Miracle-dz/UniFAR-FTUs huggingface dataset:
Symmetric coalescence of two hydraulic fractures

Significance We present an experimental investigation on the coalescence of hydraulic fractures in a brittle solid. Using a dual-fracturing setup, we obtain high-resolution experimental measurements on the time evolution of the fracture profiles and internal velocity field before, during, and after fracture coalescence. These measurements show an intermediate time self-similar coalescence during the dynamic interaction of two fractures. The work probes the dynamic formation of a fracture network, which is crucial to the industrial practice of energy resource recovery, compensation grouting, and the reservoir integrity of many confined systems involving fluid injection. The formation of a fracture network is a key process for many geophysical and industrial practices from energy resource recovery to induced seismic management. We focus on the initial stage of a fracture network formation using experiments on the symmetric coalescence of two equal coplanar, fluid-driven, penny-shaped fractures in a brittle elastic medium. Initially, the fractures propagate independently of each other. The fractures then begin to interact and coalesce, forming a bridge between them. Within an intermediate period after the initial contact, most of the fracture growth is localized along this bridge, perpendicular to the line connecting the injection sources. Using light attenuation and particle image velocimetry to measure both the fracture aperture and velocity field, we characterize the growth of this bridge. We model this behavior using a geometric volume conservation argument dependent on the symmetry of the interaction, with a 2D approximation for the bridge. We also verify experimentally the scaling for the bridge growth and the shape of the thickness profile along the bridge. The influence of elasticity and toughness of the solid, injection rate of the fluid, and initial location of the fractures are captured by our scaling.
Utility of Chest Radiographs in Children Presenting to a Pediatric Emergency Department With Acute Asthma Exacerbation and Chest Pain

Objectives Previous studies have not evaluated the utility of obtaining chest radiographs (CXR) in patients with acute asthma exacerbation reporting chest pain. The aims of this study were to evaluate the symptom of chest pain as a predictor for clinicians obtaining a CXR in these patients and to evaluate chest pain as a predictor of a positive CXR finding. Methods This was a retrospective chart review of patients, ages 2 to 18 years, presenting for acute asthma exacerbation to the emergency department from August 1, 2014, to March 31, 2016. Data collected included demographics, clinical data, provider type, and CXR results. Chest radiographs were classified as positive if they showed evidence of pneumonia, pneumothorax, or pneumomediastinum. Multivariate logistic regression models were developed with dependent variables of “obtaining a CXR” and “a positive CXR finding. ” Results Seven hundred ninety-three subjects were included in the study. Two hundred thirty-one (29.1%) reported chest pain. Chest radiographs were obtained in 184 patients (23.2%). Of those, 74 patients (40.2%) had chest pain and 21 (11.4%) had a positive CXR. Providers were more likely to obtain CXRs in patients who reported chest pain (odds ratio = 2.2 [95% confidence interval = 1.5–3.2]). Patients reporting chest pain were more likely to have a positive CXR although this difference was not statistically significant (odds ratio = 2.0 [95% confidence interval = 0.7–5.6]). Conclusions Providers are more likely to obtain CXRs in asthmatic patients complaining of chest pain; however, these CXRs infrequently yield positive findings. This further supports limiting the use of chest radiography in patients with acute asthma exacerbation.
University of Birmingham Serum testosterone, sex hormone-binding globulin and sex-specific risk of incident type 2 diabetes in a retrospective primary care cohort

Citation for published version (Harvard): O'reilly, M, Glisic, M, Kumarendran, B, Subramanian, A, Manolopoulos, K, Tahrani, A, Keerthy, D, Muka, T, Toulis, K, Hanif, W, Thomas, GN, Franco, OH, Arlt, W & Nirantharakumar, K 2019, 'Serum testosterone, sex hormone-binding globulin and sex-specific risk of incident type 2 diabetes in a retrospective primary care cohort', Clinical Endocrinology, vol. 90, no. 1, pp. 145-154. https://doi.org/10.1111/cen.13862
The jamming transition as a paradigm to understand the loss landscape of deep neural networks

Deep learning has been immensely successful at a variety of tasks, ranging from classification to artificial intelligence. Learning corresponds to fitting training data, which is implemented by descending a very high-dimensional loss function. Understanding under which conditions neural networks do not get stuck in poor minima of the loss, and how the landscape of that loss evolves as depth is increased, remains a challenge. Here we predict, and test empirically, an analogy between this landscape and the energy landscape of repulsive ellipses. We argue that in fully connected deep networks a phase transition delimits the over- and underparametrized regimes where fitting can or cannot be achieved. In the vicinity of this transition, properties of the curvature of the minima of the loss (the spectrum of the Hessian) are critical. This transition shares direct similarities with the jamming transition by which particles form a disordered solid as the density is increased, which also occurs in certain classes of computational optimization and learning problems such as the perceptron. Our analysis gives a simple explanation as to why poor minima of the loss cannot be encountered in the overparametrized regime. Interestingly, we observe that the ability of fully connected networks to fit random data is independent of their depth, an independence that appears to also hold for real data. We also study a quantity Δ which characterizes how well (Δ<0) or badly (Δ>0) a datum is learned. At the critical point it is power-law distributed on several decades, P_{+}(Δ)∼Δ^{θ} for Δ>0 and P_{-}(Δ)∼(-Δ)^{-γ} for Δ<0, with exponents that depend on the choice of activation function. This observation suggests that near the transition the loss landscape has a hierarchical structure and that the learning dynamics is prone to avalanche-like dynamics, with abrupt changes in the set of patterns that are learned.
Coarse-grained modelling of the structural properties of DNA origami

Abstract We use the oxDNA coarse-grained model to provide a detailed characterization of the fundamental structural properties of DNA origami, focussing on archetypal 2D and 3D origami. The model reproduces well the characteristic pattern of helix bending in a 2D origami, showing that it stems from the intrinsic tendency of anti-parallel four-way junctions to splay apart, a tendency that is enhanced both by less screened electrostatic interactions and by increased thermal motion. We also compare to the structure of a 3D origami whose structure has been determined by cryo-electron microscopy. The oxDNA average structure has a root-mean-square deviation from the experimental structure of 8.4 Å, which is of the order of the experimental resolution. These results illustrate that the oxDNA model is capable of providing detailed and accurate insights into the structure of DNA origami, and has the potential to be used to routinely pre-screen putative origami designs and to investigate the molecular mechanisms that regulate the properties of DNA origami.
Zoom-RNN: A Novel Method for Person Recognition Using Recurrent Neural Networks

The overwhelming popularity of social media has resulted in bulk amounts of personal photos being uploaded to the internet every day. Since these photos are taken in unconstrained settings, recognizing the identities of people among the photos remains a challenge. Studies have indicated that utilizing evidence other than face appearance improves the performance of person recognition systems. In this work, we aim to take advantage of additional cues obtained from different body regions in a zooming in fashion for person recognition. Hence, we present Zoom-RNN, a novel method based on recurrent neural networks for combining evidence extracted from the whole body, upper body, and head regions. Our model is evaluated on a challenging dataset, namely People In Photo Albums (PIPA), and we demonstrate that employing our system improves the performance of conventional fusion methods by a noticeable margin.
Arabidopsis RUP2 represses UVR8-mediated flowering in noninductive photoperiods

Arongaus et al. show that genetic mutation of REPRESSOR OF UV-B PHOTOMORPHOGENESIS 2 (RUP2) renders the facultative long day plant Arabidopsis thaliana a day-neutral plant (specifically under light conditions that include UV-B radiation) and dependent on the UV RESISTANCE LOCUS 8 (UVR8) UV-B photoreceptor.
Predicting protein secondary structure with Neural Machine Translation

We present analysis of a novel tool for protein secondary structure prediction using the recently-investigated Neural Machine Translation framework. The tool provides a fast and accurate folding prediction based on primary structure with subsecond prediction time even for batched inputs. We hypothesize that Neural Machine Translation can improve upon current predictive accuracy by better encoding complex relationships between nearby but non-adjacent amino acids. We overview our modifications to the framework in order to improve accuracy on protein sequences. We report 65.9% Q3 accuracy and analyze the strengths and weaknesses of our predictive model.
Motility and biofilm formation of the emerging gastrointestinal pathogen Campylobacter concisus differs under microaerophilic and anaerobic environments

Abstract Campylobacter concisus has been isolated from patients with gastroenteritis and inflammatory bowel disease (IBD), as well as healthy subjects. While strain differences may plausibly explain virulence differentials, an alternative hypothesis posits that the pathogenic potential of this species may depend on altered ecosystem conditions in the inflamed gut. One potential difference is oxygen availability, which is frequently increased under conditions of inflammation and is known to regulate bacterial virulence. Hence, we hypothesized that oxygen influences C. concisus physiology. We therefore characterized the effect of microaerophilic or anaerobic environments on C. concisus motility and biofilm formation, two important determinants of host colonization and dissemination. C. concisus isolates (n = 46) sourced from saliva, gut mucosal biopsies and feces of patients with IBD (n = 23), gastroenteritis (n = 8) and healthy subjects (n = 13), were used for this study. Capacity to form biofilms was determined using crystal violet assay, while assessment of dispersion through soft agar permitted motility to be assessed. No association existed between GI disease and either motility or biofilm forming capacity. Oral isolates exhibited significantly greater capacity for biofilm formation compared to fecal isolates (p<0.03), and showed a strong negative correlation between motility and biofilm formation (r = -0.7; p = 0.01). Motility significantly increased when strains were cultured under microaerophilic compared to anaerobic conditions (p<0.001). Increased biofilm formation under microaerophillic conditions was also observed for a subset of isolates. Hence, differences in oxygen availability appear to influence key physiological aspects of the opportunistic gastrointestinal pathogen C. concisus.
Assessment of Antagonist Enamel Wear and Clinical Performance of Full‐Contour Monolithic Zirconia Crowns: One‐Year Results of a Prospective Study

PURPOSE To assess the clinical performance and survival of full-contour monolithic zirconia (MZ) crowns and enamel wear produced over a 1-year period. MATERIALS AND METHODS 60 patients requiring full-coverage restorations for endodontically treated posterior teeth opposed by healthy unrestored antagonistic teeth were selected. MZ crowns were fabricated. Vinyl polysiloxane impressions of the antagonist teeth were made, and the stone casts were digitized using a 3D laser scanner. Wear of the opposing natural teeth was evaluated at baseline (1 week), 6 months, and 1 year after crown cementation. Superimposition of the follow-up scans on the baseline scans were performed to evaluate wear. Survival and function of the restorations were evaluated by the modified USPHS rating criteria at the same timeframes. RESULTS Comparison of the baseline and the follow-up wear values was statistically tested using the paired t-test. Statistical significance was noted between the wear values at 6 months (15.5 μm) and at 12 months (16.3 μm) (p < 0.05). The Wilcoxon signed rank sum test was performed to evaluate each parameter of the modified USPHS criteria and to analyze the change in the follow-up scores of the restorations. The survival rate for the crowns was 100%. Results were classified as "excellent" over a 1-year follow up. CONCLUSIONS MZ crowns showed promising results related to antagonist enamel wear and survival/clinical performance.
Epidemiology of Aspergillus species causing keratitis in Mexico

The incidence of fungal keratitis has increased in recent years. While the epidemiology and clinical roles of various Candida and Fusarium species have been relatively well‐identified in infections of the eye, data regarding keratitis caused by Aspergillus species are scant. Accurate and rapid diagnosis is important for successful management of this infection.
High-level Expression of Tetanus Toxin Fragment C in Escherichia coli.

Fragment C is the C-terminal domain of the heavy chain of tetanus toxin that can promote the immune response against the lethal dose of this toxin. Therefore, this portion can be considered as a candidate vaccine against tetanus infection, which occurs by Clostridium tetani. The present study aimed to compare the expression of tetanus toxin fragment C in Escherichia coli BL21 (DE3) pLysS cells having a high tolerance to toxins between two different expression vectors, namely pET22b and pET28a, using the sodium dodecyl sulfate polyacrylamide gel electrophoresis and western blot analyses. After DNA extraction from Harvard CN49205 strain of C. tetani, the gene of interest was amplified using polymerase chain reaction, and then sequenced and cloned into the expression vectors of pET22b and pET28a, transformed into competent BL21 (DE3) pLysS cells, and finally expressed using an optimized protocol. The cells were induced with isopropyl β-D-1-thiogalactopyranoside (IPTG) at four different incubation temperatures (i.e., 37, 33, 30, and 25 °C) and three different incubation times (i.e., 1, 2, and 3 h). Although the SDS-PAGE and western blot analyses confirmed the expression of the recombinant fragment C (r-fragment C) ligated into both of the expression vectors, pET28a showed a higher r-fragment C expression level than the other vector (38.66 mg/L versus 32.33 mg/L, P<0.05). An optimal expression condition was acquired 3 h after 1 mM IPTG induction at 25 °C. The results demonstrated that E. coli BL21 (DE3) pLysS as an expression host in combination with pET-28a as an expression vector was a more compatible expression system to express the fragment C of tetanus toxin, compared to E. coli BL21 (DE3) pLysS/pET-22b expression system. Overall, these results may represent an opportunity to improve the expression system for the production of tetanus toxin vaccine using recombinant protein strategy.
The effect of physiotherapy on fatigue and physical functioning in chronic fatigue syndrome patients: A systematic review.

OBJECTIVE The objectives of this work were to fill the gap in the scientific literature and to evaluate the results of physical therapy treatments in individuals affected by chronic fatigue syndrome, considering only studies that employed a randomized controlled trial. METHODS A systematic review was carried out according to PRISMA guidelines. Three bibliographic databases were searched: MEDLINE, Cochrane Library, and PEDro. The minimum prerequisites for papers to be included in the systematic review were that they had to (a) employ a randomized controlled trial; (b) be published in English; and (c) be published during the last ten years (2007-2017). The studies were evaluated according to Jadad score. RESULTS Four studies were included. This systematic review suggests that a treatment that is more effective than all the others cannot be defined. This conclusion is related to the low number of investigated studies; therefore, the collected results cannot be generalized. CONCLUSION Chronic fatigue syndrome is not yet a well-understood pathology, and the physical mechanisms that influence the outcomes still need more study. Rehabilitation programs that promote physiotherapy techniques such as exercise, mobilization, and body awareness (e.g., MRT and GET) are the most effective in reducing medium and long-term fatigue severity in CFS patients.
Association of functional polymorphisms in 3′-untranslated regions of COMT, DISC1, and DTNBP1 with schizophrenia: a meta-analysis

Introduction In recent years, various studies have accumulated evidence of the involvement of single nucleotide polymorphisms (SNPs) in introns and exons in schizophrenia. The association of functional SNPs in the 3′-untranslated regions with schizophrenia has been explored in a number of studies, but the results are inconclusive because of limited meta-analyses. To systematically analyze the association between SNPs in 3′-untranslated regions and schizophrenia, we conducted a meta-analysis by combining all available studies on schizophrenia candidate genes. Materials and methods We searched candidate genes from the schizophrenia database and performed a comprehensive meta-analysis using all the available data up to August 2017. The association between susceptible SNPs and schizophrenia was assessed by the pooled odds ratio with 95% confidence interval using fixed-effect and random-effect models. Results A total of 21 studies including 8291 cases and 9638 controls were used for meta-analysis. Three investigated SNPs were rs165599, rs3737597, and rs1047631 of COMT, DISC1, and DTNBP1, respectively. Our results suggested that rs3737597 showed a significant association with schizophrenia in Europeans (odds ratio: 1.584, P: 0.002, 95% confidence interval: 1.176–2.134) under a random-effect framework. Conclusion This meta-analysis indicated that rs3737597 of DISC1 was significantly associated with schizophrenia in Europeans, and it can be suggested as an ethnic-specific risk genetic factor.
A Survey of Learning Causality with Data

This work considers the question of how convenient access to copious data impacts our ability to learn causal effects and relations. In what ways is learning causality in the era of big data different from—or the same as—the traditional one? To answer this question, this survey provides a comprehensive and structured review of both traditional and frontier methods in learning causality and relations along with the connections between causality and machine learning. This work points out on a case-by-case basis how big data facilitates, complicates, or motivates each approach.
Dimerization interface of osteoprotegerin revealed by hydrogen–deuterium exchange mass spectrometry

Previous structural studies of osteoprotegerin (OPG), a crucial negative regulator of bone remodeling and osteoclastogenesis, were mostly limited to the N-terminal ligand-binding domains. It is now known that the three C-terminal domains of OPG also play essential roles in its function by mediating OPG dimerization, OPG–heparan sulfate (HS) interactions, and formation of the OPG–HS–receptor activator of nuclear factor κB ligand (RANKL) ternary complex. Employing hydrogen–deuterium exchange MS methods, here we investigated the structure of full-length OPG in complex with HS or RANKL in solution. Our data revealed two noteworthy aspects of the OPG structure. First, we found that the interconnection between the N- and C-terminal domains is much more rigid than previously thought, possibly because of hydrophobic interactions between the fourth cysteine-rich domain and the first death domain. Second, we observed that two hydrophobic clusters located in two separate C-terminal domains directly contribute to OPG dimerization, likely by forming a hydrophobic dimerization interface. Aided by site-directed mutagenesis, we further demonstrated that an intact dimerization interface is essential for the biological activity of OPG. Our study represents an important step toward deciphering the structure–function relationship of the full-length OPG protein.
Medical Cannabis in Patients with Chronic Pain: Effect on Pain Relief, Pain Disability, and Psychological aspects. A Prospective Non randomized Single Arm Clinical Trial.

BACKGROUND There is an increasing interest in the medical use of cannabis, particularly in the treatment of chronic pain. OBJECTIVES The aim is to evaluate the effects of cannabis use and the associated benefits reported by patients with various chronic pain diagnoses. MATERIAL AND METHODS A total of 338 patients with different chro- nic pain conditions were treated with a Cannabis Flos 19% decoction for 12 months, in addition to their pharmacological therapy. Baseline levels for pain medications, pain intensity, pain disability, anxiety and depression were recorded at 1, 3, 6 and 12 months. RESULTS Pain intensity records a statistically significant reduction from Baseline to 12 months follow up (X² 61.375; P<0,001); the im- provements from Baseline to 12 months follow up are also recorded in pain disability (X² 39.423; P<0,001) and in anxiety and depression symptoms (X²30.362; P<0,001; X²27.786; P<0,001). CONCLUSIONS Our study suggest that Cannabis therapy, as an adjun- ct a traditional analgesic therapy, can be an efficacious tool to make more effective the management of chronic pain and its consequences on functional and psychological dimension. Further randomized, controlled trials are needed to confirm our conclusions.
TFAP2 transcription factors are regulators of lipid droplet biogenesis

How trafficking pathways and organelle abundance adapt in response to metabolic and physiological changes is still mysterious, although a few transcriptional regulators of organellar biogenesis have been identified in recent years. We previously found that the Wnt signaling directly controls lipid droplet formation, linking the cell storage capacity to the established functions of Wnt in development and differentiation. In the present paper, we report that Wnt-induced lipid droplet biogenesis does not depend on the canonical TCF/LEF transcription factors. Instead, we find that TFAP2 family members mediate the pro-lipid droplet signal induced by Wnt3a, leading to the notion that the TFAP2 transcription factor may function as a “master” regulator of lipid droplet biogenesis.
Hessian barrier algorithms for linearly constrained optimization problems

In this paper, we propose an interior-point method for linearly constrained optimization problems (possibly nonconvex). The method - which we call the Hessian barrier algorithm (HBA) - combines a forward Euler discretization of Hessian Riemannian gradient flows with an Armijo backtracking step-size policy. In this way, HBA can be seen as an alternative to mirror descent (MD), and contains as special cases the affine scaling algorithm, regularized Newton processes, and several other iterative solution methods. Our main result is that, modulo a non-degeneracy condition, the algorithm converges to the problem's set of critical points; hence, in the convex case, the algorithm converges globally to the problem's minimum set. In the case of linearly constrained quadratic programs (not necessarily convex), we also show that the method's convergence rate is $\mathcal{O}(1/k^\rho)$ for some $\rho\in(0,1]$ that depends only on the choice of kernel function (i.e., not on the problem's primitives). These theoretical results are validated by numerical experiments in standard non-convex test functions and large-scale traffic assignment problems.