bluuebunny/crossref_metadata_2025 huggingface dataset:
Draft Genome Assembly of Acinetobacter baumannii ATCC 19606
Authors: Davenport Karen W. , Daligault Hajnalka E. , Minogue Timothy D. , Bruce David C. , Chain Patrick S. G. , Coyne Susan R. , Jaissle James G. , Koroleva Galina I. , Ladner Jason T. , Li Po-E , Palacios Gustavo F. , Scholz Matthew B. , Teshima Hazuki , Johnson Shannon L.
Published: August 2014

Acinetobacter baumannii
is an emerging nosocomial pathogen, and therefore high-quality genome assemblies for this organism are needed to aid in detection, diagnostic, and treatment technologies. Here we present the improved draft assembly of
A. baumannii
ATCC 19606 in two scaffolds. This 3,953,621-bp genome contains 3,750 coding regions and has a 39.1% G+C content.
Draft Genome Sequence of the Pyridinediol-Fermenting Bacterium Synergistes jonesii 78-1
Authors: Holland-Moritz Hannah E. , Coil David A. , Badger Jonathan H. , Dmitrov George I. , Khouri Hoda , Ward Naomi L. , Robb Frank T. , Eisen Jonathan A.
Published: August 2014

Here we present the draft genome of
Synergistes jonesii
78-1, ATCC 49833, a member of the
Synergistes
phylum. This organism was isolated from the rumen of a Hawaiian goat and ferments pyridinediols. The assembly contains 2,747,397 bp in 61 contigs.
Complete Genome Sequence of Campylobacter iguaniorum Strain 1485E
T
, Isolated from a Bearded Dragon (
Pogona vitticeps
)
Authors: Gilbert Maarten J. , Miller William G. , Yee Emma , Kik Marja , Wagenaar Jaap A. , Duim Birgitta
Published: August 2014

Campylobacter iguaniorum
has been isolated from reptiles. This
Campylobacter
species is genetically related to
Campylobacter fetus
and
Campylobacter hyointestinalis
. Here we present the first whole-genome sequence for this species.
Mycolic Acid Biosynthesis Genes in the Genome Sequence of Corynebacterium atypicum DSM 44849
Authors: Tippelt Anna , Möllmann Sabrina , Albersmeier Andreas , Jaenicke Sebastian , Rückert Christian , Tauch Andreas
Published: August 2014

The complete chromosomal sequence of the type strain
Corynebacterium atypicum
DSM 44849 comprises 2,311,380 bp. A functional annotation revealed the presence of genes involved in the synthesis and export of mycolic acids and in trehalose corynomycolate biosynthesis, supporting the view that the cell envelope of
C. atypicum
contains mycolic acids.
Complete Genome Sequence of a Klebsiella pneumoniae Strain Isolated from a Known Cotton Insect Boll Vector
Authors: Medrano Enrique G. , Forray Marissa M. , Bell Alois A.
Published: August 2014

Klebsiella pneumoniae
(associated with bacterial pneumonia) was previously isolated from
Nezara viridula
, a significant vector of cotton boll-rot pathogens. We provide the first annotated genome sequence of the cotton opportunistic strain
K. pneumoniae
5-1. This data provides guidance to study the bases of cotton pathogenesis by bacteria associated with vectors.
Evaluating the state of the art in disorder recognition and normalization of the clinical narrative
Authors: Pradhan Sameer , Elhadad Noémie , South Brett R , Martinez David , Christensen Lee , Vogel Amy , Suominen Hanna , Chapman Wendy W , Savova Guergana
Published: August 2014

Objective The ShARe/CLEF eHealth 2013 Evaluation Lab Task 1 was organized to evaluate the state of the art on the clinical text in (i) disorder mention identification/recognition based on Unified Medical Language System (UMLS) definition (Task 1a) and (ii) disorder mention normalization to an ontology (Task 1b). Such a community evaluation has not been previously executed. Task 1a included a total of 22 system submissions, and Task 1b included 17. Most of the systems employed a combination of rules and machine learners.

Materials and methods We used a subset of the Shared Annotated Resources (ShARe) corpus of annotated clinical text—199 clinical notes for training and 99 for testing (roughly 180 K words in total). We provided the community with the annotated gold standard training documents to build systems to identify and normalize disorder mentions. The systems were tested on a held-out gold standard test set to measure their performance.

Results For Task 1a, the best-performing system achieved an F1 score of 0.75 (0.80 precision; 0.71 recall). For Task 1b, another system performed best with an accuracy of 0.59.

Discussion Most of the participating systems used a hybrid approach by supplementing machine-learning algorithms with features generated by rules and gazetteers created from the training data and from external resources.

Conclusions The task of disorder normalization is more challenging than that of identification. The ShARe corpus is available to the community as a reference standard for future studies.
Recurrent spontaneous compartment syndrome of the thigh
Authors: Rohman Lebur , Chan Sheung , Hadi Saifullah , Maruszewski Daniel
Published: August 2014

Acute comparment syndrome (ACS) is a surgical emergency, in which tissue pressure becomes greater than perfusion pressure leading to tissue ischaemia. It is typically a consequence of trauma. We present a case in which a patient suffers blunt trauma to the thigh, but develops ACS 2 years after this injury and consequently endures 10-episodes of ACS (no perciptating event or cause) in the same thigh over 10 years. On the 10th presentation the patient was found to have arteriovenous malformation on MR angiography which were embolised and the fasciotomy wound closed with a split-thickness skin graft. A thorough literature search deemed this case to be the first reported recurrent spontaneous ACS of the thigh. Prompt recognition and treatment of ACS is vital. Clinicians should thoroughly investigate such patients postoperatively and involve vascular/plastic surgeons and interventianal radiologist to provide optimum care and prevent recurrence.
Hyperinfection strongyloidiasis in renal transplant recipients
Authors: Khuroo Mehnaaz S
Published: August 2014

Strongyloidiasis is infection caused by the nematodeStrongyloides stercoralis. Chronic uncomplicated strongyloidiasis is known to occur in immunocompetent individuals while hyperinfection and dissemination occurs in selective immunosuppressed hosts particularly those on corticosteroid therapy. We report two cases of hyperinfection strongyloidiasis in renal transplant recipients and document endoscopic and pathological changes in the involved small bowel. One patient presented with features of dehydration and malnutrition while another developed ileal obstruction and strangulation, requiring bowel resection. Oesophagogastroduodenoscopy showed erythematous and thickened duodenal mucosal folds. Histopathological examination of duodenal biopsies revealedS. stercoralisworms, larvae and eggs embedded in mucosa and submucosa. Wet mount stool preparation showed filariform larvae ofS. stercoralisin both cases. Patients were managed with anthelmintic therapy (ivermectin/albendazole) and concurrent reduction of immunosuppression. Both patients had uneventful recovery. Complicated strongyloidiasis should be suspected in immunocompromised hosts who present with abdominal pain, vomiting and diarrhoea, particularly in endemic areas.
Fulminant pneumococcal infection
Authors: Naito Ryo , Miyazaki Tetsuro , Kajino Kazunori , Daida Hiroyuki
Published: August 2014

Fulminant pneumococcal infection is a fatal pneumococcal infection that tends to occur in immunocompromised hosts, such as patients who are asplenic or on immunosuppressant therapy. We experienced a case of a 73-year-old Japanese man with a medical history of coronary stent implantation and catheter ablation for atrial flutter who presented with dyspnoea at rest. The patient was diagnosed with streptococcal pneumonia based on a urine antigen test and CT. Despite the use of effective antibiotics and systemic therapies, his clinical course was rapidly progressive and he died 18 h after admission. This case of fulminant pneumococcal infection is reported along with the autopsy findings.
Granulocytic sarcoma (chloroma) presenting as colo-colic intussusception in a 16-year-old boy: an unusual presentation
Authors: Gupta Saurabh , Chawla Inderjit , Singh Vishwajeet , Singh Karnail
Published: August 2014

A 16-year-old boy presented with intestinal obstruction with left lumbar mass. On evaluation with ultrasonography and contrast-enhanced CT of abdomen he was found to have left colo-colic intussusception. On exploratory laparotomy he was found to have invagination of necrosed distal transverse colon and splenic flexure with omentum into descending colon with enlarged mesenteric lymph nodes for which left hemicolectomy was performed. Histopathology and immunohistochemistry was suggestive of submucosal infiltration by immature myeloid precursors with few metamyelocytes and occasional eosinophils and the cells showed cytoplasmic granular positivity with myeloperoxidase stain suggestive of granulocytic sarcoma (chloroma—extra-medullary manifestation of acute myeloid leukaemia). Our patient received three cycles of cytarabine+daunorubicin chemotherapy in the postoperative period and is doing well at 12 months of follow-up. Granulocytic sarcoma (chloroma) presenting as colo-colic intussusception is very rare and has not been reported in literature so far.
Managing patient complaints in China: a qualitative study in Shanghai
Authors: Jiang Yishi , Ying Xiaohua , Zhang Qian , Tang Sirui Rae , Kane Sumit , Mukhopadhyay Maitrayee , Qian Xu ,   HESVIC team authorship
Published: August 2014

Objectives

To examine the handling system for patient complaints and to identify existing barriers that are associated with effective management of patient complaints in China.

Setting

Key stakeholders of the handling system for patient complaints at the national, Shanghai municipal and hospital levels in China.

Participants

35 key informants including policymakers, hospital managers, healthcare providers, users and other stakeholders in Shanghai.

Primary and secondary outcome measures

Semistructured interviews were conducted to understand the process of handling patient complaints and factors affecting the process and outcomes of patient complaint management.

Results

The Chinese handling system for patient complaints was established in the past decade. Hospitals shoulder the most responsibility of patient complaint handling. Barriers to effective management of patient complaints included service users’ low awareness of the systems in the initial stage of the process; poor capacity and skills of healthcare providers, incompetence and powerlessness of complaint handlers and non-transparent exchange of information during the process of complaint handling; conflicts between relevant actors and regulations and unjustifiable complaints by patients during solution settlements; and weak enforcement of regulations, deficient information for managing patient complaints and unwillingness of the hospitals to effectively handle complaints in the postcomplaint stage.

Conclusions

Barriers to the effective management of patient complaints vary at the different stages of complaint handling and perspectives on these barriers differ between the service users and providers. Information, procedure design, human resources, system arrangement, unified legal system and regulations and factors shaping the social context all play important roles in effective patient complaint management.
Efficacy of a dual-ring wound protector for prevention of incisional surgical site infection after Whipple's procedure (pancreaticoduodenectomy) with preoperatively-placed intrabiliary stents: protocol for a randomised controlled trial
Authors: Bressan Alexsander K , Roberts Derek J , Edwards Janet P , Bhatti Sana U , Dixon Elijah , Sutherland Francis R , Bathe Oliver , Ball Chad G
Published: August 2014

Introduction

Among surgical oncology patients, incisional surgical site infection is associated with substantially increased morbidity, mortality and healthcare costs. Moreover, while adults undergoing pancreaticoduodenectomy with preoperative placement of an intrabiliary stent have a high risk of this type of infection, and wound protectors may significantly reduce its risk, no relevant studies of wound protectors yet exist involving this patient population. This study will evaluate the efficacy of a dual-ring wound protector for prevention of incisional surgical site infection among adults undergoing pancreaticoduodenectomy with preoperatively-placed intrabiliary stents.

Methods and analysis

This study will be a parallel, dual-arm, randomised controlled trial that will utilise a more explanatory than pragmatic attitude. All adults (≥18 years) undergoing a pancreaticoduodenectomy at the Foothills Medical Centre in Calgary, Alberta, Canada with preoperative placement of an intrabiliary stent will be considered eligible. Exclusion criteria will include patient age <18 years and those receiving long-term glucocorticoids. The trial will employ block randomisation to allocate patients to a commercial dual-ring wound protector (the Alexis Wound Protector) or no wound protector and the current standard of care. The main outcome measure will be the rate of surgical site infection as defined by the Centers for Disease Control and Prevention criteria within 30 days of the index operation date as determined by a research assistant blinded to treatment allocation. Outcomes will be analysed by a statistician blinded to allocation status by calculating risk ratios and 95% CIs and compared using Fisher's exact test.

Ethics and dissemination

This will be the first randomised trial to evaluate the efficacy of a dual-ring wound protector for prevention of incisional surgical site infection among patients undergoing pancreaticoduodenectomy. Results of this study are expected to be available in 2016/2017 and will be disseminated using an integrated and end-of-grant knowledge translation strategy.

Trial registration number

ClinicalTrials.gov identifierNCT01836237.
Developing a service user informed intervention to improve participation and ability to perform daily activities in primary Sjögren's syndrome: a mixed-methods study protocol
Authors: Hackett Katie L , Newton Julia L , Deane Katherine H O , Rapley Tim , Deary Vincent , Kolehmainen Niina , Lendrem Dennis , Ng Wan-Fai
Published: August 2014

Introduction

A significant proportion of patients with primary Sjögren's syndrome (PSS) is functionally impaired and experience difficulties participating in various aspects of everyday life. There is currently no evidence of efficacy for non-pharmacological interventions aimed specifically at supporting the patients with PSS to improve their participation and ability to perform daily activities. This paper describes a research protocol for a mixed-methods study to develop an intervention to improve these outcomes. The protocol follows the Medical Research Council framework for complex interventions.

Methods and analysis

We will use group concept mapping with the patients, adults who live with them and healthcare professionals to identify factors which prevent people with PSS from participating in daily life and performing daily activities. The factors will be prioritised by participants for importance and feasibility and will inform an intervention to be delivered within a National Health Service (NHS) setting. Evidence-based intervention techniques will be identified for the prioritised factors and combined into a deliverable intervention package. Key stakeholders will comment on the intervention content and mode of delivery through focus groups, and the data will be used to refine the intervention. The acceptability and feasibility of the refined intervention will be evaluated in a future study.

Ethics and dissemination

The study has been approved by an NHS Research Ethics Committee, REC Reference: 13/NI/0190. The findings of this study will be disseminated in peer-reviewed journals and through presentation at national and international conferences.

Trial registration number

UKCRN Study ID: 15939.
Augmented biracks and their homology
Authors: Ceniceros Jose , Elhamdadi Mohamed , Green Matthew , Nelson Sam
Published: August 2014

We introduce augmented biracks and define a (co)homology theory associated to augmented biracks. The new homology theory extends the previously studied Yang–Baxter homology with a combinatorial formulation for the boundary map and specializes to N-reduced rack homology when the birack is a rack. We introduce augmented birack 2-cocycle invariants of classical and virtual knots and links and provide examples.
Systematic wave-equation finite difference time domain formulations for modeling electromagnetic wave-propagation in general linear and nonlinear dispersive materials
Authors: Ramadan Omar
Published: August 2014

In this paper, systematic wave-equation finite difference time domain (WE-FDTD) formulations are presented for modeling electromagnetic wave-propagation in linear and nonlinear dispersive materials. In the proposed formulations, the complex conjugate pole residue (CCPR) pairs model is adopted in deriving a unified dispersive WE-FDTD algorithm that allows modeling different dispersive materials, such as Debye, Drude and Lorentz, in the same manner with the minimal additional auxiliary variables. Moreover, the proposed formulations are incorporated with the wave-equation perfectly matched layer (WE-PML) to construct a material independent mesh truncating technique that can be used for modeling general frequency-dependent open region problems. Several numerical examples involving linear and nonlinear dispersive materials are included to show the validity of the proposed formulations.
Key steps toward the creation of QCD — Notes on the logic and history of the genesis of QCD
Authors: Cao Tian Yu
Published: August 2014

The creation of QCD is one of greatest achievements in the history of science. It has radically changed our conception of the fundamental ontology of the physical world and its underlying dynamics. What it has discovered are more than new particles and a new force, but rather a deeper level of physical reality, a new kind of entities. Dynamically, the strong nuclear forces are no longer taken to be fundamental, but are relegated to the status of the un-cancelled residue of far stronger long range force mediated by gluon. From a long term perspective, perhaps more important than these discoveries is that it breaks a new path to explore many novel features of an unknown layer of the physical world, such as instanton, the theta vacuum and effective energy. The notion of effective energy allows us to conceptualize the mysterious quantum number flow and hadronization. Although the metaphysical status of effective energy is not quite clear at this moment, but a window is open for conceptualizing the physical world that is in complex processes of transmutations in a unified way.
Universal κ-Poincaré covariant differential calculus over κ-Minkowski space
Authors: Jurić Tajron , Meljanac Stjepan , Štrajn Rina
Published: August 2014

Unified graded differential algebra, generated by κ-Minkowski noncommutative (NC) coordinates, Lorentz generators and anticommuting one-forms, is constructed. It is compatible with κ-Poincaré–Hopf algebra. For time- and space-like deformations, the super-Jacobi identities are not satisfied. By introducing additional generator, interpreted as exterior derivative, we find a new unique algebra that satisfies all super-Jacobi identities. It is universal and valid for all type of deformations (time-, space-, and light-like). For time-like deformations this algebra coincides with the one in A. Sitarz, Phys. Lett. B349, 42 (1995), arXiv:hep-th/9409014. Different realizations of our algebra in terms of super-Heisenberg algebra are presented. For light-like deformations we get (4D) bicovariant calculus, with κ-Poincaré–Hopf algebra and present the corresponding twist, which is written in a new covariant way, using Poincaré generators only. In the time- and space-like case, this twist leads to κ-Snyder space. Our results might lead to applications in NC quantum field theories (especially electrodynamics and gauge theories), quantum gravity models and Planck scale physics.
Second post-Minkowskian metric for a moving Kerr black hole
Authors: He G. , Jiang C. , Lin W.
Published: August 2014

In this paper, the harmonic metric for a moving Kerr black hole is presented in the second post-Minkowskian approximation. It is further demonstrated that the obtained metric is consistent with the Liénard–Wiechert gravitational potential for a moving and spinning source with an arbitrary constant velocity. Based on the metric, we also give the post-Newtonian equations of motion for photon and massive test particle in the time-dependent gravitational field.
FINITE DURATION TREATMENT OF CANCER BY USING VACCINE THERAPY AND OPTIMAL CHEMOTHERAPY: STATE-DEPENDENT RICCATI EQUATION CONTROL AND EXTENDED KALMAN FILTER
Authors: NAZARI MOSTAFA , GHAFFARI ALI , ARAB FARHAD
Published: August 2014

The main purpose of this paper is to propose an optimal finite duration treatment method for preventing tumor growth. The obtained results show that changing the dynamics of the cancer model is essential for a finite duration treatment. Therefore, vaccine therapy is used for changing the parameters of the system and chemotherapy is applied for pushing the system to the domain of attraction of the healthy state. The state-dependent Riccati equation (SDRE)-based optimal control method is used for optimal chemotherapy. In this method, the special conditions of the patients could be considered by choosing suitable weighting matrices in the cost function and restricting the drug dosage. Also, there are infinite ways to choose these state-dependent matrices. In this paper, these interesting features of this method are used for each patient. Since measuring the states of the system is impossible at each time for states feedback; an extended Kalman filter (EKF) is designed as an observer in the nonlinear system. So, the SDRE method is employed just by measuring the population of normal cells. Numerical simulations show the flexibility and effectiveness of this treatment method.
Improved Bilinear Degenerated Shell Element
Authors: Swamy Naidu N. V. , Sateesh B.
Published: August 2014

The development of a new four node 24 degree of freedom bilinear degenerated shell element is presented for the analysis of shell structures. The present finite element formulation considers the assumed covariant transverse shear strains to avoid the shear locking problem and the assumed covariant membrane strains, which are separated from covariant in-plane strains, to overcome the membrane locking problem. The formulation also includes the deviation of the normal torsional rotation of the mid surface in the governing equation. This element is free from serious shear and membrane locking problems and undesirable spurious kinematic deformation modes. The element is tested for rigid body modes and distorted edges to meet the patch test requirements. The versatility and accuracy of this new degenerated shell element is demonstrated by solving several numerical examples for thick and thin plates.
On the periodic writing of cubic irrationals and a generalization of Rédei functions
Authors: Murru Nadir
Published: August 2014

In this paper, we provide a periodic representation (by means of periodic rational or integer sequences) for any cubic irrationality. In particular, for a root α of a cubic polynomial with rational coefficients, we study the Cerruti polynomials [Formula: see text], and [Formula: see text], which are defined via [Formula: see text] Using these polynomials, we show how any cubic irrational can be written periodically as a ternary continued fraction. A periodic multidimensional continued fraction (with pre-period of length 2 and period of length 3) is proved convergent to a given cubic irrationality, by using the algebraic properties of cubic irrationalities and linear recurrent sequences.
Biostratigraphical and palaeobiogeographical implications of Lower Silurian Radiolaria from black cherts of the Armorican Massif (France)
Authors: Tetard Martin , Danelian Taniel , Noble Paula
Published: August 2014

Abstract. A moderately well-preserved radiolarian assemblage was recovered from organic-rich black chert in a Llandovery (Lower Silurian) sequence that crops out in southern Brittany (Chalonnes-sur-Loire section, Armorican Massif, France). The assemblage is composed of two families (Rotasphaeridae and Haplotaeniatidae), four genera (?Diparvapila, Secuicollacta, Orbiculopylorum, Haplotaeniatum) and 13 species. Some were identified from whole specimens preserved in silica and extracted following dilute hydrofluoric acid processing, while others were recognized in thin-section preparations, as they are beautifully preserved as ‘carbonized’ microfossils. The age range suggested by conodonts and chitinozoans yielded after HF processing from one of the 27 studied samples is in good agreement with the previously published age based on graptolites. The recovered radiolarians are discussed, documented and compared with known Rhuddanian, Aeronian and lower Telychian assemblages in the literature. The stratigraphic ranges are extended for the species Secuicollacta bipola, S. hexactinia, S. parvitesta, Orbiculopylorum granti and O. splendens based on our new data. A significant number of radiolarians found in our samples occur in Llandovery sections from Alaska, Nevada, Arctic Canada and Sweden. These similarities are used to discuss the palaeodistribution of Lower Silurian Radiolaria and our observations support the hypothesis of a wide geographical distribution for these Palaeozoic species.
Diatom identification in the face of changing species concepts and evidence of phenotypic plasticity
Authors: Cox Eileen J.
Published: August 2014

Abstract. Although it is often suggested that diatom wall morphology is faithfully replicated at each cell division, it is also well known that the average cell size of a diatom population usually decreases as cells proliferate. Comparisons between the two valves of a single frustule may also reveal morphological differences, indicating that valve ontogenetic processes are susceptible to modification. This paper will discuss the different factors affecting valve morphology in diatoms and some of the implications for ecological and palaeo-ecological studies using diatoms. It will also consider some of the problems of evaluating variation between clonal populations, and the influence of findings from molecular biology and reproductive studies on the interpretation of morphology and species concepts.
Refining students' coding and reviewing skills
Authors: Guo Philip
Published: August 2014

The
Communications
Web site, http://cacm.acm.org, features more than a dozen bloggers in the BLOG@CACM community. In each issue of
Communications
, we'll publish selected posts or excerpts.

twitter

Follow us on Twitter at http://twitter.com/blogCACM

http://cacm.acm.org/blogs/blog-cacm

Philip Guo sees code reviews providing students "lots of pragmatic learning."
Q&A: Finding themes
Authors: Krakovsky Marina
Published: August 2014

ACM-Infosys Foundation Award recipient David Blei recalls the origins of his famous topic model, its extensions, and its uses in areas that continue to amaze him.
Puzzled: Solutions and sources
Authors: Winkler Peter
Published: August 2014

Last month (August 2014), we presented three puzzles concerning the Path Game and the Match Game, each of which can be played on any finite graph. To start, Alice marks a vertex; Bob and Alice then alternate marking vertices until one (the loser) is unable to mark any more. In the Path Game, each vertex thus marked, following the first one, must be adjacent to the most recently marked vertex. In the Match Game, only Bob has this constraint, whereas Alice can mark any vertex.
The network is reliable
Authors: Bailis Peter , Kingsbury Kyle
Published: August 2014

An informal survey of real-world communications failures.
Accountability in future internet architectures
Authors: Bechtold Stefan , Perrig Adrian
Published: August 2014

Can technical and legal aspects be happily intertwined?
Soft infrastructure challenges to scientific knowledge discovery
Authors: King John Leslie , Uhlir Paul F.
Published: August 2014

Seeking to overcome nontechnical challenges to the scientific enterprise.
Moving portraits
Authors: Kemelmacher-Shlizerman Ira , Shechtman Eli , Garg Rahul , Seitz Steven M.
Published: August 2014

We present an approach for generating face animations from large image collections of the same person. Such collections, which we call photobios, are remarkable in that they summarize a person's life in photos; the photos sample the appearance of a person over changes in age, pose, facial expression, hairstyle, and other variations. Yet, browsing and exploring photobios is infeasible due to their large volume. By optimizing the quantity and order in which photos are displayed and cross dissolving between them, we can render smooth transitions between face pose (e.g., from frowning to smiling), and create moving portraits from collections of still photos. Used in this context, the cross dissolve produces a very strong motion effect; a key contribution of the paper is to explain this effect and analyze its operating range. We demonstrate results on a variety of datasets including time-lapse photography, personal photo collections, and images of celebrities downloaded from the Internet. Our approach is completely automatic and has been widely deployed as the "Face Movies" feature in Google's Picasa.
Complex Formation and Function of Estrogen Receptor α in Transcription Requires RIP140
Authors: Rosell Meritxell , Nevedomskaya Ekaterina , Stelloo Suzan , Nautiyal Jaya , Poliandri Ariel , Steel Jennifer H. , Wessels Lodewyk F.A. , Carroll Jason S. , Parker Malcolm G. , Zwart Wilbert
Published: August 2014

RIP140 is a transcriptional coregulator involved in energy homeostasis, ovulation, and mammary gland development. Although conclusive evidence is lacking, reports have implicated a role for RIP140 in breast cancer. Here, we explored the mechanistic role of RIP140 in breast cancer and its involvement in estrogen receptor α (ERα) transcriptional regulation of gene expression. Using ChIP-seq analysis, we demonstrate that RIP140 shares more than 80% of its binding sites with ERα, colocalizing with its interaction partners FOXA1, GATA3, p300, CBP, and p160 family members at H3K4me1-demarcated enhancer regions. RIP140 is required for ERα-complex formation, ERα-mediated gene expression, and ERα-dependent breast cancer cell proliferation. Genes affected following RIP140 silencing could be used to stratify tamoxifen-treated breast cancer cohorts, based on clinical outcome. Importantly, this gene signature was only effective in endocrine-treated conditions. Cumulatively, our data suggest that RIP140 plays an important role in ERα-mediated transcriptional regulation in breast cancer and response to tamoxifen treatment. Cancer Res; 74(19); 5469–79. ©2014 AACR.
AEG-1 Promoter–Mediated Imaging of Prostate Cancer
Authors: Bhatnagar Akrita , Wang Yuchuan , Mease Ronnie C. , Gabrielson Matthew , Sysa Polina , Minn Il , Green Gilbert , Simmons Brian , Gabrielson Kathleen , Sarkar Siddik , Fisher Paul B. , Pomper Martin G.
Published: August 2014

We describe a new imaging method for detecting prostate cancer, whether localized or disseminated and metastatic to soft tissues and bone. The method relies on the use of imaging reporter genes under the control of the promoter of AEG-1 (MTDH), which is selectively active only in malignant cells. Through a systemic, nanoparticle-based delivery of the imaging construct, lesions can be identified through bioluminescence imaging and single-photon emission computed tomography in the PC3-ML murine model of prostate cancer at high sensitivity. This approach is applicable for the detection of prostate cancer metastases, including bone lesions for which there is no current reliable agent for noninvasive clinical imaging. Furthermore, the approach compares favorably with accepted and emerging clinical standards, including PET with [18F]fluorodeoxyglucose and [18F]sodium fluoride. Our results offer a preclinical proof of concept that rationalizes clinical evaluation in patients with advanced prostate cancer. Cancer Res; 74(20); 5772–81. ©2014 AACR.
SAR405838: An Optimized Inhibitor of MDM2–p53 Interaction That Induces Complete and Durable Tumor Regression
Authors: Wang Shaomeng , Sun Wei , Zhao Yujun , McEachern Donna , Meaux Isabelle , Barrière Cédric , Stuckey Jeanne A. , Meagher Jennifer L. , Bai Longchuan , Liu Liu , Hoffman-Luca Cassandra Gianna , Lu Jianfeng , Shangary Sanjeev , Yu Shanghai , Bernard Denzil , Aguilar Angelo , Dos-Santos Odette , Besret Laurent , Guerif Stéphane , Pannier Pascal , Gorge-Bernat Dimitri , Debussche Laurent
Published: August 2014

Blocking the oncoprotein murine double minute 2 (MDM2)–p53 protein–protein interaction has long been considered to offer a broad cancer therapeutic strategy, despite the potential risks of selecting tumors harboring p53 mutations that escape MDM2 control. In this study, we report a novel small-molecule inhibitor of the MDM2–p53 interaction, SAR405838 (MI-77301), that has been advanced into phase I clinical trials. SAR405838 binds to MDM2 with Ki = 0.88 nmol/L and has high specificity over other proteins. A cocrystal structure of the SAR405838:MDM2 complex shows that, in addition to mimicking three key p53 amino acid residues, the inhibitor captures additional interactions not observed in the p53–MDM2 complex and induces refolding of the short, unstructured MDM2 N-terminal region to achieve its high affinity. SAR405838 effectively activates wild-type p53 in vitro and in xenograft tumor tissue of leukemia and solid tumors, leading to p53-dependent cell-cycle arrest and/or apoptosis. At well-tolerated dose schedules, SAR405838 achieves either durable tumor regression or complete tumor growth inhibition in mouse xenograft models of SJSA-1 osteosarcoma, RS4;11 acute leukemia, LNCaP prostate cancer, and HCT-116 colon cancer. Remarkably, a single oral dose of SAR405838 is sufficient to achieve complete tumor regression in the SJSA-1 model. Mechanistically, robust transcriptional upregulation of PUMA induced by SAR405838 results in strong apoptosis in tumor tissue, leading to complete tumor regression. Our findings provide a preclinical basis upon which to evaluate SAR405838 as a therapeutic agent in patients whose tumors retain wild-type p53. Cancer Res; 74(20); 5855–65. ©2014 AACR.
Folate and Vitamin B12 May Play a Critical Role in Lowering the HPV 16 Methylation–Associated Risk of Developing Higher Grades of CIN
Authors: Piyathilake Chandrika J. , Macaluso Maurizio , Chambers Michelle M. , Badiga Suguna , Siddiqui Nuzhat R. , Bell Walter C. , Edberg Jeffrey C. , Partridge Edward E. , Alvarez Ronald D. , Johanning Gary L.
Published: August 2014

We previously reported that a higher degree of methylation of CpG sites in the promoter (positions 31, 37, 43, 52, and 58) and enhancer site 7862 of human papillomavirus (HPV) 16 was associated with a lower likelihood of being diagnosed with HPV 16–associated CIN 2+. The purpose of this study was to replicate our previous findings and, in addition, to evaluate the influence of plasma concentrations of folate and vitamin B12 on the degree of HPV 16 methylation (HPV 16m). The study included 315 HPV 16-positive women diagnosed with either CIN 2+ or ≤CIN 1. Pyrosequencing technology was used to quantify the degree of HPV 16m. We reproduced the previously reported inverse association between HPV 16m and risk of being diagnosed with CIN 2+. In addition, we observed that women with higher plasma folate and HPV 16m or those with higher plasma vitamin B12 and HPV 16m were 75% (P < 0.01) and 60% (P = 0.02) less likely to be diagnosed with CIN 2+, respectively. With a tertile increase in the plasma folate or vitamin B12, there was a 50% (P = 0.03) and 40% (P = 0.07) increase in the odds of having a higher degree of HPV 16m, respectively. This study provides initial evidence that methyl donor micronutrients, folate and vitamin B12, may play an important role in maintaining a desirably high degree of methylation at specific CpG sites in the HPV E6 promoter and enhancer that are associated with the likelihood of being diagnosed with CIN 2+. Cancer Prev Res; 7(11); 1128–37. ©2014 AACR.
The Advantages of Unilateral Pedal Lymphography in the Diagnosis of Chyluria
Authors: Liu Ding-Yi , He Hong-Chao , Zhou Wen-Long , Chao Zhi-Fu , Wang Jian , Wang Ming-Wei , He Xiao-Zhou , Xia Wei-Mu , Zhang Chong-Yu
Published: August 2014

Objectives: To evaluate the efficacy and safety of pedal lymphography (PLG) in the localization diagnosis of chyluria. Methods: Cystoscopy was performed in 153 patients and PLG in 121 cases. Unilateral or staged bilateral ligation and stripping of renal lymphatic vessel were performed according to the results of cystoscopy and/or PLG. Results: Unilateral and bilateral urinary excretion of chyle was detected in 123 and 1 case by cystoscopy, respectively. In 121 cases receiving PLG, 100 cases of unilateral fistulous connection between the renal pelvis and the lymphatic system, 18 cases of bilateral fistulas and 1 case of lymphatic bladder fistula were demonstrated. PLG has a higher diagnostic rate for the detection of bilateral lymphatic renal pelvis fistulas than cystoscopy (p < 0.05). 28 cases received renal pedicle lymphatic disconnection only according to the results of cystoscopy, and 3 of them failed (10.1%). While 121 cases had the same operation according to the results of PLG, only 1 case failed the operation (0.8%). Conclusions: PLG was efficient and safe for the localization diagnosis of chyluria, with a higher detection rate of bilateral fistulas than cystoscopy. PLG might benefit the selection of appropriate therapy and improve the surgical effect.
Fate of Finally Transplanted Deceased Donor Kidneys Initially Rejected at Other Kidney Transplantation Centers
Authors: Friedersdorff Frank , Roller Chris , Manus Philipp , Cash Hannes , Stier Katja , Schmidt Danilo , Budde Klemens , Kemkensteffen Carsten , Busch Jonas , Fuller Tom Florian , Giessing Markus
Published: August 2014

Objective: We conducted this study to determine whether it is justifiable for transplant centers to reject cadaveric donor organs based on marginal organ quality. There is a growing discrepancy between the demand for renal transplants and the number of transplants conducted. For the many patients on the renal transplant waiting list, this translates into increased dialysis-associated morbidity, mortality and a reduced quality of life. Patients and Methods: In our retrospective analysis, we focused on deceased donor kidneys that had been rejected in other transplant centers because of poor organ quality (111 patients) and then accepted for transplantation at our center, compared with a control group consisting of 343 patients. Results: Cold ischemia time was statistically significantly shorter in the control group (11 vs. 12.5 h, p = 0.005). Also, delayed graft function occurred significantly (p = 0.004) more often in the study group (45.9-30.3%). Parameters regarding perioperative data and recipient outcome did not show significant differences and except for 2 time points at 1 week and 3 months, graft function did not differ either. Conclusions: We propose that acceptance criteria for marginal donor kidneys should be expanded. Centers should reconsider their acceptance criteria in the light of these findings as the results of these transplantations may even be much better if the delay due to reallocation and retransport can be spared.
First-Trimester Screening for Down Syndrome with Serum Sampling at Different Gestational Ages: The Effect on Screening Performance
Authors: Engels Melanie A.J. , Twisk Jos W.R. , Blankenstein Marinus A. , van Vugt John M.G.
Published: August 2014

Introduction: The objective of this study was to evaluate the performance of first-trimester Down syndrome (DS) screening with serum sampling at different weeks of gestation. Material and Methods: We studied 35,431 singleton pregnancies (2005-2011), including 145 DS cases. Screening performance was determined in different maternal age groups with serum sampling between weeks 9 + 0 and 13 + 6. Results: No significant differences were found between the detection rates at different gestational weeks. The false-positive rate (FPR) in week 9 (6%) was comparable to the FPR in week 10 (6.5%; p = 0.214), whereas it was significantly lower compared to weeks 11 (7.2%; p = 0.007), 12 (7.4%; p = 0.003) and 13 (8.5%; p < 0.001). The odds of receiving a false-positive result was significantly increased with serum sampling in week 11 (OR 1.32, 95% CI 1.08-1.63; p = 0.008) for women ≥36 years and from week 12 onwards (OR 1.28, 95% CI 1.01-1.61; p = 0.04) for women <36 years. There were no differences in mean log10 multiple of the median values of pregnancy-associated plasma protein-A, free β-human chorionic gonadotrophin or nuchal translucency between both age groups, nor in mean maternal age between the different gestational weeks in either age group. Discussion: Early serum sampling (<11 weeks) resulted in higher screening performance. The impact of the increase in the FPR was highest in women ≥36 years.
Cytoarchitecture of the Telencephalon in the Coral Reef Multiband Butterflyfish (Chaetodon multicinctus: Perciformes)
Authors: Dewan Adam K. , Tricas Timothy C.
Published: August 2014

Detailed neuroanatomical studies of model species are necessary to facilitate comparative experiments which test hypotheses relevant to brain evolution and function. Butterflyfishes (Chaetodontidae) boast numerous sympatric species that differ in social behavior, aggression and feeding ecology. However, the ability to test hypotheses relevant to brain function in this family is hindered by the lack of detailed neural descriptions. The cytoarchitecture of the telencephalon in the monogamous and territorial multiband butterflyfish, Chaetodon multicinctus, was determined with Nissl-stained serial sections and an immunohistochemical analysis of arginine vasotocin (AVT), serotonin, substance P and tyrosine hydroxylase. The ventral telencephalon was similar to that of other perciform fishes studied, with one major difference. A previously undescribed postcommissural region, the cuneate nucleus, was identified and putatively assigned to the ventral telencephalon. While the function of this nucleus is unknown, preliminary studies indicate that it may be part of a behaviorally relevant subpallial neural circuit that is modulated by AVT. The dorsal telencephalon consisted of 15 subdivisions among central, medial, lateral, dorsal and posterior zones. Several regions of the dorsal telencephalon of C. multicinctus differed from many other perciform fishes examined thus far. The nucleus taenia was in a more caudal position, and the central and lateral zones were enlarged. Within the lateral zone, an unusual third, ventral subdivision and a large-celled division were present. One hypothesis is that the enlarged ventral subdivision of the lateral zone (potential hippocampus homolog) relates to an enhancement of spatial learning or olfactory memory, which are important for this coral reef fish. This study provides the neuroanatomical basis for future comparative and evolutionary studies of brain organization and neuropeptide distributions, physiological studies of neural processing and insight into the complex social behavior of butterflyfishes.
Distribution Pattern of Hepatitis C Virus Genotypes and Correlation with Viral Load and Risk Factors in Chronic Positive Patients
Authors: Petruzziello Arnolfo , Coppola Nicola , Loquercio Giovanna , Marigliano Samantha , Giordano Margherita , Azzaro Rosa , Diodato Anna Maria , Iervolino Vincenzo , Di Costanzo Gaetano , Di Macchia Catia Addolorata , Di Meo Tommaso , Paradiso Laurenza , Ferro Rosario , Giuliano Pasquale , Russo Ferdinando , Pasquale Giuseppe , Cacciapuoti Carmela
Published: August 2014

Objective: Hepatitis C virus (HCV) has emerged as a leading cause of chronic hepatitis, liver cirrhosis and hepatocellular carcinoma worldwide. The purpose of this study was to describe the distribution pattern of HCV genotypes in chronic hepatitis patients in the Campania region of southern Italy and estimate their association with risk factors and viral load. Materials and Methods: 404 consecutive HCV ribonucleic acid-positive patients were included in the study. HCV genotyping was carried out by the HCV line probe assay test and viral load estimation by the TaqMan real-time PCR system. Results: The predominant genotype was 1 (63.6%), followed by genotype 2 (29.4%), 3 (6.2%) and 4 (0.8%). Subtype 1b was more frequent in females than in males. Conversely, genotype 3 was more frequent in males. No significant difference was observed in age distribution of HCV genotypes. Surgery and dental therapy were the most frequent risk factors for genotype 1 and intravenous drug abuse and tattooing for genotype 3. Patients with genotype 1 more frequently showed high HCV viral load when compared to those with genotypes 2 and 3. Conclusion: The present study revealed that HCV genotypes 1 and 2 accounted for over 95% of all HCV infections in the Campania region, and genotype 1 was more frequently associated with a higher viral load when compared to genotypes 2 and 3.
No Tumor-Free Waiting Period after Treatment of Multilocular Cystic Renal Cell Carcinoma: A New Case and Review of the Literature
Authors: Tantisattamo Ekamol , Elam April , Cobb Jason , Ellis Carla L. , Bailey James L.
Published: August 2014

Most pretransplant malignancies require a tumor-free waiting period before transplantation. End-stage renal disease (ESRD) patients have an increased risk of renal cell carcinoma (RCC), which is mostly detected from routine screening during pre-kidney transplant evaluation. RCC must be quiescent prior to kidney transplantation. However, the tumor-free waiting period for RCC varies depending on the types of RCC. Multilocular cystic RCC (MCRCC), one subtype of clear cell RCC, has low malignant potential and may not require a tumor-free waiting period. We report a case of an ESRD patient with a newly diagnosed MCRCC that was found during routine pre-kidney transplant evaluation. A plan for kidney transplantation within 6 months of successful tumor removal by nephrectomy was made. The literature regarding MCRCC in kidney transplantation is reviewed.