Miracle-dz/UniFAR-FTUs huggingface dataset:
Empirical Data Analytics

In this paper, we propose an approach to data analysis, which is based entirely on the empirical observations of discrete data samples and the relative proximity of these points in the data space. At the core of the proposed new approach is the typicality—an empirically derived quantity that resembles probability. This nonparametric measure is a normalized form of the square centrality (centrality is a measure of closeness used in graph theory). It is also closely linked to the cumulative proximity and eccentricity (a measure of the tail of the distributions that is very useful for anomaly detection and analysis of extreme values). In this paper, we introduce and study two types of typicality, namely its local and global versions. The local typicality resembles the well‐known probability density function (pdf), probability mass function, and fuzzy set membership but differs from all of them. The global typicality, on the other hand, resembles well‐known histograms but also differs from them. A distinctive feature of the proposed new approach, empirical data analysis (EDA), is that it is not limited by restrictive impractical prior assumptions about the data generation model as the traditional probability theory and statistical learning approaches are. Moreover, it does not require an explicit and binary assumption of either randomness or determinism of the empirically observed data, their independence, or even their number (it can be as low as a couple of data samples). The typicality is considered as a fundamental quantity in the pattern analysis, which is derived directly from data and is stated in a discrete form in contrast to the traditional approach where a continuous pdf is assumed a priori and estimated from data afterward. The typicality introduced in this paper is free from the paradoxes of the pdf. Typicality is objectivist while the fuzzy sets and the belief‐based branch of the probability theory are subjectivist. The local typicality is expressed in a closed analytical form and can be calculated recursively, thus, computationally very efficiently. The other nonparametric ensemble properties of the data introduced and studied in this paper, namely, the square centrality, cumulative proximity, and eccentricity, can also be updated recursively for various types of distance metrics. Finally, a new type of classifier called naïve typicality‐based EDA class is introduced, which is based on the newly introduced global typicality. This is only one of the wide range of possible applications of EDA including but not limited for anomaly detection, clustering, classification, control, prediction, control, rare events analysis, etc., which will be the subject of further research.
Bevacizumab Induces Acute Hypoxia and Cancer Progression in Patients with Refractory Breast Cancer: Multimodal Functional Imaging and Multiplex Cytokine Analysis

Purpose: Bevacizumab, an antibody against endothelial growth factor, is a key but controversial drug in the treatment of metastatic breast cancer. We, therefore, aimed to determine the intrinsic resistance to bevacizumab at the physiologic and molecular levels in advanced breast cancer using PET, dynamic contrast-enhanced MRI, diffuse optical spectroscopic imaging (DOSI), and multiplex cytokine assays. Experimental Design: In total, 28 patients diagnosed with advanced stage III/IV breast cancer receiving single-agent bevacizumab for 1 week followed by paclitaxel combined with bevacizumab underwent 18F-fluorodeoxyglucose (FDG)-PET, 18F-fluoromisonidazole (FMISO)-PET, and MRI at both baseline and two courses after treatment initiation. Hemodynamic measurement using DOSI and blood sample collection were performed at baseline and multiple times during the first week after the initiation of single-agent bevacizumab. We distinguished nonresponders from responders by serial FDG-PET based on their glycolytic changes to chemotherapy. Results: Nonresponders showed significantly higher hypoxic activity on FMISO-PET and less tumor shrinkage than responders. Hemodynamic parameters showed higher tumor blood volume and a remarkable decrease in the tissue oxygen level in nonresponders compared with responders after the infusion of single-agent bevacizumab. Multiplex cytokine assays revealed increased plasma levels of both proangiogenic and hypoxia-related inflammatory cytokines in nonresponders and decreased levels in responders. Conclusions: Nonresponders exhibited a higher degree of angiogenesis with more severe hypoxia than responders during bevacizumab treatment. These findings demonstrated that the addition of bevacizumab to paclitaxel treatment under hypoxic conditions could be ineffective and may result in acute hypoxia and increased cytokine secretion associated with cancer progression. Clin Cancer Res; 23(19); 5769–78. ©2017 AACR.
Cell and Tissue Damage after Skin Exposure to Ionizing Radiation: Short- and Long-Term Effects after a Single and Fractional Doses

Ionizing radiation is often used to treat progressive neoplasms. However, the consequences of long-term radiation exposure to healthy skin tissue are poorly understood. We aimed to evaluate the short- and long-term radiation damage to healthy skin of the same irradiation given either as single or fractional doses. C57BL/J6 mice were randomly assigned to one of three groups: a control and two exposure groups (5 Gy ×2 or 10 Gy ×1). The inguinal area was irradiated (6-MeV beam) 1 week after depilation in the treatment groups. Skin samples were evaluated macroscopically and histologically for up to 6 months after the final exposure. After anagen hair follicle injury by irradiation, hair cycling resumed in both groups, but hair graying was observed in the 10 Gy ×1 group but not in the 5 Gy ×2 group, suggesting the dose of each fractional exposure is more relevant to melanocyte stem cell damage than the total dose. On the other hand, in the long term, the fractional double exposures induced more severe atrophy and capillary reduction in the dermis and subcutis, suggesting fractional exposure may cause more depletion of tissue stem cells and endothelial cells in the tissue. Thus, our results indicated that there were differences between the degrees of damage that occurred as a result of a single exposure compared with fractional exposures to ionizing radiation: the former induces more severe acute injury to the skin with irreversible depigmentation of hairs, while the latter induces long-term damage to the dermis and subcutis.
Impact of calcium and vitamin D insufficiencies on serum parathyroid hormone and bone mineral density: Analysis of the fourth and fifth Korea National Health and Nutrition Examination Survey (KNHANES IV‐3, 2009 and KNHANES V‐1, 2010)

The relative contributions of calcium and vitamin D to calcium metabolism and bone mineral density (BMD) have been examined previously, but not in a population with very low calcium intake. To determine the relative importance of dietary calcium intake and serum 25‐hydroxyvitamin D [25(OH)D] concentration to calcium metabolism and bone mass in a population with low calcium intake, a total of 4662 adults (2567 men and 2095 women) ≥50 years of age from the 2009–2010 Korea National Health and Nutrition Examination Survey (KNHANES) were divided into groups according to dietary calcium intakes (quintiles means: 154, 278, 400, 557, and 951 mg/d) and serum 25(OH)D concentrations (<50, 50–75, and >75 nmol/L). Serum intact parathyroid hormone (PTH) and femoral neck and lumbar spine BMD were evaluated according to dietary calcium intake and serum 25(OH)D. Mean calcium intake was 485 mg/d; mean serum 25(OH)D concentration was 48.1 nmol/L; PTH was 68.4 pg/mL; femoral neck BMD was 0.692 g/cm2; and lumbar spine BMD was 0.881 g/cm2. Lower dietary calcium intakes were significantly associated with higher serum PTH concentrations and lower femoral neck BMD, not only at lower (<50 nmol/L) but also at higher (>75 nmol/L) serum 25(OH)D concentrations. Serum PTH was highest and femoral neck BMD was lowest in the group, with a serum 25(OH)D less than 50 nmol/L. In this low‐intake population, calcium intake is a significant determinant of serum PTH and BMD at higher as well as lower 25(OH)D levels. This finding indicates that low calcium intake cannot be compensated for with higher 25(OH)D levels alone. As expected, serum 25(OH)D levels were inversely associated with serum PTH and BMD. A calcium intake of at least 668 mg/d and a serum 25(OH)D level of at least 50 nmol/L may be needed to maintain bone mass in this calcium deficient population. © 2013 American Society for Bone and Mineral Research.
Wear Behavior of Al-Based Nanocomposites Reinforced with Bimodal Micro- and Nano-Sized Al2O3 Particles Produced by Spark Plasma Sintering

Spark Plasma Sintering (SPS) has been recognized, in the recent past, as a very useful method to produce metal matrix composites with enhanced mechanical and wear properties. Obviously, the material’s final properties are strongly related to the reinforcement types and percentages and the particles’ distribution, as well as to the processing parameters employed during synthesis. The present article analyzes the effect of microscopic and nanometric alumina particles, blended to pure aluminum in different combinations, on the final properties of metal matrix composites produced via SPS. A strong variation in the microstructural behavior, mechanical, and wear properties has been observed by varying the nano- to micro-alumina particles’ percentage and the distribution of the ceramic particles blended with aluminum ones.
Optimal Switching under a Regime-Switching Model with Two-Time-Scale Markov Chains

This paper is concerned with a probabilistic approach to an optimal switching problem. The dynamics of the system consists of a set of diffusions coupled by a finite-state Markov chain. It is shown that the corresponding value function can be given in terms of the solution of an oblique reflected backward stochastic differential equation with a Markov chain. In many applications, the underlying Markov chain exhibits two-time-scale structure. In this case, the value function for the original problem is shown to converge to the value function of a limit problem as the fluctuation rate shrinks to zero. The main advantage of this two-time-scale approach is the reduction of dimensionality. The limit problem is much easier to solve, and its optimal switching solution leads to approximate solutions to the original problem. Finally, a numerical example is provided to demonstrate the convergence result.
Multiple bile‐duct hamartomas

Six cases of multiple bile‐duct hamartomas are reported as incidental findings in 875 autopsies (0.69%). All of the patients were Negroes; there were 3 males and 3 females, ranging in age from 46 to 93 years. One patient had associated bilateral congenital polycystic kidney and hemangiomas of the liver. Another patient had associated unilateral congenital cysts of the kidney and a cortical hamartoma of the ipsilateral kidney. Gross and microscopic variations of bile‐duct hamartomas are illustrated and their significance is discussed. To avoid possible oversight of the lesions, reexamination of the liver after fixation in 10% neutral formalin is recommended. It is also emphasized that the histology of the lesions may be clear‐cut hamartomas or may suggest neoplastic growths. The relationship of bile‐duct hamartomas to polycystic disease of the liver is discussed. Its association with congenital hepatic fibrosis and congenital dilatation of the intrahepatic bile ducts is presented.
Optimization of NaOH Molarity, LUSI Mud/Alkaline Activator, and Na2SiO3/NaOH Ratio to Produce Lightweight Aggregate-Based Geopolymer

This paper presents the mechanical function and characterization of an artificial lightweight geopolymer aggregate (ALGA) using LUSI (Sidoarjo mud) and alkaline activator as source materials. LUSI stands for LU-Lumpur and SI-Sidoarjo, meaning mud from Sidoarjo which erupted near the Banjarpanji-1 exploration well in Sidoarjo, East Java, Indonesia on 27 May 2006. The effect of NaOH molarity, LUSI mud/Alkaline activator (LM/AA) ratio, and Na2SiO3/NaOH ratio to the ALGA are investigated at a sintering temperature of 950 °C. The results show that the optimum NaOH molarity found in this study is 12 M due to the highest strength (lowest AIV value) of 15.79% with lower water absorption and specific gravity. The optimum LUSI mud/Alkaline activator (LM/AA) ratio of 1.7 and the Na2SiO3/NaOH ratio of 0.4 gives the highest strength with AIV value of 15.42% with specific gravity of 1.10 g/cm3 and water absorption of 4.7%. The major synthesized crystalline phases were identified as sodalite, quartz and albite. Scanning Electron Microscope (SEM) image showed more complete geopolymer matrix which contributes to highest strength of ALGA produced.
A 0.076 mm2 12 b 26.5 mW 600 MS/s 4-Way Interleaved Subranging SAR- $\Delta \Sigma $ ADC With On-Chip Buffer in 28 nm CMOS

A 0.076 mm2 12b 28 nm 600 MS/s 4-way time interleaved ADC with on chip buffer is presented. The usage of a subranging scheme consisting of a coarse SAR ADC followed by an incremental ΔΣ fine converter provides better suppression of thermal noise added during conversion for a given power compared to a conventional SAR. The ADC area has been optimized by using a segmented charge-sharing charge-redistribution DAC. The prototype achieves an SNDR of 60.7 dB and 58 dB at low and high frequency, respectively, while consuming 26 mW.
The physics of confined flow and its application to water leaks, water permeation and water nanoflows: a review

This review assesses the current state of understanding of the calculation of the rate of flow of gases, vapours and liquids confined in channels, in porous media and in permeable materials with an emphasis on the flow of water and its vapour. One motivation is to investigate the relation between the permeation rate of moisture and that of a noncondensable test gas such as helium, another is to assist in unifying theory and experiment across disparate fields. Available theories of single component ideal gas flows in channels of defined geometry (cylindrical, rectangular and elliptical) are described and their predictions compared with measurement over a wide range of conditions defined by the Knudsen number. Theory for two phase flows is assembled in order to understand the behaviour of four standard water leak configurations: vapour, slug, Washburn and liquid flow, distinguished by the number and location of phase boundaries (menisci). Air may or may not be present as a background gas. Slip length is an important parameter that greatly affects leak rates. Measurements of water vapour flows confirm that water vapour shows ideal gas behaviour. Results on carbon nanotubes show that smooth walls may lead to anomalously high slip lengths arising from the properties of ‘confined’ water. In porous media, behaviour can be matched to the four standard leaks. Traditional membrane permeation models consider that the permeant dissolves, diffuses and evaporates at the outlet side, ideas we align with those from channel flow. Recent results on graphite oxide membranes show examples where helium which does not permeate while at the same time moisture is almost unimpeded, again a result of confined water. We conclude that while there is no a priori relation between a noncondensable gas flow and a moisture flow, measurements using helium will give results within two orders of magnitude of the moisture flow rate, except in the case where there is anomalous slip or confined water, when moisture specific measurements are essential.
Graphene Oxide as a Dielectric and Charge Trap Element in Pentacene-Based Organic Thin-Film Transistors for Nonvolatile Memory

In this report, the dielectric nature of graphene oxide (GO) was exploited for the successful implementation of low-power pentacene thin-film transistors suitable for nonvolatile memory applications. Two different types of devices were fabricated on indium tin oxide-coated glass substrates with two different metals, viz., gold and aluminum, as the source and drain contacts. The performance of the devices was analyzed from their field-effect characteristics. Both the devices showed dominant p-type charge transport behavior. The breakdown electric field was determined to be 1.02 × 108 V/m. The current transport mechanism was explained from the output characteristics using the Fowler–Nordheim tunneling theory. Capacitance–voltage (C–V) measurements have been employed to determine the value of the oxide capacitance and to examine the memory effect. The hysteresis behavior observed from the C–V characteristics show the suitability of the device for memory applications with a low operating voltage of 3 V. The charge trapping behavior of GO was explained by the energy band diagram. Frequency-dependent C–V measurements in the range 100 kHz to 1 MHz were also performed to account for the memory window obtained in the devices. The charge retention and endurance characteristics were evaluated under a constant voltage stress to check the reliability of device operation.
Learning from Host-Defense Peptides: Cationic, Amphipathic Peptoids with Potent Anticancer Activity

Cationic, amphipathic host defense peptides represent a promising group of agents to be developed for anticancer applications. Poly-N-substituted glycines, or peptoids, are a class of biostable, peptidomimetic scaffold that can display a great diversity of side chains in highly tunable sequences via facile solid-phase synthesis. Herein, we present a library of anti-proliferative peptoids that mimics the cationic, amphipathic structural feature of the host defense peptides and explore the relationships between the structure, anticancer activity and selectivity of these peptoids. Several peptoids are found to be potent against a broad range of cancer cell lines at low-micromolar concentrations including cancer cells with multidrug resistance (MDR), causing cytotoxicity in a concentration-dependent manner. They can penetrate into cells, but their cytotoxicity primarily involves plasma membrane perturbations. Furthermore, peptoid 1, the most potent peptoid synthesized, significantly inhibited tumor growth in a human breast cancer xenotransplantation model without any noticeable acute adverse effects in mice. Taken together, our work provided important structural information for designing host defense peptides or their mimics for anticancer applications. Several cationic, amphipathic peptoids are very attractive for further development due to their high solubility, stability against protease degradation, their broad, potent cytotoxicity against cancer cells and their ability to overcome multidrug resistance.
NK cells exacerbate the pathology of influenza virus infection in mice

NK cells offer a first line of defense against viruses and are considered beneficial to the host during infection. Nevertheless, little is understood regarding the phenotype and function of NK cells in the lung during influenza virus infection. We found that the frequency of NK cells in mouse lung increased during influenza infection, with the majority of a mature phenotype. Cell surface CD107a and intracellular IFN‐γ were detected in cells expressing multiple NK‐cell receptors in infected lung, suggesting that NK cells were activated during infection. The activating receptor NKp46 was predominantly negative on such cells, possibly as a result of encountering influenza HA. Depletion of NK cells in vivo with anti‐asialo GM1 or anti‐NK1.1 reduced mortality from influenza infection and surviving mice recovered their body weight. Pathology induced by NK cells was only observed with high, not medium or low‐dose influenza infection, indicating that the severity of infection influences NK‐cell‐mediated pathology. Furthermore, adoptive transfer of NK cells from influenza‐infected lung, but not uninfected lung, resulted in more rapid weight loss and increased mortality of influenza‐infected mice. Our results indicate that during severe influenza infection of the lung, NK cells have a deleterious impact on the host, promoting mortality.
Adipose tissue autophagy status in obesity: Expression and flux—two faces of the picture

abstract In the context of elevated prevalence of obesity-associated metabolic diseases in the human population wordwide, interest in the autophagy degradation pathway is increasing, due to close links with energy metabolism, nutritional state, and inflammation. Here we highlight recent data focusing on adipose tissue which demonstrate alterations in fat cell autophagic flux in human obesity.
Learning Entailment Rules for Unary Templates

Most work on unsupervised entailment rule acquisition focused on rules between templates with two variables, ignoring unary rules - entailment rules between templates with a single variable. In this paper we investigate two approaches for unsupervised learning of such rules and compare the proposed methods with a binary rule learning method. The results show that the learned unary rule-sets outperform the binary rule-set. In addition, a novel directional similarity measure for learning entailment, termed Balanced-Inclusion, is the best performing measure.
Towards automated crystallographic structure refinement with phenix.refine

phenix.refine is a program within the PHENIX package that supports crystallographic structure refinement against experimental data with a wide range of upper resolution limits using a large repertoire of model parameterizations. This paper presents an overview of the major phenix.refine features, with extensive literature references for readers interested in more detailed discussions of the methods.
K2: A Stream Cipher Algorithm using Dynamic Feedback Control

A technique for maintaining the integrity of data maintained in an object in a persistent store of objects. When a modification event is initiated during a transaction to modify an object, a copy of the object is created. Modifications are made to the copy of the object, and the original object remains available to be accessed with its original value. The modifications to the copy of the object can be reviewed, or further modifications can be made to the copy before the modifications are committed and the changes to the copy applied to the original object and thus available to all users of the persistent store. Alternatively, the modification event can be canceled prior to commitment and never be made available via the persistent store.
Determining the maximal singularity-free circle or sphere of parallel mechanisms using interval analysis

SUMMARY This paper proposes a systematic algorithm based on the concept of interval analysis to obtain the maximal singularity-free circle or sphere within the workspace of parallel mechanisms. As case studies the 3-RPR planar and 6-UPS parallel mechanisms are considered to illustrate the relevance of the algorithm for 2D and 3D workspaces. To this end, the main algorithm is divided into four sub-algorithms, which eases the understanding of the main approach and leads to a more effective and robust algorithm to solve the problem. The first step is introduced to obtain the constant-orientation workspace and then the singularity locus. The main purpose is to obtain the maximal singularity-free workspace for an initial guess. Eventually, the general maximal singularity-free workspace is obtained. The main contribution of the paper is the proposition of a systematic algorithm to obtain the maximal singularity-free circle/sphere in the workspace of parallel mechanisms. The combination of a maximal singularity-free circle or sphere with the workspace analysis by taking into account the stroke of actuators, as additional constraint to the latter problem, is considered. Moreover, the center point of the circle/sphere is not restrained to a prescribed point.