bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mutational landscape, clonal evolution patterns, and role of RAS mutations in relapsed acute lymphoblastic leukemia
Authors: Oshima Koichi , Khiabanian Hossein , da Silva-Almeida Ana C. , Tzoneva Gannie , Abate Francesco , Ambesi-Impiombato Alberto , Sanchez-Martin Marta , Carpenter Zachary , Penson Alex , Perez-Garcia Arianne , Eckert Cornelia , Nicolas Concepción , Balbin Milagros , Sulis Maria Luisa , Kato Motohiro , Koh Katsuyoshi , Paganin Maddalena , Basso Giuseppe , Gastier-Foster Julie M. , Devidas Meenakshi , Loh Mignon L. , Kirschner-Schwabe Renate , Palomero Teresa , Rabadan Raul , Ferrando Adolfo A. 
Published: September 2016

Significance
Relapsed acute lymphoblastic leukemia (ALL) is associated with chemotherapy resistance and poor prognosis. This study analyzes the emergence of acquired mutations in relapsed ALL samples, identifying genes implicated in disease progression and defining the process of clonal evolution leading to relapse. These analyses revealed that ALL relapse emerges from subclonal populations sharing only part of the mutations present in the dominant leukemia population found at diagnosis. Moreover, we show mutations in genes implicated in chemotherapy resistance pathways at relapse. RAS mutations are highly prevalent in high-risk ALL, yet their capacity to confer resistance to methotrexate and sensitivity to vincristine, two core drugs used in the treatment of ALL, influences their positive or negative selection at relapse.
Strain analysis of protein structures and low dimensionality of mechanical allosteric couplings
Authors: Mitchell Michael R. , Tlusty Tsvi , Leibler Stanislas 
Published: September 2016

Significance
Regulation of biochemical activity is essential for proper cell growth and metabolism. Many proteins’ activities are regulated by interactions with other molecules binding some distance away from the proteins’ active sites. In such allosteric proteins, active sites should thus be mechanically coupled to spatially removed regulatory regions. We studied crystal and NMR structures of proteins in various regulatory and ligand-binding states. We calculated and analyzed distributions of strains throughout several proteins. Strains reveal allosteric and active sites and suggest that quasi-two-dimensional strained surfaces mediate mechanical couplings between them. Strain analysis of widely available structural data can illuminate protein function and guide future experimental investigation.
Short polyhistidine peptides penetrate effectively into Nicotiana tabacum-cultured cells and Saccharomyces cerevisiae cells
Authors: Kimura Sayaka , Kawano Tsuyoshi , Iwasaki Takashi 
Published: September 2016

Abstract
The polyhistidine peptides (PHPs) have been previously reported as novel cell-penetrating peptides and are efficiently internalized into mammal cells; however, penetration of PHPs into other cell types is unknown. In this study, the cellular uptake of PHPs in plant and yeast cells was found to be dependent on the number of histidines, and short PHPs (H6–H10 peptides) showed effective internalization. The H8 peptide showed the highest cell-penetrating capacity and localized to vacuoles in plant and yeast cells. Low-temperature conditions inhibited significantly the cellular uptake of short PHPs by both cells. However, net charge neutralization of PHPs also completely inhibited cellular uptake by plant cells, but not by yeast cells. These results indicate that short PHPs penetrate effectively into plant and yeast cells by similar mechanism with the exception of net charge dependency. The findings show the short PHPs are promising candidates for new delivery tools into plant and yeast cells.
Interlude
Authors: Gilliver Peter 
Published: September 2016

Abstract
This chapter assesses the contribution made to the ‘New English Dictionary’ by the volunteer sub-editors who worked on it during the 1860s and 1870s under the editorship of Frederick Furnivall. It examines the editorial policy as it was recommended by Furnivall and the ways in which this was interpreted by those sub-editors whose work has survived; it looks at the proposed inclusion policy, the quotations available to the sub-editors and how they were used, etymology, pronunciation, and the approach to the organization of dictionary entries, and considers how the lexicographical work carried out during this period differed from the later OED.
Manoeuvres: 1876–1879
Authors: Gilliver Peter 
Published: September 2016

Abstract
This chapter describes the search to find a publisher for the ‘New English Dictionary’, beginning with the abortive negotiations with Macmillan—in the course of which James Murray was identified as a suitable Editor of the Dictionary—and ending with the signing of contracts between Murray, the Philological Society, and Oxford University Press in 1879, following protracted negotiations between the parties over various aspects of editorial policy, the extent of the proposed dictionary, and the division of the anticipated profits. The roles of various key individuals in the negotiations, including Henry Sweet, Walter Skeat, Frederick Furnivall, Henry Liddell, Henry Hucks Gibbs, and Bartholomew Price, are described.
The road to Ant: 1879–1884
Authors: Gilliver Peter 
Published: September 2016

Abstract
This chapter describes the first five years of work on the ‘New English Dictionary’ under James Murray’s Editorship, leading up to the publication of the first fascicle in 1884. It begins with the setting up of Murray’s editorial establishment in his ‘Scriptorium’ at Mill Hill and the collection of existing materials; this is followed by the issuing of Murray’s ‘Appeal to the English-speaking and English-reading Public’ to collect more quotations, extended discussion and experimentation regarding various aspects of editorial policy (including the issuing of specimen entries), the appearance of a commercial rival to the Dictionary in the form of Cassell’s Encyclopaedic Dictionary, the dismissal of Murray’s assistant Sidney Herrtage, and the interventions made by the University’s new Vice-Chancellor, Benjamin Jowett. Murray’s financial difficulties, and the part played by Henry Hucks Gibbs both in alleviating these and in smoothing the path of the Dictionary in other ways, are explored in detail.
Limping over the finishing line: 1923–1933
Authors: Gilliver Peter 
Published: September 2016

Abstract
This chapter describes the concluding years of the first edition of the Oxford English Dictionary, and the compilation of the Supplement which appeared in 1933. It describes William Craigie’s continuing struggles with words beginning with un-, and his apparent growing disillusion with the project, culminating in his appointment to a professorship at the University of Chicago (with a brief to compile a new dictionary of American English), a position which severely diminished his contribution to the Dictionary and Supplement. The completion of the main Dictionary in 1928, and the associated celebrations, are described. The particular contributions of two OED assistants, Walter Worrall and George Watson, to the Dictionary are explored, as is that made to the Supplement by a new appointee, James Wyllie, and also the increasingly prominent role played in management of OUP’s lexicographical activities by Kenneth Sisam. The completion and publication of the Shorter OED is also described.
Secreted Frizzled-Related Protein 2 and Inflammation-Induced Skeletal Muscle Atrophy
Authors: Zhu Xiaoxi , Kny Melanie , Schmidt Franziska , Hahn Alexander , Wollersheim Tobias , Kleber Christian , Weber-Carstens Steffen , Fielitz Jens 
Published: September 2016

Objective:
In sepsis, the disease course of critically ill patients is often complicated by muscle failure leading to ICU-acquired weakness. The myokine transforming growth factor-β1 increases during inflammation and mediates muscle atrophy in vivo. We observed that the transforming growth factor-β1 inhibitor, secreted frizzled-related protein 2, was down-regulated in skeletal muscle of ICU-acquired weakness patients. We hypothesized that secreted frizzled-related protein 2 reduction enhances transforming growth factor-β1-mediated effects and investigated the interrelationship between transforming growth factor-β1 and secreted frizzled-related protein 2 in inflammation-induced atrophy.

Design:
Observational study and prospective animal trial.

Setting:
Two ICUs and research laboratory.

Patients/Subjects:
Twenty-six critically ill patients with Sequential Organ Failure Assessment scores greater than or equal to 8 underwent a skeletal muscle biopsy from the vastus lateralis at median day 5 in ICU. Four patients undergoing elective orthopedic surgery served as controls. To search for signaling pathways enriched in muscle of ICU-acquired weakness patients, a gene set enrichment analysis of our recently published gene expression profiles was performed. Quantitative reverse transcriptase-polymerase chain reaction, Western blot, and immunohistochemistry were used to analyze secreted frizzled-related protein 2 expression and protein content. A mouse model of inflammation-induced skeletal muscle atrophy due to polymicrobial sepsis and cultured myocytes were used for mechanistic analyses.

Interventions:
None.

Measurements and Main Results:
Gene set enrichment analysis uncovered transforming growth factor-β1 signaling activation in vastus lateralis from ICU-acquired weakness patients. Muscular secreted frizzled-related protein 2 expression was reduced after 5 days in ICU. Likewise, muscular secreted frizzled-related protein 2 expression was decreased early and continuously in mice with inflammation-induced atrophy. In muscle, secreted frizzled-related protein 2 was predominantly contained in fast twitch/type II myofibers. Secreted frizzled-related protein 2 physically interacted and colocalized with transforming growth factor-β1 through its cysteine-rich domain. Finally, secreted frizzled-related protein 2 prevented transforming growth factor-β1-induced atrophy in C2C12 myotubes.

Conclusions:
Muscular secreted frizzled-related protein 2 is down-regulated in ICU-acquired weakness patients and mice with inflammation-induced muscle atrophy. Decreased secreted frizzled-related protein 2 possibly establishes a positive feedback loop enhancing transforming growth factor-β1-mediated atrophic effects in inflammation-induced atrophy.
Relative Bioavailabilities of Lisdexamfetamine Dimesylate and d-Amphetamine in Healthy Adults in an Open-Label, Randomized, Crossover Study After Mixing Lisdexamfetamine Dimesylate With Food or Drink
Authors: Ermer James , Corcoran Mary , Lasseter Kenneth , Martin Patrick T. 
Published: September 2016

Background:
This open-label, crossover study examined lisdexamfetamine dimesylate (LDX) and d-amphetamine pharmacokinetics in healthy adults after administration of an intact LDX capsule or after the capsule was emptied into orange juice or yogurt and the contents consumed.

Methods:
Healthy adult volunteers (N = 30) were administered a 70-mg LDX capsule or the contents of a 70-mg capsule mixed with yogurt or orange juice using a 3-way crossover design. Blood samples were collected serially for up to 96 hours after dose. Pharmacokinetic endpoints included maximum plasma concentration (Cmax) and area under the plasma concentration versus time curve from zero to infinity (AUC0–∞) or to last assessment (AUClast). Relative LDX and d-amphetamine bioavailabilities from the contents of a 70-mg LDX capsule mixed with orange juice or yogurt were compared with those from the intact LDX capsule using bioequivalence-testing procedures.

Results:
Geometric least squares mean ratios (90% confidence intervals [CIs]) for d-amphetamine (active moiety) were within the prespecified bioequivalence range (0.80–1.25) when the contents of a 70-mg LDX capsule were mixed with orange juice [Cmax: 0.971 (0.945, 0.998); AUC0–∞: 0.986 (0.955, 1.019); AUClast: 0.970 (0.937, 1.004)] or yogurt [Cmax: 0.970 (0.944, 0.997); AUC0–∞: 0.945 (0.915, 0.976); AUClast: 0.944 (0.912, 0.977)]. Geometric least squares mean ratios (90% CIs) for LDX (inactive prodrug) were below the accepted range when the contents of a 70-mg LDX capsule were mixed with orange juice [Cmax: 0.641 (0.582, 0.707); AUC0–∞: 0.716 (0.647, 0.792); AUClast: 0.708 (0.655, 0.766)]; the lower 90% CI for Cmax [0.828 (0.752, 0.912)] was below the accepted range when the contents of a 70-mg LDX capsule were mixed with yogurt.

Conclusions:
Relative bioavailability of d-amphetamine (the active moiety) did not differ across administrations, which suggests that emptying an LDX capsule into orange juice or yogurt and consuming it is an alternative to intact capsules.
Hyperpolarized 129Xenon Magnetic Resonance Imaging to Quantify Regional Ventilation Differences in Mild to Moderate Asthma
Authors: Ebner Lukas , He Mu , Virgincar Rohan S. , Heacock Timothy , Kaushik Suryanarayanan S. , Freemann Matthew S. , McAdams H. Page , Kraft Monica , Driehuys Bastiaan 
Published: September 2016

Objectives
The aim of this study was to investigate ventilation in mild to moderate asthmatic patients and age-matched controls using hyperpolarized (HP) 129Xenon magnetic resonance imaging (MRI) and correlate findings with pulmonary function tests (PFTs).

Materials and Methods
This single-center, Health Insurance Portability and Accountability Act–compliant prospective study was approved by our institutional review board. Thirty subjects (10 young asthmatic patients, 26 ± 6 years; 3 males, 7 females; 10 older asthmatic patients, 64 ± 6 years; 3 males, 7 females; 10 healthy controls) were enrolled. After repeated PFTs 1 week apart, the subjects underwent 2 MRI scans within 10 minutes, inhaling 1-L volumes containing 0.5 to 1 L of 129Xe. 129Xe ventilation signal was quantified by linear binning, from which the ventilation defect percentage (VDP) was derived. Differences in VDP among subgroups and variability with age were evaluated using 1-tailed t tests. Correlation of VDP with PFTs was tested using Pearson correlation coefficient. Reproducibility of VDP was assessed using Bland-Altman plots, linear regression (R
2), intraclass correlation coefficient, and concordance correlation coefficient.

Results
Ventilation defect percentage was significantly higher in young asthmatic patients versus young healthy subjects (8.4% ± 3.2% vs 5.6% ± 1.7%, P = 0.031), but not in older asthmatic patients versus age-matched controls (16.8% ± 10.3% vs 11.6% ± 6.6%, P = 0.13). Ventilation defect percentage was found to increase significantly with age (healthy, P = 0.05; asthmatic patients, P = 0.033). Ventilation defect percentage was highly reproducible (R
2 = 0.976; intraclass correlation coefficient, 0.977; concordance correlation coefficient, 0.976) and significantly correlated with FEV1% (r = −0.42, P = 0.025), FEF25%–75% (r = −0.45, P = 0.019), FEV1/FVC (r = −0.71, P < 0.0001), FeNO (r = 0.69, P < 0.0001), and RV/TLC (r = 0.51, P = 0.0067). Bland-Altman analysis showed a bias for VDP of −0.88 ± 1.52 (FEV1%, −0.33 ± 7.18).

Conclusions

129Xenon MRI is able to depict airway obstructions in mild to moderate asthma and significantly correlates with PFTs.
Basal Ganglia Calcification in Psychiatric Inpatients: A Case-Control Study
Authors: Mufaddel Amir A. , Osman Ossama T. , Al-Hassani Ghanem , Al-Bedwawi Shakhbout , Hashim M. Jawad 
Published: September 2016

Background and Objective:
Several case reports have noted basal ganglia calcification (BGC) as an incidental radiologic finding in patients presenting with psychiatric manifestations. In this study, we examined the clinical correlates of mental disorders in two groups of psychiatric patients, one with BGC and one with normal radiologic studies.

Methods:
In a retrospective cross-sectional case-control study of patients admitted to the psychiatric ward in Al Ain Hospital between January 2011 and December 2013, we compared all 15 patients diagnosed with BGC and 30 control patients who had normal radiologic findings.

Results:
The BGC group’s psychiatric symptoms began when they were aged in their 30s and 40s, later than the controls’ 20s and 30s (P=0.001). More of the BGC group than the controls had cognitive symptoms (60% versus 6.7%, P=0.001). The BGC group was more likely to have chronic medical comorbidities (66.7% versus 20%, P=0.003). The BGC group’s mean serum calcium was lower than the controls’ (P=0.003) and the C-reactive protein was higher (P=0.049). We did not find significant differences between the groups in psychiatric diagnoses; five of the 15 patients with BGC had mood disorders and four of the 15 had psychotic disorders.

Conclusions:
Patients with BGC tend to develop psychiatric symptoms later in life than other psychiatric patients, and have higher rates of medical comorbidities. Many patients with BGC have cognitive symptoms, which can be concurrent with a mood or psychotic disorder.
ATX-2, theC. elegansOrtholog of Human Ataxin-2, Regulates Centrosome Size and Microtubule Dynamics
Authors: Stubenvoll Michael D. , Medley Jeffrey C. , Irwin Miranda , Song Mi Hye 
Published: September 2016

AbstractCentrosomes are critical sites for orchestrating microtubule dynamics, and exhibit dynamic changes in size during the cell cycle. As cells progress to mitosis, centrosomes recruit more microtubules (MT) to form mitotic bipolar spindles that ensure proper chromosome segregation. We report a new role for ATX-2, aC. elegansortholog of Human Ataxin-2, in regulating centrosome size and MT dynamics. ATX-2, an RNA-binding protein, forms a complex with SZY-20 in an RNA-independent fashion. Depleting ATX-2 results in embryonic lethality and cytokinesis failure, and restores centrosome duplication tozyg-1mutants. In this pathway, SZY-20 promotes ATX-2 abundance, which inversely correlates with centrosome size. Centrosomes depleted of ATX-2 exhibit elevated levels of centrosome factors (ZYG-1, SPD-5, γ-Tubulin), increasing MT nucleating activity but impeding MT growth. We show that ATX-2 influences MT behavior through γ-Tubulin at the centrosome. Our data suggest that RNA-binding proteins play an active role in controlling MT dynamics and provide insight into the control of proper centrosome size and MT dynamics.
The functional impact of alternative splicing in cancer
Authors: Climente-González Héctor , Porta-Pardo Eduard , Godzik Adam , Eyras Eduardo 
Published: September 2016

SummaryAlternative splicing changes are frequently observed in cancer and are starting to be recognized as important signatures for tumor progression and therapy. However, their functional impact and relevance to tumorigenesis remains mostly unknown. We carried out a systematic analysis to characterize the potential functional consequences of alternative splicing changes in thousands of tumor samples. This analysis revealed that a subset of alternative splicing changes affect protein domain families that are frequently mutated in tumors and potentially disrupt protein protein interactions in cancer-related pathways. Moreover, there was a negative correlation between the number of these alternative splicing changes in a sample and the number of somatic mutations in drivers. We propose that a subset of the alternative splicing changes observed in tumors may represent independent oncogenic processes that could be relevant to explain the functional transformations in cancer and some of them could potentially be considered alternative splicing drivers (AS-drivers).
A call to all L&D, OD and HR professionals: how can you increase your professional reputation?
Authors: Denton D. Keith 
Published: September 2016

PurposeTo improve the readers' ability to sell ideas, concepts and recommendations by learning to enhance their professional reputation.Design/methodology/approachThe paper is designed to help the reader through the process of enhancing their effectiveness in a work environment.FindingsThe article highlights the benefits of developing a strong professional reputation and how to promote your particular expertise.Practical implicationsProfessional managers cannot expect people to value their expertise simply on merit. You have to learn to promote that knowledge and influence.Social implicationsClearly organizations function best when all voices have had a chance to influence outcomes. Applying these techniques help ensure the reader's perspective is seen.Originality/valueThis paper describes clear steps you can take to better influence decisions and impact the organization by enhancing your professional reputation.
Design of a novel bionic prosthetic knee joint
Authors: Zhang Xiufeng , Fu Huiqun , Wang Xitai , Li Guanglin , Yang Rong , Liu Ying 
Published: September 2016

Purpose
This paper aims to find a new method that could be applied to the high and mid-grade prosthesis knee joint.

Design/methodology/approach
Based on analysis, calculation, modeling, simulation and experimental study of the motion law of knee joint, this paper not only determines the structure and parameters of the knee joint and calculates the instantaneous center but also analyzes the stance stability and completes the optimization. With the help of experimental tests (fatigue test and gait curve test), the quality and performance of the designed knee joint is verified.

Findings
The experimental results show that the gait curve of the designed knee joint is much closer to health people. The designed prosthesis knee joint, with adjustable swing speed and gait curve which are close to health limb, has a better performance when compared to the ordinary knee joint with four-bar linkage structure.

Originality/value
This paper developed a prosthesis knee joint based on a novel design method that could be applied to the “high and mid” grade prosthesis knee joint and verified its function on an amputee performed the lower amputation, which could provide theoretical support for researches and designs related to prosthesis knee joint in future.
Automatic multi-stereo-vision reconstruction method of complicated tubes for industrial assembly
Authors: Jin Peng , Liu Jian Hua , Liu Shao Li , Wang Xiao 
Published: September 2016

Purpose
Complicated tubes extensively exist in the industrial equipment. The manufacturing precision of the tubes is difficult to be ensured with bending machine. Therefore, the tubes’ 3D geometric error should be fixed according to measurement results. However, there are no convenient methods to accomplish the measurement accurately and effectively. Thus, this paper aims to propose a new tube measurement method to achieve tube's automatic measurement. The accurate measurement results can be used to fix the geometric error of the tube to achieve stress-free assembly.

Design/methodology/approach
Tubes’ shape can be determined by control points. First, the point clouds of the centre line by multi-stereo-vision technology are reconstructed. Then, the point clouds to the spine of the tube are thinned by moving least-squares and segmented into lines and arcs. Finally, the control points are calculated and the model is reconstructed. The authors can get the tube’s geometric dimensions from the model.

Findings
The experiment results indicate that the multi-stereo-vision technology can solve the occlusion problem and measure the complicated tubes efficiently and accurately.

Originality/value
The paper proposed a tube measurement method. The repeatability measuring precision was 0.12 mm, and the absolute measuring precision was within 0.78 mm. The tube spectra assessed in this paper are in the range of angles between two adjacent line segments of 3-177° and the shortest length of the line segment is greater than 5 mm, confirming that the proposed algorithm can measure various complicated tubes effectively and accurately.