bluuebunny/crossref_metadata_2025_split huggingface dataset:
Increased Microsatellite Instability and Epigenetic Inactivation of the Hmlh1 Gene in Head and Neck Squamous Cell Carcinoma
Authors: Zuo Chunlai , Zhang Haihong , Spencer Horace J. , Vural Emre , Suen James Y. , Schichman Steven A. , Smoller Bruce R. , Kokoska Mimi S. , Fan Chun‐Yang 
Published: September 2009

OBJECTIVEThe study is designed to elucidate the relationship between epigenetic silencing of the hMLH1 (human MutL homologue 1) gene and microsatellite instability (MSI) and the prognostic values of hMLH1 promoter methylation and MSI in head and neck squamous cell carcinoma (HNSCC).STUDY DESIGNCross‐sectional study.SETTINGTertiary referral center.SUBJECTS AND METHODSA total of 120 cases of HNSCC were analyzed for hMLH1 promoter hypermethylation, protein expression, and MSI by using methylation‐specific polymerase chain reaction, immunohistochemical staining, and polymerase chain reaction amplification with the use of 16 fluorescent‐labeled microsatellite markers, followed by fragment analysis.RESULTSOf 120 HNSCCs, hMLH1 promoter hypermethylation and decreased hMLH1 protein expression were shown in 39 (32.5%) and 22 (18.3%), respectively. hMLH1 promoter hypermethylation was detected in 13 of 52 (25%) normal‐appearing squamous mucosa adjacent to invasive carcinoma. MSI was detected in 21 (17.5%) tumors at two or more markers and in 99 (82.5%) tumors with no evidence of MSI or at only one marker. Hypermethylation of the hMLH1 gene is significantly associated with decreased hMLH1 protein expression (P < 0.001). High‐frequency MSI was significantly associated with promoter hypermethylation (P = 0.01) but not with decreased protein expression (P = 0.069) of hMLH1 gene. hMLH1 promoter hypermethylation is significantly associated with decreased cause‐specific survival for HNSCC patients (P = 0.03).CONCLUSIONSPromoter hypermethylation of the hMLH1 gene could be detected early in head and neck squamous carcinogenesis and may be associated with increased MSI and poor survival in HNSCC.
Nonasthmatic Nasal Polyposis Patients with Allergy Exhibit Greater Epithelial MMP Positivity
Authors: Shin Hyun‐Woo , Han Doo Hee , Lim Yune Sung , Kim Hye Jung , Kim Dong‐Young , Lee Chul Hee , Min Yang‐Gi , Rhee Chae‐Seo 
Published: September 2009

OBJECTIVETo determine the influence of allergic rhinitis (AR) on the expression of matrix metalloproteinase (MMP)‐9, MMP‐2, and tissue inhibitor‐1 of metalloproteinase (TIMP‐1) in nasal polyposis.STUDY DESIGNA case‐control study.SETTINGA tertiary referral center.SUBJECTS AND METHODSThe expression of MMP‐9, MMP‐2, and TIMP‐1 was investigated in the nasal polyp tissue (NP) and maxillary sinus mucosa (MM) samples from 20 AR patients and 20 nonallergic patients undergoing endoscopic sinus surgery. Trichrome, periodic acid‐Schiff, and hematoxylin‐eosin staining were also performed and those expression levels were compared.RESULTSInfiltration of eosinophils was shown more intensely in NP rather than in MM, especially in the presence of AR. In the NP of AR patients, increased expression of MMP‐9, MMP‐2, and TIMP‐1 was observed more prominently than in that of the control group. In case of MM, however, there was no significant difference between AR patients and the control group.CONCLUSIONThe presence of AR may enhance the expression of MMP‐9, MMP‐2, and TIMP‐1 associated with airway remodeling in nasal polyposis.
Dietary vitamin D and risk of non-Hodgkin lymphoma: the multiethnic cohort
Authors: Erber Eva , Maskarinec Gertraud , Lim Unhee , Kolonel Laurence N. 
Published: September 2009

The present study explored the association between dietary vitamin D and non-Hodgkin's lymphoma (NHL) risk. The multiethnic cohort (MEC) includes more than 215 000 Caucasians, African Americans, Native Hawaiians, Japanese Americans and Latinos, aged 45–75. After 10 years of follow-up, 939 incident NHL cases were identified. Risk was estimated using proportional hazards' models adjusted for possible confounders. Vitamin D intake was not associated with NHL risk in the entire cohort (Ptrend = 0·72 for men and Ptrend = 0·83 for women), but significantly lowered disease risk in African American women (hazard ratio (HR) = 0·50, 95 % CI: 0·28, 0·90, Ptrend = 0·03) and was borderline protective in African American men (HR = 0·68; 95 % CI: 0·39, 1·19; Ptrend = 0·31) when the highest to the lowest tertile was compared. In NHL subtype analyses, a 19, 36 and 32 % lowered risk, although not significant, was observed for diffuse large B-cell lymphoma, follicular lymphoma and small lymphocytic lymphoma/chronic lymphocytic leukemia in women, respectively. High dietary intake of vitamin D did not show a protective effect against NHL within the MEC except among African Americans, possibly because vitamin D production due to sun exposure is limited in this population.
Commensurability classes of arithmetic Fuchsian surface groups of genus 2
Authors: MACLACHLAN C. , ROSENBERGER G. 
Published: September 2009

AbstractHere we determine the arithmetic data i.e. the totally real number field and the set of ramified places of the defining quaternion algebra, of all those commensurability classes of arithmetic Fuchsian groups which contain a surface group of genus 2, i.e. a group of signature (2;– –).
Galois theory of Salem polynomials
Authors: CHRISTOPOULOS CHRISTOS , MCKEE JAMES 
Published: September 2009

AbstractLet f(x) ∈ [x] be a monic irreducible reciprocal polynomial of degree 2d with roots r1, 1/r1, r2, 1/r2, . . ., rd, 1/rd. The corresponding trace polynomial g(x) of degree d is the polynomial whose roots are r1 + 1/r1, . . ., rd + 1/rd. If the Galois groups of f and g are Gf and Gg respectively, then Gg ≅ Gf/N, where N is isomorphic to a subgroup of C2d. In a naive sense, the generic case is Gf ≅ C2d ⋊ Sd, with N ≅ C2d and Gg ≅ Sd. When f(x) has extra structure this may be reflected in the Galois group, and it is not always true even that Gf ≅ N ⋊ Gg. For example, for cyclotomic polynomials f(x) = Φn(x) it is known that Gf ≅ N ⋊ Gg if and only if n is divisible either by 4 or by some prime congruent to 3 modulo 4.In this paper we deal with irreducible reciprocal monic polynomials f(x) ∈ [x] that are ‘close’ to being cyclotomic, in that there is one pair of real positive reciprocal roots and all other roots lie on the unit circle. With the further restriction that f(x) has degree at least 4, this means that f(x) is the minimal polynomial of a Salem number. We show that in this case one always has Gf ≅ N ⋊ Gg, and moreover that N ≅ C2d or C2d−1, with the latter only possible if d is odd.
Geste de pointage enfantin et développement du lexique du stade du premier mot au stade de l'énoncé à deux mots
Authors: HUNKELER HERVÉ 
Published: September 2009

RÉSUMÉCette étude porte sur le rôle du geste enfantin dans le développement du lexique précoce chez des enfants jumeaux (garçon et fille) en interaction avec leur mère entre 15 et 26 mois en situation de livres d'images. Il ressort de ce travail que ces deux enfants produisent des combinaisons geste/mot(s), contenant le plus souvent un mot référentiel. Nous remarquons aussi que toutes ces combinaisons contiennent des informations identiques. Celles-ci semblent faciliter l'accroissement des combinaisons « pointage+énoncés à 2 mots » constaté chez nos deux sujets entre 24 et 26 mois. Ce résultat nouveau lié à la situation de livres d'images rompt avec les travaux cités dans la littérature.
Accent et syllabe dans les vers français: une synthèse possible?
Authors: PENSOM ROGER 
Published: September 2009

RESUMESelon certains critiques influents, l'équivalence métrique repose uniquement sur des équivalences en nombre syllabique, la division en unités rythmiques et la disposition interne des accents restant ‘libres’, c'est -à-dire indifférentes au mètre. A l'encontre de cette vue, depuis 1800, bon nombre d'amateurs et poètes ont discerné dans les vers français l'opération d'un principe formel fondé sur la répartition des accents au sein du vers. Suite à des travaux récents qui constatent la présence d'une occurrence statistiquement significative de répartitions d'accents régulières dans un vaste corpus d'alexandrins classiques, l'article présent cherche à démontrer une interdépendance fonctionnelle entre le décompte syllabique récurrent et la répartition des accents internes. La question de l'accent de vers étant actuellement le lieu d'âpres débats, tout comme celle de l'accent dans la langue, la réalité de l'accent de mot est affirmé au moyen d'une analyse distributionnelle de syntagmes nominaux dans un texte de Racine. Une analyse comparative prose/vers démontre que, dans les vers, la distribution des accents internes, ainsi que celle des voyelles atones, est sujette à contrainte; cette analyse fournit aussi des indications sur le statut linguistique du contre-accent en français. Un examen critique de Cornulier (1982, 1995) met en doute l'idée que l'isosyllabisme est la condition suffisante et nécessaire du vers français, et propose à sa place une conception dynamique où l'agencement formel du rythme accentuel joue un rôle indispensable à notre perception de la métrique du vers.
Optimal waist:height ratio cut-off point for cardiometabolic risk factors in Turkish adults
Authors: Selçuk Can Ahmet , Akal Yıldız Emine , Samur Gülhan , Rakıcıoğlu Neslişah , Pekcan Gülden , Özbayrakçı Sinan , Palaoğlu K Erhan , Gönen Mithat , Bersot Thomas P 
Published: September 2009

AbstractObjectiveTo identify the optimal waist:height ratio (WHtR) cut-off point that discriminates cardiometabolic risk factors in Turkish adults.DesignCross-sectional study. Hypertension, dyslipidaemia, diabetes, metabolic syndrome score ≥2 (presence of two or more metabolic syndrome components except for waist circumference) and at least one risk factor (diabetes, hypertension or dyslipidaemia) were categorical outcome variables. Receiver-operating characteristic (ROC) curves were prepared by plotting 1 − specificity on thex-axis and sensitivity on they-axis. The WHtR value that had the highest Youden index was selected as the optimal cut-off point for each cardiometabolic risk factor (Youden index = sensitivity + specificity − 1).SettingTurkey, 2003.SubjectsAdults (1121 women and 571 men) aged 18 years and over were examined.ResultsAnalysis of ROC coordinate tables showed that the optimal cut-off value ranged between 0·55 and 0·60 and was almost equal between men and women. The sensitivities of the identified cut-offs were between 0·63 and 0·81, the specificities were between 0·42 and 0·71 and the accuracies were between 0·65 and 0·73, for men and women. The cut-off point of 0·59 was the most frequently identified value for discrimination of the studied cardiometabolic risk factors. Subjects classified as having WHtR ≥ 0·59 had significantly higher age and sociodemographic multivariable-adjusted odds ratios for cardiometabolic risk factors than subjects with WHtR < 0·59, except for diabetes in men.ConclusionsWe show that the optimal WHtR cut-off point to discriminate cardiometabolic risk factors is 0·59 in Turkish adults.
Automatically classifying sentences in full-text biomedical articles into Introduction, Methods, Results and Discussion
Authors: Agarwal Shashank , Yu Hong 
Published: September 2009

Abstract
Biomedical texts can be typically represented by four rhetorical categories: Introduction, Methods, Results and Discussion (IMRAD). Classifying sentences into these categories can benefit many other text-mining tasks. Although many studies have applied different approaches for automatically classifying sentences in MEDLINE abstracts into the IMRAD categories, few have explored the classification of sentences that appear in full-text biomedical articles. We first evaluated whether sentences in full-text biomedical articles could be reliably annotated into the IMRAD format and then explored different approaches for automatically classifying these sentences into the IMRAD categories. Our results show an overall annotation agreement of 82.14% with a Kappa score of 0.756. The best classification system is a multinomial naïve Bayes classifier trained on manually annotated data that achieved 91.95% accuracy and an average F-score of 91.55%, which is significantly higher than baseline systems. A web version of this system is available online at—http://wood.ims.uwm.edu/full_text_classifier/.
Contact: hongyu@uwm.edu
Automatic assignment of reaction operators to enzymatic reactions
Authors: Leber Markus , Egelhofer Volker , Schomburg Ida , Schomburg Dietmar 
Published: September 2009

Abstract
Background: Enzymes are classified in a numerical classification scheme introduced by the Nomenclature Committee of the IUBMB based on the overall reaction chemistry. Due to the manifold of enzymatic reactions the system has become highly complex. Assignment of enzymes to the enzyme classes requires a detailed knowledge of the system and manual analysis. Frequently rearrangements and deletions of enzymes and sub-subclasses are necessary.
Results: We use the Dugundji–Ugi model for coding of biochemical reactions which is based on electron shift patterns occurring during reactions. Changes of the bonds or of non-bonded valence electrons are expressed by reaction matrices. Our program calculates reaction matrices automatically on the sole basis of substrate and product chemical structures based on a new strategy for maximal common substructure determination, which allows an accurate atom mapping of the substrate and product atoms. The system has been tested for a large set of enzymatic reactions including all sub-subclasses of the EC classification system. Altogether 147 different representative reaction operators were found in the classified enzymes, 121 of which are unique with respect to an EC sub-subclass. The other 26 comprise groups of enzymes with very similar reactions, being identical with respect to the bonds formed and broken.
Conclusion: The analysis and comparison of enzymatic reactions according to their electron shift patterns is defining enzyme groups characterised by unique reaction cores. Our results demonstrate the applicability of the Dugundji–Ugi model as a reasonable pre-classification system allowing an objective and rational view on biochemical reactions.
Availability: The program to generate reaction matrix descriptors is available upon request.
Contact: d.schomburg@tu-bs.de
Modelling the effectiveness of contraception for controlling introduced populations of elephant in South Africa
Authors: Mackey Robin L. , Page Bruce R. , Grobler Douw , Slotow Rob 
Published: September 2009

AbstractRe‐introduced African elephant (Loxodonta africanaBlumenbach) populations are growing at very high rates in many of southern Africa’s reserves, have attained densities higher than previously thought possible and may be exhibiting irruptive growth. Active management of such populations is necessary to prevent the potentially negative effects on habitat and biodiversity that are associated with elephant overpopulation. One potentially feasible method of elephant management is immunocontraception, but very little is known about the long‐term effectiveness of this method. Using demographic data from three South African elephant populations, we made model projections of the effects of contraception on population growth rates to determine whether contraception may be a feasible management tool for elephant. In comparison with noncontracepted populations, realistic reductions in population growth rate after 20 years of contraception were projected to be up to c. 64%, with 50% being a very feasible target. Through its ability to reduce population growth rates, immunocontraception should be an effective tool for preventing or minimizing irruption in elephants and, perhaps, other introduced ungulate species.
The stem cells of small intestinal crypts: where are they?
Authors: Potten C. S. , Gandara R. , Mahida Y. R. , Loeffler M. , Wright N. A. 
Published: September 2009

AbstractRecently, there has been resurgence of interest in the question of small intestinal stem cells, their precise location and numbers in the crypts. In this article, we attempt to re‐assess the data, including historical information often omitted in recent studies on the subject. The conclusion we draw is that the evidence supports the concept that active murine small intestinal stem cells in steady state are few in number and are proliferative. There are two evolving, but divergent views on their location (which may be more related to scope of capability and reversibility than to location) several lineage labelling and stem cell self‐renewing studies (based on Lgr5 expression) suggest a location intercalated between the Paneth cells (crypt base columnar cells (CBCCs)), or classical cell kinetic, label‐retention and radiobiological evidence plus other recent studies, pointing to a location four cell positions luminally from the base of the crypt The latter is supported by recent lineage labelling of Bmi‐1‐expressing cells and by studies on expression of Wip‐1 phosphatase. The situation in the human small intestine remains unclear, but recent mtDNA mutation studies suggest that the stem cells in humans are also located above the Paneth cell zone. There could be a distinct and as yet undiscovered relationship between these observed traits, with stem cell properties both in cells of the crypt base and those at cell position 4.
Bony remodelling in unilateral dermatomal cavernous haemangiomatosis of the arm
Authors: Kraus A. , Richards P. J. , Tan B. B. 
Published: September 2009

SummaryWe report a case of a massive unilateral dermatomal cavernous haemangioma (UDCH) affecting the left arm and adjacent neck in the region of the C4–C8 dermatomes, with associated bony remodelling. To our knowledge, this is the first report of the rare condition UDCH with bony abnormalities.
The effect of regular exercise on penile nitric oxide synthase expression in rats
Authors: Ozbek Emin , Tasci Ali Ihsan , Ilbey Yusuf Ozlem , Simsek Abdulmuttalip , Somay Adnan , Metin Gokhan 
Published: September 2009

SummaryErectile dysfunction (ED) is a major public health problem that seriously affects the quality of life of patients and their partners and its prevalence increases significantly with ageing. In this study, we tested the hypothesis that age‐associated decrease in penile endothelial (eNOS) and neuronal nitric oxide synthase (nNOS) activity in aged rats may be increased by regular exercise. A total of 28 young (4 m) and aged (24 m) male rats were divided into four equal groups: group 1 – young control; group 2 – young trained; group 3 – old control and group 4 – old trained group. Groups 2 and 4 rats were trained to swim for 30 min a day and 5 days a week, which lasted 8 weeks. At the end of 8 weeks, rats were sacrificed and penile tissues evaluated for eNOS and nNOS activities. eNOS and nNOS activities were evaluated by immunohistochemistry in paraffinized penile tissues and results assessed semiquantitatively. Results also were compared with healthy age‐matched and adult (4 m) controls. Serum level of testosterone (T) was determined using ELISA kits (Beckman Coulter, Fullerton, CA, USA). In penile tissues of aged control rats, eNOS and nNOS staining were weakly positive; however in trained groups, eNOS and nNOS immunoreactivity were increased. In young control group, eNOS and nNOS activities were more intense than aged control. eNOS and nNOS activities were higher in adult trained group than control. Serum T concentrations were significantly higher in young and aged trained group than in control groups. We can suggest that regular exercise upregulates eNOS and nNOS expressions in the aged and young rat penis. Regular exercise may improve penile erection by increasing penile neurotransmitter in both young and aged rats.
Elevated mtDNA diversity in introduced populations of Cynotilapia afra (Günther 1894) in Lake Malawi National Park is evidence for multiple source populations and hybridization
Authors: ZIDANA HASTINGS , TURNER GEORGE F. , Van OOSTERHOUT COCK , HÄNFLING BERND 
Published: September 2009

AbstractGenetic variation in many invasive species shows little or no signs of a founder event, suggesting that high genetic diversity may facilitate establishment success. The rocky‐shore, plankton‐feeding cichlid fish Cynotilapia afra is endemic to Lake Malawi, but naturally absent from many suitable sites. In the 1960s, this species was introduced to the southern areas of the lake, presumably as a result of the aquarium fish trade. It has now become established on a number of rocky areas within the Lake Malawi National Park. Here, we analysed DNA sequence variation in the mitochondrial control region of six native and four introduced populations of C. afra, and three populations of the closely‐related and hybridizing Pseudotropheus zebra. In contrast to previous studies of Lake Malawi rock dwelling cichlids, network analyses suggested that native populations of C. afra showed high levels of lineage sorting in mtDNA. Introduced populations showed higher sequence and haplotype diversity than their native counterparts. Our analyses suggested that the elevated gene diversity was largely attributed to the fact that the introduced C. afra populations were derived from several genetically distinct and geographically separate populations, and to a lesser extent because of introgressive hybridization with native P. zebra. The establishment and spread of C. afra may be partly because of its ability to occupy a vacant ecological niche, but it may also have been facilitated by its enhanced genetic diversity.
The first evidence that a single cellulase can be essential for cellulose degradation in a cellulolytic microorganism
Authors: Wilson David B. 
Published: September 2009

SummaryCellulose is the most abundant carbon source in nature but it is very difficult to degrade because of its insolubility, quasi‐crystalline structure and its presence in plant cell walls in a matrix with other polymers that limit access to the cellulose surface. Most cellulose in soils is degraded by cellulolytic microorganisms that use a number of different approaches to overcome the recalcitrance of cellulose in plant cell walls. All of these approaches involve multiple cellulases and, since cellulose is insoluble and microorganisms cannot ingest particles, the cellulases are present outside of the cell although they can be attached to its outer surface. An impressive article by Tolonen et al. in this issue of Molecular Microbiology shows that deletion of the single family 9 cellulase gene in Clostridium phytofermentans prevents growth on cellulose although the mutant strain grows perfectly well on glucose and its other cellulase genes are transcribed normally. These results show for the first time that a single cellulase can be essential for cellulose degradation by an organism despite the presence of several other cellulases. It will be interesting to learn the detailed mechanism that C. phytofermentans uses to degrade cellulose.