Miracle-dz/UniFAR-FTUs huggingface dataset:
Defect-Tolerant Design and Optimization of a Digital Microfluidic Biochip for Protein Crystallization

Protein crystallization is a commonly used technique for protein analysis and subsequent drug design. It predicts the 3-D arrangement of the constituent amino acids, which in turn indicates the specific biological function of a protein. Protein crystallization experiments are typically carried out in well-plates in the laboratory. As a result, these experiments are slow, expensive, and error-prone due to the need for repeated human intervention. Recently, droplet-based ¿digital¿ microfluidics have been used for executing protein assays on a chip. Protein samples in the form of nanoliter-volume droplets are manipulated using the principle of electrowetting-on-dielectric. We present the design of a multi-well-plate microfluidic biochip for protein crystallization; this biochip can transfer protein samples, prepare candidate solutions, and carry out crystallization automatically. To reduce the manufacturing cost of such devices, we present an efficient algorithm to generate a pin-assignment plan for the proposed design. The resulting biochip enables control of a large number of on-chip electrodes using only a small number of pins. Based on the pin-constrained chip design, we present an efficient shuttle-passenger-like droplet manipulation method and test procedure to achieve high-throughput and defect-tolerant well loading.
A novel context for the ‘MutT’ module, a guardian of cell integrity, in a diphosphoinositol polyphosphate phosphohydrolase

Diphosphoinositol pentakisphosphate (PP‐InsP5 or ‘InsP7’) and bisdiphosphoinositol tetrakisphosphate ([PP]2‐InsP4 or ‘InsP8’) are the most highly phosphorylated members of the inositol‐based cell signaling family. We have purified a rat hepatic diphosphoinositol polyphosphate phosphohydrolase (DIPP) that cleaves a β‐phosphate from the diphosphate groups in PP‐InsP5 (Km = 340 nM) and [PP]2‐InsP4 (Km = 34 nM). Inositol hexakisphophate (InsP6) was not a substrate, but it inhibited metabolism of both [PP]2‐InsP4 and PP‐InsP5 (IC50 = 0.2 and 3 μM, respectively). Microsequencing of DIPP revealed a ‘MutT’ domain, which in other contexts guards cellular integrity by dephosphorylating 8‐oxo‐dGTP, which causes AT to CG transversion mutations. The MutT domain also metabolizes some nucleoside phosphates that may play roles in signal transduction. The rat DIPP MutT domain is conserved in a novel recombinant human uterine DIPP. The nucleotide sequence of the human DIPP cDNA was aligned to chromosome 6; the candidate gene contains at least four exons. The dependence of DIPP's catalytic activity upon its MutT domain was confirmed by mutagenesis of a conserved glutamate residue. DIPP's low molecular size, Mg2+ dependency and catalytic preference for phosphoanhydride bonds are also features of other MutT‐type proteins. Because overlapping substrate specificity is a feature of this class of proteins, our data provide new directions for future studies of higher inositol phosphates.
Large Scale Semantic Annotation, Indexing and Search at The National Archives

This paper describes a tool developed to improve access to the enormous volume of data housed at the UK's National Archives, both for the general public and for specialist researchers. The system we have developed, TNA-Search, enables a multi-paradigm search over the entire electronic archive (42TB of data in various formats). The search functionality allows queries that arbitrarily mix any combination of full-text, structural, linguistic and semantic queries. The archive is annotated and indexed with respect to a massive semantic knowledge base containing data from the LOD cloud, data.gov. uk, related TNA projects, and a large geographical database. The semantic annotation component achieves approximately 83% F-measure, which is very reasonable considering the wide range of entities and document types and the open domain. The technologies are being adopted by real users at The National Archives and will form the core of their suite of search tools, with additional in-house interfaces.
TLAB at the NTCIR-13 AKG Task

In recent years, popular search engines are utilizing the power of Knowledge Graph(KG) to provide specific answers to queries and questions in a direct way. It is expected that search engine result pages (SERPs) will provide facts about the quires satisfying semantic meaning, which encouraging researchers to constructing more powerful Knowledge Graph. One of the major challenges is disambiguating and recognizing entities and their actions stored in KG in a context. To achieve and advance the technologies related to actionable knowledge graph presentation, Action Mining (AM) is an essential step and relatively new research direction to nurture research on generating such KG that is optimized for facilitating entity’s actions e.g. for entity“Donald J. Trump” most potential actions could be “won the US Presidential Election” or “targeting US journalists”. This paper presents the Action Mining (AM) task organized by NTCIR-13. We employ a probabilistic model to address the AM problem.
Similarity and Pattern Recognition

This paper formally defines similarities as tolerance relations, which are reflexive and symmetric binary relations. An abstract set with a similarity is called a tolerance space. The training data set in a learning task is a given database of independent identically distributed random pairs (Xi, Yi), where each Xi is a record and Yi is its label: Yi ∈ {0, 1}. The goal of the learning is to design a classifier of which the error probability is near to the theoretical limitation, the Bayes error. The learning process consists of finding a similarity of feature vectors ψ(Xi)’s and the learning result is a representative data clustering on the tolerance space of feature vectors. The information about a record X derived from the representative clustering is the set of representatives similar to the feature vector ψ(X). The percentage of the records of class 1 in the intersection of these representative clusters is used to estimate the conditional probability of Y = 1. This paper defines a θ-classifier, which assigns the record to class 1 if the conditional probability is larger than the threshold θ. If the clustering is a partition, the threshold θ = 1 2 minimizes error probability in the training data set. In general, an optimal θ-classifier has a different threshold. The experiments show the trade-off between the number of clusters and the error probabilities of the optimal
A low-noise charge sensitive amplifier for MEMS capacitive sensors

This paper describes a low-noise charge sensitive amplifier (CSA) for MEMS capacitive sensors which uses a chopper technique to reduce the low-frequency noise and offset. The feedback resistors of the CSA are implemented as a MOS-bipolar pseudo-resistors and an input common-feedback (ICMFB) is designed to prevent large output errors from input common-shift and maintain the op-amp within its input common-mode range. A simulated resolution of 5.8aF (rms) in capacitive change integrated over the signal band is achieved while chopped at 1 MHz
Distribution and Abundance of Archaeal and Bacterial Ammonia Oxidizers in the Sediments of the Dongjiang River, a Drinking Water Supply for Hong Kong

Ammonia-oxidizing archaea (AOA) and bacteria (AOB) play important roles in nitrification. However, limited information about the characteristics of AOA and AOB in the river ecosystem is available. The distribution and abundance of AOA and AOB in the sediments of the Dongjiang River, a drinking water source for Hong Kong, were investigated by clone library analysis and quantitative real-time PCR. Phylogenetic analysis showed that Group 1.1b-and Group 1.1b-associated sequences of AOA predominated in sediments with comparatively high carbon and nitrogen contents (e.g. total carbon (TC) >13 g kg−1 sediment, NH4+-N >144 mg kg−1 sediment), while Group 1.1a- and Group 1.1a-associated sequences were dominant in sediments with opposite conditions (e.g. TC <4 g kg−1 sediment, NH4+-N <93 mg kg−1 sediment). Although Nitrosomonas- and Nitrosospira-related sequences of AOB were detected in the sediments, nearly 70% of the sequences fell into the Nitrosomonas-like B cluster, suggesting similar sediment AOB communities along the river. Higher abundance of AOB than AOA was observed in almost all of the sediments in the Dongjiang River, while significant correlations were only detected between the distribution of AOA and the sediment pH and TC, which suggested that AOA responded more sensitively than AOB to variations of environmental factors. These results extend our knowledge about the environmental responses of ammonia oxidizers in the river ecosystem.
Enactment and Performance Analysis of Discrete Transform based Watermarking Algorithms for Digitized Images

A digital watermark is a kind of marker covertly embedded in a noise-tolerant signal such as audio o r image data. It is typically used to identify owners hip of the copyright of such signal. "Watermarking" is the process of hiding digital information in a carrier signal; the hidden information should, but does not need to contain a relation to the carrier signal. Digital watermarks may be used to verify the authenticity or integrity of the carrier signal or to show the identity of its owners. It is prominently used for tracing copyright Digital ima ge watermarking technology protects digital content (text, images, audio, and video) from illegal manipulations. In th is paper we proposed implementation and performance analys is of two different watermarking schemes based on DCTDWT-SVD. Both are non-blind techniques. One is bas ed on SVD of DC coefficients using second level DWT decomposition and other is SVD of all DCT values of second level DWT composition of c ver image. PSNR and NCC parameters are used to check effective ness of both techniques for Imperceptibility and ro bustness.
Jurisprudence on new developments of brain science

In recent years, western countries have made great progresses in the area of brain science, which provides advanced scientific and technological supports to the physiological study of behavioral decision. These progresses are not only of significance in natural sciences, but also demonstrate strong basic significance in humanities and social sciences. Meantime, they expanded the new vision of legal studies and brought about new waves of problems and thinking, and indicated an alternative approach of development for the research methods and research areas of legal studies.
Soft Actuators and Robots that Are Resistant to Mechanical Damage

This paper characterizes the ability of soft pneumatic actuators and robots to resist mechanical insults that would irreversibly damage or destroy hard robotic systems—systems fabricated in metals and structural polymers, and actuated mechanically—of comparable sizes. The pneumatic networks that actuate these soft machines are formed by bonding two layers of elastomeric or polymeric materials that have different moduli on application of strain by pneumatic inflation; this difference in strain between an extensible top layer and an inextensible, strain‐limiting, bottom layer causes the pneumatic network to expand anisotropically. While all the soft machines described here are, to some extent, more resistant to damage by compressive forces, blunt impacts, and severe bending than most corresponding hard systems, the composition of the strain‐limiting layers confers on them very different tensile and compressive strengths.
Decentralized Cooperative Policy for Conflict Resolution in Multivehicle Systems

In this paper, we propose a novel policy for steering multiple vehicles between assigned start and goal configurations, ensuring collision avoidance. The policy rests on the assumption that all agents are cooperating by implementing the same traffic rules. However, the policy is completely decentralized, as each agent decides its own motion by applying those rules only on the locally available information, and scalable, in the sense that the amount of information processed by each agent and the computational complexity of the algorithms do not increase with the number of agents in the scenario. The proposed policy applies to systems in which new vehicles may enter the scene and start interacting with existing ones at any time, while others may leave. Under mild conditions on the initial configurations, the policy is shown to be safe, i.e., it guarantees collision avoidance throughout the system evolution. In the paper, conditions are discussed on the desired configurations of agents, under which the ultimate convergence of all vehicles to their goals can also be guaranteed. To show that such conditions are actually necessary and sufficient, which turns out to be a challenging liveness-verification problem for a complex hybrid automaton, we employ a probabilistic verification method. The paper finally presents and discusses simulations for systems of several tens of vehicles, and reports on some experimental implementation showing the practicality of the approach.
SIGGRAPH Asia 2016: course notes directions in shape analysis towards functionality

The majority of man-made objects are designed to serve a certain function, and this is often reflected by the geometry of the objects, or the way that they are used or organized in an environment. In recent years, many efforts in shape analysis have developed methods that extract high-level structural and semantic information from geometric shapes and scenes, especially involving man-made objects. One can argue that the ultimate goal of some of these works is to understand the functionality of the objects. Moreover, there have also been works that explicitly model and incorporate functionality into the processing of shapes and scenes. Thus, functionality has been receiving increasingly more attention in shape analysis and geometric modeling, either directly or indirectly, since functionality considerations can aid in applications such as semantic classification, shape editing and synthesis, as well as product design, development, and fabrication. In this course, we discuss recent developments that incorporate functionality aspects into the analysis of 3D shapes and scenes, to provide a summary of the state-of-the-art in this area, including a discussion of key ideas and literature works. More specifically, we first discuss approaches that are precursors in this front, such as structure-aware and data-driven methods that learn relationships between shape parts or objects in scenes. Next, we cover works that more explicitly model the functionality of shapes and scenes, such as agent- and interaction-based methods. The course is structured in the form of talks given by four different speakers, aided by electronic slides that include notes for subsequent consultation.
License Plate Classification from a Binarization Perspective

For binarized license plates, there are usually two categories: one is the white-character type, of which the character is white and the background is black. The other is the black-character type. For some linearization-based algorithms, such as character segmentation, we should apply suitable approach according to different linearization results. It is still a challenging task for multi-style license plates. In this paper we propose a stroke-width-transform-based method for this problem. Firstly, we calculate the stroke width transform by using the original grey image and the inverted one, respectively. Secondly, the histograms of the corresponding stroke width transform images are generated. Thirdly, the image, corresponding to the maximum value of the histograms, is selected. Finally, if the original image is selected, the license plate is the white-character type and vice versa. The experimental results show the proposed method is superior to others by using multi-style license plates in the United States, but the time complexity is high.
A turning point for problematic alcohol users: can relationship adjustment predict desistance?

Abstract Problematic alcohol use (PAU) presents a major burden on health worldwide. Sampson and Laub’s Age-Graded Theory of Informal Social Control provides a unique lens through which to investigate desistance from PAU. This study explored the potential of relationship adjustment to act as a turning point, promoting desistance from PAU across the lifespan. Seventy-three participants (58 females, 15 males) who had previously experienced a period of PAU responded to an anonymous online survey. Contrary to the hypothesis, results showed that relationship adjustment did not act as a turning point predicting desistance from PAU across the lifespan in this sample. However, further analyses revealed that relationship adjustment did predict desistance for those aged 25 years and under. The findings provide partial support for the use of Sampson and Laub’s theory in the alcohol use literature, and highlight the importance of relationship adjustment in the drinking behaviors of youth. Replication and further research are needed. Implications for therapeutic practices, health promotion, and theoretical frameworks are discussed.
Contemporary measures of approach and avoidance goal orientations: similarities and differences.

BACKGROUND In response to a resurgence of interest in and demonstrated utility of the approach-avoidance goal distinction, a number of researchers (Elliot & Church, 1997; Midgley et al., 1998; Skaalvik, 1997) have developed instruments to assess individual differences in the tendency to adopt approach-avoidance goals. However, to date there has been no attempt to examine the psychometric properties or conceptual and measurement overlap of these instruments. AIMS (i) To determine whether three questionnaires designed to measure approach-avoidance goal orientations are assessing the same or different constructs, and (ii) to examine the psychometric properties of each of the approach-avoidance measures (i.e., internal consistency, convergent, discriminant, factorial, and construct validity). SAMPLE Participants in this study were 475 undergraduate students (N = 228 males; N = 244 females; three missing information) enrolled at two large universities in the United Kingdom. METHOD Participants completed a questionnaire which included measures of approach-avoidance goal orientations, effort regulation, test anxiety, perceived ability, and intrinsic motivation, extrinsic motivation, and amotivation. RESULTS Results revealed a degree of convergence between the three instruments. Each of the instruments demonstrated good psychometric properties although construct validity results were inconsistent across the measures. CONCLUSION There is a need for future research to clarify the operational definition and subsequent measurement of the performance avoidance construct, and in particular, to examine the role that effort, impression management, and anxiety/fear of failure play in its conceptualisation.
How a Therapy-Based Quality Improvement Intervention for Depression Affected Life Events and Psychological Well-Being Over Time: A 9-Year Longitudinal Analysis

Background:Short-term quality improvement (QI) interventions for depression can improve long-term mental health but mechanisms are unknown. We hypothesized that 1 pathway for such health benefits was an indirect effect with QI reducing risk factors for depression such as stressful life events. Objective:To determine whether 6–12 month QI programs for depression reduce negative life events at 5-year follow-up and to model the relationship between program implementation, life events and mental health over 9 years. Design:Forty-six primary care clinics in 6 managed care organizations were randomized to usual care or 1 of 2 QI interventions. We focus on the intervention that provided resources to assess and manage depression while particularly facilitating access to evidence-based psychotherapy (“QI-Therapy”). Subjects:A total of 1300 enrolled patients with current depressive symptoms, who had data at any of 4 data points: baseline, or follow-up year 1, 5, or 9. Measures:Total and negatively-evaluated life events and psychologic well-being. Results:A path model showed that QI-Therapy, in addition to improving psychologic well-being at year 1 (P = 0.0033), reduced negative life events at year 5 (P = 0.0033). This effect was not fully explained by improved psychologic well-being. Better mental health (P < 0.0001) and fewer negative life events (P = 0.0013) at year 5 were associated with improved psychologic well-being at 9 years. Conclusions:Depression QI programs that include resources for psychotherapy can reduce occurrence of life events, further protecting subsequent mental health. Implications for the design of QI programs and development of prevention interventions are discussed.
Effects of organic and inorganic selenium supplementation on selenoenzyme activity in blood lymphocytes, granulocytes, platelets and erythrocytes.

The blood selenium (Se) concentration in the U.K. population has declined by approx. 50% between 1974 and 1991, reflecting a large decrease in dietary Se supply, with intakes only half the reference nutrient intake of 1 microg/kg body weight. Tissue levels of Se are readily influenced by dietary intake. Therefore selenoprotein activity may be sub-optimal due to low Se status, and thus compromise normal cell function. To examine the effects of changing Se intake on selenoproteins, we have determined the relative effectiveness of organic selenomethionine and inorganic sodium selenite (50 microg of Se daily for 28 days) in modulating glutathione peroxidase activities in blood cells from 45 healthy men and women, from a U.K. population. Transient and acute changes in lymphocyte, granulocyte and platelet phospholipid-hydroperoxide glutathione peroxidase (GPx4) activity occurred by day 7 or 14 of sodium selenite treatment and by day 7 in lymphocytes from selenomethionine-treated subjects compared with controls taking a placebo. In contrast, GPx4 activity in granulocytes and platelets in the selenomethionine group increased gradually over the 28 days. Cytosolic glutathione peroxidase (GPx1) activity in these blood cells from both treatment groups increased gradually over the 28 days. For each cellular selenoenzyme activity a significant inter-individual difference (P<0.001) in the extent of the response to Se supplementation was observed, but this was not related to blood Se concentrations either before or after treatments. Significant inverse correlations were evident between baseline enzyme activities and percentage change in activity after 28 days of supplementation [e.g. lymphocyte GPx4, r=-0.695 (P<0.001)], indicating that pre-treatment activity may be sub-optimal as a result of poor Se status. The different and contrasting effects that Se supplementation had on blood selenoenzyme activities may be indicative of a difference in metabolic need for Se regulated at the level of Se-dependent cell function.
Local states in distributed computations: a few relations and formulas

If events produced by processes of a distributed computation are generally supposed to be instantaneous, it is not the case for local states generated by these events. Due to message exchanges and synchronization local states have some duration. This paper defines notions about local states such as weak precedence, strong precedence, weak concurrency and strong concurrency. Moreover a few formulas based on vector clocks, and consequently usable in an operational context, are introduced to decide about relations between local states. These relations and formulas can be used either to debug, test or analyze distributed programs (especially for global properties detection) or to define consistent checkpoints.