Miracle-dz/UniFAR-FTUs huggingface dataset:
Acquiring Chondrocyte Phenotype from Human Mesenchymal Stem Cells under Inflammatory Conditions

An inflammatory milieu breaks down the cartilage matrix and induces chondrocyte apoptosis, resulting in cartilage destruction in patients with cartilage degenerative diseases, such as rheumatoid arthritis or osteoarthritis. Because of the limited regenerative ability of chondrocytes, defects in cartilage are irreversible and difficult to repair. Mesenchymal stem cells (MSCs) are expected to be a new tool for cartilage repair because they are present in the cartilage and are able to differentiate into multiple lineages of cells, including chondrocytes. Although clinical trials using MSCs for patients with cartilage defects have already begun, its efficacy and repair mechanisms remain unknown. A PubMed search conducted in October 2014 using the following medical subject headings (MeSH) terms: mesenchymal stromal cells, chondrogenesis, and cytokines resulted in 204 articles. The titles and abstracts were screened and nine articles relevant to “inflammatory” cytokines and “human” MSCs were identified. Herein, we review the cell biology and mechanisms of chondrocyte phenotype acquisition from human MSCs in an inflammatory milieu and discuss the clinical potential of MSCs for cartilage repair.
Evaluation of free-to-total prostate specific antigen (F/T PSA), prostate specific antigen density (PSAD) and (F/T)/PSAD sensitivity on reduction of unnecessary prostate biopsies for patients with PSA in gray zone.

AIM We evaluated the influence of ratio between free-to-total prostate specific antigen (F/T PSA) and prostate specific antigen density (PSAD)-(F/T)/PSAD on reduction of unnecessary prostate biopsies in grey zone (prostate specific antigen (psa) value 4.0-10.0 ng/ml). METHODS The study included 108 patients. For all patients serum total PSA (T PSA), free PSA (F PSA), F/T PSA and PSAD were analyzed. The group was divided due to the prostate volume into: entire group (regardless the prostate VOL-Group 1) and group with prostate VOL<40 (Group 2). RESULTS Seventy five patients were diagnosed with benign prostatic hyperplasia (BPH) and 33 with prostate cancer (CaP). F/T PSA and (F/T)/PSAD showed significantly lower values in patients with CaP versus those with BPH, while PSAD had significantly higher values. For the cutoff values of 1.12 for (F/T)/PSAD, we found sensitivity to be 67% and specificity 60%, and the (AUC) 0.701. For patients with VOL<40, statistical significance remained with AUC of 0.732 (p=0.003), cutoff was 0.82, and with sensitivity 77% and specificity 68%. CONCLUSIONS Most significant prostate carcinoma predictors were PSAD and (F/T)/PSAD, where we proposed that patients with (F/T)/PSAD values below 1.49 ± 0.94 and PSAD values above 0.17±0.06 should be included for biopsy.
Secure group key management scheme based on dual receiver cryptosystem

Providing the confidentiality to the messages delivered between group members in secure group communication model is a critical networking issue. Key management is a challenging task in secure group communication. Tree based group key management scheme is believed to provide a very powerful approach for group key management. In this paper, we provide a new approach to group key management based on the dual receiver crypto system in which a sender can encrypt a message that can be decrypted by two receivers. The proposed scheme is a distributed scheme and uses the key tree to manage the keys. Some of the existing distributed schemes assume the key tree as binary and ternary. Our scheme can be extended to key tree of varying degree. For a group with $n$ users, only two encryptions are needed for rekeying during member join event and ≤ [d/3] logdn (d > 1 is degree) encryptions are required for rekeying upon user leave event. We compare the proposed scheme with the other tree based distributed schemes and show that the proposed scheme is efficient.
Optimization of resource allocation in relay assisted multi-user SCMA uplink network

In this paper, we study the optimization of resource allocation in dual-hop relay assisted multi-user sparse code multiple access (SCMA) uplink network. Based on this, an uplink transmission strategy with the combination of SCMA and orthogonal frequency division multiple access (OFDMA) is considered, where the user equipments (UEs) transmit information to a relay station (RS) via SCMA codebook assignment and then the RS amplifies and forwards the information to the base station (BS) through OFDMA subcarrier pairing. Under the individual power constraints on both UEs and RS, a problem of maximizing the weighted sum-rate of the system by joint power allocation, codebook assignment and subcarrier pairing is conceived. To tackle the complex issue, a two-step wise algorithm is proposed. Alternatively, we find the optimal power and codebook allocation based on the special feature of SCMA codebook, and then obtain the solution to subcarrier pairing with a new criteria for each possible subcarrier pair. Numerical results verify the effectiveness of the proposed algorithm in both weighted sum-rate and energy efficiency (EE).
Sustained Atrial Tachycardia in Adult Patients: Electrophysiological Characteristics, Pharmacological Response, Possible Mechanisms, and Effects of Radiofrequency Ablation

BackgroundMechanisms and electropharmacological characteristics in adult patients with atrial tachycardia (AT) are not well described. We proposed that a combination of electropharmacological characteristics, recording of monophasic action potential, and effects of radiofrequency ablation could further determine the mechanisms and achieve a new classification in adults with various types of AT because they were important in regard to the correlation between mecha-nisms and pathophysiology, clinical syndrome, and responses to specific pharmacological or nonpharmacological therapies. Methods and ResultsThirty-six patients (11 female, 25 male; mean age, 57±13 years) with AT were referred for electropharmacological studies and radiofrequency ablation. Resetting response pattern, entrainment phenomenon, recording of monophasic action potential, serial drug test, response to Valsalva maneuver, endocardial mapping technique, and radiofrequency ablation were performed. Seven patients had automatic AT provocable with isoproterenol; neither initiation nor termination was related to programmed electrical stimulation. The other 29 patients had AT initiated or terminated by electrical stimulation and mechanisms related to triggered activity or reentry; nine of them needed isopro-terenol to facilitate initiation of AT, associated with delayed afterdepolarization in monophasic action potential. All responded to adenosine (15 to 60 μg/kg) and Valsalva maneuver. Dipyridamole terminated AT and decreased the slope of afterdepolarization. Afterdepolarization was not found in the patients with automatic or reentrant AT. In 40 of 41 (98%), AT was ablated successfully, with late recurrence in 2 of 40 (5%) (follow-up, 18±4 months). ConclusionsThis study demonstrates the diverse mechanisms and electropharmacological characteristics of AT in adults. Furthermore, radiofrequency ablation of various types of AT could achieve high success and low recurrence rates.
Classification of fingerprints using singular points and their principal axes

This paper proposes a rule-based algorithm for classification of a fingerprint into one of six well-known classes: plain arch, tented arch, right loop, left loop, whorl and twin loop. The rules are formed using the relative locations and types of singular points and the relative directions of their associated principal axes. The reliable and fast classification algorithm is made possible by a simple but effective combination of ridge flow-code technique and orientation variance calculation in the determination of singular points and principal axes. The Poincare indices of these singular points are used to determine their type: ordinary, delta, core or double-core. For a small test sample of 157 fingerprints available to the authors, the correct classification rate is better than 90%.
Quantitative three‐dimensional ultrasound analysis of tongue protrusion, grooving and symmetry: Data from 12 normal speakers and a partial glossectomee

The functional determinants for a good speech outcome after a partial tongue resection and reconstruction are not well established. The purpose of the present study was to assess the protrusion, grooving and symmetry of the tongue during sustained speech sound production using three‐dimensional ultrasound. The participants were twelve normal speakers and one partial glossectomee. The three‐dimensional ultrasound volumes of nine sustained speech sounds were measured in three sagittal planes. The data were re‐plotted as three‐dimensional surfaces. We calculated an anteriority index, a concavity index and an asymmetry index. The glossectomee's postoperative surface plots were characterized by asymmetry and convexity of the tongue surface. The anteriority index illustrated that the glossectomee's ability to protrude her tongue was not affected by the operation. The concavity index captured a decrease in midsagittal grooving in the glossectomee's tongue. The asymmetry index demonstrated height differences in the elevation of the right and left side of the tongue. We conclude that three‐dimensional ultrasound offers us a practical tool for the detailed and concise assessment of the lingual shape and deformation in patients undergoing glossectomy surgery.
Spectral Entropy for Epileptic Seizures Detection

The electroencephalogram (EEG) is the brain signal that represented the valuable information about the brains condition. The configuration of the signals waveform may contain valuable and useful information about the different states of the brain. Since the biological signals are personal, indications may occur highly random in both time and frequency domains. Thus the computer analyzing is necessary. EEG is decomposed by wavelet transform and coefficient sets are obtained. In this paper spectral entropy is applied to these coefficient sets for epileptic seizures detection. This process is applied to three different groups of EEG signals: 1) healthy states, 2) epileptic states during a seizure-free interval (interictal EEG), 3) epileptic states during a seizure (ictal EEG). At the end the statistical analysis is applied for distinguishing the coefficient sets. This statistical process can differentiate between ictal and healthy subject (with eyes close) of cD2 coefficients (15-30 Hz) with 99% p-value.
C-Linker of Cyclic Nucleotide–gated Channels Controls Coupling of Ligand Binding to Channel Gating

Cyclic nucleotide–gated channels are composed of a core transmembrane domain, structurally homologous to the voltage-gated K+ channels, and a cytoplasmic ligand-binding domain. These two modules are joined by ∼90 conserved amino acids, the C-linker, whose precise role in the mechanism of channel activation by cyclic nucleotides is poorly understood. We examined cyclic nucleotide–gated channels from bovine photoreceptors and Caenorhabditis elegans sensory neurons that show marked differences in cyclic nucleotide efficacy and sensitivity. By constructing chimeras from these two channels, we identified a region of 30 amino acids in the C-linker (the L2 region) as an important determinant of activation properties. An increase in both the efficacy of gating and apparent affinity for cGMP and cAMP can be conferred onto the photoreceptor channel by the replacement of its L2 region with that of the C. elegans channel. Three residues within this region largely account for this effect. Despite the profound effect of the C-linker region on ligand gating, the identity of the C-linker does not affect the spontaneous, ligand-independent open probability. Based on a cyclic allosteric model of activation, we propose that the C-linker couples the opening reaction in the transmembrane core region to the enhancement of the affinity of the open channel for agonist, which underlies ligand gating.
Dynamic and Adaptive Calling Context Encoding

Calling context has been widely used in many software development processes such as testing, event logging, and program analysis. It plays an even more important role in data race detection and performance bottleneck analysis for multi-threaded programs. This paper presents DACCE (Dynamic and Adaptive Calling Context Encoding), an efficient runtime encoding/decoding mechanism for single-threaded and multi-threaded programs that captures dynamic calling contexts. It can dynamically encode all call paths invoked at runtime, and adjust the encodings according to program's execution behavior. In contrast to existing context encoding method, DACCE can work on incomplete call graph, and it does not require source code analysis and offline profiling to conduct context encoding. DACCE has significantly expanded the functionality and applicability of calling context with even lower runtime overhead. DACCE is very efficient based on experiments with SPEC CPU2006 and Parsec 2.1 (with about 2% of runtime overhead) and effective for all tested benchmarks.
A Virtualized Environment Security (VES) model for a secure virtualized environment

Security in virtualized environments has become a serious concern, as it gained acceptance in corporate data centers. The importance of the operational, organizational and economic context has been placed into the background, while much of the focus remained on the virtualization technology itself. The security of a virtualized environment requires a multi-faceted approach, where technical as well as non-technical aspects need to be taken into account. For example, securing the virtual machine alone will not secure the virtualized environment. The management of the virtual machines, users' roles and permissions, as well as the implementation of policies and procedures in the organization all plays a role in the overall security of the virtualized environment. Without compliance and best practice guidelines, amongst others, the organization is at risk. This paper will discuss the Virtualized Environment Security (VES) model, illustrating the necessary dimensions needed in order to secure a virtualized environment.
Causal inference and the data-fusion problem

We review concepts, principles, and tools that unify current approaches to causal analysis and attend to new challenges presented by big data. In particular, we address the problem of data fusion—piecing together multiple datasets collected under heterogeneous conditions (i.e., different populations, regimes, and sampling methods) to obtain valid answers to queries of interest. The availability of multiple heterogeneous datasets presents new opportunities to big data analysts, because the knowledge that can be acquired from combined data would not be possible from any individual source alone. However, the biases that emerge in heterogeneous environments require new analytical tools. Some of these biases, including confounding, sampling selection, and cross-population biases, have been addressed in isolation, largely in restricted parametric models. We here present a general, nonparametric framework for handling these biases and, ultimately, a theoretical solution to the problem of data fusion in causal inference tasks.
Reduced Expression of miRNA-27a Modulates Cisplatin Resistance in Bladder Cancer by Targeting the Cystine/Glutamate Exchanger SLC7A11

Purpose: Resistance to cisplatin-based chemotherapy is a major obstacle to bladder cancer treatment. We aimed to identify microRNAs (miRNA) that are dysregulated in cisplatin-resistant disease, ascertain how these contribute to a drug-resistant phenotype, and how this resistance might be overcome. Experimental Design: miRNA expression in paired cisplatin-resistant and -sensitive cell lines was measured. Dysregulated miRNAs were further studied for their ability to mediate resistance. The nature of the cisplatin-resistant phenotype was established by measurement of cisplatin/DNA adducts and intracellular glutathione (GSH). Candidate miRNAs were examined for their ability to (i) mediate resistance and (ii) alter the expression of a candidate target protein (SLC7A11); direct regulation of SLC7A11 was confirmed using a luciferase assay. SLC7A11 protein and mRNA, and miRNA-27a were quantified in patient tumor material. Results: A panel of miRNAs were found to be dysregulated in cisplatin-resistant cells. miRNA-27a was found to target the cystine/glutamate exchanger SLC7A11 and to contribute to cisplatin resistance through modulation of GSH biosynthesis. In patients, SLC7A11 expression was inversely related to miRNA-27a expression, and those tumors with high mRNA expression or high membrane staining for SLC7A11 experienced poorer clinical outcomes. Resistant cell lines were resensitized by restoring miRNA-27a expression or reducing SLC7A11 activity with siRNA or with sulfasalazine. Conclusion: Our findings indicate that miRNA-27a negatively regulates SLC7A11 in cisplatin-resistant bladder cancer, and shows promise as a marker for patients likely to benefit from cisplatin-based chemotherapy. SLC7A11 inhibition with sulfasalazine may be a promising therapeutic approach to the treatment of cisplatin-resistant disease. Clin Cancer Res; 20(7); 1990–2000. ©2014 AACR.
Mathematical modeling of mixed‐culture biofilms

About 10 years ago a set of mass balance equations for mathematical modeling of mixed‐culture biofilms (MCBs) was presented. That model was able to describe the progression of the biofilm thickness and the spatial distribution and development in time of particulate and dissolved components in the biofilm as a function of transport and transformation processes. Experimental observations made in the past years have shown that some of the assumptions made in that MCB model were too simple. Therefore, an extended MCB model with additional processes has been developed. This model includes a more flexible description of transport of dissolved components in the biofilm and considers diffusive transport of particulate components in the biofilm solid matrix, changes of the biofilm liquid phase volume fraction (porosity), and simultaneous detachment and attachment of cells and particles at the biofilm surface. The extended MCB model is implemented in AQUASIM, a new computer program designed for the analysis of aquatic systems, which is used here to illustrate and discuss the effect of the additional processes on MCB behavior. © 1996 John Wiley & Sons, Inc.
A Matter of gravity–mechanotransduction: how mechanical forces influence biological materials

Gravity has a major influence on the synthesis and catabolism of biological macromolecules; tissues are added or removed in response to the addition or loss of mechanical stimulation, respectively [1]. Transduction of mechanical energy into chemical energy represents the means by which biological tissues have adapted to life in a gravitational field [1,2]. The human body is a composite of macromolecular structures that support the musculoskeleton, provide a mechanism for locomotion and movement, and allow for homeostasis by regulating physiological functions [3]. They are primarily composed of extracellular matrix (ECM) containing collagen, the most abundant protein found in the human body [3,4]. Collagen fibers are found either in a mineralized form, in bone, or in a fibrous form in most other tissues and organs [3]. Fibrous collagen is a protein in the form of a coiled-coil that stores, transmits and dissipates mechanical energy in tissues as well as prevents premature mechanical failure [4,5].
Interstitial Collagen Catabolism*

Interstitial collagen mechanical and biological properties are altered by proteases that catalyze the hydrolysis of the collagen triple-helical structure. Collagenolysis is critical in development and homeostasis but also contributes to numerous pathologies. Mammalian collagenolytic enzymes include matrix metalloproteinases, cathepsin K, and neutrophil elastase, and a variety of invertebrates and pathogens possess collagenolytic enzymes. Components of the mechanism of action for the collagenolytic enzyme MMP-1 have been defined experimentally, and insights into other collagenolytic mechanisms have been provided. Ancillary biomolecules may modulate the action of collagenolytic enzymes.
Using Cognitive Models to Transfer the Strengths of Computer Games into Human Computer Interfaces

This paper extends techniques from affective psychology to show how cognitive models can be used to represent and reason about interaction with computer games. It is argued that this modeling activity provides insights into the motivational appeal that often distinguishes computer games from other forms of human computer interaction. The long-term aim behind this research is to use our improved understanding of interaction with computer games to inform the subsequent development of more general classes of interactive systems. Barnard's Interacting Cognitive Subsystems (ICS) is used throughout this paper. This decision is justified by the fact that ICS has already been applied to analyze the negative emotions surrounding clinical depression. This previous work provides a useful starting point for our investigation of the more positive emotions evoked during interaction with computer games. A further justification is that ICS has also been successfully used to represent and reason about the design of human computer interfaces.
Vertebrate Phylogenomics: Reconciled Trees and Gene Duplications

Ancient gene duplication events have left many traces in vertebrate genomes. Reconciled trees represent the differences between gene family trees and the species phylogeny those genes are sampled from, allowing us to both infer gene duplication events and estimate a species phylogeny from a sample of gene families. We show that analysis of 118 gene families yields a phylogeny of vertebrates largely in agreement with other data. We formulate the problem of locating episodes of gene duplication as a set cover problem: given a species tree in which each node has a set of gene duplications associated with it, the smallest set of species nodes whose union includes all gene duplications specifies the locations of gene duplication episodes. By generating a unique mapping from this cover set we can determine the minimal number of such episodes at each location. When applied to our data, this method reveals a complex history of gene duplications in vertebrate evolution that does not conform to the "2R" hypothesis.
:telephone::person::sailboat::whale::okhand: ; or “Call me Ishmael” – How do you translate emoji?

We report on an exploratory analysis of Emoji Dick, a project that leverages crowdsourcing to translate Melville's Moby Dick into emoji. This distinctive use of emoji removes textual context, and leads to a varying translation quality. In this paper, we use statistical word alignment and part-of-speech tagging to explore how people use emoji. Despite these simple methods, we observed differences in token and part-of-speech distributions. Experiments also suggest that semantics are preserved in the translation, and repetition is more common in emoji.
HYPOXIA IN THE NORTHERN GULF OF MEXICO

As a foundation for the IA, six topical reports were written by teams of experts. Public comments on the six reports were received from 34 organizations and individuals. Those reports and the public comments received on them, were used to draft the IA. The draft of the IA was also made available for public comment and those comments considered in completing the IA. Public comments on the draft IA were received from 16 organizations and individuals. The reports, the draft IA, and the public comments are available at <http://www.nos.noaa.gov/products/pubs_hypox. html>.