bluuebunny/crossref_metadata_2025_split huggingface dataset:
Barnacle: detecting and characterizing tandem duplications and fusions in transcriptome assemblies
Authors: Swanson Lucas , Robertson Gordon , Mungall Karen L , Butterfield Yaron S , Chiu Readman , Corbett Richard D , Docking T Roderick , Hogge Donna , Jackman Shaun D , Moore Richard A , Mungall Andrew J , Nip Ka Ming , Parker Jeremy DK , Qian Jenny Qing , Raymond Anthony , Sung Sandy , Tam Angela , Thiessen Nina , Varhol Richard , Wang Sherry , Yorukoglu Deniz , Zhao YongJun , Hoodless Pamela A , Sahinalp S Cenk , Karsan Aly , Birol Inanc 
Published: August 2013

Abstract

Background
Chimeric transcripts, including partial and internal tandem duplications (PTDs, ITDs) and gene fusions, are important in the detection, prognosis, and treatment of human cancers.

Results
We describe Barnacle, a production-grade analysis tool that detects such chimeras in de novo assemblies of RNA-seq data, and supports prioritizing them for review and validation by reporting the relative coverage of co-occurring chimeric and wild-type transcripts. We demonstrate applications in large-scale disease studies, by identifying PTDs in MLL, ITDs in FLT3, and reciprocal fusions between PML and RARA, in two deeply sequenced acute myeloid leukemia (AML) RNA-seq datasets.

Conclusions
Our analyses of real and simulated data sets show that, with appropriate filter settings, Barnacle makes highly specific predictions for three types of chimeric transcripts that are important in a range of cancers: PTDs, ITDs, and fusions. High specificity makes manual review and validation efficient, which is necessary in large-scale disease studies. Characterizing an extended range of chimera types will help generate insights into progression, treatment, and outcomes for complex diseases.
The antimicrobial lysine-peptoid hybrid LP5 inhibits DNA replication and induces the SOS response in Staphylococcus aureus
Authors: Gottschalk Sanne , Ifrah Dan , Lerche Sandra , Gottlieb Caroline T , Cohn Marianne T , Hiasa Hiroshi , Hansen Paul R , Gram Lone , Ingmer Hanne , Thomsen Line E 
Published: August 2013

Abstract

Background
The increase in antibiotic resistant bacteria has led to renewed interest in development of alternative antimicrobial compounds such as antimicrobial peptides (AMPs), either naturally-occurring or synthetically-derived. Knowledge of the mode of action (MOA) of synthetic compounds mimicking the function of AMPs is highly valuable both when developing new types of antimicrobials and when predicting resistance development. Despite many functional studies of AMPs, only a few of the synthetic peptides have been studied in detail.

Results
We investigated the MOA of the lysine-peptoid hybrid, LP5, which previously has been shown to display antimicrobial activity against Staphylococcus aureus. At concentrations of LP5 above the minimal inhibitory concentration (MIC), the peptoid caused ATP leakage from bacterial cells. However, at concentrations close to the MIC, LP5 inhibited the growth of S. aureus without ATP leakage. Instead, LP5 bound DNA and inhibited macromolecular synthesis. The binding to DNA also led to inhibition of DNA gyrase and topoisomerase IV and caused induction of the SOS response.

Conclusions
Our data demonstrate that LP5 may have a dual mode of action against S. aureus. At MIC concentrations, LP5 binds DNA and inhibits macromolecular synthesis and growth, whereas at concentrations above the MIC, LP5 targets the bacterial membrane leading to disruption of the membrane. These results add new information about the MOA of a new synthetic AMP and aid in the future design of synthetic peptides with increased therapeutic potential.
Novel open-source electronic medical records system for palliative care in low-resource settings
Authors: Shah Kamal G , Slough Tara Lyn , Yeh Ping Teresa , Gombwa Suave , Kiromera Athanase , Oden Z Maria , Richards-Kortum Rebecca R 
Published: August 2013

Abstract

Background
The need for palliative care in sub-Saharan Africa is staggering: this region shoulders over 67% of the global burden of HIV/AIDS and cancer. However, provisions for these essential services remain limited and poorly integrated with national health systems in most nations. Moreover, the evidence base for palliative care in the region remains scarce. This study chronicles the development and evaluation of DataPall, an open-source electronic medical records system that can be used to track patients, manage data, and generate reports for palliative care providers in these settings.
DataPall was developed using design criteria encompassing both functional and technical objectives articulated by hospital leaders and palliative care staff at a leading palliative care center in Malawi. The database can be used with computers that run Windows XP SP 2 or newer, and does not require an internet connection for use. Subsequent to its development and implementation in two hospitals, DataPall was tested among both trained and untrained hospital staff populations on the basis of its usability with comparison to existing paper records systems as well as on the speed at which users could perform basic database functions. Additionally, all participants evaluated this program on a standard system usability scale.

Results
In a study of health professionals in a Malawian hospital, DataPall enabled palliative care providers to find patients’ appointments, on average, in less than half the time required to locate the same record in current paper records. Moreover, participants generated customizable reports documenting patient records and comprehensive reports on providers’ activities with little training necessary. Participants affirmed this ease of use on the system usability scale.

Conclusions
DataPall is a simple, effective electronic medical records system that can assist in developing an evidence base of clinical data for palliative care in low resource settings. The system is available at no cost, is specifically designed to chronicle care in the region, and is catered to meet the technical needs and user specifications of such facilities.
Comparative study of an externship program versus a corporate-academic cooperation program for enhancing nursing competence of graduating students
Authors: Tseng Chien-Ning , Hsieh Chia-Ju , Chen Kee-Hsin , Lou Meei-Fang 
Published: August 2013

AbstractBackgroundNew graduates report intense stress during the transition from school to their first work settings. Managing this transition is important to reduce turnover rates. This study compared the effects of an externship program and a corporate-academic cooperation program on enhancing junior college students’ nursing competence and retention rates in the first 3 months and 1 year of initial employment.MethodsThis two-phase study adopted a pretest and posttest quasi-experimental design. All participants were graduating students drawn from a 5-year junior nursing college in Taiwan. There were 19 and 24 students who participated in the phase I externship program and phase II corporate-academic cooperation program, respectively. The nursing competence of the students had to be evaluated by mentors within 48 hours of practicum training and after practicum training. The retention rate was also surveyed at 3 months and 1 year after beginning employment.ResultsStudents who participated in the corporate-academic cooperation program achieved a statistically significant improvement in nursing competence and retention rates relative to those who participated in the externship program (p <0.01 andp <0.05, respectively).ConclusionsThe corporate-academic cooperation program facilitates the transition of junior college nursing students into independent staff nurses, enhances their nursing competence, and boosts retention rates.
Recurrence after skin-sparing mastectomy and immediate transverse rectus abdominis musculocutaneous flap reconstruction for invasive breast cancer
Authors: Liang Tsung-Jung , Wang Being-Whey , Liu Shiuh-Inn , Yeh Ming-Hsin , Chen Yu-Chia , Chen Jin-Shyr , Mok King-Tong , Chang Hong-Tai 
Published: August 2013

Abstract

Background
The aim of this study was to evaluate the recurrence pattern after skin-sparing mastectomy (SSM) and immediate breast reconstruction (IBR) using transverse rectus abdominis musculocutaneous (TRAM) flap in patients with invasive breast cancer.

Methods
From 1995 to 2010, patients with invasive breast cancer who underwent SSM followed by IBR using TRAM flap were retrospectively reviewed. The pattern of the first recurrence event was recorded.

Results
We identified 249 consecutive patients with invasive breast cancer, two-thirds of whom (67.1%) were diagnosed with stage II or stage III disease. During a median follow-up period of 53 months, three (1.2%) local, 13 (5.2%) regional, 34 (13.7%) distant, and five (2.0%) concurrent locoregional and distant recurrences were observed. The median time to recurrences was 26 months (range, 2 to 70 months) for all recurrences, 23 months (range, 2 to 64 months) for locoregional recurrences, and 26 months (range, 8 to 70 months) for distant recurrences. All local recurrent lesions were detectable by careful physical examination, and detection of local recurrence suggested the presence of distant metastasis (60.0%). In contrast to distant metastasis, the risk of locoregional recurrence did not increase significantly with an increase in disease stage. The 5-year overall, locoregional relapse-free, and distant relapse-free survival rates were 89.7%, 90.8%, and 81.6%, respectively.

Conclusions
SSM followed by immediate reconstruction using TRAM flap is an oncologically safe procedure even in patients with advanced-stage disease. Detection of local recurrence is crucial and can be aided by a thorough physical examination.
Circulating levels and subcutaneous adipose tissue gene expression of pigment epithelium-derived factor in polycystic ovary syndrome and normal women: a case control study
Authors: Lecke Sheila B , Morsch Debora , Spritzer Poli M 
Published: August 2013

Abstract

Background
Polycystic ovary syndrome (PCOS) has been recognized as a metabolic disorder, manifested by abdominal obesity, insulin resistance, dyslipidemia and hypertension. Pigment epithelium-derived factor (PEDF), a member of the serine protease inhibitor family, is a pleiotropic protein known for its antiangiogenic, antioxidant, and neuroprotective properties and has been shown to induce insulin resistance and play a role in glucose metabolism. Recent studies investigating circulating PEDF levels show elevated serum PEDF in association with insulin resistance in normal-weight women with PCOS, but not in obese PCOS patients. The aims of this study were 1) to assess PEDF gene expression in subcutaneous adipose tissue (scAT) from women with PCOS and nonhirsute, ovulatory controls, and 2) to determine the circulating levels of PEDF in these groups.

Methods
Total RNA was extracted from adipose tissue biopsy samples and reverse-transcribed to cDNA. Real-time quantitative PCR was performed to determine relative gene expression levels.

Results
The 22 women with PCOS and 14 non-PCOS controls included in the study had similar age, BMI, and fasting glucose, triglycerides, and HDL-cholesterol levels. Participants with PCOS exhibited higher 2 h oral glucose tolerance test levels (p = 0.006), total (p = 0.026) and LDL-cholesterol (p = 0.036), Ferriman-Gallwey score (p = 0.003) and total testosterone (p = 0.001) as compared to controls. BMI-adjusted PEDF serum levels and scAT gene expression were similar in the PCOS and control groups (p = 0.622 and p = 0.509, respectively). Circulating PEDF levels were not associated with scAT PEDF gene expression. Multiple regression analysis revealed that, in women with PCOS, insulin contributed positively and significantly to serum PEDF (p = 0.027), independently of testosterone.

Conclusion
Serum PEDF levels and scAT gene expression were associated with metabolic risk factors, but did not differ between women with PCOS and age- and BMI-matched controls. Circulating levels and scAT gene expression of PEDF were not associated in the study subjects, suggesting additional sources for PEDF in addition to or instead of fat tissue.
Transport Response is a filial-specific behavioral response to maternal carrying in C57BL/6 mice
Authors: Yoshida Sachine , Esposito Gianluca , Ohnishi Ryuko , Tsuneoka Yousuke , Okabe Shota , Kikusui Takefumi , Kato Tadafumi , Kuroda Kumi O 
Published: August 2013

Abstract

Background
A mother carries her young in many altricial mammals, such as cats, lions, rats and mice. During maternal carrying, the transported young assume a compact posture. We have recently shown that, in both humans and mice, the carried infants immediately calmed down and showed reductions in heart rate, distress vocalizations, and voluntary movement. The loss of the calming response in mouse pups hindered maternal retrieval efficacy. These findings suggested that the infant calming response functioned to reduce the maternal burden of carrying and was therefore conserved in a variety of mammalian species. However, it remains unclear how and when each component of this calming response develops and whether it is a filial-specific behavior.

Results
We dissected various components of the carrying-induced responses in mouse pups, collectively called the “Transport Response” herein. We showed that during the second postnatal week, pups exhibited characteristic compact posture with limb ventroflexion. The body trunk remained paradoxically pliable, suggesting complex neural regulation throughout the body. Pups also showed an increased pain tolerance to a tail pinch during the Transport Response. Analyses of the developmental courses of distinct components of the Transport Response revealed the independent regulation of each component: in the first postnatal week, the cessation of ultrasonic vocalizations was exhibited prominently; in the second postnatal week, immobilization reached its peak; and toward the third postnatal week, the postural component became fully matured. At the end of the third postnatal week, when the pups are able to transport by themselves, the pups no longer exhibited the Transport Response.

Conclusions
This study has revealed the mouse Transport Response as a complex set of behavioral and physiological components, each of which has a specific postnatal time window but is orchestrated in a well-matched manner with the maturation of ambulatory ability in the pups. These findings collectively indicate that the Transport Response is a filial-specific, innate behavioral reaction and is distinct from a simple reflex or defensive freezing response. The Transport Response could be a novel index of primitive filial attachment behaviors, acting to smooth mother-infant interaction.
Apical root resorption during orthodontic treatment with aligners? A retrospective radiometric study
Authors: Krieger Elena , Drechsler Thomas , Schmidtmann Irene , Jacobs Collin , Haag Simeon , Wehrbein Heinrich 
Published: August 2013

Abstract

Introduction
Objective of this study was to investigate the incidence and severity of apical root resorptions (ARR) during orthodontic treatment with aligners.

Materials and methods
The sample comprised 100 patients (17–75 years of age) with a class I occlusion and anterior crowding before treatment, treated exclusively with aligners (Invisalign®, Align Technologies, Santa Clara, CA, USA). The following teeth were assessed: upper and lower anterior teeth and first molars. Root and crown lengths of a total of 1600 teeth were measured twice in pre- and post-treatment panoramic radiographs. Afterwards, relative changes of the root length during treatment were calculated by a root-crown-ratio taking pre- and post-treatment root and crown lengths into consideration. A reduction of this ratio was considered as a shortening of the initial root length. Additionally, tooth movements of the front teeth were assessed by lateral cephalograms and the 3-dimensonal set up of each patient.

Results
All patients had a reduction of the pre-treatment root length with a minimum of two teeth. On average 7.36 teeth per patient were affected. 54% of 1600 measured teeth showed no measurable root reduction. A reduction of >0%-10% of the pre-treatment root length was found in 27.75%, a distinct reduction of >10%-20% in 11.94%. 6.31% of all teeth were affected with a considerable reduction of >20%. We found no statistically significant correlation between relative root length changes and the individual tooth, gender, age or sagittal and vertical orthodontic tooth movement; except for extrusion of upper front teeth, which was considered as not clinical relevant due to the small amount of mean 4% ARR.

Conclusions
The present study is the first analyzing ARR in patients with a fully implemented orthodontic treatment with aligners (i.e. resolving anterior crowding). The variety was high and no clinical relevant influence factor could be detected. A minimum of two teeth with a root length reduction was found in every patient. On average, 7.36 teeth per patient were affected.
Studies of ab initio and Monte Carlo simulation on interaction of fluorouracil anticancer drug with carbon nanotube
Authors: Zare Karim , Najafi Fahimeh , Sadegh Hamidreza , ghoshekandi Ramin Shahryari 
Published: August 2013

Abstract
In this study, we have carried out the calculation for the interaction of fluorouracil anticancer drug with carbon nanotube using Hartree-Fock theory with 3-21G basis set and molecular mechanic/Monte Carlo simulation (with MM+, AMBER, and OPLS force field) in the gas phase, methanol, and water solvents at various temperatures (298 up to 312 K). The obtained results of potential energy, Gibbs free energy, enthalpy, entropy, and dipole moment value changes are compared in gas phase, methanol, and water, and the temperature effects on the stability of the interaction between fluorouracil anticancer drug and carbon nanotube in gas phase, methanol, and water solvents.
Regulation of Cancerous inhibitor of PP2A (CIP2A) by small molecule inhibitor for c-Jun NH2-Terminal Kinases (JNKs), SP600125, in Human Fibrosarcoma (HT1080) cells
Authors: Khanna Anchit 
Published: August 2013

Background: Protein phosphatase 2A inhibition is one of the pre-requisites for human cell transformation. Previously, we have identified an endogenous inhibitor of PP2A, CIP2A (Cancerous Inhibitor of Protein Phosphatase 2A) in human fibrosarcoma cells (HT1080) using tandem affinity purification. CIP2A over expression has been demonstrated in almost every tumour type studied so far. However, our understanding on the mechanisms regulating CIP2A expression in human cancers, especially in sarcomas, is still emerging. Methods: Human fibrosarcoma (HT1080) cells were treated with small molecule inhibitors against the three major signalling pathways, namely p38, MEK and JNK pathways to identify the pathway regulating CIP2A expression in the sarcoma cells. This was followed by verification of the results using small interfering RNAs (siRNA) for the kinases. Results: In line with previous observations, small molecule inhibitor for MEK pathway (PD98059) decreased CIP2A mRNA and protein expression. Interestingly, small molecule inhibitor for the JNK pathway, SP600125 decreased mRNA and protein levels of CIP2A oncoprotein with negligible effect of SB203580 (p38 kinase) inhibitor on CIP2A expression in HT1080 cells. However, siRNAs specific to either JNK1 or JNK2 kinases did not result in decrease in CIP2A expression. Contrarily, two different CIP2A siRNAs, which were used as positive controls, decreased JNK2 expression in HT1080 cells. Conclusion: Although it is well established that SP600125 inhibits JNK kinases, it has also been shown to inhibit a spectra of other kinases. SP600125 inhibits CIP2A protein expression both in time and concentration dependent manner. However, depletion of both JNK1 and JNK2 kinases using specific siRNAs fails to decrease CIP2A protein expression levels, thereby indicating the need to verify the results obtained by treatment with small molecular inhibitors of kinases by independent approaches like two different target specific siRNAs. Finally, fortuitously we identify JNK2 as a CIP2A downstream target in HT1080 cells.
Tamanho e Número Ideal de Amostras para Coleta de Gafanhotos na Região Depressão Central do Rio Grande do Sul
Authors: Carvalho Nathália Leal , Costa Ervandil Correa , Souza Danilo Boanerges , Garlet Juliana 
Published: August 2013

Objetivando observar a viabilidade de um novo método para amostragem de acridóideos (conhecidos vulgarmente por gafanhotos), bem como a distancia percorrida e número ideal de amostras para amostragem foi proposto o estudo. Os levantamentos foram conduzidos em duas áreas de campo nativo no município de São Sepé, localizado na região Depressão Central no RS. As coletas foram realizadas durante o verão de 2009 com o auxilio de uma rede de coleta adaptada. As distâncias avaliadas foram de 5, 10, 15, 20 e 25m, com oito repetições cada, sendo 40 coletas por área, a amostragem foi ao acaso. As variáveis respostas foram: adultos, ninfas, espécies e número total de insetos. Foram calculadas as estatísticas descritivas, o teste Qui-quadrado a 5% de probabilidade de erro e à relação mediana/pseudo-sigma, aliada a metodologia de reamostragem Jackknife. Foram coletados 969 espécimes distribuídos em 22 espécies, 17 Gêneros, três Famílias distintas Acrididae, Proscopiidae e Romaleidae, e duas Superfamílias (Acridoidea e Eumastacoidea). Evidenciou-se relativa eficiência do método proposto. A distancia percorrida de 25 m aliada ao número de sete amostras mostrou-se ideal para coleta de acridóideos.
Ideal Size and Number of Samples to Collect Grasshoppers in the Central Depression in Rio Grande do Sul
Abstract. Aiming to observe the viability of a new method for sampling acridoideos (by commonly known locusts) and the ideal distance and number of samples for the study sample was proposed. The surveys were conducted in two areas of native grassland in Sao Sepe, in Central Depression, Rio Grande do Sul State. Samples were collected during the summer of 2009 with the help of a network of collection adapted. The distances were measured 5, 10, 15, 20 and 25m, with eight repetitions each, of which 40 samples per area, sampling was random. The response variables were: adults, nymphs, and total number of species of insects. Descriptive statistics were calculated, Chi-square test and used the median ratio/pseudo-sigma methodology combined with Jackknife resampling. We collected 969 specimens representing 22 species, 17 Genres and three distinct families Acrididae, Proscopiidae and Romaleidae, and also two Superfamilies (Acridoidea and Eumastacoidea). It was evident relative efficiency of the proposed method. The distance traveled of 25 m coupled with the number seven samples proved to be ideal for collecting of grasshoppers.
Asymptotics of the Yang–Mills
flow for holomorphic vector bundles over Kähler manifolds: The canonical
structure of the limit
Authors: Sibley Benjamin 
Published: August 2013

Abstract

In the following article we study the limiting properties of the Yang–Mills
flow associated to a holomorphic vector bundle E over an arbitrary compact
Kähler manifold (X,ω). In particular we show that the flow is
determined at infinity by the holomorphic structure of E. Namely, if we
fix an integrable unitary reference connection A
0 defining the
holomorphic structure, then the Yang–Mills flow with initial condition A
0 converges (away from an appropriately defined singular set) in the
sense of the Uhlenbeck compactness theorem to a holomorphic vector bundle E
∞, which is isomorphic to the associated graded object of the
Harder–Narasimhan–Seshadri filtration of (E,A
0). Moreover, E
∞
extends as a reflexive sheaf over the singular set as the double dual of the
associated graded object. This is an extension of previous work in the cases
of one and two complex dimensions and proves the general case of a
conjecture of Bando and Siu.