Miracle-dz/UniFAR-FTUs huggingface dataset:
The concept of function in modern physiology

An overview of the scientific literature shows that the concept of function is central in physiology. However, the concept itself is not defined by physiologists. On the other hand, the teleological, namely, the ‘goal‐directed’ dimension of function, and its subsequent explanatory relevance, is a philosophical problem. Intuitively, the function of a trait in a system explains why this trait is present, but, in the early 1960s, Ernest Nagel and Carl Hempel have shown that this inference cannot be logically founded. However, they showed that self‐regulated systems are teleological. According to the selectionist theories, the function of an item is its effect that has been selected by natural selection, a process that explains its presence. As they restrict the functional attribution of a trait to its past selective value and not its current properties, these theories are inconsistent with the concept of function in physiology. A more adequate one is the causal role theory, for which a function of a trait in a system is its causal contribution to the functional capacity of the system. However, this leaves unsolved the question of the ‘surplus meaning’ of the teleological dimension of function. The significance of considering organisms as ‘purpose‐like’ (teleological) systems may reside not in its explanatory power but in its methodological fruitfulness in physiology. In this view, the teleological dimension of physiological functions is convergent to but not imported from, the teleological dimension of evolutionary biology.
A new method for the detection of siliceous microfossils on sediment microscope slides using convolutional neural networks

Diatom communities preserved in sediment samples are valuable indicators for understanding the past and present dynamics of phytoplankton communities, and their response to environmental changes. These studies are traditionally achieved by counting methods using optical microscopy, a time-consuming process that requires taxonomic expertise. With the advent of automated image acquisition workﬂows, large image datasets can now be acquired, but require eﬃcient preprocessing methods. Detecting diatom frustules on microscope images is a challenge due to their low relief, diverse shapes, and tendency to aggregate, which prevent the use of traditional thresholding techniques. Deep learning algorithms have the potential to resolve these challenges, more particularly for the task of object detection. Here we explore the use of a Faster R-CNN (Region-based Convolutional Neural Network) model to detect siliceous biominerals, including diatoms, in microscope images of a sediment trap series from the Mediterranean Sea. Our workﬂow demonstrates promising results, achieving a precision score of 0.72 and a recall score of 0.74 when applied to a test set of Mediterranean diatom images. Our model performance decreases when used to detect fragments of these microfossils; it also decreases when particles are aggregated or when images are out of focus. Microfossil detection remains high when the model is used on a microscope image set of sediments from a diﬀerent oceanic basin, demonstrating its potential for application in a wide range of contemporary and paleoenvironmental studies. This automated method provides a valuable tool for analysing complex samples, particularly for rare species under-represented in training datasets.
A Position-Aware Deep Model for Relevance Matching in Information Retrieval

In order to adopt deep learning for ad-hoc information retrieval, it is essential to establish suitable representations of query-document pairs and to design neural architectures that are able to digest such representations. In particular, they ought to capture all relevant information required to assess the relevance of a document for a given user query, including term overlap as well as positional information such as proximity and term dependencies. While previous work has successfully captured unigram term matches, none has successfully used position-dependent information on a standard benchmark test collection. In this work, we address this gap by encoding the relevance matching in terms of similarity matrices and using a deep model to digest such matrices. We present a novel model architecture consisting of convolutional layers to capture term dependencies and proximity among query term occurrences, followed by a recurrent layer to capture relevance over dierent query terms. Extensive experiments on Trec Web Track data conrm that the proposed model with similarity matrix representations yields improved search results.
Decadal scale relationship between indices of climate variability and Australian rainfall

Australia’s climate is characterised by high intra and inter annual; decadal and longer term variability of such elements as temperature and rainfall. Various drivers are responsible for variability at these tempos, for example: the Madden Julian Oscillation, El Nino Southern Oscillation (ENSO) and Pacific Decadal Oscillation respectively. Rainfall variability dramatically impacts on the nation’s economy and efforts to understand it can assist in drought mitigation and safeguard farming and infrastructure from its associated weather extrema. 1. A Pearson’s 'r' technique incorporating Lanczos filtering to track the correlation of 24 globally diverse, monthly climate indices with spatially resolved Australian summer rainfall (December, January and February) for the 11 decades from 1900 – 2008. 2. Relationship was scored (ranked) in terms of four criteria: a. population variance was assessed as non-biased indicator, b. interdecadal variance change, c. the area of significant correlation d. and the temporal stability of a significant correlation pattern. 3. Finally each index was ranked by its overall score. The highest scoring index was the BEST index a combination of the Southern Oscillation Index (SOI) and the Nino3.4 Index. A novel aspect of this study is the use of Simple Ocean Data Analysis (SODA) datasets where necessary to overcome poor availability of ocean climate data prior to the satellite age. High correlations were from some of the oceanic warm pool (WP) indices that captured the size/volume of the WP regions adjacent to the Australian continent, either in terms of ocean heat content, or a Sea Surface Temperature metric. A WP index based on the Pacific Warm Pool (PWP) region achieved a much higher variance than the Southern Oscillation Index (SOI) and the Warm Water Volume West (WWV_W) index achieved equal second rank in score. There are no pre-existent studies that correlate WP indices with Australian decadal rainfall. A large variety of climate indices were also correlated against South East Queensland rainfall where an unexplained reduction in summer rainfall had been observed since 1980. The de facto El Nino index, Nino3.4 and SOI fared worse than they do for other regions of Australia. A WP index based on the Warm Water Volume East (WWV_E) was by far the highest scoring index. Derived ENSO indices also scored well. The thesis expands on the existing literature and a subsequent paper will highlight the significance of WP indices and further investigations and applications.
Pharmacotherapy of Obsessive‐Compulsive Disorder

Obsessive‐compulsive disorder (OCD) is a potentially devastating illness, both to the patient and family members. Its etiology is unclear, but some evidence points toward dysfunction in an orbitofrontal striatal‐limbic neuronal loop. Although many agents have been used, clomipramine, a tricyclic antidepressant, appears to be the most promising therapy. Clomipramine was approved by the Food and Drug Administration and released for general use in early 1990 under the brand name Anafranil. Clomipramine's adverse effect profile is similar to that of currently marketed tricyclic antidepressants; however, it is associated with a higher frequency of seizures, estimated to be 0.7%. Although other serotonergic agents such as fluoxetine have shown promise in OCD, they have been studied only in a limited number of patients. Other agents, with the possible exception of monoamine oxidase inhibitors, either have resulted in inconsistent improvement or have been reported in an anecdotal fashion.
A new species of Antherospora supports the systematic placement of its host plant

The morphology and phylogeny of anther smut specimens on Tractema verna collected in the United Kingdom were investigated using light microscopy, scanning electron microscopy and partial rDNA sequence analyses. The anther smut of Tractema verna shows similarity to Antherospora eucomis, A. scillae, A. tourneuxii, A. urgineae, A. vaillantii, and A. vindobonensis but differs in spore size range, spore wall thickness, host plant genera and considerable divergences of ITS and LSU sequences. Consequently, the smut is described here as a new species, Antherospora tractemae. The host plant was formerly included in the genus Scilla (S. verna), but recently moved to a distinct genus Tractema. Molecular phylogenetic analyses reveal that Antherospora tractemae is sister to the lineage of Muscari-parasitizing Antherospora and only distantly related to the Scilla-parasitizing Antherospora species. Thus, the phylogenetic placement of the smut fungus supports the systematic placement of its host plant.
Encapsulating Interaction Techniques of 3D Language Editors in Visual Patterns

The implementation of three-dimensional visual languages requires a wide range of conceptional and technical knowledge on issues for 3D graphics and textual language processing. Our generator framework DEViL3D incorporates such knowledge and supports the design of visual 3D languages and their implementation from high-level specifications. Such 3D languages arise from different modeling domains that make use of three-dimensional representations, e.g., the "ball-and-stick"models of molecules. The front-end of a 3D language implementation is a dedicated 3D graphical structure editor, which offers interaction and navigation techniques to construct programs in their domain. These techniques allow to manipulate the 3D program directly using operations to insert, move, and restructure objects. We have developed canned solutions for all such techniques that are encapsulated in visual patterns, which are provided by our generator. The designer of a particular 3D language only has to apply visual patterns to constructs of the abstract syntax, which defines the basic structure of the language. We have complemented our development with a usability study. Participants had to solve several tasks with different interaction or navigation techniques. The results partially indicate a significant advantage of one technique over another.
The gist of everything new: personalized top-k processing over web 2.0 streams

Web 2.0 portals have made content generation easier than ever with millions of users contributing news stories in form of posts in weblogs or short textual snippets as in Twitter. Efficient and effective filtering solutions are key to allow users stay tuned to this ever-growing ocean of information, releasing only relevant trickles of personal interest. In classical information filtering systems, user interests are formulated using standard IR techniques and data from all available information sources is filtered based on a predefined absolute quality-based threshold. In contrast to this restrictive approach which may still overwhelm the user with the returned stream of data, we envision a system which continuously keeps the user updated with only the top-k relevant new information. Freshness of data is guaranteed by considering it valid for a particular time interval, controlled by a sliding window. Considering relevance as relative to the existing pool of new information creates a highly dynamic setting. We present POL-filter which together with our maintenance module constitute an efficient solution to this kind of problem. We show by comprehensive performance evaluations using real world data, obtained from a weblog crawl, that our approach brings performance gains compared to state-of-the-art.
Acoustic measures of temporal intervals across speaking rates: variability of syllable- and phrase-level relative timing.

It has been suggested previously that at least some levels of the temporal organization for speech production are characterized by proportional timing. The proportional timing model maintains that the duration of temporal intervals within a sequence would remain proportionally invariant across changes in overall duration of the sequence. In order to test this hypothesis for the acoustic level of speech production, 18 women produced three trials of the utterance "Buy Bobby a poppy" at each of three speaking rates (i.e., slow, normal, fast). Acoustically derived temporal intervals were paired to form ratios reflecting either syllable-level or phrase-level relative timing. Findings indicated that ratios of temporal intervals at both the syllable-level and phrase-level did not remain invariant across speaking rates. Rather, statistically significant changes in the relative duration of both types of intervals were observed as a function of overall rate of production. For most of the obtained ratios, the direction of these changes was highly consistent across individual subjects.
Methionine Regeneration and Aspartate Aminotransferase in Parasitic Protozoa

ABSTRACT Aspartate aminotransferases have been cloned and expressed fromCrithidia fasciculata, Trypanosoma brucei brucei, Giardia intestinalis, andPlasmodium falciparum and have been found to play a role in the final step of methionine regeneration from methylthioadenosine. All five enzymes contain sequence motifs consistent with membership in the Ia subfamily of aminotransferases; the crithidial and giardial enzymes and one trypanosomal enzyme were identified as cytoplasmic aspartate aminotransferases, and the second trypanosomal enzyme was identified as a mitochondrial aspartate aminotransferase. The plasmodial enzyme contained unique sequence substitutions and appears to be highly divergent from the existing members of the Ia subfamily. In addition, the P. falciparum enzyme is the first aminotransferase found to lack the invariant residue G197 (P. K. Mehta, T. I. Hale, and P. Christen, Eur. J. Biochem. 214:549–561, 1993), a feature shared by sequences discovered in P. vivax and P. berghei. All five enzymes were able to catalyze aspartate-ketoglutarate, tyrosine-ketoglutarate, and amino acid-ketomethiobutyrate aminotransfer reactions. In the latter, glutamate, phenylalanine, tyrosine, tryptophan, and histidine were all found to be effective amino donors. The crithidial and trypanosomal cytosolic aminotransferases were also able to catalyze alanine-ketoglutarate and glutamine-ketoglutarate aminotransfer reactions and, in common with the giardial aminotransferase, were able to catalyze the leucine-ketomethiobutyrate aminotransfer reaction. In all cases, the kinetic constants were broadly similar, with the exception of that of the plasmodial enzyme, which catalyzed the transamination of ketomethiobutyrate significantly more slowly than aspartate-ketoglutarate aminotransfer. This result obtained with the recombinant P. falciparum aminotransferase parallels the results seen for total ketomethiobutyrate transamination in malarial homogenates; activity in the latter was much lower than that in homogenates from other organisms. Total ketomethiobutyrate transamination in Trichomonas vaginalis and G. intestinalis homogenates was extensive and involved lysine-ketomethiobutyrate enzyme activity in addition to the aspartate aminotransferase activity. The methionine production in these two species could be inhibited by the amino-oxy compounds canaline and carboxymethoxylamine. Canaline was also found to be an uncompetitive inhibitor of the plasmodial aspartate aminotransferase, with aKi of 27 μM.
An Automatic Query Generation Approach for Arabic Corpus

of the most common problems that encounter retrieval systems is the query environment which is utilized to evaluate the performance or throughput of them. Usually data sets of queries for a specific corpus are generated using the human experiences. Manual queries are more accurate than automatic one's, but they require a huge effort in the huge corpus. This paper proposes an automatic query generation (AQG) system for Arabic language. The system generates a set of queries of different length that were applied on a query expansion system. The results show the feasibility of these queries compared with manual one in term of average recall and average precision.
Efficient Detection of Channel Predicates in Distributed Systems

This paper discusses efficient detection of global predicates in a distributed program. Previous work in this area required predicates to be specified as a conjunction of predicates defined on individual processes. Many properties in distributed systems, however, use the state of channels, such as “the channel is empty,” or “there is a token in the channel. ” In this paper, we introduce the concept of alinearchannel predicate and provide efficient centralized and distributed algorithms to detect any conjunction of local and linear channel predicates. The class of linear predicates is fairly broad. For example, classic problems such as detection of termination and computation of global virtual time are instances of conjunctions of linear channel predicates. Linear predicates can be functions of the number of messages in the channel, or can be based upon the actual contents of the messages. The main application of our results are in debugging and testing of distributed programs. For these applications it is important to detect thefirststate where some predicate is true. We show that this first state is uniquely defined if and only if linear predicates are used.
Land Subsidence Monitoring in Greater Vancouver Through Synergy of InSAR and Polarimetric Analysis

Abstract Up-to-date spatial information on ground movements and land use is useful for emergency management of coastal regions. Time series InSAR techniques have proven to be effective tools for providing the former; however, InSAR results alone cannot be used to characterize the relationship between movements and land use. The focus of this study is to evaluate the potential to use high resolution radar satellite imagery for monitoring urban land subsidence associated with the construction of new building in Canadian coastal cities. To do this, we propose to integrate InSAR and polarimetric SAR information for deformation analysis. The methodology included multidimensional small baseline subset (MSBAS) InSAR analysis, polarimetric SAR change detection, and integration of the coherence, deformation, and polarimetric information for identifying the urban surface movements related to new buildings. The study was conducted in the Vancouver region, BC using RADARSAT-2 satellite data of ultra-fine mode and fine-quad mode acquired during 2010-2016. Results demonstrated that the integration of polarimetric and InSAR data permitted identification of ground movement, and the association of these movements to the new constructions in the urban environment. Several locations have been experiencing subsidence at a rate of up to 10 cm/year, and horizontal motion of 5 cm/year.
Evolutionarily Conserved Protein Sequences of Influenza A Viruses, Avian and Human, as Vaccine Targets

Background Influenza A viruses generate an extreme genetic diversity through point mutation and gene segment exchange, resulting in many new strains that emerge from the animal reservoirs, among which was the recent highly pathogenic H5N1 virus. This genetic diversity also endows these viruses with a dynamic adaptability to their habitats, one result being the rapid selection of genomic variants that resist the immune responses of infected hosts. With the possibility of an influenza A pandemic, a critical need is a vaccine that will recognize and protect against any influenza A pathogen. One feasible approach is a vaccine containing conserved immunogenic protein sequences that represent the genotypic diversity of all current and future avian and human influenza viruses as an alternative to current vaccines that address only the known circulating virus strains. Methodology/Principal Findings Methodologies for large-scale analysis of the evolutionary variability of the influenza A virus proteins recorded in public databases were developed and used to elucidate the amino acid sequence diversity and conservation of 36,343 sequences of the 11 viral proteins of the recorded virus isolates of the past 30 years. Technologies were also applied to identify the conserved amino acid sequences from isolates of the past decade, and to evaluate the predicted human lymphocyte antigen (HLA) supertype-restricted class I and II T-cell epitopes of the conserved sequences. Fifty-five (55) sequences of 9 or more amino acids of the polymerases (PB2, PB1, and PA), nucleoprotein (NP), and matrix 1 (M1) proteins were completely conserved in at least 80%, many in 95 to 100%, of the avian and human influenza A virus isolates despite the marked evolutionary variability of the viruses. Almost all (50) of these conserved sequences contained putative supertype HLA class I or class II epitopes as predicted by 4 peptide-HLA binding algorithms. Additionally, data of the Immune Epitope Database (IEDB) include 29 experimentally identified HLA class I and II T-cell epitopes present in 14 of the conserved sequences. Conclusions/Significance This study of all reported influenza A virus protein sequences, avian and human, has identified 55 highly conserved sequences, most of which are predicted to have immune relevance as T-cell epitopes. This is a necessary first step in the design and analysis of a polyepitope, pan-influenza A vaccine. In addition to the application described herein, these technologies can be applied to other pathogens and to other therapeutic modalities designed to attack DNA, RNA, or protein sequences critical to pathogen function.
What level of domestic government health expenditure should we aspire to for universal health coverage?

Abstract Global discussions on universal health coverage (UHC) have focussed attention on the need for increased government funding for health care in many low- and middle-income countries. The objective of this paper is to explore potential targets for government spending on health to progress towards UHC. An explicit target for government expenditure on health care relative to gross domestic product (GDP) is a potentially powerful tool for holding governments to account in progressing to UHC, particularly in the context of UHC’s inclusion in the Sustainable Development Goals. It is likely to be more influential than the Abuja target, which requires decreases in budget allocations to other sectors and is opposed by finance ministries for undermining their autonomy in making sectoral budget allocation decisions. International Monetary Fund and World Health Organisation data sets were used to analyse the relationship between government health expenditure and proxy indicators for the UHC goals of financial protection and access to quality health care, and triangulated with available country case studies estimating the resource requirements for a universal health system. Our analyses point towards a target of government spending on health of at least 5% of GDP for progressing towards UHC. This can be supplemented by a per capita target of $86 to promote universal access to primary care services in low-income countries.