bluuebunny/crossref_metadata_2025_split huggingface dataset:
Trans-visceral migration of retained surgical gauze as a cause of intestinal obstruction: a case report
Authors: Grassi Nello , Cipolla Calogero , Torcivia Adriana , Bottino Alessandro , Fiorentino Eugenio , Ficano Leonardo , Pantuso Gianni 
Published: February 2008

AbstractIntroductionA retained surgical sponge in the abdomen is uncommon although it is likely that this finding is underreported in the medical literature. The intravisceral migration of retained surgical gauze is even rarer, as demonstrated by the very few cases reported.Case presentationThree years after undergoing anterior resection of the rectum, a 75-year-old man presented with symptoms of small bowel obstruction. Plain abdominal radiography and CT showed a radio-opaque marker; a foreign body was suspected, probably a piece of retained surgical gauze. An ileotomy of about 5 cm. was performed to confirm this diagnosis and remove the gauze.ConclusionAlthough rare, retained gauze in the abdomen is a complication of surgery. The authors consider that this event may be more frequent than it appears from reports in the literature, probably because of its medico-legal implications. If all such cases were reported, it would be possible to estimate their exact number, classify the occurrence as a possible surgical complication and thus modify its medico-forensic consequences.
Genome wide prediction of HNF4α functional binding sites by the use of local and global sequence context
Authors: Kel Alexander E , Niehof Monika , Matys Volker , Zemlin Rüdiger , Borlak Jürgen 
Published: February 2008

AbstractWe report an application of machine learning algorithms that enables prediction of the functional context of transcription factor binding sites in the human genome. We demonstrate that our method allowedde novoidentification of hepatic nuclear factor (HNF)4α binding sites and significantly improved an overall recognition of faithful HNF4α targets. When applied to published findings, an unprecedented high number of false positives were identified. The technique can be applied to any transcription factor.
Sequence context affects the rate of short insertions and deletions in flies and primates
Authors: Tanay Amos , Siggia Eric D 
Published: February 2008

Abstract
Background
Insertions and deletions (indels) are an important evolutionary force, making the evolutionary process more efficient and flexible by copying and removing genomic fragments of various lengths instead of rediscovering them by point mutations. As a mutational process, indels are known to be more active in specific sequences (like micro-satellites) but not much is known about the more general and mechanistic effect of sequence context on the insertion and deletion susceptibility of genomic loci.

Results
Here we analyze a large collection of high confidence short insertions and deletions in primates and flies, revealing extensive correlations between sequence context and indel rates and building principled models for predicting these rates from sequence. According to our results, the rate of insertion or deletion of specific lengths can vary by more than 100-fold, depending on the surrounding sequence. These mutational biases can strongly influence the composition of the genome and the rate at which particular sequences appear. We exemplify this by showing how degenerate loci in human exons are selected to reduce their frame shifting indel propensity.

Conclusion
Insertions and deletions are strongly affected by sequence context. Consequentially, genomes must adapt to significant variation in the mutational input at indel-prone and indel-immune loci.
Native-Language Literacy in Colonial Peru: The Question of Mundane Quechua Writing Revisited
Authors: Durston Alan 
Published: February 2008

Abstract
Scholars of indigenous societies in colonial Latin America have long noted the contrast between the abundance of indigenous-language records from Mesoamerica and their extreme scarcity in the Andes. This article evaluates the degree to which written Quechua was used in everyday communication and record keeping among the indigenous population of colonial Peru by examining a corpus of Quechua documents, mostly letters and petitions from the seventeenth century. The linguistic features and archival contexts of these documents are analyzed to determine the extent and channels of alphabetic literacy in Quechua. The article argues that a standardized written form of Quechua developed by the church was in fact widely used among the indigenous elite, but that it never became an important medium of internal administrative record keeping in indigenous communities, as did occur with Nahuatl and other Mesoamerican languages.
Vitamin D, Calcium Homeostasis, and Skeleton Accretion in Children
Authors: Weaver Connie M 
Published: February 2008

Abstract
Overt vitamin D deficiency early in life has classically been associated with the etiology of rickets. Recent interest has focused on vitamin D insufficiency and calcium homeostasis and bone health. A review of the literature suggests that the relationship between vitamin D status and calcium utilization has some important differences with life stage and race. In contrast to adults, serum 1,25-dihydroxyvitamin D, but not serum 25-hydroxyvitamin D, predicts calcium absorption in growing children. PTH suppression with increasing serum 25-hydroxyvitamin D varies with race in adolescents. A limitation of our understanding of vitamin D status on calcium homeostasis in children relates to the cross-sectional nature of the evidence and interventions that typically use too little vitamin D supplementation to affect status. Vitamin D status has predicted changes in BMD during growth, and higher doses have been associated with increased bone area and BMC of the hip in pubertal girls with low baseline vitamin D status. Bone accretion is related to calcium status, sexual maturity, race, and genetics. Current cross-sectional studies in children suggest that vitamin D status is less important for bone accrual than for bone health in adults. Intervention studies are needed to identify responsive groups.
Role of Vitamin D Deficiency in Chronic Kidney Disease
Authors: Gal-Moscovici Anca , Sprague Stuart M 
Published: February 2008

Abstract
Chronic kidney disease (CKD) has been recognized as a significant public health problem, with ∼20 million Americans, or ∼11% of the adult population, currently living with CKD. A significant source of morbidity associated with CKD is the development of disturbances of mineral metabolism, which occurs in virtually all patients during the progression of their disease, and is associated with bone loss and fractures, cardiovascular disease, immune suppression, and increased mortality. As kidney disease develops, there is decreased functional renal mass and a tendency to retain phosphorus. The reduction in functional renal mass and the retained phosphorus act to reduce renal 1α-hydroxylase activity and thus the renal production of calcitriol. Further compensation to maintain normal serum calcium and phosphorus homeostasis includes increased production and release of PTH and potentially other phosphaturic factors, such as fibroblast growth factor-23 (FGF23). This increase in FGF23 contributes to maintain normal serum phosphate independent of PTH but may worsen calcitriol deficiency by also inhibiting renal 1α-hydroxylase activity. The decrease in calcitriol also results in promoting further hyperparathyroidism and parathyroid gland hyperplasia, because calcitriol normally inhibits the production of prepro-PTH and parathyroid cell proliferation.
Targets of Vitamin D Receptor Signaling in the Mammary Gland
Authors: Welsh JoEllen 
Published: February 2008

Abstract
Since the discovery of the vitamin D receptor (VDR) in mammary cells, the role of the vitamin D signaling pathway in normal glandular function and in breast cancer has been extensively explored. In vitro studies have shown that the VDR ligand, 1,25-dihydroxyvitamin D (1,25D), modulates key proteins involved in signaling proliferation, differentiation, and survival of normal mammary epithelial cells. Similar anti-proliferative and pro-differentiating effects of 1,25D have been observed in VDR-positive breast cancer cells, indicating that transformation per se does not abolish vitamin D signaling. However, many transformed breast cancer lose sensitivity to 1,25D secondary to alterations in vitamin D metabolizing enzymes or downregulation of VDR function. Over the years, our laboratory has focused on three general areas: (1) defining mechanisms of vitamin D–mediated apoptosis in breast cancer cells, (2) examining changes in the vitamin D signaling pathway during transformation, including the development of vitamin D resistance, and (3) using mouse models to study the impact of the VDR on growth regulatory pathways in the context of development and tumorigenesis in vivo. Recent developments include detection of megalin-mediated uptake of vitamin D–binding protein (DBP) and identification of CYP27B1 and CYP24 metabolizing enzymes in mammary cells, demonstration of precocious mammary gland development in VDR-null mice, and identification of novel pathways triggered by 1,25D during apoptosis. Our preclinical studies have been complemented by emerging data from other groups suggesting that human breast cancer may be influenced by VDR genotype and vitamin D status. Collectively, these studies have reinforced the need to further define the regulation and function of the vitamin D pathway in cells in relation to prevention and treatment of breast cancer.
Therapy of Osteoporosis With Calcium and Vitamin D
Authors: Dawson-Hughes Bess , Bischoff-Ferrari Heike A 
Published: February 2008

Abstract
Inadequate intakes of vitamin D and calcium lead to reduced calcium absorption, higher bone remodeling rates, and increased bone loss. Vitamin D insufficiency has also been linked to reduced muscle function and increased risk of falling. The mechanisms for the performance and muscle effects are not well understood. Administering vitamin D to those with inadequate vitamin D status has been shown to lower fracture rates in some trials but not in others. The purpose of this presentation is (1) to examine how calcium and vitamin D work in concert, (2) to consider key evidence that increasing vitamin D intake will affect risk of falls and fractures, and (3) to estimate the 25-hydroxyvitamin D [25(OH)D] level needed to achieve maximum fracture protection.
Vitamin D–Resistant Diseases
Authors: Liberman Uri A 
Published: February 2008

Abstract
Hereditary vitamin D receptor defects (HVDRDs) is a more appropriate and precise title for an inborn error of metabolism commonly known as pseudo-vitamin D deficiency or vitamin D dependency, type II. It is a rare autosomal recessive disorder, ∼70 kindreds were described, but its main importance is elucidating the physiology of vitamin D and calcium homeostasis in humans. Patients usually develop the clinical and biochemical aberrations, identical to vitamin D deficiency, but with high serum levels of calcitriol, within the first year of life (i.e., muscle weakness, bone pain, deformities, and fractures). Defective calcium gut absorption leads to hypocalcemia, secondary hyperparathyroidism, hypophosphatemia, and defective mineralization of newly formed bone matrix. The disease is not cured by vitamin D replacement therapy, although some patients respond to very high doses of vitamin D or its metabolites. Cells derived from patients, mainly cultured skin fibroblasts, were used to assess steps in calcitriol action from cellular uptake to bioresponse and to elucidate the molecular aberrations in the vitamin D receptor (VDR). Point mutations in the VDR gene were identified in every patient examined, and the same defect was observed in the obligatory heterozygotes. The functional characterization of the patient's VDR reflected the localization of the mutation (18 different ones described to date), thus providing vital information about the structure–function relationship in the human VDR and the essentiality of the VDR as the mediator of vitamin D action.
Calcitriol as a Chemopreventive and Therapeutic Agent in Prostate Cancer: Role of Anti-Inflammatory Activity
Authors: Krishnan Aruna V , Moreno Jacqueline , Nonn Larisa , Swami Srilatha , Peehl Donna M , Feldman David 
Published: February 2008

Abstract
Calcitriol, the hormonally active form of vitamin D, inhibits the growth and development of several cancers. Inflammation has been implicated in the development and progression of many cancers, including prostate cancer (PCa). Recent research from our laboratory suggests that calcitriol exhibits anti-inflammatory actions that may contribute to its inhibitory effects in PCa. We found that calcitriol inhibits the synthesis and actions of pro-inflammatory prostaglandins (PGs) by three mechanisms: (1) inhibition of the expression of cyclooxygenase-2 (COX-2), the enzyme that synthesizes PGs, (2) induction of the expression of 15-prostaglandin dehydrogenase (15-PGDH), the enzyme that inactivates PGs, and (3) decreasing the expression of prostaglandin E and prostaglandin F PG receptors, which are the mediators of PG signaling. The combination of calcitriol and nonsteroidal anti-inflammatory drugs (NSAIDs) result in a synergistic inhibition of PCa cell growth and offers a potential therapeutic strategy. Acting on a separate anti-inflammatory pathway, calcitriol induces the expression of mitogen-activated protein kinase phosphatase 5 (MKP5), a member of a family of phosphatases that are negative regulators of MAP kinases, causing the selective dephosphorylation and inactivation of the stress-activated protein kinase p38. Because p38 activation may be both procarcinogenic and promote inflammation, this calcitriol action, especially coupled with the inhibition of the PG pathway, may contribute to the chemopreventive activity of calcitriol. We conclude that calcitriol exerts several anti-inflammatory actions in prostate cells, which contribute to its potential as a chemopreventive and therapeutic agent in PCa.
Vitamin D, Cardiovascular Disease, and Survival in Dialysis Patients
Authors: Moe Sharon M 
Published: February 2008

Abstract
Dialysis patients have an increased burden of cardiovascular disease, with &gt;70% of patients dying from a cardiovascular event. Several recent retrospective cohort studies have shown an association of treatment with calcitriol or its analogs and improved survival. The similar findings of these studies increase the validity of the observations, but these studies are subject to biases inherent in this type of study design. In particular, the nonrandom choice to treat, lack of information on concomitant medications, and differences in characteristics of patients who are treated compared with those not treated can lead to significant bias. Thus, prospective studies are needed. Two, small, uncontrolled, prospective studies showed improvement in left ventricular hypertrophy in dialysis patients treated with α-calcidiol or calcitriol, and there is abundant animal and in vitro studies showing biological plausibility. Thus, given the available evidence, it seems prudent to advise that most dialysis patients receive some form of vitamin D while we await results of a prospective interventional trial. The unknown is what type and how much to give, and whether this approach is safe, especially in patients with low levels of PTH.
Contemporary Diagnosis and Treatment of Vitamin D–Related Disorders
Authors: Jones Glenville , Horst Ronald , Carter Graham , Makin Hugh LJ 
Published: February 2008

Abstract
Plasma 25(OH)D has emerged as a valuable biomarker for the many varied health-related effects of vitamin D in the clinic mainly because of the recognition of the importance of the enzyme, CYP27B1, or the 25(OH)D-α-hydroxylase in the extrarenal, target cell production of calcitriol. This review briefly assesses current methodology for plasma 25(OH)D assay focusing mainly on currrent controversies surrounding the definition of the normal range and performance characteristics of the assay, separate measurement of both 25(OH)D2 and 25(OH)D3, and quality assurance tesing of laboratories offering the test. Clinicians have two main types of 25(OH)D assay based on either high-performance liquid chromatography with UV or mass detection or higher throughput kits based on protein (competitive protein binding assay or radioimmunoassay) binding. Based on 30 yr of experience with measuring 25(OH)D levels, it is concluded that, in the hands of appropriately trained experts, both types of assay provide reliable and accurate results, but all laboratories providing 25(OH)D data need frequent external quality assurance service to ensure that this performance is maintained.
Women talk revisited: Personal disclosures and alignment development
Authors: DeCapua Andrea , Berkowitz Diana , Boxer Diana 
Published: February 2008

Abstract
This study is an analysis of small-group talk among three different groups of women in the United States. Building upon Coates' (1996) study of female talk in a British speech community, we investigate how women build close personal relationships through their discourse. The data consist of three hours of videotaped interactions among the three all-female groups in different locations in the US and among interlocutors of differing social distance. We demonstrate here how variation in speech event norms coupled with differences in social distance relationships lead to distinct communicative enactments of friendship. The participants in the three groups are as follows: four close friends from northeastern New Jersey engaging in ordinary social conversation; four members of a Jewish Sisterhood organization in Long Island, New York, having a casual get-together; and three mothers of young children in Tampa, Florida, meeting for a playgroup date. The interlocutors in the three groups are all originally from their respective geographical areas and have lived in these areas most of their lives. All are native speakers of American English.
Our analysis focuses on small group talk among women in groups in which the relationships vary according to shared history, interests, and norms for interaction in social conversation and group meeting. From an ‘etic’ perspective, the three groups represent a continuum ranging from social, interactional talk to transactional talk that ‘gets down to business.’ However, the features of disclosures through personal narratives and the structural elements of overlap are shown here to function toward ‘women talk’ (Coates 1996). It will become clear that regardless of the social distance relationship, the all women's groups share elements of relational, or rapport talk (Tannen 1990) that are pervasive even in transactional, or information sharing encounters (Brown and Yule 1983). In all three groups we find structural elements that lend themselves to personal disclosures, accomplished via narratives (the New Jersey Group), overlaps (the Long Island Group), and Relational Identity Display and Development or RID (Boxer and Cortes-Conde 1997) (the Tampa Group).
The Theta System – a lexico-semantic approach?
Authors: Rapp Irene 
Published: February 2008

Abstract
Tanya Reinhart's “The Theta System” is mainly meant to explain the linking behaviour and the particular binding properties of experiencing verbs. Following Pesetsky (1995), Reinhart argues that verbs like worry possess three arguments: a cause, an experiencer and a subject matter role. Backwards bound anaphors are enabled only if it is the subject matter which is realized externally – it originates VP-internally and its trace is c-commanded by the experiencer:
(1) Hisi health worries every patienti. (Reinhart's example (42a)) If the subject is construed as the cause, it merges directly externally, and the c-command requirement is not met. Bound anaphors are not licensed in this case:
(2) ??Hisi doctor worried every patienti. (Reinhart's example (65b))
Yet another Theta System
Authors: Vogel Ralf 
Published: February 2008

Abstract
Tanya Reinhart's “Theta System” (henceforth: TS) is yet another version of what we call linking theories, i.e., theories that formulate generalizations about how verbs project their semantic arguments into syntactic constituent structure. The last decades of linguistic research have seen many proposals of this kind. The TS is particularly designed to fit into a minimalist theory of syntax, but, as far as I can see, there is nothing particularly minimalist in it, apart from details of technical execution. Neither is TS the only possible linking theory within minimalism.
Comparative markedness and derived environments
Authors: Mascaró Joan 
Published: February 2008

Abstract
McCarthy's paper contains a simple idea with important consequences. The simple idea is that markedness constraints come in two brands, OM and NM. Whereas a “classic” markedness constraint *M bans the structure M, OM does so only if M is present in the input and NM only if M is not present in the input. The idea is simple but the array of consequences that it entails is by no means simple. It can be implemented in different ways; some of the implementation problems are discussed by the author, others are left for the future. As for the consequences, some are theoretical (relations to local constraint conjunction, sympathy, stratal OT) others empirical. The latter involve new predictions (grandfather effects) and older empirical domains, like counter-feeding opacity and derived environment effects (DEE). In this reaction to McCarthy's paper I will concentrate on the latter.
What does comparative markedness explain, what should it explain, and how?
Authors: McCarthy John J 
Published: February 2008

Abstract

1. Introduction

These seven commentaries treat a wide range of topics in interesting and insightful ways. It is not possible to write a coherent response that addresses all of the criticisms and suggestions, large and small, that the authors have brought up. Several main themes emerge, however, that transcend the individual commentaries, and these themes supply the structure for this reply. They include alternatives to comparative markedness, possible counterexamples, comparative markedness on other dimensions of correspondence, and questions about the authenticity of opaque phonological processes. These themes will each be addressed in turn.
Comparative markedness and containment
Authors: Oostendorp Marc Van 
Published: February 2008

Abstract

Introduction

‘Comparative Markedness’ (CM) tries among other things to characterize the notion ‘possible constraint’ in Optimality Theory (OT) and in this way to both extend and constrain the scope of the theory. The author is the first to admit that the theory as it stands is not perfect in my opinion, it is the best approximation to problems such as opacity and derived environment effects within OT that is currently available; but problems remain.
Counterfeeding, derived environment effects, and comparative markedness
Authors: Blumenfeld Lev 
Published: February 2008

Abstract

0. Introduction

One of the most interesting aspects of the Comparative Markedness (CM) theory is the unification of several phenomena traditionally thought to be unrelated. Grandfathering effects, Derived Environment Effects (DEEs), and counterfeeding opacity all turn out to be different facets of the same phenomenon, due to the presence of new and old markedness in the system.