Miracle-dz/UniFAR-FTUs huggingface dataset:
THE TAXONOMY AND PHYLOGENETIC RELATIONSHIPS OF SPECIES IN THE BACTROCERA MUSAE COMPLEX OF FRUIT FLIES (DIPTERA: TEPHRITIDAE: DACINAE) IN PAPUA NEW GUINEA

Bactrocera (Bactrocera) musae (Tryon) is a major pest species of some banana varieties in northern Queensland, the Torres Strait islands, Papua New Guinea and associated islands. It is the only pest species in a complex of 17 species described herein. Five of these are new species and are described and illustrated: Bactrocera (Bactrocera) balagawii, B. (B.) parabancroftii, B. (B.) ramuensis, B. (B.) rufi vitta, B. (B.) uvariae. The remaining twelve species have been previously described and are revised with up-to-date information on host plants, attractant records and geographic distributions. Further, a molecular study was able to explore the distinction between six of the described species. A phylogeney based on 562 base pairs of the COI gene showed strong agreement between morphological and molecular data. Furthermore, for three of the species that occurred in sympatry and were represented by suffi cient sample numbers (namely, B. contermina, B. musae, B. rufi vitta), analysis of eight new microsatellite loci using STRUCTURE also supported them as distinct species.
Yeasts as the Novel Attractant of Pomacea canaliculata

Pomacea canaliculata (golden apple snail, GAS) has become a major pest, which threatens rice cultivation especially in Asia. To control this pest, many farmers use extensively synthetic molluscicides that are not only expensive but of broad spectrum, therefore affecting non-target organisms including human beings. This study aimed to explore new biological attractant that could be used to attract the snails as an essential aspect of integrated pest control. The novel potential of isolated yeasts, identified as Candida ethanolica and Pichia kudriavzevii based on the 18S rRNA identification, as microbial-based bait for attraction of GAS was elucidated. Both the male and female GAS showed the highest moving rates towards C. ethanolica strain M2 activated in 5% molasses. This is the first report on the potential of yeasts as bait or lure for GAS which can used in integrated pest management.
Wnt5a Stimulates the Bone Formation in Tension Side during Orthodontic Tooth Movement

In this study, we first investigated the expression of wnt5a in tension sites during experimental tooth movement in rats in vivo . We then assessed the effects of wnt5a on the expression of bone marker from human periodontal ligament (hPDL) cells. Twelve male 6-week old Wistar rats were subjected to an orthodontic force of 10g in order to induce the mesial tipping movement of the upper first molars for 7 days. The expression levels of wnt5a proteins in the alveolar bone were determined using an immunohistochemical analysis. Furthermore, the effects of wnt5a on the gene expressions of alkaline phosphatase (ALP) and type I collagen (COL1) were investigated using hPDL cells in vitro . Under the conditions of experimental tooth movement in vivo , the immunoreactivity for wnt5a was detected in the tension side on day 7 in the PDL tissue of rats subjected to the orthodontic force (10g). In the in vitro study, wnt5a treatment increased the gene expression of ALP and COL1 from the hPDL cells in a time-dependent manner. These results suggest that the wnt5a stimulates the alveolar bone formation in the tension side during orthodontic tooth movement.
Bilingual Text Extraction as Reading Comprehension

In this paper, we propose a method to extract bilingual texts automatically from noisy parallel corpora by framing the problem as a token-level span prediction, such as SQuAD-style Reading Comprehension. To extract a span of the target document that is a translation of a given source sentence (span), we use either QANet or multilingual BERT. QANet can be trained for a specific parallel corpus from scratch, while multilingual BERT can utilize pre-trained multilingual representations. For the span prediction method using QANet, we introduce a total optimization method using integer linear programming to achieve consistency in the predicted parallel spans. We conduct a parallel sentence extraction experiment using simulated noisy parallel corpora with two language pairs (En-Fr and En-Ja) and find that the proposed method using QANet achieves significantly better accuracy than a baseline method using two bi-directional RNN encoders, particularly for distant language pairs (En-Ja). We also conduct a sentence alignment experiment using En-Ja newspaper articles and find that the proposed method using multilingual BERT achieves significantly better accuracy than a baseline method using a bilingual dictionary and dynamic programming.
Binary autoencoder with random binary weights

Here is presented an analysis of an autoencoder with binary activations $\{0, 1\}$ and binary $\{0, 1\}$ random weights. Such set up puts this model at the intersection of different fields: neuroscience, information theory, sparse coding, and machine learning. It is shown that the sparse activation of the hidden layer arises naturally in order to preserve information between layers. Furthermore, with a large enough hidden layer, it is possible to get zero reconstruction error for any input just by varying the thresholds of neurons. The model preserves the similarity of inputs at the hidden layer that is maximal for the dense hidden layer activation. By analyzing the mutual information between layers it is shown that the difference between sparse and dense representations is related to a memory-computation trade-off. The model is similar to an olfactory perception system of a fruit fly, and the presented theoretical results give useful insights toward understanding more complex neural networks.
TACRED Revisited: A Thorough Evaluation of the TACRED Relation Extraction Task

TACRED is one of the largest, most widely used crowdsourced datasets in Relation Extraction (RE). But, even with recent advances in unsupervised pre-training and knowledge enhanced neural RE, models still show a high error rate. In this paper, we investigate the questions: Have we reached a performance ceiling or is there still room for improvement? And how do crowd annotations, dataset, and models contribute to this error rate? To answer these questions, we first validate the most challenging 5K examples in the development and test sets using trained annotators. We find that label errors account for 8% absolute F1 test error, and that more than 50% of the examples need to be relabeled. On the relabeled test set the average F1 score of a large baseline model set improves from 62.1 to 70.1. After validation, we analyze misclassifications on the challenging instances, categorize them into linguistically motivated error groups, and verify the resulting error hypotheses on three state-of-the-art RE models. We show that two groups of ambiguous relations are responsible for most of the remaining errors and that models may adopt shallow heuristics on the dataset when entities are not masked.
Les processus biogéochimiques impliqués dans la mobilité de l’arsenic : recherche de bioindicateurs

Les bacteries jouent un role majeur dans la mobilite de l’arsenic (As) dans l’environnement. L’objectif de cette these etait d’identifier les acteurs bacteriens cles de la biotransformation de l’As pouvant etre utilises comme bioindicateurs du devenir de l’As dans les sites pollues. De nouveaux outils moleculaires ont ete developpes sur les genes aoxB, codant la sous-unite catalytique de l’AsIII-oxydase, et valides pour analyser qualitativement et quantitativement les communautes AsIII-oxydantes. La pertinence de l’usage de ce gene comme marqueur fonctionnel a ete demontree par sa detection exclusive chez toutes les bacteries AsIII-oxydantes testees et une phylogenie AoxB coherente et similaire a celle de l’ARNr 16S. Les approches de DGGE et de PCR en temps reel appliquees aux genes aoxB ont permis d’evaluer rapidement et sensiblement les variations de communautes AsIII-oxydantes associees a differentes teneurs et speciations d’As dans des eaux. La coexistence de diverses bacteries AsIII-oxydantes et AsV-reductrices a egalement ete demontree dans des sols industriels et agricoles. La microflore indigene est ainsi capable d’influencer la speciation/mobilite de l’As initialement present et/ou adsorbe sur des oxy-hydroxydes de fer selon les conditions redox du milieu. L’usage des genes fonctionnels aoxB et arrA, marqueurs des bacteries AsIII-oxydantes et respirant l’AsV, est pertinent pour evaluer les transformations potentielles de l’As. L’effet de bacteries agissant indirectement sur la mobilite de l’As a egalement ete revele. La detection de ces activites bacteriennes a l’aide d’outils moleculaires est prometteuse pour evaluer la mobilite de l’As dans un ecosysteme donne.
Investigating Transferability in Pretrained Language Models

How does language model pretraining help transfer learning? We consider a simple ablation technique for determining the impact of each pretrained layer on transfer task performance. This method, partial reinitialization, involves replacing different layers of a pretrained model with random weights, then finetuning the entire model on the transfer task and observing the change in performance. This technique reveals that in BERT, layers with high probing performance on downstream GLUE tasks are neither necessary nor sufficient for high accuracy on those tasks. Furthermore, the benefit of using pretrained parameters for a layer varies dramatically with finetuning dataset size: parameters that provide tremendous performance improvement when data is plentiful may provide negligible benefits in data-scarce settings. These results reveal the complexity of the transfer learning process, highlighting the limitations of methods that operate on frozen models or single data samples.
Phylogeography of a Palaearctic sedentary passerine, the willow tit (Parus montanus)

We analysed variation of the mitochondrial control region from willow tits through its Palaearctic distribution range. Although we found high amount of genetic variation (π=1.114%), there was almost no differentiation between subspecies or geographical localities. This may be because of a combination of several ecological and genetic factors, including a relatively homogenic habitat through the distribution range, lack of geographical barriers, high gene flow and a large long‐term effective population size. On the contrary, in the songar tit, which is sometimes considered to be conspecific with the willow tit, the mitochondrial lineages seem to correlate with the geographical locality and are clearly distinct from the willow tit. We concluded that the common ancestors of willow and songar tits existed some 1.5–2 Myr ago in the south‐eastern Asia. After the last Ice Ages, the willow tit expanded all through the Palaearctic, whereas the songar tit remained in eastern Asia.
A Frequency Selective Feedback Receiver for Multi‐Bands Operation

For a frequency‐division duplex (FDD) wide‐band code‐division multiple‐access (WCDMA) system, transmit (TX) signal leakage at the receiver input degrades the receiver performance. To cancel this TX leakage, a frequency selective feedback was previously proposed, but it had an unpredictable feedback loop characteristic due to the uncertainty of the duplexer impedance. This paper presents a new method to achieve TX leakage cancellation regardless of the duplexer impedance. In addition, a local oscillator (LO) phase shift technique is proposed to apply this method for multi‐band. A receiver adopting these proposed techniques is implemented using a 0.18‐μm CMOS process to prove the concept. The measured TX attenuations of the high‐ and low‐band are 17‐dB and 20‐dB, respectively, and the measured noise Figure (NF) degradations of the high‐ and low‐band are 0.6‐dB and 0.5‐dB, respectively. The measurement results demonstrate effectiveness of the proposed techniques.
Superconducting Materials for Microwave Kinetic Inductance Detectors

The superconducting materials that make up an MKID have a significant effect on its performance. The $T_\textrm{c}$ and normal state resistivity $\rho_\textrm{N}$ of the film determine the penetration depth $\lambda$ and therefore how much kinetic inductance it has. The ratio of kinetic inductance to total inductance ($\alpha$), the volume of the inductor, and $Q_\textrm{m}$ determines the magnitude of the response to incoming energy. The quasiparticle lifetime $\tau_\textrm{qp}$ is the characteristic time during which the MKID's surface impedance is modified by the incoming energy. Many materials have been explored for use in superconducting resonators and MKIDs, but that information is often not published or scattered around the literature. This chapter contains information and references on the work that has been done with thin film lithographed circuits for MKIDs over the last two decades. Note that measured material properties such as the internal loss quality factor $Q_\textrm{i}$ and quasiparticle lifetime $\tau_\textrm{qp}$ vary significantly depending on how the MKID superconducting thin film is made and the system they are measured in, so it is best to interpret all stated values as typical but not definitive. Values are omitted in cases when there aren't enough measurements or there is too much disagreement in the literature to estimate a typical value. In order to be as complete as possible some unpublished results from the author's lab are included and can be identified by the lack of a reference. Unless noted all films are polycrystalline or amorphous.
A Benchmark Dataset of Check-worthy Factual Claims

In this paper we present the ClaimBuster dataset of 23,533 statements extracted from all U.S. general election presidential debates and annotated by human coders. The ClaimBuster dataset can be leveraged in building computational methods to identify claims that are worth fact-checking from the myriad of sources of digital or traditional media. The ClaimBuster dataset is publicly available to the research community, and it can be found at http://doi.org/10.5281/zenodo.3609356.
A New Species of the Genus Acanthosaura Gray, 1831 (Reptilia: Agamidae) from Central Vietnam

We describe a new agamid species of the genus Acanthosaura from Khanh Hoa and Phu Yen provinces, central Vietnam based on morphological and molecular data. The new species, Acanthosaura murphyi sp. nov., most closely resembles the Indochinese horned lizard ( A. capra ) and the Natalia horned lizard ( A. nataliae ), however, it can be differentiated from other congeners by the following characters: a large-sized species (snout-vent length = 103.7 – 127.3 mm in adult males, 123.0 mm in the adult female); cylindrical spine above posterior margin of eye present; spine on occiput between tympanum and nuchal crest absent; two scale rows between rostral scute and nostril; small slightly keeled scales on flank randomly intermixed with keeled medium and large scales; nuchal crests strongly developed; dorsal crests developed and separate from nuchal crests by a diastema; coloration in life of body varies from gray in adult to brown or emerald green in subadult, and brown to whitish gray ventral skin; and tail brown or greenish with indistinct light bands. Genetically, uncorrected sequence divergences of COI between the new species and its closest species, A. capra , is 6.5%. To date, the new species has been found in evergreen forest between 84 – 1060 m in Phu Yen and Khanh Hoa provinces only.
Investigation to Increase the Viricidal Capacity of Disinfectant, Germicidal and Fungicidal, Phenolic, Dry-Type

Abstract : The straight O-D-1435 Type II disinfectant had little capacity to inactivate the poliovirus type I when used in concentrations up to 15,000 mg/l with contact times up to 24 hours. The Coxsackie A9 and Echo 12 viruses showed no inactivation with 10,000 mg/l of disinfectant and contact times of 30 minutes. An increase of the pH to more than 12 did potentiate the disinfectant for poliovirus inactivation. The survival at a pH of 12.1 with 10,000 mg/l of disinfectant was less than 0.01 percent after 5 minutes of contact. The survival at this pH without the disinfectant was 58%. Anionic surfactants in concentrations from 100 to 10,000 mg/1 had little capacity for increasing the viricidal capacity of the disinfectant. Cationic and nonionic surfactants had no enhancement ability.
Presence of a Novel Methanogenic Archaeal Lineage in Anaerobic Digesters Inferred from mcrA and 16S rRNA Gene Phylogenetic Analyses

To find taxonomically novel methanogenic archaea, a clone analysis targeting mcrA gene (a functional molecular marker of methanogenic archaea) was conducted for four anaerobic granular sludges. Several mcrA gene phylotypes were clearly different from those of other groups of known methanogens. These were found to belong to an unidentified group called as MCR-2b group. Comparative phylogenetic analysis of deduced amino acid of McrA and 16S rRNA gene sequences revealed that the MCR2-b McrA group is possibly derived from a novel methanogen group; the 16S rRNA gene sequences have been classified into an uncultured archaeal group WCHA1-57. The result suggests that WCHA1-57 archaeal group may represent a putative new order of the methanogenic archaeal group that contributes to methane production in anaerobic digesters.
The effect of stimulus onset asynchrony between different response cues on reasoning in a base rate task

Recent theories of dual processing propose the existence of multiple Type 1 processes which cue responses during reasoning. If these responses do not point towards the same answer then that conflict may be detected. If the conflict is detected, Type 2 processing is initiated to resolve it. This study is concerned with the timeline and relative strength of different Type 1 processes in a modified base rate task. The task can cue congruent (stereotype and probability point towards the same answer) or incongruent responses. We varied the SOA (stimulus onset asynchrony) time between the stereotype inducing and base rate information. The study was a 2 (congruence) × 3 (SOA: 200, 800, 1400ms) experimental design. The analysis of the total data set showed a significant congruence effect regardless of SOA for both response times and confidence. Additionally, an analysis of stereotypical and base rate responses was conducted for each level of SOA. Results showed a marginal response type by SOA interaction effect. Response times decreased for the base rate and increased for stereotypical responses as SOA increased. The same effect was not found for confidence ratings. The results imply responses cued by the stereotype information decreased in strength as SOA increased. This effect may lead to a conclusion that Type 1 process strength decays over time.
TREE MORTALITY AND RECRUITMENT IN A SUBTROPICAL BROADLEAVED MONSOON FOREST IN SOUTH CHINA

BIN Y, LIAN J, WANG Z, YE W & CAO H. 2011. Tree mortality and recruitment in a subtropical broadleaved monsoon forest in south China. Mortality and recruitment are key factors influencing forest succession. Using spatial pattern and neighbourhood analyses, effects of conspecifics and heterospecifics upon mortality and recruitment of some locally dominant tree species were investigated in a 1-ha forest plot. Specifically, we were interested in how species in different layers of the forest responded to such effects in a subtropical forest in China. During a seven-year period (1992-1999), mortality rates of the studied species ranged from 2 to 7% per year while recruitment rates ranged from 0 to 3% per year. At this small spatial scale, mortality of all but one species was random in space. Unlike mortality, however, recruitment into the al-cm size class consistently occurred where local conspecific density was high. This suggests that this process may be limited by seed dispersal. Heterospecific individuals did not influence recruitment significantly for any species. Both canopy species had difficulty recruiting into the al-cm size class during the study period. In conclusion, tree mortality in this patch of forest was random and recruitment for six non-canopy species and two canopy species was possibly limited by seed availability and ecological needs respectively.
Aspects of pseudolocality in Ricci flow

This thesis explores two separate problems related to the phenomenon of pseudolocality within Ricci flow. First, we consider the regularity of noncollapsed three-dimensional Ricci limit spaces via Ricci flow. We introduce a new weakened notion of Ricci flow, termed Pyramid Ricci flow, and use it to establish that a noncollapsed three-dimensional Ricci limit space is homeomorphic to a smooth manifold via a globally-defined homeomorphism that is bi-Hӧlder once restricted to any compact subset. We include the full details of a well-known compactness result which this work relies upon. Second, we consider the pseudolocality phenomenon in an almost-hyperbolic setting. We obtain an improved pseudolocality result for Ricci flows on two-dimensional surfaces that are initially almost-hyperbolic on large hyperbolic balls. We prove that, at the central point of the hyperbolic ball, the Gauss curvature remains close to the hyperbolic value for a time that grows exponentially in the radius of the ball. This two-dimensional result allows us to precisely conjecture how the phenomenon should appear in the higher dimensional setting.
Development of peptide nucleic acid probes to detect helicobacter pylori in diverse species potable water biofilms

The application of novel technology peptide nucleic acid (PNA) molecular probes for the visualization of Helicobacter pylori in biofilms has been assessed. The probes selected were highly specific for the pathogen and did not hybridize with any of the autochthonous bacteria isolated or with any other component from the water biofilm. The use of this technique made the pathogen detection quick and reliable however, the presence of autofluorescent microorganisms and stacks in the biofilm samples implied that care had to be taken not to misidentify the bacteria. H. pylori can successfully incorporate within biofilms and all three different types of morphology were identified. PNA probes appear to be a promising new technique for the in situ visualization of microorganisms in biofilms and a further development of this technique may allow the simultaneous detection of different species.
Cellular computation using classifier systems

The EU FP6 Integrated Project PACE ('Programmable Artificial Cell Evolution') is investigating the creation, de novo, of chemical 'protocells'. These will be minimal 'wetware' chemical systems integrating molecular information carriers, primitive energy conversion (metabolism) and containment (membrane). Ultimately they should be capable of autonomous reproduction, and be 'programmable' to realise specific desired function. A key objective of PACE is to explore the application of such protocell technology to build novel nanoscale computational devices. Our contribution to this project is to investigate approaches to adding minimal computational capability to protocells. We introduce the Molecular Classifier System (MCS) to represent the internal molecular reactions of the protocell. Reactions in the MCS are constrained as follows: The products of the reaction depend on the reactants and the environment in which the reaction took place; The reactions that can happen depend on the physical and chemical structure of the reacting compounds. In our MCS, there are reactants and reaction rules. The rules determine the reactants and the products for a given interaction. These simple computational processes may also help in understanding the origins of Cell Signaling Networks(CSNs). CSNs are complex bio-chemical networks responsible for coordinating and controlling cellular activities. CSNs can therefore be regarded as computational systems. To understand the evolution of such complex computational systems as found in nature, we will distinguish the minimal computational properties fundamental for the survival of a protocell.