bluuebunny/crossref_metadata_2025 huggingface dataset:
A Biomechanical Comparison of Pitching From a Mound Versus Flat Ground in Adolescent Baseball Pitchers
Authors: Nissen Carl W. , Solomito Matthew , Garibay Erin , Õunpuu Sylvia , Westwell Melany
Published: September 2013

Background:

Baseball professionals believe that pitching from a mound can increase the stresses placed on the body.

Hypothesis:

There is no difference in kinematics or kinetics in pitching from a mound versus flat-ground conditions in adolescent baseball pitchers.

Study Design:

Laboratory investigation.

Methods:

The fastball pitching motions of 15 adolescent baseball pitchers, including upper extremity kinematics and kinetics and lead- and trail-leg kinematics, were evaluated while pitching from the mound and flat ground. Student t tests were used to determine the differences between the 2 testing conditions.

Results:

Maximum external glenohumeral rotation was similar between the 2 conditions (134° ± 14° mound vs 133° ± 14° flat ground, P = 0.10). Ankle plantar flexion of the lead leg at ball release was greater in the flat-ground condition (−20° ± 10° mound vs −15° ± 12° flat ground, P = 0.01). A statistically significant increase in glenohumeral internal rotation moment (33.6 ± 12.1 Nm mound vs 31.7 ± 11.6 Nm flat ground, P = 0.01) and an increase in elbow varus moment (33.3 ± 12.3 Nm mound vs 31.4 ± 11.8 Nm flat ground, P = 0.02) was measured when pitching from the mound as compared with flat ground.

Conclusion:

Pitching from the mound causes increased stress on the shoulder and elbow of adolescent pitchers as compared with that from flat ground.

Clinical Relevance:

The differences in kinematics as well as increased moments in the shoulder and elbow are helpful for pitchers and their coaches to know at the beginning of their season or as they return from injury or surgery. Pitchers in these situations should start their pitching progression on flat ground and progress to the mound.
Use of Complementary and Alternative Medicine in a Sample of Women With Breast Cancer
Authors: Vidal Mariana , Carvalho Cláudia , Bispo Regina
Published: September 2013

This study aims to examine the usage of complementary and alternative medicine (CAM) on a sample of Portuguese women with history of breast cancer. A total of 107 women with history of breast cancer attending Movimento Vencer e Viver Lisboa responded to a questionnaire designed to assess the use of CAM, as well as other variables, such as satisfaction with conventional care, health perception, perceived control over cancer, and health status (body mass index [BMI], smoking and alcohol consumption, hours of sleep, and physical activity). Forty-eight percent of the participants had used some kind of CAM in the past 12 months. The perceived control over cancer was significantly associated with CAM use (odds ratio [OR] = 1.5; 95% confidence interval [CI] = [1.2, 1.9]). CAM use was more prevalent among women aged 30 to 39 years, single, with high education, and a monthly income of 2,500€ to 2,999€. The CAM used most often were natural products, along with psychotherapy, breathing exercises, and meditation. The main reason mentioned for its use was the improved sense of well-being, and it was interesting to note that 60% of the participants who used CAM did not discuss it with their physicians. The findings support previous data that suggest that the participants’ perceived control over their cancer is a significant predictor of CAM usage, and more than half of the patients did not discuss CAM usage with their physician. Further studies with larger samples of cancer patients are warranted.
Resistance spot welding control based on the temperature measurement
Authors: Podržaj Primož , Simončič Samo
Published: September 2013

In this paper a novel approach for temperature measurement during resistance spot welding is presented. The temperature is measured by two thermocouples mounted at the ends of both the electrode tips. The authors chose to mount them there because it was expected that it would be possible to measure the temperature at this point using a digital camera in the near future. The research was, therefore, motivated to obtain various pieces of information about the welding process from the measured temperature profiles. The measured temperature profiles showed a good correlation with the weld strength. Other phenomena, such as expulsion and electrode wear, can also be related to a temperature profile.
Thermoelectric method for temperature measurement in friction stir welding
Authors: De Backer J , Bolmsjö G
Published: September 2013

Previous research within friction stir welding (FSW) has demonstrated that online control of welding parameters can improve the mechanical properties and is necessary for certain applications to guarantee a consistent weld quality. One approach to control the process is by adapting the heat input to maintain a stable welding temperature, within the specified operating boundaries. This requires accurate in-process temperature measurements. This paper presents a novel method to measure the temperature at the interface of the FSW tool and workpiece. The method is based on the thermoelectric effect between dissimilar materials. The measurements are compared to thermocouple measurements and to a physical model and show good correspondence to each other. Experiments demonstrate that the method can quickly detect temperature variations, due to geometrical variations of the workpiece or due to parameter changes. This allows use of the method for online control of robotic FSW.
Arc pressure and fluid flow during alternating shielding gases. Part 2: arc force determination
Authors: Campbell S W , Galloway A M , McPherson N A
Published: September 2013

The transient variation of the shielding gas present in the alternating shielding gas process produces a dynamic action within the liquid weld metal. Flow vectors opposite in direction have been reported due to the various forces acting on the weld metal when argon and helium are present; however, no data have been provided to substantiate this claim. This part of the study evaluates the various forces acting on the liquid weld metal when using argon and helium, and their effects are discussed. It was determined that argon produces a greater vertically downward force in the central region than does helium for both the arc force and Lorentz force. However, helium produces a greater radially outward force at the pool surface than does argon due to plasma shear stress and Marangoni convection. In addition, the buoyancy force, i.e. the vertically upward force in the central portion of the weld metal, was greater for helium.
Quantitative influence of minor and impurity elements on solidification cracking susceptibility of extra high purity type 310 stainless steel
Authors: Saida K , Matsushita H , Nishimoto K , Kiuchi K , Nakayama J
Published: September 2013

To evaluate the influence of minor and impurity elements on the solidification cracking susceptibility in austenitic stainless steel welds, the transverse Varestraint test was conducted using several extra high purity type 310 stainless steels with different amounts of C, Mn, P and S. The characteristic influence on solidification cracking could be expressed by the ratio of P/S/C≈1∶1·3∶0·56, while Mn affected solidification cracking to a negligible extent. A theoretical approach revealed that the reduced solidification cracking susceptibility with decreasing C, P and S contents could be attributed to the suppression of solidification segregation.
Two main genetic pathways lead to the transformation of chronic lymphocytic leukemia to Richter syndrome
Authors: Chigrinova Ekaterina , Rinaldi Andrea , Kwee Ivo , Rossi Davide , Rancoita Paola M. V. , Strefford Jonathan C. , Oscier David , Stamatopoulos Kostas , Papadaki Theodora , Berger Francoise , Young Ken H. , Murray Fiona , Rosenquist Richard , Greiner Timothy C. , Chan Wing C. , Orlandi Ester M. , Lucioni Marco , Marasca Roberto , Inghirami Giorgio , Ladetto Marco , Forconi Francesco , Cogliatti Sergio , Votavova Hana , Swerdlow Steven H. , Stilgenbauer Stephan , Piris Miguel A. , Matolcsy Andras , Spagnolo Dominic , Nikitin Eugene , Zamò Alberto , Gattei Valter , Bhagat Govind , Ott German , Zucca Emanuele , Gaidano Gianluca , Bertoni Francesco
Published: September 2013

Key Points

Richter syndrome has genomic complexity intermediate between chronic lymphocytic leukemia and diffuse large B-cell lymphoma. Inactivation of TP53 and of CDKN2A is a main mechanism in the transformation to Richter syndrome.
Primary therapy of Waldenström macroglobulinemia (WM) with weekly bortezomib, low-dose dexamethasone, and rituximab (BDR): long-term results of a phase 2 study of the European Myeloma Network (EMN)
Authors: Dimopoulos Meletios A. , García-Sanz Ramón , Gavriatopoulou Maria , Morel Pierre , Kyrtsonis Marie-Christine , Michalis Eurydiki , Kartasis Zafiris , Leleu Xavier , Palladini Giovanni , Tedeschi Alessandra , Gika Dimitra , Merlini Giampaolo , Kastritis Efstathios , Sonneveld Pieter
Published: September 2013

Key Points

BDR is an active regimen and induces long-lasting responses in patients with newly diagnosed WM. Induction with single-agent bortezomib may be effective in preventing complications of hyperviscosity or rituximab-induced IgM flare.
β1 integrin−mediated signals are required for platelet granule secretion and hemostasis in mouse
Authors: Petzold Tobias , Ruppert Raphael , Pandey Dharmendra , Barocke Verena , Meyer Hannelore , Lorenz Michael , Zhang Lin , Siess Wolfgang , Massberg Steffen , Moser Markus
Published: September 2013

Key Points

Platelet β1 integrin−mediated signals control granule secretion and hemostasis β1 integrin−mediated outside-in signaling is independent of direct kindlin-integrin interaction
Replication characteristics of porcine reproductive and respiratory syndrome virus (PRRSV) European subtype 1 (Lelystad) and subtype 3 (Lena) strains in nasal mucosa and cells of the monocytic lineage: indications for the use of new receptors of PRRSV (Lena)
Authors: Frydas Ilias S , Verbeeck Mieke , Cao Jun , Nauwynck Hans J
Published: September 2013

Recently, it has been demonstrated that subtype 3 strains of European type porcine reproductive and respiratory syndrome virus (PRRSV) are more virulent/pathogenic than subtype 1 strains. This points to differences in the pathogenesis. In the present study, a new polarized nasal mucosa explant system was used to study the invasion of the low virulent subtype 1 PRRSV strain Lelystad (LV) and the highly virulent subtype 3 PRRSV strain Lena at the portal of entry. Different cell types of the monocytic lineage (alveolar macrophages (PAM), cultured blood monocytes and monocyte-derived dendritic cells (moDC)) were enclosed to examine replication kinetics of both strains in their putative target cells. At 0, 12, 24, 48 and 72 hours post inoculation (hpi), virus production was analyzed and the infected cells were quantified and identified. Lena replicated much more efficiently than LV in the nasal mucosa explants and to a lesser extent in PAM. Differences in replication were not found in monocytes and moDC. Confocal microscopy demonstrated that for LV, almost all viral antigen positive cells were CD163+Sialoadhesin (Sn)+, which were mainly located in the lamina propria of the respiratory mucosa. In Lena-infected nasal mucosa, CD163+Sn+, CD163+Sn- and to a lesser extent CD163-Sn- monocytic subtypes were involved in infection. CD163+Sn- cells were mostly located within or in the proximity of the epithelium. Our results show that, whereas LV replicates in a restricted subpopulation of CD163+Sn+ monocytic cells in the upper respiratory tract, Lena hijacks a broader range of subpopulations to spread within the mucosa. Replication in CD163+Sn- cells suggests that an alternative entry receptor may contribute to the wider tropism of Lena.
Insights into food preference in hybrid F1 of Siniperca chuatsi (♀) × Siniperca scherzeri (♂) mandarin fish through transcriptome analysis
Authors: He Shan , Liang Xu-Fang , Sun Jian , Li Ling , Yu Ying , Huang Wei , Qu Chun-Mei , Cao Liang , Bai Xiao-Li , Tao Ya-Xiong
Published: September 2013

Background

As economically relevant traits, feeding behavior and food preference domestication determine production cost and profitability. Although there are intensive research efforts on feeding behavior and food intake, little is known about food preference. Mandarin fish accept only live prey fish and refuse dead prey fish or artificial diets. Very little is currently known about the genes regulating this unique food preference.

Results

Using transcriptome sequencing and digital gene expression profiling, we identified 1,986 and 4,526 differentially expressed genes in feeders and nonfeeders of dead prey fish, respectively. Up-regulation of Crbp, Rgr and Rdh8, and down-regulation of Gc expression, consistent with greater visual ability in feeders, could promote positive phototaxis. Altered expressions of period, casein kinase and Rev-erbα might reset circadian phase. Down-regulation of orexigenic and up-regulation of anorexigenic genes in feeders were associated with lower appetite. The mRNA levels of Creb, c-fos, C/EBP, zif268, Bdnf and Syt were dramatically decreased in feeders, which might result in significant deficiency in memory retention of its natural food preference (live prey fish). There were roughly 100 times more potential SNPs in feeders than in nonfeeders.

Conclusions

In summary, differential expression in the genes identified shed new light on why mandarin fish only feed on live prey fish, with pathways regulating retinal photosensitivity, circadian rhythm, appetite control, learning and memory involved. We also found dramatic difference in SNP abundance in feeders vs nonfeeders. These differences together might account for the different food preferences. Elucidating the genes regulating the unique food preference (live prey fish) in mandarin fish could lead to a better understanding of mechanisms controlling food preference in animals, including mammals.
Use of a promiscuous, constitutively-active bacterial enhancer-binding protein to define the σ54 (RpoN) regulon of Salmonella Typhimurium LT2
Authors: Samuels David J , Frye Jonathan G , Porwollik Steffen , McClelland Michael , Mrázek Jan , Hoover Timothy R , Karls Anna C
Published: September 2013

Background

Sigma54, or RpoN, is an alternative σ factor found widely in eubacteria. A significant complication in analysis of the global σ54 regulon in a bacterium is that the σ54 RNA polymerase holoenzyme requires interaction with an active bacterial enhancer-binding protein (bEBP) to initiate transcription at a σ54-dependent promoter. Many bacteria possess multiple bEBPs, which are activated by diverse environmental stimuli. In this work, we assess the ability of a promiscuous, constitutively-active bEBP—the AAA+ ATPase domain of DctD from Sinorhizobium meliloti—to activate transcription from all σ54-dependent promoters for the characterization of the σ54 regulon of Salmonella Typhimurium LT2.

Results

The AAA+ ATPase domain of DctD was able to drive transcription from nearly all previously characterized or predicted σ54-dependent promoters in Salmonella under a single condition. These promoters are controlled by a variety of native activators and, under the condition tested, are not transcribed in the absence of the DctD AAA+ ATPase domain. We also identified a novel σ54-dependent promoter upstream of STM2939, a homolog of the cas1 component of a CRISPR system. ChIP-chip analysis revealed at least 70 σ54 binding sites in the chromosome, of which 58% are located within coding sequences. Promoter-lacZ fusions with selected intragenic σ54 binding sites suggest that many of these sites are capable of functioning as σ54-dependent promoters.

Conclusion

Since the DctD AAA+ ATPase domain proved effective in activating transcription from the diverse σ54-dependent promoters of the S. Typhimurium LT2 σ54 regulon under a single growth condition, this approach is likely to be valuable for examining σ54 regulons in other bacterial species. The S. Typhimurium σ54 regulon included a high number of intragenic σ54 binding sites/promoters, suggesting that σ54 may have multiple regulatory roles beyond the initiation of transcription at the start of an operon.
Inter- and intraobserver variability in motor mapping of the hotspot for the abductor policis brevis muscle
Authors: Sollmann Nico , Hauck Theresa , Obermüller Thomas , Hapfelmeier Alexander , Meyer Bernhard , Ringel Florian , Krieg Sandro M
Published: September 2013

Background

For accuracy in navigated transcranial magnetic stimulation (nTMS), determination of the hotspot location of small hand muscles is crucial because it is the basis for the resting motor threshold (RMT) and, therefore, its spatial resolution. We investigated intra- and interobserver differences of hotspot mapping to provide evidence for the reproducibility of this method.

Ten subjects underwent nTMS motor mapping of the hotspot for the abductor pollicis brevis muscle (APB) three times. The first two sessions were performed by the same examiner; the third mapping was performed by a different examiner. Distances between the first and second mappings (intraobserver variability) and between the second and third mappings (interobserver variability) were measured.

Results

Intraobserver variability had a mean of 8.1 ± 3.3 mm (limits of agreement (LOA) 1.7 to 14.6 mm), whereas mean interobserver variability was 10.3 ± 3.3 mm (LOA 3.8 to 16.7 mm). Concerning RMT, CCC was 0.725 (95% CI: 0.276; 0.914). The mean variability in the same cortical depth was measured as 5.7 ± 3.3 mm (LOA −0.7 to 12.2 mm) for intraobserver and 9.2 ± 3.3 mm (LOA 2.7 to 15.8 mm) for interobserver examinations. When evaluating the RMT, CCC was 0.709 (95% CI: 0.244; 0.909).

Conclusions

Overall, intraobserver variability showed higher reliability than interobserver variability. Our findings show that we can achieve good reliability in hotspot determination, ranging within the calculated precision of the system.
Renal replacement therapy in ADPKD patients: a 25-year survey based on the Catalan registry
Authors: Martínez Víctor , Comas Jordi , Arcos Emma , Díaz Joan Manel , Muray Salomé , Cabezuelo Juan , Ballarín José , Ars Elisabet , Torra Roser
Published: September 2013

Background

Some 7-10% of patients on replacement renal therapy (RRT) are receiving it because of autosomal dominant polycystic kidney disease (ADPKD). The age at initiation of RRT is expected to increase over time.

Methods

Clinical data of 1,586 patients (7.9%) with ADPKD and 18,447 (92.1%) patients with other nephropathies were analysed from 1984 through 2009 (1984–1991, 1992–1999 and 2000–2009).

Results

The age at initiation of RRT remained stable over the three periods in the ADPKD group (56.7 ± 10.9 (mean ± SD) vs 57.5 ± 12.1 vs 57.8 ± 13.3 years), whereas it increased significantly in the non-ADPKD group (from 54.8 ± 16.8 to 63.9 ± 16.3 years, p < 0.001). The ratio of males to females was higher for non-ADPKD than for ADPKD patients (1.6–1.8 vs 1.1–1.2). The prevalence of diabetes was significantly lower in the ADPKD group (6.76% vs 11.89%, p < 0.001), as were most of the co-morbidities studied, with the exception of hypertension. The survival rate of the ADPKD patients on RRT was higher than that of the non-ADPKD patients (p < 0.001).

Conclusions

Over time neither changes in age nor alterations in male to female ratio have occurred among ADPKD patients who have started RRT, probably because of the impact of unmodifiable genetic factors in the absence of a specific treatment.
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

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

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

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

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

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

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

Panoramic 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.
Assessment of Student Learning Associated with Tree Thinking in an Undergraduate Introductory Organismal Biology Course
Authors: Smith James J. , Cheruvelil Kendra Spence , Auvenshine Stacie
Published: September 2013

Phylogenetic trees provide visual representations of ancestor–descendant relationships, a core concept of evolutionary theory. We introduced “tree thinking” into our introductory organismal biology course (freshman/sophomore majors) to help teach organismal diversity within an evolutionary framework. Our instructional strategy consisted of designing and implementing a set of experiences to help students learn to read, interpret, and manipulate phylogenetic trees, with a particular emphasis on using data to evaluate alternative phylogenetic hypotheses (trees). To assess the outcomes of these learning experiences, we designed and implemented a Phylogeny Assessment Tool (PhAT), an open-ended response instrument that asked students to: 1) map characters on phylogenetic trees; 2) apply an objective criterion to decide which of two trees (alternative hypotheses) is “better”; and 3) demonstrate understanding of phylogenetic trees as depictions of ancestor–descendant relationships. A pre–post test design was used with the PhAT to collect data from students in two consecutive Fall semesters. Students in both semesters made significant gains in their abilities to map characters onto phylogenetic trees and to choose between two alternative hypotheses of relationship (trees) by applying the principle of parsimony (Occam's razor). However, learning gains were much lower in the area of student interpretation of phylogenetic trees as representations of ancestor–descendant relationships.
A Critical Analysis of Assessment Quality in Genomics and Bioinformatics Education Research
Authors: Campbell Chad E. , Nehm Ross H.
Published: September 2013

The growing importance of genomics and bioinformatics methods and paradigms in biology has been accompanied by an explosion of new curricula and pedagogies. An important question to ask about these educational innovations is whether they are having a meaningful impact on students’ knowledge, attitudes, or skills. Although assessments are necessary tools for answering this question, their outputs are dependent on their quality. Our study 1) reviews the central importance of reliability and construct validity evidence in the development and evaluation of science assessments and 2) examines the extent to which published assessments in genomics and bioinformatics education (GBE) have been developed using such evidence. We identified 95 GBE articles (out of 226) that contained claims of knowledge increases, affective changes, or skill acquisition. We found that 1) the purpose of most of these studies was to assess summative learning gains associated with curricular change at the undergraduate level, and 2) a minority (<10%) of studies provided any reliability or validity evidence, and only one study out of the 95 sampled mentioned both validity and reliability. Our findings raise concerns about the quality of evidence derived from these instruments. We end with recommendations for improving assessment quality in GBE.
Problem- and Case-Based Learning in Science: An Introduction to Distinctions, Values, and Outcomes
Authors: Allchin Douglas
Published: September 2013

Case-based learning and problem-based learning have demonstrated great promise in reforming science education. Yet an instructor, in newly considering this suite of interrelated pedagogical strategies, faces a number of important instructional choices. Different features and their related values and learning outcomes are profiled here, including: the level of student autonomy; instructional focus on content, skills development, or nature-of-science understanding; the role of history, or known outcomes; scope, clarity, and authenticity of problems provided to students; extent of collaboration; complexity, in terms of number of interpretive perspectives; and, perhaps most importantly, the role of applying versus generating knowledge.
Post–Vision and Change: Do We Know How to Change?
Authors: D’Avanzo Charlene
Published: September 2013

The scale and importance of Vision and Change in Undergraduate Biology Education: A Call to Action challenges us to ask fundamental questions about widespread transformation of college biology instruction. I propose that we have clarified the “vision” but lack research-based models and evidence needed to guide the “change.” To support this claim, I focus on several key topics, including evidence about effective use of active-teaching pedagogy by typical faculty and whether certain programs improve students’ understanding of the Vision and Change core concepts. Program evaluation is especially problematic. While current education research and theory should inform evaluation, several prominent biology faculty–development programs continue to rely on self-reporting by faculty and students. Science, technology, engineering, and mathematics (STEM) faculty-development overviews can guide program design. Such studies highlight viewing faculty members as collaborators, embedding rewards faculty value, and characteristics of effective faculty-development learning communities. A recent National Research Council report on discipline-based STEM education research emphasizes the need for long-term faculty development and deep conceptual change in teaching and learning as the basis for genuine transformation of college instruction. Despite the progress evident in Vision and Change, forward momentum will likely be limited, because we lack evidence-based, reliable models for actually realizing the desired “change.”
Student Learning about Biomolecular Self-Assembly Using Two Different External Representations
Authors: Höst Gunnar E. , Larsson Caroline , Olson Arthur , Tibell Lena A. E.
Published: September 2013

Self-assembly is the fundamental but counterintuitive principle that explains how ordered biomolecular complexes form spontaneously in the cell. This study investigated the impact of using two external representations of virus self-assembly, an interactive tangible three-dimensional model and a static two-dimensional image, on student learning about the process of self-assembly in a group exercise. A conceptual analysis of self-assembly into a set of facets was performed to support study design and analysis. Written responses were collected in a pretest/posttest experimental design with 32 Swedish university students. A quantitative analysis of close-ended items indicated that the students improved their scores between pretest and posttest, with no significant difference between the conditions (tangible model/image). A qualitative analysis of an open-ended item indicated students were unfamiliar with self-assembly prior to the study. Students in the tangible model condition used the facets of self-assembly in their open-ended posttest responses more frequently than students in the image condition. In particular, it appears that the dynamic properties of the tangible model may support student understanding of self-assembly in terms of the random and reversible nature of molecular interactions. A tentative difference was observed in response complexity, with more multifaceted responses in the tangible model condition.
Misconceptions Are “So Yesterday!”
Authors: Maskiewicz April Cordero , Lineback Jennifer Evarts
Published: September 2013

At the close of the Society for the Advancement of Biology Education Research conference in July 2012, one of the organizers made the comment: “Misconceptions are so yesterday.” Within the community of learning sciences, misconceptions are yesterday's news, because the term has been aligned with eradication and/or replacement of conceptions, and our knowledge about how people learn has progressed past this idea. This essay provides an overview of the discussion within the learning sciences community surrounding the term “misconceptions” and how the education community's thinking has evolved with respect to students’ conceptions. Using examples of students’ incorrect ideas about evolution and ecology, we show that students’ naïve ideas can provide the resources from which to build scientific understanding. We conclude by advocating that biology education researchers use one or more appropriate alternatives in place of the term misconception whenever possible.
Partnered Research Experiences for Junior Faculty at Minority-Serving Institutions Enhance Professional Success
Authors: Campbell Andrew G. , Leibowitz Michael J. , Murray Sandra A. , Burgess David , Denetclaw Wilfred F. , Carrero-Martinez Franklin A. , Asai David J.
Published: September 2013

Scientific workforce diversity is critical to ensuring the realization of our national research goals and minority-serving institutions play a vital role in preparing undergraduate students for science careers. This paper summarizes the outcomes of supporting career training and research practices by faculty from teaching-intensive, minority-serving institutions. Support of these faculty members is predicted to lead to: 1) increases in the numbers of refereed publications, 2) increases in federal grant funding, and 3) a positive impact on professional activities and curricular practices at their home institutions that support student training. The results presented show increased productivity is evident as early as 1 yr following completion of the program, with participants being more independently productive than their matched peers in key areas that serve as measures of academic success. These outcomes are consistent with the goals of the Visiting Professorship Program to enhance scientific practices impacting undergraduate student training. Furthermore, the outcomes demonstrate the benefits of training support for research activities at minority-serving institutions that can lead to increased engagement of students from diverse backgrounds. The practices and results presented demonstrate a successful generalizable approach for stimulating junior faculty development and can serve as a basis for long-term faculty career development strategies that support scientific workforce diversity.
Were Jevons, Menger, and Walras Really Cardinalists? On the Notion of Measurement in Utility Theory, Psychology, Mathematics, and Other Disciplines, 1870-1910
Authors: Moscati Ivan
Published: September 2013

This article argues that the canonical dichotomy between cardinal utility and ordinal utility is inadequate to tell an accurate history of utility theory, and that a third form of utility consistent with the so-called classical understanding of measurement should be added to the traditional picture. According to the classical view, measuring an object consists of assessing the numerical ratio between the object and some other object taken as a unit. In particular, we show that Jevons, Menger, and Walras understood measurement in the classical sense and applied this understanding to utility measurement; therefore, they were not cardinalists in the current sense of the term, which is associated with the ranking of utility differences. We also analyze the argumentative strategies adopted by Jevons and Walras to address the conflict between the scientific importance they attributed to measurement, their classical understanding of it, and the apparent immeasurability of the utility featuring in their economic theories. Finally, in order to appreciate the broad intellectual context within which their discussions on utility measurement took place, this article reviews the understanding of measurement in disciplines that bear some relation to utility theory. The review illustrates that in the years 1870-1910, the period in which Jevons, Menger, and Walras were active, the classical understanding of measurement dominated not only utility theory but also all other disciplines surveyed. This circumstance helps to explain why the three marginalists remained committed to the classical understanding even though it did not square with their economic practices.
The Puzzle of Marx’s Missing “Results”: A Tale of Two Theories
Authors: Skillman Gilbert L.
Published: September 2013

A long-standing puzzle in the history of Marxian economic thought concerns Marx’s decision to omit the draft chapter titled “Results of the Immediate Process of Production” from the published version of volume 1 of Capital. A number of authors have explored this puzzle without satisfactorily resolving it. This article addresses the question by linking Marx’s omission to a larger set of revisions made to arguments he developed in earlier drafts of Capital. It identifies two distinct theoretical accounts of the phenomenon of surplus value in these drafts, based respectively on Marx’s historical analysis of developments in capitalist social relations and his treatment of the connection between commodity prices and values, and argues that Marx may have been driven to diminish and obscure his historical account in light of increasingly evident inconsistencies with his value-theoretic account. The argument concludes with a discussion of possible consequences of Marx’s decision for his theoretical legacy in the development of economic thought.
The Discovery of the Faustmann Formula in Natural Resource Economics
Authors: Viitala Esa-Jussi
Published: September 2013

This article examines the discovery and early development of the most fundamental of forest and natural resource economic principles, the “Faustmann formula” and the “Faustmann condition,” and links their emergence more closely to the general development of economic thought than has been done previously. In particular, it is shown that a London-based editor and book reviewer, John Houghton, should be given credit for being perhaps the first who explicitly recognized the opportunity cost of forest capital. In his writings, published in 1683 and 1701, Houghton compared forestry with other forms of land use, employing calculations that are in line with modern capital and investment theory. The emergence of this type of natural resource economic reasoning was stimulated by the extensive institutional and political changes in England in the latter part of the seventeenth century. Only much later did the capital valuation and intertemporal resource allocation approach in line with the Faustmann formula begin to gain ground in economics generally.
Limits of Visibility: Taiwan's Tongzhi Movement in Mickey Chen's Documentaries
Authors: Hong Guo-Juin
Published: September 2013

This article examines Mickey Chen's queer documentaries and their tactics of subversion, especially in his representation of both positive and negative images and in his formal strategies of mimicking mainstream media. Issues of “visibility” permeate the general landscape of documentary representation of Taiwan's GLBT or the so-called tongzhi (同志, literally “comrade”) community. Thus questions of resistance and subversion must be viewed through the lens of visibility.