bluuebunny/crossref_metadata_2025_split huggingface dataset:
Systematic Review of Prognostic Factors Related to Overall Survival in Patients with Stage IV Colorectal Cancer and Unresectable Metastases
Authors: Stillwell Andrew P. , Ho Yik‐Hong , Veitch Craig 
Published: December 2010

AbstractBackgroundWith the improvements in newer chemotherapeutic agents, the role of primary tumour resection in patients with stage IV colorectal cancer is controversial. In many cases primary tumour resection is still favoured as first‐line management. However, a detailed understanding of independent prognostic factors related to survival is necessary before making this decision.MethodA literature search was conducted using Medline and Embase. Studies that performed multivariate analysis on overall survival of patients with incurable stage IV colorectal cancer were included in this review.ResultsFourteen retrospective studies involving 3209 patients were included. Clinical variables analysed to consistently have independent prognostic significance for long‐term survival included the patients’ performance status (<2), volume of liver metastases (<50%), nodal stage (N0), disease‐free resection margins, and treatment with chemotherapy and/or primary tumour resection. Cancer antigen (CA) 19‐9, low albumin, elevated ALP levels, apical lymph node involvement, presence of ascites, and postoperative transfusion were each assessed by only one study and found to be independently associated with survival. Factors inconsistently reported to have independent prognostic significance were age, ASA score, preoperative CEA levels, primary tumour location, tumour size and differentiation, peritoneal dissemination, and extrahepatic metastases.ConclusionEach patient should be reviewed individually on the basis of the above independent prognostic factors before deciding to resect the primary tumour. Patients with a poor performance status, extensive hepatic metastases, and extensive nodal disease detected preoperatively are less likely to have a survival benefit. Nonsurgical approaches to manage these patients should be given careful consideration.
Unplanned Conversion to Thoracotomy During Video‐Assisted Thoracic Surgery Lobectomy does not Compromise the Surgical Outcome
Authors: Park Joon Suk , Kim Hong Kwan , Choi Yong Soo , Kim Jhingook , Shim Young Mog , Kim Kwhanmien 
Published: December 2010

AbstractBackgroundConcerns remain unresolved regarding the safety of unplanned conversion to open thoracotomy during video‐assisted thoracic surgery (VATS) lobectomy. We analyzed both early and late outcomes after thoracotomy conversion from VATS.MethodsFrom December 2003 to December 2008, a total of 738 VATS lobectomies were attempted. Among them were 34 unplanned conversions to open thoracotomy. Patient characteristics, operative data, and early and late postoperative outcomes were analyzed retrospectively.ResultsAmong the 34 conversion cases, 26 patients had lung cancer and 8 had benign lung disease. The conversion rate was 4.61%. Left and right upper lobectomies were most often associated with unplanned conversions. Conversion was classified into five groups: (1) problems related to anthracofibrosis of hilar lymph nodes in 14 patients; (2) intraoperative vessel or bronchus injury in 11 patients; (3) fused interlobar fissure in 4 patients; (4) oncologic problems, including mediastinal or hilar lymph node metastasis in 2 patients; and (5) vascular anomalies in 3 patients. There was one death due to postoperative pneumonia in a patient with multiple co‐morbidities. Two patients had an episode of pneumonia. The mean hospital stay was 10 days, and the median follow‐up period was 30.0 ± 11.47 months. Three patients with lung cancer developed recurrent disease, all of whom were found to have stage III disease. No cancer‐related death occurred. There was no significant difference in survival or recurrence between patients with conversion and those with successful VATS. However, the operating time and hospital stay were significantly longer in conversion patients.ConclusionsOur data support the claim that VATS lobectomy can be safely performed with an acceptable conversion rate. Unplanned conversion to open thoracotomy does not appear to compromise the prognosis.
Why do patients with psychosis use cannabis and are they ready to change their use?
Authors: Kolliakou Anna , Joseph Candice , Ismail Khalida , Atakan Zerrin , Murray Robin M. 
Published: December 2010

AbstractNumerous studies have shown that patients with psychosis are more likely to use illicit drugs than the general population, with cannabis being the most popular. There exists overwhelming evidence that cannabis use can contribute to the onset of schizophrenia and poor outcome in patients with established psychosis. Therefore, understanding why patients use cannabis and whether they are motivated to change their habits is important. The evidence is that patients with psychosis use cannabis for the same reasons the general population does, to ‘get high’, relax and have fun. There is little support for the ‘self‐medication’ hypothesis, while the literature points more towards an ‘alleviation of dysphoria’ model. There is a lack of research reporting on whether psychotic patients are ready to change their use of cannabis, which has obvious implications for identifying which treatment strategies are likely to be effective.
A probabilistic model of plasmid replication regulation by a combination of handcuffing, iteron number and dimerization of RepA protein.
Authors: Watve Milind , Tendulkar Gauri , Ghate Ketaki 
Published: December 2010

AbstractPlasmids are small circular DNA molecules in bacteria which replicate sharing the replication machinery with the bacterial chromosome. Since plasmids are much smaller than the chromosome, unless their replication is tightly regulated, their copy numbers can escalate quickly. A number of mechanisms of plasmid replication regulation are known in P1 plasmid of E. coli. Mechanisms such as autorepression of the replication initiator protein (RepA) and its dimerization are unable to explain copy number regulation by themselves. The number of RepA binding sites (iterons) is inversely related to copy numbers. Handcuffing of plasmids by RepA dimer is believed to be the main mechanism of arresting replication. We show here with a probabilistic model that for the handcuffing mechanism to work, a certain iteron number is critical without which handcuffing is unlikely to work. Further, RepA autorepression, dimerization, iteron number and handcuffing mechanism need to work in concert and no single mechanism in isolation is able to regulate plasmid replication effectively. The model also makes quantitative predictions that can be tested experimentally.
Congruences for the Andrews
spt
function
Authors: Ono Ken 
Published: December 2010

Ramanujan-type congruences for the Andrews
spt
(
n
) partition function have been found for prime moduli 5 ≤
ℓ
≤ 37 in the work of Andrews [Andrews GE, (2008)
J Reine Angew Math
624:133–142] and Garvan [Garvan F, (2010)
Int J Number Theory
6:1–29]. We exhibit unexpectedly simple congruences for all
ℓ
≥5. Confirming a conjecture of Garvan, we show that if
ℓ
≥5 is prime and

, then

(mod
ℓ
). This congruence gives (
ℓ
- 1)/2 arithmetic progressions modulo
ℓ
3
which support a mod
ℓ
congruence. This result follows from the surprising fact that the reduction of a certain mock theta function modulo
ℓ
, for every
ℓ
≥5, is an eigenform of the Hecke operator
T
(
ℓ
2
).
Improvements in the reconstruction of time-varying gene regulatory networks: dynamic programming and regularization by information sharing among genes
Authors: Grzegorczyk Marco , Husmeier Dirk 
Published: December 2010

Abstract
Method: Dynamic Bayesian networks (DBNs) have been applied widely to reconstruct the structure of regulatory processes from time series data, and they have established themselves as a standard modelling tool in computational systems biology. The conventional approach is based on the assumption of a homogeneous Markov chain, and many recent research efforts have focused on relaxing this restriction. An approach that enjoys particular popularity is based on a combination of a DBN with a multiple changepoint process, and the application of a Bayesian inference scheme via reversible jump Markov chain Monte Carlo (RJMCMC). In the present article, we expand this approach in two ways. First, we show that a dynamic programming scheme allows the changepoints to be sampled from the correct conditional distribution, which results in improved convergence over RJMCMC. Second, we introduce a novel Bayesian clustering and information sharing scheme among nodes, which provides a mechanism for automatic model complexity tuning.
Results: We evaluate the dynamic programming scheme on expression time series for Arabidopsis thaliana genes involved in circadian regulation. In a simulation study we demonstrate that the regularization scheme improves the network reconstruction accuracy over that obtained with recently proposed inhomogeneous DBNs. For gene expression profiles from a synthetically designed Saccharomyces cerevisiae strain under switching carbon metabolism we show that the combination of both: dynamic programming and regularization yields an inference procedure that outperforms two alternative established network reconstruction methods from the biology literature.
Availability and implementation: A MATLAB implementation of the algorithm and a supplementary paper with algorithmic details and further results for the Arabidopsis data can be downloaded from: http://www.statistik.tu-dortmund.de/bio2010.html
Contact: grzegorczyk@statistik.tu-dortmund.de; dirk@bioss.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
The Roles of ATP Synthase and the Cytochrome b
6/f Complexes in Limiting Chloroplast Electron Transport and Determining Photosynthetic Capacity
Authors: Yamori Wataru , Takahashi Shunichi , Makino Amane , Price G. Dean , Badger Murray R. , von Caemmerer Susanne 
Published: December 2010

Abstract
In C3 plants, CO2 assimilation is limited by ribulose 1,5-bisphosphate (RuBP) regeneration rate at high CO2. RuBP regeneration rate in turn is determined by either the chloroplast electron transport capacity to generate NADPH and ATP or the activity of Calvin cycle enzymes involved in regeneration of RuBP. Here, transgenic tobacco (Nicotiana tabacum ‘W38’) expressing an antisense gene directed at the transcript of either the Rieske iron-sulfur protein of the cytochrome (Cyt) b 6/f complex or the δ-subunit of chloroplast ATP synthase have been used to investigate the effect of a reduction of these complexes on chloroplast electron transport rate (ETR). Reductions in δ-subunit of ATP synthase content did not alter chlorophyll, Cyt b 6/f complex, or Rubisco content, but reduced ETR estimated either from measurements of chlorophyll fluorescence or CO2 assimilation rates at high CO2. Plants with low ATP synthase content exhibited higher nonphotochemical quenching and achieved higher ETR per ATP synthase than the wild type. The proportional increase in ETR per ATP synthase complex was greatest at 35°C, showing that the ATP synthase activity can vary in vivo. In comparison, there was no difference in the ETR per Cyt b 6/f complex in plants with reduced Cyt b 6/f content and the wild type. The ETR decreased more drastically with reductions in Cyt b 6/f complex than ATP synthase content. This suggests that chloroplast ETR is more limited by Cyt b 6/f than ATP synthase content and is a potential target for enhancing photosynthetic capacity in crops.
Serine Protease Inhibitors Specifically Defend Solanum nigrum against Generalist Herbivores but Do Not Influence Plant Growth and Development
Authors: Hartl Markus , Giri Ashok P. , Kaur Harleen , Baldwin Ian T. 
Published: December 2010

Abstract
Solanaceaeous taxa produce diverse peptide serine proteinase inhibitors (SPIs), known antidigestive defenses that might also control endogenous plant proteases. If and how a plant coordinates and combines its different SPIs for the defense against herbivores and if these SPIs simultaneously serve developmental functions is unknown. We examine Solanum nigrum's SPI profile, comprising four different active inhibitors, of which the most abundant proved to be novel, to understand their functional specialization in an ecological context. Transcript and activity characterization revealed tissue-specific and insect-elicited accumulation patterns. Stable and transient gene silencing of all four SPIs revealed different specificities for target proteinases: the novel SPI2c displayed high specificity for trypsin and chymotrypsin, while two other SPI2 homologs were highly active against subtilisin. In field and lab experiments, we found all four SPIs to display herbivore- and gene-specific defensive properties, with dissimilar effects on closely related species. However, we did not observe any clear developmental phenotype in SPI-silenced plants, suggesting that SPIs do not play a major role in regulating endogenous proteases under the conditions studied. In summary, specific single SPIs or their combinations defend S. nigrum against generalist herbivores, while the defense against herbivores specialized on SPI-rich diets requires other unknown defense mechanisms.
A Recycling-Defective Vacuolar Sorting Receptor Reveals an Intermediate Compartment Situated between Prevacuoles and Vacuoles in Tobacco
Authors: Foresti Ombretta , Gershlick David C. , Bottanelli Francesca , Hummel Eric , Hawes Chris , Denecke Jürgen 
Published: December 2010

Abstract
Plant vacuolar sorting receptors (VSRs) display cytosolic Tyr motifs (YMPL) for clathrin-mediated anterograde transport to the prevacuolar compartment. Here, we show that the same motif is also required for VSR recycling. A Y612A point mutation in Arabidopsis thaliana VSR2 leads to a quantitative shift in VSR2 steady state levels from the prevacuolar compartment to the trans-Golgi network when expressed in Nicotiana tabacum. By contrast, the L615A mutant VSR2 leaks strongly to vacuoles and accumulates in a previously undiscovered compartment. The latter is shown to be distinct from the Golgi stacks, the trans-Golgi network, and the prevacuolar compartment but is characterized by high concentrations of soluble vacuolar cargo and the rab5 GTPase Rha1(RabF2a). The results suggest that the prevacuolar compartment matures by gradual receptor depletion, leading to the formation of a late prevacuolar compartment situated between the prevacuolar compartment and the vacuole.
Key points in dermoscopic diagnosis of basal cell carcinoma and seborrheic keratosis in Japanese
Authors: TAKENOUCHI Tatsuya 
Published: December 2010

AbstractBasal cell carcinoma (BCC) and seborrheic keratosis (SK) are representative pigmented skin tumors, and they are differentiated as non‐melanocytic lesions in the two‐step dermoscopy algorithm proposed by the Consensus Net Meeting on Dermoscopy. Because most BCC in Japanese patients are pigmented clinically, dermoscopy plays an important role in their differential diagnosis. The dermoscopic criteria for BCC include the lack of a pigment network and the presence of at least one positive feature for BCC, such as large blue‐gray ovoid nests, multiple blue‐gray globules, leaf‐like areas, spoke wheel areas, arborizing vessels and ulceration. Whereas various dermoscopic features are seen in SK, comedo‐like openings, milia‐like cysts, and fissures and ridges are especially important features. It is necessary for clinicians to consider the pathological conditions causing the dermoscopic features of BCC and SK. In addition, the sensitivity and specificity of each feature should be taken into consideration to ensure an accurate dermoscopic diagnosis.
Trichoscopy for common hair loss diseases: Algorithmic method for diagnosis
Authors: INUI Shigeki 
Published: December 2010

AbstractIn recent years, the usefulness of trichoscopy (scalp dermoscopy) has been reported for hair loss diseases. Here, characteristic trichoscopic features of common hair loss diseases are described using a DermLite II pro or Epilight eight. Characteristic trichoscopic features of alopecia areata are black dots, tapering hairs (exclamation mark hairs), broken hairs, yellow dots and short vellus hairs. In androgenetic alopecia (AGA), hair diameter diversity (HDD), perifollicular pigmentation/peripilar sign and yellow dots are trichoscopically observed. In all cases of AGA and female AGA, HDD more than 20%, which corresponds to vellus transformation, can be seen. In cicatricial alopecia (CA), the loss of orifices, a hallmark of CA, and the associated changes including perifollicular erythema or scale and hair tufting were observed. Finally, an algorithmic method for trichoscopic diagnosing is proposed.
Key points in dermoscopic differentiation between lentigo maligna and solar lentigo
Authors: TANAKA Masaru , SAWADA Mizuki , KOBAYASHI Ken 
Published: December 2010

AbstractA clinical diagnosis of lentigo maligna at an early stage is often difficult even for experienced dermatologists. Differential diagnoses would include solar lentigo, early lesions of seborrheic keratosis, lichen planus‐like keratosis, pigmented actinic keratosis and melanocytic nevus. Dermoscopy has been shown to have higher diagnostic accuracy, especially in the diagnosis of pigmented skin lesions, in the past two decades. To aim of the present study was to review the diagnostic key points on dermoscopy in the published work to differentiate lentigo maligna from other differential diagnoses and reassess these important features on dermoscopy for specificity by describing the findings in detail. Diagnostic key points for lentigo maligna/lentigo maligna melanoma on dermoscopy are asymmetrical pigmented follicular openings, rhomboidal structures, annular‐granular structures and gray pseudo‐network. Lentigo maligna, at first, seems to occur as asymmetrical pigmented follicular openings and/or annular‐granular structures, then expand and develop into the rhomboidal structures. Annular‐granular structures and gray pseudo‐network seem to be observed also in regressive areas of solar lentigo/initial seborrheic keratosis, lichen planus‐like keratosis and pigmented actinic keratosis. The four important criteria on dermoscopy for the diagnosis of lentigo maligna have been reviewed, and the former two criteria seem to be more specific, but it might be difficult to recognize these findings without misinterpretation. The latter two seem to be not so specific as they would also be demonstrated in other pigmented epidermal lesions, although the distribution of the structures in these disorders would be inclined to be more homogeneous than that of lentigo maligna.
What dermoscopy tells us about nevogenesis
Authors: ZALAUDEK Iris , CATRICALÀ Caterina , MOSCARELLA Elvira , ARGENZIANO Giuseppe 
Published: December 2010

AbstractThe evolution of nevi is a complex process involving several constitutional and environmental factors. Although histopathology is the gold standard for the diagnosis and classification of melanocytic nevi, the widespread use of in vivo diagnostic technologies such as dermoscopy and more recently of reflectance confocal microscopy, has enriched profoundly our knowledge regarding the morphological variability of nevi in different stages of their evolution. In addition, significant progress has been made in our understanding of genetic alterations and molecular pathways involved in the formation of melanocytic tumors. All this newly acquired knowledge increasingly questions whether morphologically different nevi are also histiogenetically different. In this article, we intend to extract some of the salient points from published clinical and molecular studies on melanocytic tumors and attempt to assimilate them into an integrative concept of nevogenesis.
Key point in dermoscopic differentiation between early nail apparatus melanoma and benign longitudinal melanonychia
Authors: KOGA Hiroshi , SAIDA Toshiaki , UHARA Hisashi 
Published: December 2010

AbstractLongitudinal melanonychia presents in various conditions including neoplastic and reactive disorders. It is much more frequently seen in non‐Caucasians than Caucasians. While most cases of nail apparatus melanoma start as longitudinal melanonychia, melanocytic nevi of the nail apparatus also typically accompany longitudinal melanonychia. Identifying the suspicious longitudinal melanonychia is therefore an important task for dermatologists. Dermoscopy provides useful information for making this decision. The most suspicious dermoscopic feature of early nail apparatus melanoma is irregular lines on a brown background. Evaluation of the irregularity may be rather subjective, but through experience, dermatologists can improve their diagnostic skills of longitudinal melanonychia, including benign conditions showing regular lines. Other important dermoscopic features of early nail apparatus melanoma are micro‐Hutchinson’s sign, a wide pigmented band, and triangular pigmentation on the nail plate. Although there is as yet no solid evidence concerning the frequency of dermoscopic follow up, we recommend checking the suspicious longitudinal melanonychia every 6 months. Moreover, patients with longitudinal melanonychia should be asked to return to the clinic quickly if the lesion shows obvious changes. Diagnosis of amelanotic or hypomelanotic melanoma affecting the nail apparatus is also challenging, but melanoma should be highly suspected if remnants of melanin granules are detected dermoscopically.
This article has been retracted: Curcumin targets Akt cell survival signaling pathway in HTLV‐I‐infected T‐cell lines
Authors: Tomita Mariko , Matsuda Takehiro , Kawakami Hirochika , Uchihara Jun‐nosuke , Okudaira Taeko , Masuda Masato , Ohshiro Kazuiku , Mori Naoki 
Published: December 2010

This article has been retracted at the request of Editor‐in‐Chief & Author.The following article from Cancer Science: Tetsuro Nakazato, Taeko Okudaira, Chie Ishikawa, Shinji Nakama, Shigeki Sawada, Mariko Tomita, Jun‐nosuke Uchihara, Naoya Taira, Masato Masuda, Yuetsu Tanaka, Kazuiku Ohshiro, Nobuyuki Takasu, Naoki Mori. Anti‐adult T‐cell leukemia effects of a novel synthetic retinoid, Am80 (Tamibarotene), Cancer Science 2008; 99: 2286–2294, (doi: 10.1111/j.1349‐7006.2008.00917.x), published online on 1 September 2008 on Wiley Interscience (http://www.interscience.wiley.com), now Wiley Online Library (http://onlinelibrary.wiley.com/), has been retracted by agreement between the authors, the journal Editor‐in‐Chief, Yusuke Nakamura, and Blackwell Publishing Asia Pty Ltd. All authors wish to retract this paper due to inappropriate image utilization in three of the figures within the article.Yusuke Nakamura Editor‐in‐Chief Cancer Science
This article has been retracted: Epstein–Barr virus‐encoded latent membrane protein 1 activates β‐catenin signaling in B lymphocytes
Authors: Tomita Mariko , Dewan Md. Zahidunnabi , Yamamoto Naoki , Kikuchi Akira , Mori Naoki 
Published: December 2010

This article has been retracted at the request of Editor‐in‐Chief & Author.The following article from Cancer Science: Mariko Tomita, Zahidunnabi Dewan, Naoki Yamamoto, Akira Kikuchi and Naoki Mori. Epstein–Barr virus‐encoded latent membrane protein 1 activates β‐catenin signaling in B lymphocytes, Cancer Science 2009; 100: 807–812, (doi: 10.1111/j.1349‐7006.2009.01121.x), published online on 20 March 2009 on Wiley Interscience (http://www.interscience.wiley.com), now Wiley Online Library (http://onlinelibrary.wiley.com/), has been retracted by agreement between the authors, the journal Editor‐in‐Chief, Yusuke Nakamura, and Blackwell Publishing Asia Pty Ltd. All authors wish to retract this paper due to repeated use of images in the same gel in two figures within the article.Yusuke Nakamura Editor‐in‐Chief Cancer Science