Miracle-dz/UniFAR-FTUs huggingface dataset:
Modeling and Molecular Dynamics of HPA-1a and -1b Polymorphisms: Effects on the Structure of the β3 Subunit of the αIIbβ3 Integrin

Background The HPA-1 alloimmune system carried by the platelet integrin αIIbβ3 is the primary cause of alloimmune thrombocytopenia in Caucasians and the HPA-1b allele might be a risk factor for thrombosis. HPA-1a and -1b alleles are defined by a leucine and a proline, respectively, at position 33 in the β3 subunit. Although the structure of αIIbβ3 is available, little is known about structural effects of the L33P substitution and its consequences on immune response and integrin functions. Methodology/Principal Findings A complete 3D model of the L33-β3 extracellular domain was built and a P33 model was obtained by in silico mutagenesis. We then performed molecular dynamics simulations. Analyses focused on the PSI, I-EGF-1, and I-EGF-2 domains and confirmed higher exposure of residue 33 in the L33 β3 form. These analyses also showed major structural flexibility of all three domains in both forms, but increased flexibility in the P33 β3 form. The L33P substitution does not alter the local structure (residues 33 to 35) of the PSI domain, but modifies the structural equilibrium of the three domains. Conclusions These results provide a better understanding of HPA-1 epitopes complexity and alloimmunization prevalence of HPA-1a. P33 gain of structure flexibility in the β3 knee may explain the increased adhesion capacity of HPA-1b platelets and the associated thrombotic risk. Our study provides important new insights into the relationship between HPA-1 variants and β3 structure that suggest possible effects on the alloimmune response and platelet function.
Josephson Arbitrary Waveform System with Optoelectronic Drive

Quantum-accurate arbitrary voltage waveforms have been generated using electrical pulse driven Josephson junction arrays (JJAs) by several groups [1, 2]. An alternative method is to use optoelectronic components to convert the electrical pulse drive into an optical signal which is subsequently converted by a photodiode into an electrical drive signal connected directly to the JJA. This optoelectronic pulse drive system has several advantages. Due to the electrical isolation between electrical pulse drive and JJA, it is possible to connect several arrays in series without the requirement for complex electrical compensation circuits. This allows larger output voltages to be realized. An optoelectronic drive also offers the ability to easily tune pulse height, via continuous optical attenuation, allowing the drive signal to be tuned to the middle of the JJA constant voltage step giving optimum operation margins. We here present an optoelectronic pulse drive which forms part of a system incorporating a JJA and delta sigma feedback loop [3] for quantum-accurate digitization of arbitrary voltage waveforms. Results showing the generation of quantum-accurate voltages synchronized to the feedback loop master clock are presented.
Variational Regularized 2-D Nonnegative Matrix Factorization

A novel approach for adaptive regularization of 2-D nonnegative matrix factorization is presented. The proposed matrix factorization is developed under the framework of maximum a posteriori probability and is adaptively fine-tuned using the variational approach. The method enables: (1) a generalized criterion for variable sparseness to be imposed onto the solution; and (2) prior information to be explicitly incorporated into the basis features. The method is computationally efficient and has been demonstrated on two applications, that is, extracting features from image and separating single channel source mixture. In addition, it is shown that the basis features of an information-bearing matrix can be extracted more efficiently using the proposed regularized priors. Experimental tests have been rigorously conducted to verify the efficacy of the proposed method.
Adding Value to the Health Care System: Identifying Value-Added Systems Roles for Medical Students

To catalyze learning in Health Systems Science and add value to health systems, education programs are seeking to incorporate students into systems roles, which are not well described. The authors sought to identify authentic roles for students within a range of clinical sites and explore site leaders’ perceptions of the value of students performing these roles. From 2013 to 2015, site visits and interviews with leadership from an array of clinical sites (n = 30) were conducted. Thematic analysis was used to identify tasks and benefits of integrating students into interprofessional care teams. Types of systems roles included direct patient benefit activities, including monitoring patient progress with care plans and facilitating access to resources, and clinic benefit activities, including facilitating coordination and improving clinical processes. Perceived benefits included improved value of the clinical mission and enhanced student education. These results elucidate a framework for student roles that enhance learning and add value to health systems.
Towards Using Public Conversations to Mine Product Features in Twitter

While public conversations in Twitter have gained increasing interest in the marketing sector, relatively very little data-mining research have been conducted in this area. In this paper, we empirically evaluate whether employing reply links in public conversations can enhance the product feature extraction from tweets. We introduce a conversation-based method that considers a conversation as a reply tree and employs anaphora resolution in a backtracking mechanism to effectively extract the product features involved in the messages. We also develop a conversation filtering process based on a set of filtering measures including content relevance and social metrics. We conducted our experiments using a manually annotated Twitter corpus involving smartphones and other electronics products. The experimental results show the effectiveness of our proposed method.
LncRNA HOTAIR acts as competing endogenous RNA to control the expression of Notch3 via sponging miR-613 in pancreatic cancer

Pancreatic cancer is one of the most deadly cancers with a poor prognosis. Though studies have implicated the roles of microRNAs in pancreatic cancer progression, little is known about the role of miR-613 in pancreatic cancer. In the present study, the expression of miR-613 was down-regulated in pancreatic cancer tissues and cancer cell lines. Down-regulation of miR-613 was positively correlated with tumor differentiation, advanced TNM stage, nodal metastasis and shorter overall survival in patients with pancreatic cancer. Overexpression of miR-613 suppressed cell proliferation, invasion and migration, and induced cell apoptosis and cell cycle arrest at G0/G1 phase in pancreatic cancer cells. Bioinformatics analysis, luciferase reporter assay and rescue experiments showed that notch3 was a direct target of miR-613. MiR-613 was inversely correlated with notch3 expression in pancreatic cancer tissues. The long non-coding RNA, HOX transcript antisense RNA (HOTAIR) was up-regulated in both pancreatic cancer tissues and cancer cell lines, and HOTAIR suppressed the expression of miR-613 via functioning as a competing endogenous RNA. In vivo studies showed that stable overexpression of miR-613 or knock-down of HOTAIR suppressed tumor growth and also reduced the expression of notch3. In conclusion, these results suggest that HOTAIR functions as a competing endogenous RNA to regulate notch3 expression via sponging miR-613 in pancreatic cancer.
Optimal Trade Execution with Instantaneous Price Impact and Stochastic Resilience

We study an optimal execution problem in illiquid markets with both instantaneous and persistent price impact and stochastic resilience when only absolutely continuous trading strategies are admissible. In our model the value function can be described by a three-dimensional system of backward stochastic differential equations (BSDE) with a singular terminal condition in one component. We prove existence and uniqueness of a solution to the BSDE system and characterize both the value function and the optimal strategy in terms of the unique solution to the BSDE system. Our existence proof is based on an asymptotic expansion of the BSDE system at the terminal time that allows us to express the system in terms of a equivalent system with finite terminal value but singular driver.
Performance of AODV and OLSR routing protocols in VANET under various traffic scenarios

VANET is a subset of mobile ad hoc network MANET and it was proposed in the last few years to increase the safety value on the road. There are many routing protocols are proposed as a data dissemination method which are classified based on how they route the packet from the source to destination. In this project, the proactive OLSR routing protocol and the reactive one AODV are evaluated under different traffic scenario using the network simulator NS-3. The basic scenario is based on the common geographical topology crossroad. The mobility density is differed to be high and low-density. The congestion period has critical characteristics which are achieved always around the junction and affect the overall performance significantly. So, it is considered in this project to investigate the behavior of the network while the vast vehicles become close and around the junction. All the evaluation metrics are done in term of throughput, packet delivery ratio (PDR), and end to end delay. The results show OLSR perform better than AODV regarding throughput, PDR, and latency by 17.4%, 7%, 5%, respectively for the low-density crossroad scenario overall the simulation time. In addition, 7.9%, 6.5%, 4% the OLSR perform better than AODV in the high-density scenario. Furthermore, the OLSR still better than the other routing protocol targeted in this project when the congestion occurs.
Inbreeding Avoidance Influences the Viability of Reintroduced Populations of African Wild Dogs (Lycaon pictus)

The conservation of many fragmented and small populations of endangered African wild dogs (Lycaon pictus) relies on understanding the natural processes affecting genetic diversity, demographics, and future viability. We used extensive behavioural, life-history, and genetic data from reintroduced African wild dogs in South Africa to (1) test for inbreeding avoidance via mate selection and (2) model the potential consequences of avoidance on population persistence. Results suggested that wild dogs avoided mating with kin. Inbreeding was rare in natal packs, after reproductive vacancies, and between sibling cohorts (observed on 0.8%, 12.5%, and 3.8% of occasions, respectively). Only one of the six (16.7%) breeding pairs confirmed as third-order (or closer) kin consisted of animals that were familiar with each other, while no other paired individuals had any prior association. Computer-simulated populations allowed to experience inbreeding had only a 1.6% probability of extinction within 100 years, whereas all populations avoiding incestuous matings became extinct due to the absence of unrelated mates. Populations that avoided mating with first-order relatives became extinct after 63 years compared with persistence of 37 and 19 years for those also prevented from second-order and third-order matings, respectively. Although stronger inbreeding avoidance maintains significantly more genetic variation, our results demonstrate the potentially severe demographic impacts of reduced numbers of suitable mates on the future viability of small, isolated wild dog populations. The rapid rate of population decline suggests that extinction may occur before inbreeding depression is observed.
Maximizing achievable rate for improved AF-OFDM cooperative transmission

This manuscript develops an improved AF-OFDM (Amplify-and-Forward, Orthogonal Frequency Division Multiplexing) scheme where selective relaying policy is fully utilized to promote the spectrum efficiency of cooperative transmission, and presents an achievable rate maximizing resource allocation strategy subject to a sum-power constraint. The high computational complexity for optimization necessitates our investigation of suboptimal approaches. The proposed centralized algorithms can be implemented in a step-by-step manner. Specifically, the binary selective relaying policies are first decided for each subcarrier according to instantaneous or statistical channel state information. Then, relay selection might be conducted by those subcarriers who would like to choose a relay to assist their data transmission from network achievable rate maximization perspective, and finally power loading can be mathematically solved by employing standard Lagrange techniques. Numerical results are shown to illustrate the benefits of the improved AF-OFDM cooperative protocol with optimized resource allocation.
On a class of pseudo-logarithmic amplifiers suitable for use with digitally switched resistors: Research Articles

This paper describes three circuits that implement pseudo-logarithmic functions, which are simple and easy to implement. The circuits can be realized using operational amplifiers or current feedback amplifiers. Tuning can be achieved using switched resistors, or active resistors, or tunable transconductors, but are best suited for use with digitally switched resistors. Frequency response and stability considerations for two of the circuits are thoroughly discussed and PSPICE results confirming the theoretical results are presented alongside measured results. Copyright © 2007 John Wiley & Sons, Ltd.
Formulation and in vitro evaluation of curcumin-lactoferrin conjugated nanostructures for cancerous cells

Abstract Curcumin, a natural polyphenol, exhibits anti-oxidant, anti-inflammatory, anti-neoplastic and chemopreventive properties. In fact, targeting of this natural anticancer agent has received a great deal of attention during the recent years. In this study, we proposed that curcumin conjugation with lactoferrin molecules may lead to a potential drug delivery system targeted toward cancerous cells through both active and passive targeting. In this regard, curcumin conjugated lactoferrin was developed via a carbodiimide-based coupling reaction and the resulting conjugates were appraised for their molecular properties as a potential targeted drug delivery system. The mean diameter of the designed nanostructure was about 165 ± 26 nm with a PDI of 0.308 ± 0.045. The conjugated nanostructures showed a considerably improved cytotoxicity on HCT116 cells as illustrated by MTT assay along with a higher level of cellular uptake. Cellular uptake and targeting capability of conjugated samples were further investigated by confocal microscopy and the conjugated curcumin nanostructures showed an enhanced efficacy compared to curcumin. Furthermore, flow cytometry analysis proved that early apoptosis occurred in HCT116 cell line, after 24 h incubation with conjugated curcumin. Graphical Abstract
EUS-guided pancreatic duct drainage: Approach to a challenging procedure

Endoscopic removal of pancreatic stones is challenging because pancreatic stones tend to be spiculated and hard and are impacted behind strictures in most cases. [1] Success rate of stone retrieval by standard endoscopic retrograde cholangiopancreatography (ERCP) is only about 50%. Adding shockwave corporeal lithotripsy or ESWL increases the success rate to 60%–70%, but this is not always available. Unlike in the bile duct where percutaneous salvage is readily available, no alternative sort of surgery exists for pancreatic drainage. Therefore, endoscopic ultrasound-guided pancreatic duct drainage (EUS-PDD) has been gaining popularity because of reasonably high technical success rate and a favorable safety profile in expert hands.
Too little sleep and an unhealthy diet could increase the risk of sustaining a new injury in adolescent elite athletes

Little is known about health variables and if these variables could increase the risk of injuries among adolescent elite athletes. The primary aim was to present overall data on self‐perceived stress, nutrition intake, self‐esteem, and sleep, as well as gender and age differences, on two occasions among adolescent elite athletes. A secondary aim was to study these health variables as potential risk factors on injury incidence. A questionnaire was e‐mailed to 340 adolescent elite athletes on two occasions during a single school year: autumn semester and spring semester. The results show that during autumn semester, the recommended intake of fruits, vegetables, and fish was not met for 20%, 39%, and 43% of the adolescent elite athletes, respectively. The recommended amount of sleep during weekdays was not obtained by 19%. Multiple logistic regression showed that athletes sleeping more than 8 h of sleep during weekdays reduced the odds of injury with 61% (OR, 0.39; 95% CI, 0.16–0.99) and athletes reaching the recommended nutrition intake reduced the odds with 64% (OR, 0.36; 95% CI, 0.14–0.91). Our findings suggest that nutrition intake and sleep volume are of importance in understanding injury incidence.
Community Detection in Social Network with Node Attributes Based on Formal Concept Analysis

As far as social networks are concerned, new applications appear to analyze them. Community detection is one of the most important issues. It allows to understand the structure of complex networks and to extract useful information from the detected communities. Users have usually a social interaction with their friends because of their common interests or their similar profiles. In this paper, attributed graphs are considered, where entities of the network are described using attributes with several modalities. Then, we propose an hybrid approach based on Formal Concept Analysis (FCA) for community detection in social network with node attributes. This method, called ACDC (Attributed Community Detection based on Concepts), combines the structure of the network and the attributes of the nodes. ACDC, semantically and statically, partitions an assigned graph into k densely connected communities, using maximal cliques, with homogeneous attribute values derived from FCA. Experimental results demonstrate the effectiveness of ACDC through comparison with the state-of-the-art graph clustering and methods. Our method provides also more meaningful communities than conventional methods that consider only relationship information.
Shotgun sequencing of the mitochondrial genome of the Aldabra giant tortoise (Aldabrachelys gigantea)

Abstract The complete mitochondrial genome of the Aldabra giant tortoise [Aldabrachelys gigantea (Schweigger, 1812): Reptilia, Testudines, Testudinidae] was sequenced using a shotgun approach on an Illumina HiSeq 2500 platform (Illumina Inc., San Diego, CA). This genome was 16 467 bp long and presents the typical organization found in vertebrates. The mean coverage of sequencing was 116×. A phylogenetic analysis of the Testudinidae confirms the placement of Aldabrachelys in an Indian Ocean group (including Madagascar). This mitogenome constitutes a reference for ancient DNA analyses of the extinct Madagascan lineages of Aldabrachelys.
Race-Related Disparities in 5-Year Cognitive Level and Change in Untrained Active Participants

Objective: The current study examined a 5-year cognitive change in untrained African American and White participants from the Advanced Cognitive Training in Independent and Vital Elderly (ACTIVE) study. Method: Five-year trajectories of memory, reasoning, visual processing speed/useful field of view, digit-symbol substitution, and vocabulary were investigated. Education, health, gender, age, and retest/practice effects were controlled for, and a missing data pattern mixture approach was used to adjust for dropout effects. Results: After considering age, education, health, and gender, being African American uniquely explained 2% to 7% of the variance in cognitive performance. There were virtually no significant race differences in the rates of change. Discussion: Race-related results in the current study are consistent with previous research suggesting that social advantage factors such as education have a stronger influence on the level of performance than the rate of change. The small remaining effects of being African American on performance levels likely reflect uncontrolled variation in factors like literacy and financial advantage.
Ungulate herbivory alters leaf functional traits and recruitment of regenerating aspen

Herbivory by ungulates can affect forest regeneration success, but its long-term impacts on tree function and recruitment are less studied. We evaluated strategies of resistance, tolerance and vertical escape against ungulate herbivory by evaluating leaf traits (photosynthesis, morphology and chemistry) and growth rates of aspen in the presence and absence of ungulate herbivores 1, 2, 3 and 26 years after fires initiated aspen suckering. Over the initial 3-year period, ~60% of aspen stems in unfenced plots showed evidence of being browsed by ungulates. After 3 years, aspen in unfenced plots had smaller leaves, were 50% shorter, and had 33% lower nonstructural carbohydrate concentrations and 33% greater concentrations of condensed tannins, when compared with fenced aspen. Aspen exposed to ungulate herbivory over a 26-year period maintained smaller leaves, had lower annual radial growth rates and were still below the critical height threshold of 2 m required to escape ungulate herbivory for successful recruitment. In contrast, the average height of aspen protected from ungulates was approaching 6 m. Over the 26-year period leaves in unfenced plots had 41% lower nonstructural carbohydrate concentrations and greater expression of defense compounds-condensed tannins (63%) and phenolic glycosides (102%)-than leaves in fenced plots. Photosynthetic rates were slightly higher in aspen that experienced ungulate browsing, suggesting that changes in leaf anatomy and chemistry due to ungulate herbivory did not interfere with photosynthesis. Our data suggest that ungulate browsing increases investment in chemical defense, lowers nonstructural carbohydrate concentrations and reduces leaf area, which decreases the recruitment potential of regenerating aspen.
Analysis and verification of a miniature dolphin-like underwater glider

Purpose This paper aims to propose a novel design concept for a biomimetic dolphin-like underwater glider, which can offer the advantages of both robotic dolphins and underwater gliders to achieve high-maneuverability, high-speed and long-distance motions. Design/methodology/approach To testify the gliding capability of dolphin-like robot without traditional internal movable masses, the authors first developed a skilled and simple dolphin-like prototype with only gliding capability. The hydrodynamic coefficients, including lift, drag and pitching moment, are obtained through computational fluid dynamics method, and the hydrodynamic analysis in the steady gliding motion is also executed. Findings Experimental results have shown that the dolphin-like glider could successfully glide depending on the pitching torques only from buoyancy-driven system and controllable fins without traditional internal moveable masses. Originality/value A hybrid underwater glider scheme that combines robotic dolphin and glider is firstly proposed, shedding light on the creation of innovation gliders with maneuverability and durability.