bluuebunny/crossref_metadata_2025_split huggingface dataset:
Infarcted fibroadenoma of the breast: report of two new cases with review of the literature
Authors: Skenderi Faruk , Krakonja Fikreta , Vranic Semir 
Published: February 2013

Abstract

Introduction
Fibroadenomas are the most common benign breast tumors in young women. Infarction is rarely observed in fibroadenomas and when present, it is usually associated with pregnancy or lactation. Infarction can exceptionally occur as a complication of previous fine-needle aspiration biopsy or during lactation and pregnancy.

Materials and methods
Retrospective review of 650 cases of fibroadenomas diagnosed at our institution during the 8-years period identified two cases of fibroadenomas with infarction (rate ~0.3%).

Results
Two partially infarcted fibroadenomas were diagnosed on core biopsy and frozen section in an adolescent girl (13 years old) and in a young woman (25 years old), respectively. No preceding fine-needle aspiration biopsy was performed in these cases, nor were the patients pregnant or lactating at the time of the diagnosis.

Conclusion
Spontaneous infarction within fibroadenoma is a rare phenomenon in younger patients. The presence of necrosis on core biopsy or frozen section should be cautiously interpreted and is not a sign of malignancy.

Virtual Slides
The virtual slide(s) for this article can be found here:http://www.diagnosticpathology.diagnomx.eu/vs/1556060549847356
Ethnobotanical appraisal and medicinal use of plants in Patriata, New Murree, evidence from Pakistan
Authors: Ahmed Ejaz , Arshad Muhammad , Saboor Abdul , Qureshi Rahmatullah , Mustafa Ghazala , Sadiq Shumaila , Chaudhari Sunbal Khalil 
Published: February 2013

Abstract
Background
This paper reflects the empirical findings of an ethnobotanical survey which was undertaken in Patriata (New Murree) of district Rawalpindi in Pakistan. The aims and objectives of the study were to document indigenous knowledge of plants particularly of medicinal, veterinary, fruit, vegetable, fodder, fuel etc.

Methods
For this purpose, the whole area was surveyed for documenting folk knowledge using a semi-structured questionnaire. A total of 93 plants species belonging to 80 genera and 56 families were found in a variety of uses by the local people for the accomplishment of their basic needs. The study further employs binary logit regression model of medicinal uses of these plants so as to identify the probability of occurrence of medicinal use of woody or non-woody plants keeping other plant characteristics in view.

Results
Ethnobotanical data shows that most plants are used for medicinal and fodder purposes (27.93% each), followed by fuel (16.90%), fruit (6.55%), vegetable (5.52%) and ethno-veterinary (3.79%). There is also an established association of medicinal use of plants to the fruits use. Non-woody plants have high tendency towards medicinal use of the plants as compared to woody plants. Annual plants are less likely to be directly associated with medicinal use of plants in the surveyed vegetation. Underground plant parts are more likely to be used for medicinal purposes as revealed from the Logit expressions.

Conclusions
The study revealed that most of the plants are used for medicinal and fodder purposes. The results of Logit Model showed that the probabilities of plant species for their medicinal use are associated to the woody or non-woody, aerial or underground, perennial or annual characteristics of plants. One should be careful in completely generalizing the results as the survey findings are sensitive to the plant species and the vegetation under consideration. But it can be specified that there exists either some positive or negative association of medicinal use of plants to the various characteristics of plant species.
Phase I trial of oral etoposide in combination with radiotherapy in head and neck squamous cell carcinoma - GORTEC 2004–02
Authors: Tao Yungan , Bardet Etienne , Rosine Dominique , Rolland Frédéric , Bompas Emmanuelle , Daly-Schveitzer Nicolas , Lusinchi Antoine , Bourhis Jean 
Published: February 2013

Abstract

Purpose
This study sought to determine the maximum tolerated dose (MTD) of oral etoposide in combination with radiotherapy in head and neck squamous cell carcinoma (HNSCC).

Patients and Methods
Phase I, multicenter, open-labelled, non-comparative and dose escalating trial. Patients with locally advanced HNSCC were enrolled onto cohorts of escalating dose of etoposide. Oral etoposide was administered on five consecutive days every week for 7 weeks (7 treatment cycles) in combination with daily radiotherapy (70 Gy /35 fractions). Two dose levels (25 mg/day and 50 mg/day) of etoposide were planned and three to six patients were to be enrolled at each level according to the potential DLTs.

Results
Fourteen patients were allocated to two dose levels: 25 mg/day (3) and 50 mg/day (11). Cisplatin was contra-indicated in all the patients included. Only one patient (50 mg/day) presents a grade 4 neutropenia (DLT), no other DLTs were observed. The most frequently adverse events (AEs) were radiomucositis. Two deaths before 3 months of end of treatment were not related to treatment. Seven patients were still alive with a median follow-up of 30 months (12–58 months). Nine patients had a complete response (CR) at 3 months after the radiotherapy; Among the 9 patients, 3 patients had a local relapse; one patient with local and distant relapse.

Conclusion
Due to only one DLT experienced, it is possible to a dose of 50 mg/day for phase II studies, however this should be considered with caution.
The illusion of specific capture: surface and solution studies of suboptimal oligonucleotide hybridization
Authors: Garhyan Jaishree , Gharaibeh Raad Z , McGee Stephen , Gibas Cynthia J 
Published: February 2013

Abstract

Background
Hybridization based assays and capture systems depend on the specificity of hybridization between a probe and its intended target. A common guideline in the construction of DNA microarrays, for instance, is that avoiding complementary stretches of more than 15 nucleic acids in a 50 or 60-mer probe will eliminate sequence specific cross-hybridization reactions. Here we present a study of the behavior of partially matched oligonucleotide pairs with complementary stretches starting well below this threshold complementarity length – in silico, in solution, and at the microarray surface. The modeled behavior of pairs of oligonucleotide probes and their targets suggests that even a complementary stretch of sequence 12 nt in length would give rise to specific cross-hybridization. We designed a set of binding partners to a 50-mer oligonucleotide containing complementary stretches from 6 nt to 21 nt in length.

Results
Solution melting experiments demonstrate that stable partial duplexes can form when only 12 bp of complementary sequence are present; surface hybridization experiments confirm that a signal close in magnitude to full-strength signal can be obtained from hybridization of a 12 bp duplex within a 50mer oligonucleotide.

Conclusions
Microarray and other molecular capture strategies that rely on a 15 nt lower complementarity bound for eliminating specific cross-hybridization may not be sufficiently conservative.
Establishing a Southern Swedish Malignant Melanoma OMICS and biobank clinical capability
Authors: Welinder Charlotte , Jönsson Göran , Ingvar Christian , Lundgren Lotta , Olsson Håkan , Breslin Thomas , Végvári Ákos , Laurell Thomas , Rezeli Melinda , Jansson Bo , Baldetorp Bo , Marko‐Varga György 
Published: February 2013

AbstractBackgroundThe objectives and goals of the Southern Swedish Malignant Melanoma (SSMM)are to develop, build and utilize cutting edge biobanks and OMICS platformsto better understand disease pathology and drug mechanisms. The SSMMresearch team is a truly cross‐functional group with members from oncology, surgery, bioinformatics, proteomics, and genomics initiatives. Within theresearch team there are members who daily diagnose patients with suspectmelanomas, do follow‐ups on malignant melanoma patients and remove primaryor metastatic lesions by surgery. This inter‐disciplinary clinical patientcare ensures a competence build as well as a best practice procedure wherethe patient benefits.MethodsClinical materials from patients before, during and after treatments withclinical end points are being collected. Tissue samples as well as bio‐fluidsamples such as blood fractions, plasma, serum and whole blood will bearchived in 384‐high density sample tube formats. Standardized approachesfor patient selections, patient sampling, sample‐processing and analysisplatforms with dedicated protein assays and genomics platforms that willhold value for the research community are used. The patient biobank archivesare fully automated with novel ultralow temperature biobank storage unitsand used as clinical resources.ResultsAn IT‐infrastructure using a laboratory information management system (LIMS)has been established, that is the key interface for the research teams inorder to share and explore data generated within the project. The cross‐sitedata repository in Lund forms the basis for sample processing, together withbiological samples in southern Sweden, including blood fractions and tumortissues. Clinical registries are associated with the biobank materials, including pathology reports on disease diagnosis on the malignant melanoma(MM) patients.ConclusionsWe provide data on the developments of protein profiling and targeted proteinassays on isolated melanoma tumors, as well as reference blood standardsthat is used by the team members in the respective laboratories. These pilotdata show biobank access and feasibility of performing quantitativeproteomics in MM biobank repositories collected in southern Sweden. Thescientific outcomes further strengthen the build of healthcare benefit inthe complex challenges of malignant melanoma pathophysiology that isaddressed by the novel personalized medicines entering the market.
CD4+Foxp3+ regulatory T cells prolong drug-induced disease remission in (NZBxNZW) F1 lupus mice
Authors: Weigert Olivia , von Spee Caroline , Undeutsch Reinmar , Kloke Lutz , Humrich Jens Y , Riemekasten Gabriela 
Published: February 2013

Abstract
Introduction
The ability to ameliorate murine lupus renders regulatory T cells (Treg) a promising tool for the treatment of systemic lupus erythematosus (SLE). In consideration to the clinical translation of a Treg-based immunotherapy of SLE, we explored the potential of CD4+Foxp3+ Treg to maintain disease remission after induction of remission with an established cyclophosphamide (CTX) regimen in lupus-prone (NZBxNZW) F1 mice. As a prerequisite for this combined therapy, we also investigated the impact of CTX on the biology of endogenous Treg and conventional CD4+ T cells (Tcon).

Methods
Remission of disease was induced in diseased (NZBxNZW) F1 mice with an established CTX regimen consisting of a single dose of glucocorticosteroids followed by five day course with daily injections of CTX. Five days after the last CTX injection, differing amounts of purified CD4+Foxp3+CD25+ Treg were adoptively transferred and clinical parameters, autoantibody titers, the survival and changes in peripheral blood lymphocyte subsets were determined at different time points during the study. The influence of CTX on the numbers, frequencies and proliferation of endogenous Treg and Tcon was analyzed in lymphoid organs by flow cytometry.

Results
Apart from abrogating the proliferation of Tcon, we found that treatment with CTX induced also a significant inhibition of Treg proliferation and a decline in Treg numbers in lymphoid organs. Additional adoptive transfer of 1.5 × 106 purified Treg after the CTX regimen significantly increased the survival and prolonged the interval of remission by approximately five weeks compared to mice that received only the CTX regimen. The additional clinical amelioration was associated with an increase in the Treg frequency in the peripheral blood indicating a compensation of CTX-induced Treg deficiency by the Treg transfer.

Conclusions
Treg were capable to prolong the interval of remission induced by conventional cytostatic drugs. This study provides valuable information and a first proof-of-concept for the feasibility of a Treg-based immunotherapy in the maintenance of disease remission in SLE.
Selenoprotein K is required for palmitoylation of CD36 in macrophages: implications in foam cell formation and atherogenesis
Authors: Meiler Svenja , Baumer Yvonne , Huang Zhi , Hoffmann Fukun W , Fredericks Gregory J , Rose Aaron H , Norton Robert L , Hoffmann Peter R , Boisvert William A 
Published: February 2013

Abstract
CD36 requires palimitoylation in a selenoprotein K-dependent manner, to localize lipid rafts and function properly.
Selk is an ER transmembrane protein important for calcium flux and macrophage activation, but its role in foam cell formation and atherosclerosis has not been evaluated. BMDMs from Selk−/− mice exhibited decreased uptake of modLDL and foam cell formation compared with WT controls, and the differences were eliminated with anti-CD36 blocking antibody. CD36 expression was decreased in TNF-α-stimulated Selk−/− BMDMs compared with WT controls. Fluorescence microscopy revealed TNF-α-induced clustering of CD36 in WT BMDMs indicative of lipid raft localization, which was absent in Selk−/− BMDMs. Fractionation revealed lower levels of CD36 reaching lipid rafts in TNF-α-stimulated Selk−/− BMDMs. Immunoprecipitation showed that Selk−/− BMDMs have decreased CD36 palmitoylation, which occurs at the ER membrane and is crucial for stabilizing CD36 expression and directing its localization to lipid rafts. To assess if this phenomenon had a role in atherogenesis, a HFD was fed to irradiated Ldlr−/− mice reconstituted with BM from Selk−/− or WT mice. Selk was detected in aortic plaques of controls, particularly in macrophages. Selk−/− in immune cells led to reduction in atherosclerotic lesion formation without affecting leukocyte migration into the arterial wall. These findings suggest that Selk is important for stable, localized expression of CD36 in macrophages during inflammation, thereby contributing to foam cell formation and atherogenesis.
Non-Nuclear–Initiated Actions of the Estrogen Receptor Protect Cortical Bone Mass
Authors: Bartell Shoshana M. , Han Li , Kim Ha-neui , Kim Sung Hoon , Katzenellenbogen John A. , Katzenellenbogen Benita S. , Chambliss Ken L. , Shaul Philip W. , Roberson Paula K. , Weinstein Robert S. , Jilka Robert L. , Almeida Maria , Manolagas Stavros C. 
Published: February 2013

AbstractExtensive evidence has suggested that at least some of the effects of estrogens on bone are mediated via extranuclear estrogen receptor α signaling. However, definitive proof for this contention and the extent to which such effects may contribute to the overall protective effects of estrogens on bone maintenance have remained elusive. Here, we investigated the ability of a 17β-estradiol (E2) dendrimer conjugate (EDC), incapable of stimulating nuclear-initiated actions of estrogen receptor α, to prevent the effects of ovariectomy (OVX) on the murine skeleton. We report that EDC was as potent as an equimolar dose of E2 in preventing bone loss in the cortical compartment that represents 80% of the entire skeleton, but was ineffective on cancellous bone. In contrast, E2 was effective in both compartments. Consistent with its effect on cortical bone mass, EDC partially prevented the loss of both vertebral and femoral strength. In addition, EDC, as did E2, prevented the OVX-induced increase in osteoclastogenesis, osteoblastogenesis, and oxidative stress. Nonetheless, the OVX-induced decrease in uterine weight was unaltered by EDC but was restored by E2. These results demonstrate that the protection of cortical bone mass by estrogens is mediated, at least in part, via a mechanism that is distinct from the classic mechanism of estrogen action on reproductive organs.
Maggot learning and Synapsin function
Authors: Diegelmann Sören , Klagges Bert , Michels Birgit , Schleyer Michael , Gerber Bertram 
Published: February 2013

Summary
Drosophila larvae are focused on feeding and have few neurons. Within these bounds, however, there still are behavioural degrees of freedom. This review is devoted to what these elements of flexibility are, and how they come about. Regarding odour–food associative learning, the emerging working hypothesis is that when a mushroom body neuron is activated as a part of an odour-specific set of mushroom body neurons, and coincidently receives a reinforcement signal carried by aminergic neurons, the AC-cAMP-PKA cascade is triggered. One substrate of this cascade is Synapsin, and therefore this review features a general and comparative discussion of Synapsin function. Phosphorylation of Synapsin ensures an alteration of synaptic strength between this mushroom body neuron and its target neuron(s). If the trained odour is encountered again, the pattern of mushroom body neurons coding this odour is activated, such that their modified output now allows conditioned behaviour. However, such an activated memory trace does not automatically cause conditioned behaviour. Rather, in a process that remains off-line from behaviour, the larvae compare the value of the testing situation (based on gustatory input) with the value of the odour-activated memory trace (based on mushroom body output). The circuit towards appetitive conditioned behaviour is closed only if the memory trace suggests that tracking down the learned odour will lead to a place better than the current one. It is this expectation of a positive outcome that is the immediate cause of appetitive conditioned behaviour. Such conditioned search for reward corresponds to a view of aversive conditioned behaviour as conditioned escape from punishment, which is enabled only if there is something to escape from – much in the same way as we only search for things that are not there, and run for the emergency exit only when there is an emergency. One may now ask whether beyond ‘value’ additional information about reinforcement is contained in the memory trace, such as information about the kind and intensity of the reinforcer used. The Drosophila larva may allow us to develop satisfyingly detailed accounts of such mnemonic richness – if it exists.
Exploring text-initial words, clusters and concgrams in a newspaper corpus
Authors: O'donnell, Matthew Brook , Scott, Mike , Mahlberg, Michaela , Hoey, Michael 
Published: February 2013

AbstractThe notion of ‘textual colligation’ predicts that certain lexical items have a tendency to occur at particular points in a text, i.e. the beginning or end of texts, paragraphs or sentences. This paper describes new corpus-based methods developed to identify the profile of words, clusters (n-grams) and concgrams (non-contiguous patterns in variant order) in terms of their most common textual locations. Groups of co-occurring text-initial items are then analyzed in terms of their discourse function in relation to theories of newspaper structure. This analysis illustrates how methods from corpus linguistics, when targeted to specific textual positions, can complement text-linguistic analyses.
Clustering Analysis in Boron and Phosphorus Implanted (100) Germanium by X-Ray Absorption Spectroscopy
Authors: Sahiner M. Alper , Ansari Parviz , Carroll Malcolm S. , King C. A. , Suh Y. S. , Levy R. A. , Buyuklimanli Temel , Croft Mark 
Published: February 2013

AbstractRecently, germanium based semiconductor device technology gained renewed interest due to new developments such as the use of high-k dielectrics for high mobility Ge MOSFETS. However, a systematic local structural investigation of clustering of dopants has been lacking in the literature. In this study, we present a detailed local structural analysis of boron and phosphorus implanted Ge wafers. We have used Ge K-edge x-ray absorption fine-structure spectroscopy (XAFS) in order to probe the local structural modifications around the Ge atom under various implantation parameters and postimplantation annealing treatments. The (100) Ge wafers were implanted and with 11B+ or 31P+ using energies ranging from 20 keV to 320 keV and doses of 5×1013 to 5×1016/cm2. Pieces of the implanted wafers were subjected to thermal annealing at 400°C or 600°C for three hours in high purity nitrogen. Secondary ion mass spectrometry (SIMS) measurements on these wafers were used to correlate the dopant concentration profiles with the local structural information obtained from XAFS. B and P implanted Ge exhibit distinct responses to annealing. For the P implanted Ge samples annealing leads to recrystallization of Ge with increasing annealing temperature, but also an increase in Ge Debye-Waller factors, whereas B implanted Ge samples e×hibit recrystallization at 400°C annealing but more randomness after 600°C annealing.
Determination of Diffusivities of Si Self-Diffusion and Si Self-Interstitials using Isotopically Enriched Single-or Multi-30Si Epitaxial Layers
Authors: Matsumoto S. , Aid S.R. , Sakaguchi T. , Toyonaga K. , Nakabayashi Y. , Sakuraba M. , Shimamune Y. , Hashiba Y. , Murota J. , Wada K. , Abe T. 
Published: February 2013

AbstractSelf-diffusivity of Si has been obtained over a wide temperature range (867°C-1300°C) using highly isotopically enriched 30Si epi-layers (99.88%) as a diffusion source into natural Si substrates. 30Si epi-layers were grown on both CZ-Si substrates and non-doped epi-layers grown on CZ-Si substrates using low pressure CVD with 30SiH4. Diffusion was performed in resistance-heated furnaces under a pure Ar atmosphere. After annealing, the concentrations of the respective Si isotopes were measured with secondary ion mass spectroscopy (SIMS). Diffusivity of 30Si (called Si self-diffusivity, DSD) was determined using a numerical fitting process with 30Si SIMS profiles. We found no major differences in self-diffusivity between bulk Si and epi-Si. Within the 867°C -1300°C range investigated, DSD can be described by an Arrhenius equation with one single activation enthalpy: DSD =14 exp (—4.37 eV/kT) cm2/s. The present result is in good agreement with that of Bracht et. al.Diffusivity and thermal equilibrium concentration of Si self-interstitials have been determined using multi-30Si epi-layers consisting of alternative layers with isotopically pure 30Si and natural Si. The sample surface was oxidized and the Si self-interstitials were introduced from the surface. Spreading of 30Si spikes of each layer due to the diffusion of Si self-interstitials generated at the surface was measured with SIMS analysis. The diffusivity of Si self-interstitials, DI, is obtained by fitting with experimental results. In the temperature range between 820 -920°C, DI and thermal equilibrium concentration of Si self-interstitials, CIi, are described by the Arrhenius equations DI3.48×104 exp (—3.82eV/KT) cm2/s and CIi= 9.62×1018 exp (—0.475eV/KT) cm-3, respectively.
P-N Junction Diodes Fabricated Based on Donor Formation in Plasma Hydrogenated P-Type Czochralski Silicon
Authors: Huang Y. L. , Simoen E. , Job R. , Claeys C. , Düngen W. , Ma Y. , Fahrner W. R. , Versluys J. , Clauws P. 
Published: February 2013

AbstractA rather large amount of shallow donors is created in p-type Czochralski silicon (Cz Si) wafers after a hydrogen plasma exposure at ∼270 °C (substrate temperature) and a subsequent annealing in the temperature range of 350-450 °C. This two-step process has been used for the fabrication p-n junction diodes at low temperatures. Current-voltage characteristics show that the breakdown voltages of these diodes are higher than 100 V. The diode leakage is found to be improved after slow ramp annealing at temperatures up to 250 °C. Deep level transient spectroscopy measurements reveal that the oxygen related thermal donor is not the dominant doping species as expected before.