bluuebunny/crossref_metadata_2025_split huggingface dataset:
STEPS: efficient simulation of stochastic reaction–diffusion models in realistic morphologies
Authors: Hepburn Iain , Chen Weiliang , Wils Stefan , De Schutter Erik 
Published: May 2012

Abstract

Background
Models of cellular molecular systems are built from components such as biochemical reactions (including interactions between ligands and membrane-bound proteins), conformational changes and active and passive transport. A discrete, stochastic description of the kinetics is often essential to capture the behavior of the system accurately. Where spatial effects play a prominent role the complex morphology of cells may have to be represented, along with aspects such as chemical localization and diffusion. This high level of detail makes efficiency a particularly important consideration for software that is designed to simulate such systems.

Results
We describe STEPS, a stochastic reaction–diffusion simulator developed with an emphasis on simulating biochemical signaling pathways accurately and efficiently. STEPS supports all the above-mentioned features, and well-validated support for SBML allows many existing biochemical models to be imported reliably. Complex boundaries can be represented accurately in externally generated 3D tetrahedral meshes imported by STEPS. The powerful Python interface facilitates model construction and simulation control. STEPS implements the composition and rejection method, a variation of the Gillespie SSA, supporting diffusion between tetrahedral elements within an efficient search and update engine. Additional support for well-mixed conditions and for deterministic model solution is implemented. Solver accuracy is confirmed with an original and extensive validation set consisting of isolated reaction, diffusion and reaction–diffusion systems. Accuracy imposes upper and lower limits on tetrahedron sizes, which are described in detail. By comparing to Smoldyn, we show how the voxel-based approach in STEPS is often faster than particle-based methods, with increasing advantage in larger systems, and by comparing to MesoRD we show the efficiency of the STEPS implementation.

Conclusion
STEPS simulates models of cellular reaction–diffusion systems with complex boundaries with high accuracy and high performance in C/C++, controlled by a powerful and user-friendly Python interface. STEPS is free for use and is available at http://steps.sourceforge.net/
Oral Ezatiostat HCl (TLK199) and Myelodysplastic syndrome: A case report of sustained hematologic response following an abbreviated exposure
Authors: Quddus Fahd , Clima Jessica , Seedham Helen , Sajjad Ghulam , Galili Naomi , Raza Azra 
Published: May 2012

Abstract
Treatment options for patients with lower risk non-del(5q) myelodysplastic syndromes (MDS) who fail erythroid stimulating agents are restricted to one of the hypomethylating drugs with an expected response rate of ~50%. Ezatiostat HCl, an agent with the potential for producing multi-lineage responses in this population is currently in clinical investigation phase. This case report describes a 77 year old male who received less than two cycles of therapy with ezatiostat HCl which had to be aborted due to intolerable side effects, but which produced a sustained normalization of all three blood counts. This trilineage response has now lasted for more than a year. Interestingly, the patient began with a del(5q) abnormality and responded briefly to lenalidomide. Upon relapse of the anemia, a bone marrow showed the disappearance of the del(5q) but the appearance of a new clonal abnormality t(2;3). Given that the patient had a complete cytogenetic response to a truncated exposure to lenalidomide followed by a trilineage response to an even briefer course of ezatiostat HCl suggests a potential role for ezatiostat HCl in del(5q) patients who relapse following lenalidomide.
Current research in perineural invasion of cholangiocarcinoma
Authors: Shen Fang-Zhen , Zhang Bing-Yuan , Feng Yu-Jie , Jia Zhuo-Xia , An Bing , Liu Chang-Chang , Deng Xi-Yun , Kulkarni Anil D , Lu Yun 
Published: May 2012

Abstract

Background
Perineural invasion is a common path for cholangiocarcinoma (CCA) metastasis, and it is highly correlated with postoperative recurrence and poor prognosis. It is often an early event in a disease that is commonly diagnosed in advanced stages, and thus it could offer a timely therapeutic and diagnostic target if better understood. This article systematically reviews the progress of CCA neural invasion-related molecules.

Methods
Studies were identified by searching MEDLINE and PubMed databases for articles from January 1990 to December 2009, using the keywords "cholangiocarcinoma," "perineural invasion," "nerve growth factor"(NGF), "neural cell adhesion molecule" (NCAM), "matrix metalloproteinase"(MMP), "neurotransmitter," "acetylcholine" (Ach), and "transforming growth factor" (TGF)." Additional papers and book chapters were identified by a manual search of references from the key articles.

Results
From above we found that the molecules NGF, NCAM, MMP, Ach and TGF may have prognostic significance in, and offer clues to the mechanism of CCA neural invasion.

Conclusions
Cholangiocarcinoma's increasing worldwide incidence is especially poignant in view of both the lacking effective therapies, and the fact that it is commonly diagnosed in advanced stages. As CCA neural invasion often appears early, more complete characterization of its molecular pathology could lead to the identification of targets for the diagnosis and therapy of this devastating malignancy.
Survey of HNPCC Management Analysis of Responses from 18 International Cancer Centres
Authors: Chow Elizabeth , Macrae Finlay , Burn John ,   respondents from 18 international ICG-HNPCC Familial Cancer Clinics
Published: May 2012

Abstract
Eighteen international cancer centres responded to a questionnaire designed to determine clinic practices regarding the management of Hereditary Non-Polyposis Colorectal Cancer (HNPCC). Areas covered include definition, clinical intakes, pre-genetic testing for microsatellite instability (MSI) or expression of mismatch repair (MMR) genes by immunohistochemistry (IHC), mutational analysis, consent practices, counselling, surveillance planning, and surgical decision making. In the absence of a firm evidence base, some management practices were variable, with local access to funding and other resources being influential. More consistent responses were evident for management practices with a stronger evidence base from previous clinical research. This document provides important information to guide the management of HNPCC patients, allow comparisons to be made between the approaches of various clinics to HNPCC families, and define management issues that need to be addressed in clinical research.
Hereditary Colorectal Cancer Syndromes in Hong Kong: a Registry's Perspective
Authors: Ho Judy WC , Wei Rockson , Chan Emily MS 
Published: May 2012

Abstract
Established in 1995, the Hereditary Gastrointestinal Cancer Registry aimed at cancer prevention due to hereditary colorectal cancer syndromes in Hong Kong through early detection, timely treatment, education and ongoing research. This article details the history, structure and work of the Registry. A summary is also provided on the results of various research work conducted by the Registry which facilitates the clinical management of hereditary colorectal cancer syndromes in Hong Kong Chinese families.
Hereditary Colorectal Cancer in China
Authors: Shu Zheng , Yanqin Huang , Ying Yuan 
Published: May 2012

AbstractThe purpose of this article is to review basic research as well as clinical studies on Chinese hereditary colorectal cancer. Hereditary nonpolyposis colorectal cancer (HNPCC, Lynch syndrome) accounts for 2.2% of all colorectal cancer, and Chinese criteria for suspected HNPCC have been developed. Germline mutations as well as large genomic rearrangements of mismatch repair (MMR) genes are responsible for this syndrome. Gastric cancer is the second most common cancer in Chinese HNPCC patients. Contrary to sporadic colorectal cancer in the Chinese population, HNPCC does not typically present with rectal cancer. Incidence of familial adenomatous polyposis (FAP) in China is approximately 1.5/100,000. Polyps in Chinese FAP patients can emerge as early as 16 months old, but malignant transformation usually occurs in the third and fourth decade. Total resection of the colon and rectum is necessary in FAP patients. For unresectable duodenal polyps, chemopreventive agents may be used.
Quorums-based Replication of Multimedia Objects in Distributed Systems
Authors: Ohkawara Tadateru , Aikebaier Ailixier , Enokido Tomoya , Takizawa Makoto 
Published: May 2012

Abstract
Background
Multimedia objects like music and movies are distributed to peers through downloading and caching in peer-to-peer (P2P) overlay networks. In this paper, we consider multimedia objects which are characterized in terms of not only data structure but also quality of service (QoS) like frame rate and number of colours. For example, there are a pair of replicas o
i
and o
j
of a fully coloured movie object o. Here, a content of a replica o
i
is changed by adding a subobject but another replica o
j
is not changed. On the other hand, the colour of the replica o
j
is changed with monochromatic one but not in the replica o
i
. This means, the replica o
i
is newer than the replica o
j
with respect to the content but is older than o
j
with respect to QoS. Thus, replicas of a multimedia object are partially ordered in terms of newness of not only content but also QoS parameters.

Methods
In traditional quorum-based (QB) protocols, replicas are totally ordered just in terms of newness of content. We discuss a multimedia quorum-based (MQB) protocol to synchronize multiple replicas to make consistent on the basis of the newness-precedent relation of replicas. Here, the replicas are ordered in vectors of version counters of content and QoS parameters. Every replica in a quorum is not updated for QoS operations to reduce the communication overhead. We evaluate the MQB protocol in terms of communication overhead and show the communication overhead can be reduced in the MQB protocol compared with the traditional QB protocol.

Conclusions
We discussed the multimedia quorum-based (MQB) protocol to keep replicas of a multimedia object mutually consistent. We evaluated the MQB protocol in terms of the total volume of data transmitted among the replicas. Then, we showed the total amount of data transmitted can be reduced in the MQB protocol compared with the traditional quorum-based (QB) protocol.
Fueling the flame: bioenergy couples metabolism and inflammation
Authors: Liu Tie Fu , Brown Candice M , El Gazzar Mohamed , McPhail Linda , Millet Patrick , Rao Anuradha , Vachharajani Vidula T , Yoza Barbara K , McCall Charles E 
Published: May 2012

Abstract
Review on how the integration of bioenergetics and metabolism controls inflammation progression.
We review the emerging concept that changes in cellular bioenergetics concomitantly reprogram inflammatory and metabolic responses. The molecular pathways of this integrative process modify innate and adaptive immune reactions associated with inflammation, as well as influencing the physiology of adjacent tissue and organs. The initiating proinflammatory phase of inflammation is anabolic and requires glucose as the primary fuel, whereas the opposing adaptation phase is catabolic and requires fatty acid oxidation. The fuel switch to fatty acid oxidation depends on the sensing of AMP and NAD+ by AMPK and the SirT family of deacetylases (e.g., SirT1, -6, and -3), respectively, which couple inflammation and metabolism by chromatin and protein reprogramming. The AMP-AMPK/NAD+-SirT axis proceeds sequentially during acute systemic inflammation associated with sepsis but ceases during chronic inflammation associated with diabetes, obesity, and atherosclerosis. Rebalancing bioenergetics resolves inflammation. Manipulating cellular bioenergetics is identifying new ways to treat inflammatory and immune diseases.
Benign regional lymph nodes in gastric cancer on multidetector row CT
Authors: Park Hee Sun , Kim Young Jun , Ko Su Yeon , Yoo Moon-Won , Lee Kyung Yung , Jung Sung-Il , Jeon Hae Jeong 
Published: May 2012

Background Benign regional lymph nodes (LNs) are sometimes enlarged in gastric cancer patients due to reactive or inflammatory changes. Frequently these enlarged LNs can mimic LN metastasis and lead to overstaging. Purpose To assess frequency of benign regional LNs in gastric cancer patients compared with that in a healthy population and to assess the frequency of benign regional LNs in gastric cancer according to T-staging. Material and Methods Between August 2005 and June 2009, 177 patients with surgically proven gastric cancer without LN metastasis (T anyN0M0) who had previously undergone preoperative multidetector row CT (MDCT) and 168 healthy patients who visited the healthcare center and underwent an abdominal MDCT were included in this retrospective study. An abdominal radiologist evaluated the distribution of regional LNs and measured the short diameter of LNs ≥6 mm, ≥8 mm, and ≥10 mm. The number of enlarged benign LNs was compared between the two groups, and the distribution of LN with regard to T-stage of gastric cancer was also evaluated. Results At least one LN ≥6 mm, ≥8 mm, and ≥10 mm was detected in 64.4% (114/177), 22.0% (39/177), and 4.0% (7/177) of patients in the gastric cancer group, respectively, compared to 29.8% (50/168), 4.2% (7/168), and 0% of patients in the healthy group, respectively. The difference between the two groups was statistically significant ( P <0.0001). The LN ≥8 mm was found in 14.9% (20/134) in early gastric cancer (T1), and 44.2% (19/43) in advanced cancer (T2 or higher); the difference was statistically significant ( P = 0.0002). However, the frequency of LN ≥6 mm in mucosal cancer (T1a) and submucosal cancer (T2b) was not significantly different, regardless of its size. Conclusion Benign regional LNs ≥6 mm are more frequently detected in gastric cancer patients than in a healthy population and in advanced gastric cancer than in early cancer.
Impacts of Family Size on the Family as a Whole: Evidence from the Developing World
Authors: Cáceres-Delpiano Julio 
Published: May 2012

Abstract
Using multiple births as an Instrumental Variable (IV) for family size and data for 43 developing countries, I find evidence that a shock in fertility has a cost for a family as a whole. Mothers are more likely to live in less stable family arrangements and they are more likely to use contraceptives. Children are less likely to receive some vaccines, attend school, and live with their mothers. The analysis by level of development reveals the cost of fertility is driven by countries with lower levels of development.
The Millennium Development Program: Poised to Miss 2015 Dead Line
Authors: Ahmed Siraj U. 
Published: May 2012

AbstractThe attached article provides a comprehensive analysis of the UN Millennium Development Program that was implemented to reduce poverty around the globe. It first describes what the program itself is and then explores each of program goals by each region in the globe. It also provides author's suggestions into how improvements can be made in certain areas that have been struggling after the author has provided the reasons for the struggle.
Low Expectations: Reference‐Dependent Preferences and Labor Supply in Cape Town, South Africa
Authors: Spears Dean 
Published: May 2012

AbstractReference‐dependent decision‐making — the core of behavioral economics' prospect theory — makes people more likely to choose an outcome that they expect to receive. Reference‐dependence therefore may imply the perpetuation of disadvantage: people who do not expect an opportunity may be less likely to “seize the day” if one unexpectedly arrives. We find evidence of this possibility in labor supply decision‐making in two datasets about a high‐unemployment part of Cape Town, South Africa, including a panel. People with low expectations for finding a job — that is, people who expect to be unemployed — are less likely to report accepting several hypothetical job offers. This result is robust to a range of respecifications, including adding a range of control variables for desire and ability to work, including reservation wages. The finding appears to arise according to the theorized mechanisms. To our knowledge, this is the first indication of reference‐dependent labor supply in a developing country, where especially low expectations could have particularly important consequences.
Conditional Cash Transfers in Latin America and Anti‐Poverty Policies in Chile: Why is Chile's Market Economy Unable to Reduce Poverty and Inequality?
Authors: Borzutzky Silvia 
Published: May 2012

AbstractThe purpose of this paper is to provide a brief overview of Conditional Cash Transfers (CCTs) in Latin America and to assess Chile's anti‐poverty policies, including Chile Solidario and the Ethical Wage. The paper has a summary evaluation of the most important CCTs in Latin America, an analysis of the nature and limited impact of Chile Solidario, a discussion of poverty and vulnerability in Chile, and the Ethical Wage approach pursued by the Piñera administration The paper concludes by questioning the capacity of market oriented approaches to poverty reduction and argues that because poverty is a multifaceted situation, poverty reduction requires a multidimensional approach that includes at the very least educational, employment and labor policies.
Uric acid biorhythm, a feature of long-term variation in a clinical laboratory database
Authors: de Andrade Mauricio Pacheco , Hirata Rosario D.C. , Sandrini Fabiano , Largura Alvaro , Hirata Mario Hiroyuki 
Published: May 2012

AbstractThe biorhythm of serum uric acid was evaluated in a large sample of a clinical laboratory database by spectral analysis and the influence of the gender and age on uric acid variability.Serum uric acid values were extracted from a large database of a clinical laboratory from May 2000 to August 2006. Outlier values were excluded from the analysis and the remaining data (n=73,925) were grouped by gender and age ranges. Rhythm components were obtained by the Lomb Scargle method and Cosinor analysis.Serum uric acid was higher in men than in women older than 13 years (p<0.05). Compared with 0–12 year group, uric acid increased in men but not in women older than 13 years (p<0.05). Circannual (12 months) and transyear (17 months) rhythm components were detected, but they were significant only in adult individuals (>26 years, p<0.05). Cosinor analysis showed that midline estimating statistic of rhythm (MESOR) values were higher in men (range: 353–368 μmol/L) than in women (range: 240–278 μmol/L; p<0.05), independent of the age and rhythm component. The extent of predictable change within a cycle, approximated by the double amplitude, represented up to 20% of the corresponding MESOR.Serum uric acid biorhythm is dependent on gender and age and it may have relevant influence on preanalytical variability of clinical laboratory results.
Characterisation of a highly sensitive troponin I assay and its application to a cardio-healthy population
Authors: Koerbin Gus , Tate Jill , Potter Julia M. , Cavanaugh Juleen , Glasgow Nicholas , Hickman Peter E. 
Published: May 2012

AbstractAbbott Diagnostics have developed a new highly sensitive troponin I (hs-TnI) assay. We have assessed its analytical characteristics and applied the assay to a population of apparently cardio-healthy persons.We assessed imprecision, bias compared to the previous generation assay, matrix effects, and interferences and applied the assay to an apparently healthy population, deriving the 99th percentile limit of the distribution of values in reference populations for men and women separately.The dynamic range of the assay was ranged from 0.5–50,000 ng/L (pg/mL). The 10% CV was at a concentration of 3.9 ng/L, and the 20% CV was at a concentration of 1.8 ng/L. The new and current version of the TnI assay were highly correlated [slope: 0.98 (95%CI:0.88–1.07),This new hs-TnI assay is able to measure to an order of magnitude lower than the current generation TnI assay from the same manufacturer. With TnI being detectable in nearly all apparently healthy subject samples this suggests that TnI presence does not always indicate cardiomyocyte necrosis.
The concentration of adiponectin in breast milk is related to maternal hormonal and inflammatory status during 6 months of lactation
Authors: Ozarda Yesim , Gunes Yeliz , Tuncer Gul Ozlem 
Published: May 2012

AbstractVarying concentrations of adiponectin are present in human breast milk. This study aimed to determine the relationship between milk adiponectin concentration and the hormonal and inflammatory status of breast-feeding women.Blood and breast milk samples were collected from 157 breast-feeding women enrolled at 1–180 post-partum lactation days. The milk and serum adiponectin concentrations were measured by radioimmunoassays. The serum oestradiol, prolactin, thyroxine, triiodothyronine, cortisol and insulin concentrations were measured by the chemiluminescent immunometric method. The leptin, resistin and ghrelin concentrations were measured by the immunometric methods.The milk, but not serum, adiponectin concentration increased during the 180-day lactation period and displayed a positive correlation (r=0.748; p<0.001) to the lactation day. The milk adiponectin concentration was positively correlated to the maternal serum ghrelin concentration (r=0.299; p<0.001) and inversely to the maternal serum oestradiol (r=–0.366; p<0.001), prolactin (r=–0.444; p<0.001), thyroxine (r=–0.355; p<0.001), triiodothyronine (r=–0.291; p<0.001), cortisol (r=–0.537; p<0.001), and C-reactive protein (r=–0.483; p<0.001) concentrations. The milk adiponectin concentration was positively correlated to the milk leptin (r=0.344; p<0.001) and ghrelin (r=0.458; p<0.001) concentrations, and inversely to milk resistin concentration (r=–0.518; p<0.001). The serum adiponectin concentration in breastfed infants was positively correlated (r=0.711; p<0.001) to the adiponectin concentration in the consumed breast milk.The adiponectin concentration in breast milk increases over time during lactation and is affected by the maternal hormonal and inflammatory status.
Haematological and iron metabolism parameters in professional cyclists during the Giro d’Italia 3-weeks stage race
Authors: Corsetti Roberto , Lombardi Giovanni , Lanteri Patrizia , Colombini Alessandra , Graziani Rosella , Banfi Giuseppe 
Published: May 2012

AbstractHaematological assessment is crucial for evaluating athletes healthy status. Professional athletes experience physiological modifications during competitions and over a season: the risk of sports anaemia is high. Few descriptions of haematological parameters behaviour during a 3-weeks cycling stage race have been published.We studied nine professional cyclists engaged in the 2011Haemoglobin, red blood cells and haematocrit decreased during the race with a stabilisation in the second half, but final values were lower than baseline. Reticulocytes did not modify, whilst the immature reticulocyte fraction increased. No differences were found in red blood cells volume and corpuscular haemoglobin content, neither in iron metabolism markers. The acute phase proteins, haptoglobin and C-reactive protein, both increased over the race, while haemoglobin and haptoglobin were inversely related.These data are important for improving the knowledge of physiological modifications in haematological and iron metabolism parameters of professional athletes during highly demanding competitions. This is the first report, in the ambit of a stage race, in which the pre-analytical phase standardisation has been applied.