Miracle-dz/UniFAR-FTUs huggingface dataset:
Re-establishment of the North Sea houting in the River Rhine

The anadromous fish species North Sea houting, Coregonus oxyrinchus (L.), became extinct in the River Rhine (Kranenbarg et al. 2002) and many other rivers draining to the North Sea in the 1940s (Lelek 1987). The cause was believed to be a combination of overfishing, poor water quality, habitat loss and fragmentation and barriers hampering upstream migrations (De Groot & Nijssen 1997). Since the 1980s, water quality in the River Rhine has greatly improved, many migration barriers were facilitated with fishways (De Leeuw et al. 2005) and no commercial fisheries on houting existed after its extinction. Thus, a large part of the possible causes for extinction were mitigated. Given the small size and isolation from the only remaining houting population in Denmark, it was decided to reintroduce houting in the German section of the River Rhine (cf. Hodder & Bullock 1997). Descendants of the last known reproducing popUlation
A simple model for obstructed two-dimensional turbulent channel flow

We have investigated obstructed two-dimensional turbulent channel flow. The objective is to provide a simple building block for design models and to gain physical insight in this type of flow. We have designed a simple model with some unknown parameters to be calibrated against a CFD model. The model divides the domain between an area of main flow and recirculation areas. The model approximates these areas by polygonal shapes. The locations of the vertices of these polygons are the parameters in the model. This way, we can evaluate the simple model using the Schwarz-Christoffel integral. As a consequence, the model can be evaluated much more quickly than CFD models. The main flow is modeled to be irrotational. The recirculation area behind the obstacle is modeled as a stretched monopolar vortex and this requires 4 extra parameters. The other areas of separated flow are simply modeled to be stationary. By calibrating the simple model we have demonstrated that this physical description works reasonably well. Using only 9 parameters, the simple model reaches an error of 22\\% of the inflow velocity.
Changes in contact patterns shape the dynamics of the COVID-19 outbreak in China

Who and what next? The coronavirus 2019 (COVID-19) pandemic has brought tighter restrictions on the daily lives of millions of people, but we do not yet understand what measures are the most effective. Zhang et al. modeled virus transmission in Wuhan, China, in February 2020, investigating the effects of interventions ranging from patient management to social isolation. Age-mixing patterns were estimated by contact surveys conducted in Wuhan and Shanghai at the beginning of February 2020. Once people reduced their average daily contacts from 14 to 20 down to 2, transmission rapidly fell below the epidemic threshold. The model also showed that preemptive school closures helped to reduce transmission, although alone they would not prevent a COVID-19 outbreak. Limiting human mixing to within households appeared to be the most effective measure. Science, this issue p. 1481 Reducing social contacts on the scale achieved in Wuhan and Shanghai in early 2020 could be sufficient to bring a COVID-19 outbreak under control. Intense nonpharmaceutical interventions were put in place in China to stop transmission of the novel coronavirus disease 2019 (COVID-19). As transmission intensifies in other countries, the interplay between age, contact patterns, social distancing, susceptibility to infection, and COVID-19 dynamics remains unclear. To answer these questions, we analyze contact survey data for Wuhan and Shanghai before and during the outbreak and contact-tracing information from Hunan province. Daily contacts were reduced seven- to eightfold during the COVID-19 social distancing period, with most interactions restricted to the household. We find that children 0 to 14 years of age are less susceptible to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection than adults 15 to 64 years of age (odds ratio 0.34, 95% confidence interval 0.24 to 0.49), whereas individuals more than 65 years of age are more susceptible to infection (odds ratio 1.47, 95% confidence interval 1.12 to 1.92). Based on these data, we built a transmission model to study the impact of social distancing and school closure on transmission. We find that social distancing alone, as implemented in China during the outbreak, is sufficient to control COVID-19. Although proactive school closures cannot interrupt transmission on their own, they can reduce peak incidence by 40 to 60% and delay the epidemic.
Paralytic shellfish toxin profiles of xanthid crabs Zosimus aeneus and Atergatis floridus collected on reefs of Ishigaki Island

Toxin compositions in xanthid crabs Zosimus aeneus and Atergatis floridus were examined. Three specimens of each were collected on reefs of Ishigaki Island, Okinawa Prefecture, and were dissect ed into 6 parts; muscle of appendages, muscle of cephalothorax, skeleton of appendages, skeleton of cephalothorax, viscera, and gills. Toxicity of each tissue was determined by mouse bioassay and toxin compositions by high performance liquid chromatography (HPLC) with fluorometric detection. In both crabs, muscle of appendages gave the highest toxicities (1,100-5,900 MU/g) among the 6 tissues, and those of muscle of cephalothorax and gills were less than one tenth of it. In Z. aeneus, relative abun dances (mole%) of carbamoyl-N-hydroxyneosaxitoxin (hyneoSTX) and neosaxitoxin (neoSTX) were rather high, and 10~15% of gonyautoxins (GTXs) were contained in addition to similar amounts of carbamoyl-N-hydroxysaxitoxin (hySTX), decarbamoylsaxitoxin (dcSTX), and saxitoxin (STX) ir respective of tissues except for gills. A. floridus possessed STX predominantly over the other STXs with no detectable amount of GTXs. In both crabs, gills had a somewhat different toxin profile from the other tissues with higher neoSTX and STX but lower hyneoSTX and hySTX. A good correlation was observed between the toxicities calculated from the results of HPLC analyses and those from mouse bioassay.
Where does a ‘foreign’ accent matter? German, Spanish and Singaporean listeners’ reactions to Dutch-accented English, and standard British and American English accents

How well L2 English is understood and how L2 English speakers perceive one another within varying communication contexts has been studied relatively rarely, even though most speakers of English in the world are L2 speakers. In this matched-guise experiment (N = 1699) the effects of L1 and L2 English accents and communication context were tested on speech understandability (intelligibility, comprehensibility, interpretability) and speaker evaluations (status, affect, dynamism). German (N = 617), Spanish (N = 540), and Singaporean listeners (N = 542) were asked to evaluate three accents (Dutch-accented English, standard British English, standard American English) in three communication contexts (Lecture, Audio Tour, Job Pitch). The main finding is that the Dutch-accented English accent was understood as well as the two L1 English accents. Furthermore, Dutch-accented English evoked equally positive evaluations to the two L1 English accents in German listeners, and more positive evaluations than the two L1 English accents in Spanish and Singaporean listeners. These results suggest that accent training aimed at achieving an L1 English accent may not always be necessary for (Dutch) English language learners, especially when they are expected to mostly interact with other L2 speakers of English. More generally, our results indicate that L2 English speakers’ understanding and their evaluation of L1 and L2 Englishes would not seem to reflect traditional language norms. Instead, they seem to reflect the socio-cultural embedding of a language norm in a Lingua Franca English speech community that does not view accent varieties as a hindrance to successful communication.
The effect of weeds on the value of rotation as a practical control for Verticillium wilt of potato.

in microplot tests in Ontario rotation of potatoes with barley or fallow proved ineffective in controlling Verticillium wilt caused by Verticillium dahliae or Verticillium albo-atrum. Several weed species were excellent hosts of 1/. dahliae, and microsclerotia were produced on their roots within 2 weeks of inoculation. In soil samples averaging 1.3 microsclerotia of I/. dahliae per g of soil 80-90% of the Kennebec potato test plants became infected. It is suggested that variations in the number of viable microsclerotia in soil at the start of a rotation experiment, the effectiveness of the weed control program, and the weather during the experiment could account for the controversy surrounding the value of rotation as a means of control. The authors suggest that in Ontario rotation would be of no value in controlling Verticillium wilt of potato.
ICOS signaling promotes a secondary humoral response after re-challenge with Plasmodium chabaudi chabaudi AS

The co-stimulatory molecule ICOS is associated with the induction and regulation of T helper cell responses, including the differentiation of follicular helper T (Tfh) cells and the formation and maintenance of memory T cells. However, the role of ICOS signaling in secondary immune responses is largely unexplored. Here we show that memory T cell formation and maintenance are influenced by persistent infection with P. chabaudi chabaudi AS infection, as memory T cell numbers decline in wild-type and Icos-/- mice after drug-clearance. Following drug-clearance Icos-/- mice display a relapsing parasitemia that occurs more frequently and with higher peaks compared to wild-type mice after re-challenge. The secondary immune response in Icos-/- mice is characterized by significant impairment in the expansion of effector cells with a Tfh-like phenotype, which is associated with a diminished and delayed parasite-specific Ab response and the absence of germinal centers. Similarly, the administration of an anti-ICOSL antagonizing antibody to wild-type mice before and after reinfection with P. c. chabaudi AS leads to an early defect in Tfh cell expansion and parasite-specific antibody production, confirming a need for ICOS-ICOSL interactions to promote memory B cell responses. Furthermore, adoptive transfer of central memory T (TCM) cells from wild-type and Icos-/- mice into tcrb-/- mice to directly evaluate the ability of TCM cells to give rise to Tfh cells revealed that TCM cells from wild-type mice acquire a mixed Th1- and Tfh-like phenotype after P. c. chabaudi AS infection. While TCM cells from Icos-/- mice expand and display markers of activation to a similar degree as their WT counterparts, they displayed a reduced capacity to upregulate markers indicative of a Tfh cell phenotype, resulting in a diminished humoral response. Together these findings verify that ICOS signaling in memory T cells plays an integral role in promoting T cell effector responses during secondary infection with P. c. chabaudi AS.
Seven Challenges for the Dehumanization Hypothesis

Propagandists often compare members of stigmatized out-groups to nonhuman entities such as rats, lice, and snakes. Drawing on these horrifying descriptions, the dehumanization hypothesis proposes that out-group members are viewed as less than human and that being viewed as less than human renders them vulnerable to harm. I offer seven challenges to the dehumanization hypothesis. I argue that, even in supposedly prototypical examples of extreme dehumanization, out-group members are not treated like nonhuman entities. Furthermore, although out-group members may be denied some human qualities and states, they are attributed others. I also argue that there is reason to doubt the hypothesized causal connection between being viewed as less than human and being at risk of harm—some nonhuman organisms are treated with great care, and some groups are harmed because of how their uniquely human qualities are perceived. I close by offering an alternative account of why out-group members are sometimes referred to as nonhuman entities.
Decoding the evolution and transmissions of the novel pneumonia coronavirus (SARS-CoV-2 / HCoV-19) using whole genomic data

The outbreak of COVID-19 started in mid-December 2019 in Wuhan, China. Up to 29 February 2020, SARS-CoV-2 (HCoV-19 / 2019-nCoV) had infected more than 85 000 people in the world. In this study, we used 93 complete genomes of SARS-CoV-2 from the GISAID EpiFluTM database to investigate the evolution and human-to-human transmissions of SARS-CoV-2 in the first two months of the outbreak. We constructed haplotypes of the SARS-CoV-2 genomes, performed phylogenomic analyses and estimated the potential population size changes of the virus. The date of population expansion was calculated based on the expansion parameter tau (τ) using the formula t=τ/2u. A total of 120 substitution sites with 119 codons, including 79 non-synonymous and 40 synonymous substitutions, were found in eight coding-regions in the SARS-CoV-2 genomes. Forty non-synonymous substitutions are potentially associated with virus adaptation. No combinations were detected. The 58 haplotypes (31 found in samples from China and 31 from outside China) were identified in 93 viral genomes under study and could be classified into five groups. By applying the reported bat coronavirus genome (bat-RaTG13-CoV) as the outgroup, we found that haplotypes H13 and H38 might be considered as ancestral haplotypes, and later H1 was derived from the intermediate haplotype H3. The population size of the SARS-CoV-2 was estimated to have undergone a recent expansion on 06 January 2020, and an early expansion on 08 December 2019. Furthermore, phyloepidemiologic approaches have recovered specific directions of human-to-human transmissions and the potential sources for international infected cases.
Geochemical effects of biomass burning and land degradation on Lanyu Islet, Taiwan

Reconstructed coral skeletal Pb : Ca and Ba : Ca ratios from the Northern Coast of Lanyu Islet are shown to be sensitive indicators of land–use practices which took place on the islet during the past 30 years. Coral skeletal Pb : Ca and Ba : Ca both increased dramatically. Pb : Ca ratios are very sensitive to biomass burning on Lanyu Islet while Ba : Ca generally respond to rainfall variations except in case of instantaneous flooding. The method presented here provides a quantitative technique for identifying human effects that can be used for coastal land management and offers a way to study the environment during prehistoric times, where no written records are available.
Matrix-Assisted Laser Desorption/Ionization-Mass Spectrometry Imaging of Metabolites during Sorghum Germination1[OPEN]

Matrix-assisted laser desorption/ionization-mass spectrometry imaging reveals that biosynthesis and recycling of the plant defense compound dhurrin are key events during sorghum grain germination. Dhurrin is the most abundant cyanogenic glucoside found in sorghum (Sorghum bicolor) where it plays a key role in chemical defense by releasing toxic hydrogen cyanide upon tissue disruption. Besides this well-established function, there is strong evidence that dhurrin plays additional roles, e.g. as a transport and storage form of nitrogen, released via endogenous recycling pathways. However, knowledge about how, when and why dhurrin is endogenously metabolized is limited. We combined targeted metabolite profiling with matrix-assisted laser desorption/ionization-mass spectrometry imaging to investigate accumulation of dhurrin, its recycling products and key general metabolites in four different sorghum lines during 72 h of grain imbibition, germination and early seedling development, as well as the spatial distribution of these metabolites in two of the lines. Little or no dhurrin or recycling products were present in the dry grain, but their de novo biosynthesis started immediately after water uptake. Dhurrin accumulation increased rapidly within the first 24 h in parallel with an increase in free amino acids, a key event in seed germination. The trajectories and final concentrations of dhurrin, the recycling products and free amino acids reached within the experimental period were dependent on genotype. Matrix-assisted laser desorption/ionization-mass spectrometry imaging demonstrated that dhurrin primarily accumulated in the germinating embryo, confirming its function in protecting the emerging tissue against herbivory. The dhurrin recycling products, however, were mainly located in the scutellum and/or pericarp/seed coat region, suggesting unknown key functions in germination.
Solid waste management practices in two northern Manitoba first nations communities: community perspectives on the issues and solutions

i ACKNOWLEDGEMENTS . iii GLOSSARY OF TERMS . iv TABLE OF CONTENTS . vi LIST OF TABLES AND FIGURES . viii CHAPTER 1: INTRODUCTION . 1 1.1 Problem Statement . 3 1.2 Objectives . 4 1.3 Rationale . 4 1.4 Significance. 5 1.5 Study Area . 5 1.6 Thesis Lay-out . 7 CHAPTER 2: LITERATURE REVIEW . 9 2.1 Solid Wastes. 9 2.2 Solid Waste Management in Canadian First Nationscommunities. 11 2.3 The Concept of Integrated Solid Waste Management . 13 2.4 Management Options for Solid Wastes . 19 2.4. 1 Waste diversion and reduction. 20 2.4. 2 Source reduction. 23 2.4. 3 Recycling. 24 2.4. 4 Composting and anaerobic digestion. 26 2.4. 5 Thermal treatments. 29 2.4. 6 Landfill. 32 2.5 Solid Waste Management Legislation in Canada . 35 2.6 Waste Management and Human Behaviour . 36 2.7 Hazardous Wastes . 38 CHAPTER 3: RESEARCH METHODOLOGY AND METHODS . 52 3.
Study on the milk yield aptitudes of the Turcana sheep raised in the north-east side of the country.

The researches focused on the assessment of milking capacity of mother ewes on the growing rhythm of the own littered lambs. The biological material belonged to Turcana breed, structured on age periods as, reported to the generations. It resulted, after the researches were finished, that the average milk yield was of 94.234 l during the first 85 days of lactation, at the studied sheep population. The high performance achieved for milk yield confirmed the very good milking capacity of Turcana ewes with straight consequences on the lambs growing speed, right after parturition. The correlation coefficient for the following traits pair suckled milk quantity and lambs growing speed presented higher values, rp: 0.84 during the 0-15 days age period and rp: 0.79, for the 16-28 days period. The strength of correlation between milk yield and growing speed decreased at rp: 0.46 for the age period of 43-55 days, respectively at rp:0.24 for suckling period comprised between 71 and 85 days.
Adventitious rooting in microcuttings of selected indigenous landscape trees of Malaysia.

Rooting performance in microcuttings of five indigenous and one exotic landscape tree species was evaluated in a 60 days period. Rate of rooting varied greatly among species as Ilex cymosa, Tabebuia heterophylla and Agalaia korthalsii reached 100% rooting at 24, 42 and 48 days after insertion into the rooting medium followed by Lepisanthes rubiginosa and Hopea odorata species (95 & 80% rooting at 60 days, respectively). The poorest rooting ability (30% rooting at 60 days) was shown by Aporusa globifera and was first noticed at 30 days. Results of Ilex cymosa species for adventitious root induction per microcutting was markedly different from other species and it produced the highest number of adventitious roots (14.07 roots/microcutting). A. korthalsii generated the fewer, but the heaviest roots compared to I. cymosa. Rooting ability of microcuttings was highly correlated with its number of leaves produced during rooting (r = 0.869-0.981) as well as, with regenerative shoot length of the mother plants (r = 0.690-0.954). Regenerative leaf growth of mother plants and the rooting of their microcuttings was species-specific suggesting that developing association between the two parameters is difficult.
Why does sugarcane grow slowly

It had seemed, from juxtaposing results in a number of papers, such as those of Bull and Glasziou (1975), Begg (1965) and Wilson et al. (1973), that sugarcane grows more slowly than some other tall tropical grasses. To assess the significance of this with respect to sucrose production, unpublished data of RJ Haslam was used to directly compare sugarcane with Napier grass (Pennisetum purpureum), a tropical grass which is morphologically similar and is also vegetatively propagated, but produces little sugar.
TRIM59 Inhibits PPM1A through Ubiquitination and Activates TGF-β/Smad Signaling to Promote the Invasion of Ectopic Endometrial Stromal cells in Endometriosis.

To define the underlying molecular mechanism of TRIM59-induced invasion of ectopic endometrial stromal cells in endometriosis. Primary endometriosis ectopic endometrial stromal cells and normal endometrial cells were isolated and purified. Western blot was used to detect the expression of TRIM59, PPM1A, smad2/3 and p-smad2/3; Lentiviral vector-mediated TRIM59 interference and overexpression were established; CCK8 assay was used to detect cell proliferation and the transwell migration assay was used to detect cell invasion. MMP2 (Matrix metalloproteinase-2), MMP9, smad2/3, and p-smad2/3 expressions were also detected using western blot analysis; degradation of PPM1A was verified to be through ubiquitination. TRIM59 expression levels in the endometriosis group was significantly higher as compared to the normal group, while the expression levels of PPM1A in the endometriosis group were significantly lower. Endometriosis did not alter smad2/3 expression. However, after activating smad2/3 by phosphorylation, the expression of p-smad2/3 in the endometriosis group was significantly higher as compared with the normal group. The content of PPM1A in the TRIM59 overexpression group was significantly lower than that in the control group, whereas the content of PPM1A in the siTRIM59 group was significantly higher than that in the control group. In addition, there were no significant differences in the mRNA levels of PPM1A amongst the five groups, indicating that TRIM59 affects the expression of PPM1A at the post-translational level. Overexpression of TRIM59 significantly promoted the ubiquitination of PPM1A. TRIM59 inhibits PPM1A through ubiquitination and activates the TGF-β/Smad pathway to promote the invasion of ectopic endometrial stromal cells in endometriosis.
The Effect of the Incomplete Lactation Records for Genetic Evaluations with Random Regression Test-Day Models (RRTDM) in Holstein Cattle

The purpose of this study was to find out the effects that daughters' incomplete lactation records affect sire's breeding values through genetic evaluation using RRTDM(random regression test-day model). First, we estimated genetic parameters and breeding values on sires having complete lactation records of daughter by RRTDM, second, we changed complete lactation records of specific sires into incomplete records by various methods. Third, the breeding values were compared between complete and incomplete records. Finally, this study aimed to find out the methods to minimize the estimation errors of young bulls' breeding values. Data used in this study were collected from the dairy herd improvement program, and a total of 97,562 records were composed of 10,929 first parity with both parents known, since 1999. Breeding values on the daughters from randomly chosen sires were calculated and compared with among 90 day, 150day, and 200 day's incomplete records. For milk yields, sire's ranks of breeding values used by complete lactation records were very different from sire's ranks of breeding values obtained by incomplete lactation records(Rank_90 cut, 150cut, 200 cut). The differences were also obtained between complete lactation records(per305_full) and incomplete lactation record (per_90 cut, 150cut, 200 cut) in breeding values regarding persistency. Especially, the differences between per_90 cut and per305_full were very large(from 1.8 kg to 145kg).