bluuebunny/crossref_metadata_2025_split huggingface dataset:
Outcomes of pediatric bone marrow transplantation for leukemia and myelodysplasia using matched sibling, mismatched related, or matched unrelated donors
Authors: Shaw Peter J. , Kan Fangyu , Woo Ahn Kwang , Spellman Stephen R. , Aljurf Mahmoud , Ayas Mouhab , Burke Michael , Cairo Mitchell S. , Chen Allen R. , Davies Stella M. , Frangoul Haydar , Gajewski James , Gale Robert Peter , Godder Kamar , Hale Gregory A. , Heemskerk Martin B.A. , Horan John , Kamani Naynesh , Kasow Kimberly A. , Chan Ka Wah , Lee Stephanie J. , Leung Wing H. , Lewis Victor A. , Miklos David , Oudshoorn Machteld , Petersdorf Effie W. , Ringdén Olle , Sanders Jean , Schultz Kirk R. , Seber Adriana , Setterholm Michelle , Wall Donna A. , Yu Lolie , Pulsipher Michael A. 
Published: July 2010

AbstractAlthough some trials have allowed matched or single human leukocyte antigen (HLA)–mismatched related donors (mmRDs) along with HLA-matched sibling donors (MSDs) for pediatric bone marrow transplantation in early-stage hematologic malignancies, whether mmRD grafts lead to similar outcomes is not known. We compared patients < 18 years old reported to the Center for International Blood and Marrow Transplant Research with acute myeloid leukemia, acute lymphoblastic leukemia, chronic myeloid leukemia, and myelodysplastic syndrome undergoing allogeneic T-replete, myeloablative bone marrow transplantation between 1993 and 2006. In total, patients receiving bone marrow from 1208 MSDs, 266 8/8 allelic-matched unrelated donors (URDs), and 151 0-1 HLA-antigen mmRDs were studied. Multivariate analysis showed that recipients of MSD transplants had less transplantation-related mortality, acute graft-versus-host disease (GVHD), and chronic GVHD, along with better disease-free and overall survival than the URD and mmRD groups. No differences were observed in transplant-related mortality, acute and chronic GVHD, relapse, disease-free survival, or overall survival between the mmRD and URD groups. These data show that mmRD and 8/8 URD outcomes are similar, whereas MSD outcomes are superior to the other 2 sources. Whether allele level typing could identify mmRD recipients with better outcomes will not be known unless centers alter practice and type mmRD at the allele level.
Human NK cells of mice with reconstituted human immune system components require preactivation to acquire functional competence
Authors: Strowig Till , Chijioke Obinna , Carrega Paolo , Arrey Frida , Meixlsperger Sonja , Rämer Patrick C. , Ferlazzo Guido , Münz Christian 
Published: July 2010

Abstract
To investigate human natural killer (NK)–cell reactivity in vivo we have reconstituted human immune system components by transplantation of human hematopoietic progenitor cells into NOD-scid IL2Rγnull mice. We demonstrate here that this model allows the development of all NK-cell subsets that are also found in human adult peripheral and cord blood, including NKp46+CD56− NK cells. Similar to human cord blood, NK cells from these reconstituted mice require preactivation by interleukin-15 to reach the functional competence of human adult NK cells. Mainly the terminally differentiated CD16+ NK cells demonstrate lower reactivity without this stimulation. After preactivation, both CD16+ and CD16− NK cells efficiently produce interferon-γ and degranulate in response to stimulation with NK cell–susceptible targets, including K562 erythroleukemia cells. NK-cell lines, established from reconstituted mice, demonstrate cytotoxicity against this tumor cell line. Importantly, preactivation can as well be achieved by bystander cell maturation via poly I:C stimulation in vitro and injection of this maturation stimulus in vivo. Preactivation in vivo enhances killing of human leukocyte antigen class I negative tumor cells after their adoptive transfer. These data suggest that a functional, but resting, NK-cell compartment can be established in immune-compromised mice after human hematopoietic progenitor cell transfer.
Targeting of survivin by nanoliposomal ceramide induces complete remission in a rat model of NK-LGL leukemia
Authors: Liu Xin , Ryland Lindsay , Yang Jun , Liao Aijun , Aliaga Cesar , Watts Rebecca , Tan Su-Fern , Kaiser James , Shanmugavelandy Sriram S. , Rogers Andrew , Loughran Kathleen , Petersen Bailey , Yuen Jonathan , Meng Fanxue , Baab Kendall Thomas , Jarbadan Nancy Ruth , Broeg Kathleen , Zhang Ranran , Liao Jason , Sayers Thomas Joseph , Kester Mark , Loughran Thomas P. 
Published: July 2010

AbstractThe natural killer (NK) type of aggressive large granular lymphocytic (LGL) leukemia is a fatal illness that pursues a rapid clinical course. There are no effective therapies for this illness, and pathogenetic mechanisms remain undefined. Here we report that the survivin was highly expressed in both aggressive and chronic leukemic NK cells but not in normal NK cells. In vitro treatment of human and rat NK-LGL leukemia cells with cell-permeable, short-chain C6-ceramide (C6) in nanoliposomal formulation led to caspase-dependent apoptosis and diminished survivin protein expression, in a time- and dose-dependent manner. Importantly, systemic intravenous delivery of nanoliposomal ceramide induced complete remission in the syngeneic Fischer F344 rat model of aggressive NK-LGL leukemia. Therapeutic efficacy was associated with decreased expression of survivin in vivo. These data suggest that in vivo targeting of survivin through delivery of nanoliposomal C6-ceramide may be a promising therapeutic approach for a fatal leukemia.
A novel latent membrane 2 transcript expressed in Epstein-Barr virus–positive NK- and T-cell lymphoproliferative disease encodes a target for cellular immunotherapy
Authors: Fox Christopher P. , Haigh Tracey A. , Taylor Graham S. , Long Heather M. , Lee Steven P. , Shannon-Lowe Claire , O'Connor Simon , Bollard Catherine M. , Iqbal Javeed , Chan Wing C. , Rickinson Alan B. , Bell Andrew I. , Rowe Martin 
Published: July 2010

AbstractTherapeutic targeting of virus-encoded proteins using cellular immunotherapy has proved successful for Epstein-Barr virus (EBV)–associated posttransplant lymphoproliferative disease. However, the more limited repertoire and immunogenicity of EBV-encoded proteins in other malignancies such as Hodgkin lymphoma and extranodal natural killer (NK)/T lymphoma has been more challenging to target. The immunosubdominant latent membrane protein 2 (LMP2) is considered the optimal target in such Latency II tumors, although data relating to its expression in T/NK malignancies are limited. In addressing the validity of LMP2 as an immunotherapeutic target we found that LMP2-specific effector CD8+ T cells recognized and killed EBV-positive NK- and T-cell tumor lines, despite an apparent absence of LMP2A protein and barely detectable levels of LMP2 transcripts from the conventional LMP2A and LMP2B promoters. We resolved this paradox by identifying in these lines a novel LMP2 mRNA, initiated from within the EBV terminal repeats and containing downstream, epitope-encoding exons. This same mRNA was also highly expressed in primary (extra-nodal) NK/T lymphoma tissue, with virtually undetectable levels of conventional LMP2A/B transcripts. Expression of this novel transcript in T/NK-cell lymphoproliferative diseases validates LMP2 as an attractive target for cellular immunotherapy and implicates this truncated LMP2 protein in NK- and T-cell lymphomagenesis. This study is registered at clinicaltrials.gov as NCT00062868.
Protein structure modelling and evaluation based on a 4-distance description of side-chain interactions
Authors: Potapov Vladimir , Cohen Mati , Inbar Yuval , Schreiber Gideon 
Published: July 2010

Abstract

Background
Accurate evaluation and modelling of residue-residue interactions within and between proteins is a key aspect of computational structure prediction including homology modelling, protein-protein docking, refinement of low-resolution structures, and computational protein design.

Results
Here we introduce a method for accurate protein structure modelling and evaluation based on a novel 4-distance description of residue-residue interaction geometry. Statistical 4-distance preferences were extracted from high-resolution protein structures and were used as a basis for a knowledge-based potential, called Hunter. We demonstrate that 4-distance description of side chain interactions can be used reliably to discriminate the native structure from a set of decoys. Hunter ranked the native structure as the top one in 217 out of 220 high-resolution decoy sets, in 25 out of 28 "Decoys 'R' Us" decoy sets and in 24 out of 27 high-resolution CASP7/8 decoy sets. The same concept was applied to side chain modelling in protein structures. On a set of very high-resolution protein structures the average RMSD was 1.47 Å for all residues and 0.73 Å for buried residues, which is in the range of attainable accuracy for a model. Finally, we show that Hunter performs as good or better than other top methods in homology modelling based on results from the CASP7 experiment. The supporting web site http://bioinfo.weizmann.ac.il/hunter/ was developed to enable the use of Hunter and for visualization and interactive exploration of 4-distance distributions.

Conclusions
Our results suggest that Hunter can be used as a tool for evaluation and for accurate modelling of residue-residue interactions in protein structures. The same methodology is applicable to other areas involving high-resolution modelling of biomolecules.
MS4 - Multi-Scale Selector of Sequence Signatures: An alignment-free method for classification of biological sequences
Authors: Corel Eduardo , Pitschi Florian , Laprevotte Ivan , Grasseau Gilles , Didier Gilles , Devauchelle Claudine 
Published: July 2010

Abstract

Background
While multiple alignment is the first step of usual classification schemes for biological sequences, alignment-free methods are being increasingly used as alternatives when multiple alignments fail. Subword-based combinatorial methods are popular for their low algorithmic complexity (suffix trees ...) or exhaustivity (motif search), in general with fixed length word and/or number of mismatches. We developed previously a method to detect local similarities (the N-local decoding) based on the occurrences of repeated subwords of fixed length, which does not impose a fixed number of mismatches. The resulting similarities are, for some "good" values of N, sufficiently relevant to form the basis of a reliable alignment-free classification. The aim of this paper is to develop a method that uses the similarities detected by N-local decoding while not imposing a fixed value of N. We present a procedure that selects for every position in the sequences an adaptive value of N, and we implement it as the MS4 classification tool.

Results
Among the equivalence classes produced by the N-local decodings for all N, we select a (relatively) small number of "relevant" classes corresponding to variable length subwords that carry enough information to perform the classification. The parameter N, for which correct values are data-dependent and thus hard to guess, is here replaced by the average repetitivity κ of the sequences. We show that our approach yields classifications of several sets of HIV/SIV sequences that agree with the accepted taxonomy, even on usually discarded repetitive regions (like the non-coding part of LTR).

Conclusions
The method MS4 satisfactorily classifies a set of sequences that are notoriously hard to align. This suggests that our approach forms the basis of a reliable alignment-free classification tool. The only parameter κ of MS4 seems to give reasonable results even for its default value, which can be a great advantage for sequence sets for which little information is available.
Pleistocene glacial cycle effects on the phylogeography of the Chinese endemic bat species, Myotis davidii
Authors: You Yuyan , Sun Keping , Xu Lijie , Wang Lei , Jiang Tinglei , Liu Sen , Lu Guanjun , Berquist Sean W , Feng Jiang 
Published: July 2010

Abstract

Background
Global climatic oscillations, glaciation cycles and the unique geographic topology of China have profoundly influenced species population distributions. In most species, contemporary distributions of populations cannot be fully understood, except in a historical context. Complex patterns of Pleistocene glaciations, as well as other physiographic changes have influenced the distribution of bat species in China. Until this study, there had been no phylogeographical research on Myotis davidii, an endemic Chinese bat. We used a combination of nuclear and mitochondrial DNA markers to investigate genetic diversity, population structure, and the demographic history of M. davidii. In particular, we compared patterns of genetic variation to glacial oscillations, topography, and environmental variation during the Pleistocene in an effort to explain current distributions in light of these historical processes.

Results

M. davidii comprises three lineages (MEP, SWP and SH) based on the results of molecular variance analysis (AMOVA) and phylogenetic analyses. The results of a STRUCTURE analysis reveal multi-hierarchical population structure in M. davidii. Nuclear and mitochondrial genetic markers reveal different levels of gene flow among populations. In the case of mtDNA, populations adhere to an isolation-by-distance model, whereas the individual assignment test reveals considerable gene flow between populations. MDIV analysis indicate that the split of the MEP and SWP/SH lineages, and from the SWP and SH lineages were at 201 ka BP and 158 ka BP, respectively. The results of a mismatch distribution analysis and neutrality tests indicate a population expansion event at 79.17 ka BP and 69.12 ka BP in MEP and SWP, respectively.

Conclusions
The complex demographic history, discontinuous extant distribution of haplotypes, and multiple-hierarchy population structure of M. davidii appear associated with climatic oscillations, topography and eco-environmental variation of China. Additionally, the three regions are genetically differentiated from one another in the entire sample set. The degree of genetic differentiation, based on the analysis of mtDNA and nDNA, suggests a male-mediated gene flow among populations. Refuges were in the MEP, SH and the lower elevations of SWP regions. This study also provides insights for conservation management units (MEP, SWP and SH).
Constraints to virus infection in Nicotiana benthamiana plants transformed with a potyvirus amplicon
Authors: Calvo María , Dujovny Gabriela , Lucini Cristina , Ortuño Jesús , Alamillo Josefa M , Simón-Mateo Carmen , López-Moya Juan José , García Juan Antonio 
Published: July 2010

Abstract

Background
Plant genomes have been transformed with full-length cDNA copies of viral genomes, giving rise to what has been called 'amplicon' systems, trying to combine the genetic stability of transgenic plants with the elevated replication rate of plant viruses. However, amplicons' performance has been very variable regardless of the virus on which they are based. This has boosted further interest in understanding the underlying mechanisms that cause this behavior differences, and in developing strategies to control amplicon expression.

Results

Nicotiana benthamiana plants were transformed with an amplicon consisting of a full-length cDNA of the potyvirus Plum pox virus (PPV) genome modified to include a GFP reporter gene. Amplicon expression exhibited a great variability among different transgenic lines and even among different plants of the same line. Plants of the line 10.6 initially developed without signs of amplicon expression, but at different times some of them started to display sporadic infection foci in leaves approaching maturity. The infection progressed systemically, but at later times the infected plants recovered and returned to an amplicon-inactive state. The failure to detect virus-specific siRNAs in 10.6 plants before amplicon induction and after recovery suggested that a strong amplicon-specific RNA silencing is not established in these plants. However, the coexpression of extra viral silencing suppressors caused some amplicon activation, suggesting that a low level of RNA silencing could be contributing to maintain amplicon repression in the 10.6 plants. The resistance mechanisms that prevent amplicon-derived virus infection were also active against exogenous PPV introduced by mechanical inoculation or grafting, but did not affect other viruses. Amplicon-derived PPV was able to spread into wild type scions grafted in 10.6 rootstocks that did not display signs of amplicon expression, suggesting that resistance has little effect on virus movement.

Conclusions
Our results suggest that amplicon-derived virus infection is limited in this particular transgenic line by a combination of factors, including the presumed low efficiency of the conversion from the transgene transcript to replicable viral RNA, and also by the activation of RNA silencing and other defensive responses of the plant, which are not completely neutralized by viral suppressors.
Granulocytic sarcoma of the pancreas: A case report and review of the literatures
Authors: Rong Yefei , Wang Dansong , Lou Wenhui , Kuang Tiantao , Jin Dayong 
Published: July 2010

Abstract

Background
Granulocytic sarcoma (GS) is a form of acute myeloid leukemia (AML), also known as extramedullary myeloid tumor or chloroma. It forms a solid malignant tumor consisting of myelocytes or granulocytes and is typically located in bone while occurrence in other parts of the body is rare.

Case presentation
We reported a 40-year-old male patient who had jaundice, highly elevated bilirubin, and a mass highly suspicious of pancreatic head carcinoma. We performed surgery and the pathology and immunohistochemistry suggested GS; however the blood test and the bone marrow infiltration showed no evidence of AML. In our review of the published reports of GS, we only found six reports of the GS in the pancreas, and we suggested that immunohistochemical staining should be used to accurately differentiate GS from other pancreatic cancer and other types of leukemia.

Conclusions
The accurate diagnosis of GS is necessary for determining prognosis and deciding appropriate therapy.
Risk factors for multi-drug resistant Acinetobacter baumanniibacteremia in patients with colonization in the intensive care unit
Authors: Jung Ji Ye , Park Moo Suk , Kim Song Ee , Park Byung Hoon , Son Ji Young , Kim Eun Young , Lim Joo Eun , Lee Sang Kook , Lee Sang Hoon , Lee Kyung Jong , Kang Young Ae , Kim Se Kyu , Chang Joon , Kim Young Sam 
Published: July 2010

Abstract

Background
Epidemic outbreaks of multi-drug resistant (MDR) Acinetobacter baumannii (AB) in intensive care units (ICUs) are increasing. The incidence of MDR AB bacteremia, which develops as a result of colonization, is increasing through widespread dissemination of the pathogen, and further colonization. We sought to determine risk factors for MDR AB bacteremia in patients colonized with MDR AB in the ICU.

Methods
We conducted a retrospective, observational study of 200 patients colonized with MDR AB in the ICU at Severance Hospital, South Korea during the outbreak period between January 2008 and December 2009.

Results
Of the 200 patients colonized with MDR AB, 108 developed MDR AB bacteremia, and 92 did not. APACHE II scores were higher in bacteremic than non-bacteremic patients at the time of ICU admission and colonization (24.0 vs. 21.6; P = 0.035, 22.9 vs. 16.8; P < 0.001, respectively). There was no difference between the two groups in the duration of time from ICU admission to colonization (7.1 vs. 7.2 days; P = 0.923), but the duration of time at risk was shorter in bacteremic patients (12.1 vs. 6.0 days; P = 0.016). A recent invasive procedure was a significant risk factor for development of bacteremia (odds ratio = 3.85; 95% CI 1.45-10.24; P = 0.007). Multivariate analysis indicated infection and respiratory failure at the time of ICU admission, maintenance of mechanical ventilation, maintenance of endotracheal tube instead of switching to a tracheostomy, recent central venous catheter insertion, bacteremia caused by other microorganism after colonization by MDR AB, and prior antimicrobial therapy, were significant risk factors for MDR AB bacteremia.

Conclusions
Patients in the ICU, colonized with MDR AB, should be considered for minimizing invasive procedures and early removal of the invasive devices to prevent development of MDR AB bacteremia.
Adjuvant radiotherapy and chemotherapy in breast cancer: 30 year follow-up of survival
Authors: McArdle Colin S , McMillan Donald C , Greenlaw Nicola , Morrison David S 
Published: July 2010

Abstract

Background
The long term outcome (more than 15 years) of adjuvant treatment in patients with primary operable breast cancer has rarely been examined.

Methods
A randomised clinical trial of radiotherapy, chemotherapy (28 day cycles of cyclophosphamide, methotrexate and 5-fluorouracil) or both on women with primary operable breast cancer (n = 322) was followed-up for a median of 27 years.

Results
260 (81%) patients died, 204 (78%) from breast cancer. Cancer specific survival (SE) at 10 years, 20 years and 30 years was 41 (3)%, 34 (3)% and 33 (3)% respectively. Presence of more than 3 involved lymph nodes increased cancer-specific mortality (HR 1.88, 95% CI 1.34-2.63) after adjustment for age, socio-economic deprivation and adjuvant treatment. Both age (HR 1.63, 95% CI 1.19-2.22) and involved lymph nodes (HR 1.59, 95% CI 1.17-2.14) were significant predictors of all-cause mortality after adjustment for other factors. There was no significant difference in all-cause or cancer-specific survival between patients in each of the 3 treatment arms.

Conclusions
The present study highlights the long term impact of node positive disease but does not indicate that any regimen was associated with significantly better long-term survival.