bluuebunny/crossref_metadata_2025_split huggingface dataset:
Laparoscopic Colorectal Cancer Resection in High‐Volume Surgical Centers: Long‐Term Outcomes from the LAPCOLON Group Trial
Authors: Huscher Cristiano G. S. , Bretagnol Frederic , Corcione Francesco 
Published: March 2015

AbstractBackgroundStrong evidence has confirmed the benefit of laparoscopy in colorectal cancer resection but remains a challenging procedure. It is not clear that such promising results in selected patients translate into a favorable risk–benefit balance in real practice. We conducted a multicenter national observational registry to assess operative and oncologic long‐term outcomes following laparoscopic colorectal cancer resection.MethodsAll patients with laparoscopic colorectal cancer resection between 2001 and 2004 were included. Data were extracted from the prospective Italian national database of 10 high‐volume centers (≥40 colorectal cancer laparoscopic resections per year). Surgical technique and follow‐up were standardized. Survivals were analyzed by Kaplan–Meier method.ResultsWe reported 1832 patients with colon (58.5 %) and rectal cancer (41.5 %). TNM stage was 0–I–II in 1044 patients (57 %) and III–IV in 788 patients (43 %). Surgery included a totally laparoscopic procedure in 1820 patients (99.3 %). Conversion was 10.5 %. Postoperative morbidity and 30‐day mortality rates were 17 and 1.2 %, respectively. Clinical anastomotic leakage rate was 8.3 % (n = 152). R0 resection was 95 %. With a median follow‐up of 54.2 months, cancer recurrence rate was 13.3 %. At 5 years, cancer‐free survival was 86.7 %. Upon multivariate analysis, age (P = 0.001) and TNM stage (P < 0.001) were associated with cancer‐free survival. Predictive factors of cancer recurrence were gender (P = 0.029) and TNM stage (P < 0.001).ConclusionsIn high‐volume centers and non‐selective patients, laparoscopic colorectal resection for cancer achieves good operative results with satisfactory long‐term oncologic results. Even in the laparoscopy era, age, gender, and TNM stage remain the most powerful predictor of oncologic outcomes.
Response of the plant community and soil water status to alpine Kobresia meadow degradation gradients on the Qinghai–Tibetan Plateau, China
Authors: Li Jing , Zhang Fawei , Lin Li , Li Hongqin , Du Yangong , Li Yikang , Cao Guangmin 
Published: March 2015

AbstractDegradation of alpine Kobresia meadow in the Qinghai–Tibetan Plateau is a serious problem, but its effect on the plant community and soil water status is not fully understood. We chose four homogeneous sites with <20, 20–70, 70–90, and >90 % absolute abundance of palatable grasses, and classified them as degradation gradient categories of poor, fair, good, and excellent, respectively. The lowest aboveground biomass and infiltration rate, and the highest root biomass, thickness of mattic epipedon, topsoil (<10 cm) organic matter content and volumetric ratio of root/soil all occurred in fair plots. There was little fluctuation in plant community diversity and topsoil bulk density among the degradation gradients. Results of non‐metric multidimensional scaling suggested that vegetation dynamics along degradation processes were non‐equilibrium in the alpine Kobresia meadow. The effects of degradation on soil water content and retention were the highest in the top layer (>10 cm). The minimum topsoil water content and maximum topsoil water retention both occurred in fair plots, indicating asynchrony between soil water content and holding capacity along degradation gradients, which likely resulted in a non‐equilibrium plant community pattern through physiological desiccation and nutrient deficits. Our findings should be highly informative for threshold‐based management of the degraded alpine Kobresia meadow in the future.
Knee morphometric risk factors for acute anterior cruciate ligament injury in skeletally immature patients
Authors: Shaw K. Aaron , Dunoski Brian , Mardis Neil , Pacicca Donna 
Published: March 2015

Study design Retrospective, case–control. Purpose Knee morphometric risk factors for noncontact anterior cruciate ligament (ACL) injury have been a popular topic with skeletally mature patients. Little research has focused on the skeletally immature, with conflicting conclusions. This study performs a comprehensive analysis of identified parameters thought to predispose to ACL injury in a skeletally immature cohort. Methods A retrospective review of pediatric patients undergoing knee magnetic resonance imaging (MRI) was performed over a 4-year period. Inclusionary criteria included mid-substance ACL disruption, skeletal immaturity, noncontact injury, without associated ligamentous disruption, and no medical condition associated with ligamentous laxity. MRI studies were analyzed by a pediatric musculoskeletal radiologist, measuring identified bony parameters, and compared with an age-matched control group without ligamentous injury. Data were analyzed using unpaired t-tests and logistic regression. Results One hundred and twenty-eight patients sustained an ACL disruption, 39 met all inclusionary criteria (66 excluded for associated ligamentous disruption, 23 skeletally mature, three traumatic mechanisms, one with Marfan syndrome). When compared to an age-matched control cohort, the notch width index (NWI) was found to be significantly smaller in the ACL-injured group ( p = 0.046). Subgroups analysis demonstrated significant differences in morphometric parameters between subjects with isolated ACL injuries and concomitant medial collateral ligament (MCL) strain. Conclusions The NWI was significantly smaller in the ACL injury group. Significant differences were noted between isolated ACL injuries and ACL injuries with an MCL strain. This study further highlights the need for incorporating associated injury patterns when investigating the influence of morphometric factors for ACL injury in the skeletally immature. Level of evidence Level III.
Predicting adolescent's cyberbullying behavior: A longitudinal risk analysis
Authors: Barlett Christopher P. 
Published: March 2015

ABSTRACTThe current study used the risk factor approach to test the unique and combined influence of several possible risk factors for cyberbullying attitudes and behavior using a four‐wave longitudinal design with an adolescent US sample. Participants (N = 96; average age = 15.50 years) completed measures of cyberbullying attitudes, perceptions of anonymity, cyberbullying behavior, and demographics four times throughout the academic school year. Several logistic regression equations were used to test the contribution of these possible risk factors. Results showed that (a) cyberbullying attitudes and previous cyberbullying behavior were important unique risk factors for later cyberbullying behavior, (b) anonymity and previous cyberbullying behavior were valid risk factors for later cyberbullying attitudes, and (c) the likelihood of engaging in later cyberbullying behavior increased with the addition of risk factors. Overall, results show the unique and combined influence of such risk factors for predicting later cyberbullying behavior. Results are discussed in terms of theory.
Understanding affluent adolescent adjustment: The interplay of parental perfectionism, perceived parental pressure, and organized activity involvement
Authors: Randall Edin T. , Bohnert Amy M. , Travers Lea V. 
Published: March 2015

ABSTRACTThis cross‐sectional study examined relations between affluent adolescent adjustment and culturally salient factors within parent–child relationship and extracurricular domain. Bootstrapping techniques evaluated mediated effects among parental perfectionism, perceived parental pressure, intensity of organized activity (OA) involvement, and adolescent adjustment (i.e., depressive and anxiety symptoms, life satisfaction) within a sample of 10th graders and their parents (n = 88 parent–child pairs) from four high schools in affluent communities. Findings indicated that adolescents with more perfectionistic parents perceived more parental pressure and experienced poorer adjustment. Results also demonstrated that affluent adolescents who perceived more parental pressure were more intensely involved in OAs, but that higher OA intensity was linked to better adjustment. Findings highlight the importance of considering parental perfectionism when understanding adolescent behaviors and psychological outcomes, confirm the negative direct effects of parental pressure on adjustment, and corroborate prior research dispelling that highly intense OA involvement is linked to adolescent maladjustment.
Safety Culture and Care: A Program to Prevent Surgical Errors
Authors: Hemingway Maureen White , O'Malley Catherine , Silvestri Sandra 
Published: March 2015

AbstractSurgical errors are under scrutiny in health care as part of ensuring a culture of safety in which patients receive quality care. Hospitals use safety measures to compare their performance against industry benchmarks. To understand patient safety issues, health care providers must have processes in place to analyze and evaluate the quality of the care they provide. At one facility, efforts made to improve its quality and safety led to the development of a robust safety program with resources devoted to enhancing the culture of safety in the Perioperative Services department. Improvement initiatives included changing processes for safety reporting and performance improvement plans, adding resources and nurse roles, and creating communication strategies around adverse safety events and how to improve care. One key outcome included a 54% increase in the percentage of personnel who indicated in a survey that they would speak up if they saw something negatively affecting patient care.
A Study of Teacher–Learner Interactions: A Continuum Between Monologic and Dialogic Interactions
Authors: Kathard Harsha , Pillay Daisy , Pillay Mershen 
Published: March 2015

Purpose
Teachers and learners must be able to shift flexibly along the continuum of monologic and dialogic interactional repertoires to advance learning. This article describes how teachers and learners interacted during whole-class instruction along the continuum between monologic and dialogic interaction in primary school classrooms in Western Cape, South Africa.

Method
A video-observation method was used to analyze teacher–learner interactions (TLIs) across 15 lessons in intermediate-phase classrooms. TLIs were analyzed in relation to indicators such as authority, questions, feedback, explanation, metalevel connection, and collaboration. The transcriptions of TLIs were described using quantitative and qualitative techniques.

Results
The study found that teachers sustained dominant monologic interactions by asserting their authority, asking mainly closed-ended questions, and providing confirming/correcting feedback that constrained the interaction. Learners had limited opportunities for explanations or collaboration. Across most lessons, there were episodic shifts from monologic TLIs to transitional TLIs. These transitions were achieved by using mainly open-ended questions and feedback to expand the interaction. Dialogic TLIs were not evident.

Conclusions
Monologic TLIs were dominant, closing down opportunities for communication. Although transitional TLIs were evident, they were episodic and showed the potential for opening interaction opportunities. The absence of dialogic TLIs suggested that collaborative engagement opportunities were unavailable. The opportunity for intervention to increase dialogic TLIs is discussed.
Assessing allele-specific expression across multiple tissues from RNA-seq read data
Authors: Pirinen Matti , Lappalainen Tuuli , Zaitlen Noah A. ,   GTEx Consortium, Dermitzakis Emmanouil T. , Donnelly Peter , McCarthy Mark I. , Rivas Manuel A. 
Published: March 2015

Abstract
Motivation: RNA sequencing enables allele-specific expression (ASE) studies that complement standard genotype expression studies for common variants and, importantly, also allow measuring the regulatory impact of rare variants. The Genotype-Tissue Expression (GTEx) project is collecting RNA-seq data on multiple tissues of a same set of individuals and novel methods are required for the analysis of these data.
Results: We present a statistical method to compare different patterns of ASE across tissues and to classify genetic variants according to their impact on the tissue-wide expression profile. We focus on strong ASE effects that we are expecting to see for protein-truncating variants, but our method can also be adjusted for other types of ASE effects. We illustrate the method with a real data example on a tissue-wide expression profile of a variant causal for lipoid proteinosis, and with a simulation study to assess our method more generally.
Availability and implementation: http://www.well.ox.ac.uk/~rivas/mamba/. R-sources and data examples http://www.iki.fi/mpirinen/
Contact: matti.pirinen@helsinki.fi or rivas@well.ox.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
Identification of a small set of plasma signalling proteins using neural network for prediction of Alzheimer’s disease
Authors: Agarwal Swapna , Ghanty Pradip , Pal Nikhil R. 
Published: March 2015

Abstract
Motivation: Alzheimer’s disease (AD) is a dementia that gets worse with time resulting in loss of memory and cognitive functions. The life expectancy of AD patients following diagnosis is ∼7 years. In 2006, researchers estimated that 0.40% of the world population (range 0.17–0.89%) was afflicted by AD, and that the prevalence rate would be tripled by 2050. Usually, examination of brain tissues is required for definite diagnosis of AD. So, it is crucial to diagnose AD at an early stage via some alternative methods. As the brain controls many functions via releasing signalling proteins through blood, we analyse blood plasma proteins for diagnosis of AD.
Results: Here, we use a radial basis function (RBF) network for feature selection called feature selection RBF network for selection of plasma proteins that can help diagnosis of AD. We have identified a set of plasma proteins, smaller in size than previous study, with comparable prediction accuracy. We have also analysed mild cognitive impairment (MCI) samples with our selected proteins. We have used neural networks and support vector machines as classifiers. The principle component analysis, Sammmon projection and heat-map of the selected proteins have been used to demonstrate the proteins’ discriminating power for diagnosis of AD. We have also found a set of plasma signalling proteins that can distinguish incipient AD from MCI at an early stage. Literature survey strongly supports the AD diagnosis capability of the selected plasma proteins.
Availability and implementation: The FSRBF code is available at https://sites.google.com/site/agarwalswapna/publications.
Contact: agarwal.swapna@gmail.com or swapna_r@isical.ac.in
Supplementary information: Supplementary data are available at Bioinformatics online.
The impact of dust in host galaxies on quasar luminosity functions
Authors: Shirakata Hikari , Okamoto Takashi , Enoki Motohiro , Nagashima Masahiro , Kobayashi Masakazu A. R. , Ishiyama Tomoaki , Makiya Ryu 
Published: March 2015

Abstract
We have investigated effects of dust attenuation on quasar luminosity functions at z ∼ 2 using a semi-analytic galaxy formation model combined with a large cosmological N-body simulation. We estimate the dust attenuation of quasars self-consistently with that of galaxies by considering the dust in their host bulges. We find that the luminosity of the bright quasars is strongly dimmed by the dust attenuation, ∼2 mag in the B-band. Assuming the empirical bolometric corrections for active galactic nuclei (AGNs) by Marconi et al., we find that this dust attenuation is too strong to explain the B-band and X-ray quasar luminosity functions simultaneously. We consider two possible mechanisms that weaken the dust attenuation. As such a mechanism, we introduce a time delay for AGN activity, that is, gas fuelling to a central black hole starts sometime after the beginning of the starburst induced by a major merger. The other is the anisotropy in the dust distribution. We find that in order to make the dust attenuation of the quasars negligible, either the gas accretion into the black holes has to be delayed at least three times the dynamical time-scale of their host bulges or the dust covering factor is as small as ∼0.1.
Computational Analysis of Kilohertz Frequency Spinal Cord Stimulation for Chronic Pain Management
Authors: Lempka Scott F. , McIntyre Cameron C. , Kilgore Kevin L. , Machado Andre G. 
Published: March 2015

AbstractAbstract
Using a computational model, it was shown that kilohertz frequency spinal cord stimulation (KFSCS) used at clinical intensities probably does not cause the direct activation or conduction block of dorsal column or dorsal root fibers. Possible sites of action for KFSCS to be explored include synaptic terminals, cell bodies, and dendrites. Computational analyses suggest that KFSCS for pain management may not function through direct activation or conduction block of spinal cord fibers, and alternative concepts should be explored and evaluated.

Background:
Kilohertz frequency spinal cord stimulation (KHFSCS) is an emerging therapy for treating refractory neuropathic pain. Although KHFSCS has the potential to improve the lives of patients experiencing debilitating pain, its mechanisms of action are unknown and thus it is difficult to optimize its development. Therefore, the goal of this study was to use a computer model to investigate the direct effects of KHFSCS on specific neural elements of the spinal cord.

Methods:
This computer model consisted of two main components: (1) finite element models of the electric field generated by KHFSCS and (2) multicompartment cable models of axons in the spinal cord. Model analysis permitted systematic investigation into a number of variables (e.g., dorsal cerebrospinal fluid thickness, lead location, fiber collateralization, and fiber size) and their corresponding effects on excitation and conduction block thresholds during KHFSCS.

Results:
The results of this study suggest that direct excitation of large-diameter dorsal column or dorsal root fibers require high stimulation amplitudes that are at the upper end or outside of the range used in clinical KHFSCS (i.e., 0.5 to 5 mA). Conduction block was only possible within the clinical range for a thin dorsal cerebrospinal fluid layer.

Conclusions:
These results suggest that clinical KHFSCS may not function through direct activation or conduction block of dorsal column or dorsal root fibers. Although these results should be validated with further studies, the authors propose that additional concepts and/or alternative hypotheses should be considered when examining the pain relief mechanisms of KHFSCS.
Index-based map-to-sequence alignment in large eukaryotic genomes
Authors: Verzotto Davide , Teo Audrey S.M. , Hillmer Axel M. , Nagarajan Niranjan 
Published: March 2015

AbstractResolution of complex repeat structures and rearrangements in the assembly and analysis of large eukaryotic genomes is often aided by a combination of high-throughput sequencing and mapping technologies (e.g. optical restriction mapping). In particular, mapping technologies can generate sparse maps of large DNA fragments (150 kbp–2 Mbp) and thus provide a unique source of information for disambiguating complex rearrangements in cancer genomes. Despite their utility, combining high-throughput sequencing and mapping technologies has been challenging due to the lack of efficient and freely available software for robustly aligning maps to sequences. Here we introduce two new map-to-sequence alignment algorithms that efficiently and accurately align high-throughput mapping datasets to large, eukaryotic genomes while accounting for high error rates. In order to do so, these methods (OPTIMA for glocal and OPTIMA-Overlap for overlap alignment) exploit the ability to create efficient data structures that index continuous-valued mapping data while accounting for errors. We also introduce an approach for evaluating the significance of alignments that avoids expensive permutation-based tests while being agnostic to technology-dependent error rates. Our benchmarking results suggest that OPTIMA and OPTIMA-Overlap outperform state-of-the-art approaches in sensitivity (1.6–2× improvement) while simultaneously being more efficient (170–200%) and precise in their alignments (99% precision). These advantages are independent of the quality of the data, suggesting that our indexing approach and statistical evaluation are robust and provide improved sensitivity while guaranteeing high precision.
Visual cues determine hippocampal directional selectivity
Authors: Acharya Lavanya , M. Aghajan Zahra , Vuong Cliff , Moore Jason J. , Mehta Mayank R. 
Published: March 2015

AbstractBoth spatial and directional information are necessary for navigation. Rodent hippocampal neurons show spatial selectivity in all environments1, but directional tuning only on linear paths2–8.The sensory mechanisms underlying directionality are unknown, though vestibular and visual cues are thought to be crucial. However, hippocampal neurons are thought to show no angular modulation during two-dimensional random foraging despite the presence of vestibular and visual cues6,7. Additionally, specific aspects of visual cues have not been directly linked to hippocampal responses in rodents. To resolve these issues we manipulated vestibular and visual cues in a series of experiments. We first measured hippocampal activity during random foraging in real world (RW) where we found that neurons’ firing exhibited significant modulation by head-direction. In fact, the fraction of modulated neurons was comparable to that in the head-direction system9. These findings are contrary to commonly held beliefs about hippocampal directionality6,7. To isolate the contribution of visual cues we measured neural responses in a visually similar virtual reality (VR) where the range of vestibular inputs is minimized5,10,11. Significant directional modulation was not only found in VR, but it was comparable to that in RW. Several additional experiments revealed that changes in the angular information contained in the visual cues induced corresponding changes in hippocampal head-directional modulation. Remarkably, for head-directionally modulated neurons, the ensemble activity was biased towards the sole visual cue. These results demonstrate that robust vestibular cues are not required for hippocampal directional selectivity, while visual cues are not only sufficient but also play a causal role in driving hippocampal responses.