Miracle-dz/UniFAR-FTUs huggingface dataset:
Substrate complex competition is a regulatory motif that allows NFκB RelA to license but not amplify NFκB RelB

Significance Inflammation-responsive canonical NFκB induces many genes, two of which encode noncanonical NFκB pathway components that control developmental processes. This suggests potentially perilous cross-regulation by which inflammatory conditions could derail immune organ developmental decisions. We use mathematical modeling to propose a mechanism that functions as a brake on this connection. We report that the key enzyme mediating developmental NFκB is subject to competition from two forms of its single substrate. Termed substrate complex competition, this regulatory motif can lead to a counterintuitive decrease of signaling product in conditions of elevated substrate abundance. We propose that although noncanonical NFκB requires intact inflammatory NFκB signaling, substrate complex competition allows developmental signals to be reliably transduced without inappropriate amplification by inflammation. Signaling pathways often share molecular components, tying the activity of one pathway to the functioning of another. In the NFκB signaling system, distinct kinases mediate inflammatory and developmental signaling via RelA and RelB, respectively. Although the substrates of the developmental, so-called noncanonical, pathway are induced by inflammatory/canonical signaling, crosstalk is limited. Through dynamical systems modeling, we identified the underlying regulatory mechanism. We found that as the substrate of the noncanonical kinase NIK, the nfkb2 gene product p100, transitions from a monomer to a multimeric complex, it may compete with and inhibit p100 processing to the active p52. Although multimeric complexes of p100 (IκBδ) are known to inhibit preexisting RelA:p50 through sequestration, here we report that p100 complexes can inhibit the enzymatic formation of RelB:p52. We show that the dose–response systems properties of this complex substrate competition motif are poorly accounted for by standard Michaelis–Menten kinetics, but require more detailed mass action formulations. In sum, although tonic inflammatory signaling is required for adequate expression of the noncanonical pathway precursors, the substrate complex competition motif identified here can prevent amplification of the active RelB:p52 dimer in elevated inflammatory conditions to ensure reliable RelB-dependent developmental signaling independent of inflammatory context.
Slotting effects and high frequency signal injection for induction machine rotor speed estimation

At zero frequency the speed sensorless operation may be only possible using high frequency signal injection methods (HFSIM's). Using the HFSIM's requiring the existence of saliencies in the machine. As the slots in induction machine present intrinsically design it is advantageous to exploit its effects for rotor speed monitoring. Injecting the HF voltage to fundamental supply, the rotor position can be determined by evaluating the current response. The combination between the model including slotting effects and the use of HF signal injection voltage to track rotor saliency created by slotting effects presents the aim of this research. Because the machine contains the rotor position dependent saliency, the carrier signal current includes the information about the rotor position. To extract this spatial information, the resulting stator current treads to heterodyning process to eliminate the disturbance components then the rotor speed is tracked by a closed-loop observer. The simulation tests will be achieved to verify the validity of the proposed model. At zero speed the effectiveness of speed estimation is confirmed through simulation results.
Effects of chronic treatment with gold nanoparticles on inflammatory responses and oxidative stress in Mdx mice

Abstract Duchenne muscular dystrophy (DMD) is an X-linked recessive hereditary myopathy characterised by progressive muscle degeneration in male children. As a consequence of DMD, increased inflammation and oxidative stress occur in muscle tissue along with morphological changes. Several studies have reported anti-inflammatory and antioxidant effects of gold nanoparticles (GNP) in muscle injury models. The objective of this study was to evaluate these effects along with the impacts of the disease on histopathological changes following chronic administration of GNP to Mdx mice. Two-month-old Mdx mice were separated into five groups of eight individuals each, as follows: wild-type (WT), Mdx-modified without treatment, Mdx + 2.5 mg/kg GNP, Mdx + 7.0 mg/kg GNP and Mdx + 21 mg/kg GNP. GNP with a mean diameter of 20 nm were injected subcutaneously at concentrations of 2.5, 7.0 and 21 mg/kg. Treatments continued for 30 d with injections administered at 48-h intervals. Twenty-four hours after the last injection, the animals were killed and the central region of the gastrocnemius muscle was surgically removed. Chronic administration of GNP reduced inflammation in the gastrocnemius muscle of Mdx mice and reduced morphological alterations due to inflammatory responses to muscular dystrophy. In addition, GNP also demonstrated antioxidant potential by reducing the production of reactive oxygen and nitrogen species, reducing oxidative damage and improving antioxidant activity.
Risk of Fractures and Falls during and after 5-α Reductase Inhibitor Use: A Nationwide Cohort Study

Background Lower urinary tract symptoms are common among older men and 5-α reductase inhibitors (5-ARI) are a group of drugs recommended in treating these symptoms. The effect on prostate volume is mediated by a reduction in dihydrotestosterone; however, this reduction is counterbalanced by a 25% rise in serum testosterone levels. Therefore, 5-ARI use might have systemic effects and differentially affect bone mineral density, muscular mass and strength, as well as falls, all of which are major determinants of fractures in older men. Methods We conducted a nationwide cohort study of all Swedish men who used 5-ARI by comparing their risk of hip fracture, any type of fracture and of falls with matched control men randomly selected from the population and unexposed to 5-ARI. Results During 1 417 673 person-years of follow-up, 10 418 men had a hip fracture, 19 570 any type of fracture and 46 755 a fall requiring hospital care. Compared with unexposed men, current users of 5-ARI had an adjusted hazard ratio (HR) of 0.96 (95% CI 0.91–1.02) for hip fracture, an HR of 0.94 (95% CI 0.90–0.98) for all fracture and an HR of 0.99 (95% CI 0.96–1.02) for falls. Former users had an increased risk of hip fractures (HR 1.10, 95% CI 1.01–1.19). Conclusion 5-ARI is safe from a bone health perspective with an unaltered risk of fractures and falls during periods of use. After discontinuation of 5-ARI, there is a modest increase in the rate of fractures and falls.
The effect of testing and feedback on the forgetting curves for radiograph interpretation skills

Abstract Objectives: Forgetting curves plot skill decay over time. After exposure to a simulation-based radiograph interpretation learning system, we determined the rate of learning decay and how this was impacted by testing (with and without feedback). Further, we examined the association of initial learning parameters on the forgetting curve. Methods: This was a multicenter, four-arm randomized control trial. Medical trainees completed 80 elbow radiographs and a 20-case post-test. Group 1 had no testing until 12 months; Groups 2–4 had testing every 2 months until 12 months. At 6 months, Group 3 testing was feedback-enhanced, while Group 4 had feedback-enhanced testing at 2, 6, and 10 months. Results: There were 106 participants (n = 42 Group 1; n = 22 Groups 2 and 3; n = 20 Group 4). Group 1 showed an –8.1% learning decay at 12-months relative to other groups. In Groups 2, 3, and 4, there was no significant learning decay (+0.8%), and there were no differences in skill decay between these groups. Initial score and learning curve slope were predictive of retained skill. Conclusions: Learning decay was mitigated by exposure to 20 test cases (with and without feedback) every two months. Initial learning parameters predicted learning retention and may inform refresher education scheduling.
Centralised and decentralised control of the Broken River

In this paper centralised Model Predictive Control (MPC), tuned in two different ways, and a decentralised control scheme are proposed for the control of the Broken River in Victoria, Australia. The control objective is to improve water resource management for the benefit of irrigators and the environment. The controllers are designed based on simple time delay and integrator delay models. The controllers are evaluated in realistic simulation scenarios and compared to manual operation. The use of control offers increased operational flexibility with a significant potential for substantial water savings, improved level of service to irrigators and improved environmental benefits.
Acoustic Manipulation of Bio-Particles at High Frequencies: An Analytical and Simulation Approach

Manipulation of micro and nano particles in microfluidic devices with high resolution is a challenge especially in bioengineering applications where bio-particles (BPs) are separated or patterned. While acoustic forces have been used to control the position of BPs, its theoretical aspects need further investigation particularly for high-resolution manipulation where the wavelength and particle size are comparable. In this study, we used a finite element method (FEM) to amend analytical calculations of acoustic radiation force (ARF) arising from an imposed standing ultrasound field. First, an acoustic solid interaction (ASI) approach was implemented to calculate the ARF exerted on BPs and resultant deformation induced to them. The results were then used to derive a revised expression for the ARF beyond the small particle assumption. The expression was further assessed in numerical simulations of one- and multi-directional standing acoustic waves (SAWs). Furthermore, a particle tracing scheme was used to investigate the effect of actual ARF on separation and patterning applications under experimentally-relevant conditions. The results demonstrated a significant mismatch between the actual force and previous analytical predictions especially for high frequencies of manipulation. This deviation found to be not only because of the shifted ARF values but also due to the variation in force maps in multidirectional wave propagation. Findings of this work can tackle the simulation limitations for spatiotemporal control of BPs using a high resolution acoustic actuation.
Who is susceptible in three false memory tasks?

ABSTRACT Decades of research show that people are susceptible to developing false memories. But if they do so in one task, are they likely to do so in a different one? The answer: “No”. In the current research, a large number of participants took part in three well-established false memory paradigms (a misinformation task, the Deese-Roediger-McDermott [DRM] list learning paradigm, and an imagination inflation exercise) as well as completed several individual difference measures. Results indicate that many correlations between false memory variables in all three inter-paradigm comparisons are null, though some small, positive, significant correlations emerged. Moreover, very few individual difference variables significantly correlated with false memories, and any significant correlations were rather small. It seems likely, therefore, that there is no false memory “trait”. In other words, no one type of person seems especially prone, or especially resilient, to the ubiquity of memory distortion.
Journal of Orthopaedic Research: Special Issue on Stem Cells

Stem cell research has exploded over the past two decades, spanning a number of different types of stem cells ranging from embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs) to adult stem cells derived from various sites in the body. Each of these cell types has specific advantages and disadvantages in their potential for translation. While ESCs and iPSCs provide true pluripotent properties, they face a number of complexities with respect to the control of their differentiation, and therefore, numerous regulatory issues may impair their use in the clinical setting. This article is protected by copyright. All rights reserved.
Transcriptomic profiling reveals three molecular phenotypes of adenocarcinoma at the gastroesophageal junction

Cancers occurring at the gastroesophageal junction (GEJ) are classified as predominantly esophageal or gastric, which is often difficult to decipher. We hypothesized that the transcriptomic profile might reveal molecular subgroups which could help to define the tumor origin and behavior beyond anatomical location. The gene expression profiles of 107 treatment‐naïve, intestinal type, gastroesophageal adenocarcinomas were assessed by the Illumina‐HTv4.0 beadchip. Differential gene expression (limma), unsupervised subgroup assignment (mclust) and pathway analysis (gage) were undertaken in R statistical computing and results were related to demographic and clinical parameters. Unsupervised assignment of the gene expression profiles revealed three distinct molecular subgroups, which were not associated with anatomical location, tumor stage or grade (p > 0.05). Group 1 was enriched for pathways involved in cell turnover, Group 2 was enriched for metabolic processes and Group 3 for immune‐response pathways. Patients in group 1 showed the worst overall survival (p = 0.019). Key genes for the three subtypes were confirmed by immunohistochemistry. The newly defined intrinsic subtypes were analyzed in four independent datasets of gastric and esophageal adenocarcinomas with transcriptomic data available (RNAseq data: OCCAMS cohort, n = 158; gene expression arrays: Belfast, n = 63; Singapore, n = 191; Asian Cancer Research Group, n = 300). The subgroups were represented in the independent cohorts and pooled analysis confirmed the prognostic effect of the new subtypes. In conclusion, adenocarcinomas at the GEJ comprise three distinct molecular phenotypes which do not reflect anatomical location but rather inform our understanding of the key pathways expressed.
How to measure a Hill–Sachs lesion: a systematic review

Quantifying bone loss is important to decide the best treatment for patients with recurrent anterior glenohumeral instability. Currently, there is no standard method available to make a precise evaluation of the Hill–Sachs lesion and predict its engagement before the surgical procedure. This literature review was performed in order to identify existing published imaging methods quantifying humeral head bone loss in Hill–Sachs lesions. Searches were undertaken in Scopus and PubMed databases from January 2008 until February 2018. The search terms were “Hill-Sachs” and “measurement” for the initial search and “Hill–Sachs bone loss” for the second, to be present in the keywords, abstracts and title. All articles that presented a method for quantifying measurement of Hill–Sachs lesions were analysed. Several methods are currently available to evaluate Hill–Sachs lesions. The length, width and depth measurements on CT scans show strong inter and intra-observer correlation coefficients. Three-dimensional CT is helpful for evaluation of bony injuries; however, there were no significant differences between 3D CT and 3D MRI measurements. The on-track off-track method using MRI allows a simultaneous evaluation of the Hill–Sachs and glenoid bone loss and also predicts the engaging lesions with good accuracy. Cite this article: EFORT Open Rev 2019;4:151-157. DOI: 10.1302/2058-5241.4. 180031
Review of Published Information on Foam Sclerotherapy

BACKGROUND New data on foam sclerotherapy of varicose veins has been recently published. OBJECTIVE To identify the current treatment modalities and their effectiveness in use of foam sclerotherapy. MATERIALS AND METHODS Review of the recent literature regarding clinical treatment of varicose veins using foam sclerotherapy, with emphasis on safety and efficacy. RESULTS Foam sclerotherapy of the great saphenous vein is more effective than liquid. Higher sclerosant concentrations tend to induce higher occlusion. Catheter‐assisted sclerotherapy may further improve occlusion rates. To achieve adequate occlusion, vein diameter and volume of foam must be matched. If a critical foam volume is exceeded, the risk of deep venous thrombosis increases. Foam sclerotherapy offers the possibility of using lower sclerosant concentrations than with liquids. Foam sclerotherapy can also be used in venous malformations and periulcerous tributaries. Side effects are hyperpigmentation, skin necrosis, scotoma, and thromboembolic events. Thromboembolism prophylaxis is necessary only in patients with special risk factors. CONCLUSION Foam sclerotherapy has significantly better efficacy than liquid. It is essential to select the correct concentration and the correct foam volume. In the hands of an experienced physician, foam sclerotherapy is a safe and effective option for treating varicose veins. This study was funded by Kreussler & Co.
Perspectives on Big Data and Big Data Analytics

Nowadays companies are starting to realize the importance of using more data in order to support decision for their strategies. It was said and proved through study cases that “More data usually beats better algorithms”. With this statement companies started to realize that they can chose to invest more in processing larger sets of data rather than investing in expensive algorithms. The large quantity of data is better used as a whole because of the possible correlations on a larger amount, correlations that can never be found if the data is analyzed on separate sets or on a smaller set. A larger amount of data gives a better output but also working with it can become a challenge due to processing limitations. This article intends to define the concept of Big Data and stress the importance of Big Data Analytics.
mRNA expression, functional profiling and multivariate classification of colon biopsy specimen by cDNA overall glass microarray.

AIM To understand the local pathophysiological alterations and gene ontology-based functional classification of colonic biopsies into inflammatory and neoplastic diseases. METHODS Total RNA was extracted from frozen biopsies and amplified by T7-method. Expression profile was evaluated by Atlas Glass 1K microarrays. After microarray quality control, applicable data were available from 10 adenomas, 6 colorectal adenocarcinomas (CRCs), and 6 inflammatory bowel diseases (IBDs). Multivariate statistical and cell functional analyses were performed. Real-time RT-PCR and immunohistochemistry were used for validation. RESULTS Discriminant analysis of selected genes, could correctly reclassify all 22 samples using 4 parameters (heat shock transcription factor-1, bystin-like, calgranulin-A, TRAIL receptor 3). IBD samples were characterized by overregulated chemokine (C-X-C motif) ligand 13, replication protein A1, E74-like factor 2 and downregulated TNF receptor-associated factor 6, BCL2-interacting killer genes. In adenomas upregulation of TNF receptor-associated factor 6, replication protein A1, E74-like factor 2 and underexpression of BCL2-associated X protein, calgranulin-A genes were found. CRC cases had significantly increased epidermal growth factor receptor, topoisomerase-1, v-jun, TNF receptor-associated factor 6 and TRAIL receptor 3, and decreased RAD51 and RAD52 DNA repair gene, protein phosphatase-2A and BCL2-interacting killer mRNA levels. Epidermal growth factor receptor RT-PCR and immunohistochemistry, topoisomerase-1 RT-PCR confirmed the chip results. CONCLUSION Different histological alterations can be reclassified by functional, multivariate analysis using cDNA microarrays. Further studies with expanded sample number are needed for subclassification of pathological alterations.
Complete Genome Sequence of a Colistin-Resistant Uropathogenic Escherichia coli Sequence Type 131 fimH22 Strain Harboring mcr-1 on an IncHI2 Plasmid, Isolated in Riyadh, Saudi Arabia

We report the complete genome sequence of a colistin-resistant strain of uropathogenic Escherichia coli, isolated in January 2013 at King Abdulaziz Medical City (KAMC), Riyadh, Saudi Arabia. The isolate (named SA186) was sequence type 131 (ST131) and belonged to serotype O25b-H4 and clade B (fimH22). ABSTRACT We report the complete genome sequence of a colistin-resistant strain of uropathogenic Escherichia coli, isolated in January 2013 at King Abdulaziz Medical City (KAMC), Riyadh, Saudi Arabia. The isolate (named SA186) was sequence type 131 (ST131) and belonged to serotype O25b-H4 and clade B (fimH22).
Reliable and secure encryption key generation from fingerprints

Purpose – Biometric authentication, which requires storage of biometric templates and/or encryption keys, raises a matter of serious concern, since the compromise of templates or keys necessarily compromises the information secured by those keys. To address such concerns, efforts based on dynamic key generation directly from the biometrics have recently emerged. However, previous methods often have quite unacceptable authentication performance and/or small key spaces and therefore are not viable in practice. The purpose of this paper is to propose a novel method which can reliably generate long keys while requires storage of neither biometric templates nor encryption keys.Design/methodology/approach – This proposition is achieved by devising the use of fingerprint orientation fields for key generation. Additionally, the keys produced are not permanently linked to the orientation fields, hence, allowing them to be replaced in the event of key compromise.Findings – The evaluation demonstrates that the propo.
High-Level Synthesis for Minimum-Area Low-Power Clock Gating

Clock gating is one of useful techniques to reduce the dynamic power consumption of synchronous sequential circuits. To reduce the power consumption of clock tree, previous work has shown that clock control logic should be synthesized in the high-level synthesis stage. However, previous work may suffer from a large circuit area overhead on the clock control logic. In this paper, we present an ILP (integer linear programming) formulation to consider both the clock tree and the clock control logic. Our optimization goal is not only to conform to the constraint on the overall power consumption, but also to minimize the area overhead of clock control logic. Compared with previous work, benchmark data show that our approach can greatly reduce the circuit area overhead under the same constraint on the overall power consumption.