Miracle-dz/UniFAR-FTUs huggingface dataset:
Interactome of Radiation-Induced microRNA-Predicted Target Genes

The microRNAs (miRNAs) function as global negative regulators of gene expression and have been associated with a multitude of biological processes. The dysfunction of the microRNAome has been linked to various diseases including cancer. Our laboratory recently reported modulation in the expression of miRNA in a variety of cell types exposed to ionizing radiation (IR). To further understand miRNA role in IR-induced stress pathways, we catalogued a set of common miRNAs modulated in various irradiated cell lines and generated a list of predicted target genes. Using advanced bioinformatics tools we identified cellular pathways where miRNA predicted target genes function. The miRNA-targeted genes were found to play key roles in previously identified IR stress pathways such as cell cycle, p53 pathway, TGF-beta pathway, ubiquitin-mediated proteolysis, focal adhesion pathway, MAPK signaling, thyroid cancer pathway, adherens junction, insulin signaling pathway, oocyte meiosis, regulation of actin cytoskeleton, and renal cell carcinoma pathway. Interestingly, we were able to identify novel targeted pathways that have not been identified in cellular radiation response, such as aldosterone-regulated sodium reabsorption, long-term potentiation, and neutrotrophin signaling pathways. Our analysis indicates that the miRNA interactome in irradiated cells provides a platform for comprehensive modeling of the cellular stress response to IR exposure.
A fault-tolerant control architecture for induction motor drives in automotive applications

This paper describes a fault-tolerant control system for a high-performance induction motor drive that propels an electrical vehicle (EV) or hybrid electric vehicle (HEV). In the proposed control scheme, the developed system takes into account the controller transition smoothness in the event of sensor failure. Moreover, due to the EV or HEV requirements for sensorless operations, a practical sensorless control scheme is developed and used within the proposed fault-tolerant control system. This requires the presence of an adaptive flux observer. The speed estimator is based on the approximation of the magnetic characteristic slope of the induction motor to the mutual inductance value. Simulation results, in terms of speed and torque responses, show the effectiveness of the proposed approach.
Searching for chaotic dynamics in snowmelt runoff

Chaos analysis has altered the way we view natural systems. Complex or random-appearing phenomena may be chaotic and thus deterministic, rather than random. In this study, we used the Grassberger-Procaccia algorithm (GPA) to evaluate a runoff time series from a second-order catchment in southwestern Idaho for chaotic dynamics. GPA can identify the presence of low-dimensional chaotic dynamics for experimental time series. A daily runoff record, 8800 days in length, was examined. We found no evidence of chaotic dynamics in snowmelt runoff. Snowmelt runoff measured at a daily time step has a large number of degrees of freedom, which is characteristic of a random rather than chaotic process. These results suggest that the random-appearing behavior of snowmelt runoff is generated from the complex interactions of many factors, rather than low-dimensional chaotic dynamics.
RADIOCARBON-DATED DESTRUCTION LAYERS: A SKELETON FOR IRON AGE CHRONOLOGY IN THE LEVANT

Summary We present a full-sequence radiocarbon-based chronological system for the Iron Age in the Levant, anchored on the dating of ten destruction layers for the years 1130–730 BC. We establish the sequence using two methods – the ‘uncalibrated weighted average’ and the Bayesian modelling. Utilizing four dating tools in combination – radiocarbon measurements, field stratigraphy, pottery typology and ancient Near Eastern historical records – facilitates solutions to chronological problems that are far beyond the resolving power of 14C dating alone. The results shed light on disputed issues related to biblical and ancient Near Eastern history, such as the expansion of the early Israelite polity from the highlands to the lowlands; the nature of the Shoshenq I campaign to Canaan; and the evolution of the conflict between northern Israel and Aram Damascus.
EGCG Attenuates Autoimmune Arthritis by Inhibition of STAT3 and HIF-1α with Th17/Treg Control

Epigallocatechin-3-gallate (EGCG) is a green tea polyphenol exerting potent anti-oxidant and anti-inflammatory effects by inhibiting signaling and gene expression. The objective of the study was to evaluate the effect of EGCG on interleukin (IL)-1 receptor antagonist knockout (IL-1RaKO) autoimmune arthritis models. IL-1RaKO arthritis models were injected intraperitoneally with EGCG three times per week after the first immunization. EGCG decreased the arthritis index and showed protective effects against joint destruction in the IL-1RaKO arthritis models. The expression of pro-inflammatory cytokines, oxidative stress proteins, and p-STAT3 (Y705) and p-STAT3 (S727), mTOR and HIF-1α were significantly lower in mice treated with EGCG. EGCG reduced osteoclast markers in vivo and in vitro along with anti-osteoclastic activity was observed in EGCG-treated IL-1RaKO mice. The proportion of Foxp3+ Treg cells increased in the spleens of mice treated with EGCG, whereas the proportion of Th17 cells reduced. In vitro, p-STAT3 (Y705) and p-STAT3 (S727), HIF1α and glycolytic pathway molecules were decreased by EGCG. EGCG suppressed the activation of mTOR and subsequently HIF-1α, which is considered as a metabolic check point of Th17/Treg differentiation supporting the therapeutic potential of EGCG in autoimmune arthritis.
Authors' response to the letter of Nigel R Armfield on ‘The 60 most highly cited articles published in the Journal of Telemedicine and Telecare and Telemedicine Journal and E-health’

1. The aim of the study was not precisely stated The aim of the study was to analyse some characteristics of the 60 most cited papers published in the Journal of Telemedicine and Telecare (JTT) and Telemedicine Journal and E-health (TJEH). This is stated in the Introduction. Arguably, it is easier for the reader if the precise details of the characteristics that were analysed are left to the Methods. 2. The study did not describe the characteristics of highly cited papers in the field since the majority of papers in the field have been published in outlets other than the JTT and TJeH We agree that JTT and TJeH are not the only journals that publish papers on telemedicine. However, neither the title nor the text imply that we were trying to analyse all highly cited papers in telemedicine – the stated intention was to analyse highly cited papers in the two specialist journals. 3. The analysis was based on a single source We agree with this. However, our method for database searching was the same as many similar studies in other domains. It is obvious that a search in Google Scholar will return more hits than a search in the Web of Knowledge because of the much broader coverage of Google Scholar, which includes books and journals of perhaps lower quality. The quality of the papers was an important matter for us and we believe that papers indexed in Web of Knowledge are of high quality. Another reason for using the Web of Knowledge was to obtain the number of citations for each paper, which is not always readily available in other databases/sources. While the SCIE is very well adapted for extracting the number of citations for each paper, it would be difficult to retrieve the other data that we needed for our study. 4. The paper provides no new insight into the field We believe our paper provides useful, albeit brief, information regarding the characteristics of the telemedicine papers in the two journals. We did not attempt to extrapolate this information to obtain insights about the whole field of telemedicine – just the subset of it that the two specialist journals represent. We agree that the discussion section of our paper could have been more comprehensive. On the other hand, covering all six aims for the analysis of highly-cited publications which were mentioned in the introduction would have made our paper a great deal longer. We tried to do our best within the space constraints imposed by the journal.
A Framework and Comparative Analysis of Control Plane Security of SDN and Conventional Networks

Software defined networking implements the network control plane in an external entity, rather than in each individual device as in conventional networks. This architectural difference implies a different design for control functions necessary for essential network properties, e.g., loop prevention and link redundancy. We explore how such differences redefine the security weaknesses in the SDN control plane and provide a framework for comparative analysis which focuses on essential network properties required by typical production networks. This enables analysis of how these properties are delivered by the control planes of SDN and conventional networks, and to compare security risks and mitigations. Despite the architectural difference, we find similar, but not identical, exposures in control plane security if both network paradigms provide the same network properties and are analyzed under the same threat model. However, defenses vary; SDN cannot depend on edge based filtering to protect its control plane, while this is arguably the primary defense in conventional networks. Our concrete security analysis suggests that a distributed SDN architecture that supports fault tolerance and consistency checks is important for SDN control plane security. Our analysis methodology may be of independent interest for future security analysis of SDN and conventional networks.
Kinematic and Electromyographic Changes During 200 m Front Crawl at Race Pace

Abstract The purpose of this study was to analyse eventual kinematic and electromyographic changes during a maximal 200 m front crawl at race pace. 10 male international level swimmers performed a 200 m maximal front crawl test. Images were recorded by 2 above and 4 under water cameras, and electromyographic signals (EMG) of 7 upper and lower limbs muscles were analysed for 1 stroke cycle in each 50 m lap. Capillary blood lactate concentrations were collected before and after the test. The variables of interest were: swimming speed, stroke length, stroke and kick frequency, hand angular velocity, upper limb and foot displacement, elbow angle, shoulder and roll angle, duration of stroke phases, and EMG for each muscle in each stroke phase. Generally, the kinematic parameters decreased, and a relative duration increased for the entry and pull phases and decreased for the recovery phase. Muscle activation of flexor carpi radialis, biceps brachii, triceps brachii, peitoral major and upper trapezius increased during specific stroke phases over the test. Blood lactate concentration increased significantly after the test. These findings suggest the occurrence of fatigue, characterised by changes in kinematic parameters and selective changes in upper limbs muscle activation according to muscle action.
Drivers of variability in Arctic sea-ice drift speed

We explore the main drivers of seasonal and long-term variations in basin-scale Arctic sea-ice drift speed. To do so, we examine the relationship between the observed time-varying area-mean ice drift speed in the central Arctic and observed thickness and concentration as well as surface wind stress. Drift speeds are calculated from the positions of drifting buoys, thickness is based on submarine observations, concentration on satellite observations, and the wind stress comes from a global reanalysis. We find that seasonal changes in drift speed are correlated primarily with changes in concentration when concentration is low and with changes in thickness otherwise. The correlation between drift speed and concentration occurs because changing concentration changes how readily the ice responds to the synoptic-scale forcing of the atmosphere. Drift speed is correlated with neither concentration nor thickness in April and May. We show this behavior to be correlated with a decrease in the localization of deformation. This indicates that the increase in drift speed is caused by newly formed fractures not refreezing, leading to an overall reduced ice-cover strength without a detectable change in ice concentration. We show that a strong long-term trend exists in months of relatively low ice concentration. Using our analysis of the seasonal cycle, we show that the trend in concentration drives a significant portion of the drift-speed trend, possibly reinforced by a trend in cyclone activity. Hence, the trend in drift speed in this period is primarily caused by increased synoptic-scale movement of the ice pack.
Enter the Dragon: The Dynamic and Multifunctional Evolution of Anguimorpha Lizard Venoms

While snake venoms have been the subject of intense study, comparatively little work has been done on lizard venoms. In this study, we have examined the structural and functional diversification of anguimorph lizard venoms and associated toxins, and related these results to dentition and predatory ecology. Venom composition was shown to be highly variable across the 20 species of Heloderma, Lanthanotus, and Varanus included in our study. While kallikrein enzymes were ubiquitous, they were also a particularly multifunctional toxin type, with differential activities on enzyme substrates and also ability to degrade alpha or beta chains of fibrinogen that reflects structural variability. Examination of other toxin types also revealed similar variability in their presence and activity levels. The high level of venom chemistry variation in varanid lizards compared to that of helodermatid lizards suggests that venom may be subject to different selection pressures in these two families. These results not only contribute to our understanding of venom evolution but also reveal anguimorph lizard venoms to be rich sources of novel bioactive molecules with potential as drug design and development lead compounds.
Function of conserved histidine-243 in phosphatase activity of EnvZ, the sensor for porin osmoregulation in Escherichia coli

EnvZ and OmpR are the sensor and response regulator proteins of a two-component system that controls the porin regulon of Escherichia coli in response to osmolarity. Three enzymatic activities are associated with EnvZ: autokinase, OmpR kinase, and OmpR-phosphate (OmpR-P) phosphatase. Conserved histidine-243 is critical for both autokinase and OmpR kinase activities. To investigate its involvement in OmpR-P phosphatase activity, histidine-243 was mutated to several other amino acids and the phosphatase activity of mutated EnvZ was measured both in vivo and in vitro. In agreement with previous reports, we found that certain substitutions abolished the phosphatase activity of EnvZ. However, a significant level of phosphatase activity remained when histidine-243 was replaced with certain amino acids, such as tyrosine. In addition, the phosphatase activity of a previously identified kinase- phosphatase+ mutant was not abolished by the replacement of histidine-243 with asparagine. These data indicated that although conserved histidine-243 is important for the phosphatase activity, a histidine-243-P intermediate is not required. Our data are consistent with a previous model that proposes a common transition state with histidine-243 (EnvZ) in close contact with aspartate-55 (OmpR) for both OmpR phosphorylation and dephosphorylation. Phosphotransfer occurs from histidine-243-P to aspartate-55 during phosphorylation, but water replaces the phosphorylated histidine side chain leading to hydrolysis during dephosphorylation.
Plastic Optical Fibre Sensor for Spine Bending Monitoring with Power Fluctuation Compensation

This paper presents a study on the application of plastic optical fibre for spine bending monitoring based on an intensity modulation. The bending angle is measured as the angle between the emitting and receiving fibres is changed. The measured light attenuation is compared with a theoretical evaluation and the differences between these values are discussed. It was found that the light attenuation for the light intensity agreed well (margin of error < 15%) with the theoretical value for the range between 180° (representing no bend) and 200° and it was significantly increased for the bending angle beyond that value due to the effect of fibre gap increment which resulted in a less reliable experimental estimation.
Heterologous transmembrane and cytoplasmic domains direct functional chimeric influenza virus hemagglutinins into the endocytic pathway

Chimeric genes were created by fusing DNA sequences encoding the ectodomain of the influenza virus hemagglutinin (HA) to DNA coding for the transmembrane and cytoplasmic domains of either the G glycoprotein of vesicular stomatitis virus or the gC glycoprotein of Herpes simplex virus 1. CV-1 cells infected with SV40 vectors carrying the recombinant genes expressed large amounts of the chimeric proteins, HAG or HAgC on their surfaces. Although the ectodomains of HAG and HAgC differed in their immunological properties from that of HA, the chimeras displayed the biological functions characteristic of the wild-type protein. Both HAG and HAgC bound erythrocytes as efficiently as HA did and, after brief exposure to an acidic environment, induced the fusion of erythrocyte and CV-1 cell membranes. However, the behavior of HAG and HAgC at the cell surface differed from that of HA in several important respects. HAG and HAgC were observed to collect in coated pits whereas wild-type HA was excluded from those structures. In the presence of chloroquine, which inhibits the exit of receptors from endosomes, HAG and HAgC accumulated in intracellular vesicles. By contrast, chloroquine had no effect on the location of wild-type HA. HAG and HAgC labeled at the cell surface exhibited a temperature-dependent acquisition of resistance to extracellular protease at a rate similar to the rates of internalization observed for many cell surface receptors. HA acquired resistance to protease at a rate at least 20- fold slower. We conclude that HAG and HAgC are efficiently routed into the endocytic pathway and HA is not. However, like HA, HAG was degraded slowly, raising the possibility that HAG recycles to the plasma membrane.
The annual cycle and interannual variability of atmospheric pressure in the vicinity of the North Pole

A comparison of National Centers for Environmental Prediction–National Center for Atmospheric Research reanalysis six‐hourly sea‐level pressure data with former Soviet drifting station observations over the central Arctic Basin reveals high monthly correlations throughout the period 1950–91, but also a preferred winter season negative bias of about 1.4 hPa. Using the reanalysis, supplemented by Arctic Ocean Buoy Program fields and in situ observations, a generalized depiction of the annual cycle of pressure fields over the Arctic may be constructed. Above the Canada Basin–Laptev Sea side of the Arctic, the annual cycle of surface pressure is dominated by the first harmonic, which has an amplitude of about 5 hPa and maximum pressure occurring in March. Along the periphery of northern Greenland and extending to the North Pole, a weak semiannual cycle is found in surface pressure with maxima in May and November. The presence of the semiannual variation over time is highly variable.
Unique symptoms at midlife of women with osteoporosis and cardiovascular disease in Taiwan

ObjectiveThis study compared symptoms at midlife, menopause attitudes, and depression among three groups of late peri- or postmenopausal women, namely, women with cardiovascular disease (CVD group), women with osteoporosis (Os group), and women in generally good health (Co group). MethodsWe used a cross-sectional method. Participants were purposively sampled from a medical center and a residential community in southern Taiwan. A total of 500 women between 45 and 60 years of age participated in the study. Four measures were used: a demographics and health habits questionnaire, the Women’s Health Initiative Symptom Scale, the Attitudes Towards Menopause Scale, and the Center for Epidemiological Studies-Depression Scale. ResultsSignificant demographic differences among the groups were found in age, number of children, educational level, family income, employment status, exercise duration per session, smoking status, daily cigarette consumption, and number of years smoking. After significant covariates had been controlled for, the CVD group reported significantly more severe symptoms at midlife than did the Co group; significantly more severe “psychosomatic symptoms” than did the Co group; and significantly more severe “gastrointestinal symptoms and swelling” and “vasomotor symptoms” than did either the Os group or the Co group. The CVD group also reported significantly greater depressive symptoms than did the Os group. ConclusionsThis study identified a number of differences in symptoms at midlife and depressive symptoms among the three groups. Results support the importance of providing unique care for peri- and postmenopausal women in different health categories. Findings may help healthcare professionals better appreciate the diversity of menopausal experiences and support the development of appropriate care strategies.
Neurons with distinctive firing patterns, morphology and distribution in laminae V–VII of the neonatal rat lumbar spinal cord

It is generally accepted that neurons in the ventral spinal grey matter, a substantial proportion of which can be regarded as constituents of the spinal motor apparatus, receive and integrate synaptic inputs arising from various peripheral, spinal and supraspinal sources. Thus, a profound knowledge concerning the integrative properties of interneurons in the spinal ventral grey matter appears to be essential for a fair understanding of operational principles of spinal motor neural assemblies. Using the whole cell patch clamp configuration in a correlative physiological and morphological experimental approach, here we demonstrate that the intrinsic membrane properties of neurons vary widely in laminae V–VII of the ventral grey matter of the neonatal rat lumbar spinal cord. Based on their firing patterns in response to depolarizing current steps, we have classified the recorded neurons into four categories: ‘phasic’, ‘repetitive’, ‘single’ and ‘slow’. Neurons with firing properties characteristic of the ‘phasic’, ‘repetitive’ and ‘single’ cells have previously been reported also in the superficial and deep spinal dorsal horn, but this is the first account in the literature in which ‘slow’ neurons have been recovered and described in the spinal cord. The physiological heterogeneity in conjunction with the morphological correlation and distribution of neurons argues that different components of motor neural assemblies in the spinal ventral grey matter possess different signal processing characteristics.