Miracle-dz/UniFAR-FTUs huggingface dataset:
Optimal management of interstitial lung disease associated with dermatomyositis/polymyositis: lessons from the Japanese experience

Interstitial lung disease (ILD) is a serious complication in dermatomyositis (DM) and polymyositis (PM). In Japan, patients with DM/PM develop acute life-threatening ILD with high frequency. Physicians in Japan have shown the following: refractory acute/subacute (A/S)-ILD is not a rare complication in DM and amyopathic DM (ADM); anti-anti-melanoma differentiation-associated gene 5 (anti-MDA5) antibody (Ab) is closely related to A/S-ILD with poor outcomes in DM/ADM; and poor prognostic factors in A/S-ILD in DM/PM are ADM, DM with low creatine kinase elevation, positivity for anti-MDA5 Ab, serum ferritin elevation, and consolidation with ground-glass opacities on high-resolution computed tomography. There are subtypes in DM/PM-ILD: refractory DM/ADM A/S-ILD positive for anti-MDA5 Ab with poor prognosis; DM A/S-ILD with glucocorticoid (GC) resistance; PM A/S-ILD with GC sensitivity; chronic ILD positive for anti-aminoacyl-tRNA-synthetases (anti-ARS) Abs with GC responsive- ness; and C-ILD negative for anti-ARS Abs. For patients with A/S-ILD with poor prognosis, initial combination therapy with cyclosporine and cyclophosphamide in addition to GC has been developed, which rescues 50%-80% of the patients, although elucidation of the efficacy of the combination therapy is required. A/S-ILD with potentially fatal outcomes is found worldwide, not only in Japan. Clinicians caring for patients with DM/PM should be cautious when dealing with A/S-ILD and treat the patients based on clinical subtypes.
Electron beam lithography of bulk zinc oxide wafers using a polythiophene-based charge dissipation layer

The ability of thin conductive polythiophene layers to dissipate electrons in electron-beam lithography process on ZnO is presented for the first time. Quick and inexpensive processing method is shown for an EBL exposure of dense and highresolution patterns in hydrogen silsesquioxane (HSQ) negativetone resist deposited on bulk ZnO sample. Keywords-electron-beam lithography; zinc oxide; hydrogen silsesquioxane (HSQ); conductive polymer; PSS:PEDOT; photonic
Silver nanoparticles induce tight junction disruption and astrocyte neurotoxicity in a rat blood–brain barrier primary triple coculture model

Background Silver nanoparticles (Ag-NPs) can enter the brain and induce neurotoxicity. However, the toxicity of Ag-NPs on the blood–brain barrier (BBB) and the underlying mechanism(s) of action on the BBB and the brain are not well understood. Method To investigate Ag-NP suspension (Ag-NPS)-induced toxicity, a triple coculture BBB model of rat brain microvascular endothelial cells, pericytes, and astrocytes was established. The BBB permeability and tight junction protein expression in response to Ag-NPS, NP-released Ag ions, and polystyrene-NP exposure were investigated. Ultrastructural changes of the microvascular endothelial cells, pericytes, and astrocytes were observed using transmission electron microscopy (TEM). Global gene expression of astrocytes was measured using a DNA microarray. Results A triple coculture BBB model of primary rat brain microvascular endothelial cells, pericytes, and astrocytes was established, with the transendothelial electrical resistance values >200 Ω·cm2. After Ag-NPS exposure for 24 hours, the BBB permeability was significantly increased and expression of the tight junction (TJ) protein ZO-1 was decreased. Discontinuous TJs were also observed between microvascular endothelial cells. After Ag-NPS exposure, severe mitochondrial shrinkage, vacuolations, endoplasmic reticulum expansion, and Ag-NPs were observed in astrocytes by TEM. Global gene expression analysis showed that three genes were upregulated and 20 genes were downregulated in astrocytes treated with Ag-NPS. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that the 23 genes were associated with metabolic processes, biosynthetic processes, response to stimuli, cell death, the MAPK pathway, and so on. No GO term and KEGG pathways were changed in the released-ion or polystyrene-NP groups. Ag-NPS inhibited the antioxidant defense of the astrocytes by increasing thioredoxin interacting protein, which inhibits the Trx system, and decreasing Nr4a1 and Dusp1. Meanwhile, Ag-NPS induced inflammation and apoptosis through modulation of the MAPK pathway or B-cell lymphoma-2 expression or mTOR activity in astrocytes. Conclusion These results draw our attention to the importance of Ag-NP-induced toxicity on the neurovascular unit and provide a better understanding of its toxicological mechanisms on astrocytes.
High Prevalence of Extended-Spectrum β-Lactamase Producing Enterobacteriaceae Among Clinical Isolates From Cats and Dogs Admitted to a Veterinary Hospital in Switzerland

Objectives This study aimed to identify and characterize extended-spectrum β-lactamase (ESBL) producing Enterobacteriaceae among clinical samples of companion animals. Methods A total of 346 non-duplicate Enterobacteriaceae isolates were collected between 2012 and 2016 from diseased cats (n = 115) and dogs (n = 231). The presence of blaESBL, PMQR genes, and the azithromycin resistance gene mph(A) was confirmed by PCR and sequencing of bla genes. Isolates were further characterized by antimicrobial resistance profiling, multilocus sequence typing, phylogenetic grouping, identification of mutations in the QRDR of gyrA and parC, and screening for virulence-associated genes. Results Among the 346 isolates, 72 (20.8%) were confirmed ESBL producers [58 Escherichia coli (E. coli), 11 Klebsiella pneumoniae (K. pneumoniae), and 3 Enterobacter cloacae]. The strains were cultured from urine (n = 45), skin and skin wounds (n = 8), abscesses (n = 6), surgical sites (n = 6), bile (n = 4), and other sites (n = 3). ESBL genes included blaCTX-M-1, 14, 15, 27, 55, and blaSHV-12, predominantly blaCTX-M-15 (54.8%, 40/73), and blaCTX-M-1 (24.7%, 18/73). Further genes included qnrB (4.2%, 3/72), qnrS (9.7%, 7/72), aac(6’)-Ib-cr (47.2%, 34/72), and mph(A) (38.9%, 28/72). Seventeen (23.6%) isolates belonged to the major lineages of human pathogenic K. pneumoniae ST11, ST15, and ST147 and E. coli ST131. The most prevalent ST was E. coli ST410 belonging to phylogenetic group C. Conclusion The high prevalence of ESBL producing clinical Enterobacteriaceae from cats and dogs in Switzerland and the presence of highly virulent human-related K. pneumoniae and E. coli clones raises concern about transmission prevention as well as infection management and prevention in veterinary medicine.
Objective profiling of varied human motion based on normative assessment of magnetometer time series data

Objective: To quantify varied human motion and obtain an objective assessment of relative performance across a cohort. Approach: A wrist-worn magnetometer was used to record and quantify the complex motion patterns of 55 children aged 10 to 12 years old, generated during a fundamental movement skills programme. Sensor-based quantification of the physical activity used dynamic time warping of the magnetometer time series data for pairs of children. Pairwise comparison across the whole cohort produced a similarity matrix of all child to child correlations. Normative assessment scores were based on the Euclidean distance between n participants within an n − 1 multi-variate space, created from multi-dimensional scaling of the similarity matrix. The sensor-based scores were compared to the current standardised assessment which involves binary scoring of technique, outcome and time components by trained assessors. Main results: Visualisation of the relative performance using the first three axes of the multi-dimensional matrix, shows a ‘performance sphere’ in which children sit on concentric shells of increasing radius as performance deteriorates. Good agreement between standard and sensor scores is found, with Spearman rank correlation coefficients of the overall activity score in the range of 0.62–0.71 for different cohorts and a kappa statistic of 0.34 for categorisation of all 55 children into lower, middle, upper tertile and top 5% bands. Significance: By using multi-dimensional analysis of similarity measures between participants rather than direct parameterisation of the physiological data, complex and varied patterns of physical motion can be quantified, allowing objective and robust profiling of relative function across participant groups.
Regional Patterns of Cortical Phase Synchrony in the Resting State

Synchronized phase estimates between oscillating neuronal signals at the macroscale level reflect coordinated activities between neuronal assemblies. Recent electrophysiological evidence suggests the presence of significant spontaneous phase synchrony within the resting state. The purpose of this study was to investigate phase synchrony, including directional interactions, in resting state subdural electrocorticographic recordings to better characterize patterns of regional phase interactions across the lateral cortical surface during the resting state. We estimated spontaneous phase locking value (PLV) as a measure of functional connectivity, and phase slope index (PSI) as a measure of pseudo-causal phase interactions, across a broad range of canonical frequency bands and the modulation of the amplitude envelope of high gamma (amHG), a band that is believed to best reflect the physiological processes giving rise to the functional magnetic resonance imaging BOLD signal. Long-distance interactions had higher PLVs in slower frequencies (≤theta) than in higher ones (≥beta) with amHG behaving more like slow frequencies, and a general trend of increasing frequency band of significant PLVs when moving across the lateral surface along an anterior-posterior axis. Moreover, there was a strong trend of frontal-to-parietal directional phase synchronization, measured by PSI across multiple frequencies. These findings, which are likely indicative of coordinated and structured spontaneous cortical interactions, are important in the study of time scales and directional nature of resting state functional connectivity, and may ultimately contribute to a better understanding of how spontaneous synchrony is linked to variation in regional architecture across the lateral cortical surface.
Linearity of network proximity measures: implications for set‐based queries and significance testing

Motivation: In recent years, various network proximity measures have been proposed to facilitate the use of biomolecular interaction data in a broad range of applications. These applications include functional annotation, disease gene prioritization, comparative analysis of biological systems and prediction of new interactions. In such applications, a major task is the scoring or ranking of the nodes in the network in terms of their proximity to a given set of ‘seed’ nodes (e.g. a group of proteins that are identified to be associated with a disease, or are deferentially expressed in a certain condition). Many different network proximity measures are utilized for this purpose, and these measures are quite diverse in terms of the benefits they offer. Results: We propose a unifying framework for characterizing network proximity measures for set‐based queries. We observe that many existing measures are linear, in that the proximity of a node to a set of nodes can be represented as an aggregation of its proximity to the individual nodes in the set. Based on this observation, we propose methods for processing of set‐based proximity queries that take advantage of sparse local proximity information. In addition, we provide an analytical framework for characterizing the distribution of proximity scores based on reference models that accurately capture the characteristics of the seed set (e.g. degree distribution and biological function). The resulting framework facilitates computation of exact figures for the statistical significance of network proximity scores, enabling assessment of the accuracy of Monte Carlo simulation based estimation methods. Availability and Implementation: Implementations of the methods in this paper are available at https://bioengine.case.edu/crosstalker which includes a robust visualization for results viewing. Contact : stm@case.edu or mxk331@case.edu Supplementary information: Supplementary data are available at Bioinformatics online.
Femto-matching: Efficient traffic offloading in heterogeneous cellular networks

Heterogeneous cellular networks use small base stations, such as femtocells and WiFi APs, to offload traffic from macrocells. While network operators wish to globally balance the traffic, users may selfishly select the nearest base stations and make some base stations overcrowded. In this paper, we propose to use an auction-based algorithm - Femto-Matching, to achieve both load balancing among base stations and fairness among users. Femto-Matching optimally solves the global proportional fairness problem in polynomial time by transforming it into an equivalent matching problem. Furthermore, it can efficiently utilize the capacity of randomly deployed small cells. Our trace-driven simulations show Femto-Matching can reduce the load of macrocells by more than 30% compared to non-cooperative game based strategies.
Notes on Defects in Smoked Sheet and Crepe Rubber

Abstract In the following paragraphs a general account is given of the characteristics and the nature of commonly occurring defects in smoked sheet and crepe rubber, and of the principle underlying methods for their prevention as recommended for estate practice. Many of the defects referred to have no harmful effect on the quality of the rubber after vulcanization, and in the majority of cases the only reasonable excuse for their classification as defects is the unsightly appearance which they impart to the raw product. Since, however, standards of quality at present imposed by the market are based largely on appearance alone, methods have to be devised to prevent the occurrence of these defects.
Efficient reduction of Feynman integrals on supercomputers

Feynman integral reduction by means of integration-by-parts identities is a major power gadget in a theorist toolbox indispensable for calculation of multiloop quantum effects relevant for particle phenomenology and formal theory alike. An algorithmic approach consists of solving a large sparse non-square system of homogeneous linear equations with polynomial coefficients. While an analytical way of doing this is legitimate and was pursued for decades, it undoubtedly has its limitations when applied in complicated circumstances. Thus, a complementary framework based on modular arithmetic becomes critical on the way to conquer the current `what is possible' frontier. This calls for use of supercomputers to address the reduction problem. In order to properly utilize these computational resources, one has to efficiently optimize the technique for this purpose. Presently, we discuss and implement various methods which allow us to significantly improve performance of Feynman integral reduction within the FIRE environment.
The accuracy of adult recall for early mild traumatic brain injury

Abstract Background: Childhood mild traumatic brain injury (mTBI) has been associated with negative adult outcomes. Effective interventions require identification of the injury event. There is currently little information regarding the accuracy of adult recall of childhood mTBI. Method: Prospectively collected information from a large birth cohort was used to examine adult recall accuracy at age 25 for 161 childhood mTBI events occurring before age 10. Results: At age 25 cohort members recalled 11 outpatient injuries and 16 inpatient injuries. Recall accuracy increased with age. Logistic regression analysis distinguished between respondents who reported and did not report a childhood mTBI event correctly classifying 84.5% of cases. Age at injury, injury severity and loss of consciousness (LoC) made a unique statistically significant contribution to the model. Conclusions: Most childhood mTBI events are not recalled in adulthood. Age at injury, injury severity and LoC significantly increase likelihood of recall and should be used in measures that evaluate whether injury has occurred. Implications for rehabilitation Traumatic brain injury occurs frequently and often results in ongoing deficits in attention, concentration, executive function and later mental health problems. Identification of a history of traumatic brain injury is essential to ensure that appropriate rehabilitative input is provided. Rehabilitation professionals need to be aware that mental health problems may be secondary to a prior traumatic brain injury. It is important for rehabilitation professionals elicit an accurate history of traumatic brain injury to ensure that their treatment plans are tailored to the needs of this group.
Acute recovery from exercise in people with multiple sclerosis: an exploratory study on the effect of exercise intensities

Abstract Purpose A better understanding of how people with multiple sclerosis (pwMS) recover from exercise may help inform interventions. Methods We explored physiological and perceptual responses following exercise of different intensities, using a crossover exposure-response design, in 14 adults with multiple sclerosis (MS) and 9 controls. A cycling exercise test determined maximum capacity (Wpeak). Participants then performed 20-min exercise sessions relative to Wpeak (random order separated by 7 days): (1) 45% and (2) 60% continuous cycling and (3) 90% intermittent cycling (30 s cycling, 30 s rest). During a 45-min recovery period, tympanic temperature (Temp°C), exertion in breathing (RPEbr) and legs (RPEleg), and cortical excitability (MEParea) were measured. Results Eleven pwMS and eight controls completed the study. Controls performed better on the exercise test (p < 0.05), thus more absolute work during subsequent sessions. PwMS took longer to recover RPEleg with recovery time increasing with intensity (45%-6 min; 60%-15 min; 90%-35 min) and correlating with Temp°C. MEParea was significantly depressed in both groups at 45% and 60% (p < 0.001), in the MS group this also correlated with RPEleg. Conclusions Feelings of leg exertion may persist after exercise in some pwMS, especially at high intensities. This may relate to body temperature and, after continuous exercise, cortical excitability. These results support considering the recovery period post exercise and provide an insight into potential correlates of post-exercise fatigue. Implications for Rehabilitation A better understanding of how pwMS recover following exercise may help inform exercise prescription a long side fatigue management. This study showed that, in pwMS, the time taken to recover from feelings of leg fatigue increased with the intensity of the exercise session rather that total work performed and was related to increase in body temperature. The results of this relatively small study support the need to consider a recovery period after exercise and provide an insight into potential physiological correlates
Test coverage and impact analysis for detecting refactoring faults: a study on the extract method refactoring

Refactoring validation by automated testing is a common practice in agile development processes. However, this practice can be misleading when the test suite is not adequate. Particularly, refactoring faults can be tricky and difficult to detect. While coverage analysis is a standard practice to evaluate a test suite's fault detection capability, there is usually low correlation between coverage and fault detection. In this paper, we present an exploratory study on coverage of refactoring-impacted code, in order to identify shortcomings of test suites, focusing on the Extract Method Refactoring. We consider three open-source projects and their test suites. The results show that, in most cases, the lacking of test case calling the method changed in the refactoring increases the chance of missing faults. Also, a high proportion of test cases that do not cover the callers of that method does not reveal the fault either. Additional analysis of branch coverage on the test cases exercising impacted elements show a higher chance of detecting a fault when branch coverage is also high. It seems reasonable to conclude that a combination of impact analysis with branch coverage could be highly effective in detecting faults introduced by Extract Method.
The fabrication of Au nanowire by phase-control mode of USV-assisted AFM nanomachining

This paper proposed Au nanowire fabrication method combining the phase-control mode of nanomachining and the lift-off process. The conventional force-control mode of AFM nanomachining has many drawbacks such as stick-slip motion of machining, unable to directly control the machining depth, under-cutting and over-cutting. These drawbacks will lead to invalid nanopattern of resist or severe tip wear. The phase-control mode can avoid these drawbacks of conventional force-control mode. After patterning the nanogrooves by phase-control mode nanomachinng, the lift-off process is utilized to fabricate Au nanowire. Experimental result shows that width of fabricated nanowire is ∼ 50 nm. The present method also demonstrates the potential on the fabrication of three-dimension nanostructures and nanoelectronic device.
RF-Kinect

The rising popularity of electronic devices with gesture recognition capabilities makes the gesture-based human-computer interaction more attractive. Along this direction, tracking the body movement in 3D space is desirable to further facilitate behavior recognition in various scenarios. Existing solutions attempt to track the body movement based on computer version or wearable sensors, but they are either dependent on the light or incurring high energy consumption. This paper presents RF-Kinect, a training-free system which tracks the body movement in 3D space by analyzing the phase information of wearable RFID tags attached on the limb. Instead of locating each tag independently in 3D space to recover the body postures, RF-Kinect treats each limb as a whole, and estimates the corresponding orientations through extracting two types of phase features, Phase Difference between Tags (PDT) on the same part of a limb and Phase Difference between Antennas (PDA) of the same tag. It then reconstructs the body posture based on the determined orientation of limbs grounded on the human body geometric model, and exploits Kalman filter to smooth the body movement results, which is the temporal sequence of the body postures. The real experiments with 5 volunteers show that RF-Kinect achieves 8.7° angle error for determining the orientation of limbs and 4.4cm relative position error for the position estimation of joints compared with Kinect 2.0 testbed.
Scalable Closed-Form Trajectories for Periodic and Non-Periodic Human-Like Walking

We present a new framework to generate humanlike lower-limb trajectories in periodic and non-periodic walking. In our method, walking dynamics is encoded in 3LP, a linear simplified model composed of three pendulums to simulate falling, swing, and torso balancing dynamics. To stabilize the motion, we use an optimal time-projecting controller which suggests new footstep locations. On top of gait generation and stabilization in the simplified space, we introduce a kinematic conversion that synthesizes more humanlike trajectories by combining geometric variables of the 3LP model adaptively. Without any tuning, numerical optimization or off-line data, our walking gaits are scalable with respect to body properties and gait parameters. We can change body mass and height, walking direction, speed, frequency, double support time, torso style, ground clearance, and terrain inclinations. We can also simulate constant external dragging forces or momentary perturbations. The proposed framework offers closed-form solutions with simulation speeds orders of magnitude faster than real time. This can be used for video games and animations on portable electronic devices with limited power. It also gives insights for generation of more human-like walking gaits on humanoid robots.