bluuebunny/crossref_metadata_2025_split huggingface dataset:
Saccamminid foraminifers from anoxic sediments: implications for Proterozoic ecosystem dynamics
Authors: BERNHARD JOAN M. , HABURA ANDREA , BOWSER SAMUEL S. 
Published: April 2005

Eukaryote origin and earliest diversification occurred in the Proterozoic when Earth's atmosphere was undoubtedly different from that of today. Atmospheric oxygen levels were increasing from the primordial anoxic atmosphere due, for example, to cyanobacterial oxygenic photosynthesis. Late Proterozoic (∼0.6–0.9 Gya) deep‐ocean oxygen concentrations are less certain, but geochemical evidence suggests anoxia and hydrogen‐sulfide enrichment. It can, therefore, be postulated that initial eukaryotic diversification occurred in oxygen‐depleted, sulfide‐enriched environments. Foraminifera are aerobes and, thus, not expected in anoxic settings. Recently, however, we found a saccamminid allogromian in a deep‐water anoxic, sulfidic setting. Samples were collected from Santa Barbara Basin (California) when bottom‐water oxygen was undetectable and sediments smelled strongly of hydrogen sulfide. Foraminiferal SSU rDNA sequences recovered from sediments included one from a previously uncharacterized saccamminid. Ultrastructural analysis indicated the presence of intact Golgi, mitochondria, and prokaryotic endobionts. Saccamminid occurrence in environmental conditions known to exist during the Proterozoic supports the possibility of their origin early in eukaryotic evolution. Extant saccamminids could have competed well in the prokaryote‐dominated Proterozoic benthic ecosystem given their diet includes bacteria, bacterial biofilms and unicellular algae. Thus, Proterozoic foraminifers may have been top carnivores.Funded by NASA NRA‐01‐01‐EXB‐057, the Geological Society of America's W. Storrs Cole Memorial Research Award, and NSF OPP0003639.
The Tetrahymena thermophila genome sequence. 2. Relating macronuclear sequence scaffolds to corresponding macronuclear chromosomes
Authors: DelTORO CHRISTINA , WILLIAMSON SONDRA , ORIAS EDUARDO , HAMILTON EILEEN P. 
Published: April 2005

Tetrahymena's highly fragmented macronuclear genome contains ∼300 chromosomes that have recently been whole‐genome‐shotgun sequenced at TIGR. We had genetically mapped Random Amplified Polymorphic DNAs (RAPDs) to Tetrahymena's micro‐ and macronuclear genomes. We sized the MAC chromosomes that carry RAPDs by cloning and labeling RAPD DNA and probing Southern blots of macronuclear DNA separated by pulsed‐field electrophoresis. We now report using cloned RAPD sequences to blastn‐search the TIGR Tetrahymena scaffold database (http://www.tigr.org/tdb/e2kl/tgg/); each RAPD sequence matched a sized scaffold. Comparison of physical sizes of MAC chromosomes (as determined by hybridization) to corresponding scaffold sizes showed that:

Every complete scaffold (assembled from telomere to telomere) matches in size with its corresponding MAC chromosome within 10% experimental error.
No incomplete scaffolds (telomere‐capped at one or neither end) exceeded the size of its corresponding MAC chromosome.

This work is allowing us to relate the genetic, physical and sequence maps of the micro‐and macronuclear genomes to one another. It has also provided strong evidence for the quality and accuracy of the Tetrahymena genome sequencing and assembly carried out at TIGR. (Supported by NIH grant RR02931 and contract to TIGR NIGMS Tetrahymena genome sequencing grant. Sequence data were obtained from The Institute for Genomic Research website.)
The Tetrahymena thermophila genome sequence: 3. Completing macronuclear chromosome sequence scaffolds and ordering and aligning them along the micronuclear genome
Authors: HAMILTON EILEEN P. , WILLIAMSON SONDRA , DelTORO CHRISTINA , ORIAS EDUARDO 
Published: April 2005

In Ciliates, the diploid, mitotic, genetically silent micronucleus (MIC) is the cell's germline, while the macronucleus (MAC) is the exclusive site of gene expression. During (postzygotic) MAC differentiation in T. thermophila, several hundred chromosomes are generated by site specific fragmentation of the five germline‐derived chromosomes at highly conserved chromosome breakage sites. Telomeres are added to every newly generated end, and chromosomes are amplified to ∼45 N. The Tetrahymena thermophila macronuclear genome was recently whole‐genome‐shotgun sequenced to nine‐fold redundancy at TIGR. The sequence (publicly available at http://www.tigr.org/tdb/e2k1/ttg/) is assembled into contigs (contiguous segments of overlapping sequence reads) linked into scaffolds. Here, we report here the completion of the assembly of many scaffold ends by linking them to their corresponding telomere, using diverse bioinformatic or experimental approaches. 120 chromosomes are now assembled from telomere to telomere and 125 additional scaffolds are telomere capped at one end. The 120 complete scaffolds encompass ∼45% of the ∼105‐Mb assembly, suggesting a total of ∼290 MAC chromosomes. By using paired sequence tags flanking chromosome breakage sites, we are linking unambiguously ordered and oriented MAC chromosome DNA sequence into MIC genome assemblies.Supported by NIH grant RR02931. Preliminary sequence data were obtained from The Institute for Genomic Research website.
Ciliate diversity related to shrimps and blue crab
Authors: HONGWEI MA , OVERSTREET ROBIN M. 
Published: April 2005

Observations of ciliates using the Chatton–Lwoff wet silver method, Wilbert's protargol impregnation method, and silver carbonated method revealed the infraciliature and nuclear apparatus of species collected from the blue crab (Callinectes sapidus) and brown shrimp (Farfantepenaeus aztecus) from Mississippi, white shrimp (Litopenaeus setiferus) from South Carolina, northern shrimp (Pandalus borealis) from Maine, and water associated with each. Specimens were measured and photographed under an Evolution MP 5.0 RTV digital camera system. More than 26 ciliate species, belonging to 21 families in 11 orders, were observed. Among them, five species occurred on or in the blue crab, four on the brown shrimp, two on the white shrimp, and three on the northern shrimp. Of those, only three infested more than one host species. We have seen additional symbiotic species on other specimens of the same hosts but not on those reported here. A total of 16 free‐living ciliate species occurred in the systems associated with the decapods. Among them, scuticociliates were the most important ones that could infect the decapods. One of these, Uronema marinum, also occurred in the hemolymph of the blue crab and impaired its health.The research was supported by the USDA, CSREES Grant No. 2002‐38808‐01381 and the Blue Crab Advanced Research Consortium (BCARC), NOAA, NA17FU2841.
A new real‐time RT‐PCR method allowing reliable absolute quantification of human cytokine mRNA in paediatric malaria clinical samples
Authors: BOEUF P. , VIGAN I. , JUBLOT D. , BARALE J.‐C. , GOKA B. , KURTZHALS J. , AKANMORI B. D. , HVIID L. , PUIJALON O. , BEHR C. 
Published: April 2005

In endemic areas, clinical manifestations of Plasmodium falciparum infection range from asymptomatic parasitaemia to life‐threatening severe syndromes. Immune differences that could account for this disparity are poorly understood. Using tight criteria to classify patients into non‐overlapping clinical categories, we showed that cerebral malaria and severe anaemia were distinct immunological syndromes and that a proper quantitative description of cytokine profiles in the various clinical groups is essential to the understanding of the activation of immunocompetent cells.Due to the limited size of paediatric blood samples, we chose to measure cytokine mRNA using real‐time RT‐PCR. We showed that RT efficiency displayed intra‐and intergenic variations that have to be taken into consideration for reliable absolute RNA quantification when comparing clinical cases. We thus developed a SYBR Green I‐based real‐time RT‐PCR method using synthetic external RNA standards specific for each gene. Absolute RNA quantification is achieved by reverse transcribing known copy numbers of this RNA standard in parallel with cellular RNA. Strictly specific primers were designed to allow the quantification of any RNA in the same thermocycling parameters for future automation. Our method gave similar results for a lower cost when compared with TaqMan, and led to reproducible and reliable absolute RNA quantification. We validated it in vitro on naïve PBMC stimulated by LPS and ex vivo on PBMC from malaria patients. This new method raises the unprecedented possibility to compare cytokine mRNA levels between different clinical groups and is a powerful tool to further study the inflammation processes associated to malaria.
Preservation of ptp1 and ptp2 Gene Synteny in Two Microsporidia Parasite of Insects: Nosema locustae and Nosema grylli
Authors: POLONAIS V. , DELBAC F. , VIVARES C. P. 
Published: April 2005

Microsporidia are obligate intracellular parasites infecting a wide range of invertebrate and vertebrate hosts including human. The spore contains a specialized organelle called the polar tube involved in host cell invasion. Three polar tube proteins (PTP1‐3) have been identified in Encephalitozoon cuniculi. The genes coding for ptp1 and ptp2 are localized on the same chromosome and are at a distance of 860 bp. A similar synteny organization is found in two other Encephalitozoon species. Comparison of the E. cuniculi genome with that of Nosema locustae, an microsporidia parasite of grasshoppers, indicates that several genes are positioned in the same order and orientation. This allowed the identification of two ORFs distant of 1117 bp, that despite divergent sequence features, encode proteins having common characteristics with Encephalitozoon PTP1 and PTP2 (signal peptide, proline‐rich internal repeats for PTP1, lysine‐rich protein for PTP2 …). To test whether they correspond to PTP, polyclonal sera were raised against two recombinant proteins expressed in E. coli. In indirect immunofluorescence, the extruded polar tubes of N. locustae spores are specifically labelled. NlPTP1 and NlPTP2 have 355 and 287 amino acids, respectively, and are only soluble in the presence of high concentrations of reducing agent.Aptp1 and ptp2 containing cluster have been also identified in Nosema grylli. PTP1 from N. locustae and N. grylli present a strong variability in the proline‐rich internal repeats, whilst PTP2s are highly conserved. It would be interesting to show whether this gene synteny conservation is related to a specific interaction between PTP1 and PTP2.
Periodontal disease awareness among pregnant women and its relationship with socio‐demographic variables
Authors: Alwaeli HA , Al‐Jundi SH 
Published: April 2005

Abstract:Certain conditions may have an affect on gingival status and may aggravate pre‐existing disease, especially in persons with poor oral hygiene. Pregnancy is one of these conditions. In addition, there is evidence in the literature suggesting an association between periodontal diseases in pregnant women and giving birth to premature, low‐birth infants. The purpose of this study was to evaluate the degree of periodontal health knowledge, and awareness, among pregnant women in Jordan. This was carried out by cross‐sectional survey using self‐administered, structured questionnaires distributed at six maternity care centres in Irbid City. Questionnaire items addressed personal and socio‐demographic variables and periodontal health awareness and knowledge of pregnant women. Women (n = 300) were randomly chosen from attendants to these centres. Of the 300 questionnaires distributed, only 275 pregnant women ages 16–45 years with a mean of 29 year responded and were included in the study. Data were analysed by chi‐squared test with the level of significance set at (P < 0.05). About one‐third of the participants had secondary level of education; it appeared that a minority of the pregnant women had knowledge or ability to identify dental plaque (16.4%) and its harmful effects (22.5%), while most of them (88%) were aware that bleeding gums indicated the presence of periodontal disease. The differences in the responses to knowledge questions were only significant for question number one (What is plaque?) among different educational levels and groups. This study revealed that (71.6%) of the pregnant women knew the main cause of gum disease; however 56% of them do not believe that frequency of teeth brushing should be increased during pregnancy and only 5.1% believed there might be a relationship between gum diseases and premature labour. Knowledge and awareness for pregnant women about their teeth and gingival condition is generally poor. Pregnant women need accurate information about their teeth and oral health. Simple educational preventive programmes on oral self‐care and disease prevention before and during pregnancy should be provided to improve oral health.
The use of the Internet to access oral health‐related information by patients attending dental hygiene clinics
Authors: Harris CE , Chestnutt IG 
Published: April 2005

Abstract:Background:  The degree to which patients access the Internet for oral health‐related information is unknown.Objectives:  This study was designed to determine if patients attending student dental hygiene clinics had: (1) accessed the Internet, (2) used the Internet as a source of information on both general health and oral health, (3) bought oral health care products on‐line, and (4) were interested in being directed to appropriate on‐line oral health resources by dental professionals.Methods:  A self‐complete questionnaire was administered to a quota sample of 280 new and returning patients attending the student dental hygiene clinic at either the Cardiff Dental Hospital or a nearby Primary Dental Care Unit.Results:  A total of 269 (96%) patients consented to participate in the study. Of these, 147 (54.6%) had accessed the Internet, the majority (61.2%) from home. Internet use was significantly related to both patient age and level of education (P < 0.001). In total, 59 patients claimed accessing the Internet for information on general health topics. Only eight respondents had used the Internet for information on oral health/dental topics, with seven reporting that they found the information useful. On‐line purchase of oral health products was reported by seven patients. However, 117 (43.5% of all respondents) patients indicated that they would be interested in the Internet as a future source of oral health information and 112 (41.6%) would appreciate being directed to appropriate sites by their dentist or dental hygienist.Conclusions:  Patients attending student dental hygiene clinics make little use of the Internet for oral health information. However, reported interest in future access is such that dental professionals should develop and harness the potential of the Internet as an educational resource.
The Global CAPM and a Firm's Cost of Capital in Different Currencies
Authors: O'Brien Thomas J. 
Published: April 2005

In an integrated global market, a firm's cost of capital expressed in one currency should be consistent with its cost of capital expressed in another currency. This article presents and illustrates a process for estimating consistent costs of capital in different currencies for a U.K. based multinational. In so doing, it uses a simple, easy‐to‐use version of the global CAPM that attempts to incorporate the effect of uncertain exchange rates by calculating exchange rate “betas.” As argued in the previous article, at least part of a company's currency exposure is systematically related to the global market and thus should be treated as a component of the firm's systematic equity risk.For example, the U.K. firm featured in this article is shown to have an exchange rate beta of 0.20 from the perspective of a U.S. investor. This implies that a 10% return on the global market in U.S. dollars tends to be associated with a 2% change in the U.S. dollar value of the British pound. One interesting consequence of incorporating exchange risk in this fashion is that two firms with identical U.S. global betas and costs of equity will have different expected returns expressed in another currency if they have different exposures to that currency.
THE ASIAN CRISIS: LESSONS FOR CRISIS MANAGEMENT AND PREVENTION
Authors: Brealey Richard 
Published: April 2005

The succession of financial crises that swept through Asia, Russia, and Latin America in 1997 and 1998 has led to considerable debate about both the role of the IMF and possible actions to limit further crises. Some have argued that international financial markets do not function well and are subject to periodic contagious panics that can be stemmed by an international lender of last resort. This paper argues that the IMF has neither the resources nor the superior information to play such a role. However, there may be a need for an international financial institution that can use its leverage to secure policy changes in the affected countries.The paper also takes issue with the view that the IMF is simply bailing out imprudent international banks and that measures are needed to “bail them back in” again. The source of the Asian crisis lay in the real economy, but the effect of the crisis was greatly exacerbated by the financial structure of the affected countries. In particular, much of the risk was borne by domestic banks that borrowed dollars in the short‐term interbank market and made longerterm loans in the local currency. Public policy needs to be directed to ensuring that the risks in emerging markets are distributed efficiently across both foreign and domestic investors. That involves greater use of equity finance and structured debt, as well as possibly a more direct role for foreign banks in funding local activities.
CONVERTIBLE BONDS: MATCHING FINANCIAL AND REAL OPTIONS
Authors: Mayers David 
Published: April 2005

For companies whose value consists in large part of “real options”‐ growth opportunities that may (or may not) materialize‐convertible bonds may offer the ideal financing vehicle because of the matching financial options built into the securities. This paper proposes that convertible debt can be a key element in a financing strategy that aims not only to fund current activities, but to give companies access to low‐cost capital if and when their real investment options turn out to be valuable. In this sense, convertibles can be seen as the most cost‐effective solution to a sequential financing problem‐how to fund not only today's activities, but also tomorrow's growth opportunities (some of them not yet even foreseeable).For companies with real options, the ability of convertibles to match capital inflows with corporate outlays adds value by minimizing two sets of costs: those associated with having too much (particularly equity) capital (known as “agency costs of free cash flow”) and those associated with having too little (“new issue” costs). The key to the cost‐effectiveness of convertibles in funding real options is the call provision. Provided the stock price is “in the money” (and the call protection period is over), the call gives managers the option to force conversion of the bonds into equity. If and when the company's investment opportunity materializes, exercise of the call feature gives the firm an infusion of new equity (while eliminating the debt service burden associated with the convertible) that enables it to carry out its new investment plan.Consistent with this argument, the author's recent study of the investment and financing activities of 289 companies around the time of convertible calls reports significant increases in capital expenditures starting in the year of the call and extending three years after. The companies also showed increased financing activity following the call, mainly new long‐term debt issues (many of them also convertibles) in the year of the call.
INNOVATIONS IN PARTITIONING A SHARE OF STOCK
Authors: Francis Jack Clark , Bali Rakesh 
Published: April 2005

This paper presents a synthesis of innovations in the slicing and dicing of cash flows of a share of a firm's common stock. It begins by discussing PRIMEs and SCOREs, then Unbundled Stock Units (USUs), and finally three proposed hybrid equity options called DIVS, OWLS, and RISKS.Decomposing a share of stock into components that can be traded separately allows investors to choose between the different investment attributes constituting the underlying share. An investor who desires only cash dividend income may buy only DIVS, and another who values capital appreciation but not current income can purchase only the residual claim.Derivatives seem to go through a developmental process that is analogous to the biological phenomenon of natural selection and adaptation. The engines that drive this evolutionary process are changing domestic and international market conditions, international tax and regulatory arbitrage, and, of course, the financial innovators who learn from their own mistakes, and from the experience of others. These innovators continually develop new products that represent improvements over the old, if only by their ability to adhere more closely to the guidelines laid down by the regulators. The histories of PRIMEs and SCOREs, of USUs, and, most recently, of DIVS, OWLS and RISKS together provide a nice illustration of this developmental process.
THE HISTORY OF FINANCE: AN EYEWITNESS ACCOUNT
Authors: Miller Merton H. 
Published: April 2005

In this account of the evolution of finance theory, the “father of modern finance” uses the series of Nobel Prizes awarded finance scholars in the 1990s as the organizing principle for a discus‐sion of the major developments of the past 50 years. Starting with Harry Markowitz's 1952 Journal of Finance paper on “Portfolio Selection,” which provided the mean‐variance frame‐work that underlies modern portfolio theory (and for which Markowitz re‐ceived the Nobel Prize in 1990), the paper moves on to consider the Capi‐tal Asset Pricing Model, efficient mar‐ket theory, and the M & M irrelevance propositions. In describing these ad‐vances, Miller's major emphasis falls on the “tension” between the two main streams in finance scholarship: (1) the Business School (or “micro normative”) approach, which focuses on investors ‘attempts to maximize returns and cor‐porate managers’ efforts to maximize shareholder value, while taking the prices of securities in the market as given; and (2) the Economics Depart‐ment (or “macro normative”) approach, which assumes a “world of micro optimizers” and deduces from that assumption how the market prices actually evolve.The tension between the two ap‐proaches is resolved, and the two streams converge, in the final episode of Miller's history–the breakthrough in option pricing accomplished by Fischer Black, Myron Scholes, and Rob‐ert Merton in the early 1970s (for which Merton and Scholes were awarded the Nobel Prize in 1998, “with the late Fischer Black everywhere ac‐knowledged as the third pivotal fig‐ure”). As Miller says, the Black‐Scholes option pricing model and its many successors “mean that, for the first time in its close to 50‐year history, the field of finance can be built, or…rebuilt, on the basis of ‘observable’ magnitudes.” That option values can be calculated (almost entirely) with observable vari‐ables has made possible the spectacu‐lar growth in financial engineering, a highly lucrative activity where the prac‐tice of finance has come closest to attaining the precision of a hard sci‐ence. Option pricing has also helped give rise to a relatively new field called “real options” that promises to revolu‐tionize corporate strategy and capital budgeting.But if the practical applications of option pricing are impressive, the op‐portunities for further extensions of the theory by the “macro normative” wing of the profession are “vast,” in‐cluding the prospect of viewing all securities as options. Thus, it comes as no surprise that when Miller asks in closing, “What would I specialize in if I were starting over and entering the field today?,” the answer is: “At the risk of sounding like the character in ‘The Graduate,’ I reduce my advice to a single word: options.”