bluuebunny/crossref_metadata_2025_split huggingface dataset:
The sheep genome reference sequence: a work in progress
Authors:   The International Sheep Genomics Consortium, Archibald A. L. , Cockett N. E. , Dalrymple B. P. , Faraut T. , Kijas J. W. , Maddox J. F , McEwan J. C. , Hutton Oddy V. , Raadsma H. W. , Wade C. , Wang J. , Wang W. , Xun X. 
Published: September 2010

SummaryUntil recently, the construction of a reference genome was performed using Sanger sequencing alone. The emergence of next‐generation sequencing platforms now means reference genomes may incorporate sequence data generated from a range of sequencing platforms, each of which have different read length, systematic biases and mate‐pair characteristics. The objective of this review is to inform the mammalian genomics community about the experimental strategy being pursued by the International Sheep Genomics Consortium (ISGC) to construct the draft reference genome of sheep (Ovis aries). Component activities such as data generation, sequence assembly and annotation are described, along with information concerning the key researchers performing the work. This aims to foster future participation from across the research community through the coordinated activities of the consortium. The review also serves as a ‘marker paper’ by providing information concerning the pre‐publication release of the reference genome. This ensures the ISGC adheres to the framework for data sharing established at the recent Toronto International Data Release Workshop and provides guidelines for data users.
Platanus pollen allergen, Pla a 1: quantification in the atmosphere and influence on a sensitizing population
Authors: Fernández‐González D. , González‐Parrado Z. , Vega‐Maray A. M. , Valencia‐Barrera R. M. , Camazón‐Izquierdo B. , De Nuntiis P. , Mandrioli P. 
Published: September 2010

SummaryBackground
The allergic response in susceptible patients does not always coincide with the presence and magnitude of airborne pollen counts. The prevalence of allergy to Platanus is currently moderate, although the percentage of monosensitized patients is low. This hinders accurate interpretation of the relationship between the amount of pollen inhaled and the patient's symptoms.Objective
This study aims to investigate the relationship between the atmospheric concentration pattern of Pla a 1 aeroallergen and the Platanus pollen.Methods
The pollen sampling was carried out using a Hirst‐type volumetric trap (Burkard©) for pollen grains and a Burkard Cyclone sampler (Burkard©) for Pla a 1 allergen. Serum‐specific IgE levels to Acer sp., Artemisia vulgaris, Betula alba, Chenopodium album, Cupressus arizonica, Cynodon dactylon, Fraxinus excelsior, Lolium perenne, Pinus sp., Plantago lanceolata, Platanus acerifolia, Populus sp., Quercus ilex and Taraxacum officinale allergens were determined using the EAST System (Hytec specific IgE EIA kit; Hycor Biomedical, Kassel, Germany).Results
The aerobiological dynamics of Platanus pollen grains and Pla a 1 differed considerably, particularly during the Platanus pollination period. Of the 118 subjects tested, sera from 34 contained specific IgE to Platanus pollen and all of them had specific IgE to other pollen types.Conclusions
The presence of the aeroallergen Pla a 1 in the atmosphere appears to be independent of Platanus pollen counts over the same period, which may be contributing to allergic symptoms and sensitization. The number of polysensitized patients displaying allergy to Platanus suggested that allergic symptoms were caused by co‐sensitization or cross‐reactivity involving a number of allergenic particles. Cite this as: D. Fernández‐González, Z. González‐Parrado, A. M. Vega‐Maray, R. M. Valencia‐Barrera, B. Camazón‐Izquierdo, P. De Nuntiis and P. Mandrioli, Clinical & Experimental Allergy, 2010 (40) 1701–1708.
CCL20 is overexpressed in Mycobacterium tuberculosis-infected monocytes and inhibits the production of reactive oxygen species (ROS)
Authors: Rivero-Lezcano O M , González-Cortés C , Reyes-Ruvalcaba D , Diez-Tascón C 
Published: September 2010

Summary
CCL20 is a chemokine that attracts immature dendritic cells. We show that monocytes, cells characteristic of the innate immune response, infected with Mycobacterium tuberculosis express the CCL20 gene at a much higher level than the same cells infected with non-tuberculous mycobacteria. Interferon (IFN)-γ, a fundamental cytokine in the immune response to tuberculosis, strongly inhibits both the transcription and the translation of CCL20. We have also confirmed that dendritic cells are a suitable host for mycobacteria proliferation, although CCL20 does not seem to influence their intracellular multiplication rate. The chemokine, however, down-regulates the characteristic production of reactive oxygen species (ROS) induced by M. tuberculosis in monocytes, which may affect the activity of the cells. Apoptosis mediated by the mycobacteria, possibly ROS-dependent, was also inhibited by CCL20.
The dendritic cell mannose receptor mediates allergen internalization and maturation involving notch 1 signalling
Authors: Li J , Jiang H , Wen W , Zheng J , Xu G 
Published: September 2010

Summary
Dendritic cells (DCs) have been shown recently to play a key role in inducing and mediating T helper type 2 (Th2) responses associated with atopic disease. These responses are mediated in part by ligation to different Toll-like receptors (TLRs) and C-type lectins, e.g. the mannose receptor (MR), depending upon the DC subset involved and the respective microenvironments. Because ovalbumin (OVA) (which is structurally related to various allergens) can engage the MR, we can use OVA stimulation as a model for understanding the roles of both TLRs and the MR in allergic inflammatory responses. We examined TLR- and MR-mediated responses from mouse bone marrow-derived DCs in the context of antigen recognition and presentation in addition to examining the relationship between notch 1, TLRs and MR signalling pathways. This work demonstrated that OVA-mediated signalling up-regulated both TLR-2 and MR and that MR RNA interference (RNAi) but not TLR2 RNAi inhibited DC internalization of fluorescein isothiocyanate–OVA. Furthermore, MR RNAi inhibited OVA- and house dust mite allergen extract-induced DC maturation and MR RNAi and TLR2 RNAi influenced DC interleukin-12 production independently. Finally, we demonstrated that blocking notch 1 signalling inhibited both notch 1 and TLR-2 expression but not MR expression levels. However, MR RNAi inhibited the expression of MR, TLR-2 and notch 1. These results indicate that MR is the primary receptor mediating the internalization of environmental allergen glycoproteins. In addition, TLR-2 and notch 1 play important roles in DC maturation and antigen presentation and signals originating from the MR and TLR-2 receptors converge with the notch 1 signalling pathway.
Predictors of phyllodes tumours on core biopsy specimens of fibroepithelial neoplasms
Authors: Jara‐Lazaro Ana Richelia , Akhilesh Meenakshi , Thike Aye Aye , Lui Philip Chi‐Wai , Tse Gary Man‐Kit , Tan Puay Hoon 
Published: September 2010

Jara‐Lazaro A R, Akhilesh M, Thike A A, Lui P C‐W, Tse G M‐K & Tan P H (2010) Histopathology 57, 220–232 Predictors of phyllodes tumours on core biopsy specimens of fibroepithelial neoplasms Aims:  To establish histological and biological parameters that can predict phyllodes tumours on core biopsy specimens of indeterminate fibroepithelial neoplasms.Methods and results:  Core biopsy specimens of fibroepithelial lesions diagnosed at the Department of Pathology, Singapore General Hospital from 2002 to 2007 were reviewed. Cases in which phyllodes tumour was favoured, or could not be ruled out, were evaluated for stromal cellularity/distribution, nuclear atypia and mitoses, stromal overgrowth, epithelial fronding, epithelial hyperplasia, configuration of lesional edge, presence of pseudoangiomatous stromal hyperplasia and of adipose tissue. Antibodies to Ki67, topoisomerase IIα, CD34, CD117 and Bcl‐2 were applied to sections subjected to immunohistochemistry using the streptavidin–biotin method. Findings were correlated with subsequent excisions. Of 261 core biopsy specimens of fibroepithelial lesions, 98 (37%) comprised cases in which phyllodes tumour could not be excluded and 57 (58%) had subsequent open surgical excisions. Marked stromal hypercellularity (5/5; 100%) and nuclear atypia (1/1; 100%), stromal overgrowth (17/17; 100%), mitoses ≥2/10 high‐power fields (18/18; 100%) and ill‐defined lesional borders (16/16 phyllodes tumours; 100%) were features in core biopsy specimens that exclusively predicted phyllodes tumour on excision. Moderate stromal hypercellularity (20/27 phyllodes tumours; 74%), stromal overgrowth, moderate nuclear atypia (14/16 phyllodes tumours; 87%), pseudoangiomatous stromal hyperplasia (19/23 phyllodes tumours; 83%) significantly correlated with their subsequent excisions. Immunohistochemical markers Ki67 ≥5% and topoisomerase IIα≥5%, and reduced or patchy CD34 on core biopsy specimens correlated significantly with a diagnosis of phyllodes.Conclusions:  Stromal hypercellularity, combined with key histological features and immunohistochemical markers Ki67, topoisomerase IIα and CD34, reinforced by clinical findings, can predict phyllodes tumours on core biopsy specimens.
Drought increases freezing tolerance of both leaves and xylem of Larrea tridentata
Authors: MEDEIROS JULIANA S. , POCKMAN WILLIAM T. 
Published: September 2010

ABSTRACTDrought and freezing are both known to limit desert plant distributions, but the interaction of these stressors is poorly understood. Drought may increase freezing tolerance in leaves while decreasing it in the xylem, potentially creating a mismatch between water supply and demand. To test this hypothesis, we subjected Larrea tridentata juveniles grown in a greenhouse under well‐watered or drought conditions to minimum temperatures ranging from −8 to −24 °C. We measured survival, leaf retention, gas exchange, cell death, freezing point depression and leaf‐specific xylem hydraulic conductance (kl). Drought‐exposed plants exhibited smaller decreases in gas exchange after exposure to −8 °C compared to well‐watered plants. Drought also conferred a significant positive effect on leaf, xylem and whole‐plant function following exposure to −15 °C; drought‐exposed plants exhibited less cell death, greater leaf retention, higher kl and higher rates of gas exchange than well‐watered plants. Both drought‐exposed and well‐watered plants experienced 100% mortality following exposure to −24 °C. By documenting the combined effects of drought and freezing stress, our data provide insight into the mechanisms determining plant survival and performance following freezing and the potential for shifts in L. tridentata abundance and range in the face of changing temperature and precipitation regimes.
Living related liver transplant following bone marrow transplantation from same donor: Long‐term survival without immunosuppression
Authors: Granot E. , Loewenthal R. , Jakobovich E. , Gazit E. , Sokal E. , Reding R. 
Published: September 2010

Granot E, Loewenthal R, Jakobovich E, Gazit E, Sokal E, Reding R. Living related liver transplant following bone marrow transplantation from same donor: Long‐term survival without immunosuppression.  Pediatr Transplantation 2012: 16: E1–E4. © 2010 John Wiley & Sons A/S.Abstract:  We report long‐term (seven yr) immunological tolerance in a 16‐yr‐old boy, to a liver allograft donated by his father following a bone marrow transplant at age 2.5 yr from the same donor. The bone marrow transplant was complicated by severe GVHD leading to liver failure and the ensuing need for a liver transplant, performed under planned avoidance of immunosuppression. At one wk post‐transplant, although a liver biopsy was histologically compatible with acute rejection, favorable clinical and biochemical evolution precluded initiating immunosuppressive therapy, thus highlighting the need for caution when interpreting early histological changes so that administration of unnecessary immunosuppression can be avoided. Induction of tolerance in transplant recipients remains an elusive goal. In those patients who had received conventional bone marrow transplants and had endured the consequences of GVHD, development of macrochimerism may allow immunosuppression‐free solid organ transplantation from the same donor.
Impact of high‐consistency area evaluated under hand‐operated transrectal compression using a sonographic probe on prostate cancer detection: Clinicopathological analysis
Authors: Minagawa Tomonori , Murata Yasushi , Uehara Takeshi , Imamura Tetsuya , Ishizuka Osamu 
Published: September 2010

AbstractAim of this investigation was to determine whether the evaluation of a new dynamic finding on conventional greyscale transrectal ultrasonography (TRUS), which we named as high‐consistency area (HCA), is useful in detection of prostate cancer (PCa). Fifty‐one consecutive patients were prospectively enrolled in this study. When TRUS‐guided prostate biopsy was performed, HCA that was difficult to transform, due to transrectal compression using sonographic probe, was evaluated. HCA‐targeting biopsy, digital rectal examination (DRE)‐targeting biopsy and systematic 12‐core biopsy were performed. All biopsy cores were diagnosed histopathologically. As the results, twenty‐three PCas were detected in 51 patients. The sensitivity and specificity of HCA‐targeting biopsy for correct diagnosis were 60.9% and 78.6%, respectively. The sensitivity and specificity for DRE‐targeting biopsy were 47.8% and 78.6%, respectively. In conclusion, HCA‐targeting biopsy of this study was superior to DRE‐targeting biopsy with regard to detection of PCa. Before prostate biopsy, patients should be evaluated for DRE and HCA, and DRE and HCA‐targeting biopsy should be performed.
Twenty‐nine Leydig cell tumors: Histological features, outcomes and implications for management
Authors: Heer Rakesh , Jackson Matthew J , El‐Sherif Amira , Thomas David J 
Published: September 2010

AbstractLeydig cell tumors are the most common interstitial neoplasm of the testes. Metastatic progression is historically quoted at over 10%, fuelling uncertainty as to the safety of testis sparing surgery. Between June 1998 and March 2009, 29 patients underwent surgery for Leydig cell tumor of the testis in our cancer network. We reviewed their histological features and clinical outcomes. Four patients with sub‐5 millimetre lesions underwent testis sparing surgery and 25 were treated with radical orchidectomy. Histopathological characteristics that have been linked with risk of malignant progression were seen infrequently in our cohort: diameter greater than 50 mm, 0%; nuclear atypia, 14%; >3 mitoses per 10 high‐power fields, 3%; infiltrative borders, 10%; necrosis, 3%; and vascular invasion 0%. No patient developed local or distant recurrent disease over a median follow up of 49 months, including seven and four patients disease‐free at 5 and 10 years, respectively. The rate of metastatic progression is likely to be significantly less than 10%. Our data suggest that, in the absence of high‐risk histopathological features, this tumor can be safely regarded as benign, pending a longer‐term follow‐up evaluation.
Suppression of Plasma Glutathione Peroxidase Activity by Ifosfamide*
Authors: Saito Goichi , Yoshimura Shinichi , Iwasaki Katsuhiko , Kuroshima Yoshio , Moriuchi Tetsuya 
Published: September 2010

AbstractPlasma glutathione peroxidase (GPx) is synthesized predominantly in the kidneys. Plasma‐GPx activities were measured in 12 patients with gynecological malignancies before and after chemotherapy. The patients were treated with cisplatin alone (P); with VP16 and cisplatin (EP); with cyclophosphamide, doxorubicin, and cisplatin (CAP); or with ifosfamide, doxorubicin, and cisplatin (IAP). The protein levels of the enzyme were semi‐quantitatively determined by immuno‐blot analysis. Plasma GPx activity was decreased by an average of 61% (p < 0.01) in patients treated with IAP, while no significant decreases were observed in patients treated with any drug combinations without ifosfamide. Immuno‐blot analysis of plasma samples from a patient treated with IAP revealed no differences in the protein levels of plasma GPx either before or after IAP administration, although the plasma GPx activity decreased 83%, from 0.173 to 0.029 units/m/. The results indicate that the decrease in plasma GPx activity was not due to impaired production of the enzyme in the kidneys, and that ifosfamide is responsible for inhibition of the enzyme activity. Since GPx is an enzyme of major importance in detoxification of lipid peroxides in the brain, CNS toxicity induced by ifosfamide might be related to severe suppression of plasma GPx activity.
Dynamic changes in anger, externalizing and internalizing problems: attention and regulation
Authors: Kim Jungmeen , Deater‐Deckard Kirby 
Published: September 2010

Background:  Low levels of dispositional anger and a good attention span are critical to healthy social emotional development, with attention control reflecting effective cognitive self‐regulation of negative emotions such as anger. Using a longitudinal design, we examined attention span as a moderator of reciprocal links between changes in anger and changes in externalizing and internalizing problems from 4.5 to 11 years of age.Method:  Participants were children from the Study of Early Child Care and Youth Development (SECCYD), assessed four times between 4.5 and 11 years. Composite scores for anger and attention were computed using indicators from multiple informants. Externalizing and internalizing problems were reported by mothers.Results:  Latent difference score analysis showed reciprocal lagged effects between increased anger and elevated levels of externalizing or internalizing problems. Significant moderating effects of attention indicated more persistent effects of anger on externalizing problems in the poor attention group. Although the poor and the good attention groups did not differ regarding the effects of anger on internalizing problems, significant moderating effects of attention indicated stronger and more persistent reciprocal effects of internalizing problems on anger in the poor attention group.Conclusions:  Attention control mechanisms are involved in self‐regulation of anger and its connections with changes in behavioral and emotional problems. Strong attention regulation may serve to protect children with higher levels of dispositional anger from developing behavioral and emotional problems in middle childhood.
Thickness of the middle trapezius muscle measured by rehabilitative ultrasound imaging: description of the technique and reliability study
Authors: Bentman Susanna , O’Sullivan Cliona , Stokes Maria 
Published: September 2010

SummaryA technique is described for measuring the thickness of the middle trapezius muscle using rehabilitative ultrasound imaging (RUSI). A test–retest study was employed to investigate the reliability of the technique in a convenience sample of 16 asymptomatic participants aged 20–41  (12 women). The middle trapezius muscle was imaged using RUSI with participants in a standardized sitting position. The principal investigator took measurements on two consecutive days to examine intra‐rater reliability, and two additional investigators took measurements on the second day to investigate inter‐rater reliability of the measurement technique. Reliability was examined using intra‐class correlation coefficients (ICC), standard error of measurement (SEM), and Bland and Altman plots. The results demonstrated that inter‐rater reliability was good between raters (ICC2,3 = 0·81, SEM = 0·94 mm) and was moderate for the same rater between days (ICC3,2 = 0·67, SEM = 1·0 mm). This study demonstrates that RUSI can be used reliably to measure muscle thickness of the middle trapezius muscle following the procedure described.
The Trade‐Off between Costs and Outcomes: The Case of Acute Myocardial Infarction
Authors: Schreyögg Jonas , Stargardt Tom 
Published: September 2010

Objective. To investigate and to quantify the relationship between hospital costs and health outcomes for patients with acute myocardial infarction (AMI) in Veterans Health Administration (VHA) hospitals using individual‐level data for costs and outcomes.Data Sources. VHA administrative files for the fiscal years 2000–2006.Study Design. Costs were defined as costs incurred during the index hospitalization for treatment of AMI. Mortality and readmission, assessed 1 year after the index hospitalization, were used as measures of clinical outcome. We examined health outcomes as a function of costs and other patient‐level and hospital‐level characteristics using a two‐stage Cox proportional hazard model that accounted for competing risks within a multilevel framework. To control for patient comorbidities, we compiled a comprehensive list of comorbidities that have been found in other studies to affect mortality and readmissions.Principal Findings. We found that costs were negatively associated with mortality and readmissions. Every U.S.$100 less spent is associated with a 0.63 percent increase in the hazard of dying and a 1.24 percent increase in the hazard to be readmitted conditional on not dying. This main finding remained unchanged after a number of sensitivity checks.Conclusions. Our results suggest that there is a trade‐off between costs and outcomes. The negative association between costs and mortality suggests that outcomes should be monitored closely when introducing cost‐containment programs. Additional studies are needed to examine the cost–outcome relationship for conditions other than AMI to see whether our results are consistent.
No‐Reflow Phenomenon Following Percutaneous Coronary Intervention for Acute Myocardial Infarction: Incidence, Outcome, and Effect of Pharmacologic Therapy
Authors: REZKALLA SHEREIF H. , DHARMASHANKAR KODLIPET C. , ABDALRAHMAN IHAB B. , KLONER ROBERT A. 
Published: September 2010

Background: No‐reflow (NR) phenomenon is a well‐known problem, often accompanying percutaneous coronary intervention for acute ST elevation myocardial infarction (STEMI). There are little data on effects of pharmacologic therapy on the resolution, outcome, and long‐term natural history of NR.
Objective: Retrospectively assess incidence, management, and prognosis of NR in a tertiary referral hospital.
Methods: Study included patients with STEMI, treated with percutaneous coronary intervention (PCI). Effect of pharmacologic therapy and long‐term outcome were assessed. NR was defined by thrombolysis in myocardial infarction (TIMI) < 3 or myocardial blush grade (MBG) < 3.
Results: Of 347 identified subjects, NR occurred in 110 (32%) by TIMI and 198 (57%) by MBG. Higher incidence was identified in men versus women (34% vs. 25% by TIMI, P = 0.08; and 60% vs. 48% by MBG, P = 0.04). Pharmacologic therapy was equally effective in restoring normal flow, increasing TIMI score from 1.62 ± 0.07 to 2.78 ± 0.06 (P < 0.0001) and MBG score from 0.43 ± 0.08 to 2.09 ± 0.11 (P < 0.0001). Twenty‐three percent who did not receive pharmacologic therapy developed clinical composite of congestive heart failure, cardiogenic shock, and/or death; only 9% of patients who received pharmacologic therapy developed this composite. Patients with severe NR despite treatment had poorer prognosis. Sixty‐five percent of patients who survived and had repeat angiogram about 1.5 years later had spontaneous improvement in coronary flow by MBG.
Conclusion: NR is common in STEMI. Treatment with nicardipine, nitroprusside, and verapamil are equally effective in improving flow. If not treated, prognosis is poor. (J Interven Cardiol 2010;23:429–436)