Miracle-dz/UniFAR-FTUs huggingface dataset:
HIV Persistence and Viral Reservoirs

Although antiretroviral therapy (ART) can effectively inhibit replication of human immunodeficiency virus type 1 (HIV-1), the virus is able to persist in cellular and anatomical viral reservoirs. Latently infected resting memory CD4 T-cells are an important cellular reservoir, and the central nervous system (CNS) an important anatomical reservoir for HIV-1 infection. The overall aim of this thesis was to gain greater understanding of HIV-1 persistence, in regards to latent infection as well as the central nervous system. The initial viral decay rate after initiation of ART has been proposed as a measure of relative regimen potency. We compared initial viral decay in subjects treated with three ART regimens, and found that efavirenz-based therapy gave a faster initial viral decay than protease inhibitor (PI) treated subjects. In turn, lopinavir/ritonavir-based therapy gave a faster initial viral decay than atazanavir/ritonavir-based therapy. This may reflect different inherent antiretroviral potency between the treatment regimens. Latently infected CD4 T-cells constitute a major barrier for the eradication of HIV-1 infection. We investigated if a high dose of intravenous immunoglobulin (IVIG) given in addition to effective ART could reduce the size of the pool of latently infected resting cells, and found a reduction in the pool size in five of seven individuals where the latent reservoir was quantifiable. Our findings suggest that the reservoir became accessible through IVIG treatment, and indicate that novel modes of intervention can have an effect on the latent reservoir. Increased levels of intrathecal immune activation are often found in cerebrospinal fluid (CSF) of treated patients despite effective systemic suppression of HIV-1. We investigated intrathecal immune activation, measured as neopterin and IgG-index, in patients with several years of successful therapy, and found that although ART has a substantial effect on lowering viral replication and immune activation in the CSF, a majority of patients still have ongoing intrathecal immune activation despite effective suppression of the virus for extended periods of time. Occasional cases of CSF viral escape have been reported. We investigated the occurrence of CSF viral escape in neuroasymptomatic patients effectively treated with commonly used ART regimens. We found that 7 (10%) of 69 patients had evidence of CSF viral escape, which is more common than previously recognized and may have important implications for future treatment strategies and the use of new drug combinations.
Decay fungi of riparian trees in the Southwestern U.S.

Most of the tree species that characterize riparian woodlands are early or facultative seral species including Fremont cottonwood (Populus fremontii), Arizona alder (Alnus oblongifolia), Arizona sycamore (Platanus wrightii), Modesto ash (Fraxinus velutina), boxelder (Acer negundo), and narrowleaf poplar (Populus angustifolia). Arizona walnut (Juglans major) is a riparian species that can persist at a low density in late seral or climax forests. The Southwest is a harsh environment for trees. The frequent occurrence of early-seral tree species in riparian forests reflect the frequency, severity, and extent of disturbance events. Disturbance from fire, seasonal flooding, and landslides all provide special opportunity for injury and infection by wood decay fungi.
Community and environmental influences on reef coral calcification

Reef corals calcify faster in the presence of non‐calcareous algae. Ratios of calcification to photosynthesis appear to be affected by the ratio of alkalinity to acidity, which controls how efficiently the protons from calcification convert bicarbonate to carbon dioxide. By forcing calcifiers to calcify faster, algal proliferation on nutrient‐enriched reefs may adversely affect the reef‐builders.
The Spectrum of Big Data Analytics

ABSTRACT Big data analytics is playing a pivotal role in big data, artificial intelligence, management, governance, and society with the dramatic development of big data, analytics, artificial intelligence. However, what is the spectrum of big data analytics and how to develop the spectrum are still a fundamental issue in the academic community. This article addresses these issues by presenting a big data derived small data approach. It then uses the proposed approach to analyze the top 150 profiles of Google Scholar, including big data analytics as one research field and proposes a spectrum of big data analytics. The spectrum of big data analytics mainly includes data mining, machine learning, data science and systems, artificial intelligence, distributed computing and systems, and cloud computing, taking into account degree of importance. The proposed approach and findings will generalize to other researchers and practitioners of big data analytics, machine learning, artificial intelligence, and data science.
Dietary cation anion difference: Impact on productive and reproductive performance in animal agriculture

Various nutritional tools have been used to improve the productive and reproductive performance of animals, among which difference between certain minerals, called dietary cation anion difference (DCAD) plays a pivotal role. Low or negative DCAD diets reduce blood pH and HCO3- and animal becomes acidotic. This improves Ca absorption from the intestinal tract. It also induces mobilization of Ca from bones which improves Ca status of the animal, thus preventing the occurrence of milk fever at the time of parturition. This may increase milk production and health in subsequent lactation. However, animals fed high DCAD diets before parturition may suffer from milk fever. Milk fever affected animals have increased plasma cortisol level that causes immunosuppression at calving. It is also positively associated with other problems like retained placenta, mastitis and udder edema. On the other hand, feeding high DCAD diet results in increased ruminal pH which is pre-requisite for optimal microbial activity as well as improving the feed intake of the animal. Improved dry matter intake (DMI) is positively correlated with milk yield by providing precursors for various milk constituents. High DCAD diet results in increased milk fat percent due to shifting of ruminal volatile fatty acid production towards acetic acid and butyric acid. It also improves energy balance of the animal which causes increased blood flow towards ovaries and increased progesterone synthesis and follicular development due to positive association between energy balance and postpartum ovulation, which leads to improved reproductive performance of the animal. While feeding low DCAD diet reduces feed intake which causes negative energy balance in early lactating animals that lessens conception rate and increases services per conception. In conclusion, feeding low DCAD diets prepartum prevents the occurrence of milk fever via improving Ca status while feeding high DCAD diets results in improved productive and reproductive performance in lactating animals. Key words: Feed intake, milk yield, reproductive performance, hypocalcaemia, dietary cation anion difference.
FastMap Projection for High-Dimensional Data: A Cluster Ensemble Approach

High-dimensional data with many features present a significant challenge to current clustering algorithms.Sparsity, noise, and correlation of features are common properties of high-dimensional data.Another essential aspect is that clusters in such data often exist in various subspaces. Ensemble clusteringis emerging as a leading technique for improving robustness, stability, and accuracy of high-dimensional data clusterings. In this paper, we propose FastMap projection for generating subspace component data sets from high-dimensional data. By using component data sets, we create component clusterings and provides a new objective function that ensembles them by maximizing the average similarity between component clusterings and final clustering. Compared with the random sampling and random projection methods, the component clusterings by FastMap projection showed high average clustering accuracy without sacrificing clustering diversity in synthetic data analysis. We conducted a series of experiments on real-world data sets from microarray, text, and image domains employing three subspace component data generation methods, three consensus functions, and a proposed objective function for ensemble clustering. The experiment results consistently demonstrated that the FastMap projection method with the proposed objection function provided the best ensemble clustering results for all data sets.
Real-Time Stock Trend Prediction via Sentiment Analysis of News Article

The stock market is volatile and volatility occurs in clusters, price fluctuations based on sentiment and news reports are common. A trader uses a wide variety of publicly available information to forecast the marketing decision. This paper proposes an advice to traders for stock trading using sentimental analysis of publically available news reports. It is based on a hypothesis, that news articles have an impact on the stock market, with this hypothesis we study the relationship between news and stock trend and also proved that negative news has a persistent effect on the stock market. In order to prove this assumption semi-supervised learning technique is being used to build the final model of news classification. This research shows that SVM with TF-IDF as feature performs well in further analysis. The accuracy of the prediction model is more than 90% having 52% correlation with the return label of a stock. This paper also proposes a real-time system which fetches news of any company on a real-time basis and displays its top five news and also predicts the adjusted close price of the next seven days. Keywords: Text Mining, Human Sentiments, KNN, Random Forest, Multinomial Naive Bayes, linear SVM, News.
Genetic variation in chrysanthemum for resistance to Frankliniella occidentalis

In a choice‐experiment, 42 chrysanthemum cultivars were screened for resistance to Frankliniella occidentalis (Pergande). Oviposition preference, two types of feeding damage and thrips numbers per flower were recorded as measures of resistance. A large genetic variation in thrips resistance was found among the cultivars screened. The amount of feeding damage was strongly determined by oviposition preference. Besides, a positive correlation was found between the oviposition preference in non‐flowering chrysanthemums (number of eggs) and flowering chrysanthemums (number of thrips per flower). Thrips feeding on young, developing tissues, causes growth damage because affected cells are unable to expand and leaves become distorted. Thrips feeding on older, expanded leaves causes cells to become filled with air, resulting in ‘silver’ damage. The amounts of growth‐ and ‘silver’ damage were negatively correlated suggesting that thrips chose either young or older leaves to feed on. The order of resistance among cultivars did not change during the experiment. In order to get more insight in resistance mechanisms the influence of some plant‐ and flower characters on resistance was examined. The plant characters height, number of leaves, flower production and flower weight were all negatively correlated with resistance. It is suggested that tall chrysanthemum cultivars with many and large flowers may invest less in defence than smaller cultivars, and therefore are more damaged by thrips.
Diffusive boundary layers and the oxygen uptake of sediments and detritus1

The thickness of diffusive boundary layers and their role for the oxygen uptake of sediments and detritus were studied by the use of microelectrodes. Gradients of oxygen were always detectable within the boundary layer, which varied in thickness from 0.2 mm to > 1 mm. The thickness depended on the flow velocity of the water and on the roughness of the solid surface. Oxygen diffused through the boundary layer with a mean diffusion time of 1.2-9 min. The diffusive boundary layer constituted a transfer resistance for oxygen flux across the solid-water interface which limited the oxygen flux at high uptake rates. Sediments or detritus exposed to aerated water could therefore be almost anoxic at the surface, provided that they had sufficiently high rates of oxygen uptake. This can explain the occurrence of microaerophilic or anaerobic bacteria on exposed sediments where fully oxic conditions would intuitively have been expected.
Role of Dietary Calcium in Hypertension

Calcium level is an importance factor for control hypertension. This review tries to shade the light on the role of calcium in controlling blood pressure. Searching on the internet using the Google search engine was the main source of data as well as books was the method to explore this interaction. Calcium from supplementation and diets was the main focus of this paper.
Comparison of definitive chemoradiation with 5-fluorouracil versus capecitabine in anal cancer.

Background Capecitabine (Cap) is an established treatment alternative to 5-fluorouracil (5-FU) for chemoradiation in rectal cancer. Few studies have compared the two agents in anal cancer. We compared outcomes and toxicities using Cap versus 5-FU in non-metastatic anal cancer patients at Stanford. Methods All non-metastatic anal cancer patients treated with definitive chemoradiation at Stanford from 1997-2016 were included. Fisher's exact and Mann-Whitney U tests were used to compare nominal and continuous variables. Gray's test was used to compare incidence of recurrence and colostomy, and Log-rank test was used to compare survival. Results Sixty-eight patients were included. Thirty-six patients received Cap and 32 received 5-FU (12 received standard 5-FU and 20 received low-dose continuous 5-FU). Patient characteristics were similar between the two groups. There was no difference in the 3-year overall and disease-specific survival between Cap and 5-FU (94% vs. 80%, P=0.197; 100% vs. 86%, P=0.051). Overall incidence of recurrence was equivalent between Cap and 5-FU (11% vs. 13%, P=0.703), but incidence of locoregional recurrence was higher in the 5-FU group (0% vs. 13%, P=0.042); patients treated with Cap had longer recurrence-free intervals (18 vs. 6 months, P=0.400), and all recurrences were distant. More colostomies were needed with 5-FU (3% vs. 13%, P=0.133). Toxicities were similar between the two groups. The most common grade ≥2 toxicities were dermatitis (77%), anal pain (78%), and diarrhea (56%). Conclusions Overall survival (OS), cancer-specific survival and incidence of recurrence were equivalent between Cap and 5-FU in anal cancer. Patients treated with Cap had statistically significant lower incidence of loco-regional relapses.
Space- and Time-Efficient String Dictionaries

In modern computer science, the management of massive data is a fundamental problem because the amount of data is growing faster than we can easily handle them. Such data are often represented as strings such as documents, Web contents and genomics data; therefore, data structures and algorithms for space-efficient string processing have been developed by many researchers. In this thesis, we focus on a string dictionary that is an in-memory data structure for storing a set of strings. It has been traditionally used to manage vocabulary in natural language processing and information retrieval. The size of the dictionaries is not problematic because of Heaps’ Law. However, string dictionaries in recent applications, such as Web search engines, RDF stores, geographic information systems and bioinformatics, need to handle very large datasets. As the space usage of string dictionaries is a significant issue in those applications, it is necessary to develop space-efficient data structures. If limited to static applications, existing data structures have already achieved very high space efficiency by exploiting succinct data structures and text compression techniques. For example, state-of-the-art string dictionaries can be implemented in space up to 5% of the original dataset size. However, there remain trade-off problems among space efficiency, lookup-time performance and construction costs. For example, Re-Pair that is a powerful compression technique for a text is well used to obtain high space efficiency and fast lookup operations, but the time and space needed during construction are not practical for very large datasets. In our work, we attempt two approaches to solve the problems. One develops novel string dictionaries based on double-array tries. The double-array trie can support the fastest lookup operation, but its space usage is very large. We propose how to improve the disadvantage. The novel string dictionaries can support very fast lookup operations, although the space usage is somewhat larger compared to existing compressed ones. The other addresses to improve the high construction costs of applying Re-Pair by introducing an alternative compression strategy using dictionary encoding. Our strategy enables lightweight construction, while providing competitive space efficiency and operation speed. If allowing dynamic operations such as insertion and deletion, there are some sophisticated data structures. While they improve the space efficiency by reducing pointer overheads, they still consume much larger space than the static string dictionaries because
Vernalization response of winter x spring wheat derived doubled-haploids

The effect of vernalization on growth and yield-contributing traits was studied in winter wheat (cv. Saptdhara) x spring wheat (cv. HW 3024) derived 64 doubled-haploid (DH) lines. The material was divided into two sets- with vernalization (V) treatment at 4 ± 0.5°C temperatures and without/no vernalization (NV). There were significant differences between V and NV treatments as well as between the genotypes for all the traits, including days to flowering, plant height, total tillers per plant, effective tillers per plant, spike length, spikelets per spike, and grains per spike, grain yield per plant, 1000-grain weight, and harvest index. The performance of the DH lines significantly improved under V treatment for various traits. During the early growth stages, V had a pronounced effect on growth habit of the plants with no/low injury and improved the survival rate. Two DH lines, DH 33 and DH 59 with spring type growth habit and NV requirement were identified and can be utilized for future spring wheat improvement programs.
Abscisic acid-mediated leaf phenolic compounds, plant growth and yield is strawberry under different salt stress regimes

The present research was conducted to evaluate the interaction effects of exogenous abscisic acid (ABA) and salt stress on phenolic compounds, growth and yield of two short day strawberry cvs "Queen Elisa" and "Kurdistan". Plants were subjected to control, gradual salt stress (up to 20 mmol L-1 over 5 weeks) and salinity shock (20 mmol L-1). ABA treatments included: 0 (control), 5, 10, 20 and 40 µmol L-1. The experiment was carried out based on a complete randomized design in factorial experiment. The highest level of ferulic acid was observed by applying 40 µmol L-1 ABA in "Queen Elisa" under salt stress shock but effective increase in caffeic acid and p-coumaric acid was shown at gradual salt stress for both cultivars at the same ABA level. Maximum level of ABA led to the highest gentisic acid and gallic acid at gradual salt stress in "Kurdistan". Methyl gallate and flavonoid content showed a striking increase at the same conditions in "Queen Elisa". The interaction effect of salt stress regimes and ABA resulted in an increase in ellagic acid content for both cultivars. The interaction effect of ABA and salt shock caused higher reduction in root and shoot fresh dry weights and decrease in fruit yield in "Kurdistan". The results of this experiment accounts for the important role of exogenous ABA in the activation of antioxidant defense mechanism, growth and yield maintenance under gradual salt stress in strawberry.
Amino Acids: Incorporation into α- and β-Chains of Hemoglobin by Normal and Thalassemic Reticulocytes

After incubation of reticulocytes with radioactive amino acid, the specific activity of the β-chain of globin from the blood of patients with thalassemia was consistently lower than that of the α-chain. In subjects without this disorder, the specific activity of the β-chain was always equal to or higher than that of the α-chain.
Preserving genes: a model of the maintenance of genetic variation in a metapopulation under frequency-dependent selection

Understanding how genetic variability is maintained in natural populations is of both theoretical and practical interest. In particular, the subdivision of populations into demes linked by low levels of migration has been suggested to play an important role. But the maintenance of genetic variation in populations is also often linked to the maintenance of sexual reproduction: any force that acts to maintain sex should also act to maintain variation. One theory for the maintenance of sex, the Red Queen, states that sex and variation are maintained by antagonistic coevolutionary interactions – especially those between hosts and their harmful parasites – that give rise to negative frequency-dependent selection. In this paper I present a model to examine the relationships between population subdivision, negative frequency-dependent selection due to parasites, the maintenance of sex, and the preservation of alleles from fixation. The results show strong interactions between migration rates, negative frequency-dependent selection, and the maintenance of variability for sexual and asexual populations.
Maternal and zygotic temperature signalling in the control of seed dormancy and germination

Abstract Temperature has a key influence over seed dormancy and germination, allowing wild plants to synchronize their life history with the seasons. In this review we discuss the signalling pathways through which temperature is integrated into seed physiology and the control of primary and secondary dormancy, with an emphasis on understanding maternal effects and responses dictated by the zygotic tissues. A key emerging paradigm is that temperature signalling in seeds must be understood in relation to whole plant genetics and physiology, as overlapping pleiotropic roles for temperature sensing and hormone signalling pathways are commonplace.
A review of microRNAs related to the occurrence, diagnosis, and prognosis of non-small cell lung cancer

Non-small cell lung cancer (NSCLC) is the main most common type of lung cancer, accounting for about 80% of all cases. The five-year survival rate of patients with NSCLC is usually less than 20%. MicroRNAs (miRNAs), a type of small non-coding RNA, are closely related to the development and occurrence of tumors, including NSCLC. Here, we reviewed the miRNAs related to the occurrence, diagnosis and prognosis of NSCLC. K ey words: miRNA; non-small cell lung cancer; occurrence; diagnosis; prognosis
Application Research on the Flipped Class Mode in the Course of ‘Principle and Technology of Early Warning Satellite’

Early warning satellites is one of the important detective equipment of anti-missile early warning system. Learning its basic principle and common technology is indispensable for training qualified people to meet the needs of future anti-missile early warning operations all over the world. Based on analyzing the advantages of the application of flipping classroom teaching mode and the breakthrough of traditional teaching mode, this paper explores the specific teaching implementation method of flipping classroom to the course of ‘Principle and Technology of Early Warning Satellite’, reflecting on the shortcomings, and proposing rationalization suggestions. Keywords—Early warning satellite, Equipment teaching, flipping classroom