bluuebunny/crossref_metadata_2025_split huggingface dataset:
A METHOD FOR COMPUTING FAMILIES OF DISCRETE KNOTS USING KNOT NUMBERS
Authors: BRIBIESCA ERNESTO 
Published: June 2005

A method for generating families of particular 3D curves which differs from random self-avoiding walks is presented. This method is based on a chain code called knot numbers. The knot-number notation describes discrete knots. A discrete knot is the digitalized representation of a knot and is composed of constant orthogonal straight-line segments. The orthogonal direction changes of the contiguous straight-line segments of the knot define the chain elements. There are only five possible orthogonal direction changes for representing any discrete knot. Thus, the chain elements are considered as one base-five integer number (knot number). In this manner, we obtain a unique knot descriptor. This description is invariant under translation, rotation, starting point, and coding direction of the discrete knot.By evaluating all possible combinations of chain elements of curves and considering some restrictions, we obtain interesting families of curves which allow us to find the smallest nontrivial knot. Finally, we present a modest attempt at building the table of minimal discrete knots.
Circulating plasma cells detected by flow cytometry as a predictor of survival in 302 patients with newly diagnosed multiple myeloma
Authors: Nowakowski Grzegorz S. , Witzig Thomas E. , Dingli David , Tracz Michal J. , Gertz Morie A. , Lacy Martha Q. , Lust John A. , Dispenzieri Angela , Greipp Philip R. , Kyle Robert A. , Rajkumar S. Vincent 
Published: June 2005

Abstract
We detected circulating plasma cells (PCs) by flow cytometry in 302 patients with newly diagnosed multiple myeloma (MM) by gating on CD38+CD45- cells. The number of circulating PCs per 50 000 mononuclear cells was reported. In 80 (27%) patients, no circulating PC were seen; 106 (35%) patients had 1 to 10 and 115 (38%) patients had more than 10 circulating PCs. Median overall survival for the 302 patients was 47 months. Patients with 10 or fewer circulating PCs had a median survival of 58.7 months, whereas patients with more than 10 circulating PCs had a median survival of 37.3 months (P = .001). On multivariate analysis, the prognostic value of circulating PCs was independent of β2-microglobulin, albumin, and C-reactive protein. There was only a weak correlation between tumor mass and circulating PCs, suggesting that the appearance of circulating PCs may be a reflection of tumor biology. We conclude that the number of circulating PCs measured by flow cytometry in patients with newly diagnosed MM is an independent predictor of survival.
Tree measures and the number of segregating sites in time-structured population samples
Authors: Forsberg Roald , Drummond Alexei J , Hein Jotun 
Published: June 2005

Abstract
Background
Time-structured genetic samples are a valuable source of information in population genetics because they provide several correlated observations of the underlying evolutionary processes. In this paper we study basic properties of the genetic variation in time-structured samples as reflected in the genealogies relating individuals and the number of segregating sites observed. Our emphasis is on "measurably evolving populations" i.e. populations from which it is possible to obtain time-structured samples that span a significant interval of evolutionary time.

Results
We use results from the coalescent process to derive properties of time-structured samples. In the first section we extend existing results to attain measures on coalescent trees relating time-structured samples. These include the expected time to a most recent common ancestor, the expected total branch length and the expected length of branches subtending only ancient individuals. The effect of different sampling schemes on the latter measure is studied. In the second section we study the special case where the full sample consists of a group of contemporary extant samples and a group of contemporary ancient samples. As regards this case, we present results and applications concerning the probability distribution of the number of segregating sites where a mutation is unique to the ancient individuals and the number of segregating sites where a mutation is shared between ancient and extant individuals.

Conclusion
The methodology and results presented here is of use to the design and interpretation of ancient DNA experiments. Furthermore, the results may be useful in further development of statistical tests of e.g. population dynamics and selection, which include temporal information.
Evidence for abundant transcription of non-coding regions in the Saccharomyces cerevisiae genome
Authors: Havilio Moshe , Levanon Erez Y , Lerman Galia , Kupiec Martin , Eisenberg Eli 
Published: June 2005

Abstract
Background
Recent studies in a growing number of organisms have yielded accumulating evidence that a significant portion of the non-coding region in the genome is transcribed. We address this issue in the yeast Saccharomyces cerevisiae.

Results
Taking into account the absence of a significantly large yeast EST database, we use microarray expression data collected for genomic regions erroneously believed to be coding to study the expression pattern of non-coding regions in the Saccharomyces cerevisiae genome. We find that at least 164 out of 589 (28%) such regions are expressed under specific biological conditions. In particular, looking at the probes that are located opposing other known genes at the same genomic locus, we find that 88 out of 341 (26%) of these genes support antisense transcription. The expression patterns of these antisense genes are positively correlated. We validate these results using RT-PCR on a sample of 6 non-coding transcripts.

Conclusion
1. The yeast genome is transcribed on a scale larger than previously assumed. 2. Correlated transcription of antisense genes is abundant in the yeast genome. 3. Antisense genes in yeast are non-coding.
Comparative 3-D Modeling of tmRNA
Authors: Burks Jody , Zwieb Christian , Müller Florian , Wower Iwona , Wower Jacek 
Published: June 2005

Abstract

Background

Trans- translation releases stalled ribosomes from truncated mRNAs and tags defective proteins for proteolytic degradation using transfer-messenger RNA (tmRNA). This small stable RNA represents a hybrid of tRNA- and mRNA-like domains connected by a variable number of pseudoknots. Comparative sequence analysis of tmRNAs found in bacteria, plastids, and mitochondria provides considerable insights into their secondary structures. Progress toward understanding the molecular mechanism of template switching, which constitutes an essential step in trans- translation, is hampered by our limited knowledge about the three-dimensional folding of tmRNA.

Results
To facilitate experimental testing of the molecular intricacies of trans- translation, which often require appropriately modified tmRNA derivatives, we developed a procedure for building three-dimensional models of tmRNA. Using comparative sequence analysis, phylogenetically-supported 2-D structures were obtained to serve as input for the program ERNA-3D. Motifs containing loops and turns were extracted from the known structures of other RNAs and used to improve the tmRNA models. Biologically feasible 3-D models for the entire tmRNA molecule could be obtained. The models were characterized by a functionally significant close proximity between the tRNA-like domain and the resume codon. Potential conformational changes which might lead to a more open structure of tmRNA upon binding to the ribosome are discussed. The method, described in detail for the tmRNAs of Escherichia coli, Bacillus anthracis, and Caulobacter crescentus, is applicable to every tmRNA.

Conclusion
Improved molecular models of biological significance were obtained. These models will guide in the design of experiments and provide a better understanding of trans- translation. The comparative procedure described here for tmRNA is easily adopted for the modeling the members of other RNA families.
Differential localization of HPV16 E6 splice products with E6-associated protein
Authors: Vaeteewoottacharn Kulthida , Chamutpong Siriphatr , Ponglikitmongkol Mathurose , Angeletti Peter C 
Published: June 2005

Abstract
High-risk Human Papillomavirus (HPV) is the etiological agent associated with the majority of anogenital cancers. The primary HPV oncogenes, E6 and E7, undergo a complex splicing program resulting in protein products whose purpose is not fully understood. Previous mouse studies have confirmed the existence of a translated product corresponding to the E6*I splice product. In terms of function, the translated E6*I protein has been shown to bind to E6 protein and to E6 associated protein (E6AP). E6*I has an inhibitory effect on E6-mediated p53 degradation in E6 expressing cells. In order to analyze the relationship between E6*I and full-length E6 in relation to localization, we created a series of green fluorescent protein (GFP) fusion products. The localization of these proteins with reference to E6AP in vivo remains unclear. Therefore, we investigated the cellular distribution of different forms of E6 with reference to E6AP. E6 and E6*I proteins, expressed from a wild type E6 gene cassette, were dispersed in the nucleus and the cytoplasm. Whereas, the E6 splice donor mutant (E6MT) was primarily localized to the nucleus. E6*I protein and E6AP were found to co-localize mainly to the cytoplasm, whereas the co-localization of full-length E6 protein and E6AP, if at all, was found mainly at the perinuclear region. These results suggest a functional relationship between the E6*I and full-length E6 protein which correlates with their localization and likely is important in regulation of the E6-E6AP complex.
Habituated visual neurons in locusts remain sensitive to novel looming objects
Authors: Gray John R. 
Published: June 2005

SUMMARYMany animals must contend with visual cues that provide information about the spatiotemporal dynamics of multiple objects in their environment. Much research has been devoted to understanding how an identified pair of interneurons in the locust, the Descending Contralateral Movement Detectors(DCMDs), respond to objects on an impending collision course. However, little is known about how these neurons respond when challenged with multiple,looming objects of different complex shapes. I presented locusts with objects resembling either another locust or a bird approaching on a direct collision course at 3 m s-1 while recording from the DCMD axon within the mesothoracic ganglion. Stimulus presentations were designed to test: (i)whether DCMD habituation was related to the frequency of approach, (ii) if habituated DCMDs were able to respond to a novel stimulus and (iii) if non-looming motion within complex objects (internal object motion) during approach affects habituation. DCMD responses to simulated locusts or birds habituated more when the time interval between consecutive approaches within similar sequences decreased from 34 s to 4 s. Strongly habituated DCMDs were,however, able to respond to the same object approaching along a new trajectory or to a larger object approaching along the same trajectory. Habituation was not affected by internal object motion. These data are consistent with earlier findings that DCMD habituation occurs at localized synapses, which permits maintained sensitivity to multiple objects in the animal's environment.
Intragel oxygen promotes hypoxia tolerance of scyphomedusae
Authors: Thuesen Erik V. , Rutherford Ladd D. , Brommer Patricia L. , Garrison Kurt , Gutowska Magdalena A. , Towanda Trisha 
Published: June 2005

SUMMARYPopulations of jellyfish are known to thrive in many low oxygen environments, however, the physiological mechanisms that permit these organisms to live in hypoxia remain unknown. The oxyregulatory abilities of four species of scyphomedusae were investigated, and it was found that Aurelia labiata, Phacellophora camtschatica, Cyanea capillata and Chrysaora quinquecirrha maintain steady oxygen consumption to below 20 hPa oxygen (&lt;10% air saturation). Oxygen content of the mesoglea of A. labiata was measured using a fibre optic oxygen optode, and oxygen profiles through the gel are characterised by a gradient that decreases from just below normoxia at the aboral subsurface to ∼85% air saturation near the subumbrellar musculature. This gradient sustains oxyregulation by scyphomedusae, and it is demonstrated that A. labiata must be using intragel oxygen to meet its metabolic needs. Gel can also be used as an oxygen reservoir when A. labiata moves into hypoxia. Gel oxygen is depleted after about 2 h in anoxia and recovers to 70% of normal after 2.5 h in normoxia. Behaviour experiments in the laboratory showed that Aurelia labiata behaves similarly in normoxia and hypoxia (30% and 18% air saturation). The acute threshold for provoking behavioural changes in A. labiata is somewhere near its critical partial pressure, and oxygen stratification stimulates swimming back and forth across the oxycline. Intragel oxygen dynamics are recognised as a fundamental component of medusan physiology.
Physiological responses to feeding, fasting and estivation for anurans
Authors: Secor Stephen M. 
Published: June 2005

SUMMARY
Anuran estivation is characterized by long episodes of aphagia. To investigate whether estivating anurans downregulate intestinal performance as an adaptive mechanism to reduce energy expenditure, I compared the metabolic and intestinal responses to feeding, fasting and estivation among non-estivating and estivating species of the anuran families Bufonidae,Leptodactylidae and Ranidae. Standard metabolic rates of the estivating Bufo alvarius, Ceratophrys ornata and Pyxicephalus adspersuswere significantly less than those of the non-estivating Bufo marinus,Leptodactylus pentadactylus and Rana catesbeiana. Whereas the digestion of rodent meals equaling 15% of anuran body mass generated significant metabolic responses for all species, specific dynamic action was significantly greater for the estivating species. For estivating species,feeding triggered more than a doubling of small intestinal mass and significant upregulation of intestinal nutrient transport rates, resulting in six- to tenfold increases in total intestinal nutrient uptake capacity. The postprandial intestinal responses of the non-estivating species were much more modest, averaging a 50% increase in small intestinal mass and 69% increase in uptake capacities. Following 1 month of laboratory-induced estivation, C. ornata and P. adspersus had further depressed metabolic rates by 20%, intestinal masses by 44%, and total intestinal uptake capacities by 60%. In a fashion similar to infrequently feeding, sit-and-wait foraging snakes,estivating anurans possess the capacity to severely downregulate intestinal performance with fasting and estivation, and subsequently upregulate the gut with feeding. The depression in gut performance during estivation aids in reducing energy expenditure, thereby increasing the duration that the animal can remain dormant while relying solely upon stored energy.
Life at acidic pH imposes an increased energetic cost for a eukaryotic acidophile
Authors: Messerli Mark A. , Amaral-Zettler Linda A. , Zettler Erik , Jung Sung-Kwon , Smith Peter J. S. , Sogin Mitchell L. 
Published: June 2005

SUMMARY
Organisms growing in acidic environments, pH &lt;3, would be expected to possess fundamentally different molecular structures and physiological controls in comparison with similar species restricted to neutral pH. We begin to investigate this premise by determining the magnitude of the transmembrane electrochemical H+ gradient in an acidophilic Chlamydomonas sp. (ATCC® PRA-125) isolated from the Rio Tinto, a heavy metal laden, acidic river (pH 1.7-2.5). This acidophile grows most rapidly at pH 2 but is capable of growth over a wide pH range (1.5-7.0), while Chlamydomonas reinhardtii is restricted to growth at pH ≥3 with optimal growth between pH 5.5 and 8.5. With the fluorescent H+indicator, 2′,7′-bis-(2-carboxyethyl)-5-(and-6)-carboxyfluorescein(BCECF), we show that the acidophilic Chlamydomonas maintains an average cytosolic pH of 6.6 in culture medium at both pH 2 and pH 7 while Chlamydomonas reinhardtii maintains an average cytosolic pH of 7.1 in pH 7 culture medium. The transmembrane electric potential difference of Chlamydomonas sp., measured using intracellular electrodes at both pH 2 and 7, is close to 0 mV, a rare value for plants, animals and protists. The 40 000-fold difference in [H+] could be the result of either active or passive mechanisms. Evidence for active maintenance was detected by monitoring the rate of ATP consumption. At the peak, cells consume about 7%more ATP per second in medium at pH 2 than at pH 7. This increased rate of consumption is sufficient to account for removal of H+ entering the cytosol across a membrane with relatively high permeability to H+(7×10-8 cm s-1). Our results indicate that the small increase in the rate of ATP consumption can account for maintenance of the transmembrane H+ gradient without the imposition of cell surface H+ barriers.
Antifreeze activity in the gastrointestinal fluids ofArctogadus glacialis(Peters 1874) is dependent on food type
Authors: Præbel Kim , Ramløv Hans 
Published: June 2005

SUMMARYThe influence of two food types, Boreogadus saida (Bs) and crustaceans (Cr), on the osmolality, ion concentrations, antifreeze activity and antifreeze glycoprotein (AFGP) distribution in the gastrointestinal fluids of the Arctic gadoid Arctogadus glacialis was determined. The gastrointestinal fluids were hyperosmotic to serum but no significant differences in osmolality were found between the two food types. The food type significantly affected the antifreeze activity of the mid-gut fluids. The hysteresis freezing points, –3.27±0.30°C and–2.44±0.11°C for B. saida and crustaceans,respectively, were significantly lower than that of serum(–1.99±0.07°C). Furthermore, an exceptionally large thermal hysteresis ranging from 1.47±0.19°C to 2.04±0.30°C was observed in the intestinal fluids of fish feeding on B. saida. Native gel electrophoresis revealed that the gastrointestinal fluids contained AFGPs in all the different size groups. However, differences in band intensities for the two food types suggest that the ingested food has an influence on the concentration of the different AFGP-sizes in these fluids. A decrease in band intensities combined with a drop in thermal hysteresis from mid-gut to hind-gut fluid suggests that absorption of AFGP or possibly degradation occur during digestion.
Evolution of novel functions: cryptocyanin helps build new exoskeleton inCancer magister
Authors: Terwilliger N. B. , Ryan M. C. , Towle D. 
Published: June 2005

SUMMARYHemocyanin, the blue blood protein of many arthropods and molluscs,reversibly binds oxygen at its highly conserved copper–oxygen-binding sites and supplies tissues with oxygen. Cryptocyanin, closely related structurally and phylogenetically to arthropod hemocyanin, lacks several of the six critical copper-binding histidines, however, and has lost the ability to bind oxygen. Despite this loss of function, cryptocyanin continues to be synthesized, an indication that it has been exploited to carry out new functions. Here, we show that cryptocyanin is present in extremely high concentrations in the hemolymph of the crab during the premolt portion of the molt cycle. Both proteins are specifically expressed in the same type of cell in the hepatopancreas and secreted into the hemolymph, but cryptocyanin plays a major role in forming the new exoskeleton, while hemocyanin functions in oxygen transport. A cessation in cryptocyanin, but not hemocyanin, synthesis after eyestalk ablation supports our hypothesis that cryptocyanin is closely regulated by molting hormones. The contrasts between the two gene products illustrate how a gene duplication of a copper–oxygen protein and its subsequent mutation may work in concert with the evolution of new regulatory mechanisms, leading to the assumption of new functions.
Adhesion of echinoderm tube feet to rough surfaces
Authors: Santos Romana , Gorb Stanislav , Jamar Valérie , Flammang Patrick 
Published: June 2005

SUMMARY
Echinoderms attach strongly and temporarily to the substratum by means of specialized organs, the podia or tube feet. The latter consist of a basal extensible cylinder, the stem, which bears an apical flattened disc. The disc repeatedly attaches to and detaches from the substratum through adhesive and de-adhesive secretions. In their activities, echinoderms have to cope with substrata of varying degrees of roughness as well as with changing hydrodynamic conditions, and therefore their tube feet must adapt their attachment strength to these environmental constraints. This study is the first attempt to evaluate the influence of substratum roughness on the temporary adhesion of echinoderm tube feet and to investigate the material properties of their contact surface. It was demonstrated that tube foot discs are very soft (E-modulus of 6.0 and 8.1 kPa for sea stars and sea urchins, respectively), have viscoelastic properties and adapt their surface to the substratum profile. They also show increased adhesion on a rough substratum in comparison to its smooth counterpart, which is due mostly to an increase in the geometrical area of contact between the disc and the surface. Tenacity (force per unit area) increases with roughness [e.g. 0.18 and 0.34 MPa on smooth polymethyl-methacrylate (PMMA), 0.21 and 0.47 MPa on rough PMMA for sea stars and sea urchins, respectively] if only the projected surface area of the adhesive footprint is considered. However, if this tenacity is corrected to take into account the actual substratum 3-D profile, surface roughness no longer influences significantly the corrected adhesion strength(e.g. 0.18 and 0.34 MPa on smooth PMMA, 0.19 and 0.42 MPa on rough PMMA for sea stars and sea urchins, respectively). It can be hypothesized that, under slow self-imposed forces, disc material behaves viscously to adapt to substratum roughness while the adhesive fills out only very small surface irregularities (in the nanometer range). It is deposited as a thin film ideal for generation of strong adhesion. Under short pulses of wave-generated forces, attached discs probably behave elastically, distributing the stress along the entire contact area, in order to avoid crack generation and thus precluding disc peeling and tube foot detachment.