bluuebunny/crossref_metadata_2025_split huggingface dataset:
Segmentation and detection of fluorescent 3D spots
Authors: Ram Sundaresh , Rodríguez Jeffrey J. , Bosco Giovanni 
Published: February 2012

AbstractThe 3D spatial organization of genes and other genetic elements within the nucleus is important for regulating gene expression. Understanding how this spatial organization is established and maintained throughout the life of a cell is key to elucidating the many layers of gene regulation. Quantitative methods for studying nuclear organization will lead to insights into the molecular mechanisms that maintain gene organization as well as serve as diagnostic tools for pathologies caused by loss of nuclear structure. However, biologists currently lack automated and high throughput methods for quantitative and qualitative global analysis of 3D gene organization. In this study, we use confocal microscopy and fluorescence in‐situ hybridization (FISH) as a cytogenetic technique to detect and localize the presence of specific DNA sequences in 3D. FISH uses probes that bind to specific targeted locations on the chromosomes, appearing as fluorescent spots in 3D images obtained using fluorescence microscopy. In this article, we propose an automated algorithm for segmentation and detection of 3D FISH spots. The algorithm is divided into two stages: spot segmentation and spot detection. Spot segmentation consists of 3D anisotropic smoothing to reduce the effect of noise, top‐hat filtering, and intensity thresholding, followed by 3D region‐growing. Spot detection uses a Bayesian classifier with spot features such as volume, average intensity, texture, and contrast to detect and classify the segmented spots aseither true or false spots. Quantitative assessment of the proposed algorithm demonstrates improved segmentation and detection accuracy compared to other techniques. © 2012 International Society for Advancement of Cytometry
Aspects for untangling cross‐layer design and policy support
Authors: Sadok Djamel , Oliveira Luciana P. , Gonçalves Glauco , Kelner Judith , Rosa Nelson , Souto Eduardo 
Published: February 2012

SUMMARYProgramming language concepts have inspired some networking design decisions. For example, concepts such as object encapsulation and interface invocation have been borrowed, at the time of their adoption, from an already well established object oriented programming paradigm. The authors suggest in this paper that it may be time again to revisit emerging software engineering programming paradigms to learn from them. More specifically, this paper discusses the practical tangling problem, embedded in conventional layer‐coupling (linking) network software design and highlighted by recent research proposals for cross layer design. The adopted solution is based on the aspect‐oriented programming paradigm. We show its programming efficiency, limitations and role in the seamless enforcement of multiple policy scenarios while emphasizing little design changes. Copyright © 2012 John Wiley & Sons, Ltd.
Autofluorescence—an important ancillary technique for the detection of Mycobacterium tuberculosis: Revisited
Authors: Joshi Parul , Singh Mamta , Bhargava Anudita , Singh Mangal , Mehrotra Ravi 
Published: February 2012

AbstractTuberculosis is one of the oldest diseases known to affect humans and is caused by Mycobacterium tuberculosis. Lymph nodes are the most common site of extrapulmonary involvement. Tuberculous lymphadenitis can be presumptively diagnosed morphologically on fine‐needle aspiration biopsy of lymph nodes. Additional tests like Ziehl‐Neelsen (ZN) stain for detection of acid fast bacilli, fluorescence, and molecular markers are often employed for confirmation of diagnosis. However, culture is essential for obtaining a definitive diagnosis. Unfortunately, culture is time consuming and expensive. Newer investigative methods are required. The efficacy of autofluorescence in the diagnosis of tuberculous lymphadenitis was evaluated for this purpose. Fine‐needle aspiration biopsies were collected from patients with a clinical diagnosis of tuberculous lymphadenitis. Cytomorphological examination, ZN staining, autofluorescence, and culture were performed on all specimens. ZN staining was positive in 37.5% (30/80) of cases, while autofluorescence was positive in 57.5% (46/80) of patients and was found to have 81.8% specificity, 95% sensitivity, and a positive predictive value of 82.6%. This technique allowed rapid and early diagnosis of tuberculous lymphadenitis in a number of patients, permitting early institution of appropriate therapy. Diagn. Cytopathol. 2013;41:330–334. © 2012 Wiley Periodicals, Inc.
Role of fine‐needle aspiration cytology and fluid cytology in extra‐pulmonary tuberculosis
Authors: Narayana Reddy Roopa A. , Narayana Suma M. , Shariff Shameem 
Published: February 2012

AbstractExtra‐pulmonary tuberculosis is the presence of disease in an organ without obvious involvement of the lungs (World Health Organization, Tuberculosis Fact sheet, 2006). The present article focuses on the incidence of extra‐pulmonary tuberculosis as an emerging and clinically significant disease to be reckoned with in the present era. It also highlights fine‐needle aspiration cytology (FNAC) as an inexpensive, less invasive procedure for early diagnosis of such tuberculosis and timely initiation of specific therapy.All cases of proved tuberculosis presenting to the M.V.J. Medical College and Research Hospital were recorded over a period of two years (2008–2010); and categorized as pulmonary and extra‐pulmonary cases. A total of 96 cases of tuberculosis were observed; extra‐pulmonary tuberculosis was seen in 64 cases. Of these 56 cases were from lymphnodes and 8 from extra‐nodal sites which included tuberculous dactylitis (two cases), tuberculous mastitis (two cases), tuberculous synovial effusion (one case), pericardial effusion (one case), epididymo‐orchitis (one case), and cold abscess (one case). The cytology patterns observed included granulomatous inflammation and necrosis with or without acid fast bacilli. Diagn. Cytopathol. 2013. © 2012 Wiley Periodicals, Inc.
Focused rescreening of NILM Pap slides from women ≥30 years of age with positive high risk HPV DNA: An enhanced quality control measure
Authors: Sturgis Charles D. , Schaaf Michael R. , Tickman Ronald J. 
Published: February 2012

AbstractCLIA 88 regulations specify that at least 10% of negative for intraepithelial lesion or malignancy (NILM) Paps be rescreened as a means of quality control (QC). With the incorporation of HPV DNA testing into American Society for Colposcopy and Cervical Pathology guidelines for women ≥30 years of age, a population of NILM patients with positive HPV results exists. Slides from this cohort were rescreened to judge the value of focused QC. Three hundred and eighty‐six consecutive, NILM, HCII+, Paps (SurePath and ThinPrep, September 2009 to December 2009) from women aged ≥30 were retrieved from the CellNetix files. These slides were rescreened by cytotechnologists. Slides rescreened as atypical squamous cells (ASC) or higher by cytotechnologists were viewed by cytopathologists (CDS/RJT) who assigned a final interpretation. Of the 386 rescreened cases, 50 (12.9%) were placed in categories of ASC or higher, and 11 (2.9%) were interpreted as LSIL or above. By comparison, routine QC (including random, FocalPoint enriched, and historically high risk cases) was performed on a total of 20,580 Paps (21% of 99,501 annual cases). Concomitant routine QC revealed that 2.1% (427/20,580) were upgraded to ASC or higher and 0.3% (52/20,580) were upgraded to LSIL or higher. Focused rescreening of NILM cases with positive HPV DNA resulted in the detection of approximately ten times more SIL cases than did routine QC Pap slide review at CellNetix. Focused rescreening of this patient set may enhance QC in cytopathology laboratories performing liquid‐based Paps. An inherent potential bias in study design is recognized, as results of DNA testing were by definition known at the time of rescreen. Diagn. Cytopathol. 2013. © 2012 Wiley Periodicals, Inc.
ALK+ large B‐cell lymphoma: A rare variant of aggressive large B‐cell lymphoma mimicking carcinoma on cytology specimens
Authors: Lin Oscar , Koreishi Aashiyana , Brandt Suzanne M. , Arcila Maria , Teruya‐Feldstein Julie 
Published: February 2012

AbstractAnaplastic lymphoma kinase positive large B‐cell LYMPHOMA (ALK+ LBCL) was recognized as a distinct entity by the 2008 WHO classification of lymphomas. Histologically, the tumor cells exhibit either plasmablastic or immunoblastic morphology, with characteristic granular staining for ALK. The purpose of this study is to evaluate the cytologic findings of ALK+ LBCL. The cytologic material obtained by needle biopsy from three cases of ALK+ LBCL was evaluated. All lesions were nodal and the cytologic material analyzed included air‐dried and alcohol‐fixed slides stained with modified Giemsa and/or HE stains. The following morphologic criteria were assessed: cellularity, cluster characteristics, cell size, cytoplasmic and nuclear characteristics, and background composition. The cytology specimens obtained from the needle biopsies were moderately to highly cellular and composed of a population of large cells with immunoblastic or plasmablastic morphology. Single cells were present in all three cases, but two cases also showed the presence of clusters with acinar and papillary architecture. Multinucleation was noted in all three cases. Amorphous metachromatic background material was noted focally in the modified Giemsa stained slides in all three cases. Immunostains performed on cytology specimens showed cytoplasmic immunoreactivity for ALK, with characteristic granular features. ALK+ LBCL is a rare recently recognized type of lymphoma with unique morphologic and immunophenotypic findings that can mimic epithelial tumors. Recognition of this potential diagnostic pitfall is critical to prevent unnecessary additional work‐up and mistreatment. Diagn. Cytopathol. 2013. © 2012 Wiley Periodicals, Inc.
The diagnostic value of the thinprep pap test in endometrial carcinoma: A prospective study with histological follow‐up
Authors: Zhou Jianhong , Tomashefski, Joseph F. , Sawady Joram , Ferrer Hector , Khiyami Amer 
Published: February 2012

AbstractCase‐control studies have demonstrated that the ThinPrep Pap test may provide improved detection of endometrial carcinoma. The purpose of this study is to prospectively examine the diagnostic potential of the ThinPrep Pap test in the detection of endometrial carcinoma. ThinPrep Pap test slides were collected from high‐risk patient groups. Pap‐stained slides were reviewed and the cytological diagnosis was rendered independently by investigators. Each case was assigned to one of the four diagnostic categories: within normal limit (WNL); atypical glandular cells (AGC); atypical endometrial cells (AEC); or adenocarcinoma, probably endometrial origin. After cytological diagnosis was made, the histological follow‐up diagnosis was obtained through the laboratory information system and the cyto‐histological correlation was analyzed. Of 106 patients identified, 60 had histological follow‐up. For all eight cases interpreted by cytology as positive, endometrial carcinoma was confirmed histologically. Among 25 patients with normal endometrial cells present, histological follow‐up showed benign endometrium. Among 17 cases interpreted cytologically as AEC, 14 cases (82.4%) had benign histological follow‐up and 3 cases (17.6%) had endometrial carcinoma. All 11 cases (100%) classified as AGC had benign histological follow‐up. The sensitivity and specificity of detecting endometrial malignancy were 72.7% and 100%, respectively. The positive predictive value was 100%. In this prospective study, we demonstrated that the Thin Prep Pap test had a reasonably high sensitivity and/or specificity in detecting endometrial carcinoma. Diagn. Cytopathol. 2013. © 2012 Wiley Periodicals, Inc.
Toward new Drosophila paradigms
Authors: Andrioli Luiz Paulo 
Published: February 2012

AbstractThe fruit fly Drosophila melanogaster is a great model system in developmental biology studies and related disciplines. In a historical perspective, I focus on the formation of the Drosophila segmental body plan using a comparative approach. I highlight the evolutionary trend of increasing complexity of the molecular segmentation network in arthropods that resulted in an incredible degree of complexity at the gap gene level in derived Diptera. There is growing evidence that Drosophila is a highly derived insect, and we are still far from fully understanding the underlying evolutionary mechanisms that led to its complexity. In addition, recent data have altered how we view the transcriptional regulatory mechanisms that control segmentation in Drosophila. However, these observations are not all bad news for the field. Instead, they stimulate further study of segmentation in Drosophila and in other species as well. To me, these seemingly new Drosophila paradigms are very challenging ones. genesis 50:585–598, 2012. © 2012 Wiley Periodicals, Inc.
The impact of Pleistocene climate change on an ancient arctic–alpine plant: multiple lineages of disparate history in Oxyria digyna
Authors: Allen Geraldine A. , Marr Kendrick L. , McCormick Laurie J. , Hebda Richard J. 
Published: February 2012

AbstractThe ranges of arctic–alpine species have shifted extensively with Pleistocene climate changes and glaciations. Using sequence data from the trnH‐psbA and trnT‐trnL chloroplast DNA spacer regions, we investigated the phylogeography of the widespread, ancient (>3 million years) arctic–alpine plant Oxyria digyna (Polygonaceae). We identified 45 haplotypes and six highly divergent major lineages; estimated ages of these lineages (time to most recent common ancestor, TMRCA) ranged from ∼0.5 to 2.5 million years. One lineage is widespread in the arctic, a second is restricted to the southern Rocky Mountains of the western United States, and a third was found only in the Himalayan and Altai regions of Asia. Three other lineages are widespread in western North America, where they overlap extensively. The high genetic diversity and the presence of divergent major cpDNA lineages within Oxyria digyna reflect its age and suggest that it was widespread during much of its history. The distributions of individual lineages indicate repeated spread of Oxyria digyna through North America over multiple glacial cycles. During the Last Glacial Maximum it persisted in multiple refugia in western North America, including Beringia, south of the continental ice, and within the northern limits of the Cordilleran ice sheet. Our data contribute to a growing body of evidence that arctic–alpine species have migrated from different source regions over multiple glacial cycles and that cryptic refugia contributed to persistence through the Last Glacial Maximum.
Switching reinforcement learning for continuous action space
Authors: Nagayoshi Masato , Murao Hajime , Tamaki Hisashi 
Published: February 2012

AbstractReinforcement learning (RL) is attracting attention as a technique for realizing computational intelligence, such as adaptive and autonomous decentralized systems. In general, however, it is not easy to put RL to practical use. The difficulty includes the problem of designing a suitable action space for an agent, that is, satisfying two requirements in trade‐off: (i) to keep the characteristics (or structure) of the original search space as much as possible in order to seek strategies that lie close to the optimal, and (ii) to reduce the search space as much as possible in order to expedite the learning process.In order to design a suitable action space adaptively, we propose the Switching RL model to mimic the process of an infant's motor development, in which gross motor skills develop before fine motor skills. Then, a method for switching controllers is constructed by introducing and referring to the “entropy.” Further, the validity of the proposed method is confirmed by computational experiments using robot navigation problems with one‐ and two‐dimensional continuous action spaces. © 2012 Wiley Periodicals, Inc. Electron Comm Jpn, 95(3): 37–44, 2012; Published online in Wiley Online Library (wileyonlinelibrary.com). DOI 10.1002/ecj.10383
Evaluation of small ultrasonic probe using lead zirconate titanate poly‐crystal film deposited by hydrothermal method
Authors: Hasegawa Tomohito , Ishikawa Mutsuo , Kurosawa Minoru Kuribayashi , Takeuchi Shinichi 
Published: February 2012

AbstractTwo types of transducers for small ultrasound probes were fabricated. Titanium or epoxy resin was used for the backing material of the transducers. The piezoelectric material was lead zirconate titanate (PZT) that was deposited by the hydrothermal method. These transducers were built into a small ultrasound probe and the characteristics were evaluated. As a result, we succeeded in the fabrication of a wideband ultrasound probe with a distance resolution of 16 μm, a frequency bandwidth of 69 MHz in the range of 39 to 98 MHz, and a fractional bandwidth of 86% at the epoxy resin backing probe. © 2012 Wiley Periodicals, Inc. Electron Comm Jpn, 95(3): 1–8, 2012; Published online in Wiley Online Library (wileyonlinelibrary.com). DOI 10.1002/ecj.10419
Design, Testing and Kinetic Analysis of Bulky Monodentate Phosphorus Ligands in the Mizoroki–Heck Reaction
Authors: Dodds Deborah L. , Boele Maarten D. K. , van Strijdonck Gino P. F. , de Vries Johannes G. , van Leeuwen Piet W. N. M. , Kamer Paul C. J. 
Published: February 2012

AbstractA series of new monodentate phosphane ligands 2 have been evaluated in the Mizoroki–Heck arylation reaction of iodobenzene and styrene and compared with our previously reported ligands, 1, 3 and 4. The concept of rational ligand design is discussed, and we describe how the performance of this new ligand family could be predicted. Employing our best ligand, 3,3′‐di‐tert‐butyl‐5,5′‐dimethoxybiphenyl‐2,2′‐diyl diisopropylphosphoramidite (3b), we explored the scope of the reaction with regards to solvent and the substrate. We also investigated the electronic dependence of the reaction by analysing the relationship between the rate and Hammett constant. Sufficient steric bulk is required to enforce the catalytic reaction to proceed through the mono‐coordinated palladium species, thereby increasing its reactivity. The electronic properties determine the concentration of the active species from the monomer dimer equilibrium and their intrinsic reactivity. The cyclic phosphoramidite 3b provides an optimum in both properties within the systems studied, resulting in a rate limiting migratory insertion step.
Microporous Mixed‐Metal Layer‐Pillared [Zn1–xCux(bdc)(dabco)0.5] MOFs: Preparation and Characterization
Authors: Kozachuk Olesia , Khaletskaya Kira , Halbherr Markus , Bétard Angélique , Meilikhov Mikhail , Seidel Rüdiger W. , Jee Bettina , Pöppl Andreas , Fischer Roland A. 
Published: February 2012

AbstractA series of mixed‐metal layer‐pillared MOFs of general formula [Zn1–xCux(bdc)(dabco)0.5] (bdc = 1,4‐benzenedicarboxylate, dabco = 1,4‐diazabicyclo[2.2.2]octane, 0 < x < 1) have been synthesized by a solvothermal approach. Different amounts x of Cu2+ were introduced to substitute for Zn2+ centers. The prepared mixed‐metal MOFs were shown to be structurally very similar to their parent monometallic [Zn(bdc)(dabco)0.5] and [Cu(bdc)(dabco)0.5] frameworks by single‐crystal and powder X‐ray diffraction studies. Interestingly, upon inclusion of copper, a distortion of the paddle‐wheel units is observed. In addition, the incorporation of Cu2+ ions into the [Zn2(bdc)(dabco)0.5] framework and the formation of heterometallic Zn–Cu paddle‐wheel units along with monometallic Cu–Cu and Zn–Zn units in the prepared mixed‐metal MOFs were confirmed by continuous‐wave EPR spectroscopy. The synthesized materials [Zn1–xCux(bdc)(dabco)0.5] are thermally stable up to 260 °C and exhibit permanent porosity with BET surface areas in the range of 800–2430 m2 g–1.
2,2′‐Diborylazobenzenes with Double N–B Coordination: Control of Fluorescent Properties by Substituents and Redox Reactions
Authors: Kano Naokazu , Furuta Akiko , Kambe Tetsuya , Yoshino Junro , Shibata Yusuke , Kawashima Takayuki , Mizorogi Naomi , Nagase Shigeru 
Published: February 2012

Abstract2,2′‐Bis[bis(pentafluorophenyl)boryl]azobenzenes were synthesized. X‐ray crystallographic analysis exhibits a planar core structure of the azobenzene moiety, double intramolecular N–B coordination, and two tetracoordinate boron atoms. The 2,2′‐diborylazobenzenes show fluorescence emission with orange and red colors upon irradiation. The double N–B coordination causes redshifts in both the absorption and emission maxima and a decrease in the Stokes shifts relative to those of the 2‐borylazobenzene derivative. On the basis of the density functional theory calculations of the molecular orbitals of 2,2′‐diborylazobenzene, the π* orbital (LUMO) was found at a much lower energy level (–4.67 eV) than that in 2‐borylazobenzene (–3.70 eV). A reversible reduction wave was observed at a low reduction potential in the cyclic voltammograms of the 2,2′‐diborylazobenzenes. Single‐electron reduction of one of the 2,2′‐diborylazobenzenes generates an azobenzene radical anion, which was confirmed by an active ESR signal. The fluorescence was quenched by the reduction and recovered by air oxidation in this azobenzene.
Effects of prolonged‐release melatonin and zolpidem on postural stability in older adults
Authors: Otmani Sarah , Metzger Deborah , Guichard Nathalie , Danjou Philippe , Nir Tali , Zisapel Nava , Katz Amnon 
Published: February 2012

ObjectivesA prolonged‐release formulation of melatonin (PR‐M) is indicated for insomnia in patients aged 55 years and older. Because hypnotics result in impairments of body sway, it was important to evaluate the effect of 2 mg PR‐M on postural stability in older adults at night.MethodsTwenty‐four healthy volunteers (12 women, 12 men, aged 55–64 years) completed a randomized, double‐blind, single‐dose, three‐way crossover study of postural stability of PR‐M 2 mg, zolpidem 10 mg (active control) or placebo. Subjects were tested for body sway 30 min before, 1.5 and 4 h after dosing. Parameters tested were the area of the 95% confidence ellipse enclosing the center of pressure (COP; [A95]) and COP path length.ResultsZolpidem significantly increased the A95 (both eyes conditions at all time points) and path length of COP. PR‐M had no effect on A95 (both “eyes closed” and “eyes open” conditions at all time points) compared with placebo and increased COP path length by 10% at 4 h post‐dose in open but not closed eyes condition. No serious adverse events were observed.ConclusionsIn older adults, evening PR‐M intake did not impair postural stability during the night. The postural instability with zolpidem demonstrated assay sensitivity and validated the outcome. Copyright © 2012 John Wiley & Sons, Ltd.
Characteristics of Sinanodonta woodiana (Lea, 1834) Populations in Fish Ponds (Upper Silesia, Southern Poland) in Relation to Environmental Factors Abstract
Authors: Spyra Aneta , Strzelec Małgorzata , Lewin Iga , Krodkiewska Mariola , Michalik‐Kucharz Agnieszka , Gara Marcin 
Published: February 2012

AbstractWe analyzed the biomass, density and age structure of S. woodiana populations in relation to different environmental factors at new sites of its occurrence in southern Poland. The highest recorded biomass was 4,413 g m–2. Mussel density was 19 individuals m–2. The age structure was formed by juveniles as well as by specimens more than 8 years. The rapid expansion of S. woodiana in European countries is believed to be the result of accidental introduction of fishes bearing glochidia of this species. (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)