Miracle-dz/UniFAR-FTUs huggingface dataset:
Implications of localized charge for human influenza A H1N1 hemagglutinin evolution: Insights from deep mutational scans

Seasonal influenza A viruses of humans evolve rapidly due to strong selection pressures from host immune responses, principally on the hemagglutinin (HA) viral surface protein. Based on mouse transmission experiments, a proposed mechanism for immune evasion consists of increased avidity to host cellular receptors, mediated by electrostatic charge interactions with negatively charged cell surfaces. In support of this, the HA charge of the globally circulating H3N2 has increased over time since its pandemic. However, the same trend was not seen in H1N1 HA sequences. This is counter-intuitive, since immune escape due to increased avidity (due itself to an increase in charge) was determined experimentally. Here, we explore whether patterns of local charge of H1N1 HA can explain this discrepancy and thus further associate electrostatic charge with immune escape and viral evolutionary dynamics. Measures of site-wise functional selection and expected charge computed from deep mutational scan data on an early H1N1 HA yield a striking division of residues into three groups, separated by charge. We then explored evolutionary dynamics of these groups from 1918 to 2008. In particular, one group increases in net charge over time and consists of sites that are evolving the fastest, that are closest to the receptor binding site (RBS), and that are exposed to solvent (i.e., on the surface). By contrast, another group decreases in net charge and consists of sites that are further away from the RBS and evolving slower, but also exposed to solvent. The last group consists of those sites in the HA core, with no change in net charge and that evolve very slowly. Thus, there is a group of residues that follows the same trend as seen for the entire H3N2 HA. It is possible that the H1N1 HA is under other biophysical constraints that result in compensatory decreases in charge elsewhere on the protein. Our results implicate localized charge in HA interactions with host cells, and highlight how deep mutational scan data can inform evolutionary hypotheses.
A critical narrative analysis of psychiatrists’ engagement with psychosis as a contentious area

Background: Psychosis, characterised by altered perceptions or interpretations of reality, remains a contested area. Lately, perspectives and conceptualisations of psychosis that have traditionally been more peripheral have gained greater recognition. Both the British Psychological Society and Critical Psychiatry Network have highlighted some contentious areas in recent publications. Aims: The aim was to use critical narrative analysis to consider what facilitates and inhibits medical professionals with clinical experience of psychosis to engage with the topic of psychosis as a contentious area. Method: Semi-structured interviews were conducted with 12 medical professionals, who were at trainee or qualified level with a minimum of 6 months’ clinical experience within psychiatry, across three Trusts within the United Kingdom. This purposive sample had a diverse range of perspectives regarding psychosis. Critical narrative analysis comprising six distinct stages, informed the analysis. Results: Participants positioned themselves broadly within one of three groups: biological psychiatrists, critical psychiatrists and those more conflicted. Narrative analysis was undertaken for each participant before being integrated for this article. The research highlighted several factors which either limit or facilitate opportunities within the psychiatric profession to engage with a plurality of views regarding psychosis. These included the significance of power and hierarchy within the profession, the role of dialogue and the prevalence of reflexivity within the profession. Conclusion: A pattern was identified of psychiatrists generally associating with like-minded others and not engaging with wider evidence regarding psychosis, partly as a result of the inherent threats to the power and hierarchy of the profession. This led to new ideas being widely unknown or undervalued, potentially to the disservice of clinical practice.
Commentary: Revisiting the methods of corneal preservation in the COVID-19 era

The current COVID‐19 pandemic has brought into sharp focus the inadequacies in the corneal storage and preservation techniques. Traditionally, corneal preservation and storage have been classified as short term, intermediate, long term, and very long term. [2] The main limiting factor in donor corneal preservation is to maintain the viability of the corneal endothelium. Immediately after death, the production of aqueous humor stops, and the oxygen and nutrient supply to the endothelium ceases at room temperature. [2] It is important to limit this period of endothelial damage.
Non-Diazo C-H Insertion Approach to Cyclobutanones via Oxidative Gold Catalysis.

Cyclobutanones are synthetically versatile compounds that often requires extensive effort to access. Herein, we report a facile synthesis of cyclobutanones based on the C(sp 3 )-H insertion chemistry of oxidatively generated gold carbenes. A range of cyclobutanones was obtained in synthetically useful yields from substrates with minimal structural prefunctionalization. This discovery reveals new synthetic utilities of gold-catalyzed oxidative transformations of alkynones.
Lycosid Spiders are Friends and Enemies of the Endangered Pygmy Bluetongue Lizard (Tiliqua Adelaidensis)

Abstract The pygmy bluetongue lizard is an endangered species and the smallest member (average snoutto-vent length 95 mm) of the genus Tiliqua. It uses spider burrows with a single entrance for shelter and as sites to ambush passing prey. There is a little information about interactions between this lizard and the lycosid and mygalomorph spiders which construct the burrows they use. Surveys of the diet of pygmy bluetongue lizards show they eat lycosid spiders, and one record of a partly consumed juvenile pygmy bluetongue lizard found in a lycosid burrow suggests spiders eat lizards. This paper describes the first record of adult pygmy bluetongue lizards being killed by lycosid spiders. It suggests a complex relationship of lizards and spiders in that the lizards rely on potentially lethal co-inhabitants of their grassland habitat to construct the burrow refuges that they require. Conservation management of this endangered lizard will need to consider both the advantages and disadvantages of maintaining spiders in lizard population sites.
Studies on plasma progesterone concentrations and fertility in Friesland dairy cows during the post-partum period

SUMMARY Plasma progesterone concentrations were monitored in 69 lactating Friesland dairy cows during the post-partum period. Cyclic ovarian activity resumed in most cows within 40 days of calving. Forty-eight per cent of cows remained pregnant to their first insemination, 41% returned to oestrus before day 30 after insemination, and a further 11% returned to oestrus between days 30 and 88 after insemination. The mean of progesterone values on days 11 to 4 before insemination tended to be higher in cows that conceived than in cows that did not conceive. These differences were signficant on day –8 (P <0·05) and on days –8, –7, –6 and –5 combined (P <0·01). Cows in which the concentration of progesterone in plasma did not rise above 4·5 ng/ml during this period did not conceive. After insemination, mean progesterone concentrations between pregnant and non-pregnant cows diverged after day +8. Relatively low concentrations of plasma progesterone (< 1 ng/ml) up to day +8 after insemination did not preclude conception. There was no indication that embryo loss between days +30 and +88 after insemination was related to an insufficiency of ovarian progesterone during early pregnancy.
Temporal ordering and sound localization: association with environment and language development

Purpose: To investigate the simple temporal ordering and sonorous localization of children and the association with family environment resources and language development. Methods: Ninety-six children, 42 aged 4 years and 54 aged 5 years and 11 months, were assessed using the Inventory of Resources of the Family Environment, phonological and vocabulary tests, Child Language Test and Simplified Evaluation of Auditory Processing. Results: When age was associated to auditory processing skills, it was observed adequacy in both ages, being that male children showed better performance. Individuals who showed poor results in auditory processing skills also showed inadequacy in the areas of Family Environment Resources. Most children who showed adequate auditory processing skills, also showed adequate phonology, but inadequate vocabulary. Children with auditory processing disorders have three times more chance to show changes in vocabulary. Conclusion: Most children who had adequate skills in a simple temporal ordering and sound localization also demonstrated adequate phonology.
Histopathological and immunohistochemical study of hemangiosarcoma in lions

Two cases of hemangiosarcoma were recorded in lion during postmortem examination. Grossly, multiple variable sized reddish black hemorrhagic foci were noticed in the liver and spleen parenchyma. Histopathologically foci of liver and spleen revealed necrosed and numerous blood filled areas. Immature, plump endothelial cells forming vascular spaces and irregular vascular spaces containing variable amounts of blood were noticed. Immunohistochemically there was increased expression of vascular endothelial growth factor in endothelial cells.
Appealing broadly or narrowing down? The impact of government experience and party organization on the scope of parties’ issue agendas

Why do parties offer broad or narrow policy agendas to voters? Taking up the call to focus more on ‘issue diversity’ in election campaigns, this article argues that agenda scope is informed by (1) parties’ experience with government participation and (2) their internal organizational structure. Non-governing challengers, which are losers in the current system, seek to change the political status quo by focusing on a few issues only, whereas mainstream parties have an incentive to reinforce existing patterns of competition and thus distribute their attention across a wide range of issues. However, the extent to which parties respond to these external stimuli depends on intraparty politics. Party leaders seek to satisfy vote- and office-seeking motivations and want to ‘appeal broadly’, whereas activists want the party to ‘speak to the base’ and narrow down its issue appeals. Analyses of party agendas in 18 European democracies (1950–2013) support these expectations.
Effects of Double Injections of PGF2a at Different Intervals on Some Reproductive Traits in Tuj Ewes

The present study investigated the effects of double injections of PGF2a at different intervals (10 vs. 14 days) on plasma progesterone levels, oestrus and lambing rates in Tuj ewes during the breeding season. Thirty clinically healthy mature ewes were assigned randomly into 2 experimental groups: 2 injections of 125 µg of Cloprostenol (a PGF2a analogue) at either 10 (Group I, n = 15) or 14 day (Group II, n = 15) intervals. Blood samples were collected from the jugular vein on the day of the second injection of PGF2a, 4 days post-injection and 16 days after insemination to determine plasma progesterone levels. The oestrus and lambing rates were also determined. Findings showed that double injections of PGF2a at 10 or 14 day intervals did not significantly affect either the concentrations of plasma progesterone or the rates of oestrus and lambing. Plasma progesterone concentrations on the day of the second injection, 4 days post-injection and 16 days after insemination were 4.29 ± 1.96, 0.27 ± 0.19 and 7.39 ± 3.5 ng/ml in group I and 3.45 ± 1.45, 0.10 ± 0.02 and 9.21 ± 4.29 ng/ml in group II, respectively. The oestrus and lambing rates were 86.7% and 60.2% in group I, and 100% and 73.3% in group II, respectively. In conclusion, it appears that for oestrus synchronisation, shortening the interval of double injections of PGF2a by 4 days has little effect on plasma progesterone concentrations, oestrus or lambing rates in Tuj ewes during the breeding season.
Molecular Identification of Mullet Species of the Atlantic South Caribbean and South America and the Phylogeographic Analysis of Mugil liza

The abundance and wide distribution of mullets in the tropical, subtropical, and temperate regions of all continents make them a very important commercial species in fisheries and aquaculture of many regions in the world. However, the similar morphology among several species that inhabit all oceans makes it difficult to accurately determine morphological differences between mullet species. The objectives of the present study were to identify the different species of mullets from the Atlantic coast of the South Caribbean and South America using six mitochondrial genes and to test the hypothesis that Mugil liza is widely distributed in this region. The results indicated the existence of eight groups among our Atlantic samples, and two of them are possibly new species. Additionally, we concluded that M. liza has a wide distribution in the Atlantic coast of the South Caribbean and South America and that all specimens analyzed of this species belong to a single population.
Studies on the Efficacy of Organic Vs Inorganic Form of Nitrogen in Brinjal

A study was undertaken to compare the efficacy of organic and inorganic sources of nitrogen on the growth and yield of brinjal Cv. MDU. I. The results have indicated that substrate application of half N(50 kg) as poultry manure and half N (50 kg) as urea increased the dry matter and uptake of N, P, K, Ca and Mg. There was also higher plant height. The plants supplied with inorganic form of N showed early flowering when compared to organic sources or their combination. The highest yield of 51.03 t/ha of fruits was recorded by the plants supplied with 50 kg N as poultry manure and 50 kg N as urea followed by plants supplied with 50 kg N as pig manure and 50 kg as urea (45.80 t/ha).
The collision of the Indian plate with Asia: molecular evidence for its impact on the phylogeny of freshwater crabs (Brachyura: Potamidae)

Aim We used molecular data to answer the following questions: (1) Is morphology‐based (and to some extent, geography‐based) classification of the freshwater crab family Potamidae congruent with a molecular phylogeny? (2) What historical biogeographical event could have shaped this phylogeny?
Antioxidant and antimicrobial activities of Chowlai (Amaranthus viridis L.) leaf and seed extracts

The present study was conducted to evaluate the phenolics, antioxidant and antimicrobial activities of leaf and seed extracts from an edible herb namely Amaranthus viridis L. The extract yields of active components, produced using pure and aqueous methanol, from the leaves and seeds ranged from 5.4 to 6.0 and 2.4 to 3.7%, respectively. The extracts contained appreciable levels of total phenolic contents (1.03 to 3.64 GAE, g/100 g) and total flavonoid contents (18.4 – 5.42 QE, g/100 g) and also exhibited good 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical scavenging activity as revealed by IC50 (14.25 - 83.43 µg/ml). Besides, the tested extracts showed considerable antimicrobial activity against selected bacterial and fungal strains with minimum inhibitory concentrations (MIC) ranging from 179-645 µg/ml. Of the parts tested, the seed extracts exhibited superior antioxidant and antimicrobial activity. It was concluded that A. viridis leaf and seed can be explored as a potential source for isolation of antioxidant and antimicrobial agents for uses in functional food and pharmaceuticals. Key words: Amaranthus viridis, phytochemical constituents, minimum inhibitory concentrations (MIC), total phenolics, total flavonoids, 1,1-diphenyl-2-picrylhydrazyl (DPPH), radical scavengers.
BCL2 Family Related Genes Expression and Chemotherapy Response in Diffuse Large B-Cell Lymphoma

Background and Objective: Approximately half of patients with diffuse large B-cell lymphoma are cured with current chemotherapy regimens. The purpose of this study was to evaluate Bax and Bcl2 expression and their relationship with the response to chemotherapy. Materials and Methods: This study was a prospective analysis on 44 patients with diffuse large B-cell lymphoma. Their specimens were stained with immunohistochemistery method for Bax and Bcl2. The relationship between Bax/Bcl2 expression and the response to chemotherapy as well as some other prognostic factors were assessed. Results: Out of 44 patients, 29 were Bax+ and 15 Bax-, 31 Bcl2+ and 13 Bcl2-. We found a statistically significant relationship between IPI score and the response to chemotherapy (P = 0.002). The response rates were relatively better (but not significant) in cases with Bax + compared to Baxand in patients with Bcl2- compared to Bcl2 + tumors. The combination of immunohistochemistery results for Bcl2 and Bax could predict relatively higher response rates in a way that those with Bax+ Bcl2- had a higher response compared to Bax- Bcl2+ ( 57%% VS.22%, P=0.15). Conclusion: Although we found a relatively higher responses in our cases with Bax+vs. Bax- and in those with Bcl2- vs. Bcl2 +, the differences were not statistically significant. We suggest further studies to confirm whether the Bcl2 and Bax expressions have any effect on the response to chemotherapy and whether they could be considered as predictor factors for chemotherapy response.
Notes on the Bionomics of the Pink Stem Borer Sesamia inferens Walker (Lepidoptera: Noctuidae): An Upcoming Pest of Wheat in India

Wheat cultivation is of great significance in North-western plains of India and the crop was hitherto considered as almost free from serious insect attack. Recently, Pink stem borer (PSB), Sesamia inferens Walker (Lepidoptera: Noctuidae) has emerged as a new pest and is likely to pose serious threat to the successful cultivation of wheat in the North-western plains of India under largely adopted rice-wheat cropping system. Because of the paucity of data on the developmental biology of PSB on wheat crop regarding this emerging problem of insect damage, studies were initiated on biology of PSB under field as well as screenhouse conditions during seasons of 2010–2011 and 2011–2012. This is the first report on biology of PSB on wheat which indicated that the pest was able to survive well/build up populations on wheat and able to complete its life cycle. It laid eggs either at the base of wheat plant near to soil level or on soil-surface or in the left over stubble of rice plants. Eggs hatched within 7.40±0.08 days and the mean larval duration was 68.52±1.55 days. In the course of development, it passed through 8 larval instars and pupation took place near or within the left over rice stubble. Pupal period was 36.05±0.36 days in male while 37.78±0.17 days in female. The survival of adult moths was 5.31±0.26 days in male while 6.61±0.26 days in female. The mean fecundity was 118.38±11.93 eggs and 89.15 per cent of eggs hatched. The total life cycle took 116.92±2.17 and 119.95±2.05 days in males and females, respectively.
Effects of nitrate concentration on growth and nitrogen metabolism of tomato (Lycopersicon esculentum Mill.) under cadmic stress

Abstract Nitrate assimilation in higher plants is the main biosynthetic pathway leading to glutamate, required for synthesis of some metabolites that participate in mechanisms of biochemical adaptation to heavy metal such as cadmium. Seven day—old seedlings were grown for 14 days on hydroponic culture medium containing 2 mM or 5 mM of nitrate. Cadmium was added at 25 μM concentration. The supply of nitrate at an important concentration (5 mM) enhanced growth activity and nitrate content in leaves and roots. In parallel, nitrate and nitrite reductase activities were induced. Regardless the nitrate concentration, presence of cadmium (25 μM) exerted an inhibitory effect on plant growth, nitrate content, nitrate and nitrite reductase activities. This negative effect was more important when nitrate was added at 2 mM concentration. Aminating GDH activity was enhanced by the presence of cadmium in order to detoxify ammonium. Our results suggest that tomato plant was more sensitive to cadmium toxicity when received a low nitrogen concentration (nitrate).
Relation between apoptosis and embryonic development of Oreochromis niloticus

The present study aims to describe the development of different embryonic stages of Oreochromis niloticus (O. niloticus) and how apoptosis could be considered as a major physiological process associated with developmental stages of O. niloticus embryos, even reared at different environments. Embryonic development of different stages of O. niloticus was determined morphologicaly using specific software TPSDigression, apoptosis was assessed in the whole embryonic tissues using different techniques, agarose gel electrophoresis and ELISA. Apoptosis was detected in-situ at single cell level using TUNEL technique. Results showed that rate of growth correlates with apoptosis in different embryonic stages of O. niloticus. Embryonic stages which were collected from Ain Shams fish farm, showed a high rate of growth associated with different apoptotic activity than those collected from El-Abbassa fish farm. It should be noted that apoptotic activity varies according to the growth rate of different embryonic stages. The study concluded that apopotosis is a physiological process associated with embryonic development of O. niloticus and environmental factors, strongly, control apoptosis during development.
Timing of foetal growth spurts can explain sex ratio variation in polygynous mammals

The prediction from sex ratio theory that natural selection on sexually dimorphic mammals should favour an excess of male offspring only when mothers are in good condition, has been tested extensively but with little consistency in results. Although recent studies have shown that environmental variations may cause some of the discrepancy, there have also been reports of contrasting sex ratios under similar environmental settings. Here it is suggested that variation in timing of environmental stress and sex-specific differences in foetal growth pattern in relation to maternal condition, may explain such seeming contradictions in sex ratio variation of polygynous mammals.
Genetic variability in sunflower (Helianthus annuus L.)

Genetic variability was studied in sunflower (Helianthus annuus) comprising of 26 germplasm lines and one check i.e. TAS-82, grown during kharif 2007 at Dr. PDKV, Akola. The analysis of variance (ANOVA) revealed significant differences for all 13 characters under investigation. Variation for number of seeds per head was pronounced. All the characters showed a close relationship between phenotypic and genotypic coefficient of variation (PCV and GCV). High heritability with high genetic advance was recorded for number of unfilled seeds per head, seed yield per plant, plant height and 100 seed weight, while high heritability along with low genetic advance was observed for the oil content, days to 50% flowering, hull content and days to maturity, suggesting that these characters cannot be effectively improved by selection.