Miracle-dz/UniFAR-FTUs huggingface dataset:
A predictive method for the evaluation of peptide binding in pocket 1 of HLA‐DRB1 via global minimization of energy interactions

Human leukocyte antigens (HLA) or histocompatibility molecules are glycoproteins that play a pivotal role in the development of an effective immune response. An important function of the HLA molecules is the ability to bind and present antigen peptides to T lymphocytes. Presently there is no comprehensive way of predicting and energetically evaluating peptide binding on HLA molecules. To quantitatively determine the binding specificity of a class II HLA molecule interacting with peptides, a novel decomposition approach based on deterministic global optimization is proposed that takes advantage of the topography of HLA binding grove, and examined the interactions of the bound peptide with the five different pockets. In particular, the main focus of this paper is the study of pocket 1 of HLA DR1 (DRB1*0101 allele). The determination of the minimum energy conformation is based on the ECEPP/3 potential energy model that describes the energetics of the atomic interactions. The minimization of the total potential energy is formulated on the set of peptide dihedral angles, Euler angles, and translation variables to describe the relative position. The deterministic global optimization algorithm, αBB, which has been shown to be ϵ‐convergent to the global minimum potential energy through the solution of a series of nonlinear convex optimization problems, is utilized. The PACK conformational energy model that utilizes the ECEPP/3 model but also allows the consideration of protein chain interactions is interfaced with αBB. MSEED, a program used to calculate the solvation contribution via the area accessible to the solvent, is also interfaced with αBB. Results are presented for the entire array of naturally occurring amino acids binding to pocket 1 of the HLA DR1 molecule and very good agreement with experimental binding assays is obtained. Proteins 29:87–102, 1997. © 1997 Wiley‐Liss, Inc.
Paving the Way for Energy Efficient Cloud Data Centers: A Type-Aware Virtual Machine Placement Strategy

The rapid revolution of cloud computing model is accompanied by huge amounts of energy consumed by the cloud data centers. So, enhancing the energy efficiency of those data centers has become a major challenge. This paper tackles the problem of enhancing the energy consumption of cloud data centers by proposing a novel virtual machine placement strategy. The proposed strategy suits both static and dynamic placement process. It aims to better utilize the involved physical machines which host the virtual machines. As different types of jobs do not intensively use the compute and/or non-compute resources in the hosted physical machine, virtual machines allocated to the jobs of different types are placed on the same physical machine where possible. The paper presents a mathematical formulation of the virtual machine placement process based on the Multiple Choice Knapsack Problem which is a generalization of the classical Knapsack Problem. The performance evaluation of the proposed strategy shows that it can enhance the energy efficiency of the cloud data centers by trying to minimize the number of the involved physical machines which host the virtual machines, and by optimally utilizing the involved physical machines.
Naturally Occurring Nrf2 Activators in the Management of Diabetes

Nuclear factor erythroid-2 (NFE-2)-related factor-2 (Nrf2), a key leucine zipper transcription factor that regulate the expression of antioxidant enzymes, is an important target for mitigating the complications of diabetes. Several lines of evidences have concluded that targeted activation of Nrf2 using phytochemicals helps to protect insulin secreting pancreatic β-cells thereby reduce hyperglycemia induced changes such as retinopathy, neuropathy, nephropathy, cardiomyopathy, and many other complications. Mechanistically, Nrf2 activators promote the release of Nrf2 from Keap1 Nrf2 complex by disrupting the protein protein interactions or by promoting the degradation of Keap1 in cells. Once released, the Nrf2 translocates in to nucleus thereby trigger the transcription of genes such as NQO1, GST, HO1, HIF1 α, and many more, which are involved in controlling oxidative stress. Therefore, identification of naturally occurring Nrf2 activators and the use of diets rich in these activators is a potential strategy to control diabetes. However, further studies are warranted to test the safety and efficacy of Nrf2 activators for treating diabetes in clinical trials. In this mini-review, we have summarized the recent findings of cell-based and preclinical studies evaluating the role of Nrf2 in preventing and treating diabetes. In addition, the details of preclinical studies that have tested the Nrf2 activators are tabulated. For additional and more detailed information the readers can refer the publications listed in the references section.
Automated facial coding: validation of basic emotions and FACS AUs in FaceReader

In this study, we validated automated facial coding (AFC) software—FaceReader (Noldus, 2014)—on 2 publicly available and objective datasets of human expressions of basic emotions. We present the matching scores (accuracy) for recognition of facial expressions and the Facial Action Coding System (FACS) index of agreement. In 2005, matching scores of 89% were reported for FaceReader. However, previous research used a version of FaceReader that implemented older algorithms (version 1.0) and did not contain FACS classifiers. In this study, we tested the newest version (6.0). FaceReader recognized 88% of the target emotional labels in the Warsaw Set of Emotional Facial Expression Pictures (WSEFEP) and Amsterdam Dynamic Facial Expression Set (ADFES). The software reached a FACS index of agreement of 0.67 on average in both datasets. The results of this validation test are meaningful only in relation to human performance rates for both basic emotion recognition and FACS coding. The human emotions recognition for the 2 datasets was 85%, therefore FaceReader is as good at recognizing emotions as humans. To receive FACS certification, a human coder must reach an agreement of 0.70 with the master coding of the final test. Even though FaceReader did not attain this score, action units (AUs) 1, 2, 4, 5, 6, 9, 12, 15, and 25 might be used with high accuracy. We believe that FaceReader has proven to be a reliable indicator of basic emotions in the past decade and has a potential to become similarly robust with FACS.
Screening, Assessment, Treatment, and Outcome Evaluation of Behavioral Difficulties in an RTI Model

Outcomes for students classified as emotionally disturbed (ED) are among the poorest for any disability group and include disturbingly low graduation rates, poor academic achievement, high rates of school suspensions and school dropouts, and chronic interpersonal problems. Additionally, these students are often underserved within the school setting with an overall prevalence rate of less than one percent. This underservice may be partially due to the definition of ED provided in the Individuals with Disabilities Education Improvement Act (IDEA, 2004), which is vague, contradictory, and redundant. Additionally, IDEA does not provide guidelines for how to assess for ED, thus, assessment procedures and prevalence rates widely differ by state. We propose the use of a Response to Intervention (RTI) model for the assessment and treatment of students with ED. Within an RTI model, students are provided evidence-based interventions implemented with integrity, and their response to these interventions is continuously monitored. This article defines RTI and describes methods of screening, assessment, treatment, and outcome evaluation for ED within the model.
Graph SLAM with signed distance function maps on a humanoid robot

For such common tasks as motion planning or object recognition robots need to perceive their environment and create a dense 3D map of it. A recent breakthrough in this area was the KinectFusion algorithm [16], which relies on step by step matching a depth image to the map via ICP to recover the sensor pose and updating the map based on that pose. In so far it ignores techniques developed in the graph-SLAM area such as fusion with odometry, modeling of uncertainty and distributing an observed inconsistency over the map. This paper presents a method to integrate a dense geometric truncated signed distance function (TSDF) representation as KinectFusion uses with a sparse parametric representation as common in graph SLAM. The key idea is to have local TSDF sub-maps attached to reference nodes in the SLAM graph and derive graph-SLAM links via ICP by matching a map to a depth image. By moving these reference nodes according to the graph-SLAM estimate, the overall map can be deformed without touching individual sub-maps so that re-building of sub-maps is only needed in case of significant deformation within a sub-map. Also, further information can be added to the graph as common in graph SLAM. Examples are odometry or the fact that the ground is roughly but not exactly planar. Additionally, the paper proposes a modification of the KinectFusion algorithm to improve handling of long range data by taking the range dependent uncertainty into account.
The Significance of Transpersonal Experiences, Emotional Conflict, and Cognitive Abilities in Creativity

Nineteen visual artists and eighteen actors were compared to twenty-one imaginative controls, matched for high levels of imaginative absorption, all subjects female. Creatives had mystical experiences significantly more frequently than controls. In particular, the visual artists reported having had significantly more current, positive altered states of consciousness (lucid and archetypal-mythological dreaming, out of body experiences, and waking mystical experiences). These findings, taken with the fact that the creatives did not show a significantly greater tendency toward psychopathology as indexed by the multiple measures of trauma and emotional conflict, suggest that contrary to the stereotype, creatives may not be driven by conflict so much as by intense and constructive states of consciousness. Most previous studies of productive creatives have used lower absorption controls, making it more difficult to locate specific factors that make imaginative subjects into productive artists and actors.
Efficient Software-Based Mobile Cloud Computing Framework

This paper proposes an efficient software based data possession mobile cloud computing framework. The proposed design utilizes the characteristics of two frameworks. The first one is the provable data possession design built for resource-constrained mobile devices and it uses the advantage of trusted computing technology, and the second framework is a lightweight resilient storage outsourcing design for mobile cloud computing systems. Our software based framework utilizes the strength aspects in both mentioned frameworks to gain better performance and security. The evaluation and comparison results showed that our design has better flexibility and efficiency than other related frameworks.
Relativistic band structure of Si, Ge, and GeSi: Inversion-asymmetry effects.

We present relativistic (including spin) linear muffin-tin orbitals (LMTO) calculations of the band structures of Si, Ge, and zinc-blende-like GeSi. The errors in excitation energies introduced by the use of the local-density approximation to the exchange-correlation potential are corrected with ``ad hoc'' potentials placed at the atomic sites. Effective masses, matrix elements of p, and Luttinger parameters are evaluated. Special emphasis is placed on the effects of inversion asymmetry in GeSi, such as ionicity and spin splittings. The former is very small, probably with Ge acting as the cation. The latter are appreciable and can be related to the asymmetry in the spin-orbit splittings of both constituent atoms. A detailed study of these spin splittings is made, also with the help of k\ensuremath{\cdot}p perturbation theory. The coefficients of terms linear and cubic in k around k=0 are obtained. They should be experimentally observable when high-quality samples become available and should help to understand similar splittings in (Ge${)}_{\mathit{n}}$/(Si${)}_{\mathit{m}}$ (n,m odd) superlattices.
A 78 dB SNDR 87 mW 20 MHz Bandwidth Continuous-Time $\Delta\Sigma$ ADC With VCO-Based Integrator and Quantizer Implemented in 0.13 $\mu$m CMOS

The use of a VCO-based integrator and quantizer within a continuous-time (CT) ΔΣ analog-to-digital converter (ADC) structure is explored, and a custom prototype in a 0.13 μm CMOS with a measured performance of 81.2/78.1 dB SNR/SNDR over a 20 MHz bandwidth while consuming 87 mW from a 1.5 V supply and occupying an active area of 0.45 mm2 demonstrated. A key innovation is the explicit use of the oscillator's output phase to avoid the signal distortion that had severely limited the performance of earlier VCO-based ADCs, which had made use of its output frequency only. The proposed VCO-based integrator and quantizer structure enables fourth-order noise shaping with only three opamp-based integrators.
TEAR: TCP emulation at receivers – flow control for multimedia streaming

Congestion and flow control is an integral part of any Internet data transport protocol. It is widely accepted that the congestion avoidance mechanisms of TCP have been one of the key contributors to the success of the Internet. However, TCP is ill-suited to real-time multimedia streaming applications. Its bursty transmission, and abrupt and frequent wide rate fluctuations cause high delay jitters and sudden quality degradation of multimedia applications. For asymmetric networks such as wireless networks, cable modems, ADSL, and satellite networks, transmitting feedback for (almost) every packet received as it is done in TCP causes congestion in the reverse path. In this environment, TCP may severely underutilize the forward path throughput. Use of multicast further complicates the problem; TCP-like frequent feedback from each receiver to the sender in a large scale multicast session cause well-known scalability limitations (e.g. acknowledgment implosion). We have developed a new flow control approach for multimedia streaming, called TCP emulation at receivers (TEAR). TEAR shifts most of flow control mechanisms to receivers. In TEAR, a receiver does not send to the sender the congestion signals detected in its forward path but rather processes them immediately to determine its own appropriate receiving rate. TEAR can determine this rate using congestion signals observed at the receiver. These signals are used to emulate the TCP sender’s flow control functions at receivers.The emulation allows receivers to estimate a TCP-friendly rate for the congestion conditions observed in their forward paths. TEAR also allows receivers to adjust their receiving rates to a TCP-friendly rate without actually modulating the rates to probe for spare bandwidth, or to react to packet losses directly. Thus, the perceived rate fluctuations at the application are much more smooth than in TCP. A unicast version of TEAR is implemented. This report describes the implementation of TEAR, examine the performance of this TEAR implementation from the NS simulation and Internet experiments, and compare it with that of other TCP-friendly flow control techniques. Our preliminary tests indicate that TEAR shows superior fairness to TCP with significantly lower rate fluctuations than TCP. TEAR’s sensitivity to feedback interval is very low, so that even under high feedback latency, TEAR flows exhibit acceptable performance in terms of fairness, TCP-friendliness, and rate fluctuations. Finally, I will discuss the future extension of TEAR for multicast environments. This work is supported in part by NSF CAREER ANI-9875651.
Money, love, and hate contradiction and paradox in psychoanalysis

The way analysts talk, behave, and feel in relation to money is replete with an uneasiness that is the surface manifestation of a deep, psychocultural contradiction between money and love that cannot be thought, willed, or wished away. For the clinical project to succeed, this contradiction can and must find a temporary, reparative resolution in the paradox between love and hate. This essay takes up the question of money in the spirit of the Marx‐Freud tradition, in postmodern perspective, and through several languages, not only psychoanalysis, but social theory, anthropology, and less centrally, feminist theory as well. It addresses money's unconscious and emotional resonance, and its cultural meanings; money's clinical and theoretical vicissitudes in the context of cultural symbolism and economic change, as well as the class position of psychoanalysis and the psychology of class itself; and money's relational meaning in transference and countertransference.
Extracellular matrix fluctuations during early embryogenesis

Extracellular matrix (ECM) movements and rearrangements were studied in avian embryos during early stages of development. We show that the ECM moves as a composite material, whereby distinct molecular components as well as spatially separated layers exhibit similar displacements. Using scanning wide field and confocal microscopy we show that the velocity field of ECM displacement is smooth in space and that ECM movements are correlated even at locations separated by several hundred micrometers. Velocity vectors, however, strongly fluctuate in time. The autocorrelation time of the velocity fluctuations is less than a minute. Suppression of the fluctuations yields a persistent movement pattern that is shared among embryos at equivalent stages of development. The high resolution of the velocity fields allows a detailed spatio-temporal characterization of important morphogenetic processes, especially tissue dynamics surrounding the embryonic organizer (Hensen's node).
Crystal structure of human esterase D: a potential genetic marker of retinoblastoma

Retinoblastoma (RB), a carcinoma of the retina, is caused by mutations in the long arm of chromosome 13, band 13q14. The esterase D (ESD) gene maps at a similar location as the RB gene locus and therefore serves as a potential marker for the prognosis of retinoblastoma. Because very little is known about the structure and function of ESD, we determined the 3‐dimensional structure of the enzyme at 1.5 Å resolution using X‐ray crystallography. ESD shows a single domain with an α/α‐hydrolase fold. A number of insertions are observed in the canonical α/β‐hydrolase fold. The active site is located in a positively charged, shallow cleft on the surface lined by a number of aromatic residues. Superimposition studies helped identify the typical catalytic triad residues—Ser‐153, His264, and Asp230—involved in ca‐talysis. Mutagenesis of any of the catalytic triad residues to alanine abolished the enzyme activity. Backbone amides of Leu54 and Met150 are involved in the formation of the oxyanion hole. Interestingly, a M150A mutation increased the enzyme activity by 62%. The structure of human ESD determined in this study will aid the elucidation of the physiological role of the enzyme in the human body and will assist in the early diagnosis of retinoblastoma. — Wu, D. , Li, Y. , Song, G. , Zhang, D. , Shaw, N. , Liu, Z. J. Crystal structure of human esterase D: a potential genetic marker of retinoblastoma. FASEB J. 23, 1441–1446 (2009)
Evidence of Melanoma in Wild Marine Fish Populations

The increase in reports of novel diseases in a wide range of ecosystems, both terrestrial and marine, has been linked to many factors including exposure to novel pathogens and changes in the global climate. Prevalence of skin cancer in particular has been found to be increasing in humans, but has not been reported in wild fish before. Here we report extensive melanosis and melanoma (skin cancer) in wild populations of an iconic, commercially-important marine fish, the coral trout Plectropomus leopardus. The syndrome reported here has strong similarities to previous studies associated with UV induced melanomas in the well-established laboratory fish model Xiphophorus. Relatively high prevalence rates of this syndrome (15%) were recorded at two offshore sites in the Great Barrier Reef Marine Park (GBRMP). In the absence of microbial pathogens and given the strong similarities to the UV-induced melanomas, we conclude that the likely cause was environmental exposure to UV radiation. Further studies are needed to establish the large scale distribution of the syndrome and confirm that the lesions reported here are the same as the melanoma in Xiphophorus, by assessing mutation of the EGFR gene, Xmrk. Furthermore, research on the potential links of this syndrome to increases in UV radiation from stratospheric ozone depletion needs to be completed.
LPC(ID): A Sequent Calculus Proof System for Propositional Logic Extended with Inductive Definitions

The logic FO(ID) uses ideas from the field of logic programming to extend first order logic with non-monotone inductive definitions. Such logic formally extends logic programming, abductive logic programming and datalog, and thus formalizes the view on these formalisms as logics of (generalized) inductive definitions. The goal of this paper is to study a deductive inference method for PC(ID), which is the propositional fragment of FO(ID). We introduce a formal proof system based on the sequent calculus (Gentzen-style deductive system) for this logic. As PC(ID) is an integration of classical propositional logic and propositional inductive definitions, our sequent calculus proof system integrates inference rules for propositional calculus and definitions. We present the soundness and completeness of this proof system with respect to a slightly restricted fragment of PC(ID). We also provide some complexity results for PC(ID). By developing the proof system for PC(ID), it helps us to enhance the understanding of proof-theoretic foundations of FO(ID), and therefore to investigate useful proof systems for FO(ID).
2011the International Conference on Advanced Power System Automation and Protection Small Disturbance Voltage Stability Considering Thermostatically Controlled Load

Load model plays an important role in the power system stability analysis and digital simulation. In the composite load model there is a load controlled by thermostat controller, such as industrial heating, electric water heater and electric space heater. With the proportion of the thermostatically controlled load (Thload) increasing, the influence on the power flow distribution and static voltage stability is more significant. Aiming at these problems, this paper analyzed the impact of this load on the static voltage stability. Firstly, the model of Thload is introduced and its mechanism and characteristics are set forth. Then this paper has made analysis and comparison of the static voltage stability between Thload and other loads based on the foundation of power system analysis toolbox (PSAT) in MATLAB. , and the impact of the parameters of the Thload on the small disturbance voltage stability was discussed. At last, according to the results of small disturbance method, the effect of Thload and other loads on the electromechanical mode of single-machine infinite-bus system was analyzed comparatively.