Miracle-dz/UniFAR-FTUs huggingface dataset:
A FINITE ELEMENT ANALYSIS OF A CRACK GROWING UNDER CYCLIC LOADING

— Crack growth under cyclic loading has been studied by the finite element method. The calculation was made for plane stress conditions. The crack tip zone was modelled as a cohesive zone. The displacement of the free crack surface during unloading was found to be governed by the surrounding continuum and was independent of the details in the fracture zone. This means that crack closure upon unloading is directly related to the ultimate separation, of the cohesive zone, which in turn controls the residual plastic deformation left in the wake of the growing crack. If the distance over which closure takes place is rather small, closure may be very difficult to detect by the compliance technique.
mTOR dysregulation and tuberous sclerosis-related epilepsy

ABSTRACT Introduction. The mammalian target of rapamycin (mTOR) pathway has emerged as a key player for proper neural network development, and it is involved in epileptogenesis triggered by both genetic or acquired factors. Areas covered. The robust mTOR signaling deregulation observed in a large spectrum of epileptogenic developmental pathologies, such as focal cortical dysplasias and tuberous sclerosis complex (TSC), has been linked to germline and somatic mutations in mTOR pathway regulatory genes, increasing the spectrum of ‘mTORopathies’. The significant advances in the field of TSC allowed for the validation of emerging hypotheses on the mechanisms of epileptogenesis and the identification of potential new targets of therapy. Recently, a double-blind phase III randomized clinical trial on patients with TSC related epilepsy, demonstrated that adjunctive treatment with mTOR inhibition is effective and safe in reducing focal drug resistant seizures. Expert commentary. mTOR signaling dysregulation represents a common pathogenic mechanism in a subset of malformations of cortical development, sharing histopathological and clinical features, including epilepsy, autism, and intellectual disability. EXIST-3 trial provided the first evaluation of the optimal dosage, conferring a higher chance of reducing seizure frequency and severity, with adverse events being similar to what observed with lower dosages.
Assessing uncertainties in crop and pasture ensemble model simulations of productivity and N2O emissions

Simulation models are extensively used to predict agricultural productivity and greenhouse gas emissions. However, the uncertainties of (reduced) model ensemble simulations have not been assessed systematically for variables affecting food security and climate change mitigation, within multi‐species agricultural contexts. We report an international model comparison and benchmarking exercise, showing the potential of multi‐model ensembles to predict productivity and nitrous oxide (N2O) emissions for wheat, maize, rice and temperate grasslands. Using a multi‐stage modelling protocol, from blind simulations (stage 1) to partial (stages 2–4) and full calibration (stage 5), 24 process‐based biogeochemical models were assessed individually or as an ensemble against long‐term experimental data from four temperate grassland and five arable crop rotation sites spanning four continents. Comparisons were performed by reference to the experimental uncertainties of observed yields and N2O emissions. Results showed that across sites and crop/grassland types, 23%–40% of the uncalibrated individual models were within two standard deviations (SD) of observed yields, while 42 (rice) to 96% (grasslands) of the models were within 1 SD of observed N2O emissions. At stage 1, ensembles formed by the three lowest prediction model errors predicted both yields and N2O emissions within experimental uncertainties for 44% and 33% of the crop and grassland growth cycles, respectively. Partial model calibration (stages 2–4) markedly reduced prediction errors of the full model ensemble E‐median for crop grain yields (from 36% at stage 1 down to 4% on average) and grassland productivity (from 44% to 27%) and to a lesser and more variable extent for N2O emissions. Yield‐scaled N2O emissions (N2O emissions divided by crop yields) were ranked accurately by three‐model ensembles across crop species and field sites. The potential of using process‐based model ensembles to predict jointly productivity and N2O emissions at field scale is discussed.
Vertical wrap-gated nanowire transistors

We present a process for fabricating a field-effect transistor based on vertically standing InAs nanowires and demonstrate initial device characteristics. The wires are grown by chemical beam epitaxy at lithographically defined locations. Wrap gates are formed around the base of the wires through a number of deposition and etch steps. The fabrication is based on standard III–V processing and includes no random elements or single nanowire manipulation.
In vitro and biomechanical screening of polyethylene glycol and poly(trimethylene carbonate) block copolymers for annulus fibrosus repair

Herniated intervertebral discs (IVDs) are a common cause of back and neck pain. There is an unmet clinical need to seal annulus fibrosus (AF) defects, as discectomy surgeries address acute pain but are complicated by reherniation and recurrent pain. Copolymers of polyethylene glycol with trimethylene carbonate (TMC) and hexamethylene diisocyanate (HDI) end‐groups were formulated as AF sealants as the HDI form covalent bonds with native AF tissue. TMC adhesives were evaluated and optimized using the design criteria: stable size, strong adherence to AF tissue, high cytocompatibility, restoration of IVD biomechanics to intact levels following in situ repair, and low extrusion risk. TMC adhesives had high adhesion strength as assessed with a pushout test (150 kPa), and low degradation rates over 3 weeks in vitro. Both TMC adhesives had shear moduli (220 and 490 kPa) similar to, but somewhat higher than, AF tissue. The adhesive with three TMC moieties per branch (TMC3) was selected for additional in situ testing because it best matched AF shear properties. TMC3 restored torsional stiffness, torsional hysteresis area and axial range of motion to intact states. However, in a failure test of compressive deformation under fixed 5 ° flexion, some herniation risk was observed with failure strength of 5.9 MPa compared with 13.5 MPa for intact samples; TMC3 herniated under cyclic organ culture testing. These TMC adhesives performed well during in vitro and in situ testing, but additional optimization to enhance failure strength is required to further this material to advanced screening tests, such as long‐term degradation. Copyright © 2016 John Wiley & Sons, Ltd.
Genome-wide Transcriptional Dependence on TAF1 Functional Domains*

Transcription factor IID (TFIID) plays a central role in regulating the expression of most eukaryotic genes. Of the 14 TBP-associated factor (TAF) subunits that compose TFIID, TAF1 is one of the largest and most functionally diverse. Yeast TAF1 can be divided into four regions including a putative histone acetyltransferase domain and TBP, TAF, and promoter binding domains. Establishing the importance of each region in gene expression through deletion analysis has been hampered by the cellular requirement of TAF1 for viability. To circumvent this limitation we introduced galactose-inducible deletion derivatives of previously defined functional regions of TAF1 into a temperature-sensitive taf1ts2 yeast strain. After galactose induction of the TAF1 mutants and temperature-induced elimination of the resident Taf1ts2 protein, we examined the properties and phenotypes of the mutants, including their impact on genome-wide transcription. Virtually all TAF1-dependent genes, which comprise ∼90% of the yeast genome, displayed a strong dependence upon all regions of TAF1 that were tested. This finding might reflect the need for each region of TAF1 to stabilize TAF1 against degradation or may indicate that all TAF1-dependent genes require the many activities of TAF1. Paradoxically, deletion of the region of TAF1 that is important for promoter binding interfered with the expression of many genes that are normally TFIID-independent/SAGA (Spt-Ada-Gcn5-acetyltransferase)-dominated, suggesting that this region normally prevents TAF1 (TFIID) from interfering with the expression of SAGA-regulated genes.
Neural substrates and potential treatments for levodopa-induced dyskinesias in Parkinson’s disease

Abstract Parkinson’s disease (PD) is primarily a motor disorder that involves the gradual loss of motor function. Symptoms are observed initially in the extremities, such as hands and arms, while advanced stages of the disease can effect blinking, swallowing, speaking, and breathing. PD is a neurodegenerative disease, with dopaminergic neuronal loss occurring in the substantia nigra pars compacta, thus disrupting basal ganglia functions. This leads to downstream effects on other neurotransmitter systems such as glutamate, γ-aminobutyric acid, and serotonin. To date, one of the main treatments for PD is levodopa. While it is generally very effective, prolonged treatments lead to levodopa-induced dyskinesia (LID). LID encompasses a family of symptoms ranging from uncontrolled repetitive movements to sustained muscle contractions. In many cases, the symptoms of LID can cause more grief than PD itself. The purpose of this review is to discuss the possible clinical features, cognitive correlates, neural substrates, as well as potential psychopharmacological and surgical (including nondopaminergic and deep brain stimulation) treatments of LID.
Models projecting the fate of fish populations under climate change need to be based on valid physiological mechanisms

Some recent modelling papers projecting smaller fish sizes and catches in a warmer future are based on erroneous assumptions regarding (i) the scaling of gills with body mass and (ii) the energetic cost of ‘maintenance’. Assumption (i) posits that insurmountable geometric constraints prevent respiratory surface areas from growing as fast as body volume. It is argued that these constraints explain allometric scaling of energy metabolism, whereby larger fishes have relatively lower mass‐specific metabolic rates. Assumption (ii) concludes that when fishes reach a certain size, basal oxygen demands will not be met, because of assumption (i). We here demonstrate unequivocally, by applying accepted physiological principles with reference to the existing literature, that these assumptions are not valid. Gills are folded surfaces, where the scaling of surface area to volume is not constrained by spherical geometry. The gill surface area can, in fact, increase linearly in proportion to gill volume and body mass. We cite the large body of evidence demonstrating that respiratory surface areas in fishes reflect metabolic needs, not vice versa, which explains the large interspecific variation in scaling of gill surface areas. Finally, we point out that future studies basing their predictions on models should incorporate factors for scaling of metabolic rate and for temperature effects on metabolism, which agree with measured values, and should account for interspecific variation in scaling and temperature effects. It is possible that some fishes will become smaller in the future, but to make reliable predictions the underlying mechanisms need to be identified and sought elsewhere than in geometric constraints on gill surface area. Furthermore, to ensure that useful information is conveyed to the public and policymakers about the possible effects of climate change, it is necessary to improve communication and congruity between fish physiologists and fisheries scientists.
Cerebellar lobules and dentate nuclei mirror cortical force‐related‐BOLD responses: Beyond all (linear) expectations

The relationship between the BOLD response and an applied force was quantified in the cerebellum using a power grip task. To investigate whether the cerebellum responds in an on/off way to motor demands or contributes to motor responses in a parametric fashion, similarly to the cortex, five grip force levels were investigated under visual feedback. Functional MRI data were acquired in 13 healthy volunteers and their responses were analyzed using a cerebellum‐optimized pipeline. This allowed us to evaluate, within the cerebellum, voxelwise linear and non‐linear associations between cerebellar activations and forces. We showed extensive non‐linear activations (with a parametric design), covering the anterior and posterior lobes of the cerebellum with a BOLD‐force relationship that is region‐dependent. Linear responses were mainly located in the anterior lobe, similarly to the cortex, where linear responses are localized in M1. Complex responses were localized in the posterior lobe, reflecting its key role in attention and executive processing, required during visually guided movement. Given the highly organized responses in the cerebellar cortex, a key question is whether deep cerebellar nuclei show similar parametric effects. We found positive correlations with force in the ipsilateral dentate nucleus and negative correlations on the contralateral side, suggesting a somatotopic organization of the dentate nucleus in line with cerebellar and cortical areas. Our results confirm that there is cerebellar organization involving all grey matter structures that reflect functional segregation in the cortex, where cerebellar lobules and dentate nuclei contribute to complex motor tasks with different BOLD response profiles in relation to the forces. Hum Brain Mapp 38:2566–2579, 2017. © 2017 Wiley Periodicals, Inc.
Electrical Stimulation of Denervated Rat Skeletal Muscle Retards Capillary and Muscle Loss in Early Stages of Disuse Atrophy

The purpose of the present study is to investigate the effects of low-frequency electrical muscle stimulation (ES) on the decrease in muscle mass, fiber size, capillary supply, and matrix metalloproteinase (MMP) immunoreactivity in the early stages of denervation-induced limb disuse. Direct ES was performed on the tibialis anterior muscle following denervation in seven-week-old male rats. The rats were divided into the following groups: control (CON), denervation (DN), and denervation with direct ES (DN + ES). Direct ES was performed at an intensity of 16 mA and a frequency of 10 Hz for 30 min per day, six days a week, for one week. We performed immunohistochemical staining to determine the expression of dystrophin, CD34, and MMP-2 in transverse sections of TA muscles. The weight, myofiber cross-sectional area (FCSA), and capillary-to-fiber (C/F) ratio of the tibialis anterior (TA) muscle were significantly reduced in the DN group compared to the control and DN + ES groups. The MMP-2 positive area was significantly greater in DN and DN + ES groups compared to the control group. These findings suggest beneficial effects of direct ES in reducing muscle atrophy and capillary regression without increasing MMP-2 immunoreactivity in the early stages of DN-induced muscle disuse in rat hind limbs.
FGF23 protein expression in coronary arteries is associated with impaired kidney function.

BACKGROUND Fibroblast growth factor 23 (FGF23) levels are elevated in chronic kidney disease (CKD) and elevated values have been associated with both heart disease and mortality. Recent studies show that FGF23, a protein synthesized by osteocytes, is also present in calcified atherosclerotic plaques and may be induced by heart disease. Whether vascular expression of FGF23 is associated with progressive CKD, however, remains unknown. Therefore, the relationship between kidney function, vascular calcification and FGF23 expression was evaluated in patients with heart disease. METHODS Immunohistochemistry for FGF23 was performed in coronary arteries of all patients undergoing heart transplantation at UCLA between February 2008 and 2010. Immunohistochemical staining for Klotho, DMP1, FGFR1, and FGFR3; calcium deposition; and RNA expression of Klotho and DMP1 were assessed in a subset of eight samples. RESULTS FGF23 was detected by immunohistochemistry in 56% of the coronary artery specimens. Vascular FGF23 expression correlated with declining kidney function, as evidenced by reduced creatinine clearance. FGFR1 and FGFR3 were detected throughout the vascular tissue and in calcified plaques. Calcium deposition, Klotho expression and DMP1 expression correlated with FGF23 immunoreactivity. CONCLUSIONS The findings suggest that the Klotho-FGF23-FGFR system is active in coronary arteries and its upregulation correlates with impaired renal function and matrix calcium deposition.
NDNS: A DNS-Like Name Service for NDN

DNS provides a global-scale distributed lookup service to retrieve data of all types for a given name, be it IP addresses, service records, or cryptographic keys. This service has proven essential in today's operational Internet. Our experience with the design and development of Named Data Networking (NDN) suggests the need for a similar always-on lookup service. To fulfill this need we have designed the NDNS (NDN DNS) protocol, and learned several interesting lessons through the process. Although DNS's request-response operations seem closely resembling NDN's Interest-Data packet exchanges, they operate at different layers in the protocol stack. Comparing DNS's implementations over IP protocol stack with NDNS's implementation over NDN reveals several fundamental differences between applications designs for host-centric IP architecture and data-centric NDN architecture.
Cytologic Findings in a Neovagina Created with Vecchietti’s Technique for Treating Vaginal Aplasia

OBJECTIVE To report long-term cytologic findings after treatment of congenital vaginal aplasia or Mayer-Rokitansky-Küster-Hauser syndrome (MRKH) using progressive traction of the vulvar tissues, or Vecchietti's technique (VT). STUDY DESIGN In eight women with MRKH, neovaginal smears stained by the Harris-Schorr technique were collected 2-12 years after VT. RESULTS Eosinophilic superficial cells observed in all cases indicate that the neovaginal epithelium responds to hormonal variations. The presence of Döderlein bacilli (seven cases) suggests that the regional environment of the neovagina is almost the same as that of the normal vagina. Gardnerella vaginalis (one case) and human papilloma virus infection (low grade squamous intraepithelial lesions) (one case) were also observed. CONCLUSION Neovaginal smears taken after the cicatrization period following construction of a neovagina by VT show a remarkable resemblance to those from normal vaginal mucosa and suggest that these neovaginas are almost the same as normal vaginas.
Low noise sensitivity analysis of Lq-minimization in oversampled systems

The class of $\ell _q$-regularized least squares (LQLS) are considered for estimating $\beta \in \mathbb{R}^p$ from its $n$ noisy linear observations $y=X\beta + w$. The performance of these schemes are studied under the high-dimensional asymptotic setting in which the dimension of the signal grows linearly with the number of measurements. In this asymptotic setting, phase transition (PT) diagrams are often used for comparing the performance of different estimators. PT specifies the minimum number of observations required by a certain estimator to recover a structured signal, e.g. a sparse one, from its noiseless linear observations. Although PT analysis is shown to provide useful information for compressed sensing, the fact that it ignores the measurement noise not only limits its applicability in many application areas, but also may lead to misunderstandings. For instance, consider a linear regression problem in which $n>p$ and the signal is not exactly sparse. If the measurement noise is ignored in such systems, regularization techniques, such as LQLS, seem to be irrelevant since even the ordinary least squares (OLS) returns the exact solution. However, it is well known that if $n$ is not much larger than $p$, then the regularization techniques improve the performance of OLS. In response to this limitation of PT analysis, we consider the low-noise sensitivity analysis. We show that this analysis framework (i) reveals the advantage of LQLS over OLS, (ii) captures the difference between different LQLS estimators even when $n>p$, and (iii) provides a fair comparison among different estimators in high signal-to-noise ratios. As an application of this framework, we will show that under mild conditions LASSO outperforms other LQLS even when the signal is dense. Finally, by a simple transformation, we connect our low-noise sensitivity framework to the classical asymptotic regime in which $n/p \rightarrow \infty$, and characterize how and when regularization techniques offer improvements over ordinary least squares, and which regularizer gives the most improvement when the sample size is large.
Rapid online quantification of left ventricular volume from real-time three-dimensional echocardiographic data.

AIMS Determination of left ventricular (LV) volumes and ejection fraction (EF) from two-dimensional echocardiographic (2DE) images is subjective, time-consuming, and relatively inaccurate because of foreshortened views and the use of geometric assumptions. Our aims were (1) to validate a new method for rapid, online measurement of LV volumes from real-time three-dimensional echocardiographic (RT3DE) data using cardiac magnetic resonance (CMR) as the reference and (2) to compare its accuracy and reproducibility with standard 2DE measurements. METHODS AND RESULTS CMR, 2DE, and RT3DE datasets were obtained in 50 patients. End-systolic and end-diastolic volumes (ESV and EDV) were calculated from the 2DE images using biplane method of disks. ES and ED RT3DE datasets were analysed using prototype software designed to automatically detect the endocardial surface using a deformable shell model and calculate ESV and EDV from voxel counts. 2DE and RT3DE-derived volumes were compared with CMR (linear regression, Bland-Altman analysis). In most patients, analysis of RT3DE data required <2 min per patient. RT3DE measurements correlated highly with CMR (r: 0.96, 0.97, and 0.93 for EDV, ESV, and EF, respectively) with small biases (-14 mL, -6.5 mL, -1%) and narrow limits of agreement (SD: 17 mL, 16 mL, 6.4%). 2DE measurements correlated less well with CMR (r: 0.89, 0.92, 0.86) with greater biases (-23 mL, -15 mL, 1%) and wider limits of agreement (SD: 29 mL, 24 mL, 9.5%). RT3DE resulted in lower intra-observer (EDV: 7.9 vs. 23%; ESV: 7.6 vs. 26%) and inter-observer variability (EDV: 11 vs. 26%; ESV: 13 vs. 31%). CONCLUSION Semi-automated detection of the LV endocardial surface from RT3DE data is suitable for clinical use because it allows rapid, accurate, and reproducible measurements of LV volumes, superior to conventional 2DE methods.