Miracle-dz/UniFAR-FTUs huggingface dataset:
Introduction: neural tube defects.

This volume of Neurosurgical Focus covers an array of topics useful to many specialists who care for patients with neural tube defects and related abnormalities. These patients have specific needs at each stage of the lifespan. Today, many individuals with significant developmental abnormalities of the spinal cord are leading full lives. For example, it is important for obstetricians and anesthesiologists to be cognizant of the underlying abnormalities associated with a lipomyelomeningocele or myelomeningocele to optimally care for a woman with one of these lesions during the delivery of her child. These lesions are exceedingly interesting from a developmental perspective, and a better understanding of the pathophysiology will continue to improve our management. The paper by Kalani et al. focuses primarily on the pathophysiology of intradural spinal teratomas. Dr. Vogel and associates describe recent advances in our understanding of how primary cilia contribute to the pathogenesis of neural tube defects and hydrocephalus. Dr. Sarris and colleagues provide a useful review of the pathology, treatment, and outcomes of lipomyelomeningoceles. A review of the management of urologic dysfunction in patients with neural tube defects by Amarante and colleagues will be useful to providers from a wide range of specialties. Maintaining optimal urologic health is a challenge throughout life. Finally, Dr. Cox and colleagues describe an unusual presentation of bilateral paramedian cutaneous dermal sinus tracts that caused multiple episodes of infection prior to definitive neurosurgical treatment. (http://thejns.org/doi/abs/10.3171/2012.8.FOCUS12285)
Working Memory, Cognitive Load and Cardiorespiratory Fitness: Testing the CRUNCH Model with Near-Infrared Spectroscopy

The present study aimed to examine the effects of chronological age and cardiorespiratory fitness (CRF) on cognitive performance and prefrontal cortex activity, and to test the compensation-related utilization of neural circuits hypothesis (CRUNCH). A total of 19 young adults (18–22 years) and 37 older ones (60–77 years) with a high or low CRF level were recruited to perform a working memory updating task under three different cognitive load conditions. Prefrontal cortex hemodynamic responses were continuously recorded using functional near-infrared spectroscopy, and behavioral performances and perceived difficulty were measured. Results showed that chronological age had deleterious effects on both cognitive performance and prefrontal cortex activation under a higher cognitive load. In older adults, however, higher levels of CRF were related to increased bilateral prefrontal cortex activation patterns that allowed them to sustain better cognitive performances, especially under the highest cognitive load. These results are discussed in the light of the neurocognitive CRUNCH model.
Testing random effects in linear mixed‐effects models with serially correlated errors

In linear mixed‐effects models, random effects are used to capture the heterogeneity and variability between individuals due to unmeasured covariates or unknown biological differences. Testing for the need of random effects is a nonstandard problem because it requires testing on the boundary of parameter space where the asymptotic chi‐squared distribution of the classical tests such as likelihood ratio and score tests is incorrect. In the literature several tests have been proposed to overcome this difficulty, however all of these tests rely on the restrictive assumption of i.i. d. measurement errors. The presence of correlated errors, which often happens in practice, makes testing random effects much more difficult. In this paper, we propose a permutation test for random effects in the presence of serially correlated errors. The proposed test not only avoids issues with the boundary of parameter space, but also can be used for testing multiple random effects and any subset of them. Our permutation procedure includes the permutation procedure in Drikvandi, Verbeke, Khodadadi, and Partovi Nia (2013) as a special case when errors are i.i. d. , though the test statistics are different. We use simulations and a real data analysis to evaluate the performance of the proposed permutation test. We have found that random slopes for linear and quadratic time effects may not be significant when measurement errors are serially correlated.
Electrospun Antimicrobial Films of Poly(3-hydroxybutyrate-co-3-hydroxyvalerate) Containing Eugenol Essential Oil Encapsulated in Mesoporous Silica Nanoparticles

The main goal of this study was to develop poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) films with long-term antimicrobial capacity of interest in food packaging applications. To this end, eugenol was first highly efficiently encapsulated at 50 wt. -% in the pores of mesoporous silica nanoparticles by vapor adsorption. The eugenol-containing nanoparticles were then loaded in the 2.5–20 wt. -% range into PHBV by electrospinning and the resultant electrospun composite fibers were annealed at 155 °C to produce continuous films. The characterization showed that the PHBV films filled with mesoporous silica nanoparticles containing eugenol present sufficient thermal resistance and enhanced mechanical strength and barrier performance to water vapor and limonene. The antimicrobial activity of the films was also evaluated against foodborne bacteria for 15 days in open vs. closed conditions in order to simulate real packaging conditions. The electrospun PHBV films with loadings above 10 wt. -% of mesoporous silica nanoparticles containing eugenol successfully inhibited the bacterial growth, whereas the active films stored in hermetically closed systems increased their antimicrobial activity after 15 days due to the volatile portion accumulated in the system’s headspace and the sustained release capacity of the films. The resultant biopolymer films are, therefore, potential candidates to be applied in active food packaging applications to provide shelf life extension and food safety.
Robust Non-Rigid Motion Compensation of Free-Breathing Myocardial Perfusion MRI Data

Kinetic parameter values, such as myocardial perfusion, can be quantified from dynamic contrast-enhanced magnetic resonance imaging data using tracer-kinetic modeling. However, respiratory motion affects the accuracy of this process. Motion compensation of the image series is difficult due to the rapid local signal enhancement caused by the passing of the gadolinium-based contrast agent. This contrast enhancement invalidates the assumptions of the (global) cost functions traditionally used in intensity-based registrations. The algorithms are unable to distinguish whether the differences in signal intensity between frames are caused by the spatial motion artifacts or the local contrast enhancement. In order to address this problem, a fully automated motion compensation scheme is proposed, which consists of two stages. The first of which uses robust principal component analysis (PCA) to separate the local signal enhancement from the baseline signal, before a refinement stage which uses the traditional PCA to construct a synthetic reference series that is free from motion but preserves the signal enhancement. Validation is performed on 18 subjects acquired in free-breathing and 5 clinical subjects acquired with a breath-hold. The validation assesses the visual quality, the temporal smoothness of tissue curves, and the clinically relevant quantitative perfusion values. The expert observers score the visual quality increased by a mean of 1.58/5 after motion compensation and improvement over the previously published methods. The proposed motion compensation scheme also leads to the improved quantitative performance of motion compensated free-breathing image series [30% reduction in the coefficient of variation across quantitative perfusion maps and 53% reduction in temporal variations (p < 0.001)].
Chronic thromboembolic pulmonary hypertension (CTEPH): what do we know about it? A comprehensive review of the literature

&NA; Chronic thromboembolic disease (CTED), especially when associated with pulmonary hypertension (CTEPH), is a fearsome and under-diagnosed but potentially curable complication of pulmonary embolism, thanks to recent therapeutic options. Aspecific symptoms and signs make its diagnosis challenging, requiring clinicians to be ready to suspect its presence in patients with dyspnea of unknown origin or persistent symptoms after acute pulmonary embolism. The aim of this review is to provide an update to the general practitioner or the specialist physician on the state of the art regarding the epidemiology, pathophysiology and clinical management of chronic thromboembolic syndromes.
MTHFR C677T genotype influences the isotopic enrichment of one-carbon metabolites in folate-compromised men consuming d9-choline.

BACKGROUND Homozygosity for the variant 677T allele in the methylenetetrahydrofolate reductase (MTHFR) gene increases the requirement for folate and may alter the metabolic use of choline. The choline adequate intake is 550 mg/d for men, although the metabolic consequences of consuming extra choline are unclear. OBJECTIVE Deuterium-labeled choline (d9-choline) as tracer was used to determine the differential effects of the MTHFR C677T genotype and the effect of various choline intakes on the isotopic enrichment of choline derivatives in folate-compromised men. DESIGN Mexican American men with the MTHFR 677CC or 677TT genotype consumed a diet providing 300 mg choline/d plus supplemental choline chloride for total choline intakes of 550 (n = 11; 4 with 677CC and 7 with 677TT) or 1100 (n = 12; 4 with 677CC and 8 with 677TT) mg/d for 12 wk. During the last 3 wk, 15% of the total choline intake was provided as d9-choline. RESULTS Low but measurable enrichments of the choline metabolites were achieved, including that of d3-phosphatidylcholine (d3-PtdCho)--a metabolite produced in the de novo pathway via choline-derived methyl groups. Men with the MTHFR 677TT genotype had a higher urinary enrichment ratio of betaine to choline (P = 0.041), a higher urinary enrichment of sarcosine (P = 0.041), and a greater plasma enrichment ratio of d9-betaine to d9-PtdCho with the 1100 mg choline/d intake (P = 0.033). CONCLUSION These data show for the first time in humans that choline itself is a source of methyl groups for de novo PtdCho biosynthesis and indicate that the MTHFR 677TT genotype favors the use of choline as a methyl donor.
The closing process of the ductus arteriosus connecting the left common carotid artery and main pulmonary artery

Abstract An isolated left common carotid artery is very rare, and only 13 cases have been reported thus far. All those cases were accompanied by a right aortic arch and aberrant left subclavian artery, and the connecting vessel between the pulmonary artery and left common carotid artery was thought to be ductal tissue. However, there have been no reports that have followed the natural closure of this vessel. We present a case in whom we could observe the closing process of this vessel at the connection between the left common carotid artery and main pulmonary artery in association with a tetralogy of Fallot.
Louse flies of Eleonora’s falcons that also feed on their prey are evolutionary dead‐end hosts for blood parasites

Host shifts are widespread among avian haemosporidians, although the success of transmission depends upon parasite‐host and parasite‐vector compatibility. Insular avifaunas are typically characterized by a low prevalence and diversity of haemosporidians, although the underlying ecological and evolutionary processes remain unclear. We investigated the parasite transmission network in an insular system formed by Eleonora's falcons (the avian host), louse flies that parasitize the falcons (the potential vector), and haemosporidians (the parasites). We found a great diversity of parasites in louse flies (16 Haemoproteus and 6 Plasmodium lineages) that did not match with lineages previously found infecting adult falcons (only one shared lineage). Because Eleonora's falcon feeds on migratory passerines hunted over the ocean, we sampled falcon kills in search of the origin of parasites found in louse flies. Surprisingly, louse flies shared 10 of the 18 different parasite lineages infecting falcon kills. Phylogenetic analyses revealed that all lineages found in louse flies (including five new lineages) corresponded to Haemoproteus and Plasmodium parasites infecting Passeriformes. We found molecular evidence of louse flies feeding on passerines hunted by falcons. The lack of infection in nestlings and the mismatch between the lineages isolated in adult falcons and louse flies suggest that despite louse flies’ contact with a diverse array of parasites, no successful transmission to Eleonora's falcon occurs. This could be due to the falcons’ resistance to infection, the inability of parasites to develop in these phylogenetically distant species, or the inability of haemosporidian lineages to complete their development in louse flies.
Uric acid induced epithelial−mesenchymal transition of renal tubular cells through PI3K/p‐Akt signaling pathway

The phenotypic changes of tubular epithelial cell are hallmark features of renal diseases caused by abnormal uric acid levels. We hereby intend to investigate whether PI3K/p‐Akt signaling plays a role in uric‐acid induced epithelial−mesenchymal transition process. The normal rat kidney cell line (NRK‐52E) was used as a proximal tubular cell model in this study. NRK‐52E cells were exposed to different concentrations of uric acid, or PI3K inhibitor LY294002, or both, respectively. The effects of uric acid on cell morphology were examined by phase contrast microscopy, while molecular alternations were assessed by western blot analysis and immunofluorescence staining. We found that uric acid induced visible morphological alterations in NRK‐52E cells accompanied by increased expression of α‐smooth muscle actin and reduced expression of E‐cadherin. Moreover, phosphorylation of Akt protein was obviously increased, whereas Akt level remained stable. Furthermore, the above effects were abolished when PI3K/p‐Akt pathway was blocked by the PI3K inhibitor. These findings demonstrated that high uric acid could induce phenotypic transition of cultured renal tubular cells, which was probably via activating PI3K/p‐Akt signaling pathway.
An Evaluation of Peak Expiratory Flow Monitoring: A Comparison of Sitting Versus Standing Measurements

Introduction: Current guidelines for the diagnosis and management of asthma suggest that patients perform peak expiratory flow (PEF) measurements while standing; however, recent literature suggests this may not be necessary. The purpose of this study was to determine the impact of patient position on PEF measurements. Methods: A randomized observational analysis of PEF measurements for 211 patients in sitting and standing positions was performed. The highest PEF measurement from tests performed with correct technique in both the sitting and standing position was compared. Results: Overall, PEF measurements did not significantly differ between the sitting and standing positions (506 ± 2 L/min versus 508 ± 2 L/min; P = .45). No differences were seen between mean PEF measurements in the sitting or standing positions for either women or men, nor were there significant differences between mean PEF values for the sitting and standing positions in participants who reported a history of asthma. Conclusions: PEF measurements do not significantly differ based on sitting or standing measurements among healthy participants. Based on the results of this study it may not be necessary for the patient to stand while performing PEF measurements. Further study among patients with asthma is warranted.
Chromosomal Mapping of Repetitive DNAs in Myiopsitta monachus and Amazona aestiva (Psittaciformes, Psittacidae) with Emphasis on the Sex Chromosomes

Here, for the first time, we describe the karyotype of Myiopsitta monachus (Psittacidae, Arini). We found 2n = 48, corresponding to the lowest diploid number observed in Neotropical Psittaciformes so far, with an uncommonly large W chromosome homomorphic to the Z. In order to better understand the evolution of the sex chromosomes in this species, we applied several molecular cytogenetic approaches, including C-banding, FISH mapping of repetitive DNAs (several microsatellite repeats), and whole-chromosome painting on metaphases of M. monachus. For comparison, another species belonging to the same tribe but with a smaller W chromosome (A. aestiva) was also analyzed. The results show that the constitutive heterochromatin has a very diverse distribution pattern in these species revealing heterochromatic blocks in the centromeric region of all chromosomes and in most of the length of the W chromosome in A. aestiva, while in M. monachus they were found in interstitial and telomeric regions. Concerning the microsatellites, only the sequence (CG)n produced signals on the W chromosome of A. aestiva, in the distal region of both arms. However, in M. monachus, (CAA)n, (CAG)n, and (CG)n probes were accumulated on the W chromosome, and, in addition, the sequence (CAG)n also hybridized to heterochromatic regions in macrochromosomes, as well as in microchromosomes. Based on these results, we suggest that the increase in length of the W chromosome in M. monachus is due to the amplification of repetitive elements, which highlights their significant role in the evolutionary process of sex chromosome differentiation.
Confidence in Women’s Health: A Cross Border Survey of Adult Nephrologists

A range of women’s health issues are intimately related to chronic kidney disease, yet nephrologists’ confidence in counseling or managing these issues has not been evaluated. The women’s health working group of Cure Glomerulonephropathy (CureGN), an international prospective cohort study of glomerular disease, sought to assess adult nephrologists’ training in, exposure to, and confidence in managing women’s health. A 25-item electronic questionnaire was disseminated in the United States (US) and Canada via CureGN and Canadian Society of Nephrology email networks and the American Society of Nephrology Kidney News. Response frequencies were summarized using descriptive statistics. Responses were compared across provider age, gender, country of practice, and years in practice using Pearson’s chi-squared test or Fisher’s exact test. Among 154 respondents, 53% were women, 58% practiced in the US, 77% practiced in an academic setting, and the median age was 41–45 years. Over 65% of respondents lacked confidence in women’s health issues, including menstrual disorders, preconception counseling, pregnancy management, and menopause. Most provided contraception or preconception counseling to less than one woman per month, on average. Only 12% had access to interdisciplinary pregnancy clinics. Finally, 89% felt that interdisciplinary guidelines and/or continuing education seminars would improve knowledge. Participants lacked confidence in both counseling and managing women’s health. Innovative approaches are warranted to improve the care of women with kidney disease and might include the expansion of interdisciplinary clinics, the development of case-based teaching materials, and interdisciplinary treatment guidelines focused on this patient group.
The nexus of functional exercise capacity with health-related quality of life in lung cancer: how closely are they related?

Lung cancer is a devasting and common diagnosis worldwide. Approximately 81% of patients present once the cancer has spread beyond the primary site and consequently surgical treatment is often not an option, with chemoradiation, targeted therapy or immunotherapies being most common in stage III to IV disease. Lung cancer has a high disease burden with symptoms such as shortness of breath, cough and fatigue that significantly impact the patient’s activities of daily living. In the last 10 years clinicians and researchers have focused on measuring symptoms and patient reported outcomes, and providing interventions to improve these.
Ultrahigh‐resolution MRI reveals structural brain differences in serotonin transporter knockout rats after sucrose and cocaine self‐administration

Excessive use of cocaine is known to induce changes in brain white and gray matter. It is unknown whether the extent of these changes is related to individual differences in vulnerability to cocaine addiction. One factor increasing vulnerability involves reduced expression of the serotonin transporter (5‐HTT). Human studies have shown that inherited 5‐HTT downregulation is associated with structural changes in the brain. These genotype‐related structural changes may contribute to risk for cocaine addiction. Here, we tested this idea by using ultrahigh‐resolution structural magnetic resonance imaging (MRI) on postmortem tissue of 5‐HTT−/− and wild‐type (5‐HTT+/+) rats with a history of long access to cocaine or sucrose (control) self‐administration. We found that 5‐HTT−/− rats, compared with wild‐type control animals, self‐administered more cocaine, but not sucrose, under long‐access conditions. Ultrahigh‐resolution structural MRI subsequently revealed that, independent of sucrose or cocaine self‐administration, 5‐HTT−/− rats had a smaller amygdala. Moreover, we found an interaction between genotype and type of reward for dorsal raphe nucleus volume. The data point to an important but differential role of the amygdala and dorsal raphe nucleus in 5‐HTT genotype–dependent vulnerability to cocaine addiction.
A Deep Learning Framework for Identifying Essential Proteins by Integrating Multiple Types of Biological Information

Computational methods including centrality and machine learning-based methods have been proposed to identify essential proteins for understanding the minimum requirements of the survival and evolution of a cell. In centrality methods, researchers are required to design a score function which is based on prior knowledge, yet is usually not sufficient to capture the complexity of biological information. In machine learning-based methods, some selected biological features cannot represent the complete properties of biological information as they lack a computational framework to automatically select features. To tackle these problems, we propose a deep learning framework to automatically learn biological features without prior knowledge. We use node2vec technique to automatically learn a richer representation of protein-protein interaction (PPI) network topologies than a score function. Bidirectional long short term memory cells are applied to capture non-local relationships in gene expression data. For subcellular localization information, we exploit a high dimensional indicator vector to characterize their feature. To evaluate the performance of our method, we tested it on PPI network of S. cerevisiae. Our experimental results demonstrate that the performance of our method is better than traditional centrality methods and is superior to existing machine learning-based methods. To explore which of the three types of biological information is the most vital element, we conduct an ablation study by removing each component in turn. Our results show that the PPI network embedding contributes most to the improvement. In addition, gene expression profiles and subcellular localization information are also helpful to improve the performance in identification of essential proteins.