Miracle-dz/UniFAR-FTUs huggingface dataset:
Identifying the cellular HIV-1 reservoir in lymph nodes of antiretroviral therapy suppressed individuals.

6 Introduction . 6 Results . 8 Quantifying HIV-1 infection in lymph node cells . 8 Optimization of anti-Env J3 . 10 Single cell RNA-sequencing of in vitro infected cells to identify HIV-1 infected cells . 12 Detection of HIV-1 infection from in vitro infected HIV-1 negative lymph node cells using single-cell RNASeq . 14 Amplification of HIV-1 virus from lymph node cells . 16 Enrichment of cells most likely to harbour HIV-1 . 17 Cell phenotyping and identifying HIV-1 infected cells . 17 Flow cytometric validation of HIV-1 infected cell types . 19 Discussion . 21 Methods . 24 Study participants . 24 Primary cells . 25 Cell lines . 25 Infection . 25 Staining and flow cytometry for anti-HIV-1 p24 Gag and anti-Env 10-1074 and J3 . 26 Amplification of full-length HIV-1 genomes from lymph node cells . 27 Staining, magnetic activated cell sorting, and Seq-Well . 28 Single-cell RNA-seq of infected Rev-CEM-E7 cells using Smart-Seq2 . 28 Antibodies . 30 Flow Cytometry and sorting of in vivo infected lymph node cells . 30 References . 31 CHAPTER 3: DISCUSSION/SYNTHESIS . 37 ANNEX . 45 ETHICS CERTIFICATE . 45
Nesting biology of two species of the large carpenter bees Xylocopa pubescens and Xylocopa fenestrata (Hymenoptera: Apidae) in north-western Pakistan

Abstract The large carpenter bees are very promising pollinators for many agriculture crops. The nesting biology and some foraging activities of these large carpenter bees are documented from the north-western Pakistan, most extent of its natural distribution, as these species are potentially important pollinators of cucurbit crops and some agriculture crops in the region. Nests of the large carpenter bees, Xylocopa pubescens Spinola, 1838 and Xylocopa fenestrata Fabricius, 1798, around the Ismaila village, Swabi, Khyber Pakhtunkhwa Province, Pakistan, were observed and sampled from June to August 2012 and 2013. Nest details were recorded and foraging times on various floral species were documented, with bees preferentially nesting in dead wooden stems of Poplar (Populus deltoides) and Sesbania (Sesbania bispinosa). The dissection of nests was carried out and both nest architecture and nesting biology of the species were described. The importance of such studies on wild bees in Pakistan is important for the melittologists, as it will help in conservation of wild bees. The study is also useful in using large carpenter bees for pollination purpose.
Hematological-genetics, Reproductive Health and Family Welfare in Madhya Pradesh, India

Introduction: The sickle cell disease is a major genetic and public health challenge in Central India. In view of dubious credit of the highest infant mortality rate in Madhya Pradesh (62 as against 47 per 1000 live-births for India in 2011). Aim: It was presumed that carrier couples of sickle cell disorders might be one of the contributing factors to mortality. Materials and Methods: A total of 383 couples including their offspring with at least one affected and/or suspected case of sickle cell disorder referred to our Centre from NSCB Medical College & Hospital, Jabalpur during March 2010 to February 2013 were consecutively studied as matched case controls. Results and Discussion: Out of 383 couples, 200 were found normal and 183 couples had different sickle cell disorders. Sickle cell carrier couples had statistically significantly more relative fertility (mean number of conceptions, i.e. 3.153 versus 1.480) and more under 10 year mortality (11% versus 2.7%) and low surviving offspring (877.4 versus 970.6) than of normal controls. Neonatal and infant mortality per 1000 live-births was doubled (34.3 versus 14.7) and three-fold higher (44.1 versus 14.7), respectively in carriers of sickle cell disease than of controls. Couples with AS versus SS genotype showed high occurrence of neonatal, infant, under 10 year mortality each 214.3, respectively and low surviving offspring (785.7) per thousand live-births. Conclusions: This study indicated that afflicted couples (56.7%) of these hereditary disorders are increasing the defective (trait and disease) against 43.3% (controls) normals. This increased production of defective offspring leads to increased morbidity and mortality and might be contributing towards increased neonatal/infant mortality in Madhya Pradesh. As a preventive measure, affected families were imparted genetic/marriage counseling.
Declining patterns of Pacific Northwest steelhead trout (Oncorhynchus mykiss) adult abundance and smolt survival in the ocean

Examination of population abundance and survival trends over space and time can guide management and conservation actions with information about the spatial and temporal scale of factors affecting them. Here, we analyzed steelhead trout (anadromous Oncorhynchus mykiss) adult abundance time series from 35 coastal British Columbia and Washington populations along with smolt-to-adult return (smolt survival) time series from 48 populations from Washington, Oregon, and the Keogh River in British Columbia. Over 80% of the populations have declined in abundance since 1980. A multivariate autoregressive state-space model revealed smolt survival four groupings: Washington and Oregon coast, lower Columbia River, Strait of Juan de Fuca, and Puget Sound – Keogh River populations. Declines in smolt survival rates were seen for three of the four groupings. Puget Sound and Keogh River populations have experienced low rates since the early 1990s. Correlations between population pairs’ time series and distance apart illus.
Misidentification of megalopae as a potential source of error in studies of population genetics and ecology of the blue crab Callinectes sapidus

Inaccuracy in taxonomic identification is an unknown but potentially important source of error in studies of planktonic larval ecology and evolution. We address the misidentification of blue crab (Callinectes sapidus) megalopae (post-larvae) as a source of error in investigations of genetic variation and factors influencing settlement. Callinectes spp. megalopae were sampled monthly in spring and summer from the water column at 2 locations on the Texas (USA) coast and identified by 16S mitochondrial sequences. Most of the megalopae could be assigned to C. sapidus (62%), C. similis (36%), C. rathbunae (1.5%), or C. danae (0.12%), while 5 (0.8%) were ambiguously grouped with both C. similis and C. danae. Previously used morphological characters (rostrum length, carapace length, and their ratio) were not diagnostic. Species composition differed between locations and among monthly samples. A recurring seasonal pattern in species composition was discerned, with ~95% C. similis in April shifting to ~95% C. sapidus by May/ June, and variable proportions in August. This pattern strongly parallels changes in allozyme allele frequencies previously reported for blue crab megalopae at the same locations. Models selected by the Akaike information criterion indicated lunar phase, temperature, salinity, storms, and wind stress components all affecting megalopal abundance. The importance and sign of these factors differed between species. Temperature, the most important factor for each species analyzed separately, was not important when species were combined. This study demonstrates that misidentification of larvae could create the appearance of temporal genetic variation, inflate estimates of abundance, and obscure factors influencing settlement.
Concentration and Timing of Ethephon Drench Applications Interact to Affect Growth and Flowering of Containerized Angelonia and Geranium

Ethephon drenches have been reported to effectively control growth of containerized bedding plants. However, previous researchers have indicated that the effects of ethephon drenches on growth and ﬂowering may differ depending on the timing of applications. Our objectives were to quantify the effects of ethephon concentration, timing of substrate drench application, and their interaction on the growth, size, and ﬂowering of two annual bedding plants. Angelonia ( Angelonia angustifolia ) and geranium ( Pelargonium 3 hortorum ), seedlings were planted in 10.2-cm-diameter containers ﬁlled with a commercial, soilless growing substrate composed of (by vol.) 75% sphagnum peatmoss, and 25% perlite. Five, 10, 15, or 20 days after transplanting seedlings, 70-mL aliquots containing 0, 50, 100, or 200 mg · L L 1 ethephon were applied as substrate drenches. Species varied in their growth and ﬂowering responses to ethephon concentration, drench application timing, and their interaction. For angelonia, ﬂowering was delayed most with early applications and high concentrations, and delay was diminished with later applications. Angelonia height was unaffected by late applications, though lateral growth was suppressed20 days aftertransplantwith200 mg · L L 1 ethephon. Floweringofgeranium was only delayed when ethephon was applied 5 days after transplanting, whereas ﬂowering, vegetative height, and shoot dry weight were affected more by earlier applications and higher concentrations. Width and root weight were only affected by ethephon concentration, with growth suppression increasing as concentrations
RESEARCH REGARDING THE INFLUENCE WEED CONTROL TREATMENTS ON PRODUCTION AND QUALITATIVE INDICATORS SOYBEAN CULTIVATED IN MINIMUM TILLAGE SYSTEM

The use of herbicides abused, without a thorough knowledge can be dangerous for the environment through the introduction of toxic waste in agricultural ecosystems. It is necessary to reduce the doses used in relation to the use of conservative technology, finding solutions optimized for effective weed control. Research conducted at ARDS Turda in the years 2013 and 2014 have followed the effect of 12 variants of herbicides used to control weeds in soybean crop, sown in two tillage systems (classical system and minimal tillage system), on the soybean production and quality indicators. Tillage system significantly influenced both qualitative indices and soybean crop production (being 2635 kg/ha to the classical and 2131 kg/ha minimum tillage system). The significant influence of tillage soybeans in fat content (20.34% in minimum tillage system; 19.94% to the classical) and on protein (39.89% minimum tillage system; 40.56% in the classic).
Isolation and characterization of BpL1, a broad acting lytic bacteriophage against Brucella

We have isolated a new broad acting lytic brucellaphage (BpL1) from the sewage of a dairy farm. The phage lysed all the 12 Brucella abortus field isolates, B. abortus strain 99 and Brucella melitensis but did not lyse any of the heterologous species tested viz. Staphylococcus aureus, Pasteurella multocida, Escherichia coli, and Salmonella species. Streaking the plaques on Brucella lawn gave clear zones along the streak lines. The plaques were circular with a diameter of 0.5- 3.0 mm. At a concentration of 10−4 the phage count was 4.5 × 106 plaques per ml. It was a tailed phage with icosahedral head (62.2 nm in diameter and 73.71 nm in length), and the head to tail length was 229.21 nm. The phage belonged to the order Caudovirales and family Siphoviridae. It was inactivated within one hour at 55°C and within 4 hours at −20°C. Treatment at pH 2 for 4 hours and at pH 4 for 12 hours inactivated it. It was inactivated after 4 hours exposure to sunlight, and within 4 minutes by UV light. Chloroform and Sodium Dodecyl Sulfate inactivated it within 15 minutes. Lysozyme inactivated it within 1 hour whereas RNase treatment did not affect its activity.
How Betula ermanii Maintains a Positive Carbon Balance at the Individual Leaf Level at High Elevations

Generally, plant species with shorter leaf longevity maintain a positive carbon balance by decreasing leaf mass per area (LMA) and increasing photosynthesis. However, plants at high elevations need to increase LMA against environmental stresses. Therefore, plants need to increase both LMA and photosynthesis at high elevations. To examine how deciduous plants maintain a positive carbon balance at high elevations, photosynthesis and related leaf traits for deciduous broad-leaved tree Betula ermanii were measured at three elevations. LMA was greater at middle and high elevations than at low elevation. Leaf δ13C was greater at higher elevations, and positively correlated with LMA, indicating greater long-term deficiency of CO2 in leaves at higher elevations. However, the Ci/Ca ratio at photosynthetic measurement was not low at high elevations. Nitrogen content per leaf mass and stomatal conductance were greater at higher elevations. Photosynthetic rates and photosynthetic nitrogen use efficiency (PNUE) did not differ among the three elevations. Photosynthetic rate showed a strong positive correlation with stomatal conductance on a leaf area basis (R2 = 0.83, P B. ermanii compensates the deficiency of CO2 in leaves at high elevation by increasing stomatal conductance, and maintains photosynthesis and PNUE at high elevation as much as at low elevation.
Expression patterns of the circadian proteins PER2 and BMAL1 throughout the rodent forebrain: immunofluorescent mapping of their co-expression with Enkephalin and Substance P

Despite rhythmic clock gene expression being found throughout the central nervous system, very little is known about their function outside of the suprachiasmatic nucleus. Understanding how clock genes are expressed across a variety of neural cell types is important to elucidating how these clock genes are regulated and how they may influence the function of each brain region. Using immunofluorescence and confocal microscopy, we quantified the co-expression of the clock proteins BMAL1 and PER2 with Substance P (SubP) and Enkephalin (Enk). Regions examined included the limbic forebrain (the dorsal striatum, ventral striatum, amygdala, stria terminalis), the thalamus (medial habenula), the hypothalamus (paraventricular nucleus, arcuate nucleus) and the olfactory bulb. In most regions examined, PER2 and BMAL1 were homogenously expressed in nearly all cells (~90%), despite very different expression profiles of SubP or Enk in each nucleus. In nuclei that expressed both SubP and Enk, PER2 and BMAL1 were not preferentially co-expressed in one cell type or the other. The olfactory bulb was unique and expressed PER2 or BMAL1 in a much smaller percentage of cells, and Enk was rarely found in the same cells that expressed the clock proteins (SubP was undetectable). This indicates that clock genes are not unique to specific cell types and further studies will be required to address which factors contribute to clock gene rhythmicity. A focus on network interactions is recommended in order to determine how different cell types contribute to various aspects of rhythmicity, such as rhythm generation, amplitude and synchrony.
Yosemite: The Embattled Wilderness

'Runte focuses on the debate over the management of the natural resources of the park, deftly addressing delicate questions of the balance between preservation and use.His work is alive, and even more than his fine research and clear writing, his passion accounts for the wide readership his work enjoys' - "Environmental History Review". 'An angry book . firmly grounded in scholarship . [and placing] in historical perspective the decisions that . [resulted in] overdevelopment and pollution.Read the book. Get angry. Write your congressman! ' - "Southern California Quarterly". 'The history of Yosemite is symbolic of the environmental history of America itself. Those who read this fine study will come to understand that' - "Utah Historical Quarterly". 'A major work that has application beyond the Yosemite experience. Today, America's national parks are being destroyed by the unrestrained commercialism that Runte chronicles so effectively. His work is stimulating, thought-provoking, and valuable for its insights' - "Nevada Historical Society Quarterly". ' A powerful and important book, a critical contribution to Yosemite historiography and ideology at a time when the politicizing of the National Park Service and the vast hordes of visitors pose genuine threats.to the natural environment of Yosemite' - "Western American Literature". 'This analysis is applicable to every park, wilderness, and national treasure; it is a warning for every conservationist to be on guard against the pressures for development' - "Naturalist Review". Alfred Runte, an environmental historian based in Seattle, is the author of "National Parks: The American Experience" (1979; rev. ed., 1987), also published by the University of Nebraska Press.
In vitro Embryo Germination and Callus Induction of Cynometra cauliflora, an Underutilized Medicinal Plant

Cynometra cauliflora or known as ‘Nam-Nam’ is an underutilized medicinal plant of Malaysia. In this study, embryo from matured seed of C. cauliflora was cultured on the Murashige & Skoog medium containing 0.5 μM BAP. Embryo germination achieved up to 100% and produced an average of 8.8±2.0 shoot buds per explant and 1.7±1.5 leaves after eight weeks. Stem and shoot tips explants from in vitro plantlets were further treated with 5, 10 and 15µM Thidiazuron (TDZ) for regeneration capacity. Stem explant responded 100% to callus induction after two weeks of culture on medium containing 10 μM and 15μM TDZ. Meanwhile, shoot tip explant recorded only 12.11±0.54% to callus induction after 6 weeks of culture on medium containing 5μM TDZ. Stem explant remain at calli stages until the end of study, while shoot tips undergo shoot regeneration by inducing up to 54.45±9.27% shoots production with an average of 3.00±1.00 shoots per explant. Browning phenomenon was severely observed on the culture throughout this study. Therefore, the addition of activated charcoal to the culture medium will be beneficial to eliminate phenolics accumulation.
COMPOSITION, REPRODUCTION AND ECOLOGICAL ASPECTS OF A CAATINGA ANUROFAUNA IN PARAIBA STATE, BRAZIL

The study area is located at 7°22‘S and 36°15’W, in the Cariri Paraibano, one of the driest regions of Brazil. It has typical Caatinga vegetation and a diversity of natural and artificial water bodies. Eighteen species of anurans belonging to the families Pipidae, Leptodactylidae, Odontophrynidae, Bufonidae, Hylidae, Phyllomedusidae and Microhylidae were recorded. From each species data on activity, reproduction, behavior and microhabitat were obtained. Each of the 15 water bodies studied was described and the presence of the different forms of anurans throughout the study period, from 1982 to 1984 was recorded. All species had the reproductive period regulated only by rainfall and did not show any special adaptations or specific reproductive strategies for the semi-arid environment. The differences between species in the occupation of the water bodies and the duration of the reproductive period did not seem to be related to a temporal or spatial partition of the environment. Seven different reproductive modes have been recorded, all of which are also found in more mesic habitats.
Potential Biomarkers through Genome-wide Expression Analysis of Breast Cancer Samples from Malaysian Patients

Breast cancer is a serious health concern and still a leading cause of death among women in the world. To explore the complexity of this cancer, we performed microarray analysis on highly selective cancer and normal breast tissues. The aim of this study was to identify differentially expressed genes between both tissues and to elucidate further molecular pathways involved in breast cancer carcinogenesis. Genome-wide expression profiling was performed on fifteen cancer and five normal breast tissues using the Affymetrix GeneChip® Human Gene 1.0 ST array. Supervised hierarchical cluster analysis using filtering parameters of -1.5 to 1.5 fold-change and p-value with False Discovery Rate < 0.05 revealed 404 up-regulated and 463 down-regulated genes. Pathway analysis revealed the significant genes were involved in cell cycle regulation, DNA repair, Hedgehog pathway, histone phosphorylation, TRRAP/Tip60 chromatin remodelling and apoptosis regulation. Among the top 10 significantly overexpressed genes were CENPF, DTL and MK167 and these were related to cell cycle regulation. Among the top 10 significant down-regulated genes, HOXA5 and NRG1 were found to be associated with Wnt signalling pathway and ErbB signalling pathway respectively. Aberrations in these genes are likely to promote breast cancer carcinogenesis. Our current findings highlighted the importance of differentially expressed genes in breast cancer and their molecular pathways that linked these genes. Further studies are required to validate our findings using larger sample size.
Short communication:The effects of Chlorella vulgaris supplementation on growth performance, blood characteristics, and digestive enzymes in Koi (Cyprinus carpio)

1Department of Fisheries, College of Agricultural and Natural Resources, Science and Research Branch, Islamic Azad University, P.O. Box 14515/775,Tehran,Iran. 2Department of Aquatic Animal Health, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran. 3Department of Animal sciences, Islamic Azad University, Tehran, Iran. 4Department of Fisheries, Ahvaz Branch, Islamic Azad University, Ahvaz, Iran.
Comparative chemical compositions of the leaves of some selected antihypertensive medicinal plants in Nigeria

Leaves of Four different types of antihypertensive medicinal plants: Vernonia amygdalina, Carica papaya, Persea americana and Cnidosculous aconitifolius use in Nigeria were analysed for proximate composition, mineral profile, phytochemical screening and amino acids. The results from the study revealed that the leaves of all the plants are good sources of proteins, fibre, minerals and amino acids. However, the fat contents of the plants were very low and there were presence of some phytochemicals which accounts for their therapeutic uses. It can concluded that that the leaves of these plants contain nutrients and mineral elements that may be useful in nutrition with Persea americana and Vernonia amygdalina having nutritional superiority over Carica papaya and Cnidosculous aconitifolius.
Milk production in ewes fed high grain diets.

Eight Merino ewes (42.6 + 1.4 kg) with five-week-old lambs at foot were offered rations at 2.5 times calculated maternal maintenance net energy requirements. Three ate a diet of 85.5% whole wheat grain, 9% hammermilled lucerne hay and 5.5% meat meal, go/lo, (880 g DOM, 26.9 g N/kg DM) and five ate 50% whole wheat grain and 50% hammermilled lucerne hay, . 50/50, (745 g DOM, 26.9 g N/kg DM). The ewes and lambs were weighed; and the ewes milked, week1 entry and oxidation of 1-l x from 5 to 9 weeks after lambing. The ratesof C-acetate and U-l4 of 2-3H-glucose and C-glucose and rates of entry 14C-bicarbonate into the ewes, and the concentrations of insulin and free fatty acids in the ewes' plasma were measured.