bluuebunny/crossref_metadata_2025_split huggingface dataset:
DNA Repair Mechanisms and the Bypass of DNA Damage in Saccharomyces cerevisiae
Authors: Boiteux Serge , Jinks-Robertson Sue 
Published: April 2013

Abstract
DNA repair mechanisms are critical for maintaining the integrity of genomic DNA, and their loss is associated with cancer predisposition syndromes. Studies in Saccharomyces cerevisiae have played a central role in elucidating the highly conserved mechanisms that promote eukaryotic genome stability. This review will focus on repair mechanisms that involve excision of a single strand from duplex DNA with the intact, complementary strand serving as a template to fill the resulting gap. These mechanisms are of two general types: those that remove damage from DNA and those that repair errors made during DNA synthesis. The major DNA-damage repair pathways are base excision repair and nucleotide excision repair, which, in the most simple terms, are distinguished by the extent of single-strand DNA removed together with the lesion. Mistakes made by DNA polymerases are corrected by the mismatch repair pathway, which also corrects mismatches generated when single strands of non-identical duplexes are exchanged during homologous recombination. In addition to the true repair pathways, the postreplication repair pathway allows lesions or structural aberrations that block replicative DNA polymerases to be tolerated. There are two bypass mechanisms: an error-free mechanism that involves a switch to an undamaged template for synthesis past the lesion and an error-prone mechanism that utilizes specialized translesion synthesis DNA polymerases to directly synthesize DNA across the lesion. A high level of functional redundancy exists among the pathways that deal with lesions, which minimizes the detrimental effects of endogenous and exogenous DNA damage.
To “Bee or Not to Bee” Male or Female? An Educational Primer for Use with “The Am-tra2 Gene Is an Essential Regulator of Female Splice Regulation at Two Levels of the Sex Determination Hierarchy of the Honeybee”
Authors: Schurko Andrew M 
Published: April 2013

Abstract
An article by Nissen et al. in the November 2012 issue of GENETICS emphasizes the importance of alternative splicing in the sex determination cascade of the honeybee Apis mellifera. This study demonstrates the application of reverse transcriptase PCR and RNA interference screens as genetic tools to better understand the regulation of transcription and splicing. It also provides the opportunity to explore the evolutionary origins of genes by considering the functions of orthologs and paralogs in different species. This Primer article provides background information and explanations of the concepts and findings of Nissen et al. and offers discussion questions for use in the classroom.
Related article in GENETICS: Nissen, I., M. Müller, and M. Beye, 2012 The Am-tra2 gene is an essential regulator of female splice regulation at two levels of the sex determination hierarchy of the honeybee. Genetics 192: 1015–1026.
HIV and HBsAg Seropositivity Amongst Patients Presenting for Ocular Surgery at a Tertiary Eye Care Hospital in Nigeria
Authors: Alhassan M B , Unung P , Adejor GO 
Published: April 2013

Background:
The prevalence of HIV/AIDS and HBsAg sero-positivity is very high in sub-Saharan African. There is a risk of horizontal transmission of these diseases amongst ophthalmic patients.

Aim:
To determine the proportion patients for eye surgery who are HIV/AIDS and HBsAg sero-positive at the National Eye Centre, Kaduna, Nigeria.

Methods:
Patients selected for eye surgery during a surgical camp at the National Eye Centre, Kaduna were counseled for Voluntary Counseling and Testing (VCT) and HBsAg to determine their viral status.

Results:
A total of 650 patients who were selected were screened. The distributions of the indications for selection were as follows: cataract 483 (74.3%); glaucoma 44 (6.8%) and pterygium 123 (18.9%). Two patients (0.2%) were found to be HIV seropositive while 11 (1.5%) were HbsAg positive.

Conclusion:
Pre-operative screening of all patients going for ophthalmic surgery for HIV and HbsAg may be desirable in our environment.
Professional Skepticism: The Effects of a Partner's Influence and the Level of Fraud Indicators on Auditors' Fraud Judgments and Actions
Authors: Carpenter Tina D. , Reimers Jane L. 
Published: April 2013

ABSTRACT:
The Public Company Accounting Oversight Board (PCAOB), in its recent auditor inspections, cited a lack of professional skepticism and selection of appropriate audit procedures as serious problems for auditors, and suggested that the tone set by audit partners is critical for auditors' fraud investigations. We investigate selected components of Nelson's (2009) model of professional skepticism: the effects of the partner's emphasis on professional skepticism and the effect of the level of fraud indicators on auditors' identification of fraud risk factors, auditors' fraud risk assessments, and their selection of audit procedures. Thus, we provide an initial test of predictions of the links established in his model, and our results suggest a possible extension to his model. This study provides evidence that a partner's emphasis on professional skepticism is critical for both effective and efficient identification of relevant fraud risk factors and choice of relevant audit procedures. These results should be informative to both standard setters and academic researchers because they highlight the costs and benefits of an audit partner's attitude toward professional skepticism on the evaluation of fraud.
Rough set and teaching learning based optimization technique for optimal features selection
Authors: Satapathy Suresh , Naik Anima , Parvathi K. 
Published: April 2013

AbstractRough set theory has been one of the most successful methods used for feature selection. However, this method is still not able to find optimal subsets. But it can be made to be optimal using different optimization techniques. This paper proposes a new feature selection method based on Rough Set theory with Teaching learning based optimization (TLBO). The proposed method is experimentally compared with other hybrid Rough Set methods such as Genetic Algorithm (GA), Particle Swarm Optimization (PSO) and Differential Evolution (DE) and the empirical results reveal that the proposed approach could be used for feature selection as this performs better in terms of finding optimal features and doing so in quick time.
A job checkpointing system for computational grids
Authors: Amoon Mohammed 
Published: April 2013

AbstractFault tolerance is an important property in computational grids since the resources are geographically distributed. Job checkpointing is one of the most common utilized techniques for providing fault tolerance in computational grids. The efficiency of checkpointing depends on the choice of the checkpoint interval. Inappropriate checkpointing interval can delay job execution. In this paper, a fault-tolerant scheduling system based on checkpointing technique is presented and evaluated. When scheduling a job, the system uses both average failure time and failure rate of grid resources combined with resources response time to generate scheduling decisions. The system uses the failure rate of the assigned resources to calculate the checkpoint interval for each job. Extensive simulation experiments are conducted to quantify the performance of the proposed system. Experiments have shown that the proposed system can considerably improve throughput, turnaround time, grid load and failure tendency of computational grids.
Imaging preictal hemodynamic changes in neocortical epilepsy
Authors: Patel Kunal S. , Zhao Mingrui , Ma Hongtao , Schwartz Theodore H. 
Published: April 2013

Object
The ability to predict seizure occurrence is extremely important to trigger abortive therapies and to warn patients and their caregivers. Optical imaging of hemodynamic parameters such as blood flow, blood volume, and tissue and hemoglobin oxygenation has already been shown to successfully localize epileptic events with high spatial and temporal resolution. The ability to actually predict seizure occurrence using hemodynamic parameters is less well explored.

Methods
In this article, the authors critically review data from the literature on neocortical epilepsy and optical imaging, and they discuss the preictal hemodynamic changes and their application in neurosurgery.

Results
Recent optical mapping studies have demonstrated preictal hemodynamic changes in both human and animal neocortex.

Conclusions
Optical measurements of blood flow and oxygenation may become increasingly important for predicting and localizing epileptic events. The ability to successfully predict ictal onsets may be useful to trigger closed-loop abortive therapies.
Navigated transcranial magnetic stimulation for mapping the motor cortex in patients with rolandic brain tumors
Authors: Takahashi Satoshi , Vajkoczy Peter , Picht Thomas 
Published: April 2013

Object
Navigated transcranial magnetic stimulation (nTMS) is a novel technology in the field of neurosurgery for noninvasive delineation of cortical functional topography. This study addresses the spatial accuracy and clinical usefulness of nTMS in brain tumor surgery in or near the motor cortex based on a systematic review of observational studies.

Methods
A systematic search retrieved 11 reports published up to October 2012 in which adult patients were examined with nTMS prior to surgery. Quality criteria consisted of documentation of the influence of nTMS brain mapping on clinical decision making in a standardized prospective manner and/or performance of intraoperative direct electrical stimulation (DES) and comparison with nTMS results. Cross-observational assessment of nTMS accuracy was established by calculating a weighted mean distance between nTMS and DES.

Results
All studies reviewed in this article concluded that nTMS correlated well with the “gold standard” of DES. The mean distance between motor cortex identified on nTMS and DES by using the mean distance in 81 patients described in 6 quantitatively evaluated studies was 6.18 mm. The nTMS results changed the surgical strategy based on anatomical imaging alone in 25.3% of all patients, based on the data obtained in 87 patients in 2 studies.

Conclusions
The nTMS technique spatially correlates well with the gold standard of DES. Its functional information benefits surgical decision making and changes the treatment strategy in one-fourth of cases.
Integration of functional neuronavigation and intraoperative MRI in surgery for drug-resistant extratemporal epilepsy close to eloquent brain areas
Authors: Sommer Björn , Grummich Peter , Coras Roland , Kasper Burkhard Sebastian , Blumcke Ingmar , Hamer Hajo Martinus , Stefan Hermann , Buchfelder Michael , Roessler Karl 
Published: April 2013

Object
The authors performed a retrospective study to assess the impact of functional neuronavigation and intraoperative MRI (iMRI) on surgery of extratemporal epileptogenic lesions on postsurgical morbidity and seizure control.

Methods
Twenty-five patients (14 females and 11 males) underwent extratemporal resections for drug-resistant epilepsy close to speech/motor brain areas or adjacent to white matter tracts. The mean age at surgery was 34 years (range 12–67 years). The preoperative mean disease duration was 13.2 years. To avoid awake craniotomy, cortical motor-sensory representation was mapped during preoperative evaluation in 14 patients and speech representation was mapped in 15 patients using functional MRI. In addition, visualization of the pyramidal tract was performed in 11 patients, of the arcuate fascicle in 7 patients, and of the visual tract in 6 patients using diffusion tensor imaging. The mean minimum distance of tailored resection between the eloquent brain areas was 5.6 mm. During surgery, blood oxygen level–dependent imaging and diffusion tensor imaging data were integrated into neuronavigation and displayed through the operating microscope. The postoperative mean follow-up was 44.2 months.

Results
In 20% of these patients, further intraoperative resection was performed because of intraoperatively documented residual lesions according to iMRI findings. At the end of resection, the final iMRI scans confirmed achievement of total resection of the putative epileptogenic lesion in all patients. Postoperatively, transient complications and permanent complications were observed in 20% and 12% of patients, respectively. Favorable postoperative seizure control (Engel Classes I and II) was achieved in 84% and seizure freedom in 72% of these consecutive surgical patients.

Conclusions
By using functional neuronavigation and iMRI for treatment of epileptogenic brain lesions, the authors achieved a maximum extent of resection despite the lesions' proximity to eloquent brain cortex and fiber tracts in all cases. The authors' results underline possible benefits of this technique leading to a favorable seizure outcome with acceptable neurological deficit rates in difficult-to-treat extratemporal epilepsy.
The role of secondary motor and language cortices in morbidity and mortality: a retrospective functional MRI study of surgical planning for patients with intracranial tumors
Authors: Voss Jed , Meier Timothy B. , Freidel Robert , Kundu Bornali , Nair Veena A. , Holdsworth Ryan , Kuo John S. , Prabhakaran Vivek 
Published: April 2013

Object
Functional MRI (fMRI) is commonly used by neurosurgeons preoperatively to identify brain regions associated with essential behaviors, such as language and motor abilities. In this study the authors investigated the relationship between patient morbidity and mortality and the distance from the tumor border area to functional activations in secondary motor and language cortices.

Methods
Patients with primary or metastatic brain tumors who underwent preoperative fMRI motor and language mapping were selected from a large database of patients with tumors. The lesion-to-activation distance (LAD) was measured in each patient relative to the supplementary motor area (SMA) for motor tasks and the presupplementary motor area (pSMA) for language tasks. The association between LAD and the incidence of deficits was investigated using the Fisher exact tests of significance. The impact of other variables, including age, handedness, sex, and tumor grade, was also investigated. In a subset of patients, logistic regression was performed to identify the likelihood of deficits based on the LAD to primary and secondary regions. Finally, Mantel-Cox log-rank tests were performed to determine whether survival time was significantly related to the LAD to secondary motor and language areas.

Results
A significant association was observed between the LAD to the SMA and the incidence of motor deficits, with the percentage of patients with deficits dropping for those in the LAD > 2 cm group. The relationship between the LAD to the pSMA and the incidence of language deficits was not significant. Logistic regression demonstrated that the LAD to primary sensorimotor cortex does affect the incidence of motor deficits, but that the LAD to SMA does not. Finally, the authors observed no relationship between the LAD to secondary regions and patient mortality rates.

Conclusions
These results demonstrate that the LAD to SMA structures does affect morbidity, although not to the extent of LAD to primary structures. In addition, motor deficits are significantly associated with LAD to secondary structures, but language deficits are not. This should be considered by neurosurgeons for patient consultation and preoperative planning.
Association of functional magnetic resonance imaging indices with postoperative language outcomes in patients with primary brain tumors
Authors: Kundu Bornali , Penwarden Amy , Wood Joel M. , Gallagher Thomas A. , Andreoli Matthew J. , Voss Jed , Meier Timothy , Nair Veena A. , Kuo John S. , Field Aaron S. , Moritz Chad , Meyerand M. Elizabeth , Prabhakaran Vivek 
Published: April 2013

Object
Functional MRI (fMRI) has the potential to be a useful presurgical planning tool to treat patients with primary brain tumor. In this study the authors retrospectively explored relationships between language-related postoperative outcomes in such patients and multiple factors, including measures estimated from task fMRI maps (proximity of lesion to functional activation area, or lesion-to-activation distance [LAD], and activation-based language lateralization, or lateralization index [LI]) used in the clinical setting for presurgical planning, as well as other factors such as patient age, patient sex, tumor grade, and tumor volume.

Methods
Patient information was drawn from a database of patients with brain tumors who had undergone preoperative fMRI-based language mapping of the Broca and Wernicke areas. Patients had performed a battery of tasks, including word-generation tasks and a text-versus-symbols reading task, as part of a clinical fMRI protocol. Individually thresholded task fMRI activation maps had been provided for use in the clinical setting. These clinical imaging maps were used to retrospectively estimate LAD and LI for the Broca and Wernicke areas.

Results
There was a relationship between postoperative language deficits and the proximity between tumor and Broca area activation (the LAD estimate), where shorter LADs were related to the presence of postoperative aphasia. Stratification by tumor location further showed that for posterior tumors within the temporal and parietal lobes, more bilaterally oriented Broca area activation (LI estimate close to 0) and a shorter Wernicke area LAD were associated with increased postoperative aphasia. Furthermore, decreasing LAD was related to decreasing LI for both Broca and Wernicke areas. Preoperative deficits were related to increasing patient age and a shorter Wernicke area LAD.

Conclusions
Overall, LAD and LI, as determined using fMRI in the context of these paradigms, may be useful indicators of postsurgical outcomes. Whereas tumor location may influence postoperative deficits, the results indicated that tumor proximity to an activation area might also interact with how the language network is affected as a whole by the lesion. Although the derivation of LI must be further validated in individual patients by using spatially specific statistical methods, the current results indicated that fMRI is a useful tool for predicting postoperative outcomes in patients with a single brain tumor.
Integration of functional neuroimaging in CyberKnife radiosurgery: feasibility and dosimetric results
Authors: Conti Alfredo , Pontoriero Antonio , Ricciardi Giuseppe K. , Granata Francesca , Vinci Sergio , Angileri Filippo F. , Pergolizzi Stefano , Alafaci Concetta , Rizzo Vincenzo , Quartarone Angelo , Germanò Antonino , Foroni Roberto Israel , De Renzis Costantino , Tomasello Francesco 
Published: April 2013

Object
The integration of state-of-the-art neuroimaging into treatment planning may increase the therapeutic potential of stereotactic radiosurgery. Functional neuroimaging, including functional MRI, navigated brain stimulation, and diffusion tensor imaging–based tractography, may guide the orientation of radiation beams to decrease the dose to critical cortical and subcortical areas. The authors describe their method of integrating functional neuroimaging technology into radiosurgical treatment planning using the CyberKnife radiosurgery system.

Methods
The records of all patients who had undergone radiosurgery for brain lesions at the CyberKnife Center of the University of Messina, Italy, between July 2010 and July 2012 were analyzed. Among patients with brain lesions in critical areas, treatment planning with the integration of functional neuroimaging was performed in 25 patients. Morphological and functional imaging data sets were coregistered using the Multiplan dedicated treatment planning system. Treatment planning was initially based on morphological data; radiation dose distribution was then corrected in relation to the functionally relevant cortical and subcortical areas. The change in radiation dose distribution was then calculated.

Results
The data sets could be easily and reliably integrated into the Cyberknife treatment planning. Using an inverse planning algorithm, the authors achieved an average 17% reduction in the radiation dose to functional areas. Further gain in terms of dose sparing compromised other important treatment parameters, including target coverage, conformality index, and number of monitor units. No neurological deficit due to radiation was recorded at the short-term follow-up.

Conclusions
Radiosurgery treatments rely on the quality of neuroimaging. The integration of functional data allows a reduction in radiation doses to functional organs at risk, including critical cortical areas, subcortical tracts, and vascular structures. The relative simplicity of integrating functional neuroimaging into radiosurgery warrants further research to implement, standardize, and identify the limits of this procedure.
Characterizing the relationship between functional MRI–derived measures and clinical outcomes in patients with vascular lesions
Authors: Gallagher Thomas A. , Nair Veena A. , Regner Michael F. , Young Brittany M. , Radtke Andrew , Pankratz Joshua , Holdsworth Ryan L. , Baniulis Dovile , Kornder Nicole K. , Voss Jed , Austin Benjamin P. , Moritz Chad , Meyerand Mary E. , Prabhakaran Vivek 
Published: April 2013

Object
Functional MRI (fMRI) has proven to be an effective component of pretreatment planning in patients harboring a variety of different brain lesions. The authors have recently reported significant relationships concerning distances between brain tumor borders and areas of functional activation (lesion-to-activation distance; LAD) with regard to patient morbidity and mortality. This study further examines the relationship between LAD, focusing on a host of vascular lesions and pre- and posttreatment morbidity.

Methods
This study included a sample population of patients with vascular lesions (n = 106), primarily arteriovenous malformations (AVMs) and cavernomas. These patients underwent pretreatment fMRI-based motor mapping (n = 72) or language mapping (n = 84). The impact of LAD and other variables derived from the patient medical record were analyzed with respect to functional deficits in terms of morbidity (weakness and/or aphasia).

Results
In patients with no pretreatment deficits, there was trend for a significant relationship between the Wernicke area LAD and posttreatment language deficits. In patients with or without pretreatment deficits, a trend toward significance was observed between sensorimotor LAD and posttreatment motor deficits. Additionally, lesion type (AVMs or cavernomas) affected posttreatment deficits, with more patients with cavernomas showing posttreatment language deficits than patients with AVMs. However, this difference was not observed for posttreatment motor deficits.

Conclusions
These findings suggest that the proximity of a vascular lesion to sensorimotor and language areas is a relevant parameter in estimating patient prognosis in the perioperative period. Additionally, vascular lesion type and existence of pretreatment deficits play a significant role in outcomes.