bluuebunny/crossref_metadata_2025_split huggingface dataset:
What is PACT really?
Authors: Arias J. Salvador , Garzón‐Orduña Ivonne J. , López‐Osorio Federico , Parada‐Vargas Erika , Miranda‐Esquivel Daniel Rafael 
Published: March 2008

Abstract“Phylogenetic Analysis for Comparing Trees” (PACT) has been presented as a “new algorithm” for the study of biogeography and coevolution. However, an exploration of this algorithm revealed some important problems missed in the original description. First, PACT is not new, rather it is an extension of Tree Mapping under Maximum Codivergence (TM‐MC). Second, as was described, PACT lacks an optimality criterion, and like secondary BPA, it does not offer a solution for handling incongruent elements. We found that PACT and TM‐MC differ only in the way the final answer is presented, and in the absence of an explicit algorithm of historical reconstruction under PACT. Given the equivalence between TM‐MC and PACT in their aims and assumptions, the criticism to TM‐MC as “orthogenetic” is not well founded.© The Willi Hennig Society 2008.© The Willi Hennig Society 2008.
A genetic linkage map for coho salmon (Oncorhynchus kisutch)
Authors: McClelland E. K. , Naish K. A. 
Published: March 2008

SummaryConstruction of genetic linkage maps is an important first step for a variety of genomic applications, such as selective breeding in aquaculture, comparative studies of chromosomal evolution and identification of loci that have played key roles in the evolution of a species. Here we present a sex‐specific linkage map for coho salmon. The map was constructed using 148 AFLP markers, 133 microsatellite loci and the phenotypic locus SEX. Twenty‐four linkage groups spanning 287.4 cM were mapped in males, and 33 linkage groups spanning 429.7 cM were mapped in females. Several male linkage groups corresponded to two female linkage groups. The combination of linkage groups across both sexes appeared to characterize regions of 26 chromosomes. Two homeologous chromosomes were identified based on information from duplicated loci. Homologies between the coho and rainbow trout maps were examined. Eighty‐six loci were found to form common linkage relationships between the two maps; these relationships provided evidence for whole‐arm fissions, fusions and conservation of chromosomal regions in the evolution of these two species.
Identification of polymorphisms influencing feed intake and efficiency in beef cattle
Authors: Sherman E. L. , Nkrumah J. D. , Murdoch B. M. , Moore S. S. 
Published: March 2008

SummaryFeed efficiency is an economically important trait in beef cattle. Net feed efficiency, measured as residual feed intake (RFI), is the difference between actual feed intake and the predicted feed intake required for maintenance and gain of the animal. SNPs that show associations with RFI may be useful quantitative trait nucleotides for marker‐assisted selection. This study identified associations between SNPs underlying five RFI QTL on five bovine chromosomes (BTA2, 5, 10, 20 and 29) with measures of dry matter intake (DMI), RFI and feed conversion ratio (FCR) in beef cattle. Six SNPs were found to have effects on RFI (P < 0.05). The largest single SNP allele substitution effect for RFI was −0.25 kg/day located on BTA2. The combined effects of the SNPs found significant in this experiment explained 6.9% of the phenotypic variation of RFI. Not all the RFI SNPs showed associations with DMI and FCR even though these traits are highly correlated with RFI (r = 0.77 and r = 0.62 respectively). This shows that these SNPs may be affecting the underlying biological mechanisms of feed efficiency beyond feed intake control and weight gain efficiency. These SNPs can be used in marker‐assisted selection but first it will be important to verify these effects in independent populations of cattle.
Double‐negative regulatory T cells induce allotolerance when expanded after allogeneic haematopoietic stem cell transplantation
Authors: McIver Z. , Serio B. , Dunbar A. , O’Keefe C. L. , Powers J. , Wlodarski M. , Jin T. , Sobecks R. , Bolwell B. , Maciejewski J. P. 
Published: March 2008

SummaryDouble‐negative (DN) regulatory T cells (Tregs) are specialized T lymphocytes involved in the down‐modulation of immune responses, resulting in allotolerance after allogeneic haematopoietic stem cell transplantation (HSCT). Most of the properties of DN Tregs were identified in murine models, including the unique ability to suppress alloreactive syngeneic effector T cells in an antigen‐specific manner via Fas/Fas‐ligand interactions. We investigated the behaviour of DN Tregs following human allogeneic HSCT with regard to occurrence of graft‐versus‐host disease (GvHD) and restoration of T‐cell receptor repertoire in a cohort of 40 patients. The frequency of DN Tregs and CD4/CD8 TCR repertoire was measured serially and at the time of diagnosis of GvHD by flow cytometry. Analysis demonstrated a positive correlation between degree of alloreactivity, as measured by grade of GvHD, and the number of variable beta chain (Vβ) family expansions in both T‐cell populations. We also found that a deficiency of DN Tregs was associated with an increased number of Vβ family expansions, and most importantly, with the occurrence of GvHD. All individuals who demonstrated more than 1% DN Tregs did not develop GvHD, providing evidence that DN Tregs participate in peripheral tolerance to prevent GvHD when expanded after allogeneic HSCT.
Fetal haemoglobin response to hydroxycarbamide treatment and sar1a promoter polymorphisms in sickle cell anaemia
Authors: Kumkhaek Chutima , Taylor James G. , Zhu Jianqiong , Hoppe Carolyn , Kato Gregory J. , Rodgers Griffin P. 
Published: March 2008

SummaryThe hydroxycarbamide (HC)‐inducible small guanosine triphosphate (GTP)‐binding protein, secretion‐associated and RAS‐related (SAR) protein has recently been shown to play a pivotal role in HBG induction and erythroid maturation by causing cell apoptosis and G1/S‐phase arrest. Our preliminary analysis indicated that HC inducibility is transcriptionally regulated by elements within the SAR1A promoter. This study aimed to assess whether polymorphisms in the SAR1A promoter are associated with differences Hb F levels or HC therapeutic responses among sickle cell disease (SCD) patients. We studied 386 individuals with SCD comprised of 269 adults treated with or without HC and 117 newborns with SCD identified from a newborn screening program. Three previously unknown single nucleotide polymorphisms (SNPs) in the upstream 5′UTR (−809 C>T, −502 G>T and −385 C>A) were significantly associated with the fetal haemoglobin (HbF) response in Hb SS patients treated with HC (P < 0·05). In addition, four SNPs (rs2310991, −809 C>T, −385 C>A and rs4282891) were significantly associated with the change in absolute HbF after 2 years of treatment with HC. These data suggest that variation within SAR1A regulatory elements might contribute to inter‐individual differences in regulation of HbF expression and patient responses to HC in SCD.
Rituximab in the treatment of autoimmune haematological disorders
Authors: Garvey Bernadette 
Published: March 2008

SummaryCurrent treatment regimens for haematological autoimmune diseases are relatively non‐selective and are often associated with considerable toxicity. Recently, it has become clear that B cells play a key role in both the development and perpetuation of autoimmunity, suggesting that B‐cell depletion could be a valuable treatment approach for patients with autoimmune diseases. This article reviews data supporting the use of rituximab – an anti‐CD20 monoclonal antibody that specifically depletes B cells – in four key autoimmune haematological disorders: idiopathic thrombocytopenic purpura (ITP); autoimmune haemolytic anaemia (AIHA); acquired haemophilia; and thrombotic thrombocytopenic purpura (TTP). Although treatment of ITP, AIHA, acquired haemophilia and TTP with rituximab is still relatively uncommon, results from case series and small phase II trials indicate that patients of all ages can respond to rituximab, irrespective of the number or type of prior treatments that they have received. Moreover, patients with these diseases receiving rituximab experienced predominantly mild adverse events, with only a few serious adverse events reported. These data suggest that rituximab provides an effective and well‐tolerated alternative treatment option for patients with ITP, AIHA, acquired haemophilia and TTP, many of whom have limited treatment choices.
Outcome after autologous stem cell transplantation for multiple myeloma in patients with preceding plasma cell disorders
Authors: Kumar Shaji K. , Dingli David , Lacy Martha Q. , Dispenzieri Angela , Hayman Suzanne R. , Buadi Francis K. , Rajkumar S. Vincent , Litzow Mark R. , Gertz Morie A. 
Published: March 2008

SummaryA third of patients with multiple myeloma (MM) have a preceding diagnosis of plasma cell proliferative disorder (PCPD), mostly monoclonal gammopathy of undetermined significance (MGUS), smoldering MM (SMM) or plasmacytoma. While autologous stem cell transplantation (SCT) improves survival in MM, it is not clear if patients with preceding PCPD have a different outcome. We identified 151 patients with preceding PCPD from among 804 patients undergoing SCT, and their outcomes were compared. The response rates, including complete responses, were similar between the groups. Patients with a preceding diagnosis of MGUS had longer time to progression (TTP; 27·5 months vs. 17·2 months, P = 0·01), and longer overall survival (OS) from transplant (80·2 months vs. 48·3 months, P = 0·03) compared to those with de novo myeloma. However no differences were seen among those with a preceding diagnosis of SMM or plasmacytoma in terms of TTP or OS from transplant when compared to those with de novo myeloma. Multivariate analysis indicated that the presence of MGUS prior to myeloma was prognostic for post‐transplant relapse independent of other known risk factors. Patients with pre‐existing MGUS prior to myeloma diagnosis have a better outcome following HDT, reflecting more indolent disease and a favourable biology than those presenting with de novo myeloma.
Effect of deferasirox (ICL670) on arterial function in patients with beta‐thalassaemia major
Authors: Cheung Y. F. , Chan Godfrey C. F. , Ha S. Y. 
Published: March 2008

SummaryDeferasirox (ICL670) has been shown to have rapid accessibility to intracellular labile iron. We tested the hypothesis that oral deferasirox improves arterial dysfunction in patients with beta‐thalassaemia major. Nineteen thalassaemia patients, aged 23 ± 7 years, with normal left ventricular (LV) function were treated with deferasirox at 25–35 mg/kg/d for 12 months. LV function, brachial arterial flow‐mediated dilation (FMD), carotid arterial stiffness, and serum ferritin levels were determined at baseline prior to initiation, after 6 months and after 12 months of therapy. The baseline cardiovascular indices were compared with those of 17 age‐matched controls. Longitudinal changes in patients during the treatment period were also determined. Compared with controls, patients had similar echocardiographic indices of LV function (all P > 0·05), while their baseline brachial FMD was reduced (P < 0·001) and carotid stiffness increased (P = 0·019). An increase in FMD (P < 0·001) and a decrease in carotid stiffness (P = 0·007) were found at 6 and 12 months follow‐up. The stiffness index correlated inversely with FMD (r = −0·42, P = 0·001). Although there was an increase in ferritin level at 12 months (3303 ± 1185 ng/ml vs. 2714 ± 780 ng/ml at baseline, P = 0·006), no significant correlation existed between ferritin level and FMD or carotid stiffness. In conclusion, deferasirox therapy in thalassaemia patients is associated with improved arterial function.
Imaging of cell trafficking and metastases of paediatric rhabdomyosarcoma
Authors: Seitz G. , Warmann S. W. , Fuchs J. , Heitmann H. , Mahrt J. , Busse A.‐C. , Ruck P. , Hoffman R. M. , Wessels J. T. 
Published: March 2008

Abstract.  Objective: The aim of this study was to establish a preclinical mouse model to study metastases of paediatric rhabdomyosarcoma at the macroscopic and cellular levels, with different imaging methods. Experimental Design: The alveolar rhabdomyosarcoma cell line Rh30 was stably transfected with the red fluorescent protein (DsRed2) then was xenotransplanted (intravenous injection [n = 8], and footpad injection [n = 8]) into nude mice (NMRI nu/nu). Macroscopic imaging of metastases was performed using DsRed2‐fluorescence and flat‐panel volumetric computed tomography scan. In a further series of animals (n = 8), in vivo cell trafficking of rhabdomyosarcoma cells using cellular imaging with an Olympus OV100 variable‐magnification small‐animal imaging system was used. Results: Metastases in the pelvis, thoracic wall and skin were visualized by fluorescence imaging. Pelvic metastases were found after tail vein injection and at other metastatic sites after footpad injection. Flat‐panel volumetric computed tomography scan data allowed highly specific analysis of contrast between tumour and surrounding tissue. Correlation between fluorescence and flat‐panel volumetric computed tomography scan imaging data was observed. Single‐cell imaging visualized tumour cells in the vessels and demonstrated the arrest of tumour cells at vessel junctions followed by extravasation of the tumour cells. Conclusion: We established a model for visualization of experimental metastatic invasion and describe relevant tools for imaging childhood rhabdomyosarcoma metastases at the macroscopic and cellular levels. Imaging of cell trafficking visualized the behaviour of tumour cells and development of metastases by accumulation and extravasation of rhabdomyosarcoma cells.
Analysis of the PTPN11 gene in idiopathic short stature children and Noonan syndrome patients
Authors: Ferreira Lize V. , Souza Silvia C. A. L. , Montenegro Luciana R. , Malaquias Alexsandra C. , Arnhold Ivo J. P. , Mendonca Berenice B. , Jorge Alexander A. L. 
Published: March 2008

SummaryBackground  Mutations in the PTPN11 gene are the main cause of Noonan syndrome (NS). The presence of some NS features is a frequent finding in children with idiopathic short stature (ISS). These children can represent the milder end of the NS clinical spectrum and PTPN11 is a good candidate for involvement in the pathogenesis of ISS.Objective  To evaluate the presence of mutations in PTPN11 in ISS children who presented NS‐related signs and in well‐characterized NS patients.Patients and methods  We studied 50 ISS children who presented at least two NS‐associated signs but did not fulfil the criteria for NS diagnosis. Forty‐nine NS patients diagnosed by the criteria of van der Burgt et al.3 were used to assess the adequacy of these criteria to select patients for PTPN11 mutation screening. The coding region of PTPN11 was amplified by polymerase chain reaction (PCR), followed by direct sequencing.Results  No mutations or polymorphisms were found in the coding region of the PTPN11 gene in ISS children. Nineteen of the 49 NS patients (39%) presented mutations in PTPN11. No single characteristic enabled us to distinguish between NS patients with or without PTPN11 mutations.Conclusion  Considering that no mutations were found in the present cohort with NS‐related signs, it is unlikely that mutations would be found in unselected ISS children. The van der Burgt et al. criteria are adequate in attaining NS diagnosis and selecting patients for molecular studies. Mutations in the PTPN11 gene are commonly involved in the pathogenesis of NS but are not a common cause of ISS.
Percutaneous ethanol injection therapy: a surgery‐sparing treatment for primary hyperparathyroidism
Authors: Stratigis Spyros , Stylianou Kostas , Mamalaki Evangelia , Perakis Kostas , Vardaki Eleftheria , Tzenakis Nikolaos , Katsipi Irene , Papavasiliou Stathis , Yarmenitis Spyros , Kyriazis John , Daphnis Eugene 
Published: March 2008

SummaryObjective  To describe our 3‐year experience in the long‐term efficacy and safety of percutaneous ethanol injection therapy (PEIT), as an alternative to surgery for the management of patients with primary hyperparathyroidism (p‐HPT).Design  Prospective study with a mean follow‐up of 19·6 ± 10·6 months.Patients  Our study population included 19 consecutive high risk patients with p‐HPT, who met the criteria for surgery.Measurements  Under ultrasonic guidance, ethanol (95%) was injected into parathyroid glands with a volume of ≥ 0·15 cm3. With the aim of normalizing intact parathormone (iPTH) values, repeated ethanol injections were carried out, in an interval of 2 weeks, until normalization of iPTH was reached or until no residual blood supply was detected by ultrasound in the gland. Biochemical parameters were monitored throughout the study.Results  At 6‐month follow‐up, normalization of iPTH levels (10–65 ng/l) was achieved in 11 (58%) patients (responders). Of the eight remaining patients (nonresponders), six patients had reduced (but not normalized) iPTH levels and two patients required parathyroid surgery. Seventeen (11 responders and 6 nonresponders) of the 19 patients (89·5%) became normocalcaemic (serum Ca ≤ 2·57 mmol/l) and remained so for a mean follow‐up of 21 months (8–39 months). The odds ratio (P < 0·05) of response vs. no response to PEIT was 16·7‐fold for pretreatment iPTH < 200 vs. > 200 ng/l. The only complication was a transient dysphonia noticed in three patients.Conclusions  PEIT is a safe and effective nonsurgical treatment for patients with p‐HPT, who are unsuitable for surgical intervention.
In search of stable soil organic carbon fractions: a comparison of methods applied to soils labelled with 14C for 40 days or 40 years
Authors: Bruun S. , Thomsen I. K. , Christensen B. T. , Jensen L. S. 
Published: March 2008

SummaryA reliable method for the isolation of a stable fraction of soil organic carbon (SOC) would be very helpful for improving our understanding of the mechanisms responsible for stabilization of SOC and the dynamics of SOC turnover. We tested acid hydrolysis, physical fractionation (particle density/size), photo‐oxidation, treatment with chemical oxidants (NaOCl and NaS2O8) and thermal treatment on two soils incubated with 14C‐labelled barley straw for either 40 days or 40 years. Different intensities of the treatments were included. Acid hydrolysis, photo‐oxidation and treatment with a chemical oxidant consistently removed more 40‐year‐old C than 40‐day‐old C, which suggests that the isolated fractions contained a large proportion of material with a relatively rapid turnover. The clay + silt associated SOC fraction contained a small proportion of 40‐day‐old C and a large proportion of 40‐year‐old C. This is consistent with a SOC fraction with medium turnover. The thermal treatment removed more 40‐year‐old C than 40‐day‐old C. At 400°C there was still a small proportion of the 40‐year‐old C remaining, whereas almost all the 40‐day‐old C was removed. This is consistent with a stable SOC fraction. However, because only 2–3% of the C remained after this treatment, the isolated SOC fraction may be of little quantitative importance. Furthermore, the thermally resistant fraction is likely to be heavily altered by the treatment, and therefore unsuitable for further studies of the chemical nature of stable SOC.
Do freeze‐thaw events enhance C and N losses from soils of different ecosystems? A review
Authors: Matzner E. , Borken W. 
Published: March 2008

SummaryFreezing and thawing of soils may affect the turnover of soil organic matter and thus the losses of C and N from soils. Here we review the literature with special focus on: (i) the mechanisms involved, (ii) the effects of freezing temperature and frequency, (iii) the differences between arable soils and soils under natural vegetation, and (iv) the hypothesis that freeze‐thaw events lead to significant C and N losses from soils at the annual scale. Changes in microbial biomass and populations, root turnover and soil structure might explain increased gaseous and solute fluxes of C and N following freeze‐thaw events, but these mechanisms have seldom been addressed in detail. Effects of freeze‐thaw events appear to increase with colder frost temperatures below 0°C, but a threshold value for specific soils and processes cannot be defined. The pool of C and N susceptible to freeze‐thaw events is rather limited, as indicated by decreasing losses with short‐term repeated events. Elevated nitrate losses from soils under alpine and/or arctic and forest vegetation occurred only in the year following exceptional soil frost, with greatest reported losses of about 13 kg N ha−1. Nitrate losses are more likely caused by reduced root uptake rather than by increased N net mineralization. N2O emissions from forest soils often increased after thawing, but this lasted only for a relatively short time (days to 1–2 months), with the greatest reported cumulative N2O emissions of about 2 kg N2O‐N ha−1. The emissions of N2O after freeze‐thaw events were in some cases substantially greater from arable soils than from forest soils. Thus, freeze‐thaw events might induce gaseous and/or solute losses of N from soils that are relevant at the annual time scale. While a burst of CO2 after thawing of frozen soils is often found, there is strong evidence that, at the annual time scale, freeze‐thaw cycles either have little effect or will even reduce soil C losses as compared with unfrozen conditions. On the contrary, a milder winter climate with fewer periods of soil frost may result in greater losses of C from soils that are presently influenced by extended frost periods.
The turnover of organic carbon in subsoils. Part 1. Natural and bomb radiocarbon in soil profiles from the Rothamsted long‐term field experiments
Authors: Jenkinson D. S. , Poulton P. R. , Bryant C. 
Published: March 2008

SummaryThe Rothamsted long‐term field experiments, started more than 150 years ago, provide unique material for the study of carbon turnover in subsoils. Total organic C, 14C and 13C were measured on soil profiles taken from these experiments, before and after the thermonuclear bomb tests of the mid‐20th century. Four contrasting systems of land management were sampled: land cultivated every year for winter wheat; regenerating woodland on acid soil; regenerating woodland on calcareous soil; and old grassland. The mean radiocarbon ages of all the pre‐bomb samples from cultivated land were 1210 years (0–23 cm), 2040 years (23–46 cm), 3610 years (46–69 cm) and 5520 years (69–92 cm). Bomb radiocarbon derived from thermonuclear tests was present throughout the profile in all the post‐bomb samples, although below 23 cm the amounts were small and the pre‐ and post‐bomb radiocarbon measurements were often not significantly different. Values of δ13C increased down the profile, from −26.3‰ (0–23 cm layer, mean of all measurements) to −25.2‰ for the 69–92 cm layer. The C/N ratios decreased with depth in virtually all of the profiles sampled. Excluding the surface (0–23 cm) soils from the old grassland, the hyperbola m = 152.1 − 2341/(1 + 0.264n) gave a close fit to the radiocarbon data from all depths, all sampling times and all sites, where n is the organic C content of the soil, in t ha−1, and m is the radiocarbon content of the soil, in Δ14C units, corrected for expansion or contraction of soil layers with time. The aberrant grassland soils almost certainly contained coal: one of them was shown by 13C‐NMR to contain 0.82% coal C. In Part 2 (this issue) of this pair of papers, these radiocarbon and total C measurements are used to develop and test a new model for the turnover of organic C in subsoils.