bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fuse: multiple network alignment via data fusion
Authors: Gligorijević Vladimir , Malod-Dognin Noël , Pržulj Nataša 
Published: December 2015

Abstract
Motivation: Discovering patterns in networks of protein–protein interactions (PPIs) is a central problem in systems biology. Alignments between these networks aid functional understanding as they uncover important information, such as evolutionary conserved pathways, protein complexes and functional orthologs. However, the complexity of the multiple network alignment problem grows exponentially with the number of networks being aligned and designing a multiple network aligner that is both scalable and that produces biologically relevant alignments is a challenging task that has not been fully addressed. The objective of multiple network alignment is to create clusters of nodes that are evolutionarily and functionally conserved across all networks. Unfortunately, the alignment methods proposed thus far do not meet this objective as they are guided by pairwise scores that do not utilize the entire functional and evolutionary information across all networks.
Results: To overcome this weakness, we propose Fuse, a new multiple network alignment algorithm that works in two steps. First, it computes our novel protein functional similarity scores by fusing information from wiring patterns of all aligned PPI networks and sequence similarities between their proteins. This is in contrast with the previous tools that are all based on protein similarities in pairs of networks being aligned. Our comprehensive new protein similarity scores are computed by Non-negative Matrix Tri-Factorization (NMTF) method that predicts associations between proteins whose homology (from sequences) and functioning similarity (from wiring patterns) are supported by all networks. Using the five largest and most complete PPI networks from BioGRID, we show that NMTF predicts a large number protein pairs that are biologically consistent. Second, to identify clusters of aligned proteins over all networks, Fuse uses our novel maximum weight k-partite matching approximation algorithm. We compare Fuse with the state of the art multiple network aligners and show that (i) by using only sequence alignment scores, Fuse already outperforms other aligners and produces a larger number of biologically consistent clusters that cover all aligned PPI networks and (ii) using both sequence alignments and topological NMTF-predicted scores leads to the best multiple network alignments thus far.
Availability and implementation: Our dataset and software are freely available from the web site: http://bio-nets.doc.ic.ac.uk/Fuse/.
Contact: natasha@imperial.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
Combined effects of low pH and low oxygen on the early-life stages of the barnacle Balanus amphitrite
Authors: Campanati Camilla , Yip Stella , Lane Ackley , Thiyagarajan Vengatesen 
Published: December 2015

Abstract
Ocean acidification (OA) is anticipated to interact with the more frequently occurring hypoxic conditions in shallow coastal environments. These could exert extreme stress on the barnacle-dominated fouling communities. However, the interactive effect of these two emerging stressors on early-life stages of fouling organisms remains poorly studied. We investigated both the independent and interactive effect of low pH (7.6 vs. ambient 8.2) and low oxygen (LO; 3 mg l−1 vs. ambient 5 mg l−1) from larval development through settlement (attachment and metamorphosis) and juvenile growth of the widespread fouling barnacle, Balanus amphitrite. In particular, we focused on the critical transition between planktonic and benthic phases to examine potential limiting factors (i.e. larval energy storage and the ability to perceive cues) that may restrain barnacle recruitment under the interactive stressors. LO significantly slowed naupliar development, while the interaction with low pH (LO–LP) seemed to alleviate the negative effect. However, 20–50% of the larvae became cyprid within 4 d post-hatching, regardless of treatment. Under the two stressors interaction (LO–LP), the barnacle larvae increased their feeding rate, which may explain why their energy reserves at competency were not different from any other treatment. In the absence of a settlement-inducing cue, a significantly lower percentage of cyprids (∼15% lower) settled in LO and LO–LP. The presence of an inducing cue, however, elevated attachment up to 50–70% equally across all treatments. Post-metamorphic growth was not altered, although the condition index was different between LO and LO–LP treatments, potentially indicating that less and/or weaker calcified structures were developed when the two stressors were experienced simultaneously. LO was the major driver for the responses observed and its interaction with low pH should be considered in future studies to avoid underestimating the sensitivity of biofouling species to OA and associated climate change stressors.
Revisiting the classics: is [Mg/Fe] a good proxy for galaxy formation time-scales?
Authors: Martín-Navarro Ignacio 
Published: December 2015

Abstract
In the local Universe, massive early-type galaxies exhibit enhanced [Mg/Fe] ratios, which has been traditionally interpreted as the result of a rapid (τ ≲ 1 Gyr) collapse. However, recent claims of a non-universal, steep initial mass function call for a revision of this standard interpretation. In the present work we show how the simultaneous consideration of a high [Mg/Fe] and a steep IMF slope would imply unreasonably short (τ ∼ 7 Myr) and intense (SFR ∼105 M⊙ yr−1) formation events for massive early-type galaxies. We discuss possible caveats and explanations to this apparent inconsistency, and we suggest that further IMF determinations, both in the local Universe and at high redshift, are necessary to better understand the problem.
Playing for Work
Authors: Sakakeeny Matt 
Published: December 2015

Abstract
New Orleans is ideal to study music as a form of labor, because live musical performance is critical to its overall economic infrastructure. After the devastation of Hurricane Katrina in 2005, the reliance on the return of displaced culture bearers to facilitate recovery exposed the inner workings of the cultural economy and highlighted long-standing patterns of exploitation that are endemic to black musicians, the culture industry, and global capitalism. This case study, based on years of ethnographic study among black brass band musicians in New Orleans, offers a view of broader issues of heritage tourism, commodification and authenticity, festivalization and exhibition, racial appropriation, and the value of economic and social capital. The author’s observation of musicians provides a foundation for reevaluating live musical performance as a form of labor, extending a large body of literature on the political economy of music with emphasis on the monetary economy of musicians.
The Luwian Language
Authors: Yakubovich Ilya 
Published: December 2015

Abstract
The Luwian language belongs to the Luwic subgroup of the Indo-European Anatolian languages and is a close relative of Hittite. It was used for writing in the Empire of Hattusa and the Neo-Hittite states, which arose after its collapse (appr. 1400-700 BC). It is recorded in two scripts: an adaptation of Mesopotamian cuneiform and Anatolian hieroglyphs. The goal of this article is to provide a concise description of the Luwian language. It contains both information on its structure, with an emphasis on phonology and morphology, and sociolinguistic data. The grammatical description is predominantly synchronic, but historical and comparative information is occasionally introduced if it has a potential to clarify the synchronic state of affairs.
Cultural Poetics (Ethnopoetics)
Authors: Webster Anthony K. 
Published: December 2015

Abstract
This article argues for the continuing importance of ethnopoetics/cultural poetics in the work of linguists and anthropologists. A heuristic definition of ethnopoetics (or cultural poetics) is given as the various traditions of such recurrent patternings of linguistic forms (and the thwarting of such expectations of such patternings). The continuing relevance of a Hymesian-inspired anthropological philology is noted. After framing the discussion of poetry and poetics as both linguistic and ethnographic questions, this article engages questions of linguistic relativity and its relationship to poetics, as well as poetry and poetics as social practices. Examples of parallelism and metaphor are given and discussed both in relation to their poetic form and to their social work. A final extended illustration is given concerning Navajo poetry as an example of a cultural poetics informed by both linguistics and anthropology. It is argued that research on cultural poetics/ethnopoetics encourages patience and reflection.
Sentencing Policies and Practices in Pennsylvania
Authors: Ulmer Jeffery T. , Laskorunsky Julia A. 
Published: December 2015

Abstract
This article outlines the history and evolution of Pennsylvania’s sentencing policies and practices since the adoption of its sentencing guidelines in 1978. Pennsylvania’s sentencing practices have many features in common with other states, such as mandatory minimum sentences and intermediate punishment; however, the system also has some unique features, such as having two independent parole processes for county and state inmates and not awarding a “good time” reduction for state inmates. Major recent developments include the adoption of a sentencing risk assessment and the nullification of many of the state’s mandatory minimum laws. Pennsylvania remains one of the most studied states in sentencing research. Major empirical research on sentencing and incarceration patterns, disparity, and effects of policy changes is summarized.
The Efficacy of Pregabalin in the Treatment of Prediabetic Neuropathic Pain
Authors: González-Duarte Alejandra , Lem Mónica , Díaz-Díaz Eulises , Castillo Cinthia , Cárdenas-Soto Karla 
Published: December 2015

Objective:
We report the results of a pilot, enrichment-design, placebo-controlled crossover trial of pregabalin for the treatment of prediabetic small-fiber neuropathic pain.

Methods:
Individuals with impaired fasting glucose or impaired glucose tolerance and neuropathic pain were evaluated according to UTAH Early Neuropathy Scale (UENS), Quantitative Sensory Testing, and intraepidermal nerve fiber density (IENFD). Symptoms were graded according to the Numeric Rating Scale (NRS). Individuals who responded to the administration of placebo were not eligible. Pregabalin was initiated at a dose of 75 mg qid and tapered up to 300 mg bid. Only individuals with a reduction of pain scores ≥30% were eligible to continue with the double-blind phase, which consisted of a randomized crossover period of 1 month of pregabalin and 1 month of placebo, with 7 days of washout between periods.

Results:
Forty-five participants were enrolled in the study. There was 36% reduction in the NRS from baseline after 1 month of single-blind pregabalin (NRS=5.1±2.6). Twenty-six participants were eligible for the double-blind phase. There was further reduction of pain in the double-blind pregabalin and the placebo groups, but the pregabalin group had a statistically significant reduction of pain (NRS=3.2±2.2 vs. 4.0±2; P<0.05). Participants who did not respond showed a lower IENFD than those who responded, suggesting more severe nerve damage.

Conclusions:
This pilot study showed improvement of prediabetic neuropathic pain. Participants with higher pain scores at baseline had higher UENS scores and a lower IENFD. Limitations of the study include the small number of participants and the carry-over effect.
The Intraoperative Effect of Methadone on Somatosensory Evoked Potentials
Authors: Higgs Maureen , Hackworth Robert J. , John King , Riffenburgh Robert , Tomlin Jeffrey , Wamsley Brian 
Published: December 2015

Background:
Evoked potentials (EP), both somatosensory evoked potentials (SSEP) and transcranial motor evoked potentials (TcMEP), are often used during complex spine surgery to monitor the integrity of spinal pathways during operations in or around the spine. Changes in these monitored EP signals (increased latency and decreased amplitude) may result from ischemia, direct surgical injury, changes in blood pressure, hypoxia, changes in CO2 tension, and anesthetic agents. Typically, a clinically significant change for SSEPs is defined as an increase in latency >10% or a decrease of amplitude >50%. A clinically significant change for TcMEPs is much more complex but is also described in terms of large signal loss or decrease. Opioids have been shown to both increase latency and decrease the amplitude of SSEPs, although this change is usually not clinically significant. There has been a renewed interest in methadone for use in spine and other complex surgeries. However, the effect of methadone on intraoperative monitoring of SSEPs and TcMEPs is unknown. We present the first study to directly look at the effects of methadone on SSEP and TcMEP monitoring during complex spine surgery.

Methods:
The goal of this study was to observe the effect of methadone on an unrandomized set of patients. The primary endpoint was methadone’s effect on SSEPs, and the secondary endpoint was methadone’s effect on TcMEPs. Adult patients undergoing spine surgery requiring intraoperative neuromonitoring were induced with general anesthesia and had a baseline set of SSEPs and TcMEPs recorded. Next, methadone dosed 0.2 mg/kg/lean body weight was given. Repeat SSEPs and TcMEPs were recorded at 5, 10, and 15 minutes, with the timing based on distribution half-life of methadone between 6 and 8 minutes. Postoperatively, adverse events from methadone administration were collected.

Results:
There was a statistically significant difference found in SSEPs for N20 latency (95% confidence interval [CI], 0.17-0.53; P=0.028), P37 latency (95% CI, 0.65-1.25; P=0.001), and N20 amplitude (95% CI, 0.09-0.32; P=<0.001), but not for P37 amplitude (95% CI, −0.19 to 0.00; P=0.634). There was no significant effect found for TcMEPs, the secondary endpoint of the study, and there were minimal adverse events recorded postoperatively.

Conclusions:
The data demonstrate that a single intravenous dose of methadone has a statistically significant difference on the amplitude and latency of SSEPs. However, this statistical difference does not translate into a clinical significance.
Iodine-131 Therapy and Lacrimal Drainage System Toxicity: Nasal Localization Studies Using Whole Body Nuclear Scintigraphy and SPECT-CT
Authors: Ali Mohammad Javed , Vyakaranam Achyut Ram , Rao Jyotsna Eleshwarapu , Prasad Giri , Reddy Palkonda Vijay Anand 
Published: December 2015

Purpose:
The objective of this study was to evaluate the influence of dose on nasal localization of radioactive iodine-131 (I-131) following therapy for differentiated thyroid carcinomas.

Methods:
Retrospective evaluation of all patients who underwent post-therapy I-131 whole body scintigraphy and single photon emission computed tomography was performed. Patients were divided into 2 groups; group A were treated with 100 millicurie (mCi) and group B with ≥150 mCi. Databases were reviewed for demographics, diagnosis, and administered dosage of I-131. Whole body scintigraphy images were retrieved and nasal uptake was analyzed and classified as nil to trace, low, moderate, and high uptake and corresponding single photon emission CTs were analyzed for radioactive nasal activity.

Results:
A total of 100 patients were studied, 50 in each of the groups. The M:F ratio was 1.1:1 (27:23) in group A and 1.5:1 (30:20) in group B. The mean age was 43.12 years and 54.6 years in groups A and B, respectively. Papillary carcinoma of the thyroid was the most common type accounting for 82% (41/50) of patients in group A and 62% (31/50) in group B. Imaging studies revealed nil to trace nasal activity in 80% (40/50) in group A as compared with 56% (28/50) in group B. None of the patients in group A showed high nasal uptake, whereas 4% (2/50) in group B demonstrated such high activity.

Conclusion:
Intranasal localization of radioactive I-131 was significant in patients receiving a dose of ≥150 mCi. Intranasal localization may partly explain toxicity to nasolacrimal duct and may be a risk factor for subsequent development of nasolacrimal duct obstructions.
Gallbladder Ejection Fraction Is Unrelated to Gallbladder Pathology in Children and Adolescents
Authors: Jones Patrick M. , Rosenman Marc B. , Pfefferkorn Marian D. , Rescorla Frederick J. , Bennett William E. 
Published: December 2015

ABSTRACTObjectives:Biliary dyskinesia is a common diagnosis that frequently results in cholecystectomy. In adults, most clinicians use a cut off value for the gallbladder ejection fraction (GBEF) of <35% to define the disease. This disorder is not well characterized in children. Our aim was to determine the relation between GBEF and gallbladder pathology using a large statewide medical record repository.Methods:We obtained records from all patients of 21 years and younger who underwent hepatic iminodiacetic acid (HIDA) testing within the Indiana Network for Patient Care from 2004 to 2013. GBEF results were obtained from radiology reports using data mining techniques. Age, sex, race, and insurance status were obtained for each patient. Any gallbladder pathology obtained subsequent to an HIDA scan was also obtained and parsed for mention of cholecystitis, cholelithiasis, or cholesterolosis. We performed mixed effects logistic regression analysis to determine the influence of age, sex, race, insurance status, pathologist, and GBEF on the presence of these histologic findings.Results:Two thousand eight hundred forty‐one HIDA scans on 2558 patients were found. Of these, 310 patients had a full‐text gallbladder pathology report paired with the HIDA scan. GBEF did not correlate with the presence of gallbladder pathology (cholecystitis, cholelithiasis, or cholesterolosis) when controlling for age, sex, race, insurance status, and pathologist using a mixed effects model.Conclusions:Hypokinetic gallbladders are no more likely to have gallbladder pathology than normal or hyperkinetic gallbladders in the setting of a patient with both a HIDA scan and a cholecystectomy. Care should be used when interpreting the results of HIDA scans in children and adolescents.
The mediating role of job satisfaction in the relationship between job training satisfaction and turnover intentions
Authors: Huang Wen-Rou , Su Chih-Hao 
Published: December 2015

Purpose– The purpose of this paper is to examine the relationship among job training satisfaction (JTS), job satisfaction (JS) and turnover intention (TI) and moreover, the role of JS in the relationship between the JTS and TI.Design/methodology/approach– A survey was used in this study for a sample size of 115. The principal component analysis was carried out to examine the factors in JTS and JS. The regression and mediation analyses were applied to assess the relationship among the JTS, JS and TI.Findings– A significantly negative relationship between JTS and TI was found and mediated by JS. The paper also suggests that JS is positively related to JTS but is negatively related to TI, which is in accordance with what have been reported in the earlier studies.Practical implications– This study reinforced the significance of job training in human resource management practices. The employees’ satisfaction with job training that would lead to higher JS and lower TIs was emphasized. Therefore, it becomes important for HRD professionals to consider both the delivery of the training to the employees and the employees’ satisfaction with the training approach when designing the training program.Originality/value– While many different variables have been studied in the relationship with TI, the JTS is rarely discussed. This paper attempts to examine the relationship among JTS, JS and TI with addition of new insights.
Analysis of a trial assessing the long‐term effectiveness of salicylic acid plasters compared with scalpel debridement in facilitating corn resolution in patients with multiple corns
Authors: Stephenson John , Farndon Lisa , Concannon Michael 
Published: December 2015

AbstractThis study assesses the effect of salicylic acid plasters on the time to resolution of 324 corns experienced by 201 participants taking part in a randomized controlled trial. While the rate of corn resolution was substantively higher in the treatment group than in the control group, treatment was found to be not significantly related to time to corn recurrence when analyzed over the full 12‐month follow‐up period. Parametric survival analysis modeling of interval‐censored data and incorporating patient‐specific frailty terms was utilized, to model correlation of corns within patients (hazard ratio [HR], 1.189; 95% confidence interval [CI], 0.780–1.813; P = 0.422). Median resolution times were 10.0 months for corns in the treatment group and 13.4 months for corns in the control group. Controlling for treatment, corn type was found to be related to resolution time, with dorsal/interdigital (ID) corns showing better resolution than plantar corns (HR, 1.670; 95% CI, 1.061–2.630; P = 0.027). Median resolution times were 5.9 months for dorsal/ID corns and 14.9 months for plantar corns. Secondary measures relating to quality of life (QoL) and foot‐related disability, using the EQ‐5D questionnaire and the Manchester Foot Pain and Disability Index (MFPDI), were also assessed at the patient level in multivariate models. Treatment was not significantly related to any of these measures over the whole period of analysis. However, a trend analysis revealed a quadratic trend in QoL and MFPDI scores, arising from a substantive initial improvement between baseline and 3 months, followed by a gradual decrease between 3 and 12 months.