Miracle-dz/UniFAR-FTUs huggingface dataset:
Accurate Protein Complex Retrieval by Affinity Enrichment Mass Spectrometry (AE-MS) Rather than Affinity Purification Mass Spectrometry (AP-MS)*

Protein–protein interactions are fundamental to the understanding of biological processes. Affinity purification coupled to mass spectrometry (AP-MS) is one of the most promising methods for their investigation. Previously, complexes were purified as much as possible, frequently followed by identification of individual gel bands. However, todays mass spectrometers are highly sensitive, and powerful quantitative proteomics strategies are available to distinguish true interactors from background binders. Here we describe a high performance affinity enrichment-mass spectrometry method for investigating protein–protein interactions, in which no attempt at purifying complexes to homogeneity is made. Instead, we developed analysis methods that take advantage of specific enrichment of interactors in the context of a large amount of unspecific background binders. We perform single-step affinity enrichment of endogenously expressed GFP-tagged proteins and their interactors in budding yeast, followed by single-run, intensity-based label-free quantitative LC-MS/MS analysis. Each pull-down contains around 2000 background binders, which are reinterpreted from troubling contaminants to crucial elements in a novel data analysis strategy. First the background serves for accurate normalization. Second, interacting proteins are not identified by comparison to a single untagged control strain, but instead to the other tagged strains. Third, potential interactors are further validated by their intensity profiles across all samples. We demonstrate the power of our AE-MS method using several well-known and challenging yeast complexes of various abundances. AE-MS is not only highly efficient and robust, but also cost effective, broadly applicable, and can be performed in any laboratory with access to high-resolution mass spectrometers.
Measuring flow in an interactive tangible touch table environment

User engagement is a highly desired feature of user interfaces, yet it fails to sufficiently articulate the most extreme type of engagement - flow. The measurement of flow in this paper was motivated by action research participation at the initial field test of the "Preparing for Bushfire" touch table Tangible User Interface (TUI) (Brown et al. 2015)). It was evident that measuring engagement alone would not adequately describe and quantify the engrossed behaviour demonstrated by the general public participants. A Flow Index was constructed to measure and quantify the level of intense focus. Since no standard Flow Index exists, this paper outlines the development process of the construction of the index, including its mathematical validation. It then shows how the Flow Index was used to assess success or failure of the implemented user interface design that was strategically designed for high engagement. The flow was measured during the TUI "Preparing for Bushfire" study using 64 adult members of the general public.
Use of streambed substrate as refuge by steelhead or rainbow trout Oncorhynchus mykiss during simulated freshets.

A flume was used to estimate the carrying capacity of streambed substrates for juvenile steelhead or rainbow trout Oncorhynchus mykiss seeking refuge from simulated freshets. The simulated freshets had mean water column velocities of c. 1·1 m s(-1). The number of O. mykiss finding cover within the interstices of the substrate was documented for different substrate sizes and levels of embeddedness. The availability of suitable refuges determined the carrying capacity of the substrate for O. mykiss. For the size of the O. mykiss tested [mean ± s.d. fork length (L(F)) = 122 ± 12.6 mm], the number of interstices with depths ≥200 mm measured with a 14.0 mm diameter flexible plastic tube was the best predictor of the number of O. mykiss able to find cover (r(2) = 0.75). Oncorhynchus mykiss seeking refuge from freshets may need deeper interstices than those seeking concealment at autumn or winter base flows. The availability of interstices suitable as refuge from high flows may determine autumn and winter carrying capacity.
Three-dimensional, automated magnetic biomanipulation with subcellular resolution

In our previous work we introduced the inverted MiniMag, a magnetic manipulation system capable of 5 degree-of-freedom (5-DOF) wireless control of micro- and nano structures. In this work, we implement a depth tracking algorithm to provide feedback on the z-position of manipulated particles in the absence of a side camera. We demonstrate 3D closed-loop servoing of magnetic microbeads along predefined trajectories. We successfully position magnetic microbeads functionalized with antibodies in close proximity to macrophages with sub-cellular resolution and record the phagocytosis of the beads. We also show that the system can be used for 3D targeted microtissue manipulation inside microfabricated devices.
Logic in databases: report on the LID 2008 workshop

Th e Lo gic in Da tab ase s (LI DO0 8) w ork sh op w as h eld at th eDI S d ep artm en t of OLa S ap ien za O u n ivers ity, R om e, Italy,b etw ee n M ay 19-2 0, 2008.LI DO 08 w as estab lish ed as a foru m for b rin gin g toget h er re-se arch ers an d p rac tition ers, fro m th e acad em ia an d th e in -d u stry , wh o are fo cu sin g on all logica l asp ec ts of d ata m an -agem en t.LI DO 08 w as a con s u en ce of th ree su cce ssfu l p ast ev en ts:¥ LI DO 96,an in tern ation alw ork sh op on Lo gic in Da tab ases ,wh ich LI DO0 8 d eriv es its n am e fro m ;¥ IIDB O06, an intern ation al w ork sh op on In con sisten cyan d In com p let en ess in Da tab ase s;¥ LA A ICO 06 , an in tern ation al w orks h op on L og ical A s-p ec ts an d A p p lication s of In teg rity Co n stra ints.In ord er to gu ara n tee its con tinu ity, a S te erin g Co m m ittee,ch aired b y G eo rg G ottlob , w as fou n d ed ; its m em b ers are A n -d rea Ca l`o, Ja n Ch om ick i, H en n in g Ch ristian sen , La ks V . S . La k sh m an an , Da v id e M artin en gh i, Din o P ed res ch i, Jef Wi -jse n , an d Ca rlo Za n iolo.Th is w orks h op w as org an ized b y A n d rea C al`o, La ks V . S . La k sh m an an , an d Da v id e M artin en gh i; it attra ct ed 18 p a-p er su b m ission s ou t of wh ich 7 w ere sele ct ed for lon g p re -se n ta tion an d 6 for sh ort p re sen tation at th e w orksh op ; th ew ork sh op attra ct ed aro u n d 50 reg istered p articip an ts. De-tails an d p res en tation s are availab le at th e w orks h op W ebsite: http://conferenze.dei. polimi.it/lid2008/.
A New Ultralightweight RFID Authentication Protocol with Permutation

One of the key problems in RFID is security and privacy. The implementation of authentication protocols is a flexible and effective way to solve this problem. This letter proposes a new ultralightweight RFID authentication protocol with permutation (RAPP). RAPP avoids using unbalanced OR and AND operations and introduces a new operation named permutation. The tags only involve three operations: bitwise XOR, left rotation and permutation. In addition, unlike other existing ultralightweight protocols, the last messages exchanged in RAPP are sent by the reader so as to resist de-synchronization attacks. Security analysis shows that RAPP achieves the functionalities of the authentication protocol and is resistant to various attacks. Performance evaluation illustrates that RAPP uses fewer resources on tags in terms of computation operation, storage requirement and communication cost.
Designing of an e-learning system using adaptivity and gamification

This paper proposes the design of an adaptive e- learning system with gamification elements. In the context of the increasing need to keep learners motivated among so many distractions, our project aims to help a user acquire knowledge at his own pace, in a captivating environment and as flexible as possible. To achieve that the solution focuses on the course model, adaptive questions and a reward system using levels and points. The course model is based on knowledge items. Questions test the understanding of the knowledge items in the course. The questions' difficulty is personalized on the progress of each learner. The project was tested in a campus over a course of one week with positive results.
Common Polymorphism in the LRP5 Gene May Increase the Risk of Bone Fracture and Osteoporosis

The low-density lipoprotein receptor-related protein 5 gene (LRP5) was identified to be linked to the variation in bone mineral density and types of bone diseases. The present study was aimed at examining the association of LRP5 rs3736228 C>T gene with bone fracture and osteoporosis by meta-analysis. A systematic electronic search of literature was conducted to identify all published studies in English or Chinese on the association of the LRP5 gene with bone fracture and osteoporosis risks. All analyses were calculated using the Version 12.0 STATA software. Odds ratios (ORs) and their corresponding 95% confidence interval (95% CI) were calculated. An updated meta-analysis was currently performed, including seven independent case-control studies. Results identified that carriers of rs3736228 C>T variant in the LRP5 gene were associated with an increased risk of developing osteoporosis and fractures under 4 genetic models but not under the dominant model (OR = 1.19, 95% CI = 0.97~1.46, and P = 0.103). Ethnicity-subgroup analysis implied that LRP5 rs3736228 C>T mutation was more likely to develop osteoporosis and fractures among Asians and Caucasians in majority of subgroups. These results suggest that there is a modest effect of the LRP5 rs3736228 C>T on the increased susceptibility of bone fracture and osteoporosis.
Approximate Processing in Real-Time Problem Solving

WE PROPOSE AN APPROACH FOR MEETING REAL-TIME CONSTRAINTS IN AI SYSTEMS THAT VIEWS (1) TIME AS A RESOURCE THAT SHOULD BE CONSIDERED WHEN MAKING CONTROL DECISIONS, (2) PLANS AS WAYS OF EXPRESSING CONTROL DECISIONS, AND (3) APPROXIMATE PROCESSING AS A WAY OF SATISFYING TIME CONSTRAINTS THAT CANNOT BE ACHIEVED THROUGH NORMAL PROCESSING. IN THIS APPROACH, A REAL-TIME PROBLEM SOLVER ESTIMATES THE TIME REQUIRED TO GENERATE SOLUTIONS AND THEIR QUALITY. THIS ESTIMATE PERMITS THE SYSTEM TO ANTICIPATE WHETHER THE CURRENT OBJECTIVES WILL BE MET IN TIME. THE SYSTEM CAN THEN TAKE CORRECTIVE ACTION BY FORMING LOWER QUALITY SOLUTIONS WITHIN TIME CONSTRAINTS. THIS MAY INVOLVE MODIFYING EXISTING PLANS OR FORMING RADICALLY DIFFERENT PLANS THAT UTILIZE ONLY ROUGH DATA CHARACTERISTICS AND APPROXIMATE KNOWLEDGE TO ACHIEVE A DESIRED SPEEDUP. A DECISION ABOUT HOW TO CHANGE PROCESSING SHOULD BE SITUATION-DEPENDENT, BASED ON THE CURRENT STATE OF PROCESSING AND ON DOMAIN-DEPENDENT SOLUTION CRITERIA. WE PRESENT PRELIMINARY EXPERIMENTS THAT SHOW HOW APPROXIMATE PROCESSING HELPS A VEHICLE-MONITORING PROBLEM SOLVER MEET DEADLINES, AND OUTLINE A FRAMEWORK FOR FLEXIBLY MEETING REAL-TIME CONSTRAINTS.
Using a Dual-Sourcing Option in the Presence of Asymmetric Information about Supplier Reliability: Competition vs. Diversification

We study a buyer's strategic use of a dual-sourcing option when facing suppliers possessing private information about their disruption likelihood. We solve for the buyer's optimal procurement contract. We show that the optimal contract can be interpreted as the buyer choosing between diversification and competition benefits. Better information increases diversification benefits and decreases competition benefits. Therefore, with better information the buyer is more inclined to diversify. Moreover, better information may increase or decrease the value of the dual-sourcing option, depending on the buyer's unit revenue: for large revenue, the buyer uses the dual sourcing option for diversification, the benefits of which increase with information; for small revenue, the buyer uses the dual sourcing option for competition, the benefits of which decrease with information. Surprisingly, as the reliability of the entire supply base decreases, the buyer may stop diversifying under asymmetric information (to leverage competition), whereas it would never do so under symmetric information. Finally, we analyze the effect of codependence between supply disruptions. We find that lower codependence leads the buyer to rely less on competition. Because competition keeps the information costs in check, a reduction in supplier codependence increases the buyer's value of information. Therefore, strategic actions to reduce codependence between supplier disruptions should not be seen as a substitute for learning about suppliers' reliabilities.
Design and evaluation of a wearable AR system for sharing personalized content on ski resort maps

Winter sports like skiing and snowboarding are often group activities. Groups of skiers and snowboarders traditionally use paper maps or board-mounted larger-scale maps near ski lifts to aid decision making: which slope to take next, where to have lunch, or what hazards to avoid when going off-piste. To enrich those static maps with personal content (e.g., pictures, prior routes taken, or hazards encountered), we developed SkiAR - a wearable augmented reality system that allows groups of skiers and snowboarders to share such content on a printed panoramic resort map. The contribution of our work is twofold: (1) we developed a system that offers a novel way to review and share personal content in situ while on the slope using a resort map; (2) we report on the results from a qualitative analysis of two user studies to inform the design and validate the usability and perceived usefulness of our prototype.
FRIENDSHIP TYPE, CLIQUE FORMATION AND THE EVERYDAY USE OF COMMUNICATION TECHNOLOGIES IN A PEER GROUP

This study focuses on teens' use of communication technologies to maintain connections with people from their everyday peer group. It departs from a pre-defined network (in a secondary school in Flanders, Belgium) and investigates how friendship type and clique formation (an important dynamic in this (micro) context) are related to face-to-face communication (FTFC) and the use of email, instant messaging, text messaging, telephone and social network sites in this network. Hypotheses/expectations were derived from network theory and (qualitative and quantitative) studies on the social affordances of communication technologies for adolescents. Data were collected among the 78 pupils of a fourth grade (15–16-year-olds) in a Belgian secondary school. First, dyadic quadratic assignment procedure regression analyses were run to explain the frequency of FTFC and communication through different technologies by looking at dyad characteristics (strength of ties, number of friends in common, same sex…). Second, FTFC.
Investigating bottom-up auditory attention

Bottom-up attention is a sensory-driven selection mechanism that directs perception toward a subset of the stimulus that is considered salient, or attention-grabbing. Most studies of bottom-up auditory attention have adapted frameworks similar to visual attention models whereby local or global “contrast” is a central concept in defining salient elements in a scene. In the current study, we take a more fundamental approach to modeling auditory attention; providing the first examination of the space of auditory saliency spanning pitch, intensity and timbre; and shedding light on complex interactions among these features. Informed by psychoacoustic results, we develop a computational model of auditory saliency implementing a novel attentional framework, guided by processes hypothesized to take place in the auditory pathway. In particular, the model tests the hypothesis that perception tracks the evolution of sound events in a multidimensional feature space, and flags any deviation from background statistics as salient. Predictions from the model corroborate the relationship between bottom-up auditory attention and statistical inference, and argues for a potential role of predictive coding as mechanism for saliency detection in acoustic scenes.
Efficient fat suppression by slice-selection gradient reversal in twice-refocused diffusion encoding

Most diffusion imaging sequences rely on single‐shot echo‐planar imaging (EPI) for spatial encoding since it is the fastest acquisition available. However, it is sensitive to chemical‐shift artifacts due to the low bandwidth in the phase‐encoding direction, making fat suppression necessary. Often, spectral‐selective RF pulses followed by gradient spoiling are used to selectively saturate the fat signal. This lengthens the acquisition time and increases the specific absorption rate (SAR). However, in pulse sequences that contain two slice‐selective 180° refocusing pulses, the slice‐selection gradient reversal (SSGR) method of fat suppression can be implemented; i.e., using slice‐selection gradients of opposing polarity for the two refocusing pulses. We combined this method with the twice‐refocused spin‐echo sequence for diffusion encoding and tested its performance in both phantoms and in vivo. Unwanted fat signal was entirely suppressed with this method without affecting the water signal intensity or the slice profile. Magn Reson Med 60:1256–1260, 2008. © 2008 Wiley‐Liss, Inc.
Effect of Cognitive Mindfulness Practice Program on Depression among Elderly Thai Women

บทคดยอ ภาวะซมเศราเปนปญหาทางสขภาพจตทสำคญอยางยงในปจจบนและเปนสาเหตสำคญของความทกขและความสญเสยความสามารถโดยเฉพาะในผสงอาย ผหญงไทยสงอายมโอกาสเสยง ตอภาวะซมเศรามากกวาผชาย การวจยครงนเปนการวจยเชงทดลองแบบสองกลมเพอศกษาผลของโปรแกรมการบำบดทางสตและปญญาตอภาวะซมเศราในผหญงไทยสงอายทมภาวะซมเศราในระดบปานกลางและตำ โดยเปรยบเทยบกบผหญงไทยสงอายทไดรบการดแลตามปกตในชมชนจงหวดเชยงใหม โดยสมกลมตวอยางเขากลมทดลองและกลมควบคม กลมทดลองไดรบโปรแกรมการบำบดทางสตและปญญาทผวจยสรางขน สำหรบกลมควบคมไดรบการดแลดานจตใจและไดรบการพยาบาลตามปกตจากพยาบาลชมชน กลมตวอยางไดรบประเมนระดบความรนแรงของภาวะซมเศรากอนการทดลอง หลงเขารวมโปรแกรมทนท และ 3 เดอนหลงเขารวมโปรแกรมวเคราะหขอมลโดยใชสถตบรรยาย การวเคราะหความแปรปรวนแบบสองทางเมอมการวดซำ การทดสอบคาเฉลยสองกลมอสระตอกนและการวเคราะหความแปรปรวนรวม ผลการวจยพบวาหลงเขารวมโปรแกรม และ 3 เดอนหลงเขารวมโปรแกรม กลมทดลองทไดรบโปรแกรมการบำบด ทางสตและปญญามภาวะซมเศราลดลงอยางมาก เมอเปรยบเทยบกบกลมทไมไดรบโปรแกรม ผลการวจยครงนแสดงใหเหนวา โปรแกรมการบำบดทางสตและปญญาสามารถลดภาวะซมเศราในผหญงไทยสงอาย พยาบาลทมความร และผานการฝกอบรมสามารถใชโปรแกรมการบำบดทางสตและปญญาซงเปนการบำบดโดยไมใชยาและเหมาะสมกบวฒนธรรมสำหรบการบำบดผหญงไทยสงอายทมภาวะซมเศราในระดบปานกลางและตา คำสำคญ: โปรแกรมการบำบดทางสตและปญญา ผหญงไทยสงอาย ภาวะซมเศรา Abstract Depression is a leading mental health problem and a significant contributor to human suffering and disability, especially among the elderly. Elderly women are known to be more prone to depression than are men. Using a two group, pretest-posttest, control group design, this study sought to determine if a cognitive mindfulness practice program reduced depression among elderly Thai women, with mild to moderate depression, receiving care at a community center in Chiang Mai. Participants were randomly assigned to either the experimental or control group. The experimental group participated in a cognitive mindfulness practice program developed by the primary researcher. The control group received typical emotional support and nursing care from community nurses at the community center. Each participant’s level of depression was assessed: (a) prior to the start of the program’s protocol; (b) upon program completion; and, (c) three months thereafter. Data were analyzed using descriptive statistics, two-way mixed-design ANOVA, independent sample t-test and ANCOVA. Those who participated in the cognitive mindfulness practice program, compared to those who did not participate in the program, had a greater decrease in depression scores upon completion of the program and three months after completion of the program. Findings suggest the program may have contributed to changes in the level of depression among those who participated in the program. Nurses educated, and trained, in the use of the cognitive mindfulness program, potentially, could provide a non-biological, culturally appropriate intervention for the treatment of mild to moderate depression among elderly Thai women. Keywords: cognitive mindfulness practice program, depression, elderly Thai women
Quality and Quantity Revisited

Abstract This paper attempts to discuss the qualitative methodological approach of Jack Katz in its historical framework of production. In doing so, we aim to analyze the actual relevance of these discussions and their impact in the qualitative-quantitative dilemma. Revisiting Katz's ideas and complementing them with some critical remarks about the limits, misuses and biases of the four R's (representativeness, reactivity, reliability and replicability) in quantitative research implies a significant contribution to the understanding of qualitative research's value in its own terms. In many ways, Katz's methodological ideas anticipate later developments.
Are rural women powerless when it comes to HIV and AIDS risk? Implications for adult education programmes in South Africa.

There is an urgent need for fresh approaches to HIV&AIDS education for adults and youth in South Africa particularly for those marginalised by society such as rural black women. In this article we explore the factors which affect awareness condom use and HIV&AIDS risk among a group of women who attend classes in a rural Adult Education Centre in Limpopo province. We seek a better understanding of the factors which affect womens decisions and behaviour. In particular we examine the notion that women are powerless to protect themselves. We draw on theories of gender and power relations to emphasise that women can and do exercise power particularly at microlevel. Data were collected by means of focus group discussions with two groups of adult learners and through interviews with teachers and government officials. The article concludes by suggesting strategies for use in rural Adult Education Centres to empower women to deal with HIV&AIDS. (authors)
Transformation of the pectoral girdle in the evolutionary origin of frogs: insights from the primitive anuran Discoglossus

Using cleared‐and‐stained whole mounts and computer‐aided three‐dimensional reconstructions made from serial histological sections, we studied the development of the pectoral girdle in Discoglossus pictus, an extant member of an ancient frog lineage, represented for example by Eodiscoglossus from the Middle Jurassic to Early Cretaceous periods in Europe. Basic developmental features were compared with those of extinct Temnospondyli, considered to be the most probable anuran ancestors, and with Triadobatrachus, an early Triassic proanuran. In the endochondral girdle, the separate scapula and coracoid of Discoglossus and other anurans (completed by suprascapular and procoracoid cartilages) evolved from the compact scapulocoracoid of temnospondyls by paedomorphosis. In parallel, the dermal ossifications of the girdle were reduced to a small clavicle and cleithrum. The overall reduction in ossification of the anuran pectoral girdle supports the hypothesis of a paedomorphic origin for Anura. The almost simultaneous appearance of dermal and endochondral ossifications may be explained by the accumulation of developmental events during a short, distinct metamorphosis (which did not occur in neotenic temnospondyls living permanently in water). The sternal elements seem to be neomorphs for the most part, which help to cushion the shock of landing in jumping anurans but which also evolved as functional substitutes (insertion area for the pectoralis muscles) of the temnospondyl interclavicle.