bluuebunny/crossref_metadata_2025_split huggingface dataset:
Haskell, do you read me?
Authors: Viera Marcos , Swierstra S. Doaitse , Lempsink Eelco 
Published: June 2009

The Haskell definition and implementation of read is far from perfect. In the first place read is not able to handle the associativities defined for infix operators. Furthermore, it puts constraints on the way show is defined, and especially forces it to generate far more parentheses than expected. Lastly, it may give rise to exponential parsing times. All this is due to the compositionality requirement for read functions, which imposes a top-down parsing strategy.
We propose a different approach, based on typed abstract syntax, in which grammars describing the data types are composed dynamically. Using the transformation libraries described in a companion paper these syntax descriptions are combined and transformed into parsers at runtime, from which the required read function are constructed. In this way we obtain linear parsing times, achieve consistency with the defined associativities, and may use a version of show which generates far fewer parentheses, thus improving readability of printed values.
The described transformation algorithms can be incorporated in a Haskell compiler, thus moving most of the work involved to compile time.
Haskell
Authors: Coutts Duncan , Potoczny-Jones Isaac , Stewart Don 
Published: June 2009

The quality of a programming language itself is only one component in the ability of application writers to get the job done. Programming languages can succeed or fail based on the breadth and quality of their library collection. Over the last few years, the Haskell community has risen to the task of building the library infrastructure necessary for Haskell to succeed as a programming language suitable for writing real-world applications.
This on-going work, the Cabal and Hackage effort, is built on the open source model of distributed development, and have resulted in a flowering of development in the language with more code produced and reused now than at any point in the community's history. It is easier to obtain and use Haskell code, in a wider range of environments, than ever before.
This demonstration describes the infrastructure and process of Haskell development inside the Cabal/Hackage framework, including the build system, library dependency resolution, centralised publication, documentation and distribution, and how the code escapes outward into the wider software community.
We survey the benefits and trade-offs in a distributed, collaborative development ecosystem and look at a proposed Haskell Platform that envisages a complete Haskell development environment, batteries included.
mars and tousled-like kinase act in parallel to ensure chromosome fidelity in Drosophila
Authors: Li Hsing-Hsi , Chiang Chuen-Sheue , Huang Hsiao-Yu , Liaw Gwo-Jen 
Published: June 2009

Abstract

Background
High levels of Hepatoma Up-Regulated Protein (HURP) and Tousled-Like Kinase (TLK) transcripts are found in hepatocellular carcinoma. HURP overexpression induces anchorage-independent growth of 293-T cells and enhances a rough-eye phenotype resulting from tlk overexpression in Drosophila. In addition, both HURP and Mars, a Drosophila HURP sequence homologue, promote polymerization of mitotic spindles. Thus, the genetic interaction of mars with tlk might be required for accurate chromosome segregation.

Methods
To reveal whether chromosome fidelity was decreased, the frequency of gynandromorphy, an individual with both male and female characteristics, and of non-disjunction were measured in the progeny from parents with reduced mars and/or tlk activities and analyzed by Student's t-test. To show that the genetic interaction between mars and tlk is epistatic or parallel, a cytological analysis of embryos with either reduced or increased activities of mars and/or tlk was used to reveal defects in mitotic-spindle morphology and chromosome segregation.

Results
A significant but small fraction of the progeny from parents with reduced mars activity showed gynandromorphy and non-disjunction. Results of cytological analysis revealed that the decrease in chromosome fidelity was a result of delayed polymerization of the mitotic spindle, which led to asynchronous chromosome segregation in embryos that had reduced mars activity. By removing one copy of tousled-like kinase (tlk) from flies with reduced mars activity, chromosome fidelity was further reduced. This was indicated by an increased in the non-disjunction rate and more severe asynchrony. However, the morphology of the mitotic spindles in the embryos at metaphase where both gene activities were reduced was similar to that in mars embryos. Furthermore, tlk overexpression did not affect the morphology of the mitotic spindles and the cellular localization of Mars protein.

Conclusion
Chromosome fidelity in progeny from parents with reduced mars and/or tlk activity was impaired. The results from cytological studies revealed that mars and tlk function in parallel and that a balance between mars activity and tlk activity is required for cells to progress through mitosis correctly, thus ensuring chromosome fidelity.
Chromosome level assembly of the hybrid Trypanosoma cruzi genome
Authors: Weatherly D Brent , Boehlke Courtney , Tarleton Rick L 
Published: June 2009

Abstract

Background
In contrast to the essentially fully assembled genome sequences of the kinetoplastid pathogens Leishmania major and Trypanosoma brucei the assembly of the Trypanosoma cruzi genome has been hindered by its repetitive nature and the fact that the reference strain (CL Brener) is a hybrid of two distinct lineages. In this work, the majority of the contigs and scaffolds were assembled into pairs of homologous chromosomes based on predicted parental haplotype, inference from TriTryp synteny maps and the use of end sequences from T. cruzi BAC libraries.

Results
Ultimately, 41 pairs of chromosomes were assembled using this approach, a number in agreement with the predicted number of T. cruzi chromosomes based upon pulse field gel analysis, with over 90% (21133 of 23216) of the genes annotated in the genome represented. The approach was substantiated through the use of Southern blot analysis to confirm the mapping of BAC clones using as probes the genes they are predicted to contain, and each chromosome construction was visually validated to ensure sufficient evidence was present to support the organization. While many members of large gene families are incorporated into the chromosome assemblies, the majority of genes excluded from the chromosomes belong to gene families, as these genes are frequently impossible to accurately position.

Conclusion
Now assembled, these chromosomes bring T. cruzi to the same level of organization as its kinetoplastid relatives and have been used as the basis for the T. cruzi genome in TriTrypDB, a trypanosome database of EuPathDB. In addition, they will provide the foundation for analyses such as reverse genetics, where the location of genes and their alleles and/or paralogues is necessary and comparative genome hybridization analyses (CGH), where a chromosome-level view of the genome is ideal.
Functional polymorphism of the NFKB1 gene promoter is related to the risk of dilated cardiomyopathy
Authors: Zhou Bin , Rao Li , Peng Ying , Wang Yanyun , Li Yi , Gao Linbo , Chen Yu , Xue Hui , Song Yaping , Liao Miao , Zhang Lin 
Published: June 2009

Abstract

Background
Previous studies in experimental and human heart failure showed that nuclear factor kappa B (NF-κB) is chronically activated in cardiac myocytes, suggesting an important involvement of NF-κB in the cardiac remodeling process. A common insertion/deletion (-94 insertion/deletion ATTG, rs28362491) located between two putative key promoter regulatory elements in the NFKB1 gene was identified which seems to be the first potential functional NFKB1 genetic variation. The main goal of the present investigation was to investigate the NFKB1 -94 insertion/deletion ATTG polymorphism in relation to risk of dilated cardiomyopathy (DCM).

Methods
A total of 177 DCM patients and 203 control subjects were successfully investigated. The NFKB1 -94 insertion/deletion ATTG polymorphism was genotyped by using PCR-PAGE.

Results
Genotype frequency of NFKB1 -94 insertion/deletion ATTG polymorphism in DCM patients was significantly different from that in control subjects (P = 0.015) and the ATTG2 carrier (ATTG1/ATTG2 + ATTG2/ATTG2) was susceptible to DCM.

Conclusion
Our data suggested that NFKB1 -94 insertion/deletion ATTG polymorphism is associated with DCM.
Stem cell factor and its soluble receptor (c-kit) in serum of asthmatic patients- correlation with disease severity
Authors: Makowska Joanna S , Cieslak Malgorzata , Kowalski Marek L 
Published: June 2009

Abstract

Background
SCF (stem cell factor) is a pleiotropic cytokine exerting its role at different stages of bone marrow development and affecting eosinophil activation, mast cells and basophil chemotaxis and survival. The aim of the study was to assess concentration of SCF and its soluble receptor c-kit (sc-kit) in peripheral blood of patients with asthma referring it to asthma severity and phenotype.

Methods
The study involved 107 patients with bronchial asthma, well characterized with respect to severity and 21 healthy controls. Concentration of SCF and sc-kit in the patients serum were measured by ELISA method.

Results
Mean serum SCF level in the group of asthmatics (n = 88) was significantly higher as compared to healthy controls (1010 pg/ml ± 37 vs 799 ± 33; p < 0,001). The level of SCF was higher in patients with severe asthma as compared to patients with non-severe asthma (1054 +/- 41 pg/ml vs 819 +/- 50; p < 0,01) and correlated with dose of inhaled glucocorticosteroids taken by the patients to achieve asthma control (R = 0,28; p < 0,01). The mean sc-kit serum level did not differ between asthmatic patients and healthy controls, however the level of sc-kit in non-severe asthmatics was significantly higher as compared to patients with severe asthma and healthy controls. In asthmatic patients (n = 63) the level of sc-kit correlated positively with FEV1% predicted value (R = 0,45; p < 0,001) and MEF25% predicted value (R = 0,33; p < 0,01). The level of sc-kit inversely correlated with the dose of inhaled glucocorticosteroids taken by the patients (R = -0,26; p < 0,01).

Conclusion
Serum levels of SCF and its soluble receptor c-kit seem to be reflect asthma severity suggesting a role for these molecules in asthmatic inflammation.
An alternative methodology for the prediction of adherence to anti HIV treatment
Authors: Thompson IRichard , Bidgood Penelope , Petróczi Andrea , Denholm-Price James CW , Fielder Mark D ,   The Eu Resist Network Study Group
Published: June 2009

Abstract

Background
Successful treatment of HIV-positive patients is fundamental to controlling the progression to AIDS. Causes of treatment failure are either related to drug resistance and/or insufficient drug levels in the blood. Severe side effects, coupled with the intense nature of many regimens, can lead to treatment fatigue and consequently to periodic or permanent non-adherence. Although non-adherence is a recognised problem in HIV treatment, it is still poorly detected in both clinical practice and research and often based on unreliable information such as self-reports, or in a research setting, Medication Events Monitoring System caps or prescription refill rates. To meet the need for having objective information on adherence, we propose a method using viral load and HIV genome sequence data to identify non-adherence amongst patients.

Presentation of the hypothesis
With non-adherence operationally defined as a sharp increase in viral load in the absence of mutation, it is hypothesised that periods of non-adherence can be identified retrospectively based on the observed relationship between changes in viral load and mutation.

Testing the hypothesis
Spikes in the viral load (VL) can be identified from time periods over which VL rises above the undetectable level to a point at which the VL decreases by a threshold amount. The presence of mutations can be established by comparing each sequence to a reference sequence and by comparing sequences in pairs taken sequentially in time, in order to identify changes within the sequences at or around 'treatment change events'. Observed spikes in VL measurements without mutation in the corresponding sequence data then serve as a proxy indicator of non-adherence.

Implications of the hypothesis
It is envisaged that the validation of the hypothesised approach will serve as a first step on the road to clinical practice. The information inferred from clinical data on adherence would be a crucially important feature of treatment prediction tools provided for practitioners to aid daily practice. In addition, distinct characteristics of biological markers routinely used to assess the state of the disease may be identified in the adherent and non-adherent groups. This latter approach would directly help clinicians to differentiate between non-responding and non-adherent patients.
Radiotherapy quality assurance review in a multi-center randomized trial of limited-disease small cell lung cancer: the Japan Clinical Oncology Group (JCOG) trial 0202
Authors: Sanuki-Fujimoto Naoko , Ishikura Satoshi , Hayakawa Kazushige , Kubota Kaoru , Nishiwaki Yutaka , Tamura Tomohide 
Published: June 2009

Abstract

Background
The purpose of this study was to analyze the radiotherapy (RT) quality assurance (QA) assessment in Japan Clinical Oncology Group (JCOG) 0202, which was the first trial that required on-going RT QA review in the JCOG.

Methods
JCOG 0202 was a multi-center phase III trial comparing two types of consolidation chemotherapy after concurrent chemoradiotherapy for limited-disease small cell lung cancer. RT requirements included a total dose of 45 Gy/30 fx (bis in die, BID/twice a day) without heterogeneity correction; elective nodal irradiation (ENI) of 30 Gy; at least 1 cm margin around the clinical target volume (CTV); and interfraction interval of 6 hours or longer. Dose constraints were defined in regards to the spinal cord and the lung. The QA assessment was classed as per protocol (PP), deviation acceptable (DA), violation unacceptable (VU), and incomplete/not evaluable (I/NE).

Results
A total of 283 cases were accrued, of which 204 were fully evaluable, excluding 79 I/NE cases. There were 18 VU in gross tumor volume (GTV) coverage (8% of 238 evaluated); 4 VU and 23 DA in elective nodal irradiation (ENI) (2% and 9% of 243 evaluated, respectively). Some VU were observed in organs at risk (1 VU in the lung and 5 VU in the spinal cord). Overall RT compliance (PP + DA) was 92% (187 of 204 fully evaluable). Comparison between the former and latter halves of the accrued cases revealed that the number of VU and DA had decreased.

Conclusion
The results of the RT QA assessment in JCOG 0202 seemed to be acceptable, providing reliable results.
Menstrual Cycle and Surgical Treatment of Breast Cancer: Findings From the NCCTG N9431 Study
Authors: Grant Clive S. , Ingle James N. , Suman Vera J. , Dumesic Daniel A. , Wickerham D. Lawrence , Gelber Richard D. , Flynn Patrick J. , Weir Lorna M. , Intra Mattia , Jones Wayne O. , Perez Edith A. , Hartmann Lynn C. 
Published: June 2009

Purpose For nearly two decades, multiple retrospective reports, small prospective studies, and meta-analyses have arrived at conflicting results regarding the value of timing surgical intervention for breast cancer on the basis of menstrual cycle phase. We present the results of a multi–cooperative group, prospective, observational trial of menstrual cycle phase and outcome after breast cancer surgery, led by the North Central Cancer Treatment Group (NCCTG) in collaboration with the National Surgical Adjuvant Breast and Bowel Project (NSABP) and the International Breast Cancer Study Group (IBCSG). Patients and Methods Premenopausal women age 18 to 55 years, who were interviewed for menstrual history and who were surgically treated for stages I to II breast cancer, had serum drawn within 1 day of surgery for estradiol, progesterone, and luteinizing hormone levels. Menstrual history and hormone levels were used to determine menstrual phase: luteal, follicular, and other. Disease-free survival (DFS) and overall survival (OS) rates were determined by Kaplan-Meier method and were compared by using the log-rank test and Cox proportional hazard modeling. Results Of 1,118 women initially enrolled, 834 women comprised the study cohort: 230 (28%) in luteal phase; 363 (44%) in follicular phase; and 241 grouped as other. During a median follow-up of 6.6 years, and in analysis that accounted for nodal disease, estrogen receptor status, adjuvant radiation therapy or chemotherapy, neither DFS nor OS differed with respect to menstrual phase. The 5-year DFS rates were 82.7%, 82.1%, and 79.2% for follicular, luteal, or other phases, respectively. Corresponding OS survival rates were 91.9%, 92.2%, and 91.8%, respectively. Conclusion When menstrual cycle phases were strictly defined, neither DFS nor OS differed between women who underwent surgery during the follicular phase versus the luteal phase. Nearly 30% of the patients did not meet criteria for either follicular- or luteal-phase categories.
Short‐Term Effects of an Anti‐Inflammatory Treatment on Clinical Parameters and Serum Levels of C‐Reactive Protein and Proinflammatory Cytokines in Subjects With Periodontitis
Authors: Renvert Stefan , Lindahl Christel , Roos‐Jansåker Ann‐Marie , Lessem Jan 
Published: June 2009

Background: Periodontal disease is the most common multifactorial disease, afflicting a very large proportion of the adult population. Periodontal disease secondarily causes increases in the serum levels of C‐reactive protein (CRP) and other markers of inflammation. An increased level of CRP reflects an increased risk for cardiovascular disease. The aim of the current randomized clinical trial was to evaluate the short‐term effect of a combination of dipyridamole and prednisolone (CRx‐102) on the levels of high‐sensitivity (hs)‐CRP, proinflammatory markers in blood, and clinical signs of periodontal disease.Methods: Fifty‐seven patients with ≥10 pockets with probing depths ≥5 mm were randomized into two groups in this masked single‐center placebo‐controlled study: CRx‐102 (n = 28) and placebo (n = 29). hs‐CRP levels, inflammatory markers (interleukin [IL]‐6, −1β, −8, and −12, tumor necrosis factor‐alpha, and interferon‐gamma [IFN‐γ]), bleeding on probing (BOP), and changes in probing depths were evaluated. The subjects received mechanical non‐surgical therapy after 42 days, and the study was completed after 49 days.Results: At day 42, the differences in the hs‐CRP, IFN‐γ, and IL‐6 levels between the two groups were statistically significant (P <0.05), whereas no difference was found for the other inflammatory markers. There was no change in probing depth or BOP between the two groups.Conclusion: The administration of CRx‐102 resulted in significant decreases in hs‐CRP, IFN‐γ, and IL‐6, but it did not significantly change BOP or probing depths.
A Surgical Reentry Study on the Influence of Platelet‐Rich Plasma in Enhancing the Regenerative Effects of Bovine Porous Bone Mineral and Guided Tissue Regeneration in the Treatment of Intrabony Defects in Humans
Authors: Camargo Paulo M. , Lekovic Vojislav , Weinlaender Michael , Divnic‐Resnik Tihana , Pavlovic Marija , Kenney E. Barrie 
Published: June 2009

Background: The purpose of this study was to evaluate the additional benefits provided by the incorporation of platelet‐rich plasma (PRP) into a regenerative protocol consisting of bovine porous bone mineral (BPBM) and guided tissue regeneration (GTR) in the treatment of intrabony defects in humans.Methods: Twenty‐three paired intrabony defects were surgically treated using a split‐mouth design. Defects were treated with BPBM/GTR/PRP (experimental group) or with BPBM/GTR (control group). The clinical parameters evaluated included changes in probing depth, clinical attachment level, and defect fill as revealed by reentry surgeries at 6 months.Results: Preoperative probing depths, attachment levels, and transoperative bone measurements were similar for the two groups. Post‐surgical measurements taken at 6 months revealed that both treatment modalities resulted in a significant decrease in probing depth, gain in clinical attachment, and bone fill of the defects compared to baseline. Postoperative differences observed between the two groups were 0.72 ± 0.36 mm at buccal sites and 0.90 ± 0.32 mm at lingual sites for probing depth, 0.82 ± 0.41 mm at buccal sites and 0.78 ± 0.38 at lingual sites for gain in clinical attachment, and 0.85 ± 0.36 mm at buccal sites and 0.94 ± 0.42 mm at lingual sites for defect fill, all favoring the experimental sites. However, none of the differences were statistically significant.Conclusion: Within the limitations related to using a small sample size, PRP did not significantly augment the effects of BPBM and GTR in promoting the clinical resolution of intrabony defects.
Fetal Exposure to Oral Pathogens and Subsequent Risk for Neonatal Intensive Care Admission
Authors: Jared Heather , Boggess Kim A. , Moss Kevin , Bose Carl , Auten Richard , Beck James , Offenbacher Steven 
Published: June 2009

Background: Maternal periodontal infection has been associated with adverse maternal and neonatal outcomes. In utero fetal exposure to oral pathogens was also recognized as deleterious to the fetus. The objective of this study was to determine the relationship between fetal exposure to oral pathogens and neonatal intensive care unit (NICU) admission.Methods: This was a secondary analysis of a prospective cohort study of maternal oral health and pregnancy outcome. Fetal immunoglobulin M against oral pathogens was detected in umbilical cord serum by immunoblot. The presence of at least one oral pathogen–specific antibody was considered seropositivity. The cord level of C‐reactive protein was determined by enzyme‐linked immunosorbent assay and categorized as detectable versus undetectable. Chi‐square and logistic regression analyses were used to determine the association between cord serum seropositivity or detectable C‐reactive protein and NICU admission and length of stay.Results: Of 650 infants, 45 (6.9%) were admitted to the NICU. The admission rate was higher among seropositive infants compared to seronegative infants (11% versus 5%; P = 0.0019). Seropositive infants were also more likely than seronegative infants to stay >3 or >7 days (8% versus 3% and 6% versus 2%; P = 0.004 and 0.003, respectively). Adjusting for gestational age, the odds ratio (95% confidence interval) for NICU admission was 2.14 (1.01 to 4.54); for a length of stay >3 or >7 days, it was 2.38 (1.01 to 5.60) and 3.29 (1.13 to 9.58), respectively. The NICU admission rate was not significantly higher for those with detectable versus undetectable umbilical cord serum C‐reactive protein (8% versus 6%; P = 0.3).Conclusions: In utero fetal exposure to oral pathogens increases the risk for NICU admission and the length of stay. Interventions that interrupt fetal exposure to oral pathogens may reduce these risks.
Model theory without choice? Categoricity
Authors: Shelah Saharon 
Published: June 2009

AbstractWe prove Los conjecture = Morley theorem in ZF. with the same characterization, i.e., of first order countable theories categorical in ℵα for some (eqiuvalently for every ordinal) α > 0. Another central result here in this context is: the number of models of a countable first order T of cardinality ℵα is either ≥ ∣α∣ for every α or it has a small upper bound (independent of α close to ⊐2).