Miracle-dz/UniFAR-FTUs huggingface dataset:
Stably folded de novo proteins from a designed combinatorial library

Binary patterning of polar and nonpolar amino acids has been used as the key design feature for constructing large combinatorial libraries of de novo proteins. Each position in a binary patterned sequence is designed explicitly to be either polar or nonpolar; however, the precise identities of these amino acids are varied extensively. The combinatorial underpinnings of the “binary code” strategy preclude explicit design of particular side chains at specified positions. Therefore, packing interactions cannot be specified a priori. To assess whether the binary code strategy can nonetheless produce well‐folded de novo proteins, we constructed a second‐generation library based upon a new structural scaffold designed to fold into 102‐residue four‐helix bundles. Characterization of five proteins chosen arbitrarily from this new library revealed that (1) all are α‐helical and quite stable; (2) four of the five contain an abundance of tertiary interactions indicative of well‐ordered structures; and (3) one protein forms a well‐folded structure with native‐like features. The proteins from this new 102‐residue library are substantially more stable and dramatically more native‐like than those from an earlier binary patterned library of 74‐residue sequences. These findings demonstrate that chain length is a crucial determinant of structural order in libraries of de novo four‐helix bundles. Moreover, these results show that the binary code strategy—if applied to an appropriately designed structural scaffold—can generate large collections of stably folded and/or native‐like proteins.
What Determines an Agreeable and Adoptable Idea? A Study of User Ideas on MyStarbucksIdea.com

Rising tide of crowdsourcing as a new method of innovation is surging across diverse industries. Considering that the goal of crowdsourcing is generating ideas which can be seeds of innovation, understanding the characteristics of user-agreeable and organization-adoptable ideas can enhance the effectiveness of idea generation. In our approach, we extract idea contents characteristics such as subjectivity, negativity, publicness, and depth of idea as well as user characteristics such as user experience and reputation to examine what are the factors that affect user-agreement and organizational adoption. An analysis of 71,134 ideas from MyStarbucksIdea.com shows that there are significant differences between user-agreeable and organization-adoptable ideas. Besides, moderating effect of user reputation is found. Managerial implications are discussed.
Wearable approach for continuous ECG - and activity patient-monitoring

The paper describes an approach to monitor a person's ECG and activity continuously with functional clothing. A belt with integrated electronics has been developed and has proven long-term robustness of all electrical components. A low-power module measures the ECG signal as well as the acceleration (2-axis) and stores data continuously up to two days. A user test has been performed to evaluate the belt according to system performance at different daily-life activities like sleeping, walking and so on. System parameters are ECG-signal quality, system up-time, and ECG-signal coverage during a day.
Perspectives on Social Care Practice in Romania: Supporting the Development of Professional Learning and Practice

This paper examines the authors' experiences of developing and delivering training for workers in social care services in Romania, through a European Union PHARE1 funded project. The authors use their experiences to draw on the past and current practices of those social workers who were participants in the training and to explore their understanding of the emerging issues and themes for social work in Romania. There is also an exploration of the potential opportunities for the further development of professional social work learning and practice within Romania. The case is made that learning and development of social workers could be supported through the encouragement of participatory networks and `communities of practice'
Human progenitor cells with high aldehyde dehydrogenase activity efficiently engraft into damaged liver in a novel model

Human cord blood stem cells (hCBSCs) have been reported to generate hepatocyte‐like cells and thus hold promise for repairing damaged liver. However, the frequency of hCBSC‐derived hepatocytes varies tremendously between different studies, and it is still controversial as to whether hCBSC‐derived cells can transdifferentiate into hepatocytes or simply fuse to recipient hepatocytes. We used the β‐glucuronidase–deficient nonobese diabetic/severe combined immunodeficient/mucopolysaccharidosis type VII (NOD/SCID/MPSVII) mouse model for better identification of engrafted cells. We transplanted lineage‐depleted human umbilical cord blood–derived cells with high aldehyde dehydrogenase activity (ALDHhiLin−) into irradiated NOD/SCID/MPSVII mice followed by carbon tetrachloride administration to induced liver damage. ALDHhiLin− cells were efficiently engrafted in the recipient mouse livers and improved recovery of the mice from toxic insult. The percentage of human cells in these livers ranged between 3% and 14.2% using quantitative real‐time polymerase chain reaction. Furthermore, human‐originated cells expressing liver‐specific α1‐antitrypsin messenger RNA, albumin and hepatocyte nuclear factor 1 protein were detected in the recipient livers. Interestingly, human versus murine centromeric fluorescent in situ hybridization analysis on the liver sections demonstrated that most human cells were not fused to mouse cells. However, the majority of the human originated albumin‐expressing cells also carried mouse genetic material, hence were the product of cell fusion. Conclusion: hCBSCs or their progeny may home to the injured liver and release trophic factors that hasten tissue repair, whereas fusion of these cells with hepatocytes may occur rarely and contribute to a lesser extent to liver repair. (HEPATOLOGY 2009.)
Study of Active-Front-End design for the Acceleration Grid Power Supply of ITER Neutral Beam Injector

In order to explore strategies to reduce the high reactive power demand and to improve the current harmonic content injected into the main grid of the ITER experimental reactor, in this paper a different design approach to the ac/dc conversion system of the Acceleration Grid Power Supply (AGPS) of ITER Neutral Beam Injector based on Active Front End (AFE) solution is investigated. Particular attention has been given to the chosen modulation strategy, different from that normally used in AFE converter for high power application. Finally, the performance of AGPS realized with AFE and reference thyristor rectifiers are compared and discussed.
Mechanisms of action in integrated cognitive-behavioral treatment versus twelve-step facilitation for substance-dependent adults with comorbid major depression.

OBJECTIVE In a population of veterans with co-occurring substance use disorders and concomitant major depressive disorder, the current study compared mechanisms of change and therapeutic effects relevant to both disorders between integrated, dual disorder-specific cognitive behavioral therapy (ICBT) and twelve-step facilitation (TSF). METHOD Veterans (N = 148) were given standard pharmacotherapy for depression and were randomly assigned to receive 24 weeks of either TSF or ICBT. Process measures were selected to quantify (1) changes in self-efficacy in ICBT, (2) changes in ability to terminate negative affect in ICBT, (3) twelve-step affiliation (TSA) in TSF, and (4) changes in social support in both conditions. Measures of depression and substance use were administered to all participants before treatment, during treatment, and at the end of treatment. RESULTS Self-efficacy increased among both TSF and ICBT participants during treatment, whereas self-reported ability to regulate negative affect did not change. Consistent with predictions, TSF participants increased community TSA during treatment, whereas those receiving ICBT reduced TSA. Changes in self-efficacy and TSA were associated with improvement in substance use outcomes at the end of treatment. Hypothesized changes in social support were not supported. CONCLUSIONS Both ICBT and TSF produce improvements in self-efficacy, and these changes are related to substance use outcomes for depressed substance abusers. In TSF, intervention-specific changes in TSA occur during the course of treatment and are related to substance use outcomes.
Secure transmission over the wiretap channel using polar codes and artificial noise

In this study, the authors propose a secure transmission scheme using polar codes and artificial noise (AN) for the wiretap system without assuming the channel quality advantage of main channel over wiretap channel. They first derive lower and upper bounds on the symmetric capacity of the polarised bit-channels , which depend on the signal-to-noise ratio of each use of physical channel. According to the bounds, they prove existence of the bit-channels that are beneficial to the signal reception of the main channels but hostile to the wiretap channel, and a method based on injecting the AN at the transmitter is introduced to achieve those bit-channels. Through theoretical analysis, the security of the proposed AN method is proven. Thereafter, they elaborate two AN power allocation schemes denoted by AN-PA-I and AN-PA-II for each use of physical channel. The former proves the existence of the minimum AN power to achieve the secrecy rate that is equal to the capacity of the main channel, referred to as the maximum secrecy rate, and the latter introduces how to obtain it with an optimisation method. Numerical results show that both the two schemes can achieve the maximum secrecy rate.
Remote Direct Memory Access (RDMA) over IP Problem Statement

Overhead due to the movement of user data in the end-system network I/O processing path at high speeds is significant, and has limited the use of Internet protocols in interconnection networks, and the Internet itself -- especially where high bandwidth, low latency, and/or low overhead are required by the hosted application. This document examines this overhead, and addresses an architectural, IP- based "copy avoidance" solution for its elimination, by enabling Remote Direct Memory Access (RDMA). This memo provides information for the Internet community.
The Successes and Failures of Policing Animal Rights Extremism in the UK 2004–2010

This paper considers animal rights activism and associated extremism in the period 2004–2010 in the UK, and proposes that this post-2004 period witnessed a new era in animal rights extremism. It is argued that following the successful targeting of major pharmaceutical companies leading up to 2004 by animal rights campaigners deploying a variety of effective tactics based primarily on intimidation and harassment — the government, the police and the targeted industries robustly responded in a coordinated strategic approach to reduce animal rights crimes. However, the success of this initiative has had far-reaching implications for human rights and the ability of people to protest in a democratic society. The operational success has also led to more sophisticated tactics being used by extremists and a displacement abroad to ‘softer’ targets. This, perversely, orchestrated even more restrictive laws being passed to curb extremist incidents that were only carried out by a small minority within the animal rights movement. Animal rights activism and linked extremism have now been effectively brought under control, but, collectively, ‘protest law’ has been altered. In some cases, the law has been misused and applied disproportionately by the State, thereby fundamentally affecting freedom of assembly and free expression for all UK citizens. Ultimately, by failing to consider an individual's right to protest, the overall cost to the police service has been increased by civil litigation against it, failed prosecutions in the courts and the possible exposure of individual officers to misconduct procedures. Most damaging of all is the damage to its reputation as a service dedicated to impartially serving the interests of the community of which it is part.
Acoustic Emissions in Fracturing Sea Ice Plate Simulated by Particle System

In-plane dynamic fracture jumps and acoustic emissions in sea ice floes of different sizes are simulated by the particle system. Fracture patterns and time sequences similar to those observed in experiments are achieved. For the given spatial location of hydrophone, the acoustic signals from crack jumps in ice are calculated in the frequency domain by a modified Farmer and Xie's acoustic model for ice plate floating in shallow sea. The acoustic pressure-time histories are synthesized by the Fourier inverse transform. The calculated acoustic signals resemble the recorded signals. Their overall character is found to depend on the plate size. This is a size effect that is manifested in the calculated root-mean-square history of the acoustic pressure at hydrophone. Differences among the acoustic records for different fracture lengths are found. They offer the possibility of making inferences on the fracture characteristics of sea ice from the acoustic records.
An Efficient Spectral Method for Document Cluster Ensemble

Cluster ensemble techniques have been recently shown to be effective in improving the accuracy and stability of single clustering algorithms. A critical problem in cluster ensemble is how to combine multiple clusterers to yield a final superior clustering result. In this paper, we present an efficient spectral graph theory-based ensemble clustering method feasible for large scale applications such as document clustering. Since the EigenValue Decomposition (EVD) of Laplacian is formidable for large document sets, we first transform it to a Singular Value Decomposition (SVD) problem, and then an equivalent EVD is performed. Experiments show that our spectral algorithm yields better clustering results than other cluster ensemble techniques without high computational cost.
Induction of antigen-specific Th1-biased immune responses by plasmid DNA in schistosoma-infected mice with a preexistent dominant Th2 immune profile.

A requisite for vaccines to confer protection against intracellular infections such as Human Immunodeficiency Virus or Mycobacterium tuberculosis is their capacity to induce Th1 immune responses. However, they may fail to do so in Africa and South East Asia, where most individuals have a dominant preexistent Th2 immune profile, due to persistent helminthic parasitic infections, which may undermine any Th1 response. It is well established that DNA vaccines induce strong Th1 biased immune responses against an encoded antigen, depending on the route and mode of immunization. Here, we demonstrate that intradermal immunization with plasmid DNA encoding beta-gal (pCMV-LacZ) of Schistosoma-infected mice, with preexistent dominant Th2 immune background, induce a strong Th1 anti-beta-gal response, as opposed to immunized with beta-gal only. Importantly, the established protective Th2 immune response to schistosomes was not disrupted. These findings strongly support the possibility of using plasmid DNA as a Th1 inducing adjuvant when immunizing populations with a strong preexistent Th2 immune profile.
Astroglial IFITM3 mediates neuronal impairments following neonatal immune challenge in mice

Interferon‐induced transmembrane protein 3 (IFITM3) ıplays a crucial role in the antiviral responses of Type I interferons (IFNs). The role of IFITM3 in the central nervous system (CNS) is, however, largely unknown, despite the fact that its expression is increased in the brains of patients with neurologic and neuropsychiatric diseases. Here, we show the role of IFITM3 in long‐lasting neuronal impairments in mice following polyriboinosinic‐polyribocytidylic acid (polyI:C, a synthetic double‐stranded RNA)‐induced immune challenge during the early stages of development. We found that the induction of IFITM3 expression in the brain of mice treated with polyI:C was observed only in astrocytes. Cultured astrocytes were activated by polyI:C treatment, leading to an increase in the mRNA levels of inflammatory cytokines as well as Ifitm3. When cultured neurons were treated with the conditioned medium of polyI:C‐treated astrocytes (polyI:C‐ACM), neurite development was impaired. These polyI:C‐ACM‐induced neurodevelopmental abnormalities were alleviated by ifitm3−/− astrocyte‐conditioned medium. Furthermore, decreases of MAP2 expression, spine density, and dendrite complexity in the frontal cortex as well as memory impairment were evident in polyI:C‐treated wild‐type mice, but such neuronal impairments were not observed in ifitm3−/− mice. We also found that IFITM3 proteins were localized to the early endosomes of astrocytes following polyI:C treatment and reduced endocytic activity. These findings suggest that the induction of IFITM3 expression in astrocytes by the activation of the innate immune system during the early stages of development has non‐cell autonomous effects that affect subsequent neurodevelopment, leading to neuropathological impairments and brain dysfunction, by impairing endocytosis in astrocytes. GLIA 2013
Synthetic aperture radar imaging using nonlinear frequency modulation signal

In this paper, a new nonlinear frequency modulation (NLFM) waveform is developed that can be used as a transmitted chirp in synthetic aperture radar (SAR) imaging to improve the imaging quality compared to a linear frequency modulation (LFM) chirp signal. The new NLFM is constructed based on piecewise linear functions, which are optimized using multi-objective optimization. Different signal processing algorithms are investigated in order to use NLFM as the transmitted chirp in a SAR system. In addition, a modified motion compensation (MC) algorithm using navigation data is proposed for the range-Doppler algorithm. Strip-map SAR geometry is considered to generate a SAR raw signal, in order to validate the new offered chirp signal and the proposed MC algorithm.
Stacked multicell converter (SMC): reconstruction of flying capacitor voltages

We present in this paper a new method for the observation of the flying capacitor voltages dedicated to stacked multicell converters (SMC). Unlike the imbricated-cell converter, the new SMC topology allows increasing the input voltage level while decreasing the energy stored in the converter. This consists of a hybrid association of commutation cells, which enables to share the voltage constraint on several switches. During normal operation, the flying capacitor voltages have to be kept constant by the control strategy. Due to high voltage/high power applications, it is difficult and expensive to measure the flying capacitor voltages. Therefore, a new method has been developed to estimate those voltages. After an introduction and a brief reminder on the SMC topology, we will present a new strategy to estimate the capacitor voltages based on the determination of an image of those ones regarding the control signals and the chopped voltage. The influence of the measurement noise on our new technique has also been studied carefully and appropriate strategies have been developed. The last part will be devoted to conclusions and perspectives
Newsvendor optimization with limited distribution information

Lack of complete distribution calls for stochastically robust models that, after exploiting available limited or partial information, offer risk-shielded solutions, or in other words, solutions that are insensitive to all possible distributions of random variables. We focus on the well-known newsvendor problem in this study, where the distribution of the random demand is only specified by its mean and one of the following: its standard deviation or its support. We propose a stochastically robust model for the newsvendor problem. More specifically, our model tries to minimize the regret that is defined as the ratio of the expected cost based on limited information to that based on complete information, called Relative Expected Value of Distribution (REVD). We show how to derive an optimal solution to the REVD model. Numerical examples are provided to compare our model with other similar approaches. The goal is to establish a confidence ratio that the decision from our model is not worse, relatively, too much than the decision based on the true distribution which would be never known exactly in real-world applications.
Multilevel Deficiency of White Matter Connectivity Networks in Alzheimer's Disease: A Diffusion MRI Study with DTI and HARDI Models

Alzheimer's disease (AD) is the most common form of dementia in elderly people. It is an irreversible and progressive brain disease. In this paper, we utilized diffusion-weighted imaging (DWI) to detect abnormal topological organization of white matter (WM) structural networks. We compared the differences between WM connectivity characteristics at global, regional, and local levels in 26 patients with probable AD and 16 normal control (NC) elderly subjects, using connectivity networks constructed with the diffusion tensor imaging (DTI) model and the high angular resolution diffusion imaging (HARDI) model, respectively. At the global level, we found that the WM structural networks of both AD and NC groups had a small-world topology; however, the AD group showed a significant decrease in both global and local efficiency, but an increase in clustering coefficient and the average shortest path length. We further found that the AD patients had significantly decreased nodal efficiency at the regional level, as well as weaker connections in multiple local cortical and subcortical regions, such as precuneus, temporal lobe, hippocampus, and thalamus. The HARDI model was found to be more advantageous than the DTI model, as it was more sensitive to the deficiencies in AD at all of the three levels.
Towards Flash Disk Use in Databases - Keeping Performance While Saving Energy?

Green computing or energy saving when processing information is primarily considered a task of processor development. We, however, advocate that a holistic approach is necessary to reduce power consumption to a minimum. We explore the potential of NAND flash memory in comparison to magnetic disks for DBMS-based architectures. For this reason, we attempt to identify the IO performance of both storage types at the device level and file system interface, before we approach the most important question how DBMS applications can take advantage of the flash performance characteristics. Furthermore, based on an analysis of storage structures and related benchmark runs in our XTC system, we discuss how IO-intensive DBMS algorithms have to be adjusted to take most out of the flash technology which is entering the server area with dramatic pace. The ultimate goal is to substantially improve energy efficiency while comparable performance as in disk-based DB servers is maintained.