Miracle-dz/UniFAR-FTUs huggingface dataset:
Mutagenic Deimmunization of Diphtheria Toxin for Use in Biologic Drug Development

Background: Targeted toxins require multiple treatments and therefore must be deimmunized. We report a method of protein deimmunization based on the point mutation of highly hydrophilic R, K, D, E, and Q amino acids on the molecular surface of truncated diphtheria-toxin (DT390). Methods: Based on their surface position derived from an X-ray-crystallographic model, residues were chosen for point mutation that were located in prominent positions on the molecular surface and away from the catalytic site. Mice were immunized with a targeted toxin containing either a mutated DT390 containing seven critical point mutations or the non-mutated parental toxin form. Results: Serum analysis revealed a significant 90% reduction in anti-toxin antibodies in mice immunized with the mutant, but not the parental drug form despite multiple immunizations. The experiment was repeated in a second strain of mice with a different MHC-haplotype to address whether point mutation removed T or B cell epitopes. Findings were identical indicating that B cell epitopes were eliminated from DT. The mutant drug form lost only minimal activity in vitro as well as in vivo. Conclusion: These findings indicate that this method may be effective for deimmunizing of other proteins and that discovery of a deimmunized form of DT may lead to the development of more effective targeted toxin.
Code placement using temporal profile information

Instruction cache performance is important to instruction fetch efficiency and overall processor performance. The layout of an executable has a substantial effect on the cache miss rate and the instruction working set size during execution. This means that the performance of an executable can be improved significantly by applying a code-placement algorithm that minimizes instruction cache conflicts and improves spatial locality. We describe an algorithm for procedure placement, one type of code-placement algorithm, that significantly differs from previous approaches in the type of information used to drive the placement algorithm. In particular, we gather temporal ordering information that summarizes the interleaving of procedures in a program trace. Our algorithm uses this information along with cache configuration and procedure size information to better estimate the conflict cost of a potential procedure ordering. It optimizes the procedure placement for singleand multi-level caches. In addition to reducing instruction cache conflicts, the algorithm simultaneously minimizes the instruction working set size of the program. We compare the performance of our algorithm with a particularly successful procedure-placement algorithm and show noticeable improvements in the instruction cache behavior, while maintaining the same instruction working set size.
Growth and nodulation of symbiotic Medicago truncatula at different levels of phosphorus availability

Medicago truncatula is an important model plant for characterization of P deficiency on leguminous plants at the physiological and molecular levels. Growth optimization of this plant with regard to P supply is the first essential step for elucidation of the role of P in regulation of nodulation. Hence, a study was carried out to address the growth pattern of M. truncatula hydroponically grown at different gradual increases in P levels. The findings revealed that M. truncatula had a narrow P regime, with an optimum P level (12 μM P) which is relatively close to the concentration that induces P toxicity. The accumulated P concentration (2.7 mg g–1 dry matter), which is normal for other crops and legumes, adversely affected the growth of M. truncatula plants. Under P deficiency, M. truncatula showed a higher symbiotic efficiency with Sinorhizobium meliloti 2011 in comparison with S. meliloti 102F51, partially as a result of higher electron allocation to N2 versus H+. The total composition of free amino acids in the phloem was significantly affected by P deprivation. This pattern was found to be almost exclusively the result of the increase in the asparagine level, suggesting that asparagine might be the shoot-derived signal that translocates to the nodules and exerts the down-regulation of nitrogenase activity. Additionally, P deprivation was found to have a strong influence on the contents of the nodule carbon metabolites. While levels of sucrose and succinate tended to decrease, a higher accumulation of malate was observed. These findings have provided evidence that N2 fixation of M. truncatula is mediated through an N feedback mechanism which is closely related to nodule carbon metabolism.
Spectroscopic and Computational Study of Melittin, Cecropin A, and the Hybrid Peptide CM15

Antimicrobial peptides (AMPs), such as cecropin A from silk moth, are key components of the innate immune system. They are effective defensive weapons against invading pathogens, yet they do not target host eukaryotic cells. In contrast, peptide toxins, such as honeybee melittin, are nondiscriminating and target both eukaryotic and prokaryotic cells. An AMP-toxin hybrid peptide that is composed of cecropin A and melittin (CM15) improves upon the antimicrobial activity of cecropin A without displaying the nonspecific, hemolytic properties of melittin. Here we report fluorescence and UV resonance Raman spectra of melittin, cecropin A, and CM15 with the goal of elucidating peptide-membrane interactions that help guide specificity. We have probed the potency for membrane disruption, local environment and structure of the single tryptophan residue, backbone conformation near the peptide hinge, and amide backbone structure of the peptides in lipid environments that mimic eukaryotic and prokaryotic membranes. These experimental results suggest that melittin inserts deeply into the bilayer, whereas cecropin A remains localized to the lipid headgroup region. A surprising finding is that CM15 is a potent membrane-disruptor despite its largely unfolded conformation. A molecular dynamics analysis complements these data and demonstrates the ability of CM15 to associate favorably with membranes as an unfolded peptide. This combined experimental–computational study suggests that new models for peptide–membrane interactions should be considered.
Design of a Hybrid Controller using Differential Evolution and MIT Rule for Magnetic Levitation System

In various industrial systems, parameters variation is one of the major problems faced by control engineers now days. To overcome the problem of parameter variations, this paper proposes the hybridization of MIT rule based online tuning of classical PID controllers with Differential Evolution algorithm. The hybridization of two techniques results in the offline as well as online tuning of PID controllers at the same time. The developed hybrid controller is then applied on magnetic levitation system using MATLAB and Simulink. The paper also describes the basic steps involved in Differential Evolution (DE) algorithm and a comparison between designed hybrid controller and the simple DE algorithm based controller has been carried out. The results depict that the performance of the hybrid controller is better than the offline tuned PID controller in terms of transient parameters such as peak overshoot and settling time. Keywords–Differential evolution, hybridization, MIT rule, PID controller, soft computing.
Face to Age

A Century of Portraits is a dataset that contains frontal-facing American high school year-book photos with labels to indicate the years those photos were taken [2]. In this project we train classifiers to predict the label, given the image. We used several Deep Neural Network architectures for this task, all of which were finetuned with ImageNet pretraining. With VGGNet architecture, we demonstrate significant improvements in classification accuracy reporting test set accuracy of 67.59% and mean L1 error, as compared to 11.31 % achieved by Ginosar et al. [2]. Further, we show some visualizations of the trained model to gain insights into the learned model. The code for this project can be found at https://github.com/AshishBora/face2year.
AUTHORS' RESPONSE Deeper Into Attachment Theory

One of the explicit goals of our target article was to provoke the kind of integrative thinking and conceptual debate that can help advance the science of relationships. Surely that goal was achieved! We were challenged and inspired by what many of the commentators wrote in response to our proposed theoretical framework. For this and for the time and thought they put into their commentaries, we thank them. They highlighted the strengths and limitations of attachment theory and our extensions of it and forced consideration of some very complex issues that must be settled if research on adult attachment is to proceed in fruitful directions. Their insights and even their criticisms made it easier for us to see just how to proceed. Most of the criticisms fall into one of two major categories. On the one hand are concerns about the validity and utility of attachment theory itself. On the other hand are concerns about our application of the theory to adult relationship phenomena. An important caveat to be stated at the outset is that our article should not be seen as providing a complete explication of attachment theory. Bowlby required well more than a thousand pages for his initial presentation of it, whereas the present format allowed only a sketch of the key concepts. To respond to commentators' concerns about the theory necessitates a detailed discussion of some of its neglected features, all directly or indirectly tied to three questions raised repeatedly in the commentaries:
Effects of mental rotation, visual aids and training on inspection performance during airport baggage inspection

ii ACKNOWLEDGEMENTS I would like to thank my advisor Dr. Craig M. Harvey for making this work possible. No words of thanks are enough for his mentorship, guidance, support and patience. I must acknowledge the freedom he gave me in pursuing research topics that I found interesting. His keen observations and tremendous experience helped me a great deal in defining a path for my research. I have learned a lot from him in the last couple of years both as a researcher and as a person. I would like to thank Dr. Fereyduon Aghazadeh and Dr. Xiaoyue Jiang, for taking their valuable time out to help and guide me through my thesis. I would like to thank my parents Mr. & Mrs. Lakshmi Pathi Rao for their support and love throughout. I would also like to thank Sushma and Kaladhar for their encouragement and support. I would like to specially thank my best friend Lini, without whose love and support none of this would have been possible. No acknowledgement is complete without mentioning the friends I made at LSU. I will always remember them for making my stay away from home a most memorable one. Thank you one and all for always being there.
PR: More than Meets the Eye

In this paper, we introduce a new image descriptor for broad Image Categorization, the Progressive Randomization (PR) that uses perturbations on the values of the Least Significant Bits (LSB) of images. We show that different classes of images have a distinct behavior under our methodology and that using statistical descriptors of LSB occurrences and enough training examples, the method already performs as well or better than comparable existing techniques in the literature. With few training examples PR still has good separability and its accuracy increases with the size of the training set. We validate our method using four image databases with different categories.
Galois theory, functional Lindemann-Weierstrass, and Manin maps.

We prove several new results of Ax-Lindemann type for semiabelian varieties over the algebraic closure K of C(t), making heavy use of the Galois theory of logarithmic differential equations. Using related techniques, we also give a generalization of the theorem of the kernel for abelian varieties over K.
Effects of Caprylic Triglyceride on Cognitive Performance and Cerebral Glucose Metabolism in Mild Alzheimer’s Disease: A Single-Case Observation

Objective: To examine the effect of 109 days of caprylic triglyceride (CT) in a 70-year-old male with mild Alzheimer’s disease (AD). Background: Cerebral metabolism is limited to glucose under most conditions, and diminished cerebral glucose metabolism is a characteristic feature of AD. Another substrate available for cerebral metabolism is ketone bodies. Ketone bodies (KB) are normally derived from fat stores under conditions of low glucose availability as an alternative energy substrate to glucose. KB can also be produced by oral administration of CT. Prior studies suggest that the alternative energy source of CT may improve cognitive function due to mild to moderate AD, by circumventing the diminished glucose metabolism. Method: The effect of CT was analyzed in a single-case of mild AD with cognitive alterations in an open label study. Study outcomes included the Montreal cognitive assessment (MoCA), mini mental state exam (MMSE), and 18-fluorodeoxyglucose (18F) positron emission tomography (FDG PET) scans. Results: After 109 days of CT, MoCA scores changed from a baseline value of 24–28, and MMSE scores changed from 23 to 28. No changes were observed on FDG PET scans. Conclusion: The results suggest that, in a case of mild AD, CT may have affected cognitive function, assessed by means of MMSE and MoCA, although glucose uptake and metabolism remained unchanged.
Named entity patterns across news domains

A new event tracking approach is proposed based on the identification of named entity (NE) patterns such as Who, What, Where and When, and their relationship with news domains such as Politics, Economy, Government and Entertainment. This research comprises three parts. The first part uses a set of user studies to identify NE patterns and their relationship with news domains. Second part is to design a prototype system based on NE patterns. The final part evaluates the prototype event tracking system. This paper described the first part which is to evaluate the importance of NE across news domains. We have achieved a better understanding on NE patterns by identifying the distribution of NE across news domains.
Robustness of power systems under a democratic fiber bundle-like model

We consider a power system with N transmission lines whose initial loads (i.e., power flows) L1, . , LN are independent and identically distributed with PL(x) = P [L ≤ x]. The capacity Ci defines the maximum flow allowed on line i, and is assumed to be given by Ci = (1 + α)Li, with α > 0. We study the robustness of this power system against random attacks (or, failures) that target a p-fraction of the lines, under a democratic fiber bundle-like model. Namely, when a line fails, the load it was carrying is redistributed equally among the remaining lines. Our contributions are as follows: i) we show analytically that the final breakdown of the system always takes place through a first-order transition at the critical attack size p = 1− E[L] maxx(P[L>x](αx+E[L | L>x])) , where E [·] is the expectation operator; ii) we derive conditions on the distribution PL(x) for which the first order break down of the system occurs abruptly without any preceding diverging rate of failure; iii) we provide a detailed analysis of the robustness of the system under three specific load distributions: Uniform, Pareto, and Weibull, showing that with the minimum load Lmin and mean load E [L] fixed, Pareto distribution is the worst (in terms of robustness) among the three, whereas Weibull distribution is the best with shape parameter selected relatively large; iv) we provide numerical results that confirm our mean-field analysis; and v) we show that p is maximized when the load distribution is a Dirac delta function centered at E [L], i.e., when all lines carry the same load; we also show that optimal p equals α α+1 . This last finding is particularly surprising given that heterogeneity is known to lead to high robustness against random failures in many other systems.
Combining knowledge discovery, ontologies, annotations, and semantic wikis

Semantic Wikis provide an original and operational infrastructure for efficiently combining semantic technologies and collaborative design activities. This text presents: a running example and its context (organization of the collections in a museum); concepts of wikis as a tool to allow computer supported cooperative work (cscw); concepts of semantic technologies and knowledge representation; concepts and examples of semantic wikis; anatomy of a semantic wiki (reasoning tools, storage, querying); and research directions.
Thermal Conductivity Measurement of an Electron-Beam Physical-Vapor-Deposition Coating

An industrial ceramic thermal-barrier coating designated PWA 266, processed by electron-beam physical-vapor deposition, was measured using a steady-state thermal conductivity technique. The thermal conductivity of the mass fraction 7 % yttria-stabilized zirconia coating was measured from 100 °C to 900 °C. Measurements on three thicknesses of coatings, 170 μm, 350 μm, and 510 μm resulted in thermal conductivity in the range from 1.5 W/(m·K) to 1.7 W/(m·K) with a combined relative standard uncertainty of 20 %. The thermal conductivity is not significantly dependent on temperature.
NADPH Oxidase: A Potential Target for Treatment of Stroke

Stroke is the third leading cause of death in industrialized nations. Oxidative stress is involved in the pathogenesis of stroke, and excessive generation of reactive oxygen species (ROS) by mitochondria is thought to be the main cause of oxidative stress. NADPH oxidase (NOX) enzymes have recently been identified and studied as important producers of ROS in brain tissues after stroke. Several reports have shown that knockout or deletion of NOX exerts a neuroprotective effect in three major experimental stroke models. Recent studies also confirmed that NOX inhibitors ameliorate brain injury and improve neurological outcome after stroke. However, the physiological and pathophysiological roles of NOX enzymes in the central nervous system (CNS) are not known well. In this review, we provide a comprehensive summary of our current understanding about expression and physiological function of NOX enzymes in the CNS and its pathophysiological roles in the three major types of stroke: ischemic stroke, intracerebral hemorrhage, and subarachnoid hemorrhage.
Small Cell Transmit Power Assignment Based on Correlated Bandit Learning

Judiciously setting the base station transmit power that matches its deployment environment is a key problem in ultra-dense networks and heterogeneous in-building cellular deployments. A unique characteristic of this problem is the tradeoff between sufficient indoor coverage and limited outdoor leakage, which has to be met without explicit knowledge of the environment. In this paper, we address the small base station (SBS) transmit power assignment problem based on stochastic bandit theory. Unlike existing solutions that rely on heavy involvement of RF engineers surveying the target area, we take advantage of the human user behavior with simple coverage feedback in the network, and thus significantly reduce the planned human measurement. In addition, the proposed power assignment algorithms follow the Bayesian principle to utilize the available prior knowledge from system self-configuration. To guarantee good performance when the prior knowledge is insufficient, we incorporate the performance correlation among similar power values, and establish an algorithm that exploits the correlation structure to recover majority of the degraded performance. Furthermore, we explicitly consider power switching penalties in order to discourage frequent changes of the transmit power, which cause varying coverage and uneven user experience. Comprehensive system-level simulations are performed for both single and multiple SBS deployment scenarios, and the resulting power settings are compared with the state-of-the-art solutions. Significant performance gains of the proposed algorithms are observed. Particularly, the correlation structure enables the algorithm to converge much faster to the optimal long-term power than other methods.
Anatomy of Public Internet eXchange Points Ecosystem in Brazil

For a long time many efforts were carried to increase the understanding of the complex Internet ecosystem. Internet eXchange Points have been targets since they represent a microcosm of Internet diversity. The contribution of this paper is the first empirical analysis of the IXP ecosystem in Brazil, compiling information that comprehend the characterization of members participating of these environments, including the build of AS-level connectivity graphs. By analysing the topologies we found the average adjacency of IXP's members (vertices degree), the isolated and accumulated depth of paths in advertised routes (AS-PATH), the density of peers to highlight the peering potential within IXPs, the accounting of traffic engineering policies related to AS-Prepend and k-clique communities. Another contribution is that our dataset with more than 2.5 GB is shared with the academic community.
Probabilistic Methods for Combinational Circuits

The probabilistic methods for power estimation in combinational circuits are classified in two categories according to the adopted gate-delay model. The zero and real gate-delay power estimation methods. Under zero delay model, assuming spatiotemporal independence among the circuit signals, the switching activity, E(sw), of a circuit node, x, is given by ) 1 ( 2 2 ) ( 1 1 0 1 x x x x p p p p sw E x − = = . Thus, the problem is reduced to the computation of the
Stabilization of time-delay systems using finite-dimensional compensators

For linear time-invariant systems with one or more noncommensurate time delays, necessary and sufficient conditions are given for the existence of a finite-dimensional stabilizing feedback compensator. In particular, it is shown that a stabilizable time-delay system can always be stabilized using a finite-dimensional compensator. The problem of explicitly constructing finite-dimensional stabilizing compensators is also considered.
Correlation Between Professionalism, Job Satisfaction, and Job Performance of the Physical Therapist

Purpose: This study was conducted in order to understand the correlation between professionalism, job satisfaction, and job performance of physical therapists Methods: Subjects included 148 physiotherapists. We conducted a questionnaire survey on professionalism, job satisfaction, and business performance. We then performed a correlation analysis. Results: The highest ‘compliance of professional organization’ in professionalism, the lowest ‘vocation awareness of the profession’. In job satisfaction, the highest satisfaction was reported for ‘supervisor’, and the lowest satisfaction for ‘duty’. Professionalism and job satisfaction/job satisfaction and job performance showed a clear positive correlation, and professionalism and job performance showed a weak positive correlation. Conclusion: The results of this study indicate that, in order to improve the job performance of the physical therapist, it is necessary to improve professionalism and job satisfaction. Physical therapists should improve their professionalism in order to improve job performance. In addition, research to improve job satisfaction and job performance of the physical therapist should be continued.