Miracle-dz/UniFAR-FTUs huggingface dataset:
Locomotor activity in the Namaqua rock mouse (Micaelamys namaquensis) : entrainment by light manipulations

The locomotor activity rhythms of wild-caught Namaqua rock mice (Micaelamys namaquensis (A. Smith, 1834)) were examined under four light-cycle regimes to quantitatively describe the daily expression of locomotor activity and to study the innate relationship between activity and the light–dark cycle. Activity was always significantly higher at night than during the day; we note four trends. (1) The LD1 light cycle (12 h light : 12 h dark) established a distinct light-entrained and strongly nocturnal activity rhythm (99.11% nocturnal activity). The activity onset was prompt (zeitgeber time (ZT) 12.2 ± 0.04) and activity continued without any prominent peaks or extended times of rest until the offset of activity at ZT 23.73 ± 0.08. (2) Evidence for the internal maintenance of locomotor activity was obtained from the constant dark cycle (DD) in which locomotor activity free ran (mean τ = 23.89 h) and 77.58% of the activity was expressed during the subjective night. (3) During re-entrainment (LD2; 12 h light :.
Anatomy and Morphology of Two Hawaiian Endemic Portulaca Species

The genus Portulaca is known to withstand harsh environments with its various vegetative and reproductive features. Hawaiian Portulaca species are annual or perennial herbs that rarely form shrubs. Both native and introduced Portulaca species on the Hawaiian Islands, such as P. oleracea and P. pilosa, are relatively common. However, endemic species of P. molokiniensis and P. sclerocarpa are also present although not as widespread. Among Hawaiian Portulaca species, P. molokiniensis and P. sclerocarpa have drawn attention because of their unusual vegetative and reproductive features. The relationship between these two species and other Portulaca species has been investigated in previous studies (Kim & Carr, 1990a, 1990b). P. oleracea and P. pilosa, which is widely distributed, have particularly been of focus. This is because P. oleracea has been speculated to be the parental lineage of P. molokiniensis, and P. pilosa that of P. sclerocarpa (Yun, 1989; Wagner et al., 1999). Artificial, interspecific pollinations have yielded a hybrid between the broad-leaved P. molokiniensis (2n=40) and P. oleracea (2n=54) suggesting a close affinity and polyploid nature (Kim & Carr, 1990a). Kim and Carr (1990a) have distinguished two groups of Hawaiian Portulaca species based on their chromosome ploidy level–polyploids (2n=40, 54) in broad-leaved species versus diploids (2n=18) in cylindricalleaved species. Reproductive features have been reported with variation among taxa in studies examining the reproductive biology and uniformity of Portulaca species (Kim & Carr, 1990b) as well as their cytogenetics and hybridization (Kim & Carr, 1990a). Furthermore, the Kranz anatomy, as in C-4 syndrome, has been well-demonstrated in a study investigating structural aspects of the leaves of seven Portulaca species growing in Hawaii (Kim & Fisher, 1990). In recent works, morphological and anatomical features of seeds (Kim, 2012) and pollen grains (Kim, 2013) have revealed important structural patterns among taxa. None of these studies, however, include vegetative stomata features or other features that may have been influenced by polyploidy. Thus, Anatomy and Morphology of Two Hawaiian Endemic Portulaca Species
Efficacy of pre-lay diet

A biological study was carried out to review the Bureau of Indian Standards (BIS) recommendations for layer pullet feed. Commercial layer chicks were fed till 14 weeks of age as per BIS. At 15 weeks, pullets were randomly assigned to each of the five pre-lay feeding strategies, namely T1 (BIS control), T2 (16/2700), T3 (18/2700) (%CP/kcal ME/kg), T4 (same as T2 + lysine and methionine by 10% higher than BIS) and T5 (same as T4 with 2% oil). At 5% egg production, all groups were fed as per BIS. Pullets fed on high energy and protein pre-lay diets of 2700 kcal and 18% protein-advanced sexual maturity with good body composition. Pre-layers fed 2700/18 feed had the best hen day (85.44±1.52), hen-housed egg production (84.21±1.52), layed heavier eggs, had a higher egg mass output (47.14±0.95g), gave the best feed efficiency, had the lowest pullet production cost and high egg feed price ratio. It was concluded that pre-lay pullets have to be provided with 2700/18 kcal of metabolisable energy and protein level as against the BIS recommendation of 2500/16 dietary energy and protein level.
Short-term restoration of riverine bird assemblages after a severe flood

Capsule Diversity and abundance of birds breeding in river channels increased significantly after a severe flood in southern Poland. Flooding increased the diversity of river channels, especially on previously regulated sections, and this resulted in more breeding habitat for birds. Aims To investigate how a severe flood can alter river assemblages of bird species breeding in natural pre-flood or regulated sections. Methods Data of breeding birds within submontane river channels in southern Poland from before (2007–2009) and after (2011) a flood were collected. Bird diversity and abundance in natural and pre-flood regulated sections were compared before and after the flood. Results The presence of natural features within channels increased significantly in all the studied sections. The number of bird species and breeding pairs increased both in the regulated and natural channel sections, but was much larger in the previously regulated sections. Conclusion The underlying cause of the observed short-term increase in species and their population size was thought to be a combination of increased breeding site availability and food abundance. Floods are a major factor in river channel restoration.
ENHANCING ON-FARM VARIETAL DIVERSITY THROUGH PARTICIPATORY VARIETAL SELECTION: A CASE STUDY FOR CHAITE RICE IN NEPAL

To enhance the diversification of rice varieties for the specific needs of farmers through a participatory varietal selection (PVS) approach, four pre-release and one released chaite rice varieties were distributed in 20 villages of the Western Hills of Nepal in 1991. A survey conducted during June 1993 found that varietal diversity increased in all locations and in 80% of the study area at least two new rice varieties were reported where only CH 45 was grown before the distribution. On-farm varietal diversity was further enhanced by farmer-to-farmer dissemination of new rice varieties. All the rice varieties tested were adopted, but the adoption level varied between locations. Of the households surveyed 37% were growing the new rice varieties and a further 57% were aware of those varieties within two years of introduction. The PVS approach provided farmers with the benefits of new genetic materials five to six years in advance of the formal system and with minimum effort. Institutionalization of the PVS approach and the use of the farmers' network of information and seed exchange, involving relevant grassroots level institutions, can improve the effectiveness of the variety evaluation system.
Maximizing water yield with indigenous non‐forest vegetation: a New Zealand perspective

Provision of clean freshwater is an essential ecosystem service that is under increasing pressure worldwide from a variety of conflicting demands. Water yields differ in relation to land-cover type. Successful resource management therefore requires accurate information on yields from alternative vegetation types to adequately address concerns regarding water production. Of particular importance are upper watersheds/catchments, regardless of where water is extracted. Research in New Zealand has shown that, when in good condition, indigenous tall tussock grasslands can maximize water yield relative to other vegetation cover types. A long-term hydrological paired-catchment study revealed reductions (up to 41% after 22 years) in water yielded annually from an afforested catchment relative to adjacent indigenous grassland. Furthermore, a stable isotope assessment showed that water from fog may substantially contribute to yield in upland tussock grasslands. The tall tussock life-form and its leaf anatomy and ph.
The digestibility coefficients of myristic, palmitic and stearic acids in the diet of sheep

Summary The apparent digestibility coefficients of the various constituents of diets containing myristic, palmitic or stearic acids have been determined in an experiment with 8 sheep. The inclusion of myristic acid in the diet had no effect on the digestibility coefficient of total dry matter or crude protein, but it decreased the digestibility coefficients of crude fibre and nitrogen-free-extractives and increased the digestibility coefficients of fat and minerals. When palmitic acid was included in the diet there were decreases in the digestibility coefficients of total dry matter, crude fibre and nitrogen-free-extractives. The inclusion of stearic acid in the diet resulted in decreases in the digestibility coefficients of dry matter and nitrogen-free-extractives. There was an inverse relationship between the melting points and the digestibility coefficients of the added fatty acids. The findings of this investigation are discussed in relation to the results of a previous study on the effects of these dietary fatty acids on the yield and composition of cow's milk.
From EL to Tractable Existential Rules with Complex Role Inclusions

Ontology-based data access consists in using ontologies while querying data. Due to the high complexity of this problem, considering lightweight description logics like EL is especially relevant. Another strand of research is based on existential rules. In this paper, we use this latter formalism in order to cover EL with the same complexity of reasoning while allowing any predicate arity and some cycles on variables. We then add complex role inclusions to enhance expressivity, while staying polynomial in data complexity and generalizing existing results. In particular, we consider transitivity and right/left identity rules, which do not behave well with respect to usual decidability paradigms.
Kappa-Casein Genotypic Frequencies in Holstein-Friesian Dairy Cattle in West Java Province

Kappa casein (ĸ-cn) gene as one of the four casein genes commonly has two variant alleles. B allele is positively correlated with milk proteins, so potentially be used as MAS to improve milk protein content. This study aimed to identify genetic variation of the ĸ-casein gene in Holstein-Friesian (HF) from several dairy regions in West Java. Blood samples were taken through jugular vein of lactating heifers and cows, from intensive managements under the Local Government Dairy Breeding Station - Cikole (BBPT Cikole-SP) (82 hds), Embryo Transfer Station (BET) (50 hds), and Eco Farm of Animal Science Faculty of Bogor Agricultural University (EcoFarm) (20 hds); as well as from semi-intensive managements of small dairy farmers under the supervision of the North Lembang Cooperative Unit (KPSBU Lembang) in two villages of Cilumber (98 hds) and Pasar Kemis (92 hds). Blood samples were also taken via cocsigalis vein of AI (active and non active) HF bulls at the two National AI Stations in Lembang (25 hds) and Singosari (32 hds). Identification of genetic variation was by applying PCR-RFLP method. Three genotypes were identified, namely AA, AB, and BB, resulting two alleles of A and B. Results entirely showed that the frequencies of the BB HF female were very low, with the range of 0%-6% (vs AA genotype= 10%-54% and AB genotype= 46%-85%), despite of the relatively high frequency of the B allele over the A allele (23%-48% vs. 52%-77%). The low frequency of the observed BB females might be due to the limited AI active BB bulls used for services by the two national AI stations (0%-4%).
COVID-19 versus non-COVID-19 pneumonia: A retrospective cohort study

Background and Objective: Since the outbreak of coronavirus disease 2019 (COVID-19) in December 2019 in Wuhan, Hubei Province, China, it has spread around the world and become a global public health emergency. It is important to distinguish COVID-19 from other viral pneumonias in order to properly screen and diagnose patients, reduce nosocomial infections, and complement the inadequacy of nucleic acid testing. In this study, we retrospectively analysed the clinical data of COVID-19 versus non-COVID-19 patients treated at our hospital between January 17 and February 27, 2020 in order to summarize our clinical experience in the differential diagnosis of COVID-19. Methods: In this retrospective cohort study, 23 confirmed COVID-19 patients were consecutively enrolled from January 17 to February 27, 2020, while 29 confirmed non-COVID-19 patients were enrolled in West China Hospital of Sichuan University. We collected baseline data, epidemiological data, clinical characteristics, imaging findings, viral nucleic acid test results, and survival data. SPSS v22.0 was used for statistical analysis. Outcomes were followed up until March 25. Results: A total of 52 patients were included in this study, including 23 COVID-19 patients and 29 non-COVID-19 patients. No significant between-group difference was observed in age, sex, primary signs or symptoms, cellular immunity, or platelet count. Significant between-group differences were observed in clinical characteristics such as dry cough, contact with individuals from Wuhan, some underlying diseases, nucleated cell count, chest imaging findings, viral nucleic acid test result,28-day mortality, and 28-day survival. Conclusion: Epidemiological data, clinical symptoms, nucleic acid test results for COVID-19 and chest CT manifestation may help distinguish COVID-19 from non-COVID-19 cases, prevent imported cases and nosocomial infections.
Diagnosis and significance of antibody titers in anti-NMDA receptor encephalitis, a retrospective study

1Department of Neurology at Hospital ClinicInstitut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain 2Department of Neurology, Erasmus Medical Center, Rotterdam, The Netherlands 3Biostatistics and Data Management Platform, IDIBAPS, Hospital Clinic, Barcelona, Spain 4Department of Neurology, University of Pennsylvania, Philadelphia, PA 5Department of Neurology, University of California – Los Angeles, Los Angeles, CA 6Department of Neuroscience, University of Pennsylvania, Philadelphia, PA 7Department of Neurology, University of Pennsylvania, Philadelphia, PA 8Department of Neurology, Children’s Hospital of Philadelphia (CHOP), Philadelphia, PA 9Institució Catalana de Recerca i Estudis Avançats (ICREA)
Plant functional diversity, species diversity and climate in arid and semi-arid southern Africa

Abstract This paper analyses data on growth form (functional) diversity, species richness and climate from nine Nama-Karoo/Desert sites (predominantly summer rain) and 10 Succulent Karoo sites (predominantly winter rain) along comparable gradients of total rainfall in arid and semi-arid southern Africa. Sites from the latter region were richer in total species and succulent species, but had lower growth form diversity. Contrary to the predictions of niche theory, the more heterogeneous rocky habitats did not have significantly more species or higher growth form diversity than adjacent loamy flats at the community level (25 m 2 plot). However, significantly more species were recorded in rocky than flat habitats at the site scale (10,000 m 2 ), probably reflecting the longer resource axes and higher internal beta diversity in the former habitat. Species richness showed a significant positive relationship with growth form diversity. This relationship was much tighter for the Nama-Karoo/Desert than Succulent Karoo sites indicating a higher incidence of functional redundancy (coexistence of species with similar growth forms) in the latter region. An index of climatic heterogeneity (reflecting the diversity of conditions suitable for plant growth) and measures of rainfall evenness throughout the year, emerged as the strongest predictors of species richness and growth form diversity. These results are consistent with predictions of classical niche theory. Sites with a high percentage winter rain as well as those with evenly distributed rain (with a predictable winter component) had the highest cover of succulents and Mesembryanthema. In Succulent Karoo communities functional redundancy is associated with a high number of relatively short-lived leaf succulent shrub species, belonging largely to the Mesembryanthema. However, owing to their differential response to rare but catastrophic drought-induced mortality, the diversity within this functional type ensures long-term stability of community-level growth form mix or functional diversity.
Relationship between phenology and life form: a test with 25 Patagonian species

Soil resource availability varies across seasons and soil layers. Both plant phenology, i.e. the sequence of growth and developmental changes along the year, and plant life form, i.e. the life cycle, distribution of roots, and longevity of leaves, determine the ability to use resources. The phenological heterogeneity within and among life forms of a single community may reveal key features of community structure, such as temporal niche segregation within life forms or convergence of phenological and life form patterns. We described the phenological patterns of most species of a Patagonian steppe composed of four life forms: perennial grasses, shrubs, annual herbs, and perennial herbs. By applying standard multivariate analysis techniques, we classified the species into three phenological groups and analysed the variation among groups and life forms. One phenological group, composed exclusively by grasses, had higher autumn-winter phenological activity than the other two groups. The non-grass groups differed in the date of beginning of vegetative growth and ending of the reproductive growth, one of the groups being earlier than the other. However, the three groups coincided at the phenophase of floral buds and open flowers, which occurred around the time of the maximum rate of phenological change and maximum fraction of photosynthetically active radiation being intercepted by the entire community. Phenological groups and life forms only partially overlapped: grasses and annual herbs belonged to individual phenological groups, whereas shrubs and perennial herbs spread across two groups. Thus, some life forms of the community were strictly related to a phenological behaviour, whereas other showed high temporal niche segregation. Simultaneously, diverse life forms converged into similar phenological patterns.
BIROn - Birkbeck Institutional Research Online

Uracil-DNA glycosylase (UDG) compromises the replication strategies of diverse viruses from unrelated lineages. Virally encoded proteins therefore exist to limit, inhibit or target UDG activity for pro-teolysis. Viral proteins targeting UDG, such as the bacteriophage proteins ugi, and p56, and the HIV-1 protein Vpr, share no sequence similarity, and are not structurally homologous. Such diversity has hindered identification of known or expected UDG-inhibitory activities in other genomes. The structural basis for UDG inhibition by ugi is well characterized; yet, paradoxically, the structure of the unbound p56 protein is enigmatically unrevealing of its mechanism. To resolve this conundrum, we determined the structure of a p56 dimer bound to UDG. A helix from one of the subunits of p56 occupies the UDG DNA-binding cleft, whereas the dimer interface forms a hydrophobic box to trap a mechanistically important UDG residue. Surprisingly, these p56 inhibitory elements are unexpectedly analogous to features used by ugi despite profound architectural disparity. Contacts from B-DNA to UDG are mimicked by residues of the p56 helix, echoing the role of ugi’s inhibitory beta strand. Using mutagenesis, we propose that DNA mimicry by p56 is a targeting and specificity mechanism supporting tight inhibition via hydrophobic sequestration.
Parse Disambiguation for a Rich HPSG Grammar

In this paper, we describe experiments on HPSG parse disambiguation using the Redwoods HPSG treebank. We have explored building probabilistic models for parse disambiguation using this rich HPSG treebank, assessing the effectiveness of different kinds of information. We describe generative and discriminative models using analogous features and compare their performance on the disambiguation task.
Female-specific upregulation of insulin pathway activity mediates the sex difference in Drosophila body size plasticity

Nutrient-dependent body size plasticity differs between the sexes in most species, including mammals. Previous work in Drosophila showed that body size plasticity was higher in females, yet the mechanisms underlying the sex difference in body size plasticity remain unclear. Here, we discover that a protein-rich diet augments body size in females and not males because of a female-specific increase in activity of the conserved insulin/insulin-like growth factor signaling pathway (IIS). This increased IIS activity was triggered by a diet-induced increase in stunted, and required Drosophila insulin-like peptide 2, illuminating new sex-specific roles for these genes. Importantly, we show that sex determination gene transformer regulates the diet-induced increase in stunted and IIS activity, and mediates the sex difference in body size plasticity. This identifies one sex-specific mechanism underlying the nutrient-dependent regulation of IIS activity and body size plasticity, providing vital insight into conserved mechanisms that mediate sex differences in phenotypic plasticity.
Immunochemical and cytochemical detection of wall components of germinated pollen of gymnosperms

To elucidate wall construction of gymnosperm pollen, we studied the distributions of cell wall constituents in the germinated pollen of 14 species of gymnosperms in 8 genera and 6 families cytochemically with 4 staining dyes for polysaccharides, and immunochemically with 4 monoclonal antibodies for polysaccharides and 2 monoclonal antibodies for arabinogalactan proteins (AGPs). All intines and tube walls of the pollen examined contained AGPs and cellulose. Although having small differences, pollen of the Podocarpaceae, Pinaceae, Taxodiaceae, and Cupressaceae (Coniferales) had a similar composition of wall constituents: much AGPs occurred in both the intine and the tube wall, pectins were rare in the tube wall. On the other hand, in Cycas revoluta pollen, pectins were abundant and in Ginkgo biloba , g -(1,3)(1,4)-glucan was abundant in both the intine and the tube wall. The occurrence of g -1, 3-glucan in the intines was common to six Pinus species, but its occurrence in the tube wall differed among them. None of the gymnosperm pollen tubes examined had tube walls similar to those of angiosperm pollen, which consist of two layers, a pectic outer layer and a callosic inner layer. These results suggest that wall formation in gymnosperm pollen tubes is remarkably different from that of angiosperm pollen tubes and the composition of the wall constitutes may reflect a taxonomic relationship among gymnosperms.