Miracle-dz/UniFAR-FTUs huggingface dataset:
Modulation of Macrophage Activity by a Herbo-mineral Formulation in Murine Model

Aim: The present paper investigates the effect on immune responses by a herbo-mineral formulation, Khamira Marwarid [KM], prescribed in the Indian subcontinent as a rejuvenator, especially to convalescing patients of typhoid fever, in murine model. Study Design: KM was administered orally for short, intermediate and long duration [5, 15 and 30 days respectively] at a dose of 2g/kg body weight. Results: Administration of KM enhanced the antigenic and mitogenic activity, induced by ovalbumin and Con A (mitogenic stimuli), of mice whole splenocytes. KM caused a marked increase of production of Th-1 cytokine (IFN-) and a non significant decrease of production of Th-2 cytokine (IL-4) by splenocytes when stimulated with Concanavalin A. Oral administration of KM, by itself did not induce the production of NO by macrophages, but enhanced the production of NO in response to LPS as compared to unstimulated control. However, dose duration related suppression of NO production was observed. KM also enhanced significantly the phagocytosis that was evaluated using the phagocytic rate (PR) and phagocytic index (PI). Conclusion: The results indicate the immunomodulatory potential of KM leading to a Th1 dominant immune state and activation of macrophages and may find use in immunotherapy of tumors. Original Research Article British Journal of Medicine & Medical Research, 4(29): 4802-4811, 2014 4803
Joint estimation of sampling and turnover rates from fossil databases: capture-mark-recapture methods revisited

Abstract The estimation and interpretation of temporal patterns in origination and extinction rates is a major goal of paleobiology. However, the possibility of coincident variation in the quality and completeness of the fossil record makes the identification of such patterns particularly difficult. Previously, Nichols and Pollock (1983) proposed that capture-mark-recapture (CMR) models be adapted to address this problem. These models can be used to estimate both sampling and turnover rates, reducing the risk of confounding the two quantities. Since that time, theoretical advances have made possible the application of these tools to a much broader range of problems. This paper reviews those advances likely to be of greatest relevance in paleobiological studies. They include (1) joint estimation of per-taxon origination and extinction rates, (2) modeling sampling or turnover rates as explicit functions of causal variables, (3) ranking of alternative models according to their fit to the data, and (4) estimation of parameter values using multiple models. These are illustrated by application to an Ordovician database of benthic marine genera from key higher taxa. Robustness of these methods to violation of assumptions likely to be suspect in paleobiological studies further suggests that these models can make an important contribution to the quantitative study of macroevolutionary dynamics.
Expression and function of nuclear receptor coregulators in brain : understanding the cell-specific effects of glucocorticoids

Currently, the raising awareness of the role of glucocorticoids in the onset of numerous (neuro)-pathologies constitutes the increasing necessity of understanding the mechanisms of action of glucocorticoids in bodily processes and brain functioning. Glucocorticoids mediate their effects by binding to intracellular receptors which act as transcription factors. A remarkable and yet unexplained phenomenon described more than two decades ago, is the cell-specific effects glucocorticoids bring about on gene expression in brain. For example, while glucocorticoids suppress corticotrophin-releasing hormone (CRH) synthesis in the hypothalamus, production of CRH in the central nucleus of the amygdala (CeA) is stimulated by increased hormone levels. Inasmuch as the neuroanatomical distribution of the corticosteroid receptors does not satisfactorily explain these effects, it is of interest to decipher the role of recently discovered coregu lator proteins that modulate the direction and the magnitude of steroid receptor-driven transcription. Therefore, in the current thesis the expression and function of central coregulators was studied: the coactivators SRC1a and SRC1e along with the corepressors N-CoR and SMRT were found to be expressed in brain and involved in regulation of CRH gene expression. Finally, a method that allows detection of coregulator recruitment by steroid receptors in brain tissue was developed.
Antimutagenic Activity of Some Natural supplements on Ivermectin ge- notoxicity in Lymphocytes of Buffalo

Ivermectin is a veterinary anthelminthic drug, highly effective against a number of arthropod and nematode infestations in vertebrates. The literature reported that ivermectin have mutagenic activities. The extensive use of ivermectin in food producing animals can cause potential hazard to humanity by causing gene mutation or chromosomal aberrations. Recently, there have been considerable efforts to search for naturally occurring substances that can inhibit, reverse, retard or prevent mutagenicity. A wide array of substances derived from edibles and medicinal plants reported to possess anticarcinogenic and antimutagenic activities. Therefore, the aim of this study was to evaluate the modulator role of each of garlic, L-carnitine and wheat germ oil (WGO) against genotoxicity of ivermectin in buffalo lymphocyte cultures by using the cytokinesis block micronucleus assay and chromosomal aberrations test as cytogenetic end-points. Results showed that ivermectin induced dose dependent increase in the frequencies of the binucleated lymphocytes with micronuclei as well as the number of micronuclei in lymphocytes of river buffalo, while the number of binucleated lymphocytes significantly decreased. In addition, ivermectin low dose caused nonsignificant increase in the frequency of total chromosomal aberrations in lymphocytes of river buffalo as compared to control. Whereas, in medium and high doses the frequencies of aberrant cells increased at a significant level (P ≤ 0.001) than control. Meanwhile, the treatment with the three natural supplements (garlic, L-carnitine, wheat germ oil) in continuous with ivermectin significantly reduced the frequencies of binucleated lymphocytes with micronuclei, the number of micronuclei and the frequencies of total chromosomal aberrations induced by ivermectin tested doses, and increase the number of binucleated lymphocytes. In addition, the results indicated that there were non-significant differences between the modulator role of garlic, L-carnitine or wheat germ oil against the mutagenicity of ivermectin in blood lymphocytes. Finally, we can concluded that regular consumption of natural antioxidants, antimutagenic compounds is inversely related to the risk of cancer, since the free radicals scavenger activities of antioxidants are very important due to the de
THE PRIMARY MIXED LEUKOCYTE REACTION IN MICE

Until now, the study of dendritic cells (DC) x has required positive selection techniques. Populations enriched in DC have been shown to be powerful stimulators first of the mixed leukocyte reaction (MLR) (1) and subsequently of a number of other responses in vitro (2-11) and in situ (12, 13). Negative selection experiments have yet to be performed. Specific depletion protocols would help establish ifDC are the principal ceils required for MLR stimulation and other accessory functions. Recently we obtained a stable hybridoma, 33D1, that secretes a specific anti-DC antibody (14). The 33D1 antigen appears to be found only on DC, at a frequency of 1-1.5 × 104 antibody binding sites per cell. The antigen has yet to be identified biochemically but most likely, it is not an immune response associated or Ia antigen. In the presence of rabbit complement, 33D1 efficiently kills DC, but no other cells in spleen, node, thymus, marrow, blood, and peritoneal cavity. This monoclonal should provide a way to selectively eliminate DC and to measure the functional consequences that ensue. Here we show that selective removal of DC dramatically reduces the MLR stimulatory capacity of both unfractionated spleen and spleen adherent cells. Function is reconstituted with small numbers of DC purified by a technique that is independent of the 33D1 antibody. We propose that antigen, in combination with DC, represents the physiologic pathway for inducing the MLR and other immune responses.
DESCRIBING BODY SHAPE OF GOBY, Glossogobius giuris (HAMILTON, 1822), FROM LAKE MAINIT, SURIGAO DEL NORTE USING LANDMARK-BASED GEOMETRIC MORPHOMETRICS

Glosssogobius giuris (Hamilton, 1822) is a native fish in Lake Mainit, Surigao del Norte, Philippines. Its size can reach up to 30 cm. In this study the size of G. giuris ranges 10.5- 23.5 (female) and 10.5-27.0 (male). It is aimed in this study to determine morphological variations in body shapes between sexes of G. giuris which could be important biological information useful in biodiversity studies and implementations of proper fishery management practices. Twentyfive landmark points were assigned on the specimens to quantify its body shape. The relative warp scores were used in Discriminant Function Analysis (DFA) to test the variations of body shapes between sexes of G. giuris. DFA, PCA scatter diagram and MANOVA suggest no sexual dimorphism of the species on the basis of body shape (Wilk’s lambda = 1; p< 0.0001). Yet, some morphological variations were observed as displayed on the Box and Whisker’s plot. Females have a deep body and broader abdomen related to males to cater its reproductive role in carrying and laying eggs and males have broader caudal peduncle compared to females.
Learning Dynamic Hierarchical Topic Graph with Graph Convolutional Network for Document Classification

Constructing a graph with graph convolutional network (GCN) to explore the relational structure of the data has attracted lots of interests in various tasks. However, for document classiﬁcation, existing graph based methods often focus on the straightforward word-word and word-document relations, ignoring the hierarchical semantics. Besides, the graph construction is often independent from the task-speciﬁc GCN learning. To address these constrains, we integrate a probabilistic deep topic model into graph construction, and propose a novel trainable hierarchical topic graph (HTG), including word-level, hierarchical topic-level and document-level nodes, exhibiting semantic variation from ﬁne-grained to coarse. Regarding the document classiﬁcation as a document-node label generation task, HTG can be dynamically evolved with GCN by performing variational inference, which leads to an end-to-end document classiﬁcation method, named dynamic HTG (DHTG). Besides achieving state-of-the-art classiﬁcation results, our model learns an interpretable document graph with meaningful node embeddings and semantic edges.
Balancing Learning Speed and Stability in Policy Gradient via Adaptive Exploration

In many Reinforcement Learning (RL) applications, the goal is to find an optimal deterministic policy. However, most RL algorithms require the policy to be stochastic in order to avoid instabilities and perform a sufficient amount of exploration. Adjusting the level of stochasticity during the learning process is non-trivial, as it is difficult to assess whether the costs of random exploration will be repaid in the long run, and to contain the risk of instability. We study this problem in the context of policy gradients (PG) with Gaussian policies. Using tools from the safe PG literature, we design a surrogate objective for the policy variance that captures the effects this parameter has on the learning speed and on the quality of the final solution. Furthermore, we provide a way to optimize this objective which guarantees a stable improvement of the original performance measure. We evaluate the proposed methods on simulated continuous control tasks.
Armillaria phylogeny based on tef-1α sequences suggests ongoing divergent speciation within the boreal floristic kingdom

Armillaria plays diverse ecological roles in forests worldwide, which has inspired interest in understanding phylogenetic relationships within and among species of this genus. Previous rDNA sequence-based phylogenetic analyses of Armillaria have shown general relationships among widely divergent taxa, but rDNA sequences were not reliable for separating closely related North American species, such as A. gallica, A. calvescens, A. cepistipes, and A. sinapina, or other closely related Eurasian species (Kim et al. 2006). Recent studies have shown that translation elongation factor 1a (tef-1a ) sequences appear quite useful for phylogenetic analysis of Armillaria spp. from diverse global regions (Maphosa et al. 2006; Antonin et al. 2009; Hasegawa et al. 2010; Ota et al. 2011; Brazee et al. 2011; Mulholland et al. 2012; Ross-Davis et al. 2012; Tsykun et al. 2012). The objective of this study is to determine phylogenetic relationships among northern hemisphere Armillaria spp. based on available tef -1a sequences from well-characterized isolates.
Nanomechanics measurements of live bacteria reveal a mechanism for bacterial cell protection: the polysaccharide capsule in Klebsiella is a responsive polymer hydrogel that adapts to osmotic stress

A global health problem concerns the evolution of antibiotic-resistant bacteria. A characteristic of these super bug pathogens is their ability to form an exopolysaccharide matrix, the capsule, allowing them to resist antibiotic treatment and other environmental stresses. Here we apply atomic force microscopy (AFM) to interrogate living bacterial cells and provide the first in situ measurements of the biophysical behaviour of the capsule in physiologically relevant conditions. We prepared live Klebsiella pneumoniae, a common pathogen that has evolved super bug strains. We measured how capsule, cell wall and cell cytoplasm of wild type and capsule-deficient bacterial cells respond when indented by an AFM tip, under extreme osmotic conditions. By developing a mechanical model for the indentation of bacteria and fitting the force profiles to this model, we discovered that the organisation and hydration of the capsule alter in response to the osmotic environment, but surprisingly there is no change in cytoplasmic turgor pressure. The capsule deficient mutants however, experience extreme change in turgor pressure under altered osmotic conditions. Our results provide new insight on the biophysical behaviour of the bacterial capsule, demonstrating that it is a polymer hydrogel that acts as an ion sponge to dampen the impact of osmotic stress. Nano-mechanical screening for additives to medical plastics that alter the properties of this ion sponge represents a new way to address the problems associated with antibiotic-resistant bacteria.
Statistical and Computational Rates in Graph Logistic Regression

We consider the problem of graph logistic regression, based on partial observation of a large network, and on side information associated to its vertices. The generative model is formulated as a matrix logistic regression. The performance of the model is analyzed in a high-dimensional regime under a structural assumption. The optimal statistical rates are derived, and an estimator based on penalized maximum likelihood is shown to attain it. The algorithmic aspects of this problem are also studied, and optimal rates under computational constraints are derived, and shown to diﬀer from the information-theoretic rates - under a complexity assumption.
Bagasse Complete Rations Employing Urea or Urea Plus Fishmeal as Supplemental Nitrogen Sources

Abstract Eighteen Brown Swiss and Holstein cows were in a replicated experiment involving preliminary, adjustment, and comparison periods of 35, 7 and 105 days to compare three complete rations containing 25% bagasse and 75% concentrates. The nitrogen supplement contained urea and tuna-fish meal in the following respective proportions: Ration U2, ½; and ½; (15.9% crude protein); Ration U3, 3 4 ; and 1 4 ; (15.9% crude protein); and Ration U4, 1 and 0 (16.8% crude protein). The rations were group-fed at nearly ad libitum intake. Daily feed consumptions per head during the comparison averaged 22.39, 19.98 and 17.10kg for Rations U2, U3 and U4. The corresponding urea consumptions were 336, 450 and 513g. Daily fat corrected milk productions were 21.97, 19.65 and 18.07kg, Ration U2 being superior to U4 (P The economic estimates, in the same order, were ration cost per 100kg, 7.08, 6.88 and $6.64; feed costs per 100kg milk, 7.49, 7.10 and $6.28; and daily income over feed costs per cow, 2.49, 2.33 and $2.34.
REGULATION OF HUMAN DENDRITIC CELLS AND T CELLS BY ADENOVIRUS VECTORS TYPES 5 AND 35: IMPLICATIONS FOR VACCINE DESIGN

Following viral infection or vaccination dendritic cells (DC) perform an intricate series of roles at the interface of innate and adaptive immunity. Peripheral DC recognition of pathogen associated molecular patterns initiates signaling cascades leading to morphological and phenotypic maturation. The differentiation to a mature phenotype licenses DCs to efficiently prime Tand B-lymphocytes. Thus, DCs shape early innate immune responses that limit viral replication and initiate the generation of protective and adaptive immunological memory. In this thesis, we began by studying the interaction of human primary DCs with human adenovirus (AdV). While the causative agent of a variety of human diseases, AdVs are also a valuable research tool for probing virological, immunological, and cellular mechanisms of nature. Recombinant human AdVs (rAdV), rendered replication incompetent and thus unable to cause disease, have gained prominence as gene delivery vehicles in multiple vaccine trials. In light of the clinical importance of AdV vectors, we employed a reductionist approach to study mechanisms of virus-mediated regulation of human DC function. Since DCs activate adaptive immunity, we extended our investigations to the impact of rAdV on the activation of T-lymphocytes. These studies are particularly relevant since the induction of potent T-cell responses is one objective of rAdV based vaccine vectors. In assessing the interaction of rAdV with primary human blood myeloid and plasmacytoid DC subsets, we found that activation of these cells was dependent on rAdV type. rAdV-35 more efficiently infected DCs than rAdV-5, and matured blood DCs and strongly induced interferon-α in plasmacytoid DCs. Infection by rAdV-35 was dependent on the receptor CD46, whereas the receptor for rAdV-5 was less clear. We then showed that lactoferrin facilitated rAdV-5 infection of multiple DC subsets in a similar manner to epithelial cells. rAdV-exposed DCs were able to process and present rAdV encoded transgenes and activate polyfunctional memory T cells, which indicated that rAdV infected DCs retained their antigen presentation capacity. However, it remained unclear from these studies whether rAdV affected the activation of naive T cells, which is an important step for vaccination. To this end, rAdV-35 was found to strongly inhibit activation of naive CD4+ T cells through binding of its cellular attachment receptor, CD46. Attenuated activation was characterized by lower proliferation and IL-2 production, as well as deficient NF-κB nuclear translocation. Further studies showed that cross-linking with CD46 monoclonal antibodies and recombinant trimeric rAdV-35 knob proteins was sufficient to cause similar suppression as the whole virus, substantiating the role of CD46 in regulating CD4+ Tcell function. Our findings provide insights into the mechanisms by which host immune cells respond to rAdV and also how the virus may act to modulate host cell function. These findings may also guide the development of rAdVs as vaccine vectors.
A revision of the genus Tripterygium (Celastraceae)

To better understand the genus Tripterygium for the Flora of China , the history of the genus and its species is summarized and characters traditionally used to divide the genus re-examined. Because no reliable differentiating characters were found, all of the previously named taxa in the genus are reduced to the single species, Tripterygium wilfordii Hook.f. The range of this monospecific genus is typical of many in the East Asian flora.
Persistent infections of mammals and mammalian cell cultures with West Nile virus

Before 1990, West Nile virus (WNV) was considered to be one of many arthropod-borne viruses that caused mild febrile illness in man. However, in the 1990s, the virus was associated with severe CNS disease that produced mortality in horses and man in Europe. In 1999, WNV was identified as the etiologic agent of an outbreak of human and avian encephalitis in New York City (NY, USA). Like many other Flaviviridae family members, WNV is generally considered to cause acute infections, however, persistent WNV infections have been observed in laboratory-infected animals and in human patients. These persistent infections could be facilitated by changes to the viral genome that allow the virus to evade detection by the host cell, a property that has been studied in cell culture. This review highlights our current knowledge of persistent WNV infections in vitro and in vivo, and speculates on how persistence could influence virus transmission.
Intracellular Salivation Is the Mechanism Involved in the Inoculation of Cauliflower Mosaic Virus by Its Major Vectors Brevicoryne brassicae and Myzus persicae

Abstract Cauliflower mosaic virus (CaMV) is transmitted to crucifers in a noncirculative manner by several aphid species. CaMV is preferentially acquired from the phloem, although acquisition also occurs after brief intracellular stylet punctures of aphid vectors in nonvascular leaf tissues. In the present work, we used the electrical penetration graph technique to study the specific aphid stylet activities and behavioral events leading to the inoculation of CaMV to turnip plants by its two major vectors, Brevicoryne brassicae (L.) and Myzus persicae (Sulzer). Aphids subjected to an 8-h acquisition access time on infected plants were transferred to test plants and removed immediately after specific behavioral events were recorded. CaMV was readily inoculated after the first intracellular puncture in nonvascular tissues by both vector species. Inoculation rate of CaMV by B. brassicae was the highest after a 3-h inoculation access period, regardless of whether aphids had reached the phloem phase during that period. Consistent interspecific differences also were found in the ability of both aphid vectors to retain CaMV. B. brassicae could retain the virus after several intracellular punctures, whereas M. persicae readily lost the virus after performing the same number of intracellular stylet punctures. We concluded that salivation by aphids during successive intracellular stylet punctures in the epidermal and mesophyll cells before reaching the phloem phase are the key behavioral events associated to the inoculation of Cauliflower mosaic virus. The likely location of the viral retention site inside the aphid mouthparts is discussed.
Persistence Enhanced Graph Neural Network

Local structural information can increase the adaptability of graph convolutional networks to large graphs with heterogeneous topology. Existing methods only use relatively simple topological information, such as node degrees. We present a novel approach leveraging advanced topological information, i.e., persistent homology, which measures the information ﬂow eﬃciency at diﬀerent parts of the graph. To fully exploit such structural information in real world graphs, we propose a new network architecture which learns to use persistent homology information to reweight messages passed between graph nodes during convolution. For node classiﬁcation tasks, our network outperforms existing ones on a broad spectrum of graph benchmarks.