Miracle-dz/UniFAR-FTUs huggingface dataset:
Combining Subword Representations into Word-level Representations in the Transformer Architecture

In Neural Machine Translation, using word-level tokens leads to degradation in translation quality. The dominant approaches use subword-level tokens, but this increases the length of the sequences and makes it difficult to profit from word-level information such as POS tags or semantic dependencies. We propose a modification to the Transformer model to combine subword-level representations into word-level ones in the first layers of the encoder, reducing the effective length of the sequences in the following layers and providing a natural point to incorporate extra word-level information. Our experiments show that this approach maintains the translation quality with respect to the normal Transformer model when no extra word-level information is injected and that it is superior to the currently dominant method for incorporating word-level source language information to models based on subword-level vocabularies.
SRPOL’s System for the IWSLT 2020 End-to-End Speech Translation Task

We took part in the offline End-to-End English to German TED lectures translation task. We based our solution on our last year’s submission. We used a slightly altered Transformer architecture with ResNet-like convolutional layer preparing the audio input to Transformer encoder. To improve the model’s quality of translation we introduced two regularization techniques and trained on machine translated Librispeech corpus in addition to iwslt-corpus, TEDLIUM2 andMust_C corpora. Our best model scored almost 3 BLEU higher than last year’s model. To segment 2020 test set we used exactly the same procedure as last year.
Coexistence of Sexual and Parthenogenetic Artemia Populations in Lake Urmia and Neighbouring Lagoons

We studied the Artemia populations existing in Lake Urmia (north-western Iran), one of the largest habitats of Artemia in the world, in order to settle the long-standing controversy over the sexual status of the endemic Artemia populations. Experiments were carried out in the laboratory and in the field. Cysts, collected from different sites of the lake and peripheral lagoons, were hatched and cultured to adults in the laboratory. Adult sexual and parthenogenetic animals were isolated and newly hatched nauplii from them were cultured to maturity in different salinities, ranging from 15–80 ppt. Survival levels and percentage of animals attaining adulthood were measured over a period of 30 days. In the field experiment, cysts taken from Lake Urmia were hatched and the resulting nauplii were inoculated into six earthen ponds (80–140 ppt) constructed in the vicinity of the lake. Population composition in each pond was determined over a period of two years. Results indicated that both sexual and parthenogenetic Artemia coexist in Lake Urmia. While the lake itself is dominated by sexual Artemia, the asexual populations were found to be restricted to particular areas in or near the lake. Artemia appearing seasonally in the lagoons adjacent to the lake were exclusively parthenogenetic. Parthenogens could grow, mature and reproduce at very low salinities (15–33 ppt), whereas higher salinities (above 50 ppt) were required for A. urmiana to attain sexual maturity. We consider salinity to be a major abiotic factor determining the distribution of these sexually different populations within and outside the lake. (© 2007 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)
Patterns of carbon allocation above ground in a deciduous (Vaccinium uliginosum) and an evergreen (Vaccinium vitis‐idaea) dwarf shrub

The carbon allocation to current-year shoots of the deciduous Vaccinium uliginosum L. and the evergreen V. vitis-idaea L. was studied in a field experiment using 14C. During the first week after labelling, 0–50% and 30–80% of the initially assimilated 14C was lost in V. vitis-idaea and V. uliginosum respectively. Later on, the losses were smaller. After leaf fall in V. uliginosum, 30, 10 and 8% of the initially assimilated 14C was recovered in the abscised leaves, in plants labelled 1 July, 1 August and 1 September, respectively. The amounts found in the old V. vitis-idaea leaves the year after labelling were 33, 20 and 10%. Only traces of past-year assimilates were found in the current-year V. vitis-idaea leaves, while it was estimated that the V. uliginosum leaves contained 10–15% of the past-year label. It is concluded that V. vitis-idaea is mainly dependent on early summer assimilates - produced by leaves that have overwintered – for the current year shoot growth, while past-years' assimilates probably make an important contribution to the leaf expansion in V. uliginosum. When fruits occurred, a large fraction of the 14C assimilates was allocated to them.
School-based intervention to address self-regulation and executive functioning in children attending primary schools in remote Australian Aboriginal communities

Executive functioning and self-regulation influence a range of outcomes across the life course including physical and mental health, educational success, and employment. Children prenatally exposed to alcohol or early life trauma (ELT) are at higher risk of impairment of these skills and may require intervention to address self-regulation deficits. Researchers partnered with the local Aboriginal health organization and schools to develop and pilot a manualized version of the Alert Program® in the Fitzroy Valley, north Western Australia, a region with documented high rates of fetal alcohol spectrum disorder and ELT. This self-controlled cluster randomized trial evaluated the effect of an 8-week Alert Program® intervention on children’s executive functioning and self-regulation skills. Following parent or caregiver consent (referred to hereafter as parent), 271 students were enrolled in the study. This reflects a 75% participation rate and indicates the strong community support that exists for the study. Teachers from 26 primary school classrooms across eight Fitzroy Valley schools received training to deliver eight, one-hour Alert Program® lessons over eight-weeks to students. Student outcomes were measured by parent and teacher ratings of children’s behavioral, emotional, and cognitive regulation. The mean number of lessons attended by children was 4.2. Although no significant improvements to children’s executive functioning skills or behavior were detected via the teacher-rated measures as hypothesized, statistically significant improvements were noted on parent-rated measures of executive functioning and behavior. The effectiveness of future self-regulation programs may be enhanced through multimodal delivery through home, school and community based settings to maximize children’s exposure to the intervention. Despite mixed findings of effect, this study was an important first step in adapting and evaluating the Alert Program® for use in remote Australian Aboriginal community schools, where access to self-regulation interventions is limited.
Energy requirements during reproduction and reproductive effort in shrews (Soricidae)

The energy requirements of reproducing and non-reproducing females of three species of Crocidura (C. russula, C. viaria, C. olivieri), and two species of Sorex (S. coronatus, S. minutus) were measured. Members of these two genera show different rates of metabolism and reproductive strategies (extreme altriciality and larger litter size in Sorex). During pregnancy, the daily energy intake (on either an absolute or a mass-specific basis) remained close to the non-reproductive value in all species. The absolute energy intake increased strongly after parturition and was influenced by the litter size. Peak energy intake of lactating females was extremely high, typically between 100% and 200% above the non-reproductive requirements in the Crocidura and about 300% above the non-reproductive intake in the Sorex. The mass-specific daily energy intake was reduced during lactation in the three smaller species but not in C. viaria and C. olivieri. This decrease probably involves the different thermoregulatory abilities and/or basal rate of metabolism of the pups. Average reproductive effort was about 50%, in the Crocidura species and above 150% in the Sorex species. The higher effort in the latter is partly due to a larger litter size. But in addition, extreme altriciality in the Sorex leads to an earlier increase in the energy requirements and thus is an energetically more expensive reproductive mode. The present results support the hypothesis that a higher basal rate of metabolism is associated with a higher reproductive effort in shrews.
Infectious Bronchitis Virus Evolution, Diagnosis and Control

RNA viruses are characterized by high mutation and recombination rates, which allow a rapid adaptation to new environments. Most of the emerging diseases and host jumps are therefore sustained by these viruses. Rapid evolution may also hinder the understanding of molecular epidemiology, affect the sensitivity of diagnostic assays, limit the vaccine efficacy and favor episodes of immune escape, thus significantly complicating the control of even well-known pathogens. The history of infectious bronchitis virus (IBV) fits well with the above-mentioned scenario. Despite being known since the 1930s, it still represents one of the main causes of disease and economic losses for the poultry industry. A plethora of strategies have been developed and applied over time, with variable success, to limit its impact. However, they have rarely been evaluated objectively and on an adequate scale. Therefore, the actual advantages and disadvantages of IBV detection and control strategies, as well as their implementation, still largely depend on individual sensibility. The present manuscript aims to review the main features of IBV biology and evolution, focusing on their relevance and potential applications in terms of diagnosis and control.
Three types of HLA-G+ extravillous trophoblasts that have distinct immune regulatory properties

Significance Fetal extravillous trophoblasts (EVT) invade maternal uterine tissues and play a key role in placental development. EVT express HLA-C, a highly polymorphic antigen that can elicit allogeneic responses, and HLA-G, which is associated with immune tolerance. EVT are difficult to study due to the low numbers that can be obtained, their lack of proliferative capacity, limited survival, and lack of cell lines that recapitulate their unique functions. We succeeded in isolating three types of HLA-G+ EVT from human first trimester and term placental tissues that have significant changes in their phenotypes, gene expression, responses to pro-inflammatory signals, and induction of regulatory T cells. These methods and insights are useful for understanding of maternal–fetal tolerance and development of pregnancy complications. During pregnancy, invading HLA-G+ extravillous trophoblasts (EVT) play a key role in placental development, uterine spiral artery remodeling, and prevention of detrimental maternal immune responses to placental and fetal antigens. Failures of these processes are suggested to play a role in the development of pregnancy complications, but very little is known about the underlying mechanisms. Here we present validated methods to purify and culture primary HLA-G+ EVT from the placental disk and chorionic membrane from healthy term pregnancy. Characterization of HLA-G+ EVT from term pregnancy compared to first trimester revealed their unique phenotypes, gene expression profiles, and differing capacities to increase regulatory T cells (Treg) during coculture assays, features that cannot be captured by using surrogate cell lines or animal models. Furthermore, clinical variables including gestational age and fetal sex significantly influenced EVT biology and function. These methods and approaches form a solid basis for further investigation of the role of HLA-G+ EVT in the development of detrimental placental inflammatory responses associated with pregnancy complications, including spontaneous preterm delivery and preeclampsia.
Patterns of polychaete communities in relation to environmental perturbations in a subtropical wetland of Hong Kong

Benthic polychaetes in the largest intertidal mudflat of Hong Kong were analysed for potentially stressed environmental conditions from pollution. Over a two-year period, a total of 14 species were recorded with the species diversity (H′(log2)) ranged from 0.54 to 2.4. The community was dominated by two large polychaetes (Neanthes glandicincta and Potamilla acuminata) and a number of small pollution tolerant species (Tharyx, Capitella capitata and Prionospio cirrifera). It was also characterized by both temporal and spatial variations in terms of abundance and species composition with the lowest species number observed at onshore Station B in August and the highest at offshore Station D in February. Two distinct polychaete communities were formed along the intertidal towards subtidal mudflat, particularly the assemblage at onshore Station B showing a significant difference from those at the other three stations (P < 0.05, N = 32). Results of the abundance–biomass comparison (ABC) indicated a typical impacted community at the whole study area, especially at Station B which was close to the Shenzhen River mouth and mangrove forest. The total organic carbon had a significant positive effect on the abundance of Capitella capitata (P = 0.037, N = 8) while sedimentary compositions were statistically related to the abundance of Potamilla acuminata, Tharyx and total abundance of polychaetes (P < 0.05, N = 8). In conclusion, both the polluted Shenzhen River and nearby mangrove may be responsible for the decline in species richness and diversity as well as changes in community structure. Polychaetes can be used as the appropriate indicators in habitat ecological condition assessment instead of the whole benthic community.
COVID-19: lessons for junior doctors redeployed to critical care

Approximately 4% of patients with coronavirus disease 2019 (COVID-19) will require admission to an intensive care unit (ICU). Governments have cancelled elective procedures, ordered new ventilators and built new hospitals to meet this unprecedented challenge. However, intensive care ultimately relies on human resources. To enhance surge capacity, many junior doctors have been redeployed to ICU despite a relative lack of training and experience. The COVID-19 pandemic poses additional challenges to new ICU recruits, from the practicalities of using personal protective equipment to higher risks of burnout and moral injury. In this article, we describe lessons for junior doctors responsible for managing patients who are critically ill with COVID-19 based on our experiences at an urban teaching hospital.
Genome-Wide Identification of Discriminative Genetic Variations in Beef and Dairy Cattle via an Information-Theoretic Approach

Analyzing the associations between genotypic changes and phenotypic traits on a genome-wide scale can contribute to understanding the functional roles of distinct genetic variations during breed development. We performed a whole-genome analysis of Angus and Jersey cattle breeds using conditional mutual information, which is an information-theoretic method estimating the conditional independency among multiple factor variables. The proposed conditional mutual information-based approach allows breed-discriminative genetic variations to be explicitly identified from tens of millions of SNP (single nucleotide polymorphism) positions on a genome-wide scale while minimizing the usage of prior knowledge. Using this data-driven approach, we identified biologically relevant functional genes, including breed-specific variants for cattle traits such as beef and dairy production. The identified lipid-related genes were shown to be significantly associated with lipid and triglyceride metabolism, fat cell differentiation, and muscle development. In addition, we confirmed that milk-related genes are involved in mammary gland development, lactation, and mastitis-associated processes. Our results provide the distinct properties of Angus and Jersey cattle at a genome-wide level. Moreover, this study offers important insights into discovering unrevealed genetic variants for breed-specific traits and the identification of genetic signatures of diverse cattle breeds with respect to target breed-specific properties.
Exploring causes of the decline of the lichen Lecanora conizaeoides in Britain: effects of experimental N and S applications

Abstract The crustose lichen Lecanora conizaeoides has declined markedly around London with progressively diminishing sulphur dioxide pollution of the air since the 1960s. To identify the immediate causes of its decline, we applied S in the form of bisulphite (0·2 & 2 mM) and sulphate (2 mM), and N as nitrate (2 mM) to relict colonies of the lichen on beech trunks in a plantation in Windsor Forest. Growth of the lichen was monitored by estimating changes in percentage cover. By the end of a 25-month period of two-weekly treatments, all the chemical treatments had resulted in significant decreases in cover of L. conizaeoides compared to distilled water controls, with the 2 mM bisulphite causing the greatest loss. Bark surface pH was also lowered by the chemical treatments, but most by the 2 mM bisulphite applications. Similar results were obtained in two laboratory experiments where the nutrient applications were repeated under a controlled environment and thallus area monitored photographically. No evidence was obtained to support the hypothesis that growth of L. conizaeoides is stimulated by an elevated sulphur supply. We conclude that the disappearance of the lichen is linked to gradual increase in bark pH caused by the combined effects of a marked reduction in SO2 emissions and rising emissions of NH3.
Meta-analysis on the long-term effectiveness of psychological and medical treatments for binge-eating disorder.

OBJECTIVE Long-term effectiveness is a critical aspect of the clinical utility of a treatment; however, a meta-analytic evaluation of psychological and medical treatments for binge-eating disorder (BED), including weight loss treatments, is outstanding. This meta-analysis sought to provide a comprehensive evaluation of the long-term effectiveness in diverse treatments for BED regarding a range of clinically relevant outcomes. METHOD Based on a systematic search up to February 2018, 114 published and unpublished randomized-controlled (RCTs), nonrandomized, and uncontrolled treatment studies, totaling 8,862 individuals with BED (DSM-IV, DSM-5), were identified and analyzed using within-group random-effect modeling. RESULTS Effectiveness (regarding binge-eating episodes and abstinence, eating disorder and general psychopathology) up to 12 months following treatment was demonstrated for psychotherapy, structured self-help treatment, and combined treatment, while the results regarding body weight reduction were inconsistent. These results were confirmed in sensitivity analyses with RCTs on the most common treatments-cognitive-behavioral therapy and self-help treatment based on this approach. Follow-up intervals longer than 12 months were rarely reported, mostly supporting the long-term effectiveness of psychotherapy. Few follow-up data were available for pharmacotherapy, and behavioral and self-help weight loss treatment, while follow-up data were lacking for pharmacological and surgical weight loss treatment. Study quality varied widely. DISCUSSION This comprehensive meta-analysis demonstrated the medium-term effectiveness of psychotherapy, structured self-help treatment, and combined treatment for patients with BED, and supported the long-term effectiveness of psychotherapy. The results were derived from uncontrolled comparisons over time. Further long-term high quality research on psychological and medical treatments for BED is required.
NICHE SEPARATION IN COMMUNITY ANALYSIS: A NEW METHOD

The design and objective of a community study imply the selection of the appropriate ordination technique in terms of species response models and weighting options. In this paper, we start from the observation that existing two-table ordination techniques and related measures of niche breadth inevitably weight a sample in proportion to its abundance. We introduce a new multivariate method, which gives a more even weight to all sampling units, including those which are species poor or individual poor. We use this new method of analysis which we call OMI (for Outlying Mean Index) to address the question of niche separation and niche breadth. The Outlying Mean Index, or species marginality, measures the distance between the mean habitat conditions used by species (species centroid), and the mean habitat conditions of the sampling area (origin of the niche hyperspace), and OMI analysis places species along habitat conditions using a maximization of their mean OMI. Therefore, the position of the species depends on their niche deviation from a reference, which represents neither the mean nor the most abundant species, but a theoretical ubiquitous species that tolerates the most general habitat conditions (i.e., a hypothetical species uniformly distributed among habitat conditions). We demonstrate that OMI analysis is well suited for the investigation of multidimensional niche breadths in the case of strong limiting factors (e.g., meteorological conditions) or strong driving forces (e.g., longitudinal stream gradient). Furthermore, the analysis helps in finding which eco- logical factors are most important for community structure and organization and provides a separation of species based on their niche characteristics.
Sand goby males trade off between defence against egg predators and sneak intrusions

According to life-history theory, a care-taking parent should balance investment in current and future reproduction in such a way that it maximizes lifetime reproductive success. In the sand goby Pomatoschistus minutus, a small marine fish with paternal care, nest-guarding males may lose current reproductive success to both parasitically fertilizing males and egg predators. Here, we observed sand gobies at a marine and a brackish site, two geographically distant and ecologically different habitats. In a field experiment, we found that sand gobies at the marine site suffered from severe egg predation by netted dogwhelks Nassarius nitidus, which are lacking at the brackish site. Because egg laying takes hours and several females often lay eggs sequentially in one nest, the risk of parasitic spawnings and egg predation overlaps in time during breeding activities. Hypothesizing that egg predators might influence the success of parasitic spawnings, we then simulated these natural conditions in a laboratory experiment with the presence or absence of egg predators, combined with the presence of sneaker males. As expected, in the egg predator treatment, egg-guarding males had to compromise between defence behaviours and thus had less time to devote to defence against sneaker males. Sneaker males took advantage of the situation and approached the nests more actively than in the predator-free treatment. However, the increase in approaches did not result in more successful parasitic fertilizations by sneaker males, as determined using microsatellite DNA. Nevertheless, in nature the adjustment of time budgets by the egg-guarding male are likely to have serious fitness consequences, both if the male fails to defend his paternity and if he fails to defend his offspring.