Miracle-dz/UniFAR-FTUs huggingface dataset:
Detection of HER2 Gene Polymorphism in Breast Cancer: PCR Optimization Study

Cancers are the most deadly diseases in the world and their incidences continue to increase over time. Particularly, breast cancer in females places 1st rank among other types of cancers in term of cancer cases (23%) and death incidence (14%). Recent findings support the correlation between Ile655Val SNP in the HER2 gene with breast cancer risk. Moreover, the Ile655Val HER2 gene polymorphism could be a predictive factor in a neoadjuvant therapy setting. Precise detection of the Ile655Val HER2 gene SNP in early breast cancer patients will be beneficial in designing the most suitable treatment and in increasing the efficacy of anticancer drugs. Here we develop a rapid and inexpensive method for Ile655Val SNP detection in the HER2 gene based on allele-specific PCR technology. Two forward primers and one common reverse primer were designed to anneal specifically either on the HER2 gene fragment containing the GG genotype or to the HER2 gene fragment containing the AA genotype where one of these primers had been added with poly-GC at 5’ upstream. Moreover, to increase discrimination level, mismatch bases at the SNP site and the 3rd base of each forward primers from 3’end were added. To test the performance of the designed primers in discriminating a polymorphism and its annealing temperature, breast cancer specimen-derived genomic DNA (with GG genotype) and pGEM_HER2/AA (with AA genotype) were used as templates in the PCR reaction. The optimal annealing temperature for SNP detection was at 51.5°C as showed by the appearance of a 150 base pair (bp) band as AA genotype (pGEM_HER2/AA template), 116bp band as GG genotype (genomic DNA template), and both types of bands as AG genotype (mix of pGEM_HER2/AA and genomic DNA template). Allelic types of breast cancer patients were also determined using this optimized method compared to sanger sequencing. The 100% accordance was shown for all types of genotypes in both methods. The allele-specific PCR in this study may have application in determining polymorphisms of the breast cancers-originated Ile655Val HER2 gene.
Increased arterial wall stiffness limits flow volume in the lower extremities in type 2 diabetic patients.

OBJECTIVE To document an association between arterial wall stiffness and reduced flow volume in the lower-extremity arteries of diabetic patients. RESEARCH DESIGN AND METHODS We recruited 60 consecutive type 2 diabetic patients who had no history or symptoms of peripheral arterial disease (PAD) in the lower extremities and normal ankle/brachial systolic blood pressure index at the time of the study (non-PAD group) and 20 age-matched nondiabetic subjects (control group). We used an automatic device to measure pulse wave velocity (PWV) in the lower extremities as an index of arterial wall stiffness. At the popliteal artery, we evaluated flow volume and the resistive index as an index of arterial resistance to blood flow using gated two-dimensional cine-mode phase-contrast magnetic resonance imaging. RESULTS Consistent with previous reports, we confirmed that the non-PAD group had an abnormally higher PWV compared with that of the control group (P < 0.001). To further demonstrate decreased flow volume and abnormal flow pattern at the popliteal artery in patients with a higher degree of arterial wall stiffness, we assigned the 60 non-PAD patients to tertiles based on their levels of PWV. In the highest group, magnetic resonance angiograms of the calf and foot arteries showed decreased intravascular signal intensity, indicating the decreased arterial inflow in those arteries. The highest group was also characterized by the lowest late diastolic and total flow volumes as well as the highest resistive index among the groups. From stepwise multiple regression analysis, PWV and autonomic function were identified as independent determinants for late diastolic flow volume (r(2) = 0.300; P < 0.001). CONCLUSIONS Arterial wall stiffness was associated with reduced arterial flow volume in the lower extremities of diabetic patients.
Resonantly coupled antennas for passive sensors

Wireless resonant coupling can enhance the performance of wireless passive sensors. Very efficient transfer of both energy and information is possible. Resonant coupling implies that a weak wireless coupling is compensated by resonance. In ideal situations power conversion efficiencies of 10-50 percent can be achieved from the transceiver to the sensor. The cost is a limited bandwidth and an increased sensitivity to relative positional - especially angular - variations. The limited bandwidth is hardly a problem for most sensor applications. An analysis based on the theory for coupled circuits is presented. The capabilities and deficiencies are quantified by simple analytical and numerical calculations.
Sequential Optimum Selection: A Categorical Alternative to Discriminant Analysis for Conducting Research in Assessment

Sequential Optimum Selection, SOS, a nonparametric computer-assisted alternative to discriminant analysis, was introduced and explicated. SOS is an iterative procedure that develops ongoing decision rules for discriminating among groups, successively expunging frequency distributions or classes until all cases are accounted for. In three illustrative comparisons using clinical assessment data, SOS proved competitive with discriminant analysis in terms of over-all hit rates for parsimonious extraction of meaningful variables. Further, in one demonstration using parametric data, SOS held up better on cross-validation, While discriminant analysis will, in most cases, yield better discrimination than SOS, the latter does not make parametric assumptions and should therefore be considered a viable alternative as an exploratory procedure.
Selective detection with adaptive channel estimation for MIMO OFDM

In this paper, we investigate the performance of a new selective detection algorithm that is a modification of that proposed in [1]. The channel estimation used is based on adaptive model-based regularization in Multi Input Multi Output (MIMO) OFDM systems. The Basis Expansion Model (BEM) approach is employed for channel estimation. For the adaptive regularization, regularization matrices are computed for a set of uniform power delay profiles. The generalized cross-validation method is then used to select a best matrix from the precomputed set. We compare the performance of the detector implementing the channel estimation with adaptive regularization with the performance of the detector using the Linear Minimum Mean Square Error (LMMSE) channel estimation.
Alcohol drinking and the risk of colorectal adenoma: a dose–response meta-analysis

The International Agency for Research on Cancer concluded that alcohol consumption was positively related to colorectal cancer. However, the association between alcohol consumption and colorectal adenoma (CRA), the established precancerous lesion of colorectal cancer, remains unclear. We identified studies from a literature search of MEDLINE, EMBASE, and ISI Web of Science through 31 October 2013, and by searching reference lists of pertinent articles. Summary relative risks with 95% confidence intervals were calculated using a random-effects model. A total of 30 studies with 26 145 incident CRA cases were included. Overall, an increase of 25 g (two drinks) per day of alcohol consumption was related to an increased risk of CRA (summary relative risk=1.27, 95% confidence interval: 1.17–1.37). There was considerable heterogeneity between studies not explained by study design, sex, geographic location, publication year, site or size of the lesions, type of adenoma, number of cases, endoscopic assessment, or adjustment for main confounders. The positive association was evident for both men and women and for colonic adenoma, but not for rectal adenoma. Increased alcohol consumption is associated with an increased risk of CRA for both men and women and for adenoma in the colon, but not in the rectum.
Pelleted Bone Marrow Derived Mesenchymal Stem Cells Are Better Protected from the Deleterious Effects of Arthroscopic Heat Shock

Introduction: The impact of arthroscopic temperature on joint tissues is poorly understood and it is not known how mesenchymal stem cells (MSCs) respond to the effects of heat generated by the device during the process of arthroscopy assisted experimental cell-based therapy. In the present study, we isolated and phenotypically characterized human bone marrow mesenchymal stem cells (hBMMSCs) from osteoarthritis (OA) patients, and evaluated the effect of arthroscopic heat on cells in suspension and pellet cultures. Methods: Primary cultures of hBMMSCs were isolated from bone marrow aspirates of OA patients and cultured using DMEM supplemented with 10% FBS and characterized for their stemness. hBMMSCs (1 × 106 cells) cultured as single cell suspensions or cell pellets were exposed to an illuminated arthroscope for 10, 20, or 30 min. This was followed by analysis of cellular proliferation and heat shock related gene expression. Results: hBMMSCs were viable and exhibited population doubling, short spindle morphology, MSC related CD surface markers expression and tri-lineage differentiation into adipocytes, chondrocytes and osteoblasts. Chondrogenic and osteogenic differentiation increased collagen production and alkaline phosphatase activity. Exposure of hBMMSCs to an illuminated arthroscope for 10, 20, or 30 min for 72 h decreased metabolic activity of the cells in suspensions (63.27% at 30 min) and increased metabolic activity in cell pellets (62.86% at 10 min and 68.57% at 20 min). hBMMSCs exposed to 37, 45, and 55°C for 120 s demonstrated significant upregulation of BAX, P53, Cyclin A2, Cyclin E1, TNF-α, and HSP70 in cell suspensions compared to cell pellets. Conclusions: hBMMSC cell pellets are better protected from temperature alterations compared to cell suspensions. Transplantation of hBMMSCs as pellets rather than as cell suspensions to the cartilage defect site would therefore support their viability and may aid enhanced cartilage regeneration.
On lossy transmission of correlated sources over a multiple access channel

We study lossy communication of correlated sources over a multiple access channel. In particular, we provide a joint source-channel coding scheme for transmitting correlated sources with decoder side information, and study the conditions under which separate source and channel coding is optimal. For the latter, the encoders and/or the decoder have access to a common observation conditioned on which the two sources are independent. By establishing necessary and sufficient conditions, we show the optimality of separation when the encoders and the decoder both have access to the common observation. We also demonstrate that separation is optimal when only the encoders have access to the common observation whose lossless recovery is required at the decoder. As a special case, we study separation for sources with a common part. Our results indicate that side information can have significant impact on the optimality of source-channel separation in lossy transmission.
Psychiatric disorders and large interdialytic weight gain in patients on chronic haemodialysis

Aims: Psychiatric disorders have been considered in terms of non‐compliant behaviour and low life quality in haemodialysis patients. The aim of this study is to investigate the potential association of psychiatric disorders with compliance of fluid restriction and nutritional status and to measure the effects of psychiatric disorders on the life quality in chronic renal failure patients on haemodialysis.
IL-10/HMOX1 Signaling Modulates Cochlear Inflammation via Negative Regulation of MCP-1/CCL2 Expression in Cochlear Fibrocytes

Cochlear inflammatory diseases, such as tympanogenic labyrinthitis, are associated with acquired sensorineural hearing loss. Although otitis media is extremely frequent in children, tympanogenic labyrinthitis is not commonly observed, which suggests the existence of a potent anti-inflammatory mechanism modulating cochlear inflammation. In this study, we aimed to determine the molecular mechanism involved in cochlear protection from inflammation-mediated tissue damage, focusing on IL-10 and hemoxygenase-1 (HMOX1) signaling. We demonstrated that IL-10Rs are expressed in the cochlear lateral wall of mice and rats, particularly in the spiral ligament fibrocytes (SLFs). The rat SLF cell line was found to inhibit nontypeable Haemophilus influenzae (NTHi)-induced upregulation of monocyte chemotactic protein-1 (MCP-1; CCL2) in response to IL-10. This inhibition was suppressed by silencing IL-10R1 and was mimicked by cobalt Protoporphyrin IX and CO-releasing molecule-2. In addition, IL-10 appeared to suppress monocyte recruitment through reduction of NTHi-induced rat SLF cell line–derived chemoattractants. Silencing of HMOX1 was found to attenuate the inhibitory effect of IL-10 on NTHi-induced MCP-1/CCL2 upregulation. Chromatin immunoprecipitation assays showed that IL-10 inhibits NTHi-induced binding of p65 NF-κB to the distal motif in the promoter region of MCP-1/CCL2, resulting in suppression of NTHi-induced NF-κB activation. Furthermore, IL-10 deficiency appeared to significantly affect cochlear inflammation induced by intratympanic injections of NTHi. Taken together, our results suggest that IL-10/HMOX1 signaling is involved in modulation of cochlear inflammation through inhibition of MCP-1/CCL2 regulation in SLFs, implying a therapeutic potential for a CO-based approach for inflammation-associated cochlear diseases.
The Time Course and Determinants of Temperature within the First 48 h after Ischaemic Stroke

Background and Purpose: Previous research has attempted to analyze the relationship between post-stroke hyperthermia and prognosis. These analyses have been hindered by a lack of information about the time course and determinants of temperature change after stroke. Methods: Serial temperatures were measured until 48 h after ischaemic stroke in a prospectively recruited cohort. Potential determinants of temperature, including stroke severity [measured using the National Institutes of Health Stroke Scale (NIHSS)], infection and paracetamol use were recorded. Mixed-effects models were used to model serial temperature measurements over time, adjusted for significant determinants. Results: In 155 patients the mean temperature rose from 36.5°C at the time of stroke to 36.7°C approximately 36 h later. The factors with significant multivariable associations with serial temperatures were: first- and second-order time components, infection, paracetamol administration and the interaction between stroke severity (NIHSS ≧6) and time (all p < 0.1). Patients with admission NIHSS ≧6 had a mean temperature rise of 0.35°C during the first 36 h after stroke, compared with a rise of 0.17°C in those with NIHSS ≤5. Conclusions: Temperature spontaneously rises during the first 36 h after stroke, particularly after severer stroke and in the presence of infection.
Fractal Dimension‐Based Damage Detection Method for Beams with a Uniform Cross‐Section

Abstract: For civil structures, damage usually occurs in localized areas. As fractal dimension (FD) analysis can provide insight to local complexity in geometry, a damage detection approach based on Katz's estimation of the FD measure of displacement mode shape for homogeneous, uniform cross‐sectional beam structures is proposed in this study. An FD‐based index for damage localization (FDIDL) is developed utilizing the difference of angles of sliding windows between two successive points, which is expressed in FD. To improve robustness against noise, FDIDL is calculated using multisliding windows. The influence of the spatial sampling interval length and the number of 2‐sampling sliding windows on sensitivity to damage and robustness against noise is investigated. The relationship between the angle expressed in FD and the modal strain energy is established and thereby an FD‐based index for the estimation of damage extent (FDIDE) is presented. The two damage indices are applied to a simply supported beam to detect the simulated damage in the beam. The results indicate that the proposed FDIDL can locate the single or multiple damages, and FDIDE can reliably quantify the damage extent. The optimal spatial sampling interval and the number of sliding windows are investigated. Furthermore, the simulation with measurement noise is carried out to demonstrate the effectiveness and robustness of the two defined FD‐based damage indices. Finally, experiments are conducted on simply supported steel beams damaged at different locations. It is demonstrated that the proposed approach can locate the damages to a satisfactory precision.
First-order Definable String Transformations

The connection between languages defined by computational models and logic for languages is well-studied. Monadic second-order logic and finite automata are shown to closely correspond to each-other for the languages of strings, trees, and partial-orders. Similar connections are shown for first-order logic and finite automata with certain aperiodicity restriction. Courcelle in 1994 proposed a way to use logic to define functions over structures where the output structure is defined using logical formulas interpreted over the input structure. Engelfriet and Hoogeboom discovered the corresponding "automata connection" by showing that two-way generalised sequential machines capture the class of monadic-second order definable transformations. Alur and Cerny further refined the result by proposing a one-way deterministic transducer model with string variables - called the streaming string transducers - to capture the same class of transformations. In this paper we establish a transducer-logic correspondence for Courcelle's first-order definable string transformations. We propose a new notion of transition monoid for streaming string transducers that involves structural properties of both underlying input automata and variable dependencies. By putting an aperiodicity restriction on the transition monoids, we define a class of streaming string transducers that captures exactly the class of first-order definable transformations.
Simulation of Multi-Formalism Models with ModHel'X

A step in the validation of a system is to check its behavior by simulation. Simulation is also used to validate the behavior of the model of the system against test patterns. For complex systems, models are made of parts which use different modeling formalisms. The main issues in the simulation of such systems are the specification of the semantics of each modeling formalism, and of the interactions between heterogeneous parts of a model. ModHel'X relies on component based modeling and models of computation to address these problems and focuses on the computation of one possible behavior of a model. This includes simulation and code generation. ModHel'X defines a MOF meta-model for describing the structural elements of a modeling language. The semantics of modeling languages is expressed in an imperative style and addresses three aspects: control, data and time. ModHel'X is supported by a simulator of multi-formalism models.
Novel and Distinct Operational Principles of Intralaminar Thalamic Neurons and Their Striatal Projections

Neurons of the intralaminar thalamus, including central lateral (CL) and parafascicular (Pf) nuclei, innervate the cortex and striatum and are important for cognitive, sensory, and motor processes. We tested the hypothesis that CL and Pf neurons provide functionally distinct inputs to the striatum. We performed recordings of single CL and Pf neurons in anesthetized rats and, after juxtacellularly labeling the neurons, their somatodendritic features and synaptic connections were characterized. All CL neurons (n = 31) discharged classic low-threshold Ca2+ spike bursts during cortical slow-wave activity in vivo. In contrast, Pf neurons (n = 52) rarely fired such bursts, but instead discharged groups of spikes at relatively low frequencies. The activity of CL and Pf neurons was often temporally coupled to cortical slow oscillations. Identified CL neurons possessed archetypal “bushy” dendrites and preferentially established synapses with dendritic spines (91% of synapses) of striatal projection neurons. Pf neurons possessed “reticular-like” dendrites, and, on average, preferentially established synapses with dendritic shafts (63%) in striatum, although connectivity was markedly heterogeneous across neurons. Two of the six Pf neurons studied exclusively targeted dendritic shafts, whereas another neuron almost exclusively (97%) targeted spines. The remaining three neurons preferentially targeted dendritic shafts (53–70%). Thus, the fundamental properties of CL and Pf neurons differ (the latter do not express the typical operational principles of thalamic relay neurons), and they provide different temporally patterned inputs to distinct striatal targets. This mechanistic diversity likely underpins the transmission of specific and discrete information from intralaminar thalamic nuclei to striatal and cortical targets.
When Can Helper Node Selection Improve Regenerating Codes? Part I: Graph-Based Analysis

Regenerating codes (RCs) can significantly reduce the repair-bandwidth of distributed storage networks. Initially, the analysis of RCs was based on the assumption that during the repair process, the newcomer does not distinguish (among all surviving nodes) which nodes to access, i.e., the newcomer is oblivious to the set of helpers being used. Such a scheme is termed the blind helper selection (BHS) scheme. Nonetheless, it is intuitive in practice that the newcomer should choose to access only those "good" helpers. In this two-part paper, a new characterization of the effect of choosing the helper nodes in terms of the storage-bandwidth tradeoff is given. Specifically, the answer to the following fundamental question is provided: Under what condition does proactively choosing the helper nodes improve the storage-bandwidth tradeoff? Through a graph-based analysis, this Part I paper answers this question by providing a necessary and sufficient condition under which optimally choosing good helpers strictly improves the storage-bandwidth tradeoff. A low-complexity helper selection solution, termed the family helper selection (FHS) scheme, is proposed and the corresponding storage/repair-bandwidth curve is characterized. This Part I paper also proves that under some design parameters, the FHS scheme is indeed optimal among all helper selection schemes. In the Part II paper, an explicit construction of an exact-repair code is proposed that achieves the minimum-bandwidth-regenerating (MBR) point of the FHS scheme. The new exact-repair code can be viewed as a generalization of the existing fractional repetition code.
WATERMARKING TECHNIQUES – BINARY AND TRANSPARENCY AUTHENTICATION IN VISUAL CRYPTOGRAPHY

With the rapid growth of internet technology, services and devices, transferring of images over internet becomes increasingly popular. This paper proposes a watermarking using binary scheme and transparency authentication scheme used in visual cryptography. Watermarking using binary scheme offers better security than Hwang’s method, so that ownership information will not be detected by the attackers. In addition, transparency authentication scheme is embedded in the same image, so that secret image can be perceptible when stacking transparency. In authentication scheme, the Watermark image is half of the size of the secret image and both are encrypted at the same time. Experimental results shows that the scheme effective and practical.