bluuebunny/crossref_metadata_2025_split huggingface dataset:
Management of sarcomatoid salivary duct carcinoma of the submandibular gland duct with coexisting seropositive human immunodeficiency virus
Authors: Mourad W F , Hu K S , Shourbaji R A , Harrison L B 
Published: April 2013

AbstractBackground:Sarcomatoid salivary duct carcinoma of the submandibular gland is extremely rare. This paper highlights the impact of surgery and adjuvant radiation therapy on the outcome of this disease.Methods:A 59-year-old man with human immunodeficiency virus presented with a painless, rapidly growing left neck mass. Biopsy followed by surgical excision of the left submandibular gland revealed sarcomatoid salivary duct carcinoma of the submandibular gland duct with perineural invasion and close margins, for which he underwent adjuvant radiotherapy. Post-operative positron emission tomography and computed tomography revealed no residual or metastatic disease. Pathological analysis of tumour–node–metastasis staging revealed a T2 N0 M0 (stage II) tumour.Results:The patient tolerated his treatment without serious acute or long-term side effects. There was no evidence of disease on comprehensive examination or on positron emission tomography or computed tomography scans at the 4.6-year follow up.Conclusion:Surgery followed by adjuvant radiotherapy provided practical locoregional control with acceptable toxicity. Further detailed case reports are warranted to optimise the management of this rare malignancy.
ELOPER: elongation of paired-end reads as a pre-processing tool for improved de novo genome assembly
Authors: Silver David H. , Ben-Elazar Shay , Bogoslavsky Alexei , Yanai Itai 
Published: April 2013

Abstract
Motivation: Paired-end sequencing resulting in gapped short reads is commonly used for de novo genome assembly. Assembly methods use paired-end sequences in a two-step process, first treating each read-end independently, only later invoking the pairing to join the contiguous assemblies (contigs) into gapped scaffolds. Here, we present ELOPER, a pre-processing tool for pair-end sequences that produces a better read library for assembly programs.
Results: ELOPER proceeds by simultaneously considering both ends of paired reads generating elongated reads. We show that ELOPER theoretically doubles read-lengths while halving the number of reads. We provide evidence that pre-processing read libraries using ELOPER leads to considerably improved assemblies as predicted from the Lander–Waterman model.
Availability: http://sourceforge.net/projects/eloper.
Contact: yanai@technion.ac.il
Supplementary information: Supplementary data are available at Bioinformatics online.
APP2: automatic tracing of 3D neuron morphology based on hierarchical pruning of a gray-weighted image distance-tree
Authors: Xiao Hang , Peng Hanchuan 
Published: April 2013

Abstract
Motivation: Tracing of neuron morphology is an essential technique in computational neuroscience. However, despite a number of existing methods, few open-source techniques are completely or sufficiently automated and at the same time are able to generate robust results for real 3D microscopy images.
Results: We developed all-path-pruning 2.0 (APP2) for 3D neuron tracing. The most important idea is to prune an initial reconstruction tree of a neuron’s morphology using a long-segment-first hierarchical procedure instead of the original termini-first-search process in APP. To further enhance the robustness of APP2, we compute the distance transform of all image voxels directly for a gray-scale image, without the need to binarize the image before invoking the conventional distance transform. We also design a fast-marching algorithm-based method to compute the initial reconstruction trees without pre-computing a large graph. This method allows us to trace large images. We bench-tested APP2 on ∼700 3D microscopic images and found that APP2 can generate more satisfactory results in most cases than several previous methods.
Availability: The software has been implemented as an open-source Vaa3D plugin. The source code is available in the Vaa3D code repository http://vaa3d.org.
Contact: hanchuanp@alleninstitute.org
Supplementary information: Supplementary data are available at Bioinformatics online.
rRNA:mRNA pairing alters the length and the symmetry of mRNA-protected fragments in ribosome profiling experiments
Authors: O’Connor Patrick B. F. , Li Gene-Wei , Weissman Jonathan S. , Atkins John F. , Baranov Pavel V. 
Published: April 2013

Abstract
Motivation: Ribosome profiling is a new technique that allows monitoring locations of translating ribosomes on mRNA at a whole transcriptome level. A recent ribosome profiling study demonstrated that internal Shine–Dalgarno (SD) sequences have a major global effect on translation rates in bacteria: ribosomes pause at SD sites in mRNA. Therefore, it is important to understand how SD sites effect mRNA movement through the ribosome and generation of ribosome footprints.
Results: Here, we provide evidence that in addition to pausing effect, internal SD sequences induce a caterpillar-like movement of mRNA through the ribosome cavity. Once an SD site binds to the ribosome, it remains attached to it while the ribosome decodes a few subsequent codons. This leads to asymmetric progressive elongation of ribosome footprints at the 3′-end. It is likely that internal SD sequences induce a pause not on a single, but on several adjacent codons. This finding is important for our understanding of mRNA movement through the ribosome and also should facilitate interpretation of ribosome profiling data.
Contact: brave.oval.pan@gmail.com
Decrease in dendritic cells in endomyocardial biopsies of human dilated cardiomyopathy
Authors: Pistulli Rudin , König Sebastian , Drobnik Stefanie , Kretzschmar Daniel , Rohm Ilonka , Lichtenauer Michael , Fritzenwanger Michael , Mall Gerhard , Mall Gita , Figulla Hans‐Reiner , Yilmaz Atilla 
Published: April 2013

AimsDendritic cells (DCs) are sentinels of the immune system—their role in myocardial disease is unknown as yet. We investigated their myocardial presence in human dilated cardiomyopathy (DCM).Methods and resultsEndomyocardial biopsies from 72 patients with DCM (EF ∼30%), as well as myocardial specimens from 18 suicide or accident victims were immunohistochemically analysed for myeloid and plasmacytoid DCs, antigen‐presenting cells (APCs), and other leucocytes; also tissue fibrosis and apoptosis were histologically quantified. The myocardial viral genome was identified through polymerase chain reaction, and patients underwent clinical follow‐up in 3–6 months. We found myocardial DCs of all examined subtypes and maturation stages (fascin, CD11c, CD209, CD83, and CD304), as well as markers for APCs (HLA‐DR and CD40) and T‐cell activation (CD69) to be significantly decreased in DCM compared with controls. In contrast, regulatory T cells (the GITR epitope), apoptosis (by TUNEL reaction and immunostaining with BCL‐2), and a DC chemokine receptor (CCR7) were overexpressed, while no significant differences were observed for macrophages (CD68). Immature myeloid and plasmacytoid DCs strongly correlated with endothelial progenitor cells (CD34), which were similarly reduced in DCM, and inversely correlated with fibrosis. Myeloid DCs were especially reduced in virus‐positive biopsies, and their numbers correlated with positive change in EF (ΔEF) at follow‐up.ConclusionMyocardial DCs are reduced in heart biopsies of symptomatic DCM patients. Such a reduction correlates with an unfavourable short‐term outcome in terms of EF, and could result from myocardial tissue damage, cellular death, and insufficient vascularization in chronic heart failure.
Why do assessments of demersal stocks largely ignore habitat?
Authors: Caddy John F. 
Published: April 2013

AbstractThe divergence between most stock assessments and studies in marine ecology is characterized by the low priority usually given to assessing the holding capacity of marine habitats. Habitats of high structural complexity are relatively uncommon in shelf waters, are contagiously distributed, and are damaged incidentally by bottom-towed gear. Structurally complex habitats are used by many demersal fish and crustaceans for predation abatement and as a site for feeding forays. Successive life-history stages typically migrate through several structurally complex habitats which recent studies show often to have fractal properties. One consequence of fractal structures as cover is a rapid reduction of protection from predators with growth in size: migration is the only response possible when further growth of the recruiting age class renders individuals in that habitat vulnerable to predation. A common feature of structurally complex habitats with high vulnerability at size is the occurrence of population bottlenecks. It is suggested that identifying and rectifying shortages of structured habitat, and eliminating habitat bottlenecks, will be effective in stock enhancement. This will require placing strict spatial constraints on the operation of bottom gear. This paper reviews new methods of estimating juvenile predation mortality, including mortality-at-age and mortality-at-life-history stage, which depend on the fractal characteristics of structurally complex habitats.
Management of Cholestatic Pruritus in Paediatric Patients With Alagille Syndrome
Authors: Kronsten Victoria , Fitzpatrick Emer , Baker Alastair 
Published: April 2013

ABSTRACTObjectives:The aims of the study were to perform a retrospective observational review of the present management and outcome of cholestatic pruritus in children with Alagille syndrome (AGS) at King's College Hospital and to use results to inform appropriate guidelines.Methods:A retrospective review of 62 patients diagnosed as having AGS from January 1995 to November 2010 treated at King's College Hospital was performed. The departmental database of the Paediatric Liver Centre was searched to identify all patients and the clinical records were then analysed.Results:Fifty‐one (82.3%) patients experienced pruritus and 50 (80.6%) received antipruritic medication. Ursodeoxycholic acid was the most prescribed drug (n = 40). Other drugs prescribed were rifampicin (n = 39), cholestyramine (n = 18), naltrexone (n = 14), alimemazine (n = 13), nonsedating antihistamine agents (n = 7), ondansetron (n = 5), and phenobarbitone (n = 1). Albumin dialysis using the molecular adsorbent recirculation system was used in 1 patient. Sixteen patients (25.8%) were listed for liver transplantation, and 11 had undergone transplantation by November 2010. Patient survival was high at 95.2%. Pruritus resolved permanently in 39.2% (n = 20) of patients. Fifty‐five percent (n = 11) of such patients had undergone liver transplantation. Pruritus was controlled by medication in 41.2% (n = 21). Itching remained a significant problem, affecting quality of life in 19.6% of patients (n = 10).Conclusions:The management of cholestatic pruritus in AGS is difficult and often suboptimal. Pruritus may remain intractable even with combination medical treatment, and at this stage, surgery or liver transplantation is indicated. At our centre, pruritus was successfully treated in 80.4% of patients with medical and surgical management.
Patterning and Lifetime of Plasma Membrane-Localized Cellulose Synthase Is Dependent on Actin Organization in Arabidopsis Interphase Cells
Authors: Sampathkumar Arun , Gutierrez Ryan , McFarlane Heather E. , Bringmann Martin , Lindeboom Jelmer , Emons Anne-Mie , Samuels Lacey , Ketelaar Tijs , Ehrhardt David W. , Persson Staffan 
Published: April 2013

Abstract
The actin and microtubule cytoskeletons regulate cell shape across phyla, from bacteria to metazoans. In organisms with cell walls, the wall acts as a primary constraint of shape, and generation of specific cell shape depends on cytoskeletal organization for wall deposition and/or cell expansion. In higher plants, cortical microtubules help to organize cell wall construction by positioning the delivery of cellulose synthase (CesA) complexes and guiding their trajectories to orient newly synthesized cellulose microfibrils. The actin cytoskeleton is required for normal distribution of CesAs to the plasma membrane, but more specific roles for actin in cell wall assembly and organization remain largely elusive. We show that the actin cytoskeleton functions to regulate the CesA delivery rate to, and lifetime of CesAs at, the plasma membrane, which affects cellulose production. Furthermore, quantitative image analyses revealed that actin organization affects CesA tracking behavior at the plasma membrane and that small CesA compartments were associated with the actin cytoskeleton. By contrast, localized insertion of CesAs adjacent to cortical microtubules was not affected by the actin organization. Hence, both actin and microtubule cytoskeletons play important roles in regulating CesA trafficking, cellulose deposition, and organization of cell wall biogenesis.
Genetic Analysis of the Biosynthesis of 2-Methoxy-3-Isobutylpyrazine, a Major Grape-Derived Aroma Compound Impacting Wine Quality
Authors: Guillaumie Sabine , Ilg Andrea , Réty Stéphane , Brette Maxime , Trossat-Magnin Claudine , Decroocq Stéphane , Léon Céline , Keime Céline , Ye Tao , Baltenweck-Guyot Raymonde , Claudel Patricia , Bordenave Louis , Vanbrabant Sandra , Duchêne Eric , Delrot Serge , Darriet Philippe , Hugueney Philippe , Gomès Eric 
Published: April 2013

AbstractMethoxypyrazines (MPs) are strongly odorant volatile molecules with vegetable-like fragrances that are widespread in plants. Some grapevine (Vitis vinifera) varieties accumulate significant amounts of MPs, including 2-methoxy-3-isobutylpyrazine (IBMP), which is the major MP in grape berries. MPs are of particular importance in white Sauvignon Blanc wines. The typicality of these wines relies on a fine balance between the pea pod, capsicum character of MPs and the passion fruit/grapefruit character due to volatile thiols. Although MPs play a crucial role in Sauvignon varietal aromas, excessive concentrations of these powerful odorants alter wine quality and reduce consumer acceptance, particularly in red wines. The last step of IBMP biosynthesis has been proposed to involve the methoxylation of the nonvolatile precursor 2-hydroxy-3-isobutylpyrazine to give rise to the highly volatile IBMP. In this work, we have used a quantitative trait loci approach to investigate the genetic bases of IBMP biosynthesis. This has led to the identification of two previously uncharacterized S-adenosyl-methionine-dependent O-methyltransferase genes, termed VvOMT3 and VvOMT4. Functional characterization of these two O-methyltransferases showed that the VvOMT3 protein was highly specific and efficient for 2-hydroxy-3-isobutylpyrazine methylation. Based on its differential expression in high- and low-MP-producing grapevine varieties, we propose that VvOMT3 is a key gene for IBMP biosynthesis in grapevine.
Estimating structural change in US crop insurance experience
Authors: Coble Keith H. , Knight Thomas O. , Miller Mary Frances , Goodwin Barry J. , Rejesus Roderick M. , Boyles Ryan 
Published: April 2013

PurposeThe purpose of this research is to investigate the degree to which trends and structural change may have altered crop insurance expected loss cost ratios across time. Because loss experience is used to set rates for the program, these changes can impact the premiums paid by producers and cost to the government.Design/methodology/approachCounty level adjusted loss cost data was merged with climate division weather data for the 1980‐2009 period. Crop‐specific regional‐level regression models were estimated to test for trends and structural changes in the loss experience for major crops (corn, soybeans, sorghum, cotton, winter wheat, and spring wheat). Climate data was used to control for the effect of weather.FindingsFor several crops and regions, a significant break point in the loss cost data is found at 1995. This is consistent with the policy changes that occurred in in the program due to the 1994 legislative change. In most instances loss experience prior to 1995 is higher than more recent years even when controlling for the effect of weather. The exception is in winter wheat where it appears recent experience may be worse rather than older experience.Originality/valueThis paper provides a large‐scale assessment of the magnitude of improved crop insurance loss experience across time.
Attitude coordination of satellite swarms with communication delays
Authors: Liang Haizhao , Sun Zhaowei , Wang Jianying 
Published: April 2013

PurposeThis paper aims to investigate the fast attitude coordinated control problem for rigid satellite swarms with communication delays.Design/methodology/approachBased on behavior‐based control approach, the attitude control system is designed to guarantee that the attitude of the satellite swarm converge to a dynamic reference state in finite time. A fast sliding mode is developed to improve the convergence rate and robustness of the control system. All the effects of communication delays, parameter uncertainties and external disturbances are taken into account simultaneously, and the communication topology of the satellite swarm can be arbitrary types. Numerical simulations are provided to demonstrate the analytic results.FindingsDespite the existence of communication delays, parameter uncertainties and external disturbances, the stability of the closed‐loop system can be successfully guaranteed and the proposed control strategies are effective to overcome these unexpected phenomena subject to arbitrary communication topology.Originality/valueThis paper introduces a fast terminal sliding mode control method which can guarantee the fast convergence of the attitude state of the satellite swarm in the presence of communication delays, switched communication topology, parameter uncertainties and external disturbances.
The use of welfare by migrants in Italy
Authors: Pellizzari Michele 
Published: April 2013

PurposeThe purpose of this paper is to analyse the issue of welfare use by migrants in Italy and overcome the limitations of previous studies related to the quality of the data and to the high level of fragmentation of the Italian welfare system.Design/methodology/approachIn this paper the author is able to overcome the limitations of previous research by using an original administrative archive of means tests, performed at all levels of the public administration, to establish individual's and households’ eligibility to all kinds of benefits, both in cash and kind.FindingsResults show that, without controlling for observable characteristics, migrants from outside the EU are more likely to apply for welfare. Once individual and household characteristics are controlled for, such a residual welfare dependency is greatly reduced but does not disappear. Geographical location is a key factor, given that migrants tend to locate in the richest areas of the country, which also happen to be the ones where local welfare is most generous.Originality/valueTo the best of the author's knowledge, the administrative database used in this paper has never been used for analysing the use of welfare by migrants. Moreover, the role of geographical sorting of migrants has never been investigated in this area.
Retaliation against reporters of unequal treatment
Authors: Svensson Jörgen , van Genugten Marieke 
Published: April 2013

PurposeEqual treatment in the workplace is considered one of the most fundamental rights of employees. This right also implies that employees must be able to address any form of unequal treatment freely and effectively, without fear of retaliation. The purpose of this paper is to investigate the prevalence of retaliation against complaints of unequal treatment in The Netherlands and its underlying factors.Design/methodology/approachThis article is based on a telephone survey among employees who filed a formal complaint about unequal treatment at work to the Dutch Equal Treatment Commission.FindingsThe main finding is that retaliation against equal treatment reports is commonplace in The Netherlands and in many cases takes on serious forms. Furthermore it is found that the nature and extent of retaliation are primarily explained by the circumstances in which unequal treatment develops and that the extent of retaliation is neither explained by the manner in which unequal treatment is addressed nor by the level of institutionalized protection that is available.Originality/valueThe need for a better understanding of retaliation is high, because retaliation and fear of retaliation have broad consequences for the psychological and physical well‐being of individual employees and for employment relationships. Yet, studies on retaliation in the context of employment discrimination are rare, especially outside the USA. This article contributes to a better understanding of retaliation, which may be used by policy makers, employees and employers to address it more effectively.
Self‐reflexivity scrutinized: (pro‐)feminist men learning that gender matters
Authors: Styhre Alexander , Tienari Janne 
Published: April 2013

PurposeThe purpose of this paper is to contribute to the debate on reflexivity in organization and management studies by scrutinizing the possibilities of self‐reflexivity.Design/methodology/approachBy means of auto‐ethnography, the authors analyze their own experiences as (pro‐)feminist men in the field of gender studies.FindingsThe authors argue that self‐reflexivity is partial, fragmentary and transient: it surfaces in situations where the authors’ activities and identities as researchers are challenged by others and they become aware of their precarious position.Originality/valueThe paper's perspective complements more instrumental understandings of self‐reflexivity, and stimulates further debate on its limits as well as potential.
Women at the top
Authors: Atewologun Doyin , Doldor Elena 
Published: April 2013

PurposeThis paper reviews the recent “Women at the Top” Conference held in London by the British Psychological Society's Division of Occupational Psychology and offers some suggestions for future research on women at the top.Design/methodology/approachThe report is generated from attendee observations, notes, other reviews and podcast recordings following the conference.FindingsConference proceedings highlighted key areas of interest and current work for psychologists tackling the dearth of women leaders. A majority of presentations examined the role of stereotyping and prejudice in understanding leadership and gender, while a few others discussed contextual factors shaping women's leadership journeys such as life experiences and external parties such as head‐hunters. The limited focus on other diversity dimensions such as racio‐ethnicity is noted.Originality/valueIn light of the conference proceedings, the authors discuss how psychological research could further contribute to addressing the lack of women at the top of organisations. The authors suggest that models of stereotyping and prejudice in leadership need further contextualization and call for more research on multiple stakeholders accountable for women's leadership experiences, particularly those in positions of power and privilege such as current male leaders and Chairmen. Also stressed is the need for an intersectional approach which takes into account the multiple identities of women at the top.