Miracle-dz/UniFAR-FTUs huggingface dataset:
Prognostic significance of neutrophil to lymphocyte ratio in patients with hepatocellular carcinoma after transcatheter arterial chemoembolization

Background Accumulating evidence indicates that systemic inflammation response is associated with the prognosis of various cancers. The aim of this study was to investigate the neutrophil‐lymphocyte ratio (NLR), which is one of the systemic inflammation markers, in the prognosis of hepatocellular carcinoma (HCC) after treatment of transcatheter arterial chemoembolization (TACE). Methods The clinical data of 178 HCC patients who received TACE were retrospectively analyzed. The optimal NLR cutoff was determined according to the receiver operating characteristic (ROC) analysis. All patients were divided into NLR‐normal group and NLR‐elevated group according to the cutoff, and the clinical features of these two groups were comparatively analyzed. Meanwhile, the overall survival and disease free survival (DFS) were analyzed using the Kaplan‐Meier method. The risk factors of postoperative survival were investigated using univariate and multivariate Cox regression analyses. Results The optimal NLR cutoff was defined at 1.85 and 42 (23.6%) patients had an elevated NLR (NLR>1.85). The median survival time was 9.5 months (range 1–99 months). The clinical data between the two groups were comparable, except for á‐fetoprotein. Follow‐up results showed that the median survival of patients with normal NLR was 17.5 months (range: 1–99 months) compared with 8 months (range: 8–68 months) of patients with elevated NLR. The 1, 3 and 5‐year overall survival of patients in the NLR‐normal group and NLR‐elevated group were 57.3%, 44.1%, and 27.2% and 42.1%, 19.6%, and 9.5% respectively (&khgr;2=194.2, P <0.001). Similarly, the disease free survival also has a significant difference (&khgr;2=39.3, P <0.001). Multivariate Cox regression analysis showed that a high NLR was an independent factor affecting the survival rate of HCC after TACE (P=0.04). Conclusion Preoperative NLR was an important prognostic factor to predict the prognosis of patients with intermediate HCC treated with TACE.
Automated chest wall line detection for whole-breast segmentation in sagittal breast MR images.

PURPOSE Breast magnetic resonance imaging (MRI) plays an important role in the clinical management of breast cancer. Computerized analysis is increasingly used to quantify breast MRI features in applications such as computer-aided lesion detection and fibroglandular tissue estimation for breast cancer risk assessment. Automated segmentation of the whole-breast as an organ from the other parts imaged is an important step in aiding lesion localization and fibroglandular tissue quantification. For this task, identifying the chest wall line (CWL) is most challenging due to image contrast variations, intensity discontinuity, and bias field. METHODS In this work, the authors develop and validate a fully automated image processing algorithm for accurate delineation of the CWL in sagittal breast MRI. The CWL detection is based on an integrated scheme of edge extraction and CWL candidate evaluation. The edge extraction consists of applying edge-enhancing filters and an edge linking algorithm. Increased accuracy is achieved by the synergistic use of multiple image inputs for edge extraction, where multiple CWL candidates are evaluated by the dynamic time warping algorithm coupled with the construction of a CWL reference. Their method is quantitatively validated by a dataset of 60 3D bilateral sagittal breast MRI scans (in total 3360 2D MR slices) that span the full American College of Radiology Breast Imaging Reporting and Data System (BI-RADS) breast density range. Agreement with manual segmentation obtained by an experienced breast imaging radiologist is assessed by both volumetric and boundary-based metrics, including four quantitative measures. RESULTS In terms of breast volume agreement with manual segmentation, the overlay percentage expressed by the Dice's similarity coefficient is 95.0% and the difference percentage is 10.1%. More specifically, for the segmentation accuracy of the CWL boundary, the CWL overlay percentage is 92.7% and averaged deviation distance is 2.3 mm. Their method requires ≈ 4.5 min for segmenting each 3D breast MRI scan (56 slices) in comparison to ≈ 35 min required for manual segmentation. Further analysis indicates that the segmentation performance of their method is relatively stable across the different BI-RADS density categories and breast volume, and also robust with respect to a varying range of the major parameters of the algorithm. CONCLUSIONS Their fully automated method achieves high segmentation accuracy in a time-efficient manner. It could support large scale quantitative breast MRI analysis and holds the potential to become integrated into the clinical workflow for breast cancer clinical applications in the future.
On the Properties And Design of Stable IIR Transfer Functions Generated Using Fibonnaci Numbers

This paper considers z-domain transfer functions whose denominator polynomial possesses the property that the coefficient of zi is greater than the coefficient of zi-1. Such transfer functions can be shown to be always stable and their denominator polynomials can be formed as a finite length time reversed Fibonacci sequence of numbers. Appropriate numerator polynomials can be configured to design lowpass, highpass, bandpass, band-elimination and allpass IIR filters. It is observed that the phase response closely approximates a linear behavior. This study is on the design of IIR filters using Fibonacci numbers. The advantages are that frequency selective filters with an approximately linear phase characteristic can be obtained with neither a stability test nor an analog prototype
Stratos: A Network-Aware Orchestration Layer for Middleboxes in the Cloud

We see an increasing demand for in-the-cloud middlebox processing as applications and enterprises want their cloud deployments to leverage the same beneﬁts that such services offer in traditional deployments. Unfortunately, today’s cloud middlebox deployments lack the same abstractions for ﬂex-ible deployment and elastic scaling that have been instrumental to the adoption and success of cloud-based compute and storage services. The key challenge here is that such network processing workloads are fundamentally different from traditional virtualized compute and storage services. These differences arise as a consequence of the ways in which ten-ants need to compose different middlebox services and the network-level factors (e.g., placement, load balancing) that impact application performance. To address this challenge, we present the design and implementation of Stratos. Stratos allows tenants to specify logical middlebox deployments and provides efﬁcient scaling, placement, and distribution algorithms that abstract away low-level issues in ensuring effective application performance. We demonstrate the effectiveness of Stratos using an experimental prototype, a limited deployment over EC2, and large-scale simulations.
A Quantitative Description of KcsA Gating I: Macroscopic Currents

The prokaryotic K+ channel KcsA is activated by intracellular protons and its gating is modulated by transmembrane voltage. Typically, KcsA functions have been studied under steady-state conditions, using macroscopic Rb+-flux experiments and single-channel current measurements. These studies have provided limited insights into the gating kinetics of KcsA due to its low open probability, uncertainties in the number of channels in the patch, and a very strong intrinsic kinetic variability. In this work, we have carried out a detailed analysis of KcsA gating under nonstationary conditions by examining the influence of pH and voltage on the activation, deactivation, and slow-inactivation gating events. We find that activation and deactivation gating of KcsA are predominantly modulated by pH without a significant effect of voltage. Activation gating showed sigmoidal pH dependence with a pKa of ∼4.2 and a Hill coefficient of ∼2. In the sustained presence of proton, KcsA undergoes a time-dependent decay of conductance. This inactivation process is pH independent but is modulated by voltage and the nature of permeant ion. Recovery from inactivation occurs via deactivation and also appears to be voltage dependent. We further find that inactivation in KcsA is not entirely a property of the open-conducting channel but can also occur from partially “activated” closed states. The time course of onset and recovery of the inactivation process from these pre-open closed states appears to be different from the open-state inactivation, suggesting the presence of multiple inactivated states with diverse kinetic pathways. This information has been analyzed together with a detailed study of KcsA single-channel behavior (in the accompanying paper) in the framework of a kinetic model. Taken together our data constitutes the first quantitative description of KcsA gating.
Fourier-Padé approximations and filtering for spectral simulations of an incompressible Boussinesq convection problem

In this paper, we present rational approximations based on Fourier series representation. For periodic piecewise analytic functions, the well-known Gibbs phenomenon hampers the convergence of the standard Fourier method. Here, for a given set of the Fourier coefficients from a periodic piecewise analytic function, we define Fourier-Pade-Galerkin and Fourier-Pade collocation methods by expressing the coefficients for the rational approximations using the Fourier data. We show that those methods converge exponentially in the smooth region and successfully reduce the Gibbs oscillations as the degrees of the denominators and the numerators of the Pade approximants increase. Numerical results are demonstrated in several examples. The collocation method is applied as a postprocessing step to the standard pseudospectral simulations for the one-dimensional inviscid Burgers' equation and the two-dimensional incompressible inviscid Boussinesq convection flow.
Purification and Characterization of a Natural Brazilian Clay Blend

Clay blends are products used in several industrial sectors, such as petrochemical or pharmaceutical. In this work we describe a natural clay blend occurring in northeastern Brazil. The aim was to purify and investigate their rheological and physical-chemical properties. Foster essays with water and organic solvents were utilized to access the swelling properties of the analyzed sample. Powder X-ray diffractograms (PXRD) were utilized to analyze qualitatively the clay minerals presents in the sample blend. Scanning eletronic microscopy (SEM) and Malvern techniques were used to investigate the sample clay morphology. The purification proceeding allowed separate distinct clay phases with different colors. PXRD analysis demonstrated that each clay phase presents similar structure. SEM and Malvern analysis showed distinct morphology and different size distribution for each clay phase. Our results revealed that the analyzed sample clay may be classified as smectite blend with strong potential for use in pharmaceutical and cosmetic products.
Regulation of the sperm calcium channel CatSper by endogenous steroids and plant triterpenoids

Significance The calcium channel of sperm—CatSper—is vital for male fertility. CatSper is activated by the hormone progesterone, but its pharmacological profile is not well studied. By exploring steroid selectivity of CatSper activation, we found one additional agonist—pregnenolone sulfate—and the two plant-derived inhibitors pristimerin and lupeol. By averting sperm hyperactivation, both inhibitors can prevent fertilization, thus acting as contraceptive agents. Additionally, by exploring CatSper regulation by endogenous steroids, we explain why CatSper is silent within the male reproductive tract and is only activated in close proximity to the egg. Interestingly, both testosterone and hydrocortisone antagonize the action of progesterone at physiological concentrations, which may explain why elevated levels of these steroids in the female organism affect fertility. The calcium channel of sperm (CatSper) is essential for sperm hyperactivated motility and fertility. The steroid hormone progesterone activates CatSper of human sperm via binding to the serine hydrolase ABHD2. However, steroid specificity of ABHD2 has not been evaluated. Here, we explored whether steroid hormones to which human spermatozoa are exposed in the male and female genital tract influence CatSper activation via modulation of ABHD2. The results show that testosterone, estrogen, and hydrocortisone did not alter basal CatSper currents, whereas the neurosteroid pregnenolone sulfate exerted similar effects as progesterone, likely binding to the same site. However, physiological concentrations of testosterone and hydrocortisone inhibited CatSper activation by progesterone. Additionally, testosterone antagonized the effect of pregnenolone sulfate. We have also explored whether steroid-like molecules, such as the plant triterpenoids pristimerin and lupeol, affect sperm fertility. Interestingly, both compounds competed with progesterone and pregnenolone sulfate and significantly reduced CatSper activation by either steroid. Furthermore, pristimerin and lupeol considerably diminished hyperactivation of capacitated spermatozoa. These results indicate that (i) pregnenolone sulfate together with progesterone are the main steroids that activate CatSper and (ii) pristimerin and lupeol can act as contraceptive compounds by averting sperm hyperactivation, thus preventing fertilization.
A comprehensive multi-mode performance analysis of interleaved boost converters

Interleaved power converter topologies have received increasing attention in recent years for high performance applications. In this paper, a comprehensive multi-mode performance analysis is presented for interleaved boost converters operating over the entire duty ratio range (0 ≤ switch duty ratio ≤ 1) under the continuous conduction mode (CCM) and two discontinuous conduction modes (DCMs). With inductor coupling factor and converter loading as parameters, key performance indicators such as the dc voltage gain, input ripple current, inductor ripple current, and output ripple voltage are presented in a normalized form to aid the converter design process. Transitions among the CCM and two DCM modes are clearly defined for the entire switch duty ratio range. Advantages of DCM operation such as reduced switching loss at the expense of undesired ringing are discussed. The comprehensive multi-mode analysis has been experimentally verified using a 250 W, 70 kHz prototype converter unit.
National University of Singapore at the TREC 13 Question Answering Main Task

In the past two years in our participation in TREC, our efforts (Yang et al., 2002, 2003) have been focused on incorporating external knowledge for boosting document and passage retrieval performance in event-based open domain question answering (QA). Despite our previous successes, we have identified three weaknesses of our system with respect to this year’s task guidelines. First, our system works at the surface level to extract answers, by picking the first occurrence of a string that matches the question target type from the highest-ranked passage. As such, our answer extraction relies heavily on the results of passage retrieval and named entity tagging. However, a passage that contains the correct answer may contain other strings of the same target type (Light et al., 2001) which can lead to an incorrect string being extracted. A technique to select the answer string that has the correct relationships with respect to the other words in the question is needed. Second, our definitional QA system utilizes manually-constructed definition patterns. While these patterns are precise in selecting definition sentences, they are strict in matching (slot-by-slot matching using regular expressions), failing to match correct sentences with minor variations. Third, this year’s guidelines state that factoid and list questions are not independent; instead, they are all related to given topics. Under such contextual QA scenario, we need to revise our framework to exploit existing topic-relevant knowledge in answering such questions. Accordingly, we focus on the following three features in this year’s TREC: (1) To give appropriate evidence to answer extraction, we use grammatical dependency relations among question terms to reinforce answer selection. In contrast to previous work in matching dependency relations, we propose to measure the similarity between relations to rank answer strings.
Effect of Tumor Necrosis Factor on Epithelial Tight Junctions and Transepithelial Permeability1

The serum factor inducing hemorrhagic necrosis of transplantable tumors (tumor necrosis factor (TNF)|, and the macrophage hormone associated with cachexia in cancer and certain infectious diseases [cach-ectin| are known to be the same protein. Because an association may exist between l M and the cachectic state, we wished to examine the effect of TNF on the permeability of epithelial barriers. We present data showing that TNF affects the tight junctional region between epithelial cells, lowering the transepithelial resistance and potential difference, and increasing the flow of solute between cells and across the epithelium. These effects are dose dependent, rapidly reversible, and inhibited by a monoclonal antibody to TNF-o. We suggest that the release of TNF at various sites throughout the body will cause a general breakdown in the barrier function of an epithelial cell sheet. This may relate to the cachexia observed in certain disease states. These findings are similar to our earlier published effects of phorbol esters and diacylglycerols on tight junctions, suggesting that protein kinase C activation may be involved.
Polo-Like Kinase 1 Depletion Induces DNA Damage in Early S Prior to Caspase Activation

ABSTRACT Polo-like kinase 1 (Plk1) plays several roles in mitosis, and it has been suggested to have a role in tumorigenesis. We have previously reported that Plk1 depletion results in cell death in cancer cells, whereas normal cells survive similar depletion. However, Plk1 depletion together with p53 depletion induces cell death in normal cells as well. This communication presents evidence on the sequence of events that leads to cell death in cancer cells. DNA damage is detected at the first S phase following Plk1 depletion and is more severe in Plk1-depleted p53-null cancer cells. As a consequence of Plk1 depletion using lentivirus-based small interfering RNA techniques, prereplicative complex (pre-RC) formation is disrupted at the G1/S transition, and DNA synthesis is reduced during S phase of the first cycle after depletion. The levels of geminin, an inhibitor of DNA pre-RC, and Emi1, an inhibitor of anaphase-promoting complex/cyclosome, are elevated in Plk1-depleted cells. The rate of cell cycling is slower in Plk1-depleted cells than in control cells when synchronized by serum starvation. Plk1 depletion results in disrupted DNA pre-RC formation, reduced DNA synthesis, and DNA damage before cells display severe mitotic catastrophe or apoptosis. Our data suggest that Plk1 is required for cell cycle progression not only in mitosis but also for DNA synthesis, maintenance of DNA integrity, and prevention of cell death.
A routability constrained scan chain ordering technique for test power reduction

For scan-based testing, the high test power consumption may cause test power management problems, and the extra scan chain connections may cause routability degradation during the physical design stage. In this paper, a scan chain ordering technique for test power reduction under user-specified routability constraints is presented. The proposed technique allows the user to explicitly set the routing constraints and the achievable power reduction is rather insensitive to the routing constraints. The proposed method is applied to six industrial designs. The achievable power reduction is in the range of 37-48% without violating any user-specified routing constraint.
Feasibility studies on active damage detection for CFRP aircraft bonding structures

This paper presents a part of the feasibility study for employing a damage monitoring system using a PZT actuator/FBG sensor. The goal of this research is to improve the present safety level of aircrafts by ensuring structural integrity and reducing maintenance/operation costs of advanced composite materials that will be employed for the primary structures of the new generation aircraft. Our novel sensor system employing a PZT actuator and an FBG optical fiber sensor can detect several types of damage, such as delamination and debonding, which are expected to occur in the highly efficient bonding structures of an aircraft wing box when the main/tail wing section is designed using composite materials. In this system, elastic waves will be transmitted into the structure by PZT actuators and received by small-diameter FBG optical fiber sensors that are embedded in the critical section of the primary structure of an aircraft. The onset and growth of damage can be detected with a very high accuracy through the change in the received elastic waves. In this study, a conceptual design was implemented in order to employ the novel system. We also selected the optimum application candidate area in order to verify the effects of the system. Further, the investigation and experiment on the novel sensor system that uses a bonded PZT actuator and an FBG sensor was carried out, and the basic damage detection technique was established based on the experimental results of the received elastic wave. Furthermore, compressive tests were carried out using the coupon specimen with an embedded small-diameter or standard-diameter optical fiber sensor. It was verified that the coupon specimen with an embedded small-diameter optical fiber suffered no degradation of its material properties.
Figure-ground Segmentation using Metrics Adaptation in Level Set Methods

We present an approach for hypothesis-based image segmen- tation basing on the integration of level set methods and discriminative feature clustering techniques. Building up on previous work, we investigate Localized Generalized Matrix Learning Vector Quantization (LGMLVQ) to train a classifier for fore- and background of an image. We extend this concept towards level set segmentation algorithms, where region descrip- tors are used to adapt the object contour according to the image features. The fusion of both methods outperforms their individual applications and improve the performance compared to other state of the art segmentation methods.
Elevating the vitamin E content of plants through metabolic engineering.

alpha-Tocopherol (vitamin E) is a lipid-soluble antioxidant synthesized only by photosynthetic organisms. alpha-Tocopherol is an essential component of mammalian diets, and intakes in excess of the U.S. recommended daily allowance are correlated with decreased incidence of a number of degenerative human diseases. Plant oils, the main dietary source of tocopherols, typically contain alpha-tocopherol as a minor component and high levels of its biosynthetic precursor, gamma-tocopherol. A genomics-based approach was used to clone the final enzyme in alpha-tocopherol synthesis, gamma-tocopherol methyltransferase. Overexpression of gamma-tocopherol methyltransferase in Arabidopsis seeds shifted oil compositions in favor of alpha-tocopherol. Similar increases in agricultural oil crops would increase vitamin E levels in the average U.S. diet.