Miracle-dz/UniFAR-FTUs huggingface dataset:
Refining the Definition of Plant Mitochondrial Presequences through Analysis of Sorting Signals, N-Terminal Modifications, and Cleavage Motifs1[W][OA]

Mitochondrial protein import is a complex multistep process from synthesis of proteins in the cytosol, recognition by receptors on the organelle surface, to translocation across one or both mitochondrial membranes and assembly after removal of the targeting signal, referred to as a presequence. In plants, import has to further discriminate between mitochondria and chloroplasts. In this study, we determined the precise cleavage sites in the presequences for Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) mitochondrial proteins using mass spectrometry by comparing the precursor sequences with experimental evidence of the amino-terminal peptide from mature proteins. We validated this method by assessments of false-positive rates and comparisons with previous available data using Edman degradation. In total, the cleavable presequences of 62 proteins from Arabidopsis and 52 proteins from rice mitochondria were determined. None of these proteins contained amino-terminal acetylation, in contrast to recent findings for chloroplast stromal proteins. Furthermore, the classical matrix glutamate dehydrogenase was detected with intact and amino-terminal acetylated sequences, indicating that it is imported into mitochondria without a cleavable targeting signal. Arabidopsis and rice mitochondrial presequences had similar isoelectric points, hydrophobicity, and the predicted ability to form an amphiphilic α-helix at the amino-terminal region of the presequence, but variations in length, amino acid composition, and cleavage motifs for mitochondrial processing peptidase were observed. A combination of lower hydrophobicity and start point of the amino-terminal α-helix in mitochondrial presequences in both Arabidopsis and rice distinguished them (98%) from Arabidopsis chloroplast stroma transit peptides. Both Arabidopsis and rice mitochondrial cleavage sites could be grouped into three classes, with conserved −3R (class II) and −2R (class I) or without any conserved (class III) arginines. Class II was dominant in both Arabidopsis and rice (55%–58%), but in rice sequences there was much less frequently a phenylalanine (F) in the −1 position of the cleavage site than in Arabidopsis sequences. Our data also suggest a novel cleavage motif of (F/Y)↓(S/A) in plant class III sequences.
A review of analgesic and emotive breathing: a multidisciplinary approach

The diaphragm is the primary muscle involved in breathing and other non-primarily respiratory functions such as the maintenance of correct posture and lumbar and sacroiliac movement. It intervenes to facilitate cleaning of the upper airways through coughing, facilitates the evacuation of the intestines, and promotes the redistribution of the body’s blood. The diaphragm also has the ability to affect the perception of pain and the emotional state of the patient, functions that are the subject of this article. The aim of this article is to gather for the first time, within a single text, information on the nonrespiratory functions of the diaphragm muscle and its analgesic and emotional response functions. It also aims to highlight and reflect on the fact that when the diaphragm is treated manually, a daily occurrence for manual operators, it is not just an area of musculature that is treated but the entire body, including the psyche. This reflection allows for a multidisciplinary approach to the diaphragm and the collaboration of various medical and nonmedical practitioners, with the ultimate goal of regaining or improving the patient’s physical and mental well-being.
Epigenetic Regulation of Multiple Tumor-Related Genes Leads to Suppression of Breast Tumorigenesis by Dietary Genistein

Breast cancer is one of the most lethal diseases in women; however, the precise etiological factors are still not clear. Genistein (GE), a natural isoflavone found in soybean products, is believed to be a potent chemopreventive agent for breast cancer. One of the most important mechanisms for GE inhibition of breast cancer may involve its potential in impacting epigenetic processes allowing reversal of aberrant epigenetic events during breast tumorigenesis. To investigate epigenetic regulation for GE impedance of breast tumorigenesis, we monitored epigenetic alterations of several key tumor-related genes in an established breast cancer transformation system. Our results show that GE significantly inhibited cell growth in a dose-dependent manner in precancerous breast cells and breast cancer cells, whereas it exhibited little effect on normal human mammary epithelial cells. Furthermore, GE treatment increased expression of two crucial tumor suppressor genes, p21WAF1 (p21) and p16INK4a (p16), although it decreased expression of two tumor promoting genes, BMI1 and c-MYC. GE treatment led to alterations of histone modifications in the promoters of p21 and p16 as well as the binding ability of the c-MYC–BMI1 complex to the p16 promoter contributing to GE-induced epigenetic activation of these tumor suppressor genes. In addition, an orally-fed GE diet prevented breast tumorigenesis and inhibited breast cancer development in breast cancer mice xenografts. Our results suggest that genistein may repress early breast tumorigenesis by epigenetic regulation of p21 and p16 by impacting histone modifications as well as the BMI1-c-MYC complex recruitment to the regulatory region in the promoters of these genes. These studies will facilitate more effective use of soybean product in breast cancer prevention and also help elucidate the mechanisms during the process of early breast tumorigenesis.
Stimulation of N2O emission by manure application to agricultural soils may largely offset carbon benefits: a global meta‐analysis

Animal manure application as organic fertilizer does not only sustain agricultural productivity and increase soil organic carbon (SOC) stocks, but also affects soil nitrogen cycling and nitrous oxide (N2O) emissions. However, given that the sign and magnitude of manure effects on soil N2O emissions is uncertain, the net climatic impact of manure application in arable land is unknown. Here, we performed a global meta‐analysis using field experimental data published in peer‐reviewed journals prior to December 2015. In this meta‐analysis, we quantified the responses of N2O emissions to manure application relative to synthetic N fertilizer application from individual studies and analyzed manure characteristics, experimental duration, climate, and soil properties as explanatory factors. Manure application significantly increased N2O emissions by an average 32.7% (95% confidence interval: 5.1–58.2%) compared to application of synthetic N fertilizer alone. The significant stimulation of N2O emissions occurred following cattle and poultry manure applications, subsurface manure application, and raw manure application. Furthermore, the significant stimulatory effects on N2O emissions were also observed for warm temperate climate, acid soils (pH < 6.5), and soil texture classes of sandy loam and clay loam. Average direct N2O emission factors (EFs) of 1.87% and 0.24% were estimated for upland soils and rice paddy soils receiving manure application, respectively. Although manure application increased SOC stocks, our study suggested that the benefit of increasing SOC stocks as GHG sinks could be largely offset by stimulation of soil N2O emissions and aggravated by CH4 emissions if, particularly for rice paddy soils, the stimulation of CH4 emissions by manure application was taken into account.
Screening after hypertensive pregnancy disorders: She can do best

Over the past decades several female-specific risk factors have been identified indicating an elevated future cardiovascular disease (CVD) risk. These can be related to hormonal status such as early/late menarche, menstrual irregularities, polycystic ovary syndrome, endometriosis and early natural or surgical menopause. Most important risk factors, however, are related to pregnancy disorders, such as recurrent miscarriages, gestational diabetes and hypertensive pregnancy disorders (HPDs) with preeclampsia/HELLP as the most severe manifestations. It is unclear yet to what extent and within which stage(s) of life these female-specific risk factors are relevant to CVD risk estimation in women. When considering all agegroups together, reproductive and pregnancy related disorders do not seem to affect 10 years risk estimation. For younger women (<60 years), however, who are often considered to be at low risk, there is now overwhelming evidence that a previous history of preeclampsia is a major tool in identifying elevated and premature CVD risk. This has resulted in the addition of preeclampsia/HELLP as a female-specific risk factor in several guidelines, such as the 2014 American Heart Association stroke prevention guideline and the 2016 European Society of Cardiology guideline CVD prevention. It remains to be determined how this risk should be weighed against the well known lifestyle and traditional risk factors and at what moment in time which preventive measures should be taken. Moreover, less severe and more heterogeneous expressions of HPD, occurring in 10–15% of all pregnancies, are 4–5 times more common than preeclampsia, and follow-up measures after HPDs have not been clearly defined. In this journal a systematic review by Groenhof et al. is published in which the appearance of CVD risk factors in female populations is evaluated in the first two decades after HPD. In 6904 women from 44 studies, levels of blood pressure (BP), glucose and lipids were evaluated and compared with those of age-matched women within three different healthy reference cohorts. It was found that 20% of women after HPD had hypertension around the age of 45 years, on average 15 years post index pregnancy. No differences were found in glucose and lipid levels between affected women and women in the reference cohorts. It should be noted, however, that most of these women were still premenopausal, which may have favourably affected these metabolic and lipid parameters. The authors express their uncertainty of how to optimally manage prevention after HPD, whereas the rapid developing field of eHealth applications may be an obvious solution for this relatively young at risk patient group.
Association of Retinal Vascular Diameter and Vascular Branching Angle with Diabetic Retinopathy Stage: A Cross-Sectional Study

Purpose: To determine the association between retinal vascular diameter and its branching angles with diabetic retinopathy (DR) stages in diabetic patients Methods: A descriptive analytic cross-sectional study was conducted in 62 diabetic patients (120 eyes) referred to Farabi Eye Hospital between June 2008 and December 2009. Digital fundus photography pictures were imported into Photoshop software and diameters of arterioles and venules at their second branches from the disc were calculated. Meanwhile branching angles were measured in the same arterioles and venules. DR was graded by retinal specialists according to Airlie House classification of DR. Retinal vascular diameters and their branching angles were compared in different DR stages. Results: There was a significant difference between retinal vascular diameters in different retinopathy stages. The diameter was significantly more in proliferative stage compared with mild nonproliferative stage (P 0.05). Conclusion: Retinal vascular diameter, but not retinal vascular angle, seems to be related with retinopathy stage regardless of age and hypertention in these patients.
A Risk-Centric Model of Demand Recessions and Speculation

We provide a continuous-time “risk-centric” representation of the New Keynesian model, which we use to analyze the interactions between asset prices, financial speculation, and macroeconomic outcomes when output is determined by aggregate demand. In principle, interest rate policy is highly effective in dealing with shocks to asset valuations. However, in practice monetary policy faces a wide range of constraints. If these constraints are severe, a decline in risky asset valuations generates a demand recession. This reduces earnings and generates a negative feedback loop between asset prices and aggregate demand. In the recession phase, average beliefs matter because they not only affect asset valuations but also determine the strength of the amplification mechanism. In the ex ante boom phase, belief disagreements (or heterogeneous asset valuations) matter because they induce investors to speculate. This speculation exacerbates the crash by reducing high-valuation investors’ wealth when the economy transitions to recession, which depresses (wealth-weighted) average beliefs. Macroprudential policy that restricts speculation in the boom can Pareto improve welfare by increasing asset prices and aggregate demand in the recession.
Designing a Willing-to-Use-in-Public Hand Gestural Interaction Technique for Smart Glasses

Smart glasses suffer from obtrusive or cumbersome interaction techniques. Studies show that people are not willing to publicly use, for example, voice control or mid-air gestures in front of the face. Some techniques also hamper the high degree of freedom of the glasses. In this paper, we derive design principles for socially acceptable, yet versatile, interaction techniques for smart glasses based on a survey of related work. We propose an exemplary design, based on a haptic glove integrated with smart glasses, as an embodiment of the design principles. The design is further refined into three interaction scenarios: text entry, scrolling, and point-and-select. Through a user study conducted in a public space we show that the interaction technique is considered unobtrusive and socially acceptable. Furthermore, the performance of the technique in text entry is comparable to state-of-the-art techniques. We conclude by reflecting on the advantages of the proposed design.
Are Outcomes of Surgical Versus Transcatheter Balloon Valvotomy Equivalent in Neonatal Critical Aortic Stenosis?

Background—For neonates with critical aortic valve stenosis who are selected for biventricular repair, valvotomy can be achieved surgically (SAV) or by transcatheter balloon dilation (BAV). Methods and Results—Data regarding 110 neonates with critical aortic valve stenosis were evaluated in a study by the Congenital Heart Surgeons Society from 1994 to 1999. Reduced left ventricular function was present in 46% of neonates. The initial procedure was SAV in 28 patients and BAV in 82 patients. Mean percent reduction in systolic gradient was significantly greater with BAV (65±17%) than SAV (41±32%;P <0.001). Higher residual median gradients were present in the SAV versus BAV group (36 mm Hg [range, 10 to 85 mm Hg] versus 20 mm Hg [0 to 85 mm Hg], P <0.001). Important aortic regurgitation was more often present after BAV (18%) than SAV (3%;P =0.07). Time-related survival after valvotomy was 82% at 1 month and 72% at 5 years, with no significant difference for SAV versus BAV, even after adjustment for differences in patient and disease characteristics. Independent risk factors for mortality were mechanical ventilation before valvotomy, smaller aortic valve annulus (z score), smaller aortic diameter at the sinotubular junction (z score), and a smaller subaortic region. A second procedure was performed in 46 survivors. Estimates for freedom from reintervention were 91% at 1 month and 48% at 5 years after the initial valvotomy and did not differ significantly between groups. Conclusions—SAV and BAV for neonatal critical aortic stenosis have similar outcomes. There is a greater likelihood of important aortic regurgitation with BAV and of residual stenosis with SAV.
Biomineralization of Engineered Spider Silk Protein-Based Composite Materials for Bone Tissue Engineering

Materials based on biodegradable polyesters, such as poly(butylene terephthalate) (PBT) or poly(butylene terephthalate-co-poly(alkylene glycol) terephthalate) (PBTAT), have potential application as pro-regenerative scaffolds for bone tissue engineering. Herein, the preparation of films composed of PBT or PBTAT and an engineered spider silk protein, (eADF4(C16)), that displays multiple carboxylic acid moieties capable of binding calcium ions and facilitating their biomineralization with calcium carbonate or calcium phosphate is reported. Human mesenchymal stem cells cultured on films mineralized with calcium phosphate show enhanced levels of alkaline phosphatase activity suggesting that such composites have potential use for bone tissue engineering.
THE FINE STRUCTURE OF EMBRYONIC CHICK SKELETAL MUSCLE CELLS DIFFERENTIATED IN VITRO

Dissociated myoblasts from 12-day chick embryos were cultured in monolayer, and the differentiation of skeletal muscle cells was studied by electron microscopy. The results have revealed a striking ultrastructural similarity between the in vivo and the in vitro developing muscle, particularly with respect to the myofibrils and sarcoplasmic reticulum. This study demonstrates that all the characteristic organelles of mature skeletal muscle can develop in vitro in the absence of nerves.
Variation in Genomic Methylation in Natural Populations of Chinese White Poplar

Background It is thought that methylcytosine can be inherited through meiosis and mitosis, and that epigenetic variation may be under genetic control or correlation may be caused by neutral drift. However, DNA methylation also varies with tissue, developmental stage, and environmental factors. Eliminating these factors, we analyzed the levels and patterns, diversity and structure of genomic methylcytosine in the xylem of nine natural populations of Chinese white poplar. Principal Findings On average, the relative total methylation and non-methylation levels were approximately 26.567% and 42.708% (P<0.001), respectively. Also, the relative CNG methylation level was higher than the relative CG methylation level. The relative methylation/non-methylation levels were significantly different among the nine natural populations. Epigenetic diversity ranged from 0.811 (Gansu) to 1.211 (Shaanxi), and the coefficients of epigenetic differentiation (GST = 0.159) were assessed by Shannon’s diversity index. Co-inertia analysis indicated that methylation-sensitive polymorphism (MSP) and genomic methylation pattern (CG-CNG) profiles gave similar distributions. Using a between-group eigen analysis, we found that the Hebei and Shanxi populations were independent of each other, but the Henan population intersected with the other populations, to some degree. Conclusions Genome methylation in Populus tomentosa presented tissue-specific characteristics and the relative 5′-CCGG methylation level was higher in xylem than in leaves. Meanwhile, the genome methylation in the xylem shows great epigenetic variation and could be fixed and inherited though mitosis. Compared to genetic structure, data suggest that epigenetic and genetic variation do not completely match.
Modified Phase-Extracted Basis Functions for Efficient Analysis of Scattering From Electrically Large Targets

In this paper, phase-extracted (MPE) basis functions with both the traveling wave terms and the standing wave terms have been proposed to analyze the scattering from the electrically large targets. This kind of basis functions, called modified phase-extracted (MPE) basis function, can be defined on the relatively large patches and constructed with the higher order hierarchical vector basis functions. The constructing idea of the MPE basis function is first introduced. Then, their characteristics were compared with the relevant basis functions. It has been demonstrated that the MPE basis function is suitable for the scattering analysis of the perfect electric conductors (PECs) with smooth convex surfaces as well as the concave structures, such as the electrically large cavities. The numerical solutions to the electromagnetic scattering from both the convex targets and the cavity-like targets with strong mutual couplings have been given to show the capability of the MPE basis functions in the description of the complex distribution of the induced current on the PEC surfaces. Some numerical examples have been given to demonstrate the validation of this kind of basis functions.
Variability and anatomical specificity of the orbitofrontothalamic fibers of passage in the ventral capsule / ventral striatum ( VC / VS ) : precision care for Citation

Deep Brain Stimulation (DBS) is a neurosurgical procedure that can reduce symptoms in medically intractable obsessive-compulsive disorder (OCD). Conceptually, DBS of the ventral capsule/ventral striatum (VC/VS) region targets reciprocal excitatory connections between the orbitofrontal cortex (OFC) and thalamus, decreasing abnormal reverberant activity within the OFC-caudate-pallidal-thalamic circuit. In this study, we investigated these connections using diffusion magnetic resonance imaging (dMRI) on human connectome datasets of twenty-nine healthy young-adult volunteers with two-tensor unscented Kalman filter based tractography. We studied the morphology of the lateral and medial orbitofrontothalamic connections and estimated their topographic variability within the VC/VS region. Our results showed that the morphology of the individual orbitofrontothalamic fibers of passage in the VC/VS region is complex and inter-individual variability in their topography is high. We applied this method to an example OCD patient case who underwent DBS surgery, formulating an initial proof of concept for a tractography-guided patient-specific approach in DBS for medically intractable OCD. This may improve on current surgical practice, which involves implanting all patients at identical stereotactic coordinates within the VC/VS region.
Mechanical integrity of carbon nanotubes for bending and torsion

The mechanical integrity of single-walled carbon nanotubes for bending and torsional deformations is evaluated using molecular dynamics simulations. A cantilever type nanotube loaded by a follower lateral force at the free end of the tube exhibits an unstable local buckling near the fixed end. A hysteresis loop is observed, accompanied by an irreversible thermodynamically stable topological transition from four hexagons to two pairs of pentagons and heptagons. The finite deformation can be described by a linear elastic solution almost up to the point of buckling. The initial torsional deformation gives a linear relationship between the torsional moment and the angle of twist per unit length. After buckling, an anti-plane distorted structure is generated, whose rigidity is weaker that of the original structure. The critical bending stress and the shear stress in torsion depend not only on the geometry of the cross section but also on the tube length.
Azine- and Azole-Functionalized Oligo´ and Polythiophene Semiconductors for Organic Thin-Film Transistors

In the organic electronics research field, several strategies have been used to modulate the transport properties of thiophene-derived semiconductors via sequential functionalization of their π-conjugated cores. This review summarizes the major design and synthetic strategies for tuning thiophene-containing small molecule and polymer properties by introducing electron-deficient nitrogen-containing azine and azole moieties. Several examples are presented which elucidate the structural, optical, and electronic consequences of incorporating these electron-deficient fragments in the conjugated skeletons, particularly relating to applications in organic thin-film transistors.