Miracle-dz/UniFAR-FTUs huggingface dataset:
Disease-specific motifs can be identified in circulating nucleic acids from live elk and cattle infected with transmissible spongiform encephalopathies

To gain insight into the disease progression of transmissible spongiform encephalopathies (TSE), we searched for disease-specific patterns in circulating nucleic acids (CNA) in elk and cattle. In a 25-month time-course experiment, CNAs were isolated from blood samples of 24 elk (Cervus elaphus) orally challenged with chronic wasting disease (CWD) infectious material. In a separate experiment, blood-sample CNAs from 29 experimental cattle (Bos taurus) 40 months post-inoculation with clinical bovine spongiform encephalopathy (BSE) were analyzed according to the same protocol. Next-generation sequencing provided broad elucidation of sample CNAs: we detected infection-specific sequences as early as 11 months in elk (i.e. at least 3 months before the appearance of the first clinical signs) and we established CNA patterns related to BSE in cattle at least 4 months prior to clinical signs. In elk, a progression of CNA sequence patterns was found to precede and correlate with macro-observable disease progression, including delayed CWD progression in elk with PrP genotype LM. Some of the patterns identified contain transcription-factor-binding sites linked to endogenous retroviral integration. These patterns suggest that retroviruses may be connected to the manifestation of TSEs. Our results may become useful for the early diagnosis of TSE in live elk and cattle.
Cardiac fibrosis and down regulation of GLUT4 in experimental diabetic cardiomyopathy are ameliorated by chronic exposures to intermittent altitude

Introduction: Chronic intermittent hypoxia is considered as a preconditioning status in cardiovascular health to inducing resistance to the low oxygen supply. Diabetic cardiomyopathy leads to inability of the heart to effective circulation of blood preventing of consequent tissue damages so; the aim of this study was elucidation of effect of chronic exposure to hypoxia on Cardiac fibrosis and expression of GLUT4 in experimental diabetic cardiomyopathy. Methods: A total number of 30 rats were randomly divided into three groups; 1: Normoxia control group (NN, n = 10). 2: Normoxia diabetic group (ND, n = 10) that took fat diet for 2 weeks then were injected by streptozotocin (37 mg/kg) and 3: Hypoxia diabetic group (HD, n = 10): that were exposed to chronic intermittent hypoxia (CIH) (altitude ≈3400 m, 14% oxygen for 8 weeks). After hypoxia challenge, plasma metabolic parameters including: fasting blood glucose (FBS), triglyceride (TG) and total cholesterol (TC) were measured by colorimetric assay. Cardiac expression of GLUT4 protein and cardiac collagen accumulation were determined in the excised left ventricle by western blotting, and Masson trichrome staining respectively. Results: Based on resultant data, FBS, TG and TC were significantly (P < 0.05) decreased in HD vs. ND. Homeostasis Model Assessment (HOMA) were also significantly attenuated after exposed to CIH in HD group compared to ND group (P < 0.05). Significant increase in packed cell volume and hemoglobin concentration was observed in HD group compared to ND group (P < 0.05). Comparison of heart wet weight between three groups showed a significant difference (P < 0.05) with lower amount in HD and ND versus NN. Myocardial fibrosis was significantly more pronounced in ND when compared to NN. Eight weeks exposure to hypoxia ameliorated this increase in HD group. Intermittent hypoxia significantly increased GLUT4 protein expression in HD compared to ND group (P < 0.05). Conclusion: Data suggested that CIH might potentiate to improve glucose homeostasis and cardiac tissue structural damages created in type 2 diabetes (T2D).
Infants' knowledge of their own species

Recognition of individuals at first sight is important for social species and can be achieved by attending to facial or body information. Previous research suggests that infants possess a perceptual template for evolutionarily relevant stimuli, which may include humans, dangerous animals (e.g. snakes), but not non-dangerous animals. To be effective, such a mechanism should result in a systematic preference for attending to humans over non-dangerous animals. Using a preferential looking paradigm, the present studies investigated the nature of infants' early representation of humans. We show that 3.5- and six-month-old infants attend more to human beings than non-human primates (a gorilla or monkey) which are examplars of non-dangerous animals. This occurred when infants were presented with head or body information in isolation, as well as when both are presented simultaneously. This early preference for humans by 3.5 months of age suggests that there is a basic representation for humans, which includes both head and/or body information. However, neonates demonstrated a preference only for human faces over non-human primate faces, not for humans over non-human primates when the stimuli were presented with both head and body simultaneously. The results show that although neonates display a preference for human faces over others, preference for the human body only develops later, in the first few months of life. This suggests that infants have acquired some knowledge about the human body at 3.5 months of age that may have developed from their privileged experience with other humans in the first few months of life, rather than an innate ability to detect humans in their entirety.
Andersen's syndrome: A distinct periodic paralysis

A previous study of 4 patients defined Andersen's syndrome (AS) as a triad of potassium‐sensitive periodic paralysis, ventricular dysrhythmias, and dysmorphic features. AS appears to be distinct in terms of its genetic defect from the α‐subunit of skeletal muscle sodium channel and the cardiac potassium channel responsible for most long QT syndromes (LQT1). We studied 11 additional patients with AS from 5 kindreds. Spontaneous attacks of paralysis were associated with hypokalemia, normokalemia, or hyperkalemia. All 11 patients had similar dysmorphic features. The QT interval was prolonged in all patients although only 4 were sympotomatic. Genetic linkage studies excluded linkage to the α‐subunit of the skeletal muscle sodium channel and to four distinct LQT loci. In addition, none of the common dihydropyridine receptor mutations responsible for hypokalemic periodic paralysis were present. We conclude that (1) AS is a genetically unique channelopathy affecting both cardiac and skeletal membrane excitability, (2) attacks of paralysis may be either hypokalemic or hyperkalemic, (3) a prolonged QT interval is an integral feature of this syndrome, and (4) a prolonged QT interval may be the only sign in an individual from an otherwise typical AS kindred. This may be confused with more common, potentially lethal LQT syndromes.
High-Throughput Discovery of Mutations in Tef Semi-Dwarfing Genes by Next-Generation Sequencing Analysis

Tef (Eragrostis tef) is a major cereal crop in Ethiopia. Lodging is the primary constraint to increasing productivity in this allotetraploid species, accounting for losses of ∼15–45% in yield each year. As a first step toward identifying semi-dwarf varieties that might have improved lodging resistance, an ∼6× fosmid library was constructed and used to identify both homeologues of the dw3 semi-dwarfing gene of Sorghum bicolor. An EMS mutagenized population, consisting of ∼21,210 tef plants, was planted and leaf materials were collected into 23 superpools. Two dwarfing candidate genes, homeologues of dw3 of sorghum and rht1 of wheat, were sequenced directly from each superpool with 454 technology, and 120 candidate mutations were identified. Out of 10 candidates tested, six independent mutations were validated by Sanger sequencing, including two predicted detrimental mutations in both dw3 homeologues with a potential to improve lodging resistance in tef through further breeding. This study demonstrates that high-throughput sequencing can identify potentially valuable mutations in under-studied plant species like tef and has provided mutant lines that can now be combined and tested in breeding programs for improved lodging resistance.
The influence of happiness, anger, and anxiety on the blood pressure of borderline hypertensives.

&NA; Differences in blood pressure associated with reported happiness, anger, and anxiety are examined among 90 borderline hypertensives during 24‐hr blood pressure monitoring. There were 1152 individual ambulatory blood pressure readings for which subjects classified their emotional state as happy (n = 628), angry (n = 67), or anxious (n = 457) on scales from one (low) to ten (high). Pressures were transformed to z‐scores using the subject's 24‐hr mean and standard deviation to assess relative elevation during reported emotional arousal. The results show that emotional arousal significantly increases systolic and diastolic pressure (p less than 0.00001), an effect independent of posture and location of subject during measurement (at work, home, or elsewhere). On average, pressures during reported angry or anxious states were higher than those during a happy state (p less than 0.01). Examination of arousal intensity showed that scores on the happiness scale were inversely related to systolic pressure (p less than 0.01) whereas the degree of anxiety was positively associated with diastolic pressure (p less than 0.02). Emotional effects were also related to the degree of individual daily pressure variation such that the greater the variability, the larger the blood pressure change associated with the emotions. The results suggest that happiness, anger, and anxiety increase blood pressure to differing degrees and that emotional effects may be greater in individuals with more labile blood pressure.
Haemodialysis catheters increase mortality as compared to arteriovenous accesses especially in elderly patients.

BACKGROUND Catheter use has been associated with an increased mortality risk in haemodialysis patients. However, differences in the all-cause and cause-specific mortality risk between catheter use and arteriovenous access use in young and elderly haemodialysis patients have not yet been investigated. METHODS In this prospective cohort study of 1109 incident haemodialysis patients from 38 centres in the Netherlands, hazard ratios (HRs) with 95% confidence intervals (95% CIs) were calculated for 2-year all-cause, infection-related and cardiovascular mortality in patients with a catheter as compared to patients with an arteriovenous access stratified for age (< 65 years and ≥ 65 years). RESULTS Of the 1109 patients, 919 had an arteriovenous access and 190 had a catheter. The mortality rate was 76 per 1000 person-years in young patients with an arteriovenous access, 129 per 1000 person-years in young patients with a catheter, 222 per 1000 person-years in elderly patients with an arteriovenous access and 427 per 1000 person-years in elderly patients with a catheter. The adjusted HR was 3.15 (95% CI: 2.09-4.75) for elderly patients with a catheter as compared to young patients with an arteriovenous access. The adjusted HRs in elderly patients with a catheter as compared to elderly patients with an arteriovenous access were 1.54 (95% CI: 1.13-2.12) for all-cause mortality, 1.60 (95%: CI 0.62-4.19) for infection-related mortality and 1.67 (95% CI: 1.04-2.68) for cardiovascular mortality. CONCLUSIONS Especially, elderly haemodialysis patients with a catheter have an increased all-cause, infection-related and cardiovascular mortality risk as compared to patients with an arteriovenous access.
Interpreting Sonority-Projection Experiments: The Role of Phonotactic Modeling

A variety of experiments support the existence of “sonority projection”: speakers represent severe sonority sequencing violations ([lba]) as less wellformed than modest ones ([bda]), even though neither is present in their native language. One interpretation of such findings is that the Sonority Sequencing Principle [9] is part of Universal Grammar. Modeling study, however, suggests that the results could be explained with more modest assumptions about UG. I use the Hayes-Wilson phonotactic learner [6] to show that sonority projection is possible in a system that merely attends to sonority differences and can generalize in the right way from the learning data.
Treatment of Severe Hypothyroidism Reduced Serum Creatinine Levels in Two Chronic Renal Failure Patients

Short-term hypothyroidism has been associated with a reversible rise in serum creatinine levels in patients with normal renal function. A remarkable decline in serum creatinine levels associated with a treatment of severe and prolonged hypothyroidism has rarely been reported so far. We present here 2 patients with chronic renal failure in whom treatment for hypothyroidism resulted in a significant and sustained reduction of their serum creatinine levels. These cases indicate that because hypothyroidism may aggravate the serum creatinine levels, TSH should be considered in screening procedures of patients with chronic renal failure presenting with recent accelerated aggravation of renal function. Hypothyroidism per se, one of its complications or one of its associated autoimmune diseases might play a role in modifying the underlying renal problem.
Both Toffoli and controlled-NOT need little help to do universal quantum computing

What additional gates are needed for a set of classical universal gates to do universal quantum computation? We answer this question by proving that any single-qubit real gate suffices, except those that preserve the computational basis. The result of Gottesman and Knill[quant-ph/9807006] implies that any quantum circuit involving only the Controlled-NOT and Hadamard gates can be efficiently simulated by a classical circuit. In contrast, we prove that Controlled-NOT plus any single-qubit real gate that does not preserve the computational basis and is not Hadamard (or its alike) are universal for quantum computing. Previously only a ``generic'' gate, namely a rotation by an angle incommensurate with pi, is known to be sufficient in both problems, if only one single-qubit gate is added.
Dental injuries in younger emergency department patients.

BACKGROUND Dental trauma is a relatively common occurrence in childhood, with an impact exceeding that of periodontal diseases. It places a significant burden on the public health system because of its high frequency, impact on quality of life and consumption of resources. OBJECTIVES To identify changing trends of dental injury in patients between 0-18 years of age in Canada and provide a detailed assessment of dental injury patterns in patients attending a large pediatric tertiary care hospital. METHODS This retrospective study was carried out in two parts. Firstly, data from patients who presented to the emergency departments of the 15 Canadian hospitals involved in the Injury Reporting and Prevention Program (CHIRPP) from 1st January 1990 to 31st December 2013 was collected. Secondly, at the Hospital for Sick Children, charts of patients identified from the aforementioned database from the years 2008, 2012 and 2015 were accessed for additional clinical data. RESULTS Based on CHIRPP data there appears to be an increasing incidence in dental injuries presenting to emergency departments nationally. Participation in sports and cycling contributed to the majority of dental injuries. The use of safety equipment such as helmets with a face-grill and mouth-guard was low. CONCLUSIONS Our study demonstrates a rising incidence of dental injuries in young patients. Most dental injuries occurred during sports and playground related activities. The low rate of use of safety equipment and playground safety measures suggests that Canadian Standards Association standards for playgrounds could be more effective if strengthened by mandatory legislation.
Structural organization of the actin-spectrin–based membrane skeleton in dendrites and soma of neurons

Significance Actin, spectrin, and associated molecules form a quasi-1D periodic membrane skeleton in neurons, which organizes membrane proteins in periodic distributions and provides mechanical stability for axons. Here, we provide detailed quantifications of this periodic structure in neurons and show that it develops substantially more slowly in dendrites than in axons. Moreover, we observed a 2D, polygonal lattice structure of these molecules in the somatodendritic compartment. The diverse structural organizations and different developmental courses of the membrane skeleton in different neuronal compartments suggest the membrane skeleton is differentially regulated across these neuronal compartments. The observation of the polygonal lattice structure in cells in addition to erythrocytes suggests a potentially general presence of this structure across diverse cell types. Actin, spectrin, and associated molecules form a membrane-associated periodic skeleton (MPS) in neurons. In the MPS, short actin filaments, capped by actin-capping proteins, form ring-like structures that wrap around the circumference of neurites, and these rings are periodically spaced along the neurite by spectrin tetramers, forming a quasi-1D lattice structure. This 1D MPS structure was initially observed in axons and exists extensively in axons, spanning nearly the entire axonal shaft of mature neurons. Such 1D MPS was also observed in dendrites, but the extent to which it exists and how it develops in dendrites remain unclear. It is also unclear whether other structural forms of the membrane skeleton are present in neurons. Here, we investigated the spatial organizations of spectrin, actin, and adducin, an actin-capping protein, in the dendrites and soma of cultured hippocampal neurons at different developmental stages, and compared results with those obtained in axons, using superresolution imaging. We observed that the 1D MPS exists in a substantial fraction of dendritic regions in relatively mature neurons, but this structure develops slower and forms with a lower propensity in dendrites than in axons. In addition, we observed that spectrin, actin, and adducin also form a 2D polygonal lattice structure, resembling the expanded erythrocyte membrane skeleton structure, in the somatodendritic compartment. This 2D lattice structure also develops substantially more slowly in the soma and dendrites than the development of the 1D MPS in axons. These results suggest membrane skeleton structures are differentially regulated across different subcompartments of neurons.
Direct Renin Inhibition With Aliskiren Protects Against Myocardial Ischemia/Reperfusion Injury by Activating Nitric Oxide Synthase Signaling in Spontaneously Hypertensive Rats

Background We tested the hypothesis that direct renin inhibition with aliskiren protects against myocardial ischemia/reperfusion (I/R) injury in spontaneously hypertensive rats (SHR), and examined the mechanism by which this occurs. Methods and Results Male SHR were treated (orally, 4 weeks) with saline or aliskiren (30 or 60 mg kg−1 day−1) and subjected to 30 minutes of left anterior descending coronary artery occlusion followed by 6 or 24 hours of reperfusion. Only the higher dose significantly lowered systolic blood pressure, the lower dose causing a smaller apparent lowering that was nonsignificant. Despite this difference in blood pressure‐lowering effect, both doses increased the ejection fraction and fractional shortening and reduced myocardial infarct size equally. I/R decreased cardiac expression of phosphatidylinositol 3‐kinase (PI3K), phospho‐Akt and phospho‐endothelial nitric oxide synthase (phospho‐eNOS), but increased expression of inducible nitric oxide synthase (iNOS); these changes were all abrogated by aliskiren. Moreover, aliskiren decreased superoxide anion generation and increased cyclic guanosine‐3′,5′‐monophosphate, an index of bioactive nitric oxide, in myocardium. It also decreased the expression of myocardial matrix metalloproteinase‐2, matrix metalloproteinase‐9, and tissue inhibitor of metalloproteinases‐1 (TIMP‐1) following I/R. In a Langendorff heart preparation, the detrimental cardiac effects of I/R were abrogated by aliskiren, and these protective effects were abolished by NOS or PI3K inhibition. In a parallel study, although specific iNOS inhibition reduced plasma malondialdehyde and myocardial superoxide anion generation, it did not affect the deleterious effects of I/R on myocardial structure and function. Conclusions Direct renin inhibition protects against myocardial I/R injury through activation of the PI3K‐Akt‐eNOS pathway.
IPCA-CMI: An Algorithm for Inferring Gene Regulatory Networks based on a Combination of PCA-CMI and MIT Score

Inferring gene regulatory networks (GRNs) is a major issue in systems biology, which explicitly characterizes regulatory processes in the cell. The Path Consistency Algorithm based on Conditional Mutual Information (PCA-CMI) is a well-known method in this field. In this study, we introduce a new algorithm (IPCA-CMI) and apply it to a number of gene expression data sets in order to evaluate the accuracy of the algorithm to infer GRNs. The IPCA-CMI can be categorized as a hybrid method, using the PCA-CMI and Hill-Climbing algorithm (based on MIT score). The conditional dependence between variables is determined by the conditional mutual information test which can take into account both linear and nonlinear genes relations. IPCA-CMI uses a score and search method and defines a selected set of variables which is adjacent to one of or Y. This set is used to determine the dependency between X and Y. This method is compared with the method of evaluating dependency by PCA-CMI in which the set of variables adjacent to both X and Y, is selected. The merits of the IPCA-CMI are evaluated by applying this algorithm to the DREAM3 Challenge data sets with n variables and n samples () and to experimental data from Escherichia coil containing 9 variables and 9 samples. Results indicate that applying the IPCA-CMI improves the precision of learning the structure of the GRNs in comparison with that of the PCA-CMI.
Readiness for change as a predictor of treatment effectiveness: An application of the transtheoretical model.

Clinical research suggests that adolescent offenders often do not view their criminal behaviors as problematic and, therefore, are not motivated for treatment. Although customarily defined as a static characteristic, the transtheoretical model (TTM) proposes treatment amenability is dynamic and can be achieved through tailored interventions that motivate individuals for treatment. The current study examines the predictive validity of TTM measures for adolescent offenders at a maximum security correctional facility. In particular, the Stages of Change Scale (SOCS) and Decisional Balance for Adolescent Offenders (DBS-AO) were compared with a more traditional assessment tool utilized in evaluating treatment amenability of juvenile offenders (i.e., Risk-Sophistication-Treatment Inventory; RSTI). One hundred adolescent offenders from the Gainesville State School completed two waves of data collection with a 3-month time interval. Information was collected on offenders' treatment progress between waves. Consistent with TTM research, predictors of treatment progress included low scores on the Cons scale on the DBS-AO and on the Precontemplation scale on the SOCS. Participants in the most advanced levels of treatment also scored high on the Sophistication-Maturity scale on the RSTI and the Impression Management scale on the Paulhus Deception Scale.