Miracle-dz/UniFAR-FTUs huggingface dataset:
Continental Refugium in the Mongolian Plateau during Quaternary Glacial Oscillations: Phylogeography and Niche Modelling of the Endemic Desert Hamster, Phodopus roborovskii

The Mongolian Plateau (MP), which is situated in the interior of Asia and possesses a typical continental climate, experienced harsh climatic conditions during the Quaternary glacial fluctuations. Although these events likely had huge impacts on the local animal populations, the current effects have hardly been explored. To investigate whether the MP supported a refugium along an oceanic-continental gradient (ROCG), and whether this refugium was glacial or interglacial, we investigated the demographic and phylogeographic history of an endemic mammal species, the desert hamster Phodopus roborovskii. We reconstructed the demographic variation, the phylogeographic diffusion, and modelled the potential habitat during historical periods. The genetic diversity in the MP was the highest among all the localities, and the MP was a suitable habitat throughout the modelled historical periods. A phylogeographic diffusion analysis emphasized the importance of the MP as the centre of origin, preservation and spread for P. roborovskii. The homogeneous landscape provided the opportunity for a wide gene flow, which resulted in low resolution of the phylogenetic relationships. Moreover, P. roborovskii was favoured by the interglacial condition, with both its demographical and geographical ranges expanded within the interglacial periods. The range variation from the Last Glacial Maximum to the current condition reflects a distinct longitudinal shift, while both ranges largely contracted from that of the Last Interglacial. Our results support that the MP served as a refugium and spread centre for P. roborovskii during the Quaternary climate fluctuations. The interglacial expansion and the longitudinal shifts highlighted the important effects of precipitations on the distribution range of species adapted to arid and semi-arid during glacial oscillations.
Sound development of secure service-based systems

<i>Service-based software systems</i> are a useful concept recently developed to support the development of systems offering functions (the so-called <i>services</i>) which may be interrelated or may mutually depend on each other. Although appealing from a practical point of view, the development of service-based software for security-critical systems is, unfortunately, not well understood. Services may easily interact with each other in a way which may have unforeseen consequences on the various security properties provided. In this work, we propose a method for facilitating the development of security-critical service-based software systems using the computer-aided systems engineering tool A<sc>uto</sc>F<sc>ocus</sc> based on the formal method F<sc>ocus</sc>. We explain our method at the example of a service-based system from the automotive domain.
An assessment of Lot Quality Assurance Sampling to evaluate malaria outcome indicators: extending malaria indicator surveys.

BACKGROUND Large investments and increased global prioritization of malaria prevention and treatment have resulted in greater emphasis on programme monitoring and evaluation (M&E) in many countries. Many countries currently use large multistage cluster sample surveys to monitor malaria outcome indicators on a regional and national level. However, these surveys often mask local-level variability important to programme management. Lot Quality Assurance Sampling (LQAS) has played a valuable role for local-level programme M&E. If incorporated into these larger surveys, it would provide a comprehensive M&E plan at little, if any, extra cost. METHODS The Mozambique Ministry of Health conducted a Malaria Indicator Survey (MIS) in June and July 2007. We applied LQAS classification rules to the 345 sampled enumeration areas to demonstrate identifying high- and low-performing areas with respect to two malaria program indicators-'household possession of any bednet' and 'household possession of any insecticide-treated bednet (ITN)'. RESULTS As shown by the MIS, no province in Mozambique achieved the 70% coverage target for household possession of bednets or ITNs. By applying LQAS classification rules to the data, we identify 266 of the 345 enumeration areas as having bednet coverage severely below the 70% target. An additional 73 were identified with low ITN coverage. CONCLUSIONS This article demonstrates the feasibility of integrating LQAS into multistage cluster sampling surveys and using these results to support a comprehensive national, regional and local programme M&E system. Furthermore, in the recommendations we outlined how to integrate the Large Country-LQAS design into macro-surveys while still obtaining results available through current sampling practices.
TCP is competitive against a limited adversary

While the well-known Transport Control Protocol (TCP) is a de facto standard for reliable communication on the Internet, and performs well in practice, the question "how good is the TCP/IP congestion control algorithm? " is not completely resolved. In this paper, we provide some answers to this question using the competitive analysis framework. First, we prove that for networks with a single bottleneck (or point of congestion), TCP is competitive to the optimal global algorithm in minimizing the user-perceived latency or flow time of the sessions. Specifically, we show that with O(1) times as much bandwidth and O(1) extra time per job, TCP is O(1)-competitive against an optimal global algorithm. We motivate the need for allowing TCP to have extra resources by observing that existing lower bounds for non-clairvoyant scheduling algorithms imply that no online, distributed, non-clairvoyant algorithm can be competitive with an optimal offline algorithm if both algorithms were given the same resources. Second, we show that TCP is fair by proving that it converges quickly to allocations where every session gets its fair share of network bandwidth.
Indexing for Fast Categorisation

Automatic categorisation is an important technique for the management of large document collections. Categorisation can be used to store or locate documents that satisfy an information need when the need cannot be expressed as a concise list of query terms. Inverted indexes are used in all query-based retrieval systems to allow efficient query processing. In this paper, we propose the application of inverted indexes to categorisation with the aim of developing a fast, scalable, and accurate approach. Specifically, we propose successful variants of inverted indexing to reduce index size: first, quantisation of term-category weights; second, compression of the quantised weights; and, last, storing only those weights that significantly impact the categorisation process. We show that our techniques permits fast, accurate categorisation: index size is reduced by orders of magnitude compared to conventional inverted indexing and the accuracy of categorisation is preserved.
A Social Media Analytics Capabilitiy Framework for Firm's Competitive Advantage

Social media analytics (SMA) can provide an organization with insights that would generate greater customer value and subsequently lead to better organizational performance and, thus enable the organization to have a competitive advantage over its rivals. In this paper, we develop a conceptual SMA capability framework which identifies SMA capabilities that an organization should have in order to take full advantage of social media data. We analyzed the business analytics (BA) and SMA literature in order to present a case for the need of a SMA capability framework. Using a thematic analysis of SMA and BA literature, we identified the most relevant SMA capabilities leading to a conceptual SMA framework.
Corruption: A General Equilibrium Approach

Most theoretical studies of corruption develop micro models of individual acts while empirical papers study corruption at the country level. We build an agent-based model to provide the missing link between these two groups. Here the societal corruption level is derived from individual corruption levels optimally chosen by agents with varying risk aversion and human capital. It, in turn, affects the risk-return profile of corruption for the individual agents. Simulating a multi-generational economy with heterogeneous agents we show that there are locally stable equilibrium corruption levels with certain socio-economic determinants. However there are situations when corruption can rise till it stifles all economic activity.
Living in the city ain't so bad : cultural diversity of South Auckland rangatahi : a thesis submitted in partial fulfilment of a Masters of Philosophy in Psychology

Establishing a ‘secure’ Maori identity based solely on particular criteria of Maori culture (te reo Maori, tikanga, marae, etc.) continues to be problematic for some Maori. Those who are not seen as connected in this way are often defined by what they are seen as lacking, hence terms such as disconnected, distanced, detached and dissociated. Although young Maori may define themselves in terms of difference from others there is an increasing danger of some urban youth being defined as different from Maori who are ‘culturally connected’ and for this to be seen primarily as a negative demarcation. Although it may be the aspiration of some to have greater cultural connection, what this means for different groups and individuals may have both congruence and divergence with what are usually considered to be markers of cultural inclusion. This thesis presents the findings from a wider research project funded by the Health Research Council of New Zealand. The project objective was to gather data that can inform and contribute to existing knowledge about cultural identity of rangatahi Maori with a view to establishing a framework(s) for greater youth development and a more positive and embracing perspective of culture. Kaupapa Maori and social constructionist framings are used to centre the focused life story interviews that were conducted with young people aged between 13-21 years, who identified as Maori and lived in the South Auckland area. Findings suggest that conventional and experiential indicators of Maori identity as well as a strong localised identity are key factors in this exploration. Challenges for identity theorists, societal institutions and other Maori are discussed.
Investigation of the association between SLC1A3 gene polymorphisms and normal tension glaucoma

Purpose To investigate whether the solute carrier family 1, member 3 (SLC1A3) gene, which encodes the glutamate aspartate transporter, is associated with normal tension glaucoma (NTG) in Japanese patients. Methods Two hundred and ninety-five Japanese patients with NTG and 518 Japanese healthy controls were recruited. Patients exhibiting comparatively early NTG onset were selected because early onset suggests that genetic factors may show stronger involvement. We genotyped 5 single-nucleotide polymorphisms (SNPs) in SLC1A3 and assessed the allelic and genotypic diversity among cases and controls. Results There were no statistically significant differences in the frequency of SLC1A3 alleles and genotypes between cases and controls. Conclusions Our study showed no association between SLC1A3 and NTG, suggesting that the SLC1A3 gene may not be an associated factor in NTG pathogenesis.
Cyclic and Macrocyclic Peptides as Chemical Tools To Recognise Protein Surfaces and Probe Protein–Protein Interactions

Targeting protein surfaces and protein–protein interactions (PPIs) with small molecules is a frontier goal of chemical biology and provides attractive therapeutic opportunities in drug discovery. The molecular properties of protein surfaces, including their shallow features and lack of deep binding pockets, pose significant challenges, and as a result have proved difficult to target. Peptides are ideal candidates for this mission due to their ability to closely mimic many structural features of protein interfaces. However, their inherently low intracellular stability and permeability and high in vivo clearance have thus far limited their biological applications. One way to improve these properties is to constrain the secondary structure of linear peptides by cyclisation. Herein we review various classes of cyclic and macrocyclic peptides as chemical probes of protein surfaces and modulators of PPIs. The growing interest in this area and recent advances provide evidence of the potential of developing peptide‐like molecules that specifically target these interactions.
Group-Based Noncoherent Space-Frequency Codes and Efficient Decoding

In this paper, we focus on noncoherent space-frequency (SF) coded multiple-input-multiple-output orthogonal-frequency-division-multiplexing (MIMO-OFDM) systems. Based on OFDM subcarrier grouping, a group-based unitary space- frequency code is proposed and the effect of grouping on system performance is studied. Comparing to the coding scheme without grouping, which implements SF coding among all the OFDM tones, the proposed group-based coding scheme can greatly reduce the decoding complexity, making the noncoherent SF codes more applicable to practical use. By relating the noncoherent SF codes with packings in Grassmann manifold, we propose an efficient decoding method by restricting the implementation of decoding within a subset of the codebook. Numerical results are presented to demonstrate and verify our proposals.
Automatic Interpretation of Music Structure Analyses: A Validated Technique for Post-Hoc Estimation of the Rationale for an Annotation

Annotations of musical structure usually provide a low level of detail: they include boundary locations and section labels, but do not indicate what makes the sections similar or distinct, or what changes in the music at each boundary. For those studying annotated corpora, it would be useful to know the rationale for each annotation, but collecting this information from listeners is burdensome and difficult. We propose a new algorithm for estimating which musical features formed the basis for each part of an annotation. To evaluate our approach, we use a synthetic dataset of music clips, all designed to have ambiguous structure, that was previously used and validated in a psychology experiment. We find that, compared to a previous optimization-based algorithm, our correlation-based approach is better able to predict the rationale for an analysis. Using the best version of our algorithm, we process examples from the SALAMI dataset and demonstrate how we can augment the structure annotation data with estimated rationales, inviting new ways to research and use the data.
Geometrically Accurate Topology-Correction of Cortical Surfaces Using Nonseparating Loops

In this paper, we focus on the retrospective topology correction of surfaces. We propose a technique to accurately correct the spherical topology of cortical surfaces. Specifically, we construct a mapping from the original surface onto the sphere to detect topological defects as minimal nonhomeomorphic regions. The topology of each defect is then corrected by opening and sealing the surface along a set of nonseparating loops that are selected in a Bayesian framework. The proposed method is a wholly self-contained topology correction algorithm, which determines geometrically accurate, topologically correct solutions based on the magnetic resonance imaging (MRI) intensity profile and the expected local curvature. Applied to real data, our method provides topological corrections similar to those made by a trained operator
Sprint Training Increases Muscle Oxidative Metabolism During High-Intensity Exercise in Patients With Type 1 Diabetes

OBJECTIVE—To investigate sprint-training effects on muscle metabolism during exercise in subjects with (type 1 diabetic group) and without (control group) type 1 diabetes. RESEARCH DESIGN AND METHODS—Eight subjects with type 1 diabetes and seven control subjects, matched for age, BMI, and maximum oxygen uptake (V̇o2peak), undertook 7 weeks of sprint training. Pretraining, subjects cycled to exhaustion at 130% V̇o2peak. Posttraining subjects performed an identical test. Vastus lateralis biopsies at rest and immediately after exercise were assayed for metabolites, high-energy phosphates, and enzymes. Arterialized venous blood drawn at rest and after exercise was analyzed for lactate and [H+]. Respiratory measures were obtained on separate days during identical tests and during submaximal tests before and after training. RESULTS—Pretraining, maximal resting activities of hexokinase, citrate synthase, and pyruvate dehydrogenase did not differ between groups. Muscle lactate accumulation with exercise was higher in type 1 diabetic than nondiabetic subjects and corresponded to indexes of glycemia (A1C, fasting plasma glucose); however, glycogenolytic and glycolytic rates were similar. Posttraining, at rest, hexokinase activity increased in type 1 diabetic subjects; in both groups, citrate synthase activity increased and pyruvate dehydrogenase activity decreased; during submaximal exercise, fat oxidation was higher; and during intense exercise, peak ventilation and carbon dioxide output, plasma lactate and [H+], muscle lactate, glycogenolytic and glycolytic rates, and ATP degradation were lower in both groups. CONCLUSIONS—High-intensity exercise training was well tolerated, reduced metabolic destabilization (of lactate, H+, glycogenolysis/glycolysis, and ATP) during intense exercise, and enhanced muscle oxidative metabolism in young adults with type 1 diabetes. The latter may have clinically important health benefits.
Discriminative language modeling using simulated ASR errors

In this paper, we approach the problem of discriminatively training language models using a weighted finite state transducer (WFST) framework that does not require acoustic training data. The phonetic confusions prevalent in the recognizer are modeled using a confusion matrix that takes into account information from the pronunciation model (word-based phone confusion log likelihoods) and information from the acoustic model (distances between the phonetic acoustic models). This confusion matrix, within the WFST framework, is used to generate confusable word graphs that serve as inputs to the averaged perceptron algorithm to train the parameters of the discriminative language model. Experiments on a large vocabulary speech recognition task show significant word error rate reductions when compared to a baseline using a trigram model trained with the maximum likelihood criterion.
Impact of lactic acid on cell proliferation and free radical‐induced cell death in monolayer cultures of neural precursor cells

Biomaterials prepared from polyesters of lactic acid and glycolic acid, or a mixture of the two, degrade in the presence of water into the naturally occurring metabolites, lactic acid and glycolic acid. While the lactic acid degradation product that is released from biomaterials is well tolerated by the body, lactic acid can influence the metabolic function of cells; it can serve as an energy substrate for cells, and has been shown to have antioxidant properties. Neural precursor cells, a cell population of considerable interest as a source of cells for neural tissue regeneration strategies, generate a high amount of reactive oxygen species, and when associated with a degradable biomaterial, may be impacted by released lactic acid. In this work, the effect of lactic acid on a neural cell population containing proliferative neural precursor cells was examined in monolayer culture. Lactic acid was found to scavenge exogenously added free radicals produced in the presence of either hydrogen peroxide or a photoinitiator (I2959) commonly utilized in the preparation of photopolymerizable biomaterials. In addition to its effect on exogenously added free radicals, lactic acid reduced intracellular redox state, increased the proliferation of the cell population, and modified the cell composition. The findings of this study provide insight into the role that lactic acid plays naturally on developing neural cells and are also of interest to biomaterials scientists that are focused on the development of degradable lactic‐acid‐based polymers for cell culture devices. The effect of lactic acid on other cell populations may differ and should be characterized to best understand how cells function in degradable cell culture devices. Biotechnol. Bioeng. 2009;103: 1214–1223. © 2009 Wiley Periodicals, Inc.
NEURAL SYSTEMS FOR COMPLEX IDENTIFICATION TASKS: THE ACCESS CONTROL SYSTEM ZN-FACE AND THE ALARM IDENTIFICATION SENECA FOR STEEL CASTING PROCESSES

Neural systems have become a widely used tool in many industrial and commercial applications. We report in this contribution on new applications of diagnosis and identiication systems in two areas. Firstly, we present the access control system ZN-Face, a product developped at the ZN, which makes automated face recognition available for commercial access control systems. Neural systems have the necessary exibility to analyse the visual information correctly, which we perceive so easily as a person's face. ZN-Face combines high recognition rates (99 %) with fast computation (3 sec) on standard hardware components (PC). The system is integrated into an easy-to-use GUI. ZN-Face is in daily operation at a large company since summer 1995. { Secondly, we report on a neural system for industrial process diagnosis, namely alarm identiication in continuous steel casting , where a neural net in combination with a fuzzy system detects dangerous \hot spot"-process faults (breakouts) from the observation of high-dimensional temperature data. The system successfully detects previously undetected alarms and reduces the false alarm rate by a factor of 7. It is now (since spring 1995) installed at a major Ger-man steel manufacturing company.
Reusing invariants: a new strategy for correlated queries

Correlated queries are very common and important in decision support systems. Traditional nested iteration evaluation methods for such queries can be very time consuming. When they apply, query rewriting techniques have been shown to be much more efficient. But query rewriting is not always possible. When query rewriting does not apply, can we do something better than the traditional nested iteration methods? In this paper, we propose a new invariant technique to evaluate correlated queries efficiently. The basic idea is to recognize the part of the subquery that is not related to the outer references and cache the result of that part after its first execution. Later, we can reuse the result and combine it with the result of the rest of the subquery that is changing for each iteration. Our technique applies to arbitrary correlated subqueries. This paper introduces algorithms to recognize the invariant part of a data flow tree, and to restructure the evaluation plan to reuse the stored intermediate result. We also propose an efficient method to teach an existing join optimizer to understand the invariant feature and thus allow it to be able to generate better join plans in the new context. Some other related optimization techniques are also discussed. The proposed techniques were implemented within three months on an existing real commercial database system. We also experimentally evaluate our proposed technique. Our evaluation indicates that, when query rewriting is not possible, the invariant technique is significantly better than the traditional nested iteration method. Even when query rewriting applies, the invariant technique is sometimes better than the query rewriting technique. Our conclusion is that the invariant technique should be considered as one of the alternatives in evaluating correlated queries since it fills the gap left by rewriting techniques.