Miracle-dz/UniFAR-FTUs huggingface dataset:
Protein-ligand binding sites. Identification, characterization and interrelations

Motivation: A variety of pocket detection algorithms are now freely or commercially available to the scientific community for the analysis of static protein structures. However, since proteins are dynamic entities, enhancing the capabilities of these programs for the straightforward detection and characterization of cavities taking into account protein conformational ensembles should be valuable for capturing the plasticity of pockets, and therefore allow gaining insight into structure-function relationships. Results: This paper describes a new method, called MDpocket, providing a fast, free and open source tool for tracking small molecule binding sites and gas migration pathways on MD trajectories or other conformational ensembles. MDpocket is based on the fpocket cavity detection algorithm and a valuable contribution to existing analysis tools. The capabilities of MDpocket are illustrated for three relevant cases: i) the detection of transient sub-pockets using an ensemble of crystal structures of HSP90 ii) the detection of known xenon binding sites and migration pathways in myoglobin, and iii) the identification of suitable pockets for molecular docking in P38 Map kinase. Availability: MDpocket is free and open source software and can be downloaded at http://fpocket.sourceforge. net. Contact: pschmidtke@ub.edu Supplementary information: Supplementary data are available at Bioinformatics online.
THE PROMISES OF MONSTERS:

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Man's Performance Degradation during Simulated Small Boat Slamming

A research program has been developed and preliminary data obtained on man's performance in a repetitive slamming environment such as would be encountered in a high-performance craft traversing rough seas. The Naval Ship Research and Development Center (NSRDC) slam simulator was used to test human volunteers in two series of laboratory-controlled studies that simulated ship slamming. The results indicate (1) that man's performance is degraded in a slamming environment, (2) that the subjective reactions of the volunteers do not reflect their performance scores, (3) that the test data are highly reproducible, and (4) that only minor muscular skeletal discomforts occurred during the test sessions. The report includes background material on man's known tolerance to single impacts and vibration.
Steel Bridges

New materials, new design concepts, and a better understanding of the trade-off between structural reliability and life-cycle costs make the next millennium an exciting time for steel technology. In evaluating the trade-off between structural reliability and life-cycle costs, engineers need to keep in mind the potential advantages steel structures can offer. These include but are not limited to the following:
Does addition of craving management tools in a stop smoking app improve quit rates among adult smokers? Results from BupaQuit pragmatic pilot randomised controlled trial

Objectives Delivery of craving management tools via smartphone applications (apps) may improve smoking cessation rates, but research on such programmes remains limited, especially in real-world settings. This study evaluated the effectiveness of adding craving management tools in a cessation app (BupaQuit). Methods The study was a two-arm pragmatic pilot parallel randomised controlled trial, comparing a fully-automated BupaQuit app with craving management tool with a control app version without craving management tool. A total of 425 adult UK-based daily smokers were enrolled through open online recruitment (February 2015–March 2016), with no researcher involvement, and individually randomised within the app to the intervention (n = 208) or control (n = 217). The primary outcome was self-reported 14-day continuous abstinence assessed at 4-week follow-up. Secondary outcomes included 6-month point-prevalence and sustained abstinence, and app usage. The primary outcome was assessed with Fisher's exact test using intent to treat with those lost to follow-up counted as smoking. Participants were not reimbursed. Results Re-contact rates were 50.4% at 4 weeks and 40.2% at 6 months. There was no significant difference between intervention and control arms on the primary outcome (13.5% vs 15.7%; p = 0.58; relative risk = 0.86, 95% confidence interval = 0.54–1.36) or secondary cessation outcomes (6-month point prevalence: 14.4% vs 17.1%, p = 0.51; relative risk = 0.85, 95% confidence interval = 0.54–1.32; 6-month sustained: 11.1% vs 13.4%, p = 0.55; relative risk = 0.83, 95% confidence interval = 0.50–1.38). Bayes factors supported the null hypothesis (B[0, 0, 1.0986] = 0.20). Usage was similar across the conditions (mean/median logins: 9.6/4 vs 10.5/5; time spent: 401.8/202 s vs 325.8/209 s). Conclusions The addition of craving management tools did not affect cessation, and the limited engagement with the app may have contributed to this.
Manufacturing network flows : a generalized network flow model for manufacturing process modelling

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The Vaccine Coverage and Vaccine Immunity Status and Risk Factors of Non-Protective Levels of Antibodies Against Vaccines in Children with Juvenile Idiopathic Arthritis: Russian Tertiary Centre Study.

Background: Immunosuppressive drugs, decreased vaccine coverage, aberrant immunity might be factors of low anti-vaccine antibodies in JIA patients. The study aimed to evaluate vaccine coverage, post-vaccine immunity and risk factors of non-protective levels of antibodies against measles, mumps, rubella, hepatitis B and diphtheria in JIA patients. Methods: A prospective study included 170 children diagnosed with JIA aged 2 to 17 years, who received routine vaccinations against measles, rubella, mumps (MMR) diphtheria and hepatitis B. In all patients, the levels of post-vaccination antibodies (IgG) for measles, rubella, mumps, hepatitis B and diphtheria measured with ELISA.Results: Protective level of antibodies were 50% against hepatitis B, 52% - diphtheria, 58% - measles, 80% - mumps, 98% rubella. The best coverage for MMR had patients with enthesytis-related arthritis-85%, compare to oligoarthritis-70%, polyarthritis-69%, systemic arthritis-63%. Diphtheria coverage was 50%, 51%, 46%, 63%, respectively. Incomplete MMR vaccination had 39% patients, treated with biologics, 22% with methotrexate and 14% with NSAID (p=0.025), and 61%, 46%, 36% for diphtheria (p=0.021). Incomplete vaccination was a risk factor of non-protective level of antibodies against measles (HR=2.03 [95%CI: 1.02; 4.0], p=0.042), parotitis (HR=6.25 [95%CI: 2.13; 17.9], p=0.0008) and diphtheria (HR=2.39 [95%CI: 1.18; 4.85], p=0.016) vaccines, as well as JIA category, biologics, corticosteroids and long-term methotrexate treatment for distinct vaccines.Conclusion: Children with JIA may have lower anti-vaccine antibodies levels and required routine check, especially in children with incomplete vaccination, biologics, systemic arthritis and long-term methotrexate treatment.
Households Willingness to Pay for Improved Water Services: The Case of Burayu Town Administration: Application of Contingent Valuation Method

This study is initiated by the current deep rooted problem of improved water supply prevailing in Burayu town and its primary objective is to estimate mean willingness to pay of households using contingent valuation method. A total of 239 sampled households are interviewed in person. A single bounded closed ended followed by open-ended format were used to elicit willingness to pay for improved water. Of 217 respondents 160(73.3%) accepted bid values of improved water provided to them. The data was analyzed both in descriptive and econometric models. The probit and tobit models were used for empirical analyses. In closed ended format, the households’ mean willingness to pay for one Jeri can of improved water was 31.5 cents and 42.7 cents in open ended format. Households characteristics’ such as age, income, occupation and education are positively determine the probability of accepting the given bid value of improved water. The bid value, dummy variables such as source of water, quantity and quality negatively affect the willingness to pay for improved water in probit model. Those variables affecting the likely of willingness to pay positively also have the same sign in tobit model of determining the maximum willingness to pay. The aggregate willingness to pay of households was estimated to be 1613942.62 birr per month. The current average revenue of the town’s water supply and sewerage enterprise is estimated to 515009.95 birr for one per month. The study revealed that households are willing to pay more of the current tariff blocks for improvement. Therefore if the improvement scenario comes to effect in one way it solves the shortage of improved water problems in the other way the town’s water supply and sewerage enterprise can collect more revenue from service charges.
Understanding of Förster Resonance Energy Transfer (FRET) in Ionic Materials

Herein, an ionic material (IM) with Förster Resonance Energy Transfer (FRET) characteristics is reported for the first time. The IM is designed by pairing a Nile Blue A cation (NBA+) with an anionic near-infrared (NIR) dye, IR820−, using a facile ion exchange reaction. These two dyes absorb at different wavelength regions. In addition, NBA+ fluorescence emission spectrum overlaps with IR820− absorption spectrum, which is one requirement for the occurrence of the FRET phenomenon. Therefore, the photophysical properties of the IM were studied in detail to investigate the FRET mechanism in IM for potential dye sensitized solar cell (DSSCs) application. Detailed examination of photophysical properties of parent compounds, a mixture of the parent compounds, and the IM revealed that the IM exhibits FRET characteristics, but not the mixture of two dyes. The presence of spectator counterion in the mixture hindered the FRET mechanism while in the IM, both dyes are in close proximity as an ion pair, thus exhibiting FRET. All FRET parameters such as spectral overlap integral, Förster distance, and FRET energy confirm the FRET characteristics of the IM. This article presents a simple synthesis of a compound with FRET properties which can be further used for a variety of applications.
Key Factors Contributing to The Anchorage Loss of Maxillary First Molars: A Retrospective Study of 726 Extraction Cases

Background: Anchorage control is one of the key components in the treatment of extraction cases. However, why anchorage loss happens is still an unanswered question. The purpose of this study was to investigate the most important factors contributing to the anchorage loss of maxillary first molars in premolar extraction cases. The study enrolled 726 upper premolar extraction cases, including 214 male patients and 512 female patients, and the average age was 14 (range: 9-45 years old). Factors including physiological characteristics, treatment mechanics and cephalometric variables were collected and their influences on the angulation changes of maxillary first molars were analyzed. Results: The average angulation change of maxillary first molar after treatment was 2.81°, meaning the molar tipped forward during treatment by 2.81°. The change of UM/PP showed statistically significant difference in different sex ( male 3.84°±5.26 ° vs female 2.38°±5.10°), age (adult -0.05°±4.73 ° vs teenager 3.46°±5.07°), and molar relationship(Class II 3.28°±5.15°vs Class I 2.36°±5.19°). There are six variables accounted in the regression analysis (R=0.608, R²=37.0%). Among them, the pre-treatment molar tipping (Standardized Coefficients：-0.65) and the pre-treatment incisor/molar height ratio (Standardized Coefficients：-0.27)were the most important factors influencing anchorage loss during treatment.Conclusion: Compared with treatment-related factors, the patient’s physiological characteristics play a more important role in anchorage loss. The pre-treatment angulation of the maxillary first molar is the most contributing factor of the maxillary molar angulation changes, which are often predisposing anchorage loss.
Construction of an Economic Activity Indicator for Turkey

ABSTRACT In this paper, a monthly economic activity indicator is constructed for the Turkish economy for the period of 1988–2020. A dynamic factor modeling framework is utilized in the process. The variables are first categorized into five types as activity (hard data), activity (survey-based data or soft data), trade, employment, and financial variables. After determining the candidate variables for each category, data selection is finalized by using the hard-thresholding method. Results indicate that our monthly economic activity indicator is successful in detecting the past recessionary periods of the Turkish economy and providing timelier information about the course of economic activity.
Comparison between urban and suburban environments

Comparison between urban and suburban environments 2 Suxia Yang1,2, Bin Yuan1,2*, Yuwen Peng1,2, Shan Huang1,2, Wei Chen3, Weiwei Hu3, 3 Chenglei Pei3,4,5,6, Jun Zhou1,2, David D. Parrish1, Wenjie Wang7, Xianjun He1,2, 4 Chunlei Cheng2,8, Xiaobing Li1,2, Xiaoyun Yang1,2, Yu Song7, Haichao Wang9, Jipeng 5 Qi1,2, Baolin Wang10, Chen Wang10, Chaomin Wang1,2, Zelong Wang1,2, Tiange Li1,2, 6 E Zheng1,2, Sihang Wang1,2, Caihong Wu1,2, Mingfu Cai1,2, Chenshuo Ye7, Wei Song3, 7 Peng Cheng7, Duohong Chen6, Xinming Wang3, Zhanyi Zhang1,2, Xuemei Wang1,2, 8 Junyu Zheng1,2, Min Shao1,2* 9
Practical Determination Method of Initial Cable Forces in Cable-Stayed Bridges

A rational method for determination of initial cable forces in cable-stayed bridges without complicated nonlinear analysis is presented. Initial shape analysis for cable-stayed bridges should be able to find optimizated initial cable forces and unstrained length that minimize deflection and vending moments of the deck and pylon. A presented method utilizing the idea of force equilibrium organizes initial shape analysis for each types of cable-stayed bridges. The results of that analysis were compared to several existing methods for 2D numerical examples. And for 3D actual bridges, the improved TCUD method was performed to demonstrate the accuracy of this study.
An Autonomous Adaptive Multiagent Model for Building Automation

Abstract A layered multiagent model is presented for the management of buildings by utilizing agent capabilities (i.e. reactive, proactive and adaptive behaviour) at various levels of automation within a building (i.e. at the physical, reactive, planning and adaptive level). A framework for the application of the model is also described, employing three different types of agents within a building: personal agents, building agents and a facilitator, which is mediating between the former agents to satisfy the needs of their human owners. Although the agents have different tasks and complexity, it is demonstrated that the presented model can be used for each of the various agents in a unified manner by taking advantage of the modularity of the model. An example application shows how the proposed agent typology can be applied to building automation so that both real-time tasks (e.g. negotiating the temperature of a room) and planning tasks (e.g. booking and customizing a room including a fee for service) can be realized.
How practice breakdowns disclose existing structures and contribute to practice innovation

Practice breakdowns provide fertile ground for practice innovation because they demand a shift from structure to process. Practice breakdowns are fruitful subjects for research and practice because they disclose existing structures by prompting situated actors to become reflective on the otherwise pervasive structures underlying their business practices. Practice breakdowns typically occur whenever there is a confrontation between the goals that situated actors aim for and the practical circumstances which they are faced and that prevent an existing business practice from continuing. This research aims to improve our understanding of how the relationship between structure and process is mediated through various degrees of practice breakdowns. Empirically, we draw on two case studies. In the first case, we examined the occurrence of practice breakdowns during the implementation of a new business activity in the context of a long-standing business relationship. The second cases concentrates on the occurrence of practice breakdowns in the practices of six nonprofits responsible for landscape maintenance. Actors at these nonprofits struggled with forthcoming drastic changes in the subsidy regime which necessitated that they adopt entrepreneurial practices and enlarge the scope of their operations from the local to a regional scale through collaboration with other nonprofits. In the research approach taken, we applied four theoretical lenses with each having its own perspective-horizon. Each lens draws on distinct foundations regarding the compositional and ontological characteristics of structure and process, which are considered the triggers of change and human agency. We used a social system, a time-based, and a socio-material perspective, applying each of these separately to the first case study. A practice-driven approach was applied in the second case study to examine simultaneously aspects of the first three lenses in practice. We report the following key findings. Firstly, the occurrence of practice breakdowns in a business relationship is critical, especially when there is an absence of a shared breakdown experience. Secondly, major practice breakdowns imply that situated actors are engaged in an a building mode of agency that permits them to reflect, articulate, and implement effective changes to current practice. Thirdly, major practice breakdowns will only lead to practice innovation if and when actors are able to reconstruct both the past and future in relation to current practice. Finally, minor practice breakdowns simply lead to the perpetuation of ongoing practices in which situated actors remain routinely engaged. Therefore, it is only major practice breakdowns that have the potential to drive effective, worthwhile and sustainable improvement in business practices.
Multimodal Guidance for Land Navigation

Abstract : This report describes the third in a series of collaborative experiments between the U.S. Army Research Laboratory and TNO Human Factors (Soesterberg, The Netherlands). In each experiment, a personal tactile navigation (PTN) system for land navigation was compared with alternate land navigation systems in wooded terrain at Fort Benning, Georgia, during high workload conditions that included secondary tasks such as radio communications, target detection, and determination of location coordinates. This report briefly summarizes results of the first and second studies and describes in further detail the third experiment which assessed navigation and target detection performance when the PTN and a hand-held commercial global positioning system (GPS) device were used singly and together. Most important are findings relevant to how systems can be used most effectively when Soldiers have both. Results demonstrate the effectiveness and high Soldier appreciation of having both systems. This report also contains Soldier recommendations for how both systems can be improved and how best to use both systems when in operations.
AN EMPIRICAL ANALYSIS OF THE TECHNOLOGY CAMEL

The new technology product adoption lifecycle (TALC) has been classified as including five groups: innovators, early adopters, early majority, late majority and laggards and is visualized as a bell curve. Ghaffari and McNurlin introduced a modification of this with their concept of the technology camel. They renamed the innovators to be Eager Beavers and the laggards to be Technically Averse and they posited that the technology camel was applicable for both individuals and organizations. The focus of this study was to investigate whether the technology camel is a good model for explaining the adoption of information technology. It was found that the adoption curve has shifted to the left, with fewer individuals/companies belonging to the technically adverse group. Moreover, the results showed that individuals are ahead of organizations in the adoption of new technologies and males are more willing to adopt new technologies than females. Possible explanations are given for the differences.
Electropolishing—A Practical Method for Accessing Voids in Metal Films for Analyses

In many applications, voids in metals are observed as early degradation features caused by fatigue. In this publication, electropolishing is presented in the context of a novel sample preparation method that is capable of accessing voids in the interior of metal thin films along their lateral direction by material removal. When performed at optimized process parameters, material removal can be well controlled and the surface becomes smooth at the micro scale, resulting in the voids being well distinguishable from the background in scanning electron microscopy images. Compared to conventional cross-sectional sample preparation (embedded mechanical cross-section or focused ion beam), the accessed surface is not constrained by the thickness of the investigated film and laterally resolved void analyses are possible. For demonstrational purposes of this method, the distribution of degradation voids along the metallization of thermo-mechanically stressed microelectronic chips has been quantified.
Analysis of Diversity And Identification of SSR, SCoT, And ITAP Informative Amplicons For Grain Fe And Zn Content In Wheat Genotypes

Biofortification provides a promising method of solving microelement malnutrition in developing countries. For this purpose, a study was conducted to understand the grain Fe and Zn content variation in seventy prevalent Iranian wheat genotypes across three consecutive years, to assess genetic diversity, and to identify informative amplicons for high grain Fe and Zn content using three simple sequence repeat (SSR), start codon targeted (SCoT) polymorphism, and intron targeted amplified polymorphism (ITAP) markers. Grain Fe and Zn content was highly variable each year with high heritability. Despite the highly significant effect of year-genotype interaction, some stable genotypes were ranked highly all the three years for grain Fe and Zn content. The grain Fe and Zn contents were positively correlated in the second and third years. High genetic diversity was detected among the wheat genotypes using three different marker systems. A number of informative SSR, SCoT, and ITAP amplicons for high grain Fe and Zn were identified overall or in individual years. A few informative amplicons were common and stable for grain Fe and Zn content in the different years. The SSR alleles located on 3A, 4A, 4B, and 6B chromosomes were positively correlated with high Fe and Zn content, indicating that co-location of genes affected Fe and Zn content. Identification of informative alleles and amplicons for high grain Fe and Zn content could contribute to the development of sequence-based markers and improve the selection of genotypes with high micronutrient content.