Miracle-dz/UniFAR-FTUs huggingface dataset:
Effects of mining waste waters on fish in lakes of NW Russia

The Kostomuksha Mining Plant in NW Russia (64• 30' N, 30• 30' E) extracts and processes iron ore into pellets (ca. 7 million t year-') for the meta! industry. The main environmental effects of the production operations are air pollution (70,000 t SO, year-') and wastewater emissions. The process and mining waters (ca. 3 million m year-') enter a 34-km' waste depository, dammed in 1982 from the former Lake Kostomuksha. The waters then seep into a lake-river system, which flows for ca. 250 km to the White Sea. The waste water contains high amounts of minerals, nitrogen and heavy metals. The depository has been reporred to overflow during spring floods; overfilling is also thought to increase the risk of dam breakdown. The aim of this srudy was to provide a general description of the chemistry and biology of two lakes below the mining plant, in comparison to a clean reference lake in the same catchment area. The main emphasis of the project was on the effects of pollution on fish populations and on individual fish (TKATCHEVA et al. 2000).
Recommending verbs for rename method using association rule mining

An identifier is one of the crucial elements for program readability. Method names in an object-oriented program are important identifiers because method names are used for understanding the behavior of the methods without reading a part of the program. It is well-known that each method name should consist of a verb and objects according to general guidelines. However, it is not easy to name methods consistently since each of the developers may have a different understanding of the verbs and objects used in the method names. As a first step to enable developers to name methods consistently and easily, we focus on the verbs used in the method names. In this paper, we present a technique to recommend candidate verbs for a method name so that developers can use consistent verbs for method names. Given a method, we recommend a list of verbs used in many other methods similar to the given method, by using association rules. We have extracted association rules from 445 OSS projects and applied these rules to two projects. As a result, the extracted rules could recommend the current verbs in the top 10 candidates for 60.6% of the methods covered by our approach. Furthermore, we have identified four meaningful groups of rules for verb recommendation.
Histochemical and Morphometric Analyses of the Musculature of the Forelimb of the Subterranean Rodent Ctenomys talarum (Octodontoidea)

Histochemical and morphometric analyses were performed to characterize the fibre‐type composition of two forelimb muscles of the South American subterranean rodent Ctenomys talarum. The studied muscles were the triceps lateralis, an extensor of the elbow, and the teres major, a flexor of the shoulder. It was found that these muscles had an elevated proportion of fast oxidative‐glycolytic (FOG) fibres, and lower proportions of slow oxidative (SO) and fast glycolytic (FG) fibres. This composition probably qualifies the teres major and triceps muscles to perform the sustained effort required in tunnelling excavation. The results were discussed considering published data on fibre‐type composition of mammals having different modes of life and digging behaviour. We here suggest that C. talarum has the potential of generating forces linked to rapid, powerful movements during sustained periods by means of an elevated proportion of FOG fibres, together with osteological changes that result in a great mechanical advantage of the forelimb muscles.
Chatrooms in MOOCs: all talk and no action

We study effects of introducing a real-time chatroom into a massive open online course with several thousand students, supplementing an existing forum. The chatroom was supported by teaching assistants, and generated thousands of lines of discussion by 28\% of 681 consenting chat condition participants, mostly on-topic. Despite this, chat activity remained low ($\mu=8.2$ messages per hour) and we could find no significant effect of chat use on objective or subjective dependent variables such as grades, retention, forum participation, or students' sense of community. Further investigation reveals that only 12\% of chat participants have substantive interactions, while the remainder are either passive or have trivial interactions that are unlikely to result in learning. We also find that pervasive, highly visible chat interfaces are highly effective in encouraging both active and substantive participation in chat. When compared to chat interfaces that are restricted to a single webpage, the pervasive interface exhibits \changes{2.8 times} as many users with substantive interactions.
Attenuation in the mantle, from spectral analysis of short-period seismic waves

Various techniques for estimating t* (travel time/quality factor Q) from short period array records of body waves have been investigated. Spectral analysis in the frequency domain seems to be more appropriate for this purpose than time domain methods, because of the relative ease in which source and instrument effects can be removed. Of the techniques available, those based on maximum likelihood and homomorphic deconvolution give estimates of relative power versus frequency which best represent the power contained in a time domain wavelet of short duration. The latter technique seemed to have better noise-eliminating properties than the former, without the need to resort to pre-whitening. Homomorphic deconvolution was therefore used to obtain estimates of t* values from P, PcP, ScP and S phases recorded at the Warramunga array in the Northern Territory of Australia. The source regions for the events studied were the Sunda, Mariana, New Hebrides, Kermadec and Tonga trench zones. The short-period t* estimates obtained by this means were much smaller than estimates from published Free-oscillation Q models, indicating that the values of Q for compressional and shear waves are frequency dependent. It was found that the short-period and free oscillation data could be satisfied by assuming a linear relationship between Q and frequency, and that this relationship was consistent with other published data. The variation of Q /Qn > and phase velocity with frequency were also examined. The results of this investigation suggest new directions from which the Q structure of the mantle can be studied.
The complete mitochondrial genome of the desert darkling beetle Asbolus verrucosus (Coleoptera, Tenebrionidae)

Abstract The complete mitochondrial genome of the desert darkling beetle Asbolus verrucosus (LeConte, 1851) was sequenced using paired-end technology to an average depth of 42,111× and assembled using De Bruijn graph-based methods. The genome is 15,828 bp in length and conforms to the basal arthropod mitochondrial gene composition with the same gene orders and orientations as other darkling beetle mitochondria. This arrangement includes a control region, 22 tRNA genes, 2 rRNA genes and 13 protein-coding genes. The main coding strand is probably replicated as the lagging strand (GC skew of −0.36 and AT skew of +0.19). Phylogenomics analyses are consistent with taxonomic classifications and indicate that Tenebrio molitor is the closest relative that has a completely sequenced mitochondrial genome available for analysis. This is the first fully assembled mitogenome sequence for a darkling beetle in the subfamily Pimeliinae and will be useful for population studies on members of this ecologically important group of beetles.
Bearing Rigidity and Almost Global Bearing-Only Formation Stabilization

A fundamental problem that the bearing rigidity theory studies is to determine when a framework can be uniquely determined up to a translation and a scaling factor by its inter-neighbor bearings. While many previous works focused on the bearing rigidity of two-dimensional frameworks, a first contribution of this paper is to extend these results to arbitrary dimensions. It is shown that a framework in an arbitrary dimension can be uniquely determined up to a translation and a scaling factor by the bearings if and only if the framework is infinitesimally bearing rigid. In this paper, the proposed bearing rigidity theory is further applied to the bearing-only formation stabilization problem where the target formation is defined by inter-neighbor bearings and the feedback control uses only bearing measurements. Nonlinear distributed bearing-only formation control laws are proposed for the cases with and without a global orientation. It is proved that the control laws can almost globally stabilize infinitesimally bearing rigid formations. Numerical simulations are provided to support the analysis.
Lithography Optimization for Sub-22 Nanometer Technologies Student :

Continuing scaling of complementary metal-oxidesemiconductor (CMOS) is crucial for the electronic industry because an integrated circuit (IC) with a smaller feature size can provide a smaller silicon area, lower power consumption, higher performance, cheaper price, etc. As the IC process nodes continue to shrink to 22nm and below, the IC industry will face severe manufacturing challenges with conventional optical lithography technologies. According to recent surveys, three most expected technologies may push the limits of lithography: multiple patterning lithography (MPL), electron beam lithography (EBL) and extreme ultraviolet lithography (EUVL). However, each of which encounters different design difficulties and requires solutions for breakthroughs. In this study, we investigate the most critical design challenges of the three technologies: the layout decomposition problem in MPL, the accumulated heating problem in EBL, and the flare effect in EUVL. To overcome these challenges, we transform the original problems into corresponding optimization problems and develop novel algorithms to solve these problems. Experimental results show that the proposed algorithms can efficiently and effectively generate good layout decomposition solutions for MPL, mitigate the thermal problem in EBL, and alleviate flare level and flare variation in EUVL. These results not only can enhance process manufacturability, but also can contribute to the continuing scaling of the CMOS technology.
Performance and Scalability of Discriminative Metrics for Comparative Gene Identification in 12 Drosophila Genomes

Comparative genomics of multiple related species is a powerful methodology for the discovery of functional genomic elements, and its power should increase with the number of species compared. Here, we use 12 Drosophila genomes to study the power of comparative genomics metrics to distinguish between protein-coding and non-coding regions. First, we study the relative power of different comparative metrics and their relationship to single-species metrics. We find that even relatively simple multi-species metrics robustly outperform advanced single-species metrics, especially for shorter exons (≤240 nt), which are common in animal genomes. Moreover, the two capture largely independent features of protein-coding genes, with different sensitivity/specificity trade-offs, such that their combinations lead to even greater discriminatory power. In addition, we study how discovery power scales with the number and phylogenetic distance of the genomes compared. We find that species at a broad range of distances are comparably effective informants for pairwise comparative gene identification, but that these are surpassed by multi-species comparisons at similar evolutionary divergence. In particular, while pairwise discovery power plateaued at larger distances and never outperformed the most advanced single-species metrics, multi-species comparisons continued to benefit even from the most distant species with no apparent saturation. Last, we find that genes in functional categories typically considered fast-evolving can nonetheless be recovered at very high rates using comparative methods. Our results have implications for comparative genomics analyses in any species, including the human.
Alkaline phosphatase in amelogenesis

I n tlie several studies which have been reported concerning tlie histochemical localization of alkaline pliosphatase in the developing tooth, considerable disagreement exists among various investigators. This is especially true in regard to the ameloblasts, the cells which are intimately associated with tlie process of enamel formation. On the one hand, Rabat and Furth ( '41), Engel and Furuta ( '42) and Gomori ('43) assert that ameloblasts do not contain phosphatase. Other observers, however, Horowitz ( '42), Bevelander and Joliiisoii ('45), and Greep, Fischer and Morse ('48), maintain that ameloblasts do contain tlie enzyme. In view of the diversity of opinion concerning the presence of this enzyme in the ameloblasts, we decided to investigate this problem again and extend our previous observations to iiiclude the entire developmental and functioiial span of these cells. By extending our observatioiis to encompass not only the very young pre-calcification stages, or isolated developmental stages as previous investigators have done, we ascertained first the phosphatase localization during the histogenesis of the aineloblast, and second observed whether this enzyme was present in these cells during matrix formation and subsequent calcification.
Fidelity of δ18O as a proxy for sea surface temperature: Influence of variable coral growth rates on the coral Porites lutea from Hainan Island, China

The extremely high temporal resolution (nearly daily interval) measurement was conducted on the coral (Porites lutea) oxygen isotope compositions (δ18Oc) to examine the detailed relationship between δ18Oc and sea surface temperature (SST) and seawater oxygen isotope composition (δ18Ow) from Hainan Island, China. Although SST and sea surface salinity (SSS) or δ18Ow varied in a wide range at the studied site, the dynamic range of δ18Oc recorded in coral was much smaller than expected from SST and SSS (δ18Ow) changes. The extremely high (>30°C) and low (<22°C) SST and low (<27) SSS are not suitable for coral calcification, and coral could not record the information as their skeletal δ18O. Estimated coral extension rates (the overall rate is 15 mm/year) varied by a factor of about 18 within one year, from very slow in winter to very fast in spring. Light availability could affect the extension rate of coral skeleton through the activity of photosynthesis of symbiont algae. Such cessation and acceleration of calcification cause a serious distortion of the δ18O profile, which makes it difficult to make a correlation between δ18O and SST. Because high and low extension rates correspond to low‐ and high‐density bands, respectively, a detailed examination of the density structure may assist the correction for distortion of the δ18O profile.
Neutron-encoded Signatures Enable Product Ion Annotation From Tandem Mass Spectra*

We report the use of neutron-encoded (NeuCode) stable isotope labeling of amino acids in cell culture for the purpose of C-terminal product ion annotation. Two NeuCode labeling isotopologues of lysine, 13C615N2 and 2H8, which differ by 36 mDa, were metabolically embedded in a sample proteome, and the resultant labeled proteins were combined, digested, and analyzed via liquid chromatography and mass spectrometry. With MS/MS scan resolving powers of ∼50,000 or higher, product ions containing the C terminus (i.e. lysine) appear as a doublet spaced by exactly 36 mDa, whereas N-terminal fragments exist as a single m/z peak. Through theory and experiment, we demonstrate that over 90% of all y-type product ions have detectable doublets. We report on an algorithm that can extract these neutron signatures with high sensitivity and specificity. In other words, of 15,503 y-type product ion peaks, the y-type ion identification algorithm correctly identified 14,552 (93.2%) based on detection of the NeuCode doublet; 6.8% were misclassified (i.e. other ion types that were assigned as y-type products). Searching NeuCode labeled yeast with PepNovo+ resulted in a 34% increase in correct de novo identifications relative to searching through MS/MS only. We use this tool to simplify spectra prior to database searching, to sort unmatched tandem mass spectra for spectral richness, for correlation of co-fragmented ions to their parent precursor, and for de novo sequence identification.
Some thoughts on the concept of colimitation: Three definitions and the importance of bioavailability

We discuss the concept of colimitation of primary productivity in aquatic environments, with an emphasis on reconciling this concept with recent advances in marine bioinorganic chemistry. Colimitations are divided into three categories on the basis of their mathematical formulations and visualizations: type I, independent nutrient colimitation (e.g., N and P); type II, biochemical substitution colimitation (e.g., Co and Zn); and type III, biochemically dependent colimitation (e.g., Zn and C), where the ability to acquire one nutrient is dependent upon sufficient supply of another. The potential for colimitation occurring in the marine environment and the critical importance of understanding nutrient bioavailability are discussed.
Over-the-horizon time and frequency synchronization for maneuverable radar system based on troposcatter

Time and frequency synchronization is prerequisite of coordinating multi-static radar system. However, available synchronization methods do not provide practical beyond line-of-sight synchronization especially under the condition of maneuver. Therefore, a novel time and frequency synchronization mechanism based on troposcatter has been proposed. And the main motivations of this paper are to analyze and calculate the main time delay errors, including equipment delay errors and path time delay errors, in the process of time signal transmission and calibration. The result indicates that, the time delay errors of the proposed synchronization method fulfill the requirement of beyond line-of-sight time and frequency synchronization for maneuverable radar system.
Question Answering over Linked Data Using First-order Logic

Question Answering over Linked Data (QALD) aims to evaluate a question answering system over structured data, the key objective of which is to translate questions posed using natural language into structured queries. This technique can help common users to directly access open-structured knowledge on the Web and, accordingly, has attracted much attention. To this end, we propose a novel method using first-order logic. We formulate the knowledge for resolving the ambiguities in the main three steps of QALD (phrase detection, phrase-tosemantic-item mapping and semantic item grouping) as first-order logic clauses in a Markov Logic Network. All clauses can then produce interacted effects in a unified framework and can jointly resolve all ambiguities. Moreover, our method adopts a pattern-learning strategy for semantic item grouping. In this way, our method can cover more text expressions and answer more questions than previous methods using manually designed patterns. The experimental results using open benchmarks demonstrate the effectiveness of the proposed method.
Graph Coalition Structure Generation

We give the first analysis of the computational complexity of {\it coalition structure generation over graphs}. Given an undirected graph $G=(N,E)$ and a valuation function $v:2^N\rightarrow\RR$ over the subsets of nodes, the problem is to find a partition of $N$ into connected subsets, that maximises the sum of the components' values. This problem is generally NP--complete; in particular, it is hard for a defined class of valuation functions which are {\it independent of disconnected members}---that is, two nodes have no effect on each other's marginal contribution to their vertex separator. Nonetheless, for all such functions we provide bounds on the complexity of coalition structure generation over general and minor free graphs. Our proof is constructive and yields algorithms for solving corresponding instances of the problem. Furthermore, we derive polynomial time bounds for acyclic, $K_{2,3}$ and $K_4$ minor free graphs. However, as we show, the problem remains NP--complete for planar graphs, and hence, for any $K_k$ minor free graphs where $k\geq 5$. Moreover, our hardness result holds for a particular subclass of valuation functions, termed {\it edge sum}, where the value of each subset of nodes is simply determined by the sum of given weights of the edges in the induced subgraph.
Graphical Analysis of Kampé De Fériet's Series with Implementation of MATLAB

the present Era, MATLAB has become a standard instructional tool for introductory and advanced courses in Mathematics, Engineering, and Science. In industry, MATLAB is now the tool of choice for high-productivity research, development and analysis. It is widely applied in applied algebra, statistics processing, automation and digital communication. In this paper, the Kampe de Feriet's series is analyzed and interpreted. The remarkable thing of this paper is the crucial MATLAB coding for Kampe de Feriet's series using the MATLAB(R2012a) and interpretation has also be taken on database as well as graphical for different parameters.
Mutations in the Circadian Gene CLOCK in Colorectal Cancer

The circadian clock regulates daily variations in physiologic processes. CLOCK acts as a regulator in the circadian apparatus controlling the expression of other clock genes, including PER1. Clock genes have been implicated in cancer-related functions; in this work, we investigated CLOCK as a possible target of somatic mutations in microsatellite unstable colorectal cancers. Combining microarray gene expression data and public gene sequence information, we identified CLOCK as 1 of 790 putative novel microsatellite instability (MSI) target genes. A total of 101 MSI colorectal carcinomas (CRC) were sequenced for a coding microsatellite in CLOCK. The effect of restoring CLOCK expression was studied in LS180 cells lacking wild-type CLOCK by stably expressing GST-CLOCK or glutathione S-transferase empty vector and testing the effects of UV-induced apoptosis and radiation by DNA content analysis using flow cytometry. Putative novel CLOCK target genes were searched by using ChIP-seq. CLOCK mutations occurred in 53% of MSI CRCs. Restoring CLOCK expression in cells with biallelic CLOCK inactivation resulted in protection against UV-induced apoptosis and decreased G2-M arrest in response to ionizing radiation. Using ChIP-Seq, novel CLOCK-binding elements were identified near DNA damage genes p21, NBR1, BRCA1, and RAD50. CLOCK is shown to be mutated in cancer, and altered response to DNA damage provides one plausible mechanism of tumorigenesis. Mol Cancer Res; 8(7); 952–60. ©2010 AACR.
A comparative study of BNF and DNN multilingual training on cross-lingual low-resource speech recognition

This paper presents a comparative study of bottle-neck feature (BNF) and Deep Neural Network (DNN) multilingual training for low-resource language speech recognition. Besides, we also compared the system performances after ﬁne-tuning. The evaluation was conducted on the IARPA Babel data. The source languages are Cantonese, Pashto, Tagalog, and Turkish, while the target languages are Vietnamese and Tamil. As compared to the monolingual baseline systems, the BNF and DNN methods similarly achieved relative WER reductions of 3.0-5.1% on the Limited Language Pack (LLP) data and 6.1-8.6% on the Very LLP (VLLP) data. By ﬁne-tuning, the BNF method further gained signiﬁcant performance improvement, while the DNN method obtained marginal gains. Overall, we observed the DNN method performs worse on the smaller size data (VLLP), as well as on the noisier data (Tamil) of the target languages, in the cross-lingual transfer and ﬁne-tuning cases respectively.