bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transferring genomics to the clinic: distinguishing Burkitt and diffuse large B cell lymphomas
Authors: Sha Chulin , Barrans Sharon , Care Matthew A. , Cunningham David , Tooze Reuben M. , Jack Andrew , Westhead David R. 
Published: June 2015

Abstract
Background
Classifiers based on molecular criteria such as gene expression signatures have been developed to distinguish Burkitt lymphoma and diffuse large B cell lymphoma, which help to explore the intermediate cases where traditional diagnosis is difficult. Transfer of these research classifiers into a clinical setting is challenging because there are competing classifiers in the literature based on different methodology and gene sets with no clear best choice; classifiers based on one expression measurement platform may not transfer effectively to another; and, classifiers developed using fresh frozen samples may not work effectively with the commonly used and more convenient formalin fixed paraffin-embedded samples used in routine diagnosis.

Methods
Here we thoroughly compared two published high profile classifiers developed on data from different Affymetrix array platforms and fresh-frozen tissue, examining their transferability and concordance. Based on this analysis, a new Burkitt and diffuse large B cell lymphoma classifier (BDC) was developed and employed on Illumina DASL data from our own paraffin-embedded samples, allowing comparison with the diagnosis made in a central haematopathology laboratory and evaluation of clinical relevance.

Results
We show that both previous classifiers can be recapitulated using very much smaller gene sets than originally employed, and that the classification result is closely dependent on the Burkitt lymphoma criteria applied in the training set. The BDC classification on our data exhibits high agreement (~95 %) with the original diagnosis. A simple outcome comparison in the patients presenting intermediate features on conventional criteria suggests that the cases classified as Burkitt lymphoma by BDC have worse response to standard diffuse large B cell lymphoma treatment than those classified as diffuse large B cell lymphoma.

Conclusions
In this study, we comprehensively investigate two previous Burkitt lymphoma molecular classifiers, and implement a new gene expression classifier, BDC, that works effectively on paraffin-embedded samples and provides useful information for treatment decisions. The classifier is available as a free software package under the GNU public licence within the R statistical software environment through the link http://www.bioinformatics.leeds.ac.uk/labpages/softwares/ or on github https://github.com/Sharlene/BDC.
Cartilage in facet joints of patients with ankylosing spondylitis (AS) shows signs of cartilage degeneration rather than chondrocyte hypertrophy: implications for joint remodeling in AS
Authors: Bleil Janine , Sieper Joachim , Maier Rene , Schlichting Uwe , Hempfing Axel , Syrbe Uta , Appel Heiner 
Published: June 2015

Abstract
Introduction
In ankylosing spondylitis (AS), joint remodeling leading to joint ankylosis involves cartilage fusion. Here, we analyzed whether chondrocyte hypertrophy is involved in cartilage fusion and subsequent joint remodeling in AS.

Methods
We assessed the expression of chondrocyte hypertrophy markers runt-related transcription factor 2 (Runx2), type X collagen (COL10), matrix metalloproteinase 13 (MMP13), osteocalcin and beta-catenin and the expression of positive bone morphogenic proteins (BMPs) and negative regulators (dickkopf-1 (DKK-1)), sclerostin, (wingless inhibitory factor 1 (wif-1)) of chondrocyte hypertrophy in the cartilage of facet joints from patients with AS or osteoarthritis (OA) and from autopsy controls (CO) by immunohistochemistry. Sex determining region Y (SRY)-box 9 (Sox9) and type II collagen (COL2) expression was assessed as indicators of chondrocyte integrity and function.

Results
The percentage of hypertrophic chondrocytes expressing Runx2, COL10, MMP13, osteocalcin or beta-catenin was significantly increased in OA but not in AS joints compared to CO joints. Frequencies of sclerostin-positive and DKK-1-positive chondrocytes were similar in AS and CO. In contrast, wif-1- but also BMP-2- and BMP-7-expressing and Sox9-expressing chondrocytes were drastically reduced in AS joints compared to CO as well as OA joints whereas the percentage of COL2-expressing chondrocytes was significantly higher in AS joints compared to CO joints.

Conclusions
We found no evidence for chondrocyte hypertrophy within hyaline cartilage of AS joints even in the presence of reduced expression of the wnt inhibitor wif-1 suggesting that chondrocyte hypertrophy is not a predominant pathway involved in joint fusion and remodeling in AS. In contrast, the reduced expression of Sox9, BMP-2 and BMP-7 concomitantly with induced COL2 expression rather point to disturbed cartilage homeostasis promoting cartilage degeneration in AS.
Yema Djamila Sahraoui
Authors: Bedjaoui Ahmed 
Published: June 2015

Filmmaker Djamila Sahraoui is a product of the feminization of Algerian cinema that became dominant in the last decade of the twentieth century. More than thirty years since novelist Assia Djebar came onto the scene with her feminist stance, Algerian women are finally rendering representations of Algerian society different from those of their male counterparts. Considering her three earlier documentaries, one finds recurring themes that also run through Sahraoui’s latest film, Yema, including violence against women, the urgent need to resist, and the Kabyle landscape with its olive groves and wild mountains.
Yema is a film about the struggles being waged around the world and throughout history by men who aim to conquer. Vincent Ostria has called this into question in his review for the magazine Les InRocks; however, I would argue that Djamila Sahraoui’s film, seen through the Islamic experience, belongs to a universal discourse, much like the Greek tragedies the filmmaker has compared it to.
Quality, Subjectivity, and Sustained Superior Performance at the Olympic Games
Authors: Waguespack David M. , Salomon Robert 
Published: June 2015

In some competitions, performance evaluation includes a substantial subjective component. We argue that the inherent uncertainty and ambiguity in subjective evaluation can lead to favorable ex post treatment for reputationally privileged competitors. Post consumption, judges may infer quality that is not directly observed and/or make conservative choices to assuage accountability concerns. We examine these issues in the context of the Olympic Games, comparing country-level performance outcomes across Olympic sports. We find that past performance is predictive of current performance in all sports, but the effect is stronger in subjective outcome sports versus objective outcome sports. That is, past performance is a better predictor of future performance in sports where external judges and referees can influence the outcomes. We find the same pattern in individual boxing matches, with past country-level performance having a stronger effect on subjective boxing outcomes (judges’ decisions) than objective boxing outcomes (knockouts). Data, as supplemental material, are available at http://dx.doi.org/10.1287/mnsc.2014.2144 . This paper was accepted by Jesper Sørensen, organizations.
"THE LADIES OF TRENTON: WOMEN'S POLITICAL AND PUBLIC ACTIVISM IN REVOLUTIONARY NJ"
Authors: Hudak Catherine 
Published: June 2015

The Ladies of Trenton: Women's Political and Public Activism in Revolutionary NJBy Catherine HudakAbstractUsing the Ladies of Trenton as a case study, this article examines the extent and forms of women's public and political activism in the early national period. An analysis of the Ladies of Trenton's efforts demonstrates the pivotal roles women played in the formation of the vibrant political culture that emerged in late eighteenth century America. These elite NJ women had access to rich worlds of social and educational refinement coupled with strong political connections. The Ladies of Trenton used their literacy skills, knowledge of the patriot cause, and high social standings to captivate the nation as they entered male-dominated spaces of politics and print culture. Among the civic acts organized by the Ladies of Trenton include a fundraising campaign to assist the Continental Army and a public tribute honoring newly-elected President Washington. Contemporaries publicly recognized the significance of their fundraising to the success of the war effort as these NJ women refashioned gender roles for women by assembling to establish a committee, managing financial matters, and delving into military concerns. The Ladies of Trenton's public tribute for Washington included profound symbolism commemorating the battles of Trenton and Princeton as well as being reflective of the new nation. The contributions of the Ladies of Trenton demonstrate the presence of active public roles for women during this critical historical period of nation building in the United States.
Asilo y detención. Los guatemaltecos de 1954 en la Argentina.
Authors: Rostica Julieta Carla , Pedroni Nicolás , Sala Laura 
Published: June 2015

<p>Tras el golpe de Estado de junio de 1954, en Guatemala se produjo un asilo político en masa. El gobierno argentino recibió cerca de doscientas personas, entre las que se encontraban importantes figuras del Partido Guatemalteco del Trabajo. No obstante, a los pocos días de haber llegado al país, un grupo de más de treinta guatemaltecos fueron detenidos y apresados en la cárcel de Villa Devoto. El artículo tiene por objetivo abordar tres dimensiones, desde la perspectiva de la sociología histórica, que permiten dar cuenta de las condiciones de posibilidad de este acontecimiento: la ideológica, la normativa y la política exterior del gobierno de Juan Domingo Perón. El trabajo nos permitirá adentrarnos en la complejidad y ambigüedad que caracterizó a los populismos clásicos de América Latina y resultará una excusa para reponer la década del cincuenta, generalmente opacada por las décadas del sesenta y setenta, como coyuntura crítica para explicar las condiciones sociohistóricas de la violencia política en América Latina.</p><p> </p><p>After the coup of June 1954, in Guatemala there was a mass political asylum. The Argentine government received about two hundred people, including leading figures of the Guatemalan Labor Party. However, a few days after arriving in the country, a group of over thirty Guatemalans were arrested and imprisoned in the prison of Villa Devoto. The article seeks to address three dimensions, from the perspective of historical sociology, which allow to account for the conditions of possibility of this event: ideology, law and foreign policy of the government of Juan Domingo Perón. The work will allow us to explore the complexity and ambiguity that characterized the classical populism in Latin America and will be an excuse to relocate the fifties, usually overshadowed by the sixties and seventies, as critical juncture to explain the historical conditions of the political violence in Latin America.</p>
Unexpected toxicity to aquatic organisms of some aqueous bisphenol A samples treated by advanced oxidation processes
Authors: Tišler Tatjana , Erjavec Boštjan , Kaplan Renata , Şenilă Marin , Pintar Albin 
Published: June 2015

Abstract
In this study, photocatalytic and catalytic wet-air oxidation (CWAO) processes were used to examine removal efficiency of bisphenol A from aqueous samples over several titanate nanotube-based catalysts. Unexpected toxicity of bisphenol A (BPA) samples treated by means of the CWAO process to some tested species was determined. In addition, the CWAO effluent was recycled five- or 10-fold in order to increase the number of interactions between the liquid phase and catalyst. Consequently, the inductively coupled plasma mass spectrometry (ICP-MS) analysis indicated higher concentrations of some toxic metals like chromium, nickel, molybdenum, silver, and zinc in the recycled samples in comparison to both the single-pass sample and the photocatalytically treated solution. The highest toxicity of five- and 10-fold recycled solutions in the CWAO process was observed in water fleas, which could be correlated to high concentrations of chromium, nickel, and silver detected in tested samples. The obtained results clearly demonstrated that aqueous samples treated by means of advanced oxidation processes should always be analyzed using (i) chemical analyses to assess removal of BPA and total organic carbon from treated aqueous samples, as well as (ii) a battery of aquatic organisms from different taxonomic groups to determine possible toxicity.
Long-term effects of engineered nanoparticles on enzyme activity and functional bacteria in wastewater treatment plants
Authors: Zheng Xiong , Huang Haining , Su Yinglong , Wei Yuanyuan , Chen Yinguang 
Published: June 2015

AbstractThe pervasive use of engineered nanoparticles (NPs) in a wide range of fields raises concerns about their potential environmental impacts. Previous studies confirmed that some NPs had already entered wastewater treatment plants (WWTPs). Wastewater nutrient removal depends on the metabolisms of activated sludge bacteria and their related key enzymes. Therefore, this study compared the possible influences of Al2O3, SiO2, TiO2, and ZnO NPs on the key enzymes activities and microbial community structures involved in wastewater treatment facilities. It was found that long-term exposure to these NPs significantly affected the microbial communities and changed the relative abundances of key functional bacteria, such as ammonia-oxidizing bacteria. Also, the gene expressions and catalytic activities of essential enzymes, such as ammonia monooxygenase, nitrite oxidoreductase, nitrate reductase, and nitrite reductase, were decreased, which finally resulted in a lower efficiency of biological nitrogen removal.
Presence and persistence of wastewater pathogen Escherichia coli O157:H7 in hydroponic reactors of treatment wetland species
Authors: VanKempen-Fryling R. J. , Stein O. R. , Camper A. K. 
Published: June 2015

Abstract
Treatment wetlands (TWs) efficiently remove many pollutants including a several log order reduction of pathogens from influent to effluent; however, there is evidence to suggest that pathogen cells are sequestered in a subsurface wetland and may remain viable months after inoculation. Escherichia coli is a common pathogen in domestic and agricultural wastewater and the O157:H7 strain causes most environmental outbreaks in the United States. To assess attachment of E. coli to the TW rhizosphere, direct measurements of E. coli levels were taken. Experiments were performed in chemostats containing either Teflon nylon as an abiotic control or roots of Carex utriculata or Schoenoplectus acutus. Flow of simulated wastewater through the chemostat was set to maintain a 2 hour residence time. The influent was inoculated with E. coli O157:H7 containing DsRed fluorescent protein. Root samples were excised and analyzed via epifluorescent microscopy. E. coli O157:H7 was detected on the root surface at 2 hours after inoculation, and were visible as single cells. Microcolonies began forming at 24 hours post-inoculation and were detected for up to 1 week post-inoculation. Image analysis determined that the number of microcolonies with &gt;100 cells increased 1 week post-inoculation, confirming that E. coli O157:H7 is capable of growth within biofilms surrounding wetland plant roots.
Improved data evaluation methodology for energy ranges with missing experimental data
Authors: Konobeyev A. Yu. , Fischer U. , Capote R. 
Published: June 2015

Abstract
A number of improvements of the data evaluation concerning nuclear model calculations and evaluation procedures are considered. A promising combination of the hybrid Monte Carlo simulation model of M. Blann for the modelling of non-equilibrium particle emission and the Hauser-Feshbach model, and a possible correction of simulations using intranuclear cascade evaporation model are discussed. In the last case the modelling of particle emission is improved by the consideration of nucleon-cluster interactions. The approach for reliable predictions of cross-sections using “optimal” nuclear model parameters and the method of their generation is discussed.
The Perceptual Dimensions of Sonority-Driven Epenthesis
Authors: Fullwood Michelle Alison 
Published: June 2015

<p>Vowel epenthesis often appears to preferentially target consonant clusters with rising sonority. One explanation for this is perceptual faithfulness (Fleischhacker, 2002; Steriade, 2006): rising sonority clusters are more susceptible to epenthesis because the perceptual distance between the underlying /C1-C2/ sequence and its correspondent output sequence [C1-V-C2] is small, thus incurring a smaller faithfulness cost. This raises the question of how to compute the perceptual distance between two sonority contours /C1-C2/ and [C1-V-C2] in terms of the sonority of C1, C2 and V. In this paper, I propose the metric Sonority Angle, the angle formed by the contours /C1-C2/ and [C1-V]. I apply it in analysing two case studies of sonority-driven epenthesis, Chaha and Irish. A comparison is made to another possible metric, Sonority Rise (Flemming, 2008), the ratio of the gradients of the two contours, as well as to Syllable Contact and Sonority Sequencing, which represent an alternative, markedness-based approach to the problem of sonority-driven epenthesis.</p>
Vowel Epenthesis and Consonant Deletion in Japanese Loanwords from English
Authors: Shoji Shinichi , Shoji Kazuko 
Published: June 2015

<p>The current study examines Japanese loanwords from English in the framework of optimality theory (OT). The goal of this study is to investigate which vowels native Japanese-speaking borrowers epenthesize and when they delete consonants in modifying English source words. We aim to offer (i) a unified explanation with a single ranking of constraints for vowel epenthesis and (ii) a perceptual explanation for consonant deletion. Two experiments with native Japanese speakers were conducted to support the proposed analyses. The first experiment demonstrated that, when modifying illicit phonotactics in foreign words, native Japanese speakers select epenthetic vowels based on the constraint ranking of: Complex, CodaCond &gt;&gt; Max-IO &gt;&gt; Palatal-Front, SyllableInventoryStructure (SIS), Ident-IO &gt;&gt; *Round, *Low &gt;&gt; *Front &gt;&gt; High &gt;&gt; Back &gt;&gt; Dep-IO. The second experiment revealed that Japanese loanwords can be subject to deletion of consonants rather than vowel epenthesis, due to the lack of perceptual salience; Japanese speakers delete consonants when they fail to perceive consonants in coda and clusters in source words, especially when the source words are aurally given.</p>
Idiosyncratically Transparent Vowels in Kazakh
Authors: Bowman Samuel R. , Lokshin Benjamin 
Published: June 2015

<p>Idiosyncratically transparent vowels—those that fail to either undergo or trigger harmony in a particular morpheme but do both elsewhere—have not been documented in any language, and have been claimed to be impossible as recently as Mahanta (2012). We present two affixes in Kazakh that contain idiosyncratic vowels, and present evidence from wordlist elicitations and phonetic studies with two native speakers from different regions. We discuss the implications of these findings for constraint-based theories of vowel harmony: we show that they cannot be readily analyzed in conventional strictly-local harmony system, and present analyses in two recent systems that allow for non-local representations. Both Rhodes's (2010) system for vowel harmony in Agreement by Correspondence and Kimper's (2011) Trigger Competition can be made to accommodate lexical specifications that force vowels in particular morphemes to act as transparent, and we show that implementing these lexical specifications in Trigger Competition forces us to make somewhat stronger predictions about the rarity of idiosyncratic transparency. </p>
Distinctive Features and the Liquids in Picard
Authors: Hendrickson Ryan 
Published: June 2015

<p>The class of liquid consonants, which traditionally groups laterals and rhotics, is called into question due to a lack of shared phonological feature with a phonetic correlate. Following recent work on the liquid consonants, this paper examines these consonants in Picard, a Gallo-Romance variety spoken in Northern France and Southern Belgium. The behavior of these consonants is analyzed both word-initially in liquid-glide clusters where we observe resyllabification, epenthesis, and sometimes deletion, as well as in word-final complex clusters. We find that the lateral consonant is more prone to deletion next to coronal consonants in both positions, leading to the analysis that the lateral is phonologically specified as [coronal], whereas the rhotic, which is phonetically coronal in Picard, is unspecified for place in the phonology.</p>
Two scrambling strategies in German: Evidence from PPs
Authors: Kucerova Ivona 
Published: June 2015

<div class="page" title="Page 1"><div class="layoutArea"><div class="column"><p><span>We argue that scrambling to the middle field in German does not form a syntactically homogeneous class. Instead, there are two distinct types of movement involved: (i) feature-triggered movement typically targeting the left periphery (Rizzi, 1997; Miyagawa, 1997, a.o.), i.e., movement which is determined within syntax proper; and (ii) semantically licensed, and competition based type of movement (Reinhart, 1995, 2006; Fox, 2000; Kucerová, 2007, 2012), determined at the syntax- semantics interface. The empirical evidence comes from scrambling of definite PPs in German. </span></p></div></div></div>
The Strict Locality of Phonological Processes
Authors: Chandlee Jane 
Published: June 2015

<p>This paper addresses the question of ‘what is a possible phonological <span>process’ from a computational perspective. Many previous studies have offered explanations </span>for why certain processes are attested and/or common while others are unattested or rare <span>(see Hume &amp; Johnson 2001, Hayes et al. 2004, Blevins 2004, among others). Following work on phonotactics by Heinz (2007, 2009, 2010), the goal of the present study is to demonstrate </span>the extent to which computational properties can distinguish the subset of what is phonologically possible from the larger set of logically possible processes. <span>Specifically, I identify a strong computational property of the mapping from underlying </span>representation (UR) to surface representation (SR) in local phonological processes. This property is called Input Strict Locality (ISL) after the well-studied Strictly Local formal languages (McNaughton &amp; Papert 1971, Rogers &amp; Pullum 2011, Rogers et al. 2013). I demonstrate <span>that this property has broad empirical coverage and describe its </span>utility in phonological learning.</p>
The prosody of negative ‘yeah’
Authors: Freeman Valerie , Wright Richard , Levow Gina-Anne 
Published: June 2015

<p>Normally, <em>yeah</em> has positive polarity, but with a change in prosody, it can convey a negative stance (e.g., polite disagreement/rejection). This study examines acoustic-prosodic features of ‘negative yeahs’ in a stance-rich corpus of collaborative tasks. Four categories are identified based on degree of agreement/acceptance and distinguished by an interaction between pitch and intensity: while two groups have low, flat pitch, and two have high domed or dipping contours, this division is cross-cut by intensity, again low-flat vs. high domed. These patterns show that fine-grained stance analysis can reveal word-level acoustic patterns that are not apparent in coarser approaches. </p>