Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluation of Quantitative Structure-Activity Relationship Methods for Large-Scale Prediction of Chemicals Binding to the Estrogen Receptor

Three different QSAR methods, Comparative Molecular Field Analysis (CoMFA), classical QSAR (utilizing the CODESSA program), and Hologram QSAR (HQSAR), are compared in terms of their potential for screening large data sets of chemicals as endocrine disrupting compounds (EDCs). While CoMFA and CODESSA (Comprehensive Descriptors for Structural and Statistical Analysis) have been commercially available for some time, HQSAR is a novel QSAR technique. HQSAR attempts to correlate molecular structure with biological activity for a series of compounds using molecular holograms constructed from counts of sub-structural molecular fragments. In addition to using r2 and q2 (cross-validated r2) in assessing the statistical quality of QSAR models, another statistical parameter was defined to be the ratio of the standard error to the activity range. The statistical quality of the QSAR models constructed using CoMFA and HQSAR techniques were comparable and were generally better than those produced with CODESSA. It is notable that only 2D-connectivity, bond and elemental atom-type information were considered in building HQSAR models. Since HQSAR requires no conformational analysis or structural alignment, it is straightforward to use and lends itself readily to the rapid screening of large numbers of compounds. Among the QSAR methods considered, HQSAR appears to offer many attractive features, such as speed, reproducibility and ease of use, which portend its utility for prioritizing large numbers of potential EDCs for subsequent toxicological testing and risk assessment.
An Experimental Test of Insect-Mediated Colonisation of Damaged Pinus radiata Trees by Sapstain Fungi

Vector-pathogen dynamics play a central role in understanding tree health and forest dynamics. There is substantial evidence that bark beetles act as spore vectors for many species of fungi that cause ‘sapstain’ discolouration of damaged trees and timber. However, the direct quantitative link between vector-mediated spore dispersal and subsequent sapstain colonisation of wood is not fully understood. Here, we used caged versus uncaged experimental logs to test whether the exclusion of bark beetles quantitatively alters the distribution and intensity of sapstain fungal spread within damaged trees. Using generalised linear mixed models, we tested the effect of bark beetle exclusion on sapstain intensity within and among cut logs at two plantation forest sites. Overall, sapstain was found on all logs regardless of caging treatment, indicating that sapstain colonisation can occur (to some degree) without arthropod vectors, probably via wind, rain-splash and, potentially, latent endophytic development. This was supported by the dominance of Diplodia pinea in fungal isolations taken from trees felled at the site, as this fungal species is known to disperse independently of bark beetles. However, the intensity of sapstain within and among experimental logs was significantly greater in uncaged than in caged logs, where beetle colonisation was significantly greater. This appeared to be driven by a significant within-log association between the intensity of staining and the intensity of beetle, and other arthropod, tunnelling and feeding activities. Taken together, these results strongly suggest that the dominant mechanism underlying the role of bark beetles in sapstain development in this study system is not vector-mediated spore dispersal, per se, but rather the facilitation of spore entry and hyphal development through tunnelling and feeding activities. We discuss the implications of these findings for forest management and the effective salvage-harvest of trees damaged by stochastic climate events such as storm and fire damage.
Inline process characterization and control for robust BEOL reliability

In advanced technology node, the complexity of process, materials selection and limitation of tools' capability, becomes very challenging with respect to meet tight reliability targets. In our fabrication of low-k based BEOL integration scheme, we have demonstrated that by proper inline process characterization, feedback and control at critical process modules, a robust Time Dependent Dielectric Breakdown (TDDB) and Electromigration (EM) performance can be achieved. In this paper, we proposed a working model with inline process parameters characterization, reliability performance evaluation, root causes identification and solutions, to establish a relationship between inline process parameters and BEOL TDDB, EM performance. Our data shows that, to pass TDDB E-model (field driven), Mx final critical dimension (FCD) must be within very tight control of less than FCD target + 0.5nm, and greater than FCD target − 2nm. On the other hand, to pass TDDB SQRT E-model, FCD target − 2nm < Mx FCD < FCD target + 6nm control is required. To pass EM, Mx FCD > FCD target − 2nm is needed. Through this working model, we are able to justify and identify the critical process modules and to determine the process window to achieve robust BEOL TDDB and EM performance.
Intraoperative Ultrasound Guidance Is Associated with Clear Lumpectomy Margins for Breast Cancer: A Systematic Review and Meta-Analysis

Purpose Margin status is one of the most important predictors of local recurrence after breast conserving surgery (BCS). Intraoperative ultrasound guidance (IOUS) has the potential to improve surgical accuracy for breast cancer. The purpose of the present meta-analysis was to determine the efficacy of IOUS in breast cancer surgery and to compare the margin status to that of the more traditional Guide wire localization (GWL) or palpation-guidance. Methods We searched the database of PubMed for prospective and retrospective studies about the impact of IOUS on margin status of breast cancer, and a meta-analysis was conducted. Results Of the 13 studies included, 8 were eligible for the impact of IOUS on margin status of non-palpable breast cancers, 4 were eligible for palpable breast cancers, and 1 was for both non-palpable and palpable breast cancers. The rate of negative margins of breast cancers in IOUS group was significantly higher than that in control group without IOUS (risk ratio (RR) = 1.37, 95% confidence interval (CI) = 1.18–1.59 from 7 prospective studies, odds ratio (OR) = 2.75, 95% CI = 1.66–4.55 from 4 retrospective studies). For non-palpable breast cancers, IOUS-guidance enabled a significantly higher rate of negative margins than that of GWL-guidance (RR = 1.26, 95% CI = 1.09–1.46 from 6 prospective studies; OR = 1.45, 95% CI = 0.86–2.43 from 2 retrospective studies). For palpable breast cancers, relative to control group without IOUS, the RR for IOUS associated negative margins was 2.36 (95% CI = 1.26–4.43) from 2 prospective studies, the OR was 2.71 (95% CI = 1.25–5.87) from 2 retrospective studies. Conclusion This study strongly suggests that IOUS is an accurate method for localization of non-palpable and palpable breast cancers. It is an efficient method of obtaining high proportion of negative margins and optimum resection volumes in patients undergoing BCS.
Control of fracture reduction robot based on biomechanical property of human leg

For femoral fracture reduction, we have developed a surgical robotic system. Indirect traction is employed in our system. Indirect traction in fracture reduction is a generally used surgical method for preventing complications such as bone splits caused by high stress on bones. For traction, a patientpsilas foot is gripped by a jig and pulled to the distal side. Indirect traction has the advantage of distributing bone stress by utilizing a strong traction force; however, this procedure does not accurately control the proper positioning of fractured fragments when a surgical robot is used. The human leg has knee and an ankle joints, and thus robotic motion presents problems in not being able to directly propagate reduction motion to a fractured femoral fragment, rendering control of bone position difficult. We propose two control methods for fracture reduction robots using external force/torque measurements of the human leg. First proposed method is using a transform function which transform from a force/torque space to a position space. Second is using a simple ligament model. Results showed that the first proposed method reduced repositioning error from 6.8 mm and 15.9 degrees to 0.7 mm and 5.3 degrees and second reduced from 2.1 mm to 0.9 mm.
Reduction of AC loss in Ag sheathed PbBi2223 tapes with twisted filaments in external and self-fields

The hysteretic AC losses in multifilament tapes can be reduced by filament twisting with a pitch shorter than a critical pitch which is dependent upon the material parameters of the tape and dB/dt. To determine the effectiveness of twisting, measurements of AC losses have been carried out on Ag sheathed multifilamentary PbBi2223 tapes with different twist pitches (minimum 10 mm). Self-field loss measurements showed clear uncoupling of filaments for current up to 50% of Ic for a twist pitch shorter than 15 mm. In parallel external fields, the effect of filaments uncoupling by twisting was identified with 10 mm pitch showing a reduction in the hysteretic loss of the superconducting core, at power frequency, between 10 mT and 35 mT. This corresponds well with the theoretical predictions for a tape with a twist pitch of 10 mm and Ic=40 A (/spl sim/20 kAcm/sup -2/) operating at 43 Hz. We also observed that the losses in the normal matrix are dominant for fields above 30 mT although losses in the superconductor are reduced by twisting.
Global convergence of trust-region algorithms for constrained minimization without derivatives

In this work we propose a trust-region algorithm for the problem of minimizing a function within a convex closed domain. We assume that the objective function is differentiable but no derivatives are available. The algorithm has a very simple structure and allows a great deal of freedom in the choice of the models. Under reasonable assumptions for derivative-free schemes, we prove global convergence for the algorithm, that is to say, that all accumulation points of the sequence generated by the algorithm are stationary.
Getting along: composition of visualization paradigms

This paper describes how focus+context techniques can be composed with other high-level visualization paradigms to mutual advantage. Examples are given showing composition both with a pan\&zoom system, and with a treemap implementation. The examples illustrate how focus+context can be used as an exploration and navigation tool within those paradigms.
A Longitudinal Twin Study of the Direction of Effects between ADHD Symptoms and IQ

While the negative association between ADHD symptoms and IQ is well documented, our knowledge about the direction and aetiology of this association is limited. Here, we examine the association of ADHD symptoms with verbal and performance IQ longitudinally in a population-based sample of twins. In a population-based sample of 4,771 twin pairs, DSM-IV ADHD symptoms were obtained from the Conners’ Parent Rating Scale-Revised. Verbal (vocabulary) and performance (Raven’s Progressive Matrices) IQ were assessed online. ADHD symptom ratings and IQ scores were obtained at ages 12, 14 and 16 years. Making use of the genetic sensitivity and time-ordered nature of our data, we use a cross-lagged model to examine the direction of effects, while modelling the aetiologies of the association between ADHD symptoms with vocabulary and Raven’s scores over time. Although time-specific aetiological influences emerged for each trait at ages 14 and 16 years, the aetiological factors involved in the association between ADHD symptoms and IQ were stable over time. ADHD symptoms and IQ scores significantly predicted each other over time. ADHD symptoms at age 12 years were a significantly stronger predictor of vocabulary and Raven’s scores at age 14 years than vice versa, whereas no differential predictive effects emerged from age 14 to 16 years. The results suggest that ADHD symptoms may put adolescents at risk for decreased IQ scores. Persistent genetic influences seem to underlie the association of ADHD symptoms and IQ over time. Early intervention is likely to be key to reducing ADHD symptoms and the associated risk for lower IQ.
Acetylcholine receptor distribution on myotubes in culture correlated to acetylcholine sensitivity.

1. A linear relation, with a slope of 0‐9 +/‐ 0‐2 on a log‐log plot, was obtained between acetylcholine (ACh) sensitivity and alpha‐bungarotoxin (alpha‐BTX) binding site density in developing L6 and rat primary myotubes. ACh sensitivity was defined as g/Qn where g is conductance, Q is ACh charge and n is the Hill coefficient. Experimentally we found n approximately 1‐7 for our myotubes, which is similar in value to that reported for adult systems. 2. The linear relationship is compatible with an organization whereby each ion channel is always complexed with a fixed number of ACh receptors such that the dose‐response characteristics of each such complex are independent of average ACh receptor density. 3. Light microscope autoradiography showed that the alpha‐bungarotoxin binding sites on L6 myotubes are uniformly distributed over the surface, while primary rat myotubes exhibit gradients and hot spots. Electron microscope autoradiography indicated that about 70% of the [125I]alpha‐bungarotoxin label was on the surface of the myotubes. The alpha‐bungarotoxin site density, after subtracting myoblast background, varied from 5 to 400 sites/micrometer2 on different L6 myotubes, and from 54 to 900 sites/micrometer2 on primary rat myotubes, with occasional hot spots of 3000‐4000 sites/micrometer2. The conductance sensitivities varied from 10(‐4) to 2 X 10(‐2) Momega‐1/nC1‐7.
A Recurrent Germline Mutation in the 5’UTR of the Androgen Receptor Causes Complete Androgen Insensitivity by Activating Aberrant uORF Translation

A subset of patients with monogenic disorders lacks disease causing mutations in the protein coding region of the corresponding gene. Here we describe a recurrent germline mutation found in two unrelated patients with complete androgen insensitivity syndrome (CAIS) generating an upstream open reading frame (uORF) in the 5’ untranslated region (5’-UTR) of the androgen receptor (AR) gene. We show in patient derived primary genital skin fibroblasts as well as in cell-based reporter assays that this mutation severely impacts AR function by reducing AR protein levels without affecting AR mRNA levels. Importantly, the newly generated uORF translates into a polypeptide and the expression level of this polypeptide inversely correlates with protein translation from the primary ORF of the AR thereby providing a model for AR-5′UTR mediated translational repression. Our findings not only add a hitherto unrecognized genetic cause to complete androgen insensitivity but also underline the importance of 5′UTR mutations affecting uORFs for the pathogenesis of monogenic disorders in general.
Using ICT to Reduce Transaction Costs in Agriculture through Better Communication: A Case Study from Sri Lanka

This paper considers the specific role of information and communication technologies [ICT] in reducing transaction costs in agriculture by enabling timely and affordable communication. Segmenting transaction costs in to several components, the paper isolates the costs associated with information search as the specific costs that could be influenced through ICT. Analyzing the findings of a case study among a group of smallholder vegetable farmers in Sri Lanka the paper identifies the specific information needs of these farmers along the agriculture value chain starting with the decision on the crop to be planted and ending with the sale of produce at the wholesale market and measures the information search costs associated with this group of farmers. The paper concludes by indicating the possibility of dramatic reductions of transaction costs with the use of ICT to reduce information search costs to enable greater farmer participation in commercial agriculture as opposed to subsistence farming that continue to force so many farmers in developing countries in to poverty.
Case Study Report: Agile Product Management at Planon

Abstract With the advent of agile development methods such as SCRUM, the unpredictable and dynamic process of softwaredevelopment has for the rst time become manageable in an ecient manner. It is no surprise that these devel-opments have resulted in an increased interest in the expansion of agile principles to other domains. One of thesedomains is product management, which involves mainly the elicitation, selection and prioritization of requirementsas input for the development process. Up until now, sparse literature has been published concerning attempts toimplement an agile product management process. In this work, we present the unique case of a company thatsuccessfully implemented an agile product management process. In this technical report we describe the relevantconcepts, the product management and product development processes, and the lessons learned from implementingagile product management. 1 Introduction One of the major innovations in software development methodology of the last few years hasbeen the introduction of agile principles. Since the creation of the Agile Manifesto in 2001, in-cluding the years leading to its creation, several agile software development methods have beendeveloped (Abrahamsson et al., 2003). Examples of such methods are DSDM (Stapleton, 1999),Extreme Programming (Beck, 1999) and Feature Driven Development (Palmer & Felsing, 2002). The strong points of such methods are that by employing them, the development process becomesmore responsive to a changing environment, working software is chosen over extensive documen-tation, individuals and interactions are considered more important than tools and processes, andcustomer collaboration is valued more than contract negotiation
Sensory Attributes of Complex Tasting Divalent Salts Are Mediated by TRPM5 and TRPV1 Channels

Complex tasting divalent salts (CTDS) are present in our daily diet, contributing to multiple poorly understood taste sensations. CTDS evoking metallic, bitter, salty, and astringent sensations include the divalent salts of iron, zinc, copper, and magnesium. To identify pathways involved with the complex perception of the above salts, taste preference tests (two bottles, brief access) were performed in wild-type (WT) mice and in mice lacking (1) the T1R3 receptor, (2) TRPV1, the capsaicin receptor, or (3) the TRPM5 channel, the latter being necessary for the perception of sweet, bitter, and umami tasting stimuli. At low concentrations, FeSO4 and ZnSO4 were perceived as pleasant stimuli by WT mice, and this effect was fully reversed in TRPM5 knock-out mice. In contrast, MgSO4 and CuSO4 were aversive to WT mice, but for MgSO4 the aversion was abolished in TRPM5 knock-out animals, and for CuSO4, aversion decreased in both TRPV1- and TRPM5-deficient animals. Behavioral tests revealed that the T1R3 subunit of the sweet and umami receptors is implicated in the hedonically positive perception of FeSO4 and ZnSO4. For high concentrations of CTDS, the omission of TRPV1 reduced aversion. Imaging studies on heterologously expressed TRPM5 and TRPV1 channels are consistent with the behavioral experiments. Together, these results rationalize the complexity of metallic taste by showing that at low concentrations, compounds such as FeSO4 and ZnSO4 stimulate the gustatory system through the hedonically positive T1R3–TRPM5 pathway, and at higher concentrations, their aversion is mediated, in part, by the activation of TRPV1.
PROBABILISTIC MODEL BASED IMAGE SEGMENTATION

There exists a plethora of algorithms to perform image segmentation and there are several issues related to execution time of these algorithms. Image Segmentation is nothing but label relabeling problem under probability framework. To estimate the label configuration, an iterative optimization scheme is implemented to alternately carry out the maximum a posteriori (MAP) estimation and the maximum likelihood (ML) estimations. In this paper this technique is modified in such a way so that it performs segmentation within stipulated time period. The extensive experiments shows that the results obtained are comparable with existing algorithms. This algorithm performs faster execution than the existing algorithm to give automatic segmentation without any human intervention. Its result match image edges very closer to human perception.
A longitudinal analysis of the behavioural patterns in teachers using blogs for knowledge interactions

Introduction Compared to traditional online forums, blogs have features such as knowledge-filtering, personal logs, and digital notebooks (Blood, 2002). Many researches explored the applications of blogs in education (e.g., Churchill, 2009), and the feasibility of using blogs as a tool for professional development was discussed (e.g., Hou et al., 2009). By analyzing interactions recorded on teacher-blogs, we may explore the behavioral patterns of teachers using blogs. However, long-term, large-scale empirical longitudinal researches on teachers’ interactions in blogs are still quite limited. Using cluster analysis, we can place interaction behaviors into different clusters, and this allows us to explore different types of interactions as well as their proportions, characteristics and limitations. Therefore, this study applied cluster analysis to explore the behavioral patterns among 11,724 teachers on the 107 teacher-blogs for 46 months in Taiwan and discuss potential interaction-related limitations. We then propose suggestions for teacher-trainers in their use of blogs for professional development.
"Are you watching this film or what?": interruption and the juggling of cohorts

A proliferation of mobile devices in everyday life has increased the likelihood of technologically mediated interruptions. We examine ethnographic data from an SMS-based pervasive game in order to explicate the situated character of interruption. Ethnomethodological analysis of gameplay in the context of participants' everyday lives shows that interruption handling is shaped by its accountability to the various people or 'cohorts' whose concerns participants need to juggle simultaneously. Findings inform existing approaches to design where certain presuppositions regarding the nature of interruption prevail. Accordingly, we propose an approach to interruption handling that respects the ways in which people orient to and reason about interruptions locally in the conduct of situated action.
Book Reviews: Computational and Conversational Discourse: Burning Issues-An Interdisciplinary Account

The array of perspectives from which discourse processing is pursued can be mindboggling to students of discourse, both new and experienced. We are bombarded with concepts from various arenas that require sorting out: topic and focus, given and new, cohesion and coherence; the list goes on. Many questions loom for the computational linguistics (CL) researcher. What do notions such as topic and focus and given and new have to say about how discourses are interpreted, as modeled by formal approaches to coherence resolution? More generally, do works from traditionally functional perspectives contain deep insights, obscured by the lack of formal tools necessary to make them concrete, or does the articulate yet complex prose in these works obscure a lack of methodological rigor in their analyses? Is it time to follow other subdisciplines within CL and eschew theoretical work in favor of purely empirical approaches, or would such a move be wildly premature? Computational and Conversational Discourse, an outgrowth of a workshop entitled "Burning Issues in Discourse" held in April 1993 in Maratea, Italy, captures a snapshot of current discourse studies at the breadth necessary to begin addressing these questions.