Miracle-dz/UniFAR-FTUs huggingface dataset:
Classification of DNA methylation patterns in tumor cell genomes using a CpG island microarray

Our group has initiated experiments to epigenetically profile CpG island hypermethylation in genomic DNA from tissue specimens of head and neck squamous cell carcinoma (HNSCC) using a microarray of 12,288 CpG island clones. Our technique, known as a methylation-specific restriction enzyme (MSRE) analysis, is a variation of the differential methylation hybridization (DMH) technique, in that it is not an array comparison of two DNA samples using methylation-specific restriction enzymes. Instead, it is a comparison of a single DNA sample’s response to a methylation-sensitive restriction enzyme (HpaII) and its corresponding methylation-insensitive isoschizomer (MspI). Estimation of the reproducibility of this microarray assay by intraclass correlation (ICC) demonstrated that in four replicate experiments for three tumor specimens, the ICC observed for a given tumor specimen ranged from 0.68 to 0.85 without filtering of data. Repeated assays achieved 87% concordance or greater for all tumors after filtering of array data by fluorescence intensity. We utilized hierarchical clustering on a population of 37 HNSCC samples to cluster tumor samples with similar DNA methylation profiles. Supervised learning techniques are now being utilized to allow us to identify associations between specific epigenetic signatures and clinical parameters. Such techniques will allow us to identify select groups of CpG island loci that could be used as epigenetic markers for both diagnosis and prognosis in HNSCC.
Selective induction of Th2 cells in murine Peyer's patches by oral immunization.

We have used three different methods to determine the T helper (Th) cell response, including Th1 and Th2 types, in murine Peyer's patches (PP) following oral immunization with sheep red blood cells (SRBC). These include: (i) use of cytokine-specific (IFN-gamma and IL-5), single cell assays to estimate the frequencies of Th1 and Th2 cells respectively, (ii) cytokine-specific mRNA--cDNA dot blot and Northern gel hybridizations to detect levels of specific mRNA, and (iii) T cell cloning techniques to determine the frequency of Th1 and Th2 clones. Mice were immunized with SRBC by either the oral or i.p. route. The PP and splenic (SP) CD3+ and CD3+ CD4+ T cell subsets were isolated and cultured with antigen, feeder cells, and IL-2, and were assessed at various intervals (days 0, 1, 3, and 6) for numbers of T cells producing either IFN-gamma or IL-5 by use of an enzyme-linked immunospot (ELISPOT) procedure. Cultures of T cells from PP or SP of mice given SRBC by the oral route had a high frequency of IL-5 spot forming cells (SFC), with lower numbers of IFN-gamma SFC. However, cultures of CD3+ T cells and CD3+ CD4+ Th cells from spleens of i.p. immunized mice exhibited predominantly IFN-gamma SFC, with smaller but significant numbers of IL-5 SFC. This distinct pattern of cytokine production was supported by mRNA analysis where high IL-5 specific mRNA levels were noted in PP T cell cultures of orally primed mice, while IFN-gamma mRNA was predominant in the SP CD3+ T cell and CD3+ CD4+ Th cell cultures from i.p. immunized mice. When the frequencies of IFN-gamma or IL-5 SFC were assessed among cloned Th cells from orally- or systemically-immunized mice, 74% of Th cell clones from PP of mice orally immunized with SRBC were IL-5 producers (Th2 type), while 67% of Th cell clones from SP of mice immunized by the i.p. route were IFN-gamma producers (Th1 type). Our studies show that higher frequencies of IFN-gamma producing Th1-type cells occur in SP of mice given antigen by the systemic route, while oral immunization results in predominantly IL-5 producing, Th2-type cells in PP.
Effect of Display Size on Visual Attention

Attention plays an important role in the design of human-machine interfaces. However, current knowledge about attention is largely based on data obtained when using devices of moderate display size. With advancement in display technology comes the need for understanding attention behavior over a wider range of viewing sizes. The effect of display size on test participants' visual search performance was studied. The participants (N = 12) performed two types of visual search tasks, that is, parallel and serial search, under three display-size conditions (16°, 32°, and 60°). Serial, but not parallel, search was affected by display size. In the serial task, mean reaction time for detecting a target increased with the display size.
Human Vagus Nerve Electrophysiology: A Guide to Vagus Nerve Stimulation Parameters

Summary The authors studied human vagus nerve electrophysiology intraoperatively on 21 patients (age range: 4 to 31 years) during implantation of a vagus nerve stimulator for seizure control. The study was performed with direct electrical stimulation of the vagus nerve with various stimulation parameters resembling those employed by the Cyberonics NeuroCybernetic Prosthesis System (Houston, TX), which is used clinically for vagus nerve stimulation for treatment of seizures. Recordings were made directly from the rostral end of the vagus nerve. The response of the vagus nerve to various stimulus parameters in patients of different ages was studied. Based on the vagus nerve characteristics, age-related adjustments for stimulus parameters were recommended.
Non-Orthogonal Multiple Access Using Intra-Beam Superposition Coding and SIC in Base Station Cooperative MIMO Cellular Downlink

This paper extends our previously proposed non-orthogonal multiple access (NOMA) scheme to the base station (BS) cooperative multiple-input multiple-output (MIMO) cellular downlink for future radio access. The proposed NOMA scheme employs intra-beam superposition coding of a multiuser signal at the transmitter and the spatial filtering of inter-beam interference followed by the intra-beam successive interference canceller (SIC) at the user terminal receiver. The intra-beam SIC cancels out the inter-user interference within a beam. This configuration achieves reduced overhead for the downlink reference signaling for channel estimation at the user terminal in the case of non-orthogonal user multiplexing and also achieves the applicability of the SIC receiver in MIMO downlink. The transmitter beamforming (precoding) matrix is controlled based on open loop-type random beamforming using a block-diagonalized beamforming matrix, which is very efficient in terms of the amount of feedback information from the user terminal. Simulation results show that the proposed NOMA scheme with block-diagonalized random beamforming in BS cooperative multiuser MIMO and the intra-beam SIC achieves better system-level throughput compared to orthogonal multiple access (OMA), which is assumed in LTE-Advanced. We also show that BS cooperative operation along with the proposed NOMA in particular achieves a high cell-edge user throughput gain which implies better user fairness and universal connectivity.
Prehospital care delivery and triage of stroke with emergent large vessel occlusion (ELVO): report of the Standards and Guidelines Committee of the Society of Neurointerventional Surgery

Recent randomized clinical trials1–5 established the superiority of endovascular recanalization techniques, specifically mechanical embolectomy, compared with best medical therapy alone for the treatment of patients with emergent large vessel occlusion (ELVO) stroke. ELVO stroke is defined as a stroke secondary to anterior circulation large vessel occlusion (LVO) of the internal carotid, middle cerebral (M1 segments) arteries documented by imaging, without large completed infarct and presenting within 6 hours of symptom onset.6 Given the overwhelming clinical evidence provided by these trials, recent American Heart Association (AHA) guidelines concluded that “embolectomy needs to be performed as rapidly as possible for the greatest clinical benefit, and is best when performed within 6 h from onset of symptoms” (AHA class I, level of evidence A). 6 In addition, cost modeling derived from trial outcomes data and claims databases in the USA strongly suggests that cost-effectiveness and an overall societal benefit is associated with investment in access to these endovascular techniques.7 Rapid access to endovascular services depends upon optimization of prehospital stroke care and transport within stroke systems of care, focusing on the unique needs of patients with ELVO through their diagnostic investigation and treatment pathway. The Society of NeuroInterventional Surgery (SNIS) proposed process time metrics for ELVO stroke treatment, including door to IV tissue plasminogen activator (t-PA) of <30 min, comprehensive stroke center (CSC) door to puncture of <60 min, CSC door to recanalization of <90 min and primary stroke certification (PSC) picture to CSC puncture of <90 min.8 Early team awareness of the patient with potential ELVO, coupled with efficient interdisciplinary communication, triage and transport assist in meeting these ideal time metrics, and also contribute to improved clinical outcomes through efficiency gains and maximization of endovascular care delivery. The Standards and Guidelines Committee of the SNIS, a multidisciplinary society representing leaders in the field of …
Virtual Constraints Paradigm for Robotic Locomotion Control

Background. Designing highly mobile biologically inspired legged, winged, and limbless robots has advanced considerably in the past decade. Developing motion control algorithms for these robotic systems, however, is mainly carried out using ad-hoc techniques resulting in motions that are far less agile and efficient than the biological species that have inspired the robot morphology. A recent design paradigm, which has been originally introduced for biped robot agile and efficient control [1], is based on controlling robots using virtual constraints (VC). Virtual constraints are relations among the biped generalized coordinates encoding stable walking gaits that can be re-programmed on-the-fly and are enforced via feedback (see Figure 1). Under virtual constraints, bipeds are capable of achieving stable motions over a wide variety of terrain profiles [1]. MABLE, which is the world’s fastest planar biped with knees, employs virtual constraint-based algorithms in its motion control system [2]. This methodology has recently been applied to control of powered prosthetic legs for amputation patients [3], [4].
A small-gain-type improved criterion via preservation of iISS/ISS dissipation inequalities

This paper pursues a stability criterion by which better Lyapunov functions establishing stability of interconnected nonlinear systems can be constructed. Component systems are assumed to be integral input-to-state stable (iISS). Although the iISS small-gain condition in the literature is a necessary and sufficient condition in an appropriate sense, the Lyapunov function constructed for the interconnected system by the existing results is virtually unusable when stability margins are small. To identify the origin of the undesirable feature, this paper investigates techniques of iISS preservation. For developing a powerful remedy, the usage of the Legendre-Fenchel transformation in the preservation is generalized to remove all unnecessary assumptions used in previously existing results. The development is useful for establishing input-to-state stability of an interconnection from iISS components.
Scattering Performance of Log-Periodic Dipole Array

In this letter, the scattering performance of a log-periodic dipole array (LPDA) is numerically and experimentally demonstrated. Radiation and scattering performance of the LPDA is shown. Numerical simulations clarify that a 3-dB bandwidth of an LPDA scatterer becomes narrow due to the distortion of its RCS pattern. Relation between the total length and bandwidth performance of the LPDA scatterer is numerically examined to extend its narrow bandwidth. The optimized LPDA scatterer achieves the bandwidth of 1:1.8. The optimized LPDA scatterer is fabricated, and the measured scattering performance is shown to confirm the numerical results.
Construction and Characterization of a Highly Efficient Francisella Shuttle Plasmid

ABSTRACT Francisella tularensis is a facultative intracellular pathogen that infects a wide variety of mammals and causes tularemia in humans. It is recognized as a potential agent of bioterrorism due to its low infectious dose and multiple routes of transmission. To date, genetic manipulation in Francisella spp. has been limited due to the inefficiency of DNA transformation, the relative lack of useful selective markers, and the lack of stably replicating plasmids. Therefore, the goal of this study was to develop an enhanced shuttle plasmid that could be utilized for a variety of genetic procedures in both Francisella and Escherichia coli. A hybrid plasmid, pFNLTP1, was isolated that was transformed by electroporation at frequencies of >1 × 107 CFU μg of DNA−1 in F. tularensis LVS, Francisella novicida U112, and E. coli DH5α. Furthermore, this plasmid was stably maintained in F. tularensis LVS after passage in the absence of antibiotic selection in vitro and after 3 days of growth in J774A.1 macrophages. Importantly, F. tularensis LVS derivatives carrying pFNLTP1 were unaltered in their growth characteristics in laboratory medium and macrophages compared to wild-type LVS. We also constructed derivatives of pFNLTP1 containing expanded multiple cloning sites or temperature-sensitive mutations that failed to allow plasmid replication in F. tularensis LVS at the nonpermissive temperature. In addition, the utility of pFNLTP1 as a vehicle for gene expression, as well as complementation, was demonstrated. In summary, we describe construction of a Francisella shuttle plasmid that is transformed at high efficiency, is stably maintained, and does not alter the growth of Francisella in macrophages. This new tool should significantly enhance genetic manipulation and characterization of F. tularensis and other Francisella biotypes.
Global Analysis of Truncated RNA Ends Reveals New Insights into Ribosome Stalling in Plants[OPEN]

In a global analysis of free 5′ mRNA ends, it is shown that the plant RNA degradome contains in vivo ribosome footprints and is useful to investigate ribosome stalling during translation. High-throughput approaches for profiling the 5′ ends of RNA degradation intermediates on a genome-wide scale are frequently applied to analyze and validate cleavage sites guided by microRNAs (miRNAs). However, the complexity of the RNA degradome other than miRNA targets is currently largely uncharacterized, and this limits the application of RNA degradome studies. We conducted a global analysis of 5′-truncated mRNA ends that mapped to coding sequences (CDSs) of Arabidopsis thaliana, rice (Oryza sativa), and soybean (Glycine max). Based on this analysis, we provide multiple lines of evidence to show that the plant RNA degradome contains in vivo ribosome-protected mRNA fragments. We observed a 3-nucleotide periodicity in the position of free 5′ RNA ends and a bias toward the translational frame. By examining conserved peptide upstream open reading frames (uORFs) of Arabidopsis and rice, we found a predominance of 5′ termini of RNA degradation intermediates that were separated by a length equal to a ribosome-protected mRNA fragment. Through the analysis of RNA degradome data, we discovered uORFs and CDS regions potentially associated with stacked ribosomes in Arabidopsis. Furthermore, our analysis of RNA degradome data suggested that the binding of Arabidopsis ARGONAUTE7 to a noncleavable target site of miR390 might directly hinder ribosome movement. This work demonstrates an alternative use of RNA degradome data in the study of ribosome stalling.
A fully-integrated differential transceiver for C-band radar application

A fully-integrated differential transceiver for C-band, based on polyphase filters (PPFs) to achieve a high image rejection ratio (IRR), is proposed in the paper. The transceiver meets the requirements for the 5GHz band radar application, which is implemented in 1P6M 0. 18μm CMOS technology. The receiver achieves 7.2dB NF, 29.3dB gain and 50.7dB IRR with 3-level digital gain controllability, while draws 93.1mA from 3.3V power supply. The transmitter achieves 16.4dBm output peak power, 29.5dB gain and 65.6dB IRR, which dissipates 138.4mA from 3.3V power supply. The die area is 2.7mm×2.9mm.
Long-term outcome of endovascular reconstruction with the Pipeline embolization device in the management of unruptured dissecting aneurysms of the intracranial vertebral artery.

OBJECT Use of a flow-diverting device has shown promising short-term results in the management of vertebral artery (VA) dissecting aneurysms, but there is still uncertainty regarding its long-term efficacy and safety. The authors report their initial experience with respect to the potential utility and long-term clinical outcomes of using a flow-diverting device in the treatment of unruptured dissecting VA aneurysms. METHODS The authors conducted a retrospective review of all cases of unruptured intracranial VA dissecting aneurysms treated at their institution (Tuen Mun Hospital) with a flow-diverting device. They describe the clinical presentations and angiographic features of the cases and report the clinical outcome (with modified Rankin Scale [mRS] scores) at most recent follow-up, as well as results of the latest angiographic assessment, with particular focus on in-stent patency and side-branch occlusion. RESULTS A total of 4 aneurysms were successfully obliterated by using flow-diverting devices alone. Two devices were deployed in a telescoping fashion in each of 2 aneurysms, whereas only 1 device was inserted in each of the other 2 aneurysms. No periprocedural complication was encountered. No patient showed any angiographic evidence of recurrence, in-stent thrombosis, or side-branch occlusion in angiographic reassessment at a mean of 22 months after treatment (range 18-24 months). As of the most recent clinical follow-up (mean 30 months after treatment, range 24-37 months), all patients had favorable outcomes (mRS Score 0). CONCLUSIONS Reconstruction using a flow-diverting device is an attractive alternative in definitive treatment of dissecting VA aneurysms, demonstrating favorable long-term clinical and angiographic outcomes and the ability to maintain parent artery and side-branch patency. It is particularly useful in cases with eloquent side-branch or dominant VA involvement.
Fronto-Orbito Zygomatic Approach: A Technical Modification

The fronto-orbito zygomatic approach is part of the surgical armamentarium of modern skull base surgery. As described in the literature, it requires costly technological tools such as powerful drills and saws, to be performed. In the present communication we describe a technical modification that allows the zygoma to be elevated "en bloc" together with the fronto-orbital bone flap by means of appropriate use of the Gigli's saw. Using this technique, adequate replacement of the craniotomy flap requires only two silk sutures. This technical modification, which was already successfully used in over 20 cases, would also allow this useful approach to be performed in those neurosurgical environments where modern costly technology for cranial base surgery is not available.
Dynamic identification of robots with power model

This paper presents a new approach to identify the minimum dynamic parameters of robots using least squares techniques (LS) and a power model. Theoretical analysis is carried out from a filtering point of view and clearly shows the superiority of the power model over the energy one and over the dynamic identification model which has been used to carry out a classical ordinary LS estimation and a new weighted LS estimation. These results are checked from comparing experimental identification of the dynamic parameters of a planar SCARA prototype robot.
Macelignan: A New Modulator of P-Glycoprotein in Multidrug-Resistant Cancer Cells

The effect of macelignan, a phytoestrogen, on P-gp function was investigated using multidrug resistant cancer cells overexpressing P-gp (NCI/ADR-RES) and the fluorescent P-gp substrates, daunorubicin and rhodamine 123. Macelignan (40 μM) increased the cellular accumulation of daunorubicin by approximately threefold in NCI/ADR-RES cells, whereas it did not alter the cellular accumulation of daunorubicin in MCF-7/sensitive cells. Similarly, the presence of macelignan also enhanced significantly (P < 0.05) the cellular accumulation of rhodamine 123 in a concentration-dependent manner in NCI/ADR-RES cells. Furthermore, cancer cells were more susceptible to the cytotoxicity of vinblastine, a P-gp substrate, in the presence of macelignan. Those results suggest that macelignan has inhibitory effects on P-gp mediated cellular efflux. However, P-gp activity did not affect the cellular accumulation of macelignan itself. Taken all together, macelignan was identified as a novel inhibitor of P-gp activity and may be a promising lead compound for the rational design of more efficacious drugs to reverse multidrug resistance in cancer.
Reliability-Based Transmission Line Design

It is well known that environmental loads, e.g., wind and ice, acting on power transmission lines are highly uncertain, as are the structural strengths of the towers supporting the lines. The design of such systems must take uncertainty into account in order to achieve acceptable reliability at a reasonable cost. The paper presents a simulation-based methodology for the optimal design of a transmission line which considers uncertainties in both environmental loads and structural resistance. The methodology is developed and illustrated for the simple problem of determining the optimal span length required for designing against tower failure. Wind, ice, and tower resistances are simulated over the extent of the transmission line and over the design life of the transmission system. Total expected system cost, along with the estimated probability of lifetime failure, are produced for a range of possible span lengths, allowing an informed decision regarding the optimum span length for the tower strength limit state.
Structure and function of the b/HLH/Z domain of USF.

The basic/helix‐loop‐helix/leucine zipper (b/HLH/Z) transcription factor upstream stimulatory factor (USF) and its isolated DNA binding domain undergo a random coil to alpha‐helix folding transition on recognizing their cognate DNA. The USF b/HLH cocrystal structure resembles the structure of the b/HLH/Z domain of the homologous protein Max and reveals (i) that the truncated, b/HLH DNA binding domain homodimerizes, forming a parallel, left‐handed four‐helix bundle, and (ii) that the basic region becomes alpha‐helical on binding to the major groove of the DNA sequence CACGTG. Hydrodynamic measurements show that the b/HLH/Z DNA binding domain of USF exists as a bivalent homotetramer. This tetramer forms at the USF physiological intranuclear concentration, and depends on the integrity of the leucine zipper motif. The ability to bind simultaneously to two independent sites suggests a role in DNA looping for the b/HLH/Z and Myc‐related families of eukaryotic transcription factors.