bluuebunny/crossref_metadata_2025_split huggingface dataset:
Generation of CD19-chimeric antigen receptor modified CD8+ T cells derived from virus-specific central memory T cells
Authors: Terakura Seitaro , Yamamoto Tori N. , Gardner Rebecca A. , Turtle Cameron J. , Jensen Michael C. , Riddell Stanley R. 
Published: October 2011

AbstractThe adoptive transfer of donor T cells that have been genetically modified to recognize leukemia could prevent or treat leukemia relapse after allogeneic HSCT (allo-HSCT). However, adoptive therapy after allo-HSCT should be performed with T cells that have a defined endogenous TCR specificity to avoid GVHD. Ideally, T cells selected for genetic modification would also have the capacity to persist in vivo to ensure leukemia eradication. Here, we provide a strategy for deriving virus-specific T cells from CD45RA−CD62L+CD8+ central memory T (TCM) cells purified from donor blood with clinical grade reagents, and redirect their specificity to the B-cell lineage marker CD19 through lentiviral transfer of a gene encoding a CD19-chimeric Ag receptor (CAR). Virus-specific TCM were selectively transduced by exposure to the CD19 CAR lentivirus after peptide stimulation, and bi-specific cells were subsequently enriched to high purity using MHC streptamers. Activation of bi-specific T cells through the CAR or the virus-specific TCR elicited phosphorylation of downstream signaling molecules with similar kinetics, and induced comparable cytokine secretion, proliferation, and lytic activity. These studies identify a strategy for tumor-specific therapy with CAR-modified T cells after allo-HSCT, and for comparative studies of CAR and TCR signaling.
Variation in chromosome copy number influences the virulence of Cryptococcus neoformans and occurs in isolates from AIDS patients
Authors: Hu Guanggan , Wang Joyce , Choi Jaehyuk , Jung Won Hee , Liu Iris , Litvintseva Anastasia P , Bicanic Tihana , Aurora Rajeev , Mitchell Thomas G , Perfect John R , Kronstad James W 
Published: October 2011

Abstract

Background
The adaptation of pathogenic fungi to the host environment via large-scale genomic changes is a poorly characterized phenomenon. Cryptococcus neoformans is the leading cause of fungal meningoencephalitis in HIV/AIDS patients, and we recently discovered clinical strains of the fungus that are disomic for chromosome 13. Here, we examined the genome plasticity and phenotypes of monosomic and disomic strains, and compared their virulence in a mouse model of cryptococcosis

Results
In an initial set of strains, melanin production was correlated with monosomy at chromosome 13, and disomic variants were less melanized and attenuated for virulence in mice. After growth in culture or passage through mice, subsequent strains were identified that varied in melanin formation and exhibited copy number changes for other chromosomes. The correlation between melanin and disomy at chromosome 13 was observed for some but not all strains. A survey of environmental and clinical isolates maintained in culture revealed few occurrences of disomic chromosomes. However, an examination of isolates that were freshly collected from the cerebrospinal fluid of AIDS patients and minimally cultured provided evidence for infections with multiple strains and copy number variation.

Conclusions
Overall, these results suggest that the genome of C. neoformans exhibits a greater degree of plasticity than previously appreciated. Furthermore, the expression of an essential virulence factor and the severity of disease are associated with genome variation. The occurrence of chromosomal variation in isolates from AIDS patients, combined with the observed influence of disomy on virulence, indicates that genome plasticity may have clinical relevance.
Systematic review of clinical trials on dietary interventions to prevent excessive weight gain during pregnancy among normal weight, overweight and obese women
Authors: Tanentsapf Ida , Heitmann Berit L , Adegboye Amanda RA 
Published: October 2011

AbstractBackgroundExcessive weight gain during pregnancy and subsequent postpartum weight retention may contribute to the epidemic of obesity among women of childbearing age. Preventing excessive gestational weight gain (GWG) to optimize maternal, fetal and infant wellbeing is therefore of great importance. A number of dietary interventions in this area has been conducted with inconsistent results, which has made it difficult to identify effective strategies to prevent excessive weight gain during pregnancy among normal weight, overweight and obese women. The primary objective of this review was to evaluate the effect of dietary interventions for reducing GWG. The secondary objective was to examine the impact of these interventions on different child and maternal health outcomes.MethodThe PUBMED, the Cochrane Central Register of Controlled Trials (CENTRAL) and the LILACS databases were searched for relevant articles. All published randomized controlled trials (RCT) and quasi-randomized controlled trials (QCT), with concurrent controls, on dietary interventions during pregnancy were considered. Results were presented using relative risk (RR) for categorical data and weighted mean difference (WMD) for continuous data. Data were primarily analyzed with a fixed-effect model and a random-effects model was used in the presence of heterogeneity. No date and language restrictions were applied.ResultsIn total, 13 studies were included in this review and 10 trials contributed data on total GWG. Dietary intervention significantly reduced total GWG (n = 1434; WMD = -1.92 kg; 95% CI = -3.65/-0.19; p = 0.03), weight retention at six months postpartum (n = 443; WMD = -1.90 kg; 95% CI = -2.69/-1.12; p < 0.0001) and incidence of cesarean section (n = 609; RR = 0.75; 95% CI = 0.60/0.94; p = 0.013). However, dietary intervention had no significant effect on weight retention at six weeks postpartum, birth weight, preeclampsia, gestational diabetes and preterm birth.ConclusionDietary advice during pregnancy appears effective in decreasing total GWG and long-term postpartum weight retention, but so far there is limited evidence for further benefits on infant and maternal health.
Comprehensive analysis of clinical significance of stem-cell related factors in renal cell cancer
Authors: Liu Yongchao , Zhang Changcun , Fan Jie , Xiao Lei , Yin Bingde , Zhou Libin , Xia Shujie 
Published: October 2011

Abstract

Background
C-MYC, LIN28, OCT4, KLF4, NANOG and SOX2 are stem cell related factors. We detected whether these factors express in renal cell carcinoma (RCC) tissues to study their correlations with the clinical and pathological characteristics.

Methods
The expressions of c-MYC, LIN28, SOX2, KLF4, OCT4 and NANOG in 30 RCC patients and 5 non-RCC patients were detected with quantitative real-time reverse transcription-PCR (qRT-PCR). The data were analyzed with Wilcoxon signed rank sum test and x2 test.

Results
In RCC group, c-MYC expression was significantly higher in RCC tissues compared with normal tissues (P < 0.05). The expression levels of OCT4, KLF4, NANOG and SOX2 were significantly lower in RCC tissues compared with normal tissues (P < 0.05). LIN28 expression level was not significant. No difference was observed when it comes to clinical and pathological characteristics such as gender, age, tumor size, cTNM classification and differentiation status (P > 0.05). Also the expression levels of all above factors were not significantly changed in non-RCC group (P > 0.05).

Conclusions
The present analysis strongly suggests that altered expression of several stem cell related factors may play different roles in RCC. C-MYC may function as an oncogene and OCT4, KLF4, NANOG and SOX2 as tumor suppressors.
High expression of HLA-E in colorectal carcinoma is associated with a favorable prognosis
Authors: Benevolo Maria , Mottolese Marcella , Tremante Elisa , Rollo Francesca , Diodoro Maria Grazia , Ercolani Cristiana , Sperduti Isabella , Monaco Elisa Lo , Cosimelli Maurizio , Giacomini Patrizio 
Published: October 2011

AbstractBackgroundHuman Leukocyte Antigen (HLA)-E is a non-classical class I HLA molecule that can be stabilized by ligands donated by other classical (HLA-A, -B, -C) and non-classical (HLA-G) family members. HLA-E engages a variety of immune receptors expressed by cytotoxic T lymphocytes (CTLs), Natural killer (NK) cells and NK-CTLs. In view of the opposing outcomes (activation or inhibition) of the different HLA-E receptors, the preferred role (if any) of HLA-E expressedin vivoon tumor cells remains to be established.MethodsTaking advantage of MEM-E/02, a recently characterized antibody to denatured HLA-E molecules, HLA-E expression was assessed by immunohistochemistry on an archival collection (formalin-fixed paraffin-embedded) of 149 colorectal primary carcinoma lesions paired with their morphologically normal mucosae. Lymphoid infiltrates were assessed for the expression of the HLA-E-specific, inhibitory, non-rearranging receptor NKG2A.ResultsHigh HLA-E expression did not significantly correlate with the expression of classical HLA-B and HLA-C molecules, but it did correlate with high expression of its preferential ligand donor HLA-A. In addition, it correlated with lymphoid cell infiltrates expressing the inhibitory NKG2A receptor, and was an independent predictor of good prognosis, particularly in a subset of patients whose tumors express HLA-A levels resembling those of their paired normal counterparts (HLA-A). Thus, combination phenotypes (HLA-Elo-int/HLA-AE and HLA-Ehi/HLA-AE) of classical and non-classical class I HLA molecules mark two graded levels of good prognosis.ConclusionsThese results suggest that HLA-E favors activating immune responses to colorectal carcinoma. They also provide evidence in humans that tumor cells entertain extensive negotiation with the immune system until a compromise between recognition and escape is reached. It is implied that this process occurs stepwise, as predicted by the widely accepted 'immunoediting' model.
Comparative analysis of the quality of a global algorithm and a local algorithm for alignment of two sequences
Authors: Polyanovsky Valery O , Roytberg Mikhail A , Tumanyan Vladimir G 
Published: October 2011

Abstract

Background
Algorithms of sequence alignment are the key instruments for computer-assisted studies of biopolymers. Obviously, it is important to take into account the "quality" of the obtained alignments, i.e. how closely the algorithms manage to restore the "gold standard" alignment (GS-alignment), which superimposes positions originating from the same position in the common ancestor of the compared sequences. As an approximation of the GS-alignment, a 3D-alignment is commonly used not quite reasonably. Among the currently used algorithms of a pair-wise alignment, the best quality is achieved by using the algorithm of optimal alignment based on affine penalties for deletions (the Smith-Waterman algorithm). Nevertheless, the expedience of using local or global versions of the algorithm has not been studied.

Results
Using model series of amino acid sequence pairs, we studied the relative "quality" of results produced by local and global alignments versus (1) the relative length of similar parts of the sequences (their "cores") and their nonhomologous parts, and (2) relative positions of the core regions in the compared sequences. We obtained numerical values of the average quality (measured as accuracy and confidence) of the global alignment method and the local alignment method for evolutionary distances between homologous sequence parts from 30 to 240 PAM and for the core length making from 10% to 70% of the total length of the sequences for all possible positions of homologous sequence parts relative to the centers of the sequences.

Conclusion
We revealed criteria allowing to specify conditions of preferred applicability for the local and the global alignment algorithms depending on positions and relative lengths of the cores and nonhomologous parts of the sequences to be aligned. It was demonstrated that when the core part of one sequence was positioned above the core of the other sequence, the global algorithm was more stable at longer evolutionary distances and larger nonhomologous parts than the local algorithm. On the contrary, when the cores were positioned asymmetrically, the local algorithm was more stable at longer evolutionary distances and larger nonhomologous parts than the global algorithm. This opens a possibility for creation of a combined method allowing generation of more accurate alignments.
Spatial and temporal dynamics of cellulose degradation and biofilm formation by Caldicellulosiruptor obsidiansis and Clostridium thermocellum
Authors: Wang Zhi-Wu , Lee Seung-Hwan , Elkins James G , Morrell-Falvey Jennifer L 
Published: October 2011

AbstractCellulose degradation is one of the major bottlenecks of a consolidated bioprocess that employs cellulolytic bacterial cells as catalysts to produce biofuels from cellulosic biomass. In this study, we investigated the spatial and temporal dynamics of cellulose degradation byCaldicellulosiruptfor obsidiansis, which does not produce cellulosomes, andClostridium thermocellum, which does produce cellulosomes. Results showed that the degradation of either regenerated or natural cellulose was synchronized with biofilm formation, a process characterized by the formation and fusion of numerous crater-like depressions on the cellulose surface. In addition, the dynamics of biofilm formation were similar in both bacteria, regardless of cellulosome production. Only the areas of cellulose surface colonized by microbes were significantly degraded, highlighting the essential role of the cellulolytic biofilm in cellulose utilization. After initial attachment, the microbial biofilm structure remained thin, uniform and dense throughout the experiment. A cellular automaton model, constructed under the assumption that the attached cells divide and produce daughter cells that contribute to the hydrolysis of the adjacent cellulose, can largely simulate the observed process of biofilm formation and cellulose degradation. This study presents a model, based on direct observation, correlating cellulolytic biofilm formation with cellulose degradation.
The draft genome and transcriptome of Cannabis sativa
Authors: van Bakel Harm , Stout Jake M , Cote Atina G , Tallon Carling M , Sharpe Andrew G , Hughes Timothy R , Page Jonathan E 
Published: October 2011

Abstract
Background
Cannabis sativa has been cultivated throughout human history as a source of fiber, oil and food, and for its medicinal and intoxicating properties. Selective breeding has produced cannabis plants for specific uses, including high-potency marijuana strains and hemp cultivars for fiber and seed production. The molecular biology underlying cannabinoid biosynthesis and other traits of interest is largely unexplored.

Results
We sequenced genomic DNA and RNA from the marijuana strain Purple Kush using shortread approaches. We report a draft haploid genome sequence of 534 Mb and a transcriptome of 30,000 genes. Comparison of the transcriptome of Purple Kush with that of the hemp cultivar 'Finola' revealed that many genes encoding proteins involved in cannabinoid and precursor pathways are more highly expressed in Purple Kush than in 'Finola'. The exclusive occurrence of Δ9-tetrahydrocannabinolic acid synthase in the Purple Kush transcriptome, and its replacement by cannabidiolic acid synthase in 'Finola', may explain why the psychoactive cannabinoid Δ9-tetrahydrocannabinol (THC) is produced in marijuana but not in hemp. Resequencing the hemp cultivars 'Finola' and 'USO-31' showed little difference in gene copy numbers of cannabinoid pathway enzymes. However, single nucleotide variant analysis uncovered a relatively high level of variation among four cannabis types, and supported a separation of marijuana and hemp.

Conclusions
The availability of the Cannabis sativa genome enables the study of a multifunctional plant that occupies a unique role in human culture. Its availability will aid the development of therapeutic marijuana strains with tailored cannabinoid profiles and provide a basis for the breeding of hemp with improved agronomic characteristics.
Prolactin as a Marker of Successful Catheterization during IPSS in Patients with ACTH-Dependent Cushing's Syndrome
Authors: Sharma S. T. , Raff H. , Nieman L. K. 
Published: October 2011

Context:
Anomalous venous drainage can lead to false-negative inferior petrosal sinus sampling (IPSS) results. Baseline inferior petrosal sinus to peripheral (IPS/P) prolactin ratio higher than 1.8 ipsilateral to the highest ACTH ratio has been proposed to verify successful catheterization. Prolactin-normalized ACTH IPS/P ratios may differentiate Cushing's disease (CD) from ectopic ACTH syndrome (EAS).

Objective:
Our objective was to examine the utility of prolactin measurement during IPSS.

Design, Setting, and Participants:
We conducted a retrospective analysis of prolactin levels in basal and CRH-stimulated IPSS samples in ACTH-dependent Cushing's syndrome (2007–2010).

Results:
Twenty-five of 29 patients had a pathologically proven diagnosis (17 CD and eight EAS). IPSS results were partitioned into true positive for CD (n = 16), true negative (n = 7), false negative (n = 1), and false positive (n = 1). Prolactin IPS/P ratio suggested successful IPSS in eight of 11 with abnormal venograms. Baseline prolactin IPS/P ratio was helpful in two patients with abnormal venograms and false-negative (catheterization unsuccessful) or true-negative (catheterization successful) IPSS results; the normalized ratio correctly diagnosed their disease. Normalized ACTH IPS/P ratio was at least 1.3 in all with CD, but prolactin IPS/P ratios were misleadingly low in two. One patient with cyclic EAS had a false-positive IPSS when eucortisolemic (baseline prolactin IPS/P = 1.7; normalized ratio = 5.6). All other EAS patients had normalized ratios no higher than 0.7.

Conclusion:
Prolactin measurement and evaluation of the venogram can improve diagnostic accuracy when IPSS results suggest EAS but is not necessary with positive IPSS results. Confirmation of hypercortisolemia remains a prerequisite for IPSS. A normalized ratio of 0.7–1.3 was not diagnostic.
A Comparative Borate Adsorption Study of Ettringite and Metaettringite
Authors: Hongo Teruhisa , Tsunashima Yusuke , Sakai Yuka , Iizuka Atsushi , Yamasaki Akihiro 
Published: October 2011

Abstract
Ettringite and metaettringite samples were used to compare adsorption capacity for borate. The metaettringite, prepared from the ettringite calcined at 175 °C, showed approximately five times higher adsorption capacity for borate.
Increased use of pre-operative imaging and laparoscopy has no impact on clinical outcomes in patients undergoing appendicectomy
Authors: Markar SR , Karthikesalingam A , Cunningham J , Burd C , Bond-Smith G , Kurzawinski TR 
Published: October 2011

INTRODUCTION The aim of this study was to review changes in the management of acute appendicitis in a ten-year period at a large university teaching hospital in London. METHODS This was a retrospective cohort study reviewing the medical records of patients who underwent an appendicectomy over a period of 12 months either in 1999 or 2009. Data collected included use of radiological investigations (ultrasonography, computed tomography [CT]), technique of appendicectomy (open [OA] or laparoscopic [LA]), operative time, histopathology and post-operative complications. Univariate and multivariate analysis was performed to assess the influence of variables on the incidence of negative appendicectomy, appendiceal perforation and post-operative complications. RESULTS All of the patients operated on in 1999 (n=109) had OA. Of the patients operated on in 2009 (n=164), 67 had OA, 91 had LA and 6 had LA converted to OA. None of the patients in 1999 had CT whereas in 2009 26% of patients had CT (sensitivity 94.7%, specificity 75.0%). This increased use of pre-operative imaging had no effect on negative appendicectomy (25.7% vs 12.8%, p=0.445), perforation (30.0% vs 21.3%, p=0.308) or complication rates (9.2% vs 10.4%). The complication rate was also similar regardless of whether patients had OA or LA (11.9% vs 9.9%). Multivariate analysis revealed that age was the only predictor of negative appendicectomy (p=0.029) or perforation (p=0.014). CONCLUSIONS This study shows that significant increase in the use of pre-operative imaging and laparoscopy in the management of patients with acute appendicitis failed to reduce negative appendicectomy, perforation and complications rates. The patient's age was the only predictor of negative appendicectomy and perforation.
Total adventitial resection of the cardia: ‘optimal local resection’ for tumours of the oesophagogastric junction
Authors: Botha AJ , Odendaal W , Patel V , Watcyn-Jones T , Mahadeva U , Chang F , Deere H 
Published: October 2011

INTRODUCTION Little is published about the local resection of oesophageal cancers. We adopted the principles of rectal cancer surgery, ie standard surgical dissection techniques as well as standard pathological processing and reporting, and assessed the feasibility of applying them to oesophagogastric junction (OGJ) cancer. METHODS Over a two-year period consecutive patients with invasive cancers of the OGJ were studied. Following staging and neoadjuvant chemotherapy (NAC), a standard dissection defined as a total adventitial resection of the cardia (TARC) was performed. Standard histopathological processing involved external inking, photographing, transverse slicing and mounting of cut samples on megablocks. Hospital morbidity and mortality as well as survival at five years' follow-up were assessed. RESULTS Forty consecutive patients had a TARC for OGJ carcinoma. Of these, 32 were offered NAC. Introducing TARC did not result in increased morbidity or mortality. Twenty-seven patients (68%) had an R0 resection that was directly related to the tumour stage and significantly related to a response to chemotherapy. Sixteen patients (42%) were alive five years after their TARC operation. CONCLUSIONS Although the adventitia of the OGJ is not as well developed as that of the rectum, TARC can be performed safely as a standardised resection for OGJ cancers. Whereas the R0 rate for early stage tumours is very high, it remains disappointingly low for T3N1 tumours despite NAC. Improved long-term survival for these advanced tumours will only be achieved with better neoadjuvant and adjuvant therapies.
Metaphors in the description of seizure experiences: Common expressions and differential diagnosis
Authors: Plug Leendert , Sharrack Basil , Reuber Markus 
Published: October 2011

AbstractThis paper explores the use of metaphorical expressions in the description of seizure experiences by patients with epilepsy and patients with psychogenic non-epileptic seizures. The paper addresses two main questions. First, what is the range of metaphorical expressions which patients use to describe their seizure experiences, and can these be related to conventional metaphors used by healthy individuals? Second, is the difference in the underlying cause of our patients' seizure experiences in any way reflected in their use of metaphorical expressions? The paper suggests that the answer to both of these questions is affirmative, which strengthens the embodiment hypothesis. Implications for our understanding of patients' experiences of seizures and of the difference between epileptic and non-epileptic seizures are also discussed.