Miracle-dz/UniFAR-FTUs huggingface dataset:
Bioforensics: Characterization of biological weapons agents by NanoSIMS

The anthrax attacks of Fall 2001 highlight the need to develop forensic methods based on multiple identifiers to determine the origin of biological weapons agents. Genetic typing methods (i.e., DNA and RNA-based) provide one attribution technology, but genetic information alone is not usually sufficient to determine the provenance of the material. Non-genetic identifiers, including elemental and isotopic signatures, provide complementary information that can be used to identify the means, geographic location and date of production. Under LDRD funding, we have successfully developed the techniques necessary to perform bioforensic characterization with the NanoSIMS at the individual spore level. We have developed methods for elemental and isotopic characterization at the single spore scale. We have developed methods for analyzing spore sections to map elemental abundance within spores. We have developed rapid focused ion beam (FIB) sectioning techniques for spores to preserve elemental and structural integrity. And we have developed a high-resolution depth profiling method to characterize the elemental distribution in individual spores without sectioning. We used these newly developed methods to study the controls on elemental abundances in spores, characterize the elemental distribution of in spores, and to study elemental uptake by spores. Our work under this LDRD project attracted FBI andmore » DHS funding for applied purposes. « less
The Effect of Intellectual Capital on Firm's Value using Ownership Structure as Moderating Variable on Company Listed in Indonesia Stock Exchange period 2008-2015

— This research aims to examine the effect of intellectual capital on firm’s value using ownership structure as moderating variable. The intellectual capital was measured using a model of Value Added Intellectual Coefficient (VAIC tm ) while the value of the company was measured using Tobin’s Q. The proxy of ownership structure as a moderating variable is the percentage of managerial ownership and institutional ownership. Population of this research is the listed companies in Indonesia Stock Exchange with research period from 2008 to 2015. The data analysis used multiple regression equation with path analysis to test residual moderating variables. The result of this research indicates that intellectual capital has a positive effect on firm value while managerial ownership is moderating variable in this research. From this research, it is found that institutional ownership does not work as moderating variable.
Role of MicroRNAs as Tumor Suppressor

MicroRNAs are important regulators of gene expression that control both physiological and pathological processes such as development and cancer . Although their mode of action has attracted great attention, the principles governing their expression and activity are only beginning to emerge. Recent studies have introduced a paradigm shift in our understanding of the microRNA biogenesis pathway, which was previously believed to be universal to all microRNAs. Maturation steps specific to individual microRNAs have been uncovered, and these offer a plethora of regulatory options after transcription with multiple proteins affecting microRNA processing efficiency. More than 50% of miRNA genes are located in cancer- associated genomic regions or in fragile sites, suggesting that miRNAs may play a more important role in the pathogenesis of a limited range of human cancers than previously thought. Overexpressed miRNAs in cancers, such as mir-17-92, may function as oncogenes and promote cancer development by negatively regulating tumor suppressor genes and/ or genes that control cell differentiation or apoptosis. Underexpressed miRNAs in cancers, such as let-7 , function as tumor suppressor genes and may inhibit cancers by regulating oncogenes and/ or genes that control cell differentiation or apoptosis.
PEMBUATAN GULA SEMUT KELAPA (KAJIAN pH GULA KELAPA DAN KONSENTRASI NATRIUM BIKARBONAT) [IN PRESS JANUARI 2016]

Gula kelapa cetak sebagai alternatif bahan untuk membuat gula semut sangat potensial. Tujuan dari penelitian ini adalah mengetahui pengaruh pH gula kelapa dan konsentrasi penambahan Natrium bikarbonat terhadap karakteristik gula semut kelapa. Penelitian ini disusun dengan menggunakan metode Rancangan Acak Kelompok. Faktor 1 yaitu pH gula kelapa yang terdiri dari 3 level (6.50(±0.10); 7.00(±0.10); 7.50(±0.10)) dan faktor 2 konsentrasi penambahan Natrium bikarbonat yang terdiri dari 3 level (0.75%; 1.00%; 1.25% b/b), dengan 3 kali ulangan. Pemilihan perlakuan terbaik dengan metode Multiple Attribute atau Zeleny dan uji organoleptik pada produk gula semut kelapa dianalisi menggunakan uji kesukaan. Perlakuan terbaik organoleptik diperoleh pada gula kelapa dengan pH 7.00(±0.10) dan konsentrasi Natrium bikarbonat 1,25% dan perlakuan terbaik fisiko-kimia ialah perlakuan gula kelapa dengan pH 7.50(±0.10) dan konsentrasi penambahan Natrium bikarbonat 0.75%. Kata Kunci: Gula Semut Kelapa, Natrium bikarbonat, pH Gula Kelapa
Defensins in Ulcerative Colitis

Defensins and cathelicidins are the two major endogenous antimicrobial peptide families in mammals, which are abundant components of phagocytic leukocytes and are released by epithelial cells at mucosal surfaces. Defensins are antimicrobial peptides produced at a variety of epithelial surfaces. In the small intestine Paneth cells secrete ┙-defensins and additional antimicrobial peptides at high levels in response to cholinergic stimulation and when exposed to bacterial antigens. In the intestinal tract ┙and ┚-defensins contribute to host immunity and assist in maintaining the balance between protection from pathogens and tolerance to normal flora. However, attenuated expression of these defensins compromises host immunity and hence may alter the balance toward inflammation. Altered defensins production is suggested to be an integral element in the pathogenesis of ulcerative colitis (UC). Recent years, the defensins have attracted great attention because of their roles in the organism defense system. This review highlights the current knowledge of defensins, distribution, structures, the diverse functions in the immune response and the changes of defensins expression in UC and the potential role in the pathogenesis of UC.
The colonizing fungus as a food provider

Filamentous fungi colonize food ingredients, penetrating into them, releasing a variety of enzymes, raising metabolites and reaction products and increasing their biomass. In many cases, this sequence of events is considered as spoilage (Pitt and Hocking, 1985) because of off-odours, unwanted discolourations, taste defects, and toxicity. Interestingly, however, mankind experienced that in certain situations, colonizing filamentous fungi (moulds in short) bring about desirable changes in foods, and termed them fermentations (Fukushima, 1985). Considering the chiefly aerobic metabolism of moulds, the usage of the term fermentations indicating the anaerobic mechanism of energy generation is incorrect by definition. Nevertheless the term fungal food fermentation is widely accepted in the sense of bioprocesses resulting in improvements of quality. Whereas the origin of fungal food fermentation is the Orient, some specific processes have developed in Europe. Increasing international travel and trade have been the vehicle for the worldwide distribution of some of the derived products. In principle, the birth of fungal food fermentations must have been from "spoilage"; from an ecological point-of-view it may thus be expected that the concept of "spoilage associations" (Dalgaard et al., 2003) also applies to fungal food fermentations. This implies ecological niches consisting of suitable substrate, microbial competition, and favourable envi ronmental conditions. It therefore seems quite logical to encounter moulds with optimum growth temperature (Topt) of 20-30 °C in the moderate climates, and those with Topt of 30-40 °C in the humid tropics. Table 1 presents an overview of selected filamentous fungi, the fermented foods in which they feature, their role in quality improvement, and some recent literature references. In the following sections these cases will be discussed in some detail, with a focus on the scientific questions of recent interest.
Human IgG Monoclonal Anti-αIIbβ3-Binding Fragments Derived from Immunized Donors Using Phage Display1

Previous studies of the immune response in polytransfused Glanzmann thrombasthenia (GT) patients and in autoimmune thrombocytopenic purpura (AITP) have relied on serum analysis and have shown the frequent development of Abs directed against the αIIbβ3 integrin. However, little is known about the molecular diversity of the humoral immune response to αIIbβ3 due to the paucity of mAbs issuing from these pathologies. We have isolated human IgG anti-αIIbβ3 binding fragments using combinatorial libraries of single-chain IgG created from the B cells of a GT and an AITP patient, both with serum Abs. Ab screening was performed using activated platelets or activated αIIbβ3-expressing Chinese hamster ovary cells. Sequencing of selected phage Abs showed that a broad selection of genes from virtually all V gene families had been used, indicating the diversity of the immune response. About one-half of the VH and VL segments of our IgG anti-αIIbβ3 fragments displayed extensive hypermutations in the complementarity-determining region, supporting the idea that an Ag-driven immune response was occurring in both patients. The H chain complementarity-determining region 3 analysis of phage Abs revealed motifs other than the well-known RGD and KQAGDV integrin-binding sequences. To our knowledge, our study is the first to illustrate multiple human IgG anti-αIIbβ3 reactivities and structural variations linked to the anti-platelet human immune response. Human αIIbβ3 Abs preferentially directed against the activated form of the integrin were further characterized because platelet αIIbβ3 inhibitors are potential therapeutic reagents for treating acute coronary syndromes. Currently available αIIbβ3 antagonists do not specifically recognize the activated form of the integrin.
Determinación y evaluación de los componentes presentes en las pinturas anti-incrustantes utilizadas en la acuicultura y sus posibles efectos en sedimentos marinos en el sur de Chile

Sediment samples were taken in three areas related to the use of antifouling paints in salmon farming in southern Chile, in order to detect changes in the abundance and diversity of benthic macrofauna due to the accumulation of metals such as Cu and Zn in sediments. The results show that if there especially Cu accumulation in sediments adjacent to cages each crop, but there were no significant changes in the composition or abundance of benthic macrofauna that accompanies these farms, even when concentrations Cu exceeded 800 µg g -1 in sediments.
THE ETHNOBOTANY OF CHITRAL VALLEY, PAKISTAN WITH PARTICULAR REFERENCE TO MEDICINAL PLANTS

An ethnobotanical survey was carried out to collect information regarding the various indigenous uses, especially the medicinal plants in Chitral valley. A total of 83 taxa are reported as being used locally for various purposes. Our results suggest that root is the major plant part used in most of the recipes. Majority of the recipes are prepared in the form of decoction from freshly collected plant parts. Mostly a single species is used and are mainly taken orally. All of these plants are collected from the wild, 7 of which are reported as scarce locally. Unsustainable collection methods, poor post harvest methods, soil erosion and intense deforestation are the main causes of the depletion of local flora. As the Chitrali people still partly depend on medicinal plants for majority of their ailments, therefore loss of these plant resources will, to a certain extent, hamper the existing healthcare system in the area. Measures for the conservation of plant resources especially medicinal plants of Chitral valley are urgently needed.
Estresse salino em plântulas de milho: parte II distribuição dos macronutrientes catiônicos e suas relações com sódio

The work was performed in the greenhouse, aiming to evaluate the effect of salt stress on distribution of nutrients in different parts of maize cultivars differing in their tolerance to salinity. The experiment was carried out on 2 x 5 factorial arrangement with two maize cultivars (P-3051 and BR-5011) and five sodium chloride levels in nutrient solution (0, 25, 50, 75 or 100 mol m-3). Salt stress increased Na+ content and decreased K+ content in all plant parts. Na+ content was higher in stalk and sheath than in leaf blade tissue. Ca++ content decreased in root, stalk and leaf blade while Mg++ content decreased only in root and in stalk tissue. Root Ca++ content in the cultivar P-3051 under 100 mol m-3 NaCl was 60% higher than in the cultivar BR-5011. The salt treatment increased Na+/K+, Na+/Ca++ and Na+/Mg++ ratios in all plant parts, and the increment was higher in the P-3051 than in the BR-5011 cultivar.
Date seed and date seed oil

Date palm is an important plant in arid regions with more than 20 varieties reported all over the world. Date seed is a byproduct of date fruit industry which is normally being discarded, used as animal feed ingredient or turned into non-caffeinated coffee by the Arabs. About 11-18% of date fruit weight is the seed which is composed of carbohydrates, dietary fiber, fat, ash and protein. In addition, the antioxidant content in date seed oil (DSO) was found to be comparable with olive oil, which can be as a good source of antioxidant in order to fulfill the consumers demand. Oleic acid is the major fatty acid found in DSO, followed by lauric, linoleic, palmitic and myristic acid. However, different varieties of date fruits have different fatty acid compositions. This paper reviewed the potential use of date seed and date seed oil in order to discover and develop its usage and find out the suitable application of these seed and oil.
Reconstructing Human Origins: A Modern Synthesis

Time, climate and human evolution finding, dating and naming fossil hominids before the bipeds - human antecedents among the Miocene hominoids the earliest hominids - the Australopithecines Australopithicine palaeobiology and phyogeny the origin of the genus homo quo vadis homo erectus? almost but not quite - archaic homo sapiens between apes and humanity - what the molecules say about "modern" human origins between apes and humanity - what the fossils say about "modern" human origins epilogue. (Part contents)
Correlating Cryptosporidium and Giardia with microbial indicators

Concentrations of Cryptosporidium oocysts, Giardia cysts, fecal and total coliforms, fecal streptococci, Aeromonas sp. , Pseudomonas aeruginosa, Clostridium perfringens, algae, and coliphages were measured in each of 51 raw water samples from rivers in the Ottawa (Canada) region over three months. This study also examined correlations between the protozoa concentrations and current or potential indicators of water quality in raw surface water. The article also reports the concentrations of Cryptosporidium oocysts and Giardia lamblia cysts in two water treatment plants and in one wastewater plant. Significant correlations between fecal streptococci and Cryptosporidium oocysts and between Giardia and both somatic coliphages and algae were observed in raw surface water samples, but the relationships appear to be watershed-dependent. No significant correlation was obtained between the presence of the protozoa and that of Clostridium perfringens or any of the other indicators.
Impact of probiotics on numbers, ability to hemolysis and on changes in drug-resistance of selected Escherichia coli isolates recovered from faeces of dairy cattle

The investigations were conducted on 60 Holstein-Friesian dairy cows (at age 3 year and weight 590 kg) kept in tie-stall barn. The animals were divided into 3 groups of 20 heads each. The control group (K) was fed diets without probiotics, group (EM) – was fed diet with the addition of EM probiotic (dose of 150 ml × t–1 TMR) and group (T) – was fed diet with the addition of ToyoCerin probiotic (dose of 0.2 kg × t–1 TMR). Strains of Escherichia coli were isolated from faeces with the aim to determine their numbers, capability for hemolysis and assessment of their drug-resistance. The isolates were identified as E. coli on the basis of their biochemical properties API 20E (BioMerieux) and the PCR method. When analysing the capability of Escherichia coli for hemolysis, the highest number of haemolytic strains was determined in the faeces of animals fed diets with the addition of the EM probiotic. The examined isolates were characterised by different degrees of resistance to the antibiotics used in experiments. The smallest (P<0.05) number of resistant isolates was determined in group T.
Scar/WAVE complex suppresses cell invasion and cancer cell transformation

The mechanisms by which cancer cells hijack the actin cytoskeleton to invade and disseminate to distant sites of metastasis remains one of the great frontiers in cancer research. Many actin-regulating proteins have been identified to be important in cancer cell invasion and metastasis. However the role of a major actin assembly promoting complex, Scar/WAVE regulatory complex (WRC) in cancer cell invasion is poorly understood. WRC has a well-known motility-promoting role in 2D planar cell migration, but a recent study on human epithelial cancers suggests WRC may be anti-invasive in vivo. To investigate the controversy, human epithelial cancer cells with reduced WRC expression were tested in multiple 3D cell motility assays. Interestingly, WRC demonstrates a robust anti-invasive role in these exciting experiments. To understand how loss of WRC promotes invasion, the molecular mechanism is investigated. N-WASP is the other major actin assembly promoting protein. Unlike WRC, N-WASP is interestingly not required for 2D planar cell migration, but is important for motility in 3D. The interplay of the two major actin assembly promoting proteins has not been explored in 3D cell motility. I report here that loss of WRC promotes hyper-activation of focal adhesion kinase that leads to N-WASP accumulation and activation at the invasive front. This chain of events results in enhanced invasion providing a molecular mechanism of WRC’s anti-invasive function. ￼￼￼ In addition to this FAK-N-WASP core mechanism, I also identified a novel pro- invasive role of HSPC300 independently of WRC. Loss of WRC possibly releases free HSPC300 that could subsequently interact with and regulate N-WASP activation during invasion providing a potential direct molecular link between the two proteins. Furthermore, WRC also supresses focal adhesion kinase mediated cell transformation and tumour formation in vivo. In this thesis I therefore demonstrate novel anti-invasion and anti-tumourigenesis functions of WRC. I also show how a novel WRC binding protein, NHS, could negatively regulate WRC function.
Novel enterovirus inhibitors; Viral and host targets

A novel compound, TTP-8307, was identified as a potent inhibitor of the replication of several rhinoand enteroviruses. TTP-8307 inhibits viral RNA synthesis in a dose-dependent manner, without affecting polyprotein synthesis and/or processing. Drug-resistant variants of coxsackievirus B3 were all shown to carry at least one amino acid mutation in the nonstructural protein 3A. In particular three mutations located in a nonstructured region preceding the hydrophobic domain (V45A, I54F and H57Y) appeared to contribute to the drug-resistant phenotype. This region has previously been identified as a hot sport for mutations that resulted in resistance to enviroxime, the sole 3A-targeting enterovirus inhibitor reported thus far. This was corroborated by the fact that TTP-8307 and enviroxime proved cross-resistant. It is hypothesized that TTP-8307 and enviroxime disrupt proper interactions of 3A(B) with other viral or cellular proteins that are required for efficient replication.
Population Biology of Grasses: Competition between grasses and woody plants

Introduction Grasses are good models for studying the role of competition in forming ecological patterns because they contribute to obvious patterns, such as the boundary between prairie and forest. Further, grasses are suitable for short-term experiments because they achieve full size and reproductive maturity quickly. In this review I examine competition in the context of the replacement of grasses by trees along gradients of increasing evapotranspiration or productivity. Grasses are also replaced by shrubs as grassland merges into desert, and I have drawn examples from that system where appropriate. The boundary between grass and woody vegetation is especially interesting because its causes are unknown. The boundary is associated with very small differences in climate, making it likely to be highly responsive to global change (Emanuel, Shugart & Stevenson, 1985). Its abrupt nature may reflect feedbacks between plants and resources (Wilson & Agnew, 1992). Temporal shifts between grass and woody vegetation are also often sudden, prompting Westoby, Walker & Noy-Meir (1989) to suggest that grassland vegetation dynamics are best described using state and transition models. In spite of many examples of competition between grasses and trees, however, it is not at all clear how competition contributes to the boundaries between them. Here I review what features distinguish grass competition from competition involving other kinds of plants. Because the grass plant has a unique morphology, I examine the possible contribution of niche partitioning to the distribution of grasses. General models relating species distributions to competition are evaluated using mostly experimental evidence. The role of feedbacks is assessed. Finally, I try to identify promising avenues for future research.
Functional Domain Motions and Processivity in Bacterial Hyaluronate Lyase

Processive enzymes are a special class of enzymes which presumably remain attached to their polymeric substrates between multiple rounds of catalysis. Due to this property, the substrate slides along the enzyme and reduces the time for the random diffusional enzyme-substrate encounters thereby increasing the efficiency of these enzymes manifold. Although structural information from many processive enzymes is available, the atomistic details of particularly the substrate sliding process, which is an inherently dynamic process, remain largely unknown. We take first steps to understand the sliding process by investigating a prototypic processive enzyme: Streptococcus Pneumoniae Hyaluronate lyase, a bacterial enzyme that degrades the polysaccharide substrate hyaluronan. Here we have investigated the flexibility of the enzyme as observed from essential dynamics simulations and its relation to the enzyme-substrate interactions by employing several free and enforced molecular dynamics simulations (on sub-microsecond timescale). This way we have identified a coupling between domain motions of the enzyme and the processivity or the sliding phase of the substrate. In the putative mechanism for the substrate translocation phase we observed an energy barrier along the processive direction and it is speculated that this may arise because of the reorientation of the sugar inside the cleft of the protein. This view was supported from the Force probe molecular dynamics simulations and umbrella sampling simulations that were employed to obtain a preliminary free energy proﬁle underlying the mechanism. The observed free energy barrier is low enough to be easily crossed by thermal fluctuations, renderring essential slow collective domain rearrangements as likely rate-limiting factor for the processive cycle. The collective conformational motions of the protein along with particular interactions of individual amino acids may be involved in this translocation phase. Experimental validation along with further computational studies will be useful to understand this complex mechanism.