bluuebunny/crossref_metadata_2025_split huggingface dataset:
Automatic registration of multi-modal microscopy images for integrative analysis of prostate tissue sections
Authors: Lippolis Giuseppe , Edsjö Anders , Helczynski Leszek , Bjartell Anders , Overgaard Niels Chr 
Published: September 2013

Abstract

Background
Prostate cancer is one of the leading causes of cancer related deaths. For diagnosis, predicting the outcome of the disease, and for assessing potential new biomarkers, pathologists and researchers routinely analyze histological samples. Morphological and molecular information may be integrated by aligning microscopic histological images in a multiplex fashion. This process is usually time-consuming and results in intra- and inter-user variability. The aim of this study is to investigate the feasibility of using modern image analysis methods for automated alignment of microscopic images from differently stained adjacent paraffin sections from prostatic tissue specimens.

Methods
Tissue samples, obtained from biopsy or radical prostatectomy, were sectioned and stained with either hematoxylin & eosin (H&E), immunohistochemistry for p63 and AMACR or Time Resolved Fluorescence (TRF) for androgen receptor (AR).
Image pairs were aligned allowing for translation, rotation and scaling. The registration was performed automatically by first detecting landmarks in both images, using the scale invariant image transform (SIFT), followed by the well-known RANSAC protocol for finding point correspondences and finally aligned by Procrustes fit. The Registration results were evaluated using both visual and quantitative criteria as defined in the text.

Results
Three experiments were carried out. First, images of consecutive tissue sections stained with H&E and p63/AMACR were successfully aligned in 85 of 88 cases (96.6%). The failures occurred in 3 out of 13 cores with highly aggressive cancer (Gleason score ≥ 8). Second, TRF and H&E image pairs were aligned correctly in 103 out of 106 cases (97%).
The third experiment considered the alignment of image pairs with the same staining (H&E) coming from a stack of 4 sections. The success rate for alignment dropped from 93.8% in adjacent sections to 22% for sections furthest away.

Conclusions
The proposed method is both reliable and fast and therefore well suited for automatic segmentation and analysis of specific areas of interest, combining morphological information with protein expression data from three consecutive tissue sections. Finally, the performance of the algorithm seems to be largely unaffected by the Gleason grade of the prostate tissue samples examined, at least up to Gleason score 7.
District health managers’ perceptions of supervision in Malawi and Tanzania
Authors: Bradley Susan , Kamwendo Francis , Masanja Honorati , de Pinho Helen , Waxman Rachel , Boostrom Camille , McAuliffe Eilish 
Published: September 2013

Abstract

Background
Mid-level cadres are being used to address human resource shortages in many African contexts, but insufficient and ineffective human resource management is compromising their performance. Supervision plays a key role in performance and motivation, but is frequently characterised by periodic inspection and control, rather than support and feedback to improve performance. This paper explores the perceptions of district health management teams in Tanzania and Malawi on their role as supervisors and on the challenges to effective supervision at the district level.

Methods
This qualitative study took place as part of a broader project, “Health Systems Strengthening for Equity: The Power and Potential of Mid-Level Providers”. Semi-structured interviews were conducted with 20 district health management team personnel in Malawi and 37 council health team members in Tanzania. The interviews covered a range of human resource management issues, including supervision and performance assessment, staff job descriptions and roles, motivation and working conditions.

Results
Participants displayed varying attitudes to the nature and purpose of the supervision process. Much of the discourse in Malawi centred on inspection and control, while interviewees in Tanzania were more likely to articulate a paradigm characterised by support and improvement. In both countries, facility level performance metrics dominated. The lack of competency-based indicators or clear standards to assess individual health worker performance were considered problematic. Shortages of staff, at both district and facility level, were described as a major impediment to carrying out regular supervisory visits. Other challenges included conflicting and multiple responsibilities of district health team staff and financial constraints.

Conclusion
Supervision is a central component of effective human resource management. Policy level attention is crucial to ensure a systematic, structured process that is based on common understandings of the role and purpose of supervision. This is particularly important in a context where the majority of staff are mid-level cadres for whom regulation and guidelines may not be as formalised or well-developed as for traditional cadres, such as registered nurses and medical doctors. Supervision needs to be adequately resourced and supported in order to improve performance and retention at the district level.
MicroRNA-9 regulates survival of chondroblasts and cartilage integrity by targeting protogenin
Authors: Song Jinsoo , Kim Dongkyun , Chun Churl-Hong , Jin Eun-Jung 
Published: September 2013

Abstract

Background
Studies have shown the roles of miR-9 and its validated target, protogenin (PRTG) in the differentiation of chondroblasts to chondrocyte and in the pathogenesis of osteoarthritis (OA). We hypothesized that miR-9 plays a distinct role in endochondral ossification and OA pathogenesis and the present study was undertaken to identify this role. In the studies, chondroblasts were isolated from limb bud of chick and mouse embryos and articular chondrocytes were isolated from rabbit and human cartilage. Osteoarthritic chondrocytes were isolated from cartilage from patients undergoing total knee replacement. Using these cells, we analyzed the changes in the expression of genes and proteins, tested the expression level of miR-9, and applied a target validation system. We also performed functional study of miR-9 and PRTG.

Results
With the progression of chondrogenesis, decreased miR-9 level was observed at the time of numerous apoptotic cell deaths. And chondrocytes isolated from normal human articular cartilage expressed miR-9, and this expression was significantly reduced in OA chondrocytes, especially decreased its expression in parallel with the degree of cartilage degradation. Over-expression of PRTG induced the activation of caspase-3 signaling and increased apoptosis. However, the co-treatment with the miR-9 precursor or PRTG-specific siRNA blocked this apoptotic signaling.

Conclusion
This study shows that PRTG is regulated by miR-9, plays an inhibitory action on survival of chondroblasts and articular chondrocytes during chondrogenesis and OA pathogenesis.
Efficient link scheduling for rechargeable wireless ad hoc and sensor networks
Authors: Sun Guodong , Qiao Guofu , Zhao Lin 
Published: September 2013

Abstract
We study the link scheduling for rechargeable wireless ad hoc and sensor networks to improve network throughput. Efficient link scheduling is highly critical for wireless networks, and a lot of efforts have been made to address this issue. The previous work which only considers how to reduce interference within close-by links, however, fails to improve the network throughput for rechargeable wireless network in which a node, powered by ambient energy (such like solar and vibration) has to be recharged before it can communicate with other nodes. Thus, link scheduling with rechargeable nodes is constrained not only by co-channel interference but also by energy replenishment of the node. In this paper, we develop efficient link scheduling algorithms to improve the network throughput of rechargeable wireless ad hoc and sensor networks. The proposed design, based on realistic network models and mathematical formulation, achieves constant ratio of the best solution. Besides the theoretical analysis, simulation experiments are conducted to evaluate our algorithms.
An online model composition tool for system biology models
Authors: Coskun Sarp A , Cicek A Ercument , Lai Nicola , Dash Ranjan K , Ozsoyoglu Z Meral , Ozsoyoglu Gultekin 
Published: September 2013

Abstract

Background
There are multiple representation formats for Systems Biology computational models, and the Systems Biology Markup Language (SBML) is one of the most widely used. SBML is used to capture, store, and distribute computational models by Systems Biology data sources (e.g., the BioModels Database) and researchers. Therefore, there is a need for all-in-one web-based solutions that support advance SBML functionalities such as uploading, editing, composing, visualizing, simulating, querying, and browsing computational models.

Results
We present the design and implementation of the Model Composition Tool (Interface) within the PathCase-SB (PathCase Systems Biology) web portal. The tool helps users compose systems biology models to facilitate the complex process of merging systems biology models. We also present three tools that support the model composition tool, namely, (1) Model Simulation Interface that generates a visual plot of the simulation according to user’s input, (2) iModel Tool as a platform for users to upload their own models to compose, and (3) SimCom Tool that provides a side by side comparison of models being composed in the same pathway. Finally, we provide a web site that hosts BioModels Database models and a separate web site that hosts SBML Test Suite models.

Conclusions
Model composition tool (and the other three tools) can be used with little or no knowledge of the SBML document structure. For this reason, students or anyone who wants to learn about systems biology will benefit from the described functionalities. SBML Test Suite models will be a nice starting point for beginners. And, for more advanced purposes, users will able to access and employ models of the BioModels Database as well.
Antimicrobial activity of novel nanostructured Cu-SiO2 coatings prepared by chemical vapour deposition against hospital related pathogens
Authors: Varghese Sajnu , ElFakhri Souad O , Sheel David W , Sheel Paul , Bolton Frederick J Eric , Foster Howard A 
Published: September 2013

Abstract
There is increasing recognition that the healthcare environment acts as an important reservoir for transmission of healthcare acquired infections (HCAI). One method of reducing environmental contamination would be use of antimicrobial materials. The antimicrobial activity of thin silica-copper films prepared by chemical vapour deposition was evaluated against standard strains of bacteria used for disinfectant testing and bacteria of current interest in HCAI. The structure of the coatings was determined using Scanning Electron Microscopy and their hardness and adhesion to the substrate determined. Antimicrobial activity was tested using a method based on BS ISO 22196:2007. The coatings had a pale green-brown colour and had a similar hardness to steel. SEM showed nano-structured aggregates of Cu within a silica matrix. A log10 reduction in viability of >5 could be obtained within 4 h for the disinfectant test strains and within 6 h for producing Acinetobacter baumannii, Klebsiella pneumoniae and Stenotrophomonas maltophilia. Activity against the other hospital isolates was slower but still gave log10 reduction factors of >5 for extended spectrum β-lactamase producing Escherichia coli and >3 for vancomycin resistant Enterococcus faecium, methicillin resistant Staphylococcus aureus and Pseudomonas aeruginosa within 24 h. The results demonstrate the importance of testing antimicrobial materials destined for healthcare use against isolates of current interest in hospitals as well as standard test strains. The coatings used here can also be applied to substrates such as metals and ceramics and have potential applications where reduction of microbial environmental contamination is desirable.
Panoramic human structure maintenance based on invariant features of video frames
Authors: Chang Shih-Ming , Chang Hon-Hang , Yen Shwu-Huey , Shih Timothy K 
Published: September 2013

AbstractPanoramic photography is becoming a very popular and commonly available feature in the mobile handheld devices nowadays. In traditional panoramic photography, the human structure often becomes messy if the human changes position in the scene or during the combination step of the human structure and natural background. In this paper, we present an effective method in panorama creation to maintain the main structure of human in the panorama. In the proposed method, we use an automatic method of feature matching, and the energy map of seam carving is used to avoid the overlapping of human with the natural background. The contributions of this proposal include automated panoramic creation method and it solves the human ghost generation problem in panorama by maintaining the structure of human by energy map. Experimental results prove that the proposed system can be effectively used to compose panoramic photographs and maintain human structure in panorama.
Analysis of the availability and completeness of pervious radiological examinations related to plain films
Authors: Völk M. , Strotzer M. , Lenhart M. , Wild T. , Fründ R. , Techert J. , Feuerbach S. 
Published: September 2013

Purpose: To evaluate the availability and completeness of previous radiological examinations. Material and Methods: Seven different types of examinations were analysed separately: 1) chest examinations, 2) bedside chest examinations, 3) skeletal examinations, 4) angiographic examinations, 5) mammographic examinations, 6) CT examinations, and 7) MR examinations. A retrospective part of the study covered the calendar year 1997, while a prospective part referred to 1998. The sample size in each modality and each part of the study was 100 observations, resulting in a total number of 1,400 examinations. Results: The average availability and completeness of radiographs in the retrospective analysis was 96.9% in 1997. The average availability and completeness of radiographs in the prospective analysis was 85.5% for the year 1998. This applied to necessary previous examinations of the same or different modality irrespective whether the examination was conducted internally or externally. Conclusion: The real loss rate of radiographs derived from the retrospective investigation was 3.1%. The prospective part of the study showed that 14.5% of the required previous internal and external examinations of the same or different modality were not available completely and in time to the examining radiologist.
Does diving damage the brain?: MR control study of divers' central nervous system
Authors: Hutzelmann A. , Tetzlaff K. , Reuter M. , Müller-Hülsbeck S. , Heller M. 
Published: September 2013

Purpose: To evaluate the prevalence of cerebral white matter changes on MR imaging in healthy elderly compressed air divers with a long diving history in comparison with control subjects who have never dived. Material and Methods: The investigation employed 59 experienced elderly divers and 48 control subjects matched for age, body mass index, alcohol and smoking history. MR studies included a fluid attenuated inversion recovery sequence and T1- and T2-weighted pre- and postcontrast images in axial orientation of the whole brain to localize white matter changes. Results: MR images did not show any morphologic abnormalities in the brains of divers. Both groups - divers and controls - did not differ significantly with respect to white matter changes of the brain. Conclusion: No increased prevalence of cerebral white matter changes in compressed air divers compared with a healthy worker sample of similar age were found. Thus, extensive compressed air diving may not necessarily be related to radiological changes on MR.
Doppler ultrasonography in predicting relapse of hyperthyroidism in Graves' disease
Authors: Varsamidis K. , Varsamidou E. , Mavropoulos G. 
Published: September 2013

Purpose: To determine whether Doppler ultrasonography could be useful in the prediction of relapse of hyperthyroidism in patients with Graves' disease. Material and Methods: Forty patients with Graves' disease confirmed by laboratory tests were examined for a number of blood flow parameters in the inferior thyroid artery before and after they were subjected to proper antithyroid drug treatment. Data were retrospectively reviewed and compared with findings for a control group of 16 age-matched subjects. Results: Significantly increased blood flow parameters were observed both in patients with active hyperthyroidism before treatment and in euthyroid patients who presented a relapse shortly after withdrawal of proper antithyroid drug treatment versus normal controls. Conversely, no significant differences were observed between patients who remained in stable remission and normal controls. Conclusion: Our results support the concept that Doppler ultrasonography evaluation of patients with Graves' disease may contribute to the detection of a relapsing course of hyperthyroidism.
CT findings in tuberculous otomastoiditis: A case report
Authors: Cavallin L. , Muren C. 
Published: September 2013

Purpose: Otomastoiditis is a rare but important manifestation of tuberculosis and is well recognizable when information on its clinical course is considered in connection with the radiographic changes. Material and Method: A patient with a clinical history of chronic otorrhea, resistant to conventional therapy but without dramatic symptoms, was referred for CT examination. Results: CT revealed widespread soft tissue densities in the tympanic cavity and in the mastoid process, with bone erosions in the latter. Surgery and bacteriology confirmed the diagnosis of Mycobacterium tuberculosis infection. Conclusion: CT evidence of widespread bone destruction without clinical signs of aggressive infection should suggest the diagnosis of a mycobacterial process. Early treatment is essential in order to avoid propagation of the disease and lasting loss of function.
Pre-operative simultaneous stereotactic core biopsy and fine-needle aspiration biopsy in the diagnosis of invasive lobular breast carcinoma
Authors: Leifland K. , Lundquist H. , Måre K. , Erhardt K. , Fernstad R. 
Published: September 2013

Purpose: To determine the diagnostic value of stereotactic core needle biopsy (SCNB) in comparison to stereotactic fine-needle aspiration biopsy (SFNAB) in patients with invasive lobular carcinoma (ILC). Material and Methods: Twenty-two patients with clinical or mammographic findings suspicious of malignancy underwent surgery where postoperative histopathology showed ILC. Pre-operative attempts of diagnosis were made using SFNAB and SCNB. SFNAB was done with a spinal needle 0.7- or 0.9-mm and SCNB was simultaneously performed with an automated 2.1-mm biopsy gun in all patients. Results: SFNAB was diagnostic of carcinoma in 9 women, showed “probable carcinoma” in 5 and “atypia” in 3. In the remaining 5 women, SFNAB showed no atypia. SCNB diagnosed ILC in 20 patients and showed ILC as well as invasive ductal carcinoma (IDC) in 1. Ductal carcinoma in situ was suggested in the remaining patient. Conclusion: SCNB was superior to SFNAB in diagnosing ILC and did not miss any carcinoma, whereas SFNAB was non-diagnostic in 8 cases. SCNB is thus recommended in patients with suspicion of ILC of the breast.
High-resolution imaging of coronary calcifications by intense low-energy fluoroscopic X-ray obtained from synchrotron radiation
Authors: Ohtsuka S. , Sugishita Y. , Takeda T. , Itai Y. , Tada J. , Hyodo K. , Ando M. 
Published: September 2013

Purpose: To obtain an intense monochromatic low-energy X-ray from synchrotron radiation (SR) and apply it to detect coronary calcifications. Methods and Results: The SR beam was reflected with a silicon crystal to be expanded (150 mm in height and 80 mm in width) and to be monochromatized at an energy level of 37 keV. The X-ray was intermittently irradiated to obtain dynamic imaging of 30 images/s. Images were recorded by a digital fluorography system. The low-energy X-ray from SR sharply visualized calcification of coronary arteries, while conventional X-ray could not visualize coronary calcification. Conclusion: The intense monochromatic low-energy X-ray from SR is sensitive, has high-resolution for imaging coronary calcification and may serve as a screening method for coronary artery disease.
A double coaxial delivery system for deployment of a two-stage stent-graft: An experimental feasibility study
Authors: Kónya A. , Wright K. C. 
Published: September 2013

Purpose: To design and test a delivery system for successive, rapid two-stage deployment of an aortic stent graft. Material and Methods: An aortic stent graft was made that consisted of two separate parts. A delivery system composed of two independent coaxial mechanisms was fabricated and used to deploy the stages of the graft in dogs' aortas. Results: Delivery was successful in all four dogs, and required less than 2 min in each animal. Conclusion: The double coaxial delivery system enabled quick endovascular assembly of a two-stage aortic stent-graft.
Infrapopliteal percutaneous transluminal angioplasty for limb salvage
Authors: Boyer L. , Therre T. , Garcier J.M. , Perez N. , Ravel A. , Privat C. , Viallet J.-F. 
Published: September 2013

Purpose: To evaluate long-term results of infrapopliteal percutaneous transluminal angioplasty (PTA) for limb salvage. Material and Methods: A retrospective study of 71 consecutive infrapopliteal PTAs in 49 patients with rest pain (n = 20) or ulceration (n = 29) was conducted. In 18 patients, surgical minor amputation or debridment was also performed. Results: Technical success was achieved in 45 patients. Four failures necessitated 2 amputations. One patient died in the postoperative course. Global morbidity rate was 16%, including minor complications in 5 patients and major vascular complications in 3 patients. After technical success during the follow-up (median duration 21 months), restenoses occurred in 4 patients, of whom 3 had a successful re-PTA (clinical success rate 72%). Survival, primary patency, secondary patency and limb salvage rates were, respectively, 75%, 81%, 88% and 87% after 3 years. The only positive predictive factor for primary patency was the presence of diabetes mellitus. Conclusion: Infrapopliteal PTA is a safe and effective procedure, allowing good patency and limb salvage rates with low mortality and morbidity.
Impact of intraoperative ultrasonography on surgical treatment of liver tumours
Authors: Özsunar Y. , Skjoldbye B. , Court-Payen M. , Karstrup S. , Burcharth F. 
Published: September 2013

Purpose: The aim of this study was to evaluate the impact of intraoperative ultrasonography (IOUS) on surgical decision-making in patients with liver tumours. Material and Methods: IOUS of the liver was performed in 116 patients undergoing surgery for liver tumours. The patients were evaluated preoperatively by ultrasonography, CT and in some cases, by ERCP and scintigraphy. IOUS findings were compared with the results of preoperative imaging and surgical findings. Results: The surgical procedures were altered in 50 cases (43%), extended in 19 cases (16%) and reduced in 8 cases (7%). Twenty-three patients (20%) were found inoperable. Intraoperative evaluation caused surgical modification by IOUS in 13 patients (11%), by surgical findings in 14 patients (12%) and by a combination of both in 23 patients (20%). Conclusion: IOUS is a precise diagnostic method for staging the operability of liver tumours. Unnecessary surgical procedures can be avoided. In total, IOUS altered the preoperative plan in one-third of our patients and is therefore recommended as a routine procedure in connection with major liver surgery.