2a‐low mature thyrocytes interspersed in individual follicles can be distinguished. We corroborate heterogeneity within the thyrocyte population using RNA sequencing of pax2a‐high and pax2a‐low thyrocytes, which demonstrates 20% differential expression in transcriptome between the two subpopulations. Our results identify and validate transcriptional differences within the presumed homogenous thyrocyte population.
Metabolic syndrome and lifestyle factors among type 2 diabetes mellitus patients in Dessie Referral Hospital, Amhara region, Ethiopia

Background The prevalence of metabolic syndrome is rising at an alarming rate and more common among Type 2 Diabetes Mellitus patients in the world. The risk for cardiovascular disease is greater among individuals who have a combination of Type 2 Diabetes Mellitus and metabolic syndrome compared to those who have either alone. Objective To assess the proportion of metabolic syndrome and lifestyle factors among Type 2 Diabetes Mellitus Patients in Dessie Referral Hospital, Amhara Region, Ethiopia. Methods A hospital-based cross-sectional study was conducted from February to March 2017 among 343 randomly selected Type 2 Diabetes Mellitus patients. Three definitions of Metabolic syndrome were considered. Multivariable logistic regression analysis was conducted to identify factors associated with metabolic syndrome. Adjusted odds ratio (AOR) with 95% confidence intervals (CI) were reported to show the strength of association. Statistical significance was declared at P-value < 0.05. Result The proportion of metabolic syndrome was 50.3%, 59.4% and 64.5% according to 2005 International Diabetes Federation, revised ATP III and 2009 harmonized criteria, respectively. Being female (AOR = 2.43; 95% CI = 1.40, 4.21), consumption of red meat (AOR = 2.61; 95% CI = 1.28, 5.33), sedentary leisure time activity (AOR = 2.65; 95% CI = 1.47, 4.78), coffee intake (AOR = 0.43; 95% CI = 0.21, 0.86), BMI ≥ 25 kg/m2 (AOR = 9.59; 95% CI = 4.98, 18.47), 40–49 years of age (AOR = 2.74, 95% CI = (1.02, 7.37), 50–59 years of age (AOR = 4.22; 95% CI = 1.60, 11.11) and ≥70 years of age (AOR = 4.51, 95% CI = 1.44, 14.15) were significantly associated with metabolic syndrome. Conclusion and recommendation The proportion of metabolic syndrome was high among Type 2 Diabetes Mellitus patients. Overweight and obesity, being female, age of respondent, intake of coffee, regular red meat consumption, and sedentary leisure-time activity were factors associated with metabolic syndrome. Counseling of Type 2 Diabetes Mellitus patients on the need for spending leisure time with activities, intake of coffee, control of body weight, and avoidance of regular red meat consumption is recommended.
Formulation of New Baking (+)-Catechin Based Leavening Agents: Effects on Rheology, Sensory and Antioxidant Features during Muffin Preparation

The aim of this investigation was to prepare two solid mixtures containing a soluble polymorph of (+)-catechin and mucic (MUC) or tartaric (TAR) acids as new leavening agents. The solid mixtures were based on a polymorph of (+)-catechin, characterized through Powder X-ray Diffraction (PXRD) analysis and assayed in in vitro antioxidant and solubility assays. The dough samples were studied by dynamic rheological tests, while muffins were studied through Headspace Solid-Phase Microextraction (HS-SPME)/Gas Chromatography-Mass Spectrometry (GC-MS) analysis to identify volatile compounds, in vitro tests to evaluate antioxidant properties, and sensory analyses. TAR powder showed a solubility in water almost one order of magnitude increased with respect to commercial (+)-catechin (40.0 against 4.6 mg mL−1) and increased antioxidant performances. In particular, TAR showed total phenolic content (TPC) and total antioxidant capacity (TAC) values of 0.0298 ± 0.021 and 0.0081 ± 0.0009 meq CT/g, while MUC showed better results in terms of 2,2-diphenyl-1-picrylhydrazyl) acid (DPPH) and 2,2′-azino-bis (3-ethylbenzothiazoline-6-sulphonic acid (ABTS), 0.518 ± 0.015 and 0.112 ± 0.010 mg/mL, respectively. MS analysis identified different compounds derived from the lipid oxidation process. Muffins obtained using both powders showed interesting outcomes regarding dough process and appreciable appearance/olfactory/taste/texture profiles. Muffins obtained from TAR-based mixture showed also a total phenolic content of 0.00175 meq CT/g muffin, and almost two times improved TAC and scavenger activity against DPPH radical. The formulated powders could be used as suitable health-promoting ingredients in the food industry.
Microfluidics Used as a Tool to Understand and Optimize Membrane Filtration Processes

Membrane filtration processes are best known for their application in the water, oil, and gas sectors, but also in food production they play an eminent role. Filtration processes are known to suffer from a decrease in efficiency in time due to e.g., particle deposition, also known as fouling and pore blocking. Although these processes are not very well understood at a small scale, smart engineering approaches have been used to keep membrane processes running. Microfluidic devices have been increasingly applied to study membrane filtration processes and accommodate observation and understanding of the filtration process at different scales, from nanometer to millimeter and more. In combination with microscopes and high-speed imaging, microfluidic devices allow real time observation of filtration processes. In this review we will give a general introduction on microfluidic devices used to study membrane filtration behavior, followed by a discussion of how microfluidic devices can be used to understand current challenges. We will then discuss how increased knowledge on fundamental aspects of membrane filtration can help optimize existing processes, before wrapping up with an outlook on future prospects on the use of microfluidics within the field of membrane separation.
Nitrifying Microbes in the Rhizosphere of Perennial Grasses Are Modified by Biological Nitrification Inhibition

Soil nitrification (microbial oxidation of ammonium to nitrate) can lead to nitrogen leaching and environmental pollution. A number of plant species are able to suppress soil nitrifiers by exuding inhibitors from roots, a process called biological nitrification inhibition (BNI). However, the BNI activity of perennial grasses in the nutrient-poor soils of Australia and the effects of BNI activity on nitrifying microbes in the rhizosphere microbiome have not been well studied. Here we evaluated the BNI capacity of bermudagrass (Cynodon dactylon L.), St. Augustinegrass (Stenotaphrum secundatum (Walt.) Kuntze), saltwater couch (Sporobolus virginicus), seashore paspalum (Paspalum vaginatum Swartz.), and kikuyu grass (Pennisetum clandestinum) compared with the known positive control, koronivia grass (Brachiaria humidicola). The microbial communities were analysed by sequencing 16S rRNA genes. St. Augustinegrass and bermudagrass showed high BNI activity, about 80 to 90% of koronivia grass. All the three grasses with stronger BNI capacities suppressed the populations of Nitrospira in the rhizosphere, a bacteria genus with a nitrite-oxidizing function, but not all of the potential ammonia-oxidizing archaea. The rhizosphere of saltwater couch and seashore paspalum exerted a weak recruitment effect on the soil microbiome. Our results demonstrate that BNI activity of perennial grasses played a vital role in modulating nitrification-associated microbial populations.
Point-of-Care Ultrasound to Confirm the Depth of Endotracheal Tube in Children: Potential to Replace Chest Radiograph.

Pediatric Critical Care Medicine www.pccmjournal. org 1023 and we are still discovering its varied manifestations in the critically ill, such as multisystemic inflammatory syndrome of children and adolescents. There are many unknowns and the pathogenesis, clinical features, and therapeutic options are likely to be revealed over time. We thank Lanziotti et al (2) for their thoughtful letter, highlighting the many unknowns with COVID-19 in children, revealing theories of immunopathogenesis in children, and how that could impact acute disease and the development of immunity, including vaccine design. These are fundamental questions that the global community needs urgent answers on, and we encourage all of the readers to ensure maximal collaboration to answer these questions together. Given the relative rarity of pediatric disease requiring hospitalization or critical care, combining data, both biological and clinical, should be a fundamental goal of our community at this time. Understanding disease in children will provide tremendous insight into preventing and managing it across age groups, as well as guide population health interventions. The authors have disclosed that they do not have any potential conflicts of interest.
A simple, rapid, interpretable, actionable and implementable digital PCR based mortality index

ABSTRACT Mortality assessments are conducted for both civil and commercial purposes. Recent advances in epigenetics have resulted in DNA methylation tools to assess risk and aid in this task. However, widely available array-based algorithms are not readily translatable into clinical tools and do not provide a good foundation for clinical recommendations. Further, recent work shows evidence of heritability and possible racial bias in these indices. Using a publicly available array data set, the Framingham Heart Study (FHS), we develop and test a five-locus mortality-risk algorithm using only previously validated methylation biomarkers that have been shown to be free of racial bias, and that provide specific assessments of smoking, alcohol consumption, diabetes and heart disease. We show that a model using age, sex and methylation measurements at these five loci outperforms the 513 probe Levine index and approximates the predictive power of the 1030 probe GrimAge index. We then show each of the five loci in our algorithm can be assessed using a more powerful, reference-free digital PCR approach, further demonstrating that it is readily clinically translatable. Finally, we show the loci do not reflect ethnically specific variation. We conclude that this algorithm is a simple, yet powerful tool for assessing mortality risk. We further suggest that the output from this or similarly derived algorithms using either array or digital PCR can be used to provide powerful feedback to patients, guide recommendations for additional medical assessments, and help monitor the effect of public health prevention interventions.