bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improved i.p. drug delivery with bioadhesive nanoparticles
Authors: Deng Yang , Yang Fan , Cocco Emiliano , Song Eric , Zhang Junwei , Cui Jiajia , Mohideen Muneeb , Bellone Stefania , Santin Alessandro D. , Saltzman W. Mark 
Published: September 2016

Significance
Resistance to platinum-based chemotherapies and paclitaxel is common in recurrence of both high-grade ovarian and endometrial cancers. Paclitaxel resistance has been correlated with overexpression of class III β-tubulin, the preferential target of the epothilones, microtubule-stabilizing agents. Epothilone B (EB) is manifold more effective than paclitaxel, but clinical use is limited by side effects. To reduce side effects, we encapsulated EB into bioadhesive nanoparticles (BNPs), reasoning that bioadhesive nanoparticles loaded with epothilone B (EB/BNPs) would interact with abdominal tissues and gradually release EB in proximity of peritoneal cancer implants, thus maintaining EB concentration at the site of action and limiting systemic exposure and toxicity. Our experiments show the higher therapeutic activity and limited toxicity of EB/BNPs compared with nonadhesive nanoparticles loaded with EB or carrier-free EB.
Inferring interaction partners from protein sequences
Authors: Bitbol Anne-Florence , Dwyer Robert S. , Colwell Lucy J. , Wingreen Ned S. 
Published: September 2016

Significance
Specific protein−protein interactions play crucial roles in the stability of multiprotein complexes and in signal transduction. Thus, mapping these interactions is key to a systems-level understanding of cells. Systematic experimental identification of protein interaction partners is still challenging. However, a large and rapidly growing amount of sequence data is now available. Is it possible to identify which proteins interact just from their sequences? We propose an approach based on sequence covariation, building on methods used with success to predict the three-dimensional structures of proteins from sequences alone. Our method identifies specific interaction partners with high accuracy among the members of several ubiquitous prokaryotic protein families, and provides a way to predict protein−protein interactions directly from sequence data.
Oriented collagen fibers direct tumor cell intravasation
Authors: Han Weijing , Chen Shaohua , Yuan Wei , Fan Qihui , Tian Jianxiang , Wang Xiaochen , Chen Longqing , Zhang Xixiang , Wei Weili , Liu Ruchuan , Qu Junle , Jiao Yang , Austin Robert H. , Liu Liyu 
Published: September 2016

Significance
Intravasation is an early stage of metastasis that involves metastatic cells moving from the tumor into the extracellular matrix (ECM), breakthrough of the basement membrane, and entry into blood vessels. We found that the oriented fibers greatly enhance and facilitate the metastatic cell intravasation process during metastasis. We suggest that a possible “tissue treatment” therapy could be considered, in which the ECM fiber structure orientation in the tumor microenvironment might be altered to minimize the intravasation rate of metastatic cells.
Rational design of a Kv1.3 channel-blocking antibody as a selective immunosuppressant
Authors: Wang Rongsheng E. , Wang Ying , Zhang Yuhan , Gabrelow Chase , Zhang Yong , Chi Victor , Fu Qiangwei , Luo Xiaozhou , Wang Danling , Joseph Sean , Johnson Kristen , Chatterjee Arnab K. , Wright Timothy M. , Nguyen-Tran Vân T. B. , Teijaro John , Theofilopoulos Argyrios N. , Schultz Peter G. , Wang Feng 
Published: September 2016

SignificanceThere is considerable interest in developing immunosuppressants that can specifically target effector memory T cells which are key to the pathogenesis of many inflammatory disorders. The potassium channel Kv1.3 has been found to play an important role in TEMactivation, but not in naive and central memory T cells. It has proven challenging to generate small molecules or antibodies that potently and selectively block Kv1.3 function. We generated antibody fusions by grafting potent Kv1.3 blocking peptides into complementary-determining regions (CDRs) of humanized antibodies, and among those, identified a candidate with high in vitro potency, excellent physiochemical and pharmacologic properties, and in vivo efficacy in a rat model. These novel toxin-antibody fusions have therapeutic potential for a variety of TEM-mediated inflammatory diseases.
A generative model for the behavior of RNA polymerase
Authors: Azofeifa Joseph G , Dowell Robin D 
Published: September 2016

AbstractMotivationTranscription by RNA polymerase is a highly dynamic process involving multiple distinct points of regulation. Nascent transcription assays are a relatively new set of high throughput techniques that measure the location of actively engaged RNA polymerase genome wide. Hence, nascent transcription is a rich source of information on the regulation of RNA polymerase activity. To fully dissect this data requires the development of stochastic models that can both deconvolve the stages of polymerase activity and identify significant changes in activity between experiments.ResultsWe present a generative, probabilistic model of RNA polymerase that fully describes loading, initiation, elongation and termination. We fit this model genome wide and profile the enzymatic activity of RNA polymerase across various loci and following experimental perturbation. We observe striking correlation of predicted loading events and regulatory chromatin marks. We provide principled statistics that compute probabilities reminiscent of traveler’s and divergent ratios. We finish with a systematic comparison of RNA Polymerase activity at promoter versus non-promoter associated loci.Availability and ImplementationTranscription Fit (Tfit) is a freely available, open source software package written in C/C ++ that requires GNU compilers 4.7.3 or greater. Tfit is available from GitHub (https://github.com/azofeifa/Tfit).Supplementary informationSupplementary data are available at Bioinformatics online.
FastRFS: fast and accurate Robinson-Foulds Supertrees using constrained exact optimization
Authors: Vachaspati Pranjal , Warnow Tandy 
Published: September 2016

Abstract

Motivation
The estimation of phylogenetic trees is a major part of many biological dataset analyses, but maximum likelihood approaches are NP-hard and Bayesian MCMC methods do not scale well to even moderate-sized datasets. Supertree methods, which are used to construct trees from trees computed on subsets, are critically important tools for enabling the statistical estimation of phylogenies for large and potentially heterogeneous datasets. Supertree estimation is itself NP-hard, and no current supertree method has sufficient accuracy and scalability to provide good accuracy on the large datasets that supertree methods were designed for, containing thousands of species and many subset trees.

Results
We present FastRFS, a new method based on a dynamic programming method we have developed to find an exact solution to the Robinson-Foulds Supertree problem within a constrained search space. FastRFS has excellent accuracy in terms of criterion scores and topological accuracy of the resultant trees, substantially improving on competing methods on a large collection of biological and simulated data. In addition, FastRFS is extremely fast, finishing in minutes on even very large datasets, and in under an hour on a biological dataset with 2228 species.

Availability and Implementation
FastRFS is available on github at https://github.com/pranjalv123/FastRFS

Supplementary information
Supplementary data are available at Bioinformatics online.
FoldAtlas: a repository for genome-wide RNA structure probing data
Authors: Norris Matthew , Kwok Chun Kit , Cheema Jitender , Hartley Matthew , Morris Richard J , Aviran Sharon , Ding Yiliang 
Published: September 2016

Abstract

Summary
Most RNA molecules form internal base pairs, leading to a folded secondary structure. Some of these structures have been demonstrated to be functionally significant. High-throughput RNA structure chemical probing methods generate millions of sequencing reads to provide structural constraints for RNA secondary structure prediction. At present, processed data from these experiments are difficult to access without computational expertise. Here we present FoldAtlas, a web interface for accessing raw and processed structural data across thousands of transcripts. FoldAtlas allows a researcher to easily locate, view, and retrieve probing data for a given RNA molecule. We also provide in silico and in vivo secondary structure predictions for comparison, visualized in the browser as circle plots and topology diagrams. Data currently integrated into FoldAtlas are from a new high-depth Structure-seq data analysis in Arabidopsis thaliana, released with this work.

Availability and Implementation
The FoldAtlas website can be accessed at www.foldatlas.com. Source code is freely available at github.com/mnori/foldatlas under the MIT license. Raw reads data are available under the NCBI SRA accession SRP066985.

Supplementary information
Supplementary data are available at Bioinformatics online.
The challenge of measuring magnetic fields in strongly pulsating stars: the case of HD 96446
Authors: Järvinen S. P. , Hubrig S. , Ilyin I. , Schöller M. , Briquet M. 
Published: September 2016

Abstract
Among the early B-type stars, He-rich Bp stars exhibit the strongest large-scale organized magnetic fields with a predominant dipole contribution. The presence of β Cep-like pulsations in the typical magnetic early Bp-type star HD 96446 was announced a few years ago, but the analysis of the magnetic field geometry was hampered by the absence of a reliable rotation period and a sophisticated procedure for accounting for the impact of pulsations on the magnetic field measurements. Using new spectropolarimetric observations and a recently determined rotation period based on an extensive spectroscopic time series, we investigate the magnetic field model parameters of this star under more detailed considerations of the pulsation behaviour of line profiles.
KIC 2831097 – a 2-yr-orbital-period RR Lyrae binary candidate
Authors: Sódor Á. , Skarka M. , Liška J. , Bognár Zs. 
Published: September 2016

Abstract
We report the discovery of a new Kepler first-overtone RR Lyrae pulsator, KIC 2831097. The pulsation shows large, 0.1-d amplitude, systematic phase variations that can be interpreted as light traveltime effect caused by orbital motion in a binary system, superimposed on a linear pulsation-period decrease. The assumed eccentric (e = 0.47) orbit with the period of ≈2 yr is the shortest among the non-eclipsing RR Lyrae binary candidates. The binary model gives the lowest estimate for the mass of the companion of 8.4 M⊙, that places it among black hole candidates. Beside the first-overtone pulsation, numerous additional non-radial pulsation frequencies were also identified. We detected an ≈47-d Blazhko-like irregular light-curve modulation.
X-ray observations of a subhalo associated with the NGC 4839 group infalling toward the Coma cluster
Authors: Sasaki Toru , Matsushita Kyoko , Sato Kosuke , Okabe Nobuhiro 
Published: September 2016

Abstract
We report on Suzaku X-ray observations of the dark subhalo associated with the merging group of NGC 4839 in the Coma cluster. The X-ray image exhibits an elongated tail toward the southwest. The X-ray peak shifts approximately 1′ away from the weak-lensing mass center toward the opposite direction of the Coma cluster center. We investigated the temperature, normalization, pressure, and entropy distributions around the subhalo. Excluding the X-ray tail, the temperature beyond the truncation radius is 8–10 keV, which is twice as high as that of the subhalo and the X-ray tail. The pressure is nearly uniform, excluding the southern part of the subhalo at two times of the truncation radius. We computed the gas mass within the truncation radius and the X-ray tail. While the gas fraction within the truncation radius is about five times smaller than that of regular groups, the gas mass in the subhalo and the X-ray tail to weak-lensing mass ratio is consistent with that of regular groups. Assuming an infall velocity of 2000 km s−1, the ram pressure is 1.4 times greater than the gravitational force per unit area. Assuming the Kelvin–Helmholtz instabilities, the total lost mass is approximately 3 × 1011 M⊙. If this gas had originally been within the truncation radius, the gas mass fraction of the subhalo would have been comparable with those of regular groups before infalling to the Coma cluster.
The Sunyaev–Zel'dovich effect at 5″: RX J1347.5−1145 imaged by ALMA
Authors: Kitayama Tetsu , Ueda Shutaro , Takakuwa Shigehisa , Tsutsumi Takahiro , Komatsu Eiichiro , Akahori Takuya , Iono Daisuke , Izumi Takuma , Kawabe Ryohei , Kohno Kotaro , Matsuo Hiroshi , Ota Naomi , Suto Yasushi , Takizawa Motozaku , Yoshikawa Kohji 
Published: September 2016

Abstract
We present the first image of the thermal Sunyaev–Zel'dovich effect (SZE) obtained by the Atacama Large Millimeter/submillimeter Array (ALMA). Combining 7-m and 12-m arrays in Band 3, we create an SZE map toward a galaxy cluster RX J1347.5−1145 with 5″ resolution (corresponding to a physical size of 20 h−1 kpc), the highest angular and physical spatial resolutions achieved to-date for imaging the SZE, while retaining extended signals out to 40″. The 1 σ statistical sensitivity of the image is 0.017 mJy beam−1 or 0.12 mKCMB at the 5″ full width at half maximum. The SZE image shows a good agreement with an electron pressure map reconstructed independently from the X-ray data and offers a new probe of the small-scale structure of the intracluster medium. Our results demonstrate that ALMA is a powerful instrument for imaging the SZE in compact galaxy clusters with unprecedented angular resolution and sensitivity. As the first report on the detection of the SZE by ALMA, we present detailed analysis procedures including corrections for the missing flux, to provide guiding methods for analyzing and interpreting future SZE images obtained by ALMA.
Trajectory of Postoperative Wound Pain Within the First 2 Weeks Following Posterior Spinal Fusion Surgery in Adolescent Idiopathic Scoliosis Patients
Authors: Kwan Mun Keong , Chiu Chee Kidd , Chan Teik Seng , Chong Kok Ian , Mohamad Siti Mariam , Hasan Mohd Shahnaz , Chan Chris Yin Wei 
Published: September 2016

Study Design.
A prospective cohort study.

Objective.
The aim of this study was to determine and evaluate the trajectory of surgical wound pain from day 1 to day 14 after posterior spinal fusion (PSF) surgery in patients with adolescent idiopathic scoliosis (AIS).

Summary of Background Data.
Information regarding how the postoperative pain improves with time offers invaluable information not only to the patients and parents but also to assist the clinician in managing postoperative pain.

Methods.
AIS patients who were planned for elective PSF surgery from September 2015 to December 2015 were prospectively recruited into this study. All patients underwent a similar pain management regimen with patient-controlled anesthesia (PCA) morphine, acetaminophen, celecoxib, and oxycodone hydrochloride.

Results.
A total of 40 patients (36 F:4 M) were recruited. The visual analogue score (VAS) pain score was highest at 12 hours postoperation (6.0 ± 2.3). It reduced to 3.9 ± 2.2 (day 4), 1.9 ± 1.6 (day 7), and 0.7 ± 1.1 (day 14). The total PCA usage in all patients was 12.4 ± 9.9 mg (first 12 hours), 7.1 ± 8.0 mg (12 to 24 hours), 5.6 ± 6.9 (24–36 hours), and 2.1 ± 6.1 mg (36–48 hours). The celecoxib capsules usage was reducing from 215.0 ± 152.8 mg at 24 hours to 55.0 ± 90.4 mg on day 14. The acetaminophen usage was reducing from 2275 ± 1198 mg at 24 hours to 150 ± 483 mg at day 14. Oxycodone hydrochloride capsules consumption rose to the peak of 1.4 ± 2.8 mg on day 4 before gradually reducing to none by day 13.

Conclusion.
With an adequate postoperation pain regimen, significant pain should subside to a tolerable level by postoperative day 4 and negligible by postoperative day 7. Patient usually can be discharged on postoperative day 4 when the usage of PCA morphine was not required.

Level of Evidence: 2
A Topical Anesthetic and Lidocaine Mixture for Pain Relief During Keloid Treatment: A Double-Blind, Randomized Controlled Trial
Authors: Usanakornkul Arnik , Burusapat Chairat 
Published: September 2016

BACKGROUND
Keloids are abnormal overgrowth of collagen fibers, and the first-line treatment includes intralesional injection of triamcinolone acetonide (TA), which is associated with pain.

OBJECTIVE
To study the benefit of applying topical anesthetics or a 1:1 mixture of 1% lidocaine and TA at the TA injection site to alleviate pain during keloid treatment.

METHODS AND MATERIALS
A double-blind, randomized controlled trial was conducted. Four TA injection methods were tested: control, lidocaine, topical, and combined. A visual analog scale (VAS) was used to assess needle-stick and injection pain. Data on pain duration after injection were also collected.

RESULTS
Forty patients were enrolled (mean age, 37.1 years). The VAS scores of needle-stick pain in the control, lidocaine, topical, and combined groups were 4.18 ± 2.12, 3.82 ± 2.48, 2.03 ± 2.02, and 2.20 ± 1.99, respectively. Pain statistically decreased in the topical and combined groups. Intralesional injection pain (VAS) scores in the control, lidocaine, topical, and combined groups were similar as follows: 4.97 ± 2.50, 4.97 ± 2.79, 4.10 ± 2.80, and 4.43 ± 2.68, respectively.

CONCLUSION
Application of topical anesthetics significantly relieved needle-stick pain, especially at sternum and auricular keloids; administration of a lidocaine mixture did not alleviate pain during injection.
Reshaping of the Anterior Nasal Spine: An Important Step in Rhinoplasty
Authors: Marianetti Tito M. , Boccieri Armando , Pascali Michele 
Published: September 2016

Background:
The importance of analysis of the nasal spine should not be underestimated in the correct planning of rhinoplasty. Deformations in position with respect to the midline and/or in size are often present, and their correction to ensure harmony between the spine and the other components of the nasal pyramid constitutes a key step in rhinoplasty that can lead to excellent results.

Methods:
The study includes 160 patients who underwent surgical treatment of the anterior nasal spine with or without other techniques of nasal reshaping. Eighty-seven of these patients presented with hyperplasia of the nasal spine, 43 with hypoplasia, and 30 with deviation. A combination of deviation and hyperplasia was present in 15 cases.

Results:
No patients developed postoperative complications. Five patients who underwent anterior nasal spine reduction reported postoperative numbness in the premaxillary area, but sensitivity was fully regained within 4 months after surgery in these patients. All the patients reported postoperative improvement of nasal airflow. A total of 142 patients considered their postoperative aesthetic result as excellent and 18 as good.

Conclusion:
The simplicity of the surgical procedures performed on the nasal spine and the marked aesthetic improvements thus achieved suggest that greater attention should be paid to this anatomical region.
Short article: Buried bumper syndrome in children: incidence and risk factors
Authors: Stewart Claire E. , Mutalib Mohamed , Pradhan Akhilesh , Bassett Christopher , Drake David , Upadhyaya Manasvi 
Published: September 2016

Objective
Buried bumper syndrome (BBS) is a serious complication in gastrostomy-dependent children. Many need surgical correction. On account of comorbidities, this becomes a high-risk procedure. Our aim was to review the incidence of BBS in children and to identify the risk factors.

Patients and methods
Retrospective review of patients’ records over 10 years, 2006–2015, was carried out. Types of tubes, operative interventions, comorbidities and records were noted. Two-tailed Fisher’s exact test was used for statistical analysis.

Results
A total of 535 patients were reviewed. Overall, 475 had only percutaneous endoscopic gastrostomy (PEG) and 60 had a jejunal extension with percutaneous endoscopic gastrostomy (PEG-J). Twenty-nine patients (PEG-J – 16/26; PEG – 13/26) had a total of 31 BBS episodes. The overall incidence of BBS in our study was 5.4%. The age at presentation ranged from 1 to 18 years (median 8.6 years). All had significant comorbidities (neurodevelopmental 26/29, cardiorespiratory 14/29, genetic 16/29). Overall, 27/29 had two or more comorbidities. The mean time to development of BBS was 1025±634 days. BBS was found in the second or the subsequent tube in four patients with PEGs (P<0.0004) and in 10 PEG-Js (P<0.0001). Twenty-five patients needed laparotomy. There were no postoperative deaths.

Conclusion
In BBS, the two significant risk factors identified were a having PEG-J and two or more previous gastrostomy insertions. Vigilance in documentation and prolonged follow-up to provide regular education to carers can reduce the incidence of this preventable complication.
Patient, Therapist, and System Factors Influencing the Effectiveness of Prolonged Exposure for Veterans With Comorbid Posttraumatic Stress Disorder and Traumatic Brain Injury
Authors: Crawford Eric Floyd , Wolf Gregory K. , Kretzmer Tracy , Dillon Kirsten H. , Thors Christina , Vanderploeg Rodney D. 
Published: September 2016

Abstract
In contrast to concerns that cognitive limitations and neurobehavioral symptoms (NBS) associated with traumatic brain injury (TBI) may inhibit treatment effectiveness, a recent study found prolonged exposure (PE) led to large reductions in posttraumatic stress disorder (PTSD) symptoms among Iraq-Afghanistan veterans with a range of TBI severity (article by Wolf, Kretzmer, Crawford, Thors, Wagner, Strom, Eftekhari, Klenk, Hayward, and Vanderploeg [J Trauma Stress 28:339–347, 2015]). We further examined this sample of 69 veterans to determine whether system, veteran, and therapist factors predicted clinically significant responses. Results of hierarchical, logistic regressions revealed that therapist training in PE and lower service connection were associated with increased odds of large decreases in PTSD symptoms after adjusting for the robust effect of PE sessions completed. Other patient-level factors including age, time since injury, and baseline NBS were unrelated to significant improvements. Findings emphasized the impact of PE dosage, indicated greater mastery of the protocol was beneficial, and showed that service connection could impede self-reported, clinically significant change during PE in this important cohort.