bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transposome: a toolkit for annotation of transposable element families from unassembled sequence reads
Authors: Staton S. Evan , Burke John M. 
Published: February 2015

Abstract
Motivation: Transposable elements (TEs) can be found in virtually all eukaryotic genomes and have the potential to produce evolutionary novelty. Despite the broad taxonomic distribution of TEs, the evolutionary history of these sequences is largely unknown for many taxa due to a lack of genomic resources and identification methods. Given that most TE annotation methods are designed to work on genome assemblies, we sought to develop a method to provide a fine-grained classification of TEs from DNA sequence reads. Here, we present a toolkit for the efficient annotation of TE families from low-coverage whole-genome shotgun (WGS) data, enabling the rapid identification of TEs in a large number of taxa. We compared our software, Transposome, with other approaches for annotating repeats from WGS data, and we show that it offers significant improvements in run time and produces more precise estimates of genomic repeat abundance. Transposome may also be used as a general toolkit for working with Next Generation Sequencing (NGS) data, and for constructing custom genome analysis pipelines.
Availability and implementation: The source code for Transposome is freely available ( http://sestaton.github.io/Transposome ), implemented in Perl and is supported on Linux.
Contact: statonse@biodiversity.ubc.ca
Supplementary information: Supplementary data are available at Bioinformatics online.
Expitope: a web server for epitope expression
Authors: Haase Kerstin , Raffegerst Silke , Schendel Dolores J. , Frishman Dmitrij 
Published: February 2015

Abstract
Motivation: Adoptive T cell therapies based on introduction of new T cell receptors (TCRs) into patient recipient T cells is a promising new treatment for various kinds of cancers. A major challenge, however, is the choice of target antigens. If an engineered TCR can cross-react with self-antigens in healthy tissue, the side-effects can be devastating. We present the first web server for assessing epitope sharing when designing new potential lead targets. We enable the users to find all known proteins containing their peptide of interest. The web server returns not only exact matches, but also approximate ones, allowing a number of mismatches of the users choice. For the identified candidate proteins the expression values in various healthy tissues, representing all vital human organs, are extracted from RNA Sequencing (RNA-Seq) data as well as from some cancer tissues as control. All results are returned to the user sorted by a score, which is calculated using well-established methods and tools for immunological predictions. It depends on the probability that the epitope is created by proteasomal cleavage and its affinities to the transporter associated with antigen processing and the major histocompatibility complex class I alleles. With this framework, we hope to provide a helpful tool to exclude potential cross-reactivity in the early stage of TCR selection for use in design of adoptive T cell immunotherapy.
Availability and implementation: The Expitope web server can be accessed via http://webclu.bio.wzw.tum.de/expitope .
Contact: d.frishman@wzw.tum.de
CNOGpro: detection and quantification of CNVs in prokaryotic whole-genome sequencing data
Authors: Brynildsrud Ola , Snipen Lars-Gustav , Bohlin Jon 
Published: February 2015

Abstract
Motivation: The explosion of whole-genome sequencing (WGS) as a tool in the mapping and understanding of genomes has been accompanied by an equally massive report of tools and pipelines for the analysis of DNA copy number variation (CNV). Most currently available tools are designed specifically for human genomes, with comparatively little literature devoted to CNVs in prokaryotic organisms. However, there are several idiosyncrasies in prokaryotic WGS data. This work proposes a step-by-step approach for detection and quantification of copy number variants specifically aimed at prokaryotes.
Results: After aligning WGS reads to a reference genome, we count the individual reads in a sliding window and normalize these counts for bias introduced by differences in GC content. We then investigate the coverage in two fundamentally different ways: (i) Employing a Hidden Markov Model and (ii) by repeated sampling with replacement (bootstrapping) on each individual gene. The latter bypasses the complex problem of breakpoint determination. To demonstrate our method, we apply it to real and simulated WGS data and benchmark it against two popular methods for CNV detection. The proposed methodology will in some cases represent a significant jump in accuracy from other current methods.
Availability and implementation: CNOGpro is written entirely in the R programming language and is available from the CRAN repository ( http://cran.r-project.org ) under the GNU General Public License.
Contact : ola.brynildsrud@nmbu.no
Supplementary information: Supplementary data are available at Bioinformatics online.
Human placenta: relative content of antibodies of different classes and subclasses (IgG1–IgG4) containing lambda- and kappa-light chains and chimeric lambda-kappa-immunoglobulins
Authors: Lekchnov Evgenii A. , Sedykh Sergey E. , Dmitrenok Pavel S. , Buneva Valentina N. , Nevinsky Georgy A. 
Published: February 2015

Abstract
The specific organ placenta is much more than a filter: it is an organ that protects, feeds and regulates the growth of the embryo. Affinity chromatography, ELISA, SDS–PAGE and matrix-assisted laser desorption ionization mass spectrometry were used. Using 10 intact human placentas deprived of blood, a quantitative analysis of average relative content [% of total immunoglobulins (Igs)] was carried out for the first time: (92.7), IgA (2.4), IgM (2.5), kappa-antibodies (51.4), lambda-antibodies (48.6), IgG1 (47.0), IgG2 (39.5), IgG3 (8.8) and IgG4 (4.3). It was shown for the first time that placenta contains sIgA (2.5%). In the classic paradigm, Igs represent products of clonal B-cell populations, each producing antibodies recognizing a single antigen. There is a common belief that IgGs in mammalian biological fluids are monovalent molecules having stable structures and two identical antigen-binding sites. However, similarly to human milk Igs, placenta antibodies undergo extensive half-molecule exchange and the IgG pool consists of 43.5±15.0% kappa-kappa-IgGs and 41.6±17.0% lambda-lambda-IgGs, while 15.0±4.0% of the IgGs contained both kappa- and lambda-light chains. Kappa-kappa-IgGs and lambda-lambda-IgGs contained, respectively (%): IgG1 (47.7 and 34.4), IgG2 (36.3 and 44.5), IgG3 (7.4 and 11.8) and IgG4 (7.5 and 9.1), while chimeric kappa-lambda-IgGs consisted of (%): 43.5 IgG1, 41.0 IgG2, 5.6 IgG3 and 7.9 IgG4. Our data are indicative of the possibility of half-molecule exchange between placenta IgGs of various subclasses, raised against different antigens, which explains a very well-known polyspecificity and cross-reactivity of different human IgGs.
β-Lactam combinations with daptomycin provide synergy against vancomycin-resistant Enterococcus faecalis and Enterococcus faecium
Authors: Smith Jordan R. , Barber Katie E. , Raut Animesh , Aboutaleb Mostafa , Sakoulas George , Rybak Michael J. 
Published: February 2015

Abstract

Objectives
Enterococcus faecalis (Efc) and Enterococcus faecium (Efm) are frequently resistant to vancomycin and β-lactams (BLs). In vitro data suggest synergy between several BLs and glycopeptides or lipopeptides against resistant pathogens. Our objective was to conduct combination MIC and time–kill experiments to evaluate BL synergy with daptomycin against enterococci.

Methods
Fifteen Efc and 20 Efm strains were evaluated for daptomycin enhancement via combination MICs. Daptomycin MICs were obtained by microdilution in the absence and presence of ceftaroline, ertapenem, cefepime, ceftriaxone, cefotaxime, cefazolin and ampicillin. Two Efc strains (R6981 and R7808) and one isogenic daptomycin-susceptible/daptomycin-non-susceptible Efm pair (8019/5938) were evaluated in time–kill experiments. Daptomycin at 0.5 × MIC was used in combination with BL at biological free concentration. Strain 5938 was evaluated for enhancement of daptomycin binding in fluorescently labelled daptomycin (BoDipy) experiments.

Results
Ceftaroline reduced daptomycin MIC values the most against all strains. In time–kill experiments, ceftaroline, ertapenem, cefepime, ceftriaxone and ampicillin demonstrated synergy with daptomycin against all strains, cefazolin demonstrated none and cefotaxime demonstrated synergy against only R7808. Bacterial reduction at 24 h was greater for daptomycin + ceftaroline, ertapenem, cefepime, ceftriaxone or ampicillin for all strains compared with any single agent or daptomycin + cefazolin or cefotaxime (P &lt; 0.001). In BoDipy daptomycin experiments, ceftaroline enhanced daptomycin binding most compared with all other agents (P &lt; 0.001).

Conclusions
The data support the potential use of daptomycin/BL combination therapy in infections caused by VRE. Combination regimens, other than those involving cefazolin and cefotaxime, provide better kill compared with daptomycin alone. Further clinical research involving daptomycin combinations is warranted.
Romanian Cinema
Authors: Parvulescu Constantin 
Published: February 2015

Until the second decade of the 21st century, scholarship on Romanian film has been written almost exclusively in Romanian. Its pioneering representatives were D. I. Suchianu and Ion Cantacuzino, who published their first books in the 1930s. Since Romania had not generated consistent cinematic output until the 1950s, its historical studies came out also late, in the 1960s. The year 1989 was another turning point in Romanian film historiography, spurring post-socialist reconsiderations, and so was 1996, when the celebration of one hundred years of Romanian cinema triggered the publication of several historical studies. Consistent international representation started in the late 2000s, prompted by the international visibility of the New Romanian Cinema (also known as the Romanian New Wave). Since then, English-language film magazines delivered reviews of every new Romanian production, and academic scholarship started to yield its first articles. Soon, interest in Romanian film traditions also surged (both in Romania and abroad), coupled with a concentrated effort of the Romanian state to promote its cinema, both new and old. Romanian film is still approached mainly in the framework of national cinema, but recent studies tend to broaden the perspective and employ comparative, transnational, intermedial, and media-theory perspectives.
Américo Paredes
Authors: García Derek Xavier , Stavans Ilan 
Published: February 2015

Américo Paredes (b. 1915–d. 1999) was considered to be one of the foremost Mexican-American scholars of the twentieth century. Having influenced an entire generation of Chicano scholars—such as José E. Limón, David Montejano, and Ramón Saldívar—he is one of the forerunners of Chicano studies. A self-described “proto-Chicano,” he was born in Brownsville, Texas in the Rio Grande Valley. Fascinated with the border tales and ballads of his youth, Paredes soon began to write poetry. During the Great Depression, he worked as a writer for a local newspaper. In 1944, he enlisted in the US Army and was stationed in Japan as a journalist for Stars and Stripes and the Mexican newspaper El Universal. After he was discharged, he served with the American Red Cross and traveled across Asia. When he returned from Japan, Paredes enrolled at the University of Texas at Austin where he acquired his doctorate degree at the age of forty-one. In 1957, he began to teach at the University of Texas at Austin. The next year, his doctoral dissertation, With His Pistol in His Hand: A Border Ballad and its Hero, was published. An analysis of a popular corrido, the book expands several genres, presenting a folkloric, ethnographic, and sociocultural study of South Texas Mexicans. During his time at the University of Texas, Paredes was instrumental in furthering scholarship in folklore and Mexican-American studies. He successfully founded the Center for Intercultural Studies for Folklore and Musicology in 1967 and cofounded the Center for Mexican American Studies in 1970. He continued to publish studies on border folklore, such as A Texas-Mexican Cancionero: Folksongs of the Lower Border in 1976, and Folklore and Culture of the Texas-Mexican Border in 1992. He received numerous accolades during his lifetime, including a Guggenheim Fellowship in 1962 and the Charles Frankel Prize from the National Endowment for the Humanities in 1989. A year later, he was awarded the Orden del Aguila Azteca from the Mexican government, the highest honor afforded to foreign citizens. In 1991, he received the Orden de José de Escandón. In his later life, Paredes began to publish the Creative Works he originally wrote during his adolescence and time abroad. Some of these include George Washington Gómez (1990) and The Hammon and the Beans (1994). Paredes’s works concerning border life have become the focal point for numerous scholars wanting to research folklore and the Mexican-American experience.
Shanghai
Authors: Horesh Niv , Sullivan Jonathan 
Published: February 2015

Not long after its establishment as a treaty port in 1842, and roughly until the Japanese invasion of China proper in 1937, Shanghai maintained a reputation as one of Asia’s most spellbinding, entrepreneurial, and freewheeling cities. It had served as the mainland China’s commercial, industrial, and cultural hub during that period, and since 1991, it has indisputably re-emerged as China’s second most important city after the capital, Beijing. Yet, although first mentioned by name in Chinese records dating back to the 12th century, Shanghai was not among the 10 most populous cities on the mainland on the eve of Western settlement in 1842. Perched advantageously 15 km downstream from the confluence of the Huangpu River, the Yangtze River (Changjiang), and the East China Sea, Shanghai’s Chinese population numbered around two hundred thousand inhabitants in 1842, most of whom resided within the ancient city walls. By the 1930s, the city’s population exceeded three million, with new neighborhoods sprawling far beyond the historic walled area west of the Huangpu River. Today, the Shanghai Municipality (6,340 sq km) is one of four self-governing urban areas not affiliated with any other province. The city’s perimeters are thus much wider than was the case before 1949, including jurisdiction over fifteen districts, one county, and several offshore islands. Over twenty-three million people now reside in Shanghai, making it the most populous city in China, and one of the largest in the world. Shanghai’s newly built port, sprawling tens of kilometers along the East China Sea, is the busiest in the world, and the skyscrapers in the Pudong district have come to symbolize China’s re-established economic power. Interest in the city’s pre-war legacy has increased in recent years as a result of China’s rapid economic reforms and the opening up of its archives to foreign scholars. Western academics have begun engaging with these newly declassified materials in ways that often reshape our understanding of Chinese modern history. Yet the development path that makes Shanghai so vital to what may be loosely defined as “Chinese modernity,” has not yet been agreed on. One of many testaments to Shanghai’s enduring appeal, is the 2006 CBC television documentary Legendary Cities of Sin, in which Shanghai is portrayed as a megalopolis on par with Paris and Berlin between the two world wars. Shanghai’s mystique is even more potent in the realm of cinema, with scores of Hollywood and Chinese productions set in the pre-Communist era—Ang Lee’s acclaimed feature film Lust, Caution (2007) is an obvious example. Shanghai is also the city where past and present are most studied and written about by China specialists. The body of scholarly literature on post-1842 Shanghai is particularly abundant.
Transient Receptor Potential A1 Activation Prolongs Isoflurane Induction Latency and Impairs Respiratory Function in Mice
Authors: Li Fengxian , Guo Changxiong J. , Huang Cheng-Chiu , Yu Guang , Brown Sarah M. , Xu Shiyuan , Liu Qin 
Published: February 2015

AbstractAbstract
Mice not expressing Transient Receptor Potential A1 (TRPA1) had faster onset of isoflurane anesthesia than wild-type or TRPV1-deficient mice, whereas sevoflurane onset was independent of genotype. Onset of the pungent anesthetic isoflurane is delayed due to activation of TRPA1 receptor–mediated nocifensive reflexes that reduce ventilation, pulmonary compliance, and anesthetic uptake.

Background:
Isoflurane is a potent volatile anesthetic; however, it evokes airway irritation and neurogenic constriction through transient receptor potential (TRP) A1 channels and sensitizes TRPV1 channels, which colocalizes with TRPA1 in most of the vagal C-fibers innervating the airway. However, little is known about the precise effects of these two channels on the respiratory function during isoflurane anesthesia.

Methods:
By using a rodent behavioral model and whole-body plethysmograph, the authors examined the response of Trpa1

−/−
and Trpv1

−/−
mice to isoflurane anesthesia and monitored their respiratory functions during anesthesia.

Results:
This study showed that Trpa1

−/−
mice (n = 9), but not Trpv1

−/−
mice (n = 11), displayed a shortened induction latency compared with wild-type mice (n = 10) during isoflurane anesthesia (33 ± 2.0 s in wild-type and 33 ± 3.8 s in Trpv1

−/−

vs. 17 ± 1.8 in Trpa1

−/−
at 2.2 minimum alveolar concentrations). By contrast, their response to the nonpungent volatile anesthetic sevoflurane is indistinguishable from wild-type mice (24 ± 3.6 s in wild-type vs. 26 ± 1.0 s in Trpa1

−/−
at 2.4 minimum alveolar concentrations). The authors discovered that Trpa1

−/−
mice inhaled more anesthetic but maintained better respiratory function. Further respiration pattern analysis revealed that isoflurane triggered nociceptive reflexes and led to prolonged resting time between breaths during isoflurane induction as well as decreased dynamic pulmonary compliance, an indicator of airway constriction, throughout isoflurane anesthesia in wild-type and Trpv1

−/−
mice, but not in Trpa1

−/−
mice.

Conclusion:
Activation of TRPA1 by isoflurane negatively affects anesthetic induction latency by altering respiratory patterns and impairing pulmonary compliance.
The Efficacy of Epidermal Growth Factor Receptor Tyrosine Kinase Inhibitors in Non–Small Cell Lung Cancer Harboring Wild-type Epidermal Growth Factor Receptor
Authors: Sheng Zhixin , Zhang Yanxia 
Published: February 2015

Objective:
To determine the efficacy of first-generation epidermal growth factor receptor tyrosine kinase inhibitors (EGFR-TKIs) in advanced non–small cell lung cancer (NSCLC) patients with wild-type (WT) EGFR tumors, we performed an indirect meta-analysis to assess the treatment effects of EGFR-TKIs in such patients.

Methods:
We searched for randomized controlled trials in Medline, Embase, the Cochrane controlled trials register, the Science Citation Index, and the American Society of Clinical Oncology annual meetings. Effect measures used were hazard ratios (HR) for progression-free survival (PFS) and overall survival.

Results:
Out of 2134 retrieved articles, 25 randomized controlled trials including more than 4467 patients were identified. This pooled analysis showed the inferior efficacy of TKI over chemotherapy among patients with WT EGFR NSCLC in terms of PFS (HR, 1.37; 95% confidence interval [CI]: 1.10, 1.72; P=0.006). When used as first-line treatment, TKIs have also fared worse than chemotherapy when compared with standard platinum doublet regimens in patients with WT EGFR in terms of PFS (HR, 2.15; 95% CI: 1.68, 2.76; P<0.001). And, the same inferior trend was found with TKIs in those trials of second-line/third-line treatment in terms of PFS (HR, 1.35; 95% CI: 1.13, 1.61; P<0.001). However, according to the pooled results, EGFR-TKIs still produced a reduction of 19% in the risk of progression over placebo in such WT EGFR patients ineligible for further chemotherapy (HR, 0.81; 95% CI: 0.68, 0.97; P=0.02). Furthermore, addition of EGFR-TKI to chemotherapy resulted in an improvement of PFS over chemotherapy alone (HR, 0.83; 95% CI: 0.71, 0.96; P=0.01).

Conclusions:
Among patients with advanced NSCLC harboring WT EGFR, EGFR-TKIs were inferior to standard chemotherapy both for first-line treatment and for second-line/third-line treatment, but still superior to placebo in patients unfit for further chemotherapy. And, addition of EGFR-TKIs to chemotherapy could provide additive benefit over chemotherapy alone in such patients.
Apraxia, Autism, Attention-Deficit Hyperactivity Disorder: Do We Have a New Spectrum?
Authors: Schumacher Jayna , Strand Kristine E. , Augustyn Marilyn 
Published: February 2015

CASE: Gio is a bilingual 6-year 10-month-old boy new to your practice who presents for an unscheduled visit with concerns for speech and language delay. He was born in Portugal, and his native language is Portuguese. When he was 21 months old, his family moved to Italy and then moved to the United States 3 years later. He had very little contact with other children while living in Italy, but his parents report that he has made friends quickly in the United States. His family speaks Portuguese at home, although his father is fluent in English.
He started school 3 months after moving to the United States and is currently repeating kindergarten. He is in a sheltered English classroom with several other students who speak Portuguese. He is able to understand and follow directions in English. A recent school evaluation revealed solidly average nonverbal reasoning skills and relative weaknesses in verbal reasoning and working memory. His speech is described as unintelligible in conversation, both in English and Portuguese.
Results of a special education evaluation qualified him for services with a bilingual therapist. His teachers are very concerned that he may have autism spectrum disorder (ASD) and attention-deficit hyperactivity disorder (ADHD). They describe him as having limited interest in other children, poor eye contact, and hypersensitivities. He wanders at recess. He is very skilled at art and seems to prefer to draw rather than interact with others. He needs constant support and redirection throughout the school day. He has difficulty putting on his coat, using playground equipment, and following daily classroom routines. On the Vanderbilt Rating Scale, his teacher endorses 17 of 18 ADHD symptoms as present often or very often and significant impairment in his performance.
Gio presents to your clinic as a relatable young boy with childhood apraxia of speech. Only his productions of single words and short routine phrases are intelligible. He attempts to engage in conversation but averts his gaze and becomes frustrated when asked to repeat things. Scores on the Parent Conners Rating Scale and Social Responsiveness Scale are not elevated. When you bring up school's concerns, his father describes feeling somewhat badgered by his teachers about possibility of ASD.
School is considering placement in an inclusion classroom for children with ASD. What do you recommend? How would you advise his parents?