Miracle-dz/UniFAR-FTUs huggingface dataset:
Non-sequential protein structure alignment by conformational space annealing and local refinement

Protein structure alignment is an important tool for studying evolutionary biology and protein modeling. A tool which intensively searches for the globally optimal non-sequential alignments is rarely found. We propose ALIGN-CSA which shows improvement in scores, such as DALI-score, SP-score, SO-score and TM-score over the benchmark set including 286 cases. We performed benchmarking of existing popular alignment scoring functions, where the dependence of the search algorithm was effectively eliminated by using ALIGN-CSA. For the benchmarking, we set the minimum block size to 4 to prevent much fragmented alignments where the biological relevance of small alignment blocks is hard to interpret. With this condition, globally optimal alignments were searched by ALIGN-CSA using the four scoring functions listed above, and TM-score is found to be the most effective in generating alignments with longer match lengths and smaller RMSD values. However, DALI-score is the most effective in generating alignments similar to the manually curated reference alignments, which implies that DALI-score is more biologically relevant score. Due to the high demand on computational resources of ALIGN-CSA, we also propose a relatively fast local refinement method, which can control the minimum block size and whether to allow the reverse alignment. ALIGN-CSA can be used to obtain much improved alignment at the cost of relatively more extensive computation. For faster alignment, we propose a refinement protocol that improves the score of a given alignment obtained by various external tools. All programs are available from http://lee.kias. re.kr.
Adaptive Motion Estimation and Control of Intelligent Walkers

One of the most critical factors in the quality of elderly lives is their ability to move. As the size of the ageing society grows, more elderly people suffer from walking impairments. Most of them prefer to stay at home due to the shortage of the nursing care staff, since they deal with the daily challenges alone. Robotics researchers have developed various intelligent walking support systems to meet the needs of elderly and handicapped people. A particular problem in path tracking for such systems is maintaining the tracking performance, which is affected by the center of gravity (CG) shifts and load changes due to human-walker interactions. This thesis focuses on design of feedback controllers for safe motion of intelligent walker (i-walker) systems robust to CG shifts and load changes. Our design follows a two level approach, one for kinematics, the other for dynamics. The high level kinematic controller is designed based on integrator backstepping to produce desired velocities required for trajectory tracking. The low level dynamic controller is composed of a feedback linearization unit and a linear feedback controller to apply the control torque for tracking the desired velocity produced by the high level kinematic controller. As dynamic controllers, proportional-derivative (PD) and sliding mode controllers (SMCs) are designed. In our initial design, we assume that all system states are available. However, in the actual case, even if the wheel velocities can be measured with some sensor devices like tachometers, the measurements carry noise, which poses important problems in control algorithms. To obtain the estimates of the wheel velocities, avoiding the noise problems, the design of sliding mode observers and high gain observers is studied. The state feedback PD and SMC schemes are later integrated with these observers to form implementable output feedback controllers. In practice, the human mass and the distance due to the CG shift depend on the user. To address this issue, the output feedback control designs are further made adaptive, integrating with a parameter identifier to estimate these variables. The parameter identifier design involves a linear parametric model of the i-walker system dynamics and a least-square adaptive law based on this parametric model. Adaptive versions of the above observers and control designs are done utilizing estimated parameters and states. The effectiveness and applicability of the proposed controllers are verified via various simulations in MATLAB/Simulink environment.
Assessing News Ways Of Teaching Dynamics: An Ongoing Program To Improve Teaching, Learning, And Assessment

In spring 1998, a traditional lecture and problem-solving based course in introductory dynamics was infused with interactive learning activities. The enhanced course called “Interactive Dy-namics” was designed to engage students in a collaborative environment in which students have easy access to an array of technological tools (web-based simulations, spreadsheets, computational and simulation tools, etc.). They used these tools to generate and analyze data, observe graphic representations of the data, and construct and interact with simulations. To assess the innovations introduced into this course, we conducted pre-and post-tests on dynamics content in the Interactive sections and in the control (traditionally taught, lecture-style) sections of the course. Additionally, we collected data for other learning objectives congruent with ABET (Accreditation Board for Engineering Technology) 2000 Criteria, e.g. , teamwork, problem solving, communications, and computer skills. While gains in mechanics content knowledge for students in innovative sections were similar to those of students in traditional sections, students in active learning classrooms reported statistically significant gains in teamwork and computer skills. The data indicate the new course design reinforces the ABET goals of encouraging innovative practices in the classroom that enhance learning and develop skills needed in the workplace. This paper addresses several issues: (1) how do we develop measures that accurately reflect learning objectives given the innovative teaching practices, (2) what learning outcomes are affected when active learning strategies are employed in the engineering classroom, and (3) how can we use these assessments to improve teaching, learning, and assessment in future semesters? We used the data to enhance activities and assessment for classes being taught during fall 1998 and continue to look for ways to improve the teaching and assessment process.
Scattering and pair creation by a constant electric field between two capacitor plates

Using the quantum field theory approach developed in Phys. Rev. D. 93, 045002 (2016), we consider particle scattering and vacuum instability in the so-called L-constant electric field, which is a constant electric field confined between two capacitor plates separated by a finite distance L. We obtain and analyze special sets of stationary solutions of the Dirac and Klein-Gordon equations with the L-constant electric field. Then, we represent probabilities of particle scattering and characteristics of the vacuum instability (related to pair creation) in terms of the introduced solutions. From exact formulas, we derive asymptotic expressions for the differential mean numbers, for the total mean number of created particles, and for the vacuum-to-vacuum transition probability. Using the equivalence principle, we demonstrate that the distributions of particles created by the L-constant electric field and the gravitational field of a black hole have a similar thermal structure.
Equilibrium and Efficiency in the Tug-of-War

We characterize the unique Markov perfect equilibrium of a tug-of-war without exogenous noise, in which players have the opportunity to engage in a sequence of battles in an attempt to win the war. Each battle is an all-pay auction in which the player expending the greater resources wins. In equilibrium, contest effort concentrates on at most two adjacent states of the game, the 'tipping states', which are determined by the contestants’ relative strengths, their distances to final victory, and the discount factor. In these states battle outcomes are stochastic due to endogenous randomization. Both relative strength and closeness to victory increase the probability of winning the battle at hand. Patience reduces the role of distance in determining outcomes. Applications range from politics, economics and sports, to biology, where the equilibrium behaviour finds empirical support: many species have developed mechanisms such as hierarchies or other organizational structures by which the allocation of prizes are governed by possibly repeated conflict. Our results contribute to an explanation why. Compared to a single stage conflict, such structures can reduce the overall resources that are dissipated among the group of players.
INFORMATION BEHAVIOR AND TECHNOLOGY AFFINITY AMONG HIGHER INSTITUTION LEARNERS IN BORNEO

This study aims to provide an understanding of information behavior with technology based on gender. It also to investigate the relationship between information behavior and degree of technology affinity. This research has been conducted quantitatively and using survey to gain data from participants. Participant are selected randomly across Universiti Malaysia Sarawak, Sarawak. The instrument are adopted from Mills, Knezek, and Wakefield (2013) which taking interest into information behavior (ICTL) as well as technology affinity. The reliability for Information and Communication Technology Learning (ICTL) is 0.835 while for Technology Affinity Scale (TAS) is 0.831. Statistical Analysis for Social Science Package (SPSS) are used to analyze the data obtained through Independent T-test and Pearson Correlation test. Findings indicate that no significant difference found for understanding of information behavior with technology based on gender. While, another finding indicate that there is no significant relationship between information behavior and technology affinity. Improvement suggested obtain from the findings are providing understanding on the types of information behavior possess by each learner and helps educator as well as learner to plan their teaching and learning session to promote better indulgent of the knowledge.
Role of BRCA1-associated protein (BRAP) variant in childhood pulmonary arterial hypertension

Although mutations in several genes have been reported in pulmonary arterial hypertension (PAH), most of PAH cases do not carry these mutations. This study aimed to identify a novel cause of PAH. To determine the disease-causing variants, direct sequencing and multiplex ligation-dependent probe amplification were performed to analyze 18 families with multiple affected family members with PAH. In one of the 18 families with PAH, no disease-causing variants were found in any of BMPR2, ACVRL1, ENG, SMAD1/4/8, BMPR1B, NOTCH3, CAV1, or KCNK3. In this family, a female proband and her paternal aunt developed PAH in their childhood. Whole-exome next-generation sequencing was performed in the 2 PAH patients and the proband’s healthy mother, and a BRCA1-associated protein (BRAP) gene variant, p.Arg554Leu, was identified in the 2 family members with PAH, but not in the proband’s mother without PAH. Functional analyses were performed using human pulmonary arterial smooth muscle cells (hPASMCs). Knockdown of BRAP via small interfering RNA in hPASMCs induced p53 signaling pathway activation and decreased cell proliferation. Overexpression of either wild-type BRAP or p.Arg554Leu-BRAP cDNA constructs caused cell death confounding these studies, however we observed higher levels of p53 signaling inactivation and hPASMC proliferation in cells expressing p.Arg554Leu-BRAP compared to wild-type BRAP. In addition, p.Arg554Leu-BRAP induced decreased apoptosis of hPASMCs compared with wild-type BRAP. In conclusion, we have identified a novel variant of BRAP in a Japanese family with PAH and our results suggest it could have a gain-of-function. This study sheds light on new mechanism of PAH pathogenesis.
Comparative Study Reveals Insights of Sheepgrass (Leymus chinensis) Coping With Phosphate-Deprived Stress Condition

Sheepgrass [Leymus chinensis (Trin.) Tzvel] is a valuable forage plant highly significant to the grassland productivity of Euro-Asia steppes. Growth of above-ground tissues of L. chinensis is the major component contributing to the grass yield. Although it is generally known that this species is sensitive to ecosystem disturbance and adverse environments, detailed information of how L. chinensis coping with various nutrient deficiency especially phosphate deprivation (-Pi) is still limited. Here, we investigated impact of Pi-deprivation on shoot growth and biomass accumulation as well as photosynthetic properties of L. chinensis. Growth inhibition of Pi-deprived seedlings was most obvious and reduction of biomass accumulation and net photosynthetic rate (Pn) was 55.3 and 63.3%, respectively, compared to the control plants grown under Pi-repleted condition. Also, we compared these characters with seedlings subjected to low-Pi stress condition. Pi-deprivation caused 18.5 and 12.3% more reduction of biomass and Pn relative to low-Pi-stressed seedlings, respectively. Further analysis of in vivo chlorophyll fluorescence and thylakoid membrane protein complexes using 2D-BN/SDS-PAGE combined with immunoblot detection demonstrated that among the measured photosynthetic parameters, decrease of ATP synthase activity was most pronounced in Pi-deprived plants. Together with less extent of lipid peroxidation of the thylakoid membranes and increased ROS scavenger enzyme activities in the leaves of Pi-deprived seedlings, we suggest that the decreased activity of ATP synthase in their thylakoids is the major cause of the greater reduction of photosynthetic efficiency than that of low-Pi stressed plants, leading to the least shoot growth and biomass production in L. chinensis.
Lamarckian Evolution of Simulated Modular Robots

We study evolutionary robot systems where not only the robot brains but also the robot bodies are evolvable. Such systems need to include a learning period right after ‘birth' to acquire a controller that fits the newly created body. In this paper we investigate the possibility of bootstrapping infant robot learning through employing Lamarckian inheritance of parental controllers. In our system controllers are encoded by a combination of a morphology dependent component, a Central Pattern Generator (CPG), and a morphology independent part, a Compositional Pattern Producing Network (CPPN). This makes it possible to transfer the CPPN part of controllers between different morphologies and to create a Lamarckian system. We conduct experiments with simulated modular robots whose fitness is determined by the speed of locomotion, establish the benefits of inheriting optimized parental controllers, shed light on the conditions that influence these benefits, and observe that changing the way controllers are evolved also impacts the evolved morphologies.
CORPORATE OWNERSHIP AND CONTROL: NEW EVIDENCE FROM TAIWAN

Recent empirical literature on corporate governance has demonstrated that companies’ shares are generally concentrated in the hands of particular families or wealthy investors. Claessens et al. (2002) analyzed the ownership structure in East Asian eight countries, but misestimated the Taiwanese condition that made them not find the positive incentive or negative entrenchment effects in Taiwan. This study tries to clear the ultimate control in Taiwan, use the detailed data to better understand the ownership structure in Taiwan and investigates the determinants for deviation of control from cash flow rights. Based on the findings, the companies’ shares are common concentrated in the hands of the largest shareholder. We find that the deviation of control from cash flow rights is greater in the family-controlled companies than other type companies. Also the controlling shareholders use more pyramids and cross shareholding to increase their control rights that accompanies with deeply management participation. On the average, the controlling shareholders hold more than half board seats and usually occupy the chairman and general manger to enhance their control power in family-controlled companies. No matter in all sample or family-controlled companies, the controlling shareholders owns significantly less cash flow rights, occupy more board seats in deviation group companies than those without deviation. Corporate valuation is significantly lower in the companies with the divergence of control from cash flow rights than non-deviation companies.
POPULATION GENETIC ANALYSIS OF SONORAN PRONGHORN (ANTILOCAPRA AMERICANA SONORIENSIS)

Abstract The endangered Sonoran pronghorn (Antilocapra americana sonoriensis) consists of only 2 small populations, 1 in Arizona and 1 in Mexico. Mitochondrial DNA sequence data and 5 microsatellite loci were used to compare levels of genetic diversity and differentiation between the 2 Sonoran pronghorn populations and between this subspecies and other selected pronghorn populations, both proximate and distant to the Sonoran pronghorn's current range. The data support a history of recent isolation of Sonoran pronghorn populations from those in Arizona, New Mexico, and Texas. Loss of genetic diversity due to bottlenecks and drift has been severe in both populations of the Sonoran pronghorn, but is most pronounced in the Arizona population. These results are discussed in terms of conservation management strategies.
Short‒chain diacyl phosphatidylglycerols: which one to choose for the NMR structural determination of a membrane‒associated peptide from Escherichia coli?

Diacyl phosphatidylglycerols (PG) are the major anionic lipids in the Escherichia coli membrane. Short‒chain dihexanoyl phosphatidylglycerol (DHPG) was previously utilized for the structural determination, by NMR spectroscopy, of the peptide corresponding to the N-terminal membrane anchor of the glucose‒specific enzyme IIA (IIAGlc) from E. coli. This study explores the possible use of lipid micelles of dioctanoyl phosphatidylglycerol (DOPG) and didecanoyl phosphatidylglycerol (DDPG) as alternatives to DHPG. At a peptide concentration of 1 mM, the minimum peptide/lipid molar ratios required for the formation of the lipid‒binding amphipathic helix are approximately 1 :40, 1 :5, and 1 :5 for DHPG, DOPG, and DDPG, respectively. Based on the lipid titration, the critical micelle concentration (CMC) of DHPG was estimated to be ~50 mM. The 1H spectral linewidths of the peptide bound to a variety of lipid micelles decrease in the following order: DDPG > DOPG > DHPG. The helical regions of the peptide in different anionic lipids were elucidated based on chemical shift indexes (CSI). Residues Leu2‒Leu9, Leu2‒Val10, and Leu2‒Val10 were found to be helical in DHPG, DOPG, and DDPG, respectively, indicating that the lipid chain length had only a subtle effect on the amphipathic helix of the peptide. In light of the minimum peptide/lipid ratio and the spectral linewidth, and the CSI‒derived peptide structure, DOPG is proposed as a good compromise for structural studies of this membrane‒associated peptide by solution NMR spectroscopy.
What makes the difference? Employee social media brand engagement

Purpose This paper aims to explore, using the employee lens of business-to-business firms, word use through brand engagement and social media interaction to understand the difference between employees who rate their employer brands highly on social media and those who don't. Design/methodology/approach We conducted a textual content analysis of posts published on the social media job evaluation site glassdoor.com. LIWC software package was used to analyze 30 of the top 200 business-to-business brands listed on Brandwatch using four variables, namely, analytical thinking, clout, authenticity and emotional tone. Findings The results show that employees who rate their employer’s brand low use significantly more words, are significantly less analytic and write with significantly more clout because they focus more on others than themselves. Employees who rate their employer’s brand highly, write with significantly more authenticity, exhibit a significantly higher tone and display far more positive emotions in their reviews. Practical implications Brand managers should treat social media data disseminated by individual stakeholders, like the variables used in this study (tone, word count, frequency), as a valuable tool for brand insight on their industry, competition and their own brand equity, now and especially over time. Originality/value This study provides acknowledgement that social media is a significant source of marketing intelligence that may improve brand equity by better understanding and managing brand engagement.
Capturing public views on complex and unfamiliar goods : chemical water pollution in England and Wales

This thesis (papers submission) focuses on the challenge of using public opinion to value environmental goods that are both complex to understand and unfamiliar to people. The three central papers are introduced by a literature review, which considers recent advancements in methods and knowledge associated with determining values for unfamiliar goods. The first paper then applies a stated preference choice experiment (using online surveys) and a latent class analysis to determine the value of reducing persistent chemicals from waterbodies in England and Wales. A scientific certainty attribute is included to capture the uncertainties associated with persistent chemical effects, marking a novel contribution to the literature and a development of the precautionary principle for application. The second paper uses a deliberative approach to investigate how people frame policy options for reducing chemical water pollution in England and Wales (required under the Water Framework Directive), using a representative sample of participants over two consecutive weekend workshops. The key finding here is that stated preference research aiming to be policy-relevant should improve its approach to cost fairness issues. The final paper uses a contingent valuation approach (using online surveys) to estimate the value of removing metal pollution from waterbodies in England and Wales. This paper applies a split sample to investigate the effect of a social norms information treatment on how convincing and realistic people found the stated preference scenario and payment tasks to be, which increased for the treatment group. The results indicate that the treatment has a weak direct impact on estimated mean willingness to pay (WTP), however a relative measure of WTP precision suggests that such estimates can be improved if people pay attention to the treatment. The findings from this thesis are of use to social scientists, civil servants and environmental economists interested in: improving approaches to valuing complex and unfamiliar goods; better reflecting natural decision-making in public opinion research; and applying findings from deliberative and survey-based research to create and manage more effective policies.