Miracle-dz/UniFAR-FTUs huggingface dataset:
Patents related to dengue virus infection

This review discusses patents relevant to dengue virus infection. Dengue virus is a mosquito-transmitted flavivirus that usually causes an acute self-limited febrile illness, but may result in more severe life threatening disease. The lack of animal models that replicate features of the human disease has inhibited developing an understanding of the pathophysiology of dengue virus infection and consequently, limited investigation into potential therapeutics. However, there has been considerable progress in vaccine development and recent insights into the identity of the cells infected during the course of dengue virus infection and characterisation of cell-surface receptors used to mediate infectivity, have provided important information with therapeutic implications. There is no treatment for dengue virus infection and no vaccine is yet available, new approaches are urgently needed.
PENELUSURAN MEKANISME FLAVONOID KULIT JERUK KEPROK (Citrus reticulata) SEBAGAI AGEN KEMOPREVENTIF MELALUI DOCKING MOLEKULER PADA PROTEIN TARGET CYP1A2

Subklas flavonoid khususnya golongan polimetoksiflavon menunjukan aktivitas kemopreventif pada berbagai sel kanker secara in vitro dan beberapa studi in vivo. Pada tahapan inisiasi kanker, bioaktivasi karsinogen polisiklik aromatik hidrokarbon secara signifikan dapat direduksi oleh senyawaan polimetoksiflavon melalui penghambatan sistem enzim sitokrom P450 (CYP) dalam level transkripsi gen maupun interaksi langsung dengan enzim tersebut. Pada tahapan promosi kanker, berbagai studi menunjukan bahwa proliferasi sel kanker dihambat lebih kuat oleh golongan metoksiflavon dibandingkan hidroksiflavon. Tangeretin, nobiletin, naringin dan hesperidin adalah beberapa senyawa polimetoksiflavon dari kulit jeruk keprok yang dilaporkan memiliki efek kemopreventif melalui modulasi aktivitas CYP1A2. Penelitian ini bertujuan untuk mengetahui afinitas, konformasi dan interaksi senyawa berkerangka polimetoksiflavon kulit jeruk keprok (Citrus reticulata) terhadap protein target CYP1A2 menggunakan molecular docking. Optimasi geometri struktur polimetoksiflavon dilakukan dengan piranti lunak Molecular Operating Environment for Windows. Konformasi optimum struktur polimetoksiflavon dihasilkan menggunakan metode semiempirik AMBER99. Kemudian dilakukan proses docking senyawa uji dengan bindingsite CYP1A2 (PDB ID:2HI4) menggunakan piranti lunak Molecular Operating Environment for Windows dalam kondisi tanpa air. Hasil docking senyawa golongan polimetoksiflavon dibandingkan dengan native ligan pada target CYP1A2, menunjukkan interaksi polimetoksiflavon yang lebih kuat dibanding interaksi ligan pembanding a-naphtoflavon. Kata kunci: Citrus reticulata, polimetoksiflavon, molecular docking, CYP1A2
Alzheimer's Aβ40 Studied by NMR at Low pH Reveals That Sodium 4,4-Dimethyl-4-silapentane-1-sulfonate (DSS) Binds and Promotes β-Ball Oligomerization*

The Alzheimer's Aβ40 peptide forms soluble oligomers that are extremely potent neurotoxins and strongly impede synapses function. In this study the formation and structure of the large, soluble, neurotoxic Aβ40 oligomer called “β-ball” were characterized by two-dimensional NMR, circular dichroism, fluorescence spectroscopy, hydrogen exchange, and equilibrium sedimentation. In acidic aqueous solution, half the Aβ40 molecules are in the β-ball state; the remainder are monomeric. The equilibrium between the two states is slow as judged by NMR linewidths and is stable for months. The kinetics of β-ball formation from monomer are biphasic with τ1 = 7 min and τ2 = 80 min with no transient helix formation. Monomeric Aβ40 is essentially devoid of stable secondary structure, although the central, Leu17–Ala21, and C-terminal, Gly29–Val40, hydrophobic regions show propensity toward adopting extended structure, and residues 22–25 tended to form a turn. We found that sodium 4,4-dimethyl-4-silapentane-1-sulfonate (DSS) binds to the central hydrophobic region of monomeric Aβ40. DSS binds β-balls more strongly and caused them to double in size. Plausible micelle-like models for the β-ball structure with and without bound DSS are presented.
Northern richness and southern poverty: contrasting genetic footprints of glacial refugia in the relictual tree Sciadopitys verticillata (Coniferales: Sciadopityaceae)

Sciadopitys verticillata is amongst the most relictual of all plants, being the last living member of an ancient conifer lineage, the Sciadopityaceae, and is distributed in small and disjunct populations in high rainfall regions of Japan. Although mega-fossils indicate the persistence of the species within Japan through the Pleistocene glacial– interglacial cycles, how the species withstood the colder and drier climates of the glacials is not well known. The present study utilized phylogeography and palaeodistribution modelling to test whether the species survived within pollen-based coastal temperate forest glacial refugia or within previously unidentified refugia close to its current range. Sixteen chloroplast haplotypes were found that displayed significant geographical structuring. Unexpectedly, northern populations in central Honshu most distant from coastal refugia had the highest chloroplast diversity and were differentiated from the south, a legacy of glacial populations possibly in inland river valleys close to its current northern range. By contrast, populations near putative coastal refugia in southern Japan, harboured the lower chloroplast diversity and were dominated by a single haplotype. Fragment size polymorphism at a highly variable and homoplasious mononucleotide repeat region in the trn T-,i>trn L intergenic spacer reinforced the contrasting patterns of diversity observed between northern and southern populations. The divergent histories of northern and southern populations revealed in the present study will inform the management of this globally significant conifer.
CENTROID OF WOOD DENSITY, BOLE ECCENTRICITY, AND TREE-RING WIDTH IN RELATION TO VECTOR WINDS IN WAVE FORESTS

Circular statistics are used to analyse directional data inherent in X-ray densitometric data that pertain to cross-sectional discs sampled from balsam fir wave forest trees at Spirity Cove, Newfoundland. The analysis concentrates on directionality of centroids of mean wood density, bole eccentricity, and tree-ring width in eight directions from the pith. The results show that the centroid of mean wood density, bole cross sections, and mean tree-ring width are significantly directional and correspond closely with the mean vector wind direction.
SEX‐LINKED INHERTIANCE IN POULTRY

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Improved Semidwarf Rice Lines with Tolerance to Submergence of Seedlings

Short-term submergence of rainfed lowland and deepwater rice (Oryza sativa L.) reduces yields on millions of hectares in South and Southeast Asia. Farmers in these areas lack high-yielding cultivars that are tolerant to submergence at the vegetative stage. The present study was conducted to evaluate the submergence tolerance, yields and agronomic characteristics of improved submergence-tolerant rice lines (.)
Wheat transformation using cyanamide as a new selective agent.

There is a general need for additional selectable marker genes for plant transformation. Only a few have been reported in wheat (Triticum aestivum L.) transformation experiments, some of which are under patent restriction or have other disadvantages. A new selectable marker gene was identified which can be used to select resistant callus in tissue culture and regenerate transgenic wheat plants. A gene from the soil fungus Myrothecium verrucaria (Albertini & Schwein.) Ditmar:Fr. , coding for the enzyme cyanamide hydratase which converts cyanamide into urea, was previously described. In our wheat transformation experiments, the gene conferred resistance to cyanamide at a tissue culture level and therefore cyanamide could be used to select for transformants. At the whole plant level, progeny of transformed wheat plants showed resistance to cyanamide, whereas sensitive plants expressed a lethal necrosis and yellowing when cyanamide was applied. This gene has several potential advantages when compared with other selectable marker genes. Transformed wheat plants can be selected at the tissue culture level and may be able to convert cyanamide into a useful nitrogen compound (fertilizer). The selectable marker gene could be introduced with other genes for value-added traits in wheat and might also be applicable in other transformation systems.
Nitrogen Sharing Among Ramets Increases Clonal Growth in Fragaria Chiloensis

Transport of resources among connected ramets can increase the growth of clonal plants when ramets are located in microsites with contrasting light, water, or total soil nutrient availability. To test whether this is also true for soil nitrogen availability alone, two greenhouse experiments were conducted using the stoloniferous herb Fragaria chi- loensis (beach strawberry). First, pairs of ramets were prepared in which the two ramets were connected by a stolon but rooted in separate pots. Ramets in a pair were: (1) severed from each other and given contrasting levels of soil nitrogen (high vs. low); (2) left connected and given contrasting levels of soil nitrogen; or (3) left connected and given a uniform level of soil nitrogen (both high or both low). Second, single ramets were given the high, the low, or one of three intermediate levels of soil nitrogen. Maintaining the vascular connection between ramets given contrasting levels of soil nitrogen resulted in a greater production of new stolons and new ramets by the ramet given the low nitrogen level, and in slightly greater leaf growth of the ramet given the low nitrogen level if it was also younger than the connected ramet. However, a ramet given high soil nitrogen grew much more than a ramet given low soil nitrogen, even when connected. Maintaining the vascular connection between ramets given a uniform level of soil nitrogen had no significant effect on growth. Single ramets given a higher soil nitrogen level had greater total and component masses, more stolons and new ramets, higher nitrogen concentrations, higher specific leaf area, and a higher proportional mass of leaves and of stolons and new ramets. Experiments suggested that: (1) transport of nitrogen among ramets can increase growth in F. chiloensis, but to a limited extent; (2) transport of nitrogen through a stolon may be either acropetal or basipetal but tends to promote the growth of younger ramets; (3) higher soil nitrogen availability alters plant architecture by increasing allocation to leaves and to new stolons and ramets; and (4) physiological integration among ramets modifies clonal architecture because nitro- gen acquired by roots promotes growth of both a rooted ramet and its new ramets, whereas nitrogen acquired from another ramet promotes the growth of new ramets almost exclu- sively.
Reconsideration of criteria for differentiating faunal assemblages accumulated by hyenas and hominids

Zooarchaeologists have established several criteria for differentiating hominid- and hyena-derived faunal assemblages. In some cases, however, the patterns of skeletal part representation and bone surface modification on which these criteria are ultimately based have been observed in fossil bone assemblages of unknown origin, rather than in modern assemblages of known origin. When the proposed criteria are evaluated within an actualistic framework, only three are able to differentiate between hominid- and hyena-created faunal assemblages. I suggest that only these three criteria—proportions of carnivores to ungulates in the assemblage, the preserved condition of long bone specimens (either as whole cylinders or as splintered shaft fragments), and the types of bone surface modifications—should be retained as important factors in a diagnosis of the ancient bone-collector. The remaining four criteria—the relative proportion of horn pieces in the assemblage, the relative representation of podial bones, the relative representation of small and large bovid skeletal parts, and bovid mortality profiles—are not relevant or applicable to the problem of differentiating hominid- from hyena-derived faunal assemblages. Copyright © 2002 John Wiley & Sons, Ltd.
Reduced level of creatine kinase in the plasma of Holstein cows supplemented with d-α-tocopherol acetate

The effects of daily supplementation of 1000 IU of either d-α-tocopherol acetate or dl-α-tocopherol acetate to Holstein cows from drying off to 8 wk post-partum on plasma creatine kinase and selenium levels in plasma and red blood cells were studied. Supplementation with either d-α-tocopherol acetate or dl-α-tocopherol acetate showed no effect on selenium levels in both plasma and red blood cells. However, supplementation with d-α-tocopherol acetate, but not dl-α-tocopherol acetate decreased plasma creatine kinase significantly (P < 0.05) prior to parturition. Key words: Vitamin E, creatine kinase, selenium
Purification and Partial Characterization of Maize (Zea mays L.) β-Glucosidase

Maize (Zea mays L.) beta-glucosidase (beta-d-glucoside glucohydrolase, EC 3.2.1.21) was extracted from the coleoptiles of 5- to 6-day-old maize seedlings with 50 millimolar sodium acetate, pH 5.0. The pH of the extract was adjusted to 4.6, and most of the contaminating proteins were cryoprecipitated at 0 degrees C for 24 hours. The pH 4.6 supernatant from cryoprecipitation was further fractionated by chromatography on an Accell CM column using a 4.8 to 6.8 pH gradient of 50 millimolar sodium acetate, which yielded the enzyme in two homogeneous, chromatographically different fractions. Purified enzyme was characterized with respect to subunit molecular weight, isoelectric point, amino acid composition, NH(2)-terminal amino acid sequence, pH and temperature optima, thermostability, and activity and stability in the presence of selected reducing agents, metal ions, and alkylating agents. The purified enzyme has an estimated subunit molecular mass of 60 kilodaltons, isoelectric point at pH 5.2, and pH and temperature optima at 5.8 and 50 degrees C, respectively. The amino acid composition data indicate that the enzyme is rich in Glx and Asx, the sum of which approaches 25%. The sequence of the first 20 amino acids in the N-terminal region was H(2)N-Ser-Ala-Arg-Val-Gly-Ser-Gln-Asn-Gly-Val-Gln-Met-Leu-Ser-Pro-(Ser? ) -Glu-Ile-Pro-Gln, and it shows no significant similarity to other proteins with known sequence. The enzyme is extremely stable at 0 to 4 degrees C up to 1 year but loses activity completely at and above 55 degrees C in 10 minutes. Likewise, the enzyme is stable in the presence of or after treatment with 500 millimolar 2-mercaptoethanol, and it is totally inactivated at 2000 millimolar 2-mercaptoethanol. Such metal ions as Hg(2+) and Ag(+) reversibly inhibit the enzyme at micromolar concentrations, and inhibition could be completely overcome by adding 2-mercaptoethanol at molar excess of the inhibitory metal ion. The alkylating agents iodoacetic acid and iodoacetamide irreversibly inactivate the enzyme and such inactivation is accelerated in the presence of urea.
Rescue and restoration of inner ear function: are growth factors useful?

During recent years increased understanding of the molecular mechanisms of hair cell/neuronal death in the inner ear has started to offer new possibilities for preventing traumatic hair cell loss. In search for putative therapeutic agents, growth factors (GFs) have been proposed. GFs are a class of gene products (polypeptides) that are particularly important during development, regulating cell division and differentiation but also acting as survival factors during adulthood. Neurotrophins NT‐3 and BDNF, in particular, are putative therapeutic agents for cochlear and vestibular neurons as they and their receptors are present and active in the inner ear. For GF‐based pharmacological therapy, however, limits are set by the short half‐life of recombinant polypeptides and by the fact that these large molecules do not cross the blood labyrinthine barrier. New knowledge about the molecular mechanisms involved in stress‐induced hair‐cell death suggests that the intracellular signalling cascades involved in the commitment to and execution of cell death play key roles also in cochlear damage. Acoustic overstimulation and ototoxicity are stress stimuli that lead to oxidative stress followed by the death of hair cells. At least a subset of hair cells dies by apoptosis. The JNK (c‐Jun N‐terminal kinase) intracellular signalling pathway that couples exogenous stresses and cellular death is activated in cochlear hair cells after trauma. Inhibition of JNK activation by a small non‐protein compound, CEP‐1347, attenuates noise‐ and aminoglycoside‐induced hair‐cell death. Our results suggest that therapeutic intervention in the JNK signalling cascade may offer opportunities to treat inner ear‐specific injuries.
The use of biocides to control sulphate‐reducing bacteria in biofilms on mild steel surfaces

Three different types of biocides, viz. formaldehyde (FM), glutaraldehyde (GA) and isothiozolone (ITZ) were used to control planktonic and sessile populations of two marine isolates of sulphate‐reducing bacteria (SRB). The influence of these biocides on the initial attachment of cells to mild steel surfaces, on subsequent biofilm formation and on the activity of hydrogenase enzymes within developed biofilms was evaluated. In the presence of biocides the rate and degree of colonization of mild steel by SRB depended on incubation time, bacterial isolate and the type of biocide used. Although SRB differed in their susceptibility to biocides, for all isolates the biofilm population was more resistant to the treatment than the planktonic population. GA showed highest efficiency in controlling planktonic and sessile SRB compared with the other two biocides. The activity of the enzyme hydrogenase measured in SRB biofilms varied between isolates and with the biocide treatment. No correlation was found between the.
On measuring the rate of ageing

Ageing, or senescence, is a decline in state at later ages that is manifested through a reduction in survival and fecundity. Ageing means that reproductive prospects and hence the life history options (trade-offs) open to the organism decline. Evolutionary theories of ageing suggest that it evolves in response to the level of externally imposed mortality and insults to fertility, either as part of life history optimization or as a result of mutation pressure. Several recent empirical and theoretical studies have produced apparently anomalous results. Some have suggested that the rate of ageing can decline at later ages, others that demographic evidence for ageing can appear in parallel with an improvement in state. All of these studies used measures of ageing that would not be expected to give an accurate reflection of changes in the state of the organism with age. We propose that Fisher’s ‘reproductive value’ is a natural measure of state at each age, which includes prospects for both survival and reproduction. If this measure is used, the apparently anomalous findings are not at variance with evolutionary theories of ageing.
Competitive effect is a linear function of neighbour biomass in experimental populations of Kochia scoparia

1 Neighbour size and distance are confounded in most studies of plant growth and competition at the individual level. To investigate the effects of neighbour size on competitive effect, we grew target Kochia scoparia individuals surrounded by six equidistant, even‐aged conspecific neighbours. We varied neighbour size by sowing groups of neighbours at different times, and we also varied the sowing time of the target plants to generate variation in both neighbour and target size during the process of competition. We analysed the growth of target plants over two time intervals as a function of their own size and the size of their neighbours at the beginning of the interval. 2 When competition became intense, the relative growth rate of target plants was primarily determined by the size of their neighbours. There was a negative linear relationship between the relative growth rate of target plants over an interval and the biomass of their neighbours at the beginning of the interval. The size of the target plant itself did not make a significant additional contribution to predicting its growth rate. There is a limit on the growth in biomass of the population (target + neighbours), and growth of individuals occurs within this constraint. Local biomass density, which can be primarily determined by neighbouring individuals, can be much more important for an individual's growth than its own size. 3 There was no evidence of size‐asymmetric competition. The size of neighbours was the primary determinant of a target plant's relative growth rate, but the effect of a given amount of neighbour biomass was the same for neighbours larger and those smaller than the target plant.
Bioenergetics Modeling Today: Growing Pains on the Cutting Edge

Abstract Elaborations of the mass-balance equation that partitions energy of consumed food into its various physiological fates have flourished in the past 15 years. These bioenergetics models have been converted to powerful simulation tools and used in fisheries science, most often for predicting consumption by predators or for projecting fish growth as a function of temperature and prey availability. New uses of bioenergetics models are proliferating and range from predictions of larval survival to analysis of ecosystem function. Companion technologies such as hydroacoustics and physiological telemetry promise to further broaden the spectrum of potential applications. However, the data demands and uncertain accuracy of multiparameter models may constrain their ability to address routine fish management questions. Field measures of consumption or growth failed to corroborate bioenergetics estimates consistently (differences of at least 50%) in four of six published tests. Poor agreement could be due to i.