bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chromosomes in Leukemia and Beyond: From Irrelevant to Central Players
Authors: Rowley Janet D. 
Published: August 2009

Although it was definitely not obvious at first, consistent chromosomal translocations are major contributors to cellular transformation in some leukemias, lymphomas, sarcomas, prostate cancer, and other benign and malignant neoplasms. In the 50 years since the discovery of the Ph chromosome, the elucidation of recurring abnormalities has been an ongoing challenge that has evolved as new technologies allowed an ever more accurate definition of the precise changes in DNA resulting from these abnormalities. As we enter a new era of understanding enriched by gene expression studies, we still know little about the changes in the level of critical proteins, which may be the ultimate effectors of the genetic/epigenetic abnormalities in cancer. Despite remarkable progress in identifying both obvious chromosome abnormalities and subtle changes in DNA such as mutations and small copy-number variations, the impact of this knowledge has been variable. The challenge for the future is to enhance our ability to translate these genetic changes into effective therapies for other malignant diseases.
Modern Animals: From Subjects to Agents in Literary Studies
Authors: McHugh Susan 
Published: August 2009

AbstractAdvancing theories of literature and animality requires both recognizing the failures of traditional humanist models that separate and elevate people over all "things" animal as well as identifying and developing alternative forms. Along with providing fresh readings and important insights about representative texts in the literary canon, two new books—Carrie Rohman's Stalking the Subject: Modernism and the Animal (2009) and Philip Armstrong's What Animals Mean in the Fiction of Modernity (2008)—illustrate how this challenge is being addressed. Strategically, Rohman works within established textual forms of modern humanity to expand the parameters of who counts as a subject in literature. Armstrong takes a more tactical approach, extending ideas of nonhuman agency in order to frame this very discourse of representation itself as a problem that modern narrative forms bring to a crisis. What thus emerges is a range of textual actions and actors that exceed traditional humanist calculations of the subject. Together these studies frame questions with broader implications for humanistic scholarship: how do textual forms of subjectivity, even of discourse, become historical, and historically flexible, through animal involvements in literary representations?
Considerations on Life and Death: Medieval Asceticism and the Dissolution of the Self
Authors: Newman Martha 
Published: August 2009

AbstractThis essay explores the question of whether medieval asceticism is annihilation of the self or a means of constituting the self. It reads Gary Lease's conclusion, that religion is programmed suicide, against studies of medieval asceticism that argue for an understanding of religion as an embodied discipline which forms the subject and provides a means of resisting social norms. It suggests that the project of understanding the forms of power embedded in particular concepts of religion requires not only historicizing the term "religion" but also analyzing concepts of self, body, and agency. Drawing on the writings of the twelfth-century monk Bernard of Clairvaux as a case study, it argues that Bernard's conception of religion described a variety of ways in which embodied discipline could form a subject, and that he employed these variations ideologically to define the boundaries of his community and Church.
The Excremental Vision and the Study of Religion: An Afterword
Authors: Day Matthew 
Published: August 2009

AbstractGary Lease often deployed a Swiftian "excremental vision" to upend the liberal pretensions of "religion" and religious studies. However, this essay argues that there is far more to say about the relationship between religion and defecation. Indeed, the inescapable fact of human excrement should be viewed as an under-utilized site for academic theorizing about the power of "religion."
An Algorithm for Classification and Outlier Detection of Time-Series Data
Authors: Weekley R. Andrew , Goodrich Robert K. , Cornman Larry B. 
Published: August 2009

Abstract
An algorithm to perform outlier detection on time-series data is developed, the intelligent outlier detection algorithm (IODA). This algorithm treats a time series as an image and segments the image into clusters of interest, such as “nominal data” and “failure mode” clusters. The algorithm uses density clustering techniques to identify sequences of coincident clusters in both the time domain and delay space, where the delay-space representation of the time series consists of ordered pairs of consecutive data points taken from the time series. “Optimal” clusters that contain either mostly nominal or mostly failure-mode data are identified in both the time domain and delay space. A best cluster is selected in delay space and used to construct a “feature” in the time domain from a subset of the optimal time-domain clusters. Segments of the time series and each datum in the time series are classified using decision trees. Depending on the classification of the time series, a final quality score (or quality index) for each data point is calculated by combining a number of individual indicators. The performance of the algorithm is demonstrated via analyses of real and simulated time-series data.
Review: The varied attractions of the diabetic foot
Authors: Leese Graham P 
Published: August 2009

Various advances have been seen in the management of the diabetic foot. In some areas the rate of diabetes-related major amputations is declining. Duloxetine, pregabalin, venlafaxine and oxycodone are all well proven to help alleviate the pain of diabetic neuropathy. Negative pressure wound therapy has been shown to accelerate the healing of foot ulcers. New antibiotic policies designed to reduce Clostridium difficile and methicillin-resistant Staphylococcus aureus (MRSA) infections focus on narrow spectrum short duration antibiotics, and 80% of osteomyelitis can be successfully treated without surgery. Foot screening identifies patients who will ulcerate, with high-risk patients being up to 83 times more likely to ulcerate than low-risk patients. The ‘holiday foot’ and distal peripheral vascular disease remain as major risk factors for foot ulcer development and non-healing. The diabetic foot provides many interesting and varied challenges for the interested clinician. Br J Diabetes Vasc Dis 2009;9:155—159
Extensive intraclonal diversification in a subgroup of chronic lymphocytic leukemia patients with stereotyped IGHV4-34 receptors: implications for ongoing interactions with antigen
Authors: Sutton Lesley-Ann , Kostareli Efterpi , Hadzidimitriou Anastasia , Darzentas Nikos , Tsaftaris Athanasios , Anagnostopoulos Achilles , Rosenquist Richard , Stamatopoulos Kostas 
Published: August 2009

AbstractSeveral studies indicate that the development of chronic lymphocytic leukemia (CLL) may be influenced by antigen recognition through the clonotypic B-cell receptors (BCRs). However, it is still unclear whether antigen involvement is restricted to the malignant transformation phase or whether the putative antigen(s) may continuously trigger the CLL clone and affect not only the progenitor cell but also the leukemic cells themselves. To address this issue, we conducted a large-scale subcloning study of rearranged immunoglobulin heavy variable (IGHV) genes of diverse mutational status from 71 CLL cases (total, 1496 subcloned sequences), belonging to both the common IgM/IgD variant and the rare IgG-positive variant. Although most cases showed no or low levels of intraclonal diversification (ID), we report intense ID in the IGHV genes of selected cases, especially a subgroup of 13 IgG-switched cases expressing stereotyped, mutated IGHV4-34 rearrangements (subset 4). We demonstrate that the ID evident in subset 4 cases cannot be attributed to IGHV4-34 usage, IGHV gene-mutated status, class-switch recombination, or BCR stereotypy in general; rather, it represents a unique phenomenon strongly correlated with the distinctive BCR of subset 4. In such cases, the observed ID patterns may imply a stereotyped response to an active, ongoing interaction with antigen(s).
Acute graft-versus-host disease: from the bench to the bedside
Authors: Socié Gerard , Blazar Bruce R. 
Published: August 2009

AbstractDuring the past decade, progress in basic immunology has been impressive. In parallel, whereas our understanding of the pathophysiology of acute graft-versus-host disease (GVHD) has greatly improved, so has our knowledge of the complexities of the immune system. Much of the immunobiology of acute GVHD has been gleaned from preclinical models and far less from correlations with clinical observations or therapeutic interventions. In this review, we summarize some of the major advances in GVHD pathophysiology, including the translation of these from the bench to the bedside, and discuss preclinical approaches that warrant further exploration in the clinic.
B-cell follicle development remodels the conduit system and allows soluble antigen delivery to follicular dendritic cells
Authors: Bajénoff Marc , Germain Ronald N. 
Published: August 2009

Abstract
Afferent lymph is transported throughout lymph nodes (LNs) by the conduit system. Whereas this conduit network is dense in the T-cell zone, it is sparse in B-cell follicles. In this study, we show that this differential organization emerges during lymph node development. Neonatal LNs lack B follicles, but have a developed T-cell zone and a dense conduit network. As new T and B cells enter the developing LN, the conduit network density is maintained in the T, but not the B zone, leading to a profound remodeling of the follicular network that nevertheless maintains its connectivity. In adults, the residual follicular conduits transport soluble antigen to deep regions, where follicular dendritic cells are abundant and appear to replace the fibroblastic reticular cells that enwrap conduits in the T zone. This strategic location correlates with the capacity of the follicular dendritic cells to capture antigen even in the absence of antigen-specific antibodies. Together, these results describe how the stromal organization of the T and B regions of LNs diverges during development, giving rise to distinct antigen transport and delivery modes in the 2 compartments.
Bortezomib, tacrolimus, and methotrexate for prophylaxis of graft-versus-host disease after reduced-intensity conditioning allogeneic stem cell transplantation from HLA-mismatched unrelated donors
Authors: Koreth John , Stevenson Kristen E. , Kim Haesook T. , Garcia Michael , Ho Vincent T. , Armand Philippe , Cutler Corey , Ritz Jerome , Antin Joseph H. , Soiffer Robert J. , Alyea Edwin P. 
Published: August 2009

AbstractGraft-versus-host disease (GVHD) is a significant complication of allogeneic stem cell transplantation (alloSCT). The proteasome inhibitor bortezomib has immunomodulatory properties of potential benefit for GVHD control. We undertook a phase 1 trial of bortezomib, tacrolimus, and methotrexate for GVHD prophylaxis after reduced-intensity conditioning alloSCT using human leukocyte antigen–mismatched unrelated donors. Twenty-three patients were enrolled. Bortezomib dose levels of 1, 1.3, and 1.5 mg/m2 were evaluated with 5, 3, and 5 patients, respectively. Ten additional patients were accrued at the 1.3 mg/m2 bortezomib dose level. Bortezomib-related toxicity was minimal. With a 12-month median follow-up, grade II-IV acute GVHD occurred in 3 patients, a 180-day cumulative incidence of 13%. Chronic GVHD occurred in 9 patients, a 1-year cumulative incidence of 41%. At 1-year, the nonrelapse mortality was zero, cumulative incidence of relapse/progression was 29%, and overall, progression-free, and event-free survival were 75%, 64%, and 59%, respectively. Bortezomib is a promising novel immunomodulatory agent in allogeneic transplantation. This study was registered at http://www.clinicaltrials.gov as #NCT00369226.
Inferring polyploid phylogenies from multiply-labeled gene trees
Authors: Lott Martin , Spillner Andreas , Huber Katharina T , Petri Anna , Oxelman Bengt , Moulton Vincent 
Published: August 2009

AbstractBackgroundGene trees that arise in the context of reconstructing the evolutionary history of polyploid species are often multiply-labeled, that is, the same leaf label can occur several times in a single tree. This property considerably complicates the task of forming a consensus of a collection of such trees compared to usual phylogenetic trees.ResultsWe present a method for computing a consensus tree of multiply-labeled trees. As with the well-known greedy consensus tree approach for phylogenetic trees, our method first breaks the given collection of gene trees into a set of clusters. It then aims to insert these clusters one at a time into a tree, starting with the clusters that are supported by most of the gene trees. As the problem to decide whether a cluster can be inserted into a multiply-labeled tree is computationally hard, we have developed a heuristic method for solving this problem.ConclusionWe illustrate the applicability of our method using two collections of trees for plants of the genusSilene, that involve several allopolyploids at different levels.
Golgi localisation of GMAP210 requires two distinct cis-membrane binding mechanisms
Authors: Cardenas Jesus , Rivero Sabrina , Goud Bruno , Bornens Michel , Rios Rosa M 
Published: August 2009

Abstract

Background

The Golgi apparatus in mammals appears as a ribbon made up of interconnected stacks of flattened cisternae that is positioned close to the centrosome in a microtubule-dependent manner. How this organisation is achieved and retained is not well understood. GMAP210 is a long coiled-coil cis-Golgi associated protein that plays a role in maintaining Golgi ribbon integrity and position and contributes to the formation of the primary cilium. An amphipathic alpha-helix able to bind liposomes in vitro has been recently identified at the first 38 amino acids of the protein (amphipathic lipid-packing sensor motif), and an ARF1-binding domain (Grip-related Arf-binding domain) was found at the C-terminus. To which type of membranes these two GMAP210 regions bind in vivo and how this contributes to GMAP210 localisation and function remains to be investigated.

Results

By using truncated as well as chimeric mutants and videomicroscopy we found that both the N-terminus and the C-terminus of GMAP210 are targeted to the cis-Golgi in vivo. The ALPS motif was identified as the N-terminal binding motif and appeared concentrated in the periphery of Golgi elements and between Golgi stacks. On the contrary, the C-terminal domain appeared uniformly distributed in the cis-cisternae of the Golgi apparatus. Strikingly, the two ends of the protein also behave differently in response to the drug Brefeldin A. The N-terminal domain redistributed to the endoplasmic reticulum (ER) exit sites, as does the full-length protein, whereas the C-terminal domain rapidly dissociated from the Golgi apparatus to the cytosol. Mutants comprising the full-length protein but lacking one of the terminal motifs also associated with the cis-Golgi with distribution patterns similar to those of the corresponding terminal end whereas a mutant consisting in fused N- and C-terminal ends exhibits identical localisation as the endogenous protein.

Conclusion

We conclude that the Golgi localisation of GMAP210 is the result of the combined action of the two N- and C-terminal domains that recognise different sub-regions of the cis-GA. Based on present and previous data, we propose a model in which GMAP210 would participate in homotypic fusion of cis-cisternae by anchoring the surface of cisternae via its C-terminus and projecting its distal N-terminus to bind the rims or to stabilise tubular structures connecting neighbouring cis-cisternae.
Infection by a symbiotic polydnavirus induces wasting and inhibits metamorphosis of the mothPseudoplusia includens
Authors: Pruijssers A. J. , Falabella P. , Eum J. H. , Pennacchio F. , Brown M. R. , Strand M. R. 
Published: August 2009

SUMMARYInsect pathogens and parasites often affect the growth and development of their hosts, but understanding of these processes is fragmentary. Among the most species-rich and important mortality agents of insects are parasitoid wasps that carry symbiotic polydnaviruses (PDVs). Like many PDV-carrying wasps, Microplitis demolitor inhibits growth and pupation of its lepidopteran host, Pseudoplusia includens, by causing host hemolymph juvenile hormone (JH) titers to remain elevated and preventing ecdysteroid titers from rising. Here we report these alterations only occurred if P. includens was parasitized prior to achieving critical weight, and were fully mimicked by infection with only M. demolitor bracovirus (MdBV). Metabolic assays revealed that MdBV infection of pre-critical weight larvae caused a rapid and persistent state of hyperglycemia and reduced nutrient stores. In vitro ecdysteroid assays further indicated that prothoracic glands from larvae infected prior to achieving critical weight remained in a refractory state of ecdysteroid release, whereas infection of post-critical weight larvae had little or no effect on ecdysteroid release by prothoracic glands. Taken together, our results suggest MdBV causes alterations in metabolic physiology, which prevent the host from achieving critical weight. This in turn inhibits the endocrine events that normally trigger metamorphosis.
Buccal neurons activate ciliary beating in the foregut of the pteropod molluskClione limacina
Authors: Malyshev Aleksey Y. , Balaban Pavel M. 
Published: August 2009

SUMMARYBeating of cilia lining the foregut of gastropods facilitates the swallowing of food and, therefore, plays a role in feeding behavior. Despite the fact that neural control of feeding is well studied in mollusks, no neurons controlling ciliary beating in the foregut have been identified to date. Here we describe for the first time a pair of buccal neurons innervating the foregut of Clione. Intracellular stimulation of these neurons induced vigorous activation of cilia lining the foregut in a semi-intact preparation. Using immunochemistry labeling, buccal foregut cells were found to contain peptides similar to CNP neuropeptides of the terrestrial snail Helix lucorum. Application of DYPRL-amide, a member of the Helix CNP peptide family, mimicked the effect of buccal foregut cell stimulation on ciliary activity. Induction of fictive feeding in an isolated CNS preparation resulted in the activation of buccal foregut cells suggesting that these cells control ciliary beating in the foregut during feeding. Thus,cilia-activating buccal neurons may represent a new intrinsic element of the neural control of feeding in gastropods.
A strong magnetic anomaly affects pigeon navigation
Authors: Wiltschko Roswitha , Schiffner Ingo , Wiltschko Wolfgang 
Published: August 2009

SUMMARY
Pigeons were released in a strong magnetic anomaly with fast changes in intensity and gradients directions, about 60 km from their loft, and, for comparison, at the border of the anomaly and at a control site. The vanishing bearings were found to be closely related to the home direction, but unrelated to the local gradient directions. The vector lengths and the vanishing intervals, however, were significantly correlated with the maximum difference in intensity within a 2.5 km radius around the release site. This correlation was negative for the vector lengths and positive for the vanishing intervals,indicating that steep local gradients increase scatter between pigeons and delay their departure. These findings suggest that an irregular, fast changing magnetic field as found in the anomaly leads to confusion during the navigational processes. This, in turn, implies that pigeons can sense the respective changes in magnetic intensity. Magnetic cues seem to be included in the normal navigational processes that determine the departure direction.
Activity of trunk muscles during aquatic and terrestrial locomotion inAmbystoma maculatum
Authors: Deban Stephen M. , Schilling Nadja 
Published: August 2009

SUMMARYThe activity of seven trunk muscles was recorded at two sites along the trunk in adult spotted salamander, Ambystoma maculatum, during swimming and during trotting in water and on land. Several muscles showed patterns of activation that are consistent with the muscles producing a traveling wave of lateral bending during swimming and a standing wave of bending during aquatic and terrestrial trotting: the dorsalis trunci,subvertebralis lateralis and medialis, rectus lateralis and obliquus internus. The interspinalis showed a divergent pattern and was active out of phase with the other muscles suggesting that it functions in vertebral stabilization rather than lateral bending. The obliquus internus and rectus abdominis showed bilateral activity indicating that they counteract sagittal extension of the trunk that is produced when the large dorsal muscles are active to produce lateral bending. Of the muscles examined, only the obliquus internus showed a clear shift in function from lateral bending during swimming to resistance of long-axis torsion during trotting. During terrestrial trotting, muscle recruitment was greater in several muscles than during aquatic trotting,despite similar temporal patterns of muscle activation, suggesting that the trunk is stiffened during terrestrial locomotion against greater gravitational forces whereas the basic functions of the trunk muscles in trotting are conserved across environments.
Courtship Songs of Chrysoperla nipponensis (Neuroptera: Chrysopidae) Delineate Two Distinct Biological Species in Eastern Asia
Authors: Henry Charles S , Mochizuki Atsushi , Nakahira Kengo , Haruyama Naoto , Nomura Masashi 
Published: August 2009

Abstract
The substrate-borne vibrational courtship songs of type A and type B Chrysoperla nipponensis (Okamoto) (Neuroptera: Chrysopidae) are described in detail, from populations sampled throughout Japan and near Beijing, China. The song of type A is long (≈ 5–6 s) and is made up of numerous (four to 12) volleys of four distinct forms that differ in their carrier frequencies. The song of type B is shorter (≈2 s) and functions as a repeated single-volley song, but each volley is shown here to consist of four to six distinct subsections. During heterosexual duets, partners of type A exchange their long multi-volley songs, whereas partners of type B repeatedly exchange short single-volley songs. Geographical variation within each song type is low and largely insignificant. In addition, previously recognized mitochondrial (cytochrome oxidase subunit I) haplotypes Al and A2 of type A C. nipponensis do not have different songs. These results support the hypothesis that types A and B C. nipponensis are distinct species, with type A corresponding to the nominate species (i.e., C. nipponensis s. str.) and type B as yet unnamed. Their songs are among the most complex yet found in the Chrysoperla carnea swarm of cryptic species.