Miracle-dz/UniFAR-FTUs huggingface dataset:
Adaptive Evolution of the SIV Envelope Protein During Early SIV Infection

Primate lentiviruses (PLVs), including human immunodeficiency virus type 1 (HIV-1), HIV type 2 (HIV-2), and the simian immunodeficiency viruses (SIVs), cause persistent lifelong infections despite the presence of virus-specific adaptive immune responses. The target of antibodies is the viral envelope glycoprotein (Env), which is expressed on the surface of virions and infected cells as a trimer of gp120:gp41 heterodimers. SIV env sequence variation arising from evasion of antibodies is well established and closely mimics the pattern observed in HIV-infected human patients, yet despite the experimental advantages of the macaque model, the viral dynamics during acute and early infection leading to escape within env have not been well defined. To examine the evolutionary dynamics of SIV env during early infection (< 6 months post-infection), we obtained longitudinal plasma samples from a small cohort of SIVmac251-infected rhesus macaques. We deep-sequenced the env gene from longitudinal samples spanning acute and early infection (2-29 weeks post-infection) from four SIV-infected rhesus macaques and the inoculum (a swarm stock of uncloned SIVmac251) that was used to infect the cohort (by repeated low-dose challenge). Using high-resolution next generation sequencing (NGS), we captured a population bottleneck at the point of transmission from the stock into each animal, tracked the subsequent emergence of Env diversity from the initially homogeneous population, and correlated changes with the onset of Env-specific antibodies. We identified a pattern of common substitutions, insertions, and deletions in env of animals with antibody responses, which repeatedly emerge in SIV-infected primate hosts, and found that adaptive changes clustered within short regions of the V1 and V4 loops of gp120. Surprisingly, we found multiple large in-frame deletions in V4 emerge to become dominant in the viral population in two animals with detectable antibody responses to Env. Furthermore, we developed a novel deep sequencing based viral fitness assay (Fit-Seq) and measured the relative fitness of several key in vivo
Evaluation of Antibiotic Resistance Pattern in Dental Bacteremia Detected by Multiplex PCR Technique

The aim of this study was to detect oral bacteremia and offer the antibiotic resistance patterns. Bacterial resistance pattern was evaluated in 50 patients. A spectrophotometer device equipped with UV and electrophoresis of the extracted samples on agarose gel for antibiogram test were used. PCR test 15 minutes after tooth extraction showed that bacterial strains were extracted from 16 patients. Lactobacillus, Enterococcus faecalis (E. faecalis), Streptococcus sanguinis (S. sanguinis), Streptococcus salivarius (S. salivarius), and Streptococcus mutans (S. mutans) were extracted from 5, 4, 4, 4, and 6 patients. 100% of Lactobacillus, E. faecalis, S. sanguinis, S. salivarius, and S. mutans were sensitive to tigecycline. Most of the Lactobacillus antibiotic resistance was against tetracycline and ciprofloxacin. Antibiotic resistance in S. salivarius was observed in 75% of the cases against piperacillin-tazobactam, ciprofloxacin, and cefotaxime, while in S. mutans was 84% of the cases against ceftriaxone. The results of the current study showed that tooth extraction causes bacteremia before, during, and after tooth extraction. Generally, the highest antibiotic resistance occurred against tetracycline, ciprofloxacin, and ampicillin-sulbactam. In most cases, the bacteria showed partial resistance to these antibiotics; however, tigecycline showed 100% efficacy on all types of bacteria. Streptococcus strains (salivarius, mutans, and sanguinis) were sensitive to most of the antibiotics while antibiotic sensitivity was less evident in Lactobacillus and E. faecalis. Antibiotic resistance has become a critical issue, since it leads to treatment failure when there is a need for antibiotic therapy.
Application of visible and near infrared reflectance spectroscopy to predict total nitrogen in soil

Interpretation : The application and use of precision agriculture technologies targeting reduction in agricultural inputs are associated with various raw data and their assessment to create application maps. Yield mapping and soil mapping are the two basic agricultural application maps for variable-rate applications. Creation of highresolution digital soil maps requires high resolution information. The objective of this study was to predict total nitrogen in soil, using visible and near infrared (vis-NIR) reflectance spectroscopy, which is a new technology used for making fast and accurate measurements of physical and chemical properties of soil.
Antibacterial activity and phytochemical content of Avicennia Marina collected from polluted and unpolluted site

The aim of the present study is to evaluate the phytochemical content and antibacterial activity of Avicennia marina collected from polluted and unpolluted site from the back-waters of Attipatuputhunagar. The plants were collected separately and tested for phytochemical analysis and antibacterial activity against various bacteria such as Salmonella typhi, Staphylococcus aureus, Escherichia coli and Klebsiella pneumonia. Preliminary phytochemical analysis was performed with ethanol and aqueous extract of Avicennia marina plant leaf collected from polluted and unpolluted sites that showed the presence of alkaloids, phenols, tannin, flavonoids, aminoacids, diterpenes, oxalate, cardiac glycosides, quinone, anthocyanin, leucoanthocyanin and Xanthoprotein. The ethanol extract showed the presence of higher phytochemical content when compared to the aqueous extract. The plant collected from polluted site showed the presence of only less amount of phytochemical content when compared to unpolluted site. The ethanol extract of the leaf exhibited significant antibacterial property against tested bacterial organisms. The activity of the extract was comparable with the standards amoxicillin. In conclusion, the result of the present study showed the presence of wide spectrum of antibacterial activities against all the above bacterial pathogens studied. The maximum zone of inhibition was observed in ethanol extract when compared to aqueous extract of unpolluted site plant leaf.
The breeding ecology of Mallard Anas platyrhynchos at Lake Tonga, north-eastern Algeria

The breeding ecology of Mallard Anas platyrhynchos was investigated at Lake Tonga, north-eastern Algeria, which is at the southern edge of the species’ range in the Western Palearctic. Breeding was mainly carried out in stumps of alder carr (Alnus glutinosa) that border the northern limit of the lake. The breeding season was relatively short, spanning two months. Laying occurred mainly in April but continued until end of May. The average clutch size was 8.4 ± 1.9 eggs (N = 19 clutches) with 10 eggs being the modal clutch. The overall nesting success was 54% (N = 29 clutches), whereas predation accounted for most nest failure (76%). As often happens in arid climates and instable habitats, breeding outcome was significantly and negatively related to egg-laying date with precocious nests conferring better survival to eggs. In contrast, nest predation was positively associated with a deferred laying date. Seven cases of interspecific brood parasitism were recorded, all involving the Mallard and the Ferruginous Duck Aythya nyroca, with both species acting as either a host or a parasite. Nests in dense vegetation were more likely to harbour this interspecific interaction.
Studies on the diversity of predatory coccinellid beetles (Coleoptera) in different agro-climatic zones of Himachal Pradesh.

Himachal Pradesh is a mountainous state of India situated in western Himalayas and is known for the cultivation of commercial crops especially apple and off-season vegetables. These crops are attacked by various insect pests and coccinellid beetles play important role in the suppression of different insect-pests throughout the world. The information on the predatory coccinellid beetles from Himachal Pradesh is, however, scanty. There are about 6000 species of these beetles known worldwide (Vandenberg, 2000), of which, nearly 400 species are present in the Indian sub-region (Poorani, 2002). As for as their food habits are concerned, some are specific, while, many are polyphagous. Ladybirds are also regarded as bio-indicators (Iperti and Paoletti, 1999) and provide more general information about the ecosystem in which they occur (Anderson, 1999). Coccinellid fauna of different parts of India has been studied and reported by various workers (Puttarudriah and Channabasavanna, 1953; Kapur, 1972; Pajni and Singh, 1982; Canepari, 1986; Bhagat and Mosoodi, 1988; Omkar and Parez, 1999; Sathe and Bhosale, 2001; Poorani, 2002; Kandibane et al., 2005; Joshi and Sharma, 2008; Sharma and Joshi, 2010; Choudhary et al., 2014). Nevertheless, these workers have not covered extensively or surveyed intensively, the Himachal Pradesh state of India. Himachal Pradesh also varies in agro-climatic conditions from most parts of the country. Within the state also there are extreme variations with regards to the altitude and hence the agro-climatic conditions. Due to these variations, Himachal Pradesh is expected to vary greatly in coccinellid fauna from one place to another. The present study was, therefore, conducted to investigate the diversity of predatory coccinellid fauna of different agroclimatic zones of Himachal Pradesh, India.
Rôle des protéoglycanes à héparane sulfate dans le transfert de gène des cellules CHO et HEK293

iv Table des Matières . vi Liste des Tableaux . xiv Liste des Figures . xv Liste des Sigles et Abréviations . xix Remerciements . xxiv Avant-Propos . xxvi La Tête dans les Nuages . xxvi La Production d’Anticorps Thérapeutiques . xxv
It's about time: Insights into temporal genetic patterns in oceanic zooplankton from biodiversity indices

Large population sizes and high dispersal potential should lead to temporal genetic stability in marine species; however, the magnitude of allele frequency shifts through time have varied greatly in prior studies. We investigated temporal variation in the genetic composition of populations of two planktonic copepod species at an open ocean time series site in the North Pacific Subtropical Gyre (Station ALOHA, 22.45°N, 158°W). We sequenced fragments of the mitochondrial genes cytochrome c oxidase subunit II (Haloptilus longicornis) and subunit I (Pleuromamma xiphias) from approximately 500 individuals of each species collected on 11 cruises from September 2012 to October 2013 (12–15 generations). Conventional population genetic analyses found no evidence for significant temporal variation across cruises, including results of non‐hierarchical analysis of molecular variance, pairwise ΦST values among cruises, and isolation‐by‐time Mantel tests. Generalized entropies were able to characterize the turnover of rare haplotypic variants through time using q = 0 (haplotype richness), the shifting frequencies of the less common haplotypes using q = 1 (Shannon differentiation), and the general stability of the most abundant haplotypes using q = 2 (Jost's D). With q = 1, mild seasonality was detected in the composition of P. xiphias haplotypes from three summertime cruises, in which both copepodites and adults were included in the analyses. These results highlight the complementary insights that F‐statistics and generalized entropy contribute to characterizing the nuances of population genetic composition through time. This approach may prove particularly useful for unlocking patterns in genomic datasets for marine species.
Seabird diets as bioindicators of Atlantic herring recruitment and stock size: a new tool for ecosystem-based fisheries management

Ecosystem-based fishery management requires understanding of relationships between exploited fish and their predators, such as seabirds. We used exploratory regression analyses to model relationships between Atlantic herring (Clupea harengus) in the diet of seabird chicks at nine nesting colonies in the Gulf of Maine and four types of fishery- and survey-derived herring data. We found several strong relationships, which suggests spatial structuring in herring stocks and likely patterns of herring movements before they recruit into the fishery. Some types of herring data seldom used in stock assessments — notably acoustic surveys, fixed-gear landings, and mass-at-age (i.e., weight-at-age) — correlated as strongly with seabird data as more commonly used series, such as mobile-gear landings and modeled spawning stock biomass. Seabird chick diets collected at specific locations thus offer a promising means to assess the size, distribution, and abundance of juvenile herring across a broad area prior to recruitment, which is a major source of uncertainty in fisheries. Common terns (Sterna hirundo) showed the most potential as a bioindicator, correlating well and showing consistent spatial patterns with 11 of 13 fishery data series.
SEASONAL ABUNDANCE, SCREENING OF GENOTYPES AND CHEMICAL CONTROL OF GERBERA APHID

Morning relative humidity (r = -0.567) had significant negative correlation with aphid population. While, maximum temperature (r = -0.362), minimum temperature (r = -0.227), average temperature (r = -0.341), average relative humidity (r = -0.292) and sunshine hour (r = -0.283) had negative
Effects of seed coat colour on the seed quality and initial seedling growth of red clover cultivars (Trifolium pratense)

The objective of this study was to investigate the influence of seed coat colour on the seed quality of four red clover cultivars (germination, dormancy (hard seeds), dead seeds and initial seedling growth (vigour)) produced in Serbia over a period of two years. The seeds analyzed were first separated visually into bright, dark and mixed seed groups, followed by subsequent digital colour measurements. The results obtained showed that the seed coat colour of red clover could be considered a good indicator of seed quality and seedling growth ability. The results furthermore showed that bright-coloured seeds of red clover cultivars indicated increased vigour and seed quality compared to other colours. The impact of the production area and year on the seed quality parameters was inconclusive. A high variability in hard (CV = 22.22 %) and dead seeds (CV = 40.18 %) was recorded between different seed lots of red clover. A lower variability was found in the germination parameter of brightand mixed-coloured seeds (CV = 4.53 % and CV = 8.53 %). The seed coat colour could be an important factor in determining the quality of red clover seeds, potentially increasing germination simply by removing dark-coloured seeds.
Concerns about sustainability in the poultry industry: a comparative Delphi study in Germany and Thailand

Thailand and Germany's poultry industries face different agro-ecological and socio-economic circumstances, as well as a variety of public policies on sustainability in poultry production. Based on literature, 26 sustainability issues were identified and categorised into the five dimensions of sustainability, including environmental, economic, social, political and animal welfare aspects. Through a two-round Delphi methodology with an expert panel, additional concerning issues were proposed and all the sustainability issues were weighted by level of concern, from level 1 (not at all concerned) to level 5 (very concerned). Results showed that social, animal welfare and economic issues dominate the current discussion of sustainable poultry production. The use of antibiotics in poultry production, killing of male layer chicks and the role of food retailers were rated ‘very concerning’ by the German experts, whereas the Thai experts considered the outbreak of avian influenza and other highly infectious diseases, disease control in neighbouring countries, use of antibiotics in poultry production, contamination of meat and eggs with zoonotic microorganisms, and standards for poultry products required by importing countries as the most concerning issues.
Whole-genome comparative analysis of carbapenem-resistant Escherichia coli isolated from hospitalized patients in Lebanon. (c2016)

Antibiotic resistant bacteria that are challenging and nearly impossible to treat are becoming more prevalent and this is resulting in an urgent public health concern. The horizontal gene transfer of antibiotic resistance genes between bacteria as well as the complex antibiotic resistance mechanisms involved have aided in the production of an extensive spectrum of bacterial species with multi-drug resistant patterns. Resistance mechanisms of Gram-negative bacteria, such as extraintestinal Escherichia coli (ExPEC), vary extensively and the emergence of extended spectrum β-lactamases (ESBLs) as well as carbapenemases have compromised the effectiveness of the majority of antibiotics. ExPEC is one of the major causes of communityand nosocomial-acquired infections. Distinct from intestinal pathogens and commensals, ExPEC causes infections of the bloodstream, respiratory tract, urinary tract, peritoneum and cerebrospinal fluid. The universal burden of diseases caused by such a microorganism is staggering and hundreds of thousands of people are annually affected. In this study, 27 carbapenem resistant ExPEC isolates were recovered from hospitalized patients at the AUBMC (American University of Beirut Medical Center) and were used for identification, phylogenetic typing
Rabbit management and occurrences of mange mite infestations in rabbit farms in Morogoro Municipality, Tanzania

A cross-sectional study was conducted in Morogoro Municipality between September and December 2015 to explore the rabbit farming and assess the common health problems with a focus on epidemiology of mange infestation. A total of 18 rabbit farms with 622 animals from 9 wards were investigated. A questionnaire was administered to the rabbit farmers to gather information on rabbit management and the associated challenges. All rabbits found in the farms were examined for mange lesions and skin scrapping was collected and analysed for mange mites in the laboratory using standard procedures. It was found that Morogoro Municipality had 18 rabbit farms with average of 34.6±23.1 rabbits per farm. Farmers reported to keep rabbits as sources of meat and income. Most of rabbits (83.1%) were raised in cages and were fed on green herbes, grasses and concentrates. Constraints to rabbit production were availability of good feeds, predators, lack of extension services and diseases particularly diarrhoea, infertility and skin conditions. Mange mite infestation was reported by 33.3% of respondents and poor hygiene, not resting of rabbit house and keeping of rabbits on the floor were significant (P < 0.05) factors for mange infestation. Prevalence of mange infestation was 23.2% and 33% in rabbits and farms respectively. All the mange mites observed were identified as Sarcoptes scabiei cuniculi . The observed clinical lesions were predictors of mange mite infestations (p=0.0000072283). Rabbit production in Morogoro is at infancy stage and is constrained with many drawbacks. Mange mites are prevalent in rabbit farms in Morogoro Municipality and therefore proper animal husbandry practices and application of acaricides are recommended. Keywords: Mange mites, rabbit management, diseases, prevalence
Estuarine and coastal connectivity of an estuarine-dependent fishery species, Pomadasys commersonnii (Haemulidae)

Understanding the level of connectivity between estuarine and coastal waters is essential for appropriate management of estuarine-associated taxa. Most studies have focused on the role of a single estuary, while limited research exists on the importance of multiple estuaries to individuals of estuarine-associated species. This study used acoustic telemetry to assess the usage of multiple estuaries and coastal waters by the estuarine-dependent spotted grunter Pomadasys commersonnii. Twenty-six adult fish were tagged with acoustic transmitters in the Kariega and Bushmans estuaries, South Africa, and their movements along a 300-km stretch of Indian Ocean coastline were monitored for up to 17 months. Tagged individuals spent most of their time in the estuary where they were tagged (55% and 85% for fish tagged in the two estuaries, respectively), followed by time in the sea (30% and 15%) and in other estuaries (15% and <1%). The mean durations of sea trips for fish tagged in the Kariega Estuary or Bushmans Estuary, respectively, were 25 days (range 3–55) and 12 days (range 2–22). Of the fish that went to sea, 93% from the Kariega Estuary and 60% from the Bushmans Estuary visited other estuaries. Most visits were undertaken to the Swartkops, Bushmans and Kowie estuaries, although the longest durations were spent in the Sundays Estuary. Individuals moved to estuaries up to 130 km away. The total distance travelled between estuaries by an individual during the study was ∼529 km, with means of 201 and 184 km, respectively, for fish tagged in the Kariega and Bushmans estuaries. Despite covering large distances between estuaries, individuals often returned to their tagging estuary. Residency in their tagging estuary, combined with frequent visits to a neighbouring estuary, highlights the importance of estuarine habitats for this popular fish species, even after reaching maturity.
Does one size fit all? A multispecies approach to regional landscape corridor planning

The practical value of the single‐species approach to conserve biodiversity could be minimal or negligible when sympatric species are limited by factors that are not relevant to the proposed umbrella species. In this study, we quantitatively evaluated as follows: (1) habitat suitability and potential movement corridors of a single umbrella species, giant panda (Ailuropoda melanoleuca); (2) habitat suitability of sympatric mammals; and (3) the potential effectiveness of the single‐species corridor planning to preserve suitable habitat and its connectivity of other focal species.
Influence of Bio-Fertilzer with Recommended Doses of Fertlizer on Plant Growth, Yield, Quality And Economics of Onion (Allium cepa L.) cv. NHRDF Red 2

The invstigation was carried out in the rabi season in 2016-17 at garden of department of horticulture, C.S. Azad University of Agriculture and Technology, Kanpur to study the effect of N, P and K levels with biofertilizers on growth, yield and economics of onion crop. The experiment was laid in Randomized block design with the three replications for onion (Allium cepa L.) cv. NHRDF Red 2 and the treatments were consisted of three different levels of chemical fertilizers. Among the various treatments the treatmnt T13 viz. 100 per cent RDF + Azospyrillum + PSB, has recorded significantly higher plant height, length of leaves, number of leaves, diameter of bulb, shoot thickness, fresh weight per plant and fresh weight per bulb and shoot weight at 50, 75 and 100 DAT. The bulb yield and yield components such as bulb length, bulb diameter and bulb weight were recorded significantly higher in T13 than the other treatments. The nitrogen, phosphorus and potassium ccontent (%) was observed significantly highest with the application of 100% RDF + Azospyrillum + PSB. Treatment T13 has recorded significantly higher gross returns as well as net return but highest B:C ratio was observed in 75 per cent RDF + Azospyrillum + PSB treatmnt T9 from onion over all the treatment.