bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chromosome instability induced by Mps1 and p53 mutation generates aggressive lymphomas exhibiting aneuploidy-induced stress
Authors: Foijer Floris , Xie Stephanie Z. , Simon Judith E. , Bakker Petra L. , Conte Nathalie , Davis Stephanie H. , Kregel Eva , Jonkers Jos , Bradley Allan , Sorger Peter K. 
Published: September 2014

Significance
Normal cells rarely missegregate chromosomes, but the majority of cancer cells have a chromosomal instability (CIN) phenotype that makes errors more common and results in abnormal chromosomal content (aneuploidy). Although aneuploidy promotes transformation via gain of oncogenes and loss of tumor suppressors, it also slows cell proliferation and disrupts metabolic homeostasis. Aneuploidy therefore represents a liability as well as a source of selective advantage for cancer cells. We provoked CIN in murine T cells by weakening the spindle-assembly checkpoint and then studied the consequences. We found that CIN dramatically accelerates cancer in a genetically predisposed background and that the resulting aneuploid cancers are metabolically deranged, a vulnerability that may open new avenues to treating aneuploid cancers.
Genetic variants of ApoE and ApoER2 differentially modulate endothelial function
Authors: Ulrich Victoria , Konaniah Eddy S. , Herz Joachim , Gerard Robert D. , Jung Eunjeong , Yuhanna Ivan S. , Ahmed Mohamed , Hui David Y. , Mineo Chieko , Shaul Philip W. 
Published: September 2014

Significance
Why genetic variants of the circulating protein apolipoprotein E (apoE) or its receptor apoliprotein E receptor 2 (ApoER2) confer greater cardiovascular disease risk is poorly understood. We report that in endothelial cells, which are the guardian cells of the vascular wall, the most common form of apoE, apoE3, activates ApoER2 to favorably impact endothelial function. The risk-enhancing apoE variant apoE4 lacks this capacity and instead inhibits apoE3–ApoER2 action, and a risk-conferring ApoER2 variant is nonfunctional in endothelium. Evidence is obtained in mice that the genetic variants adversely impact endothelial repair and related vascular disease severity. From these discoveries personalized treatment strategies may be developed to protect individuals with risk-altering apoE or ApoER2 variants, which comprise approximately 15% of the population.
Translation initiation factor eIF4F modifies the dexamethasone response in multiple myeloma
Authors: Robert Francis , Roman William , Bramoullé Alexandre , Fellmann Christof , Roulston Anne , Shustik Chaim , Porco John A. , Shore Gordon C. , Sebag Michael , Pelletier Jerry 
Published: September 2014

Significance
Multiple myeloma (MM) is a cancer that develops in the bone marrow and remains incurable to this day. It is a cancer type that shows hallmarks of deregulated protein synthesis control. To uncover new vulnerabilities in this disease, we performed a focused RNAi screen to identify components of the translation apparatus that, when depleted, would sensitize tumor cells to dexamethasone (DEX), a component of frontline therapy in this cancer. We found that suppression of eukaryotic initiation factor 4F, a heterotrimeric complex required for cap-dependent translation initiation, is a modifier of the DEX response in MM. Our efforts uncover a previously unidentified vulnerability in MM that should be explored clinically.
Mixtures of opposing phosphorylations within hexamers precisely time feedback in the cyanobacterial circadian clock
Authors: Lin Jenny , Chew Justin , Chockanathan Udaysankar , Rust Michael J. 
Published: September 2014

Significance
Many organisms possess biological clocks that schedule their behavior throughout the day. To function properly, these clocks must maintain a period near 24 hours despite fluctuations in conditions. In a simple three-protein oscillator from cyanobacteria, timing information is stored in KaiC, a phosphorylated protein which forms hexameric rings. We show that the feedback loop that allows oscillation depends cooperatively on phosphorylation throughout the KaiC hexamer. Two phosphorylation sites with different kinetics have opposing effects, and this creates a sharp transition between the day and night states of the ring. This mechanism, based on opposing modifications, generates circadian rhythms across the relevant range of protein stochiometries and may be used generally in biochemical networks for precise timing.
Human oxygen sensing may have origins in prokaryotic elongation factor Tu prolyl-hydroxylation
Authors: Scotti John S. , Leung Ivanhoe K. H. , Ge Wei , Bentley Michael A. , Paps Jordi , Kramer Holger B. , Lee Joongoo , Aik WeiShen , Choi Hwanho , Paulsen Steinar M. , Bowman Lesley A. H. , Loik Nikita D. , Horita Shoichiro , Ho Chia-hua , Kershaw Nadia J. , Tang Christoph M. , Claridge Timothy D. W. , Preston Gail M. , McDonough Michael A. , Schofield Christopher J. 
Published: September 2014

SignificanceThe Fe(II)- and 2-oxoglutarate (2OG)-dependent hypoxia-inducible transcription factor prolyl-hydroxylases play a central role in human oxygen sensing and are related to other prolyl-hydroxylases involved in eukaryotic collagen biosynthesis and ribosomal modification. The finding that a PHD-related prolyl-hydroxylase inPseudomonas spp.regulates pyocyanin biosynthesis supports prokaryotic origins for the eukaryotic prolyl-hydroxylases. The identification of the switch I loop of elongation factor Tu (EF-Tu) as aPseudomonasprolyl-hydroxylase domain containing protein (PPHD) substrate provides evidence of roles for 2OG oxygenases in both translational and transcriptional regulation. A structure of the PPHD:EF-Tu complex, the first to the authors' knowledge of a 2OG oxygenase with its intact protein substrate, reveals that major conformational changes occur in both PPHD and EF-Tu and will be useful in the design of new prolyl-hydroxylase inhibitors.
Optogenetic activation of septal cholinergic neurons suppresses sharp wave ripples and enhances theta oscillations in the hippocampus
Authors: Vandecasteele Marie , Varga Viktor , Berényi Antal , Papp Edit , Barthó Péter , Venance Laurent , Freund Tamás F. , Buzsáki György 
Published: September 2014

Significance
Theta oscillations are a prominent rhythm of the brain occurring during active behavior and rapid eye movement sleep and thought to provide the temporal frame for the encoding of information. Acetylcholine modulation is a major player in hippocampal theta rhythm, as demonstrated by lesion and pharmacological manipulations of cholinergic receptors, yet the link between the activity of septal cholinergic neurons and the theta rhythm is not fully understood. We used specific optogenetic stimulation of the septo-hippocampal cholinergic neurons in the anesthetized and behaving mouse to decipher the effects of cholinergic stimulation on hippocampal network activity and show that in addition to promoting theta oscillations it suppresses sharp wave ripples and peri-theta band activity.
Assembly and molecular order of two-dimensional peptoid nanosheets through the oil–water interface
Authors: Robertson Ellen J. , Olivier Gloria K. , Qian Menglu , Proulx Caroline , Zuckermann Ronald N. , Richmond Geraldine L. 
Published: September 2014

Significance
Peptoid nanosheets are an emerging class of 2D nanomaterials that have the potential for use in a variety of applications ranging from molecular sensors to artificial enzymes. Because peptoids are highly designable polymers, nanosheets provide a general platform on which to display an enormous diversity of functionalities. Nanosheets are known to form through a unique monolayer compression mechanism, catalyzed by the air–water interface. Here we demonstrate that nanosheets can be formed via adsorption of peptoids at an oil–water interface. Using vibrational sum frequency spectroscopy, we show that electrostatic interactions are essential in the formation of an ordered peptoid monolayer at the interface, a critical intermediate in the nanosheet assembly pathway. These findings open the door for enhancing the complexity and functionality of 2D nanomaterials.
Electronic Recognition of Hand Hygiene Technique and Duration
Authors: Galluzzi Valerie , Herman Ted , Shumaker D. J. , Macinga D. R. , Arbogast J. W. , Segre Elena M. , Segre Alberto M. , Polgreen Philip M. 
Published: September 2014

We captured 3-dimensional accelerometry data from the wrists of 116 healthcare professionals as they performed hand hygiene (HH). We then used these data to train a k-nearest-neighbors classifier to recognize specific aspects of HH technique (ie, fingertip scrub) and measure the duration of HH events.Infect Control Hosp Epidemiol 2014;35(10):1298–1300
Protective Effect of Methicillin-Susceptible Staphylococcus aureus Carriage against Methicillin-Resistant S. aureus Acquisition in Nursing Homes: A Prospective Cross-Sectional Study
Authors: Datta Rupak , Quan Victor , Kim Diane , Peterson Ellena M. , Reynolds Courtney , Meyers Hildy , Cheung Michele , Huang Susan S. 
Published: September 2014

Objective.To evaluate whether an ecologic inverse association exists between methicillin-susceptible Staphylococcus aureus (MSSA) prevalence and methicillin-resistant S. aureus (MRSA) prevalence in nursing homes.Methods.We conducted a secondary analysis of a prospective cross-sectional study of S. aureus prevalence in 26 nursing homes across Orange County, California, from 2008–2011. Admission prevalence was assessed using bilateral nares swabs collected from all new residents within 3 days of admission until 100 swabs were obtained. Point prevalence was assessed from a representative sample of 100 residents. Swab samples were plated on 5% sheep blood agar and Spectra MRSA chromogenic agar. If MRSA was detected, no further tests were performed. If MRSA was not detected, blood agar was evaluated for MSSA growth. We evaluated the association between MRSA and MSSA admission and point prevalence using correlation and linear regression testing.Results.We collected 3,806 total swabs. MRSA and MSSA admission prevalence were not correlated (r = −0.40, P = .09). However, MRSA and MSSA point prevalence were negatively correlated regardless of whether MSSA prevalence was measured among all residents sampled (r = −0.67, P = .0002) or among those who did not harbor MRSA (r = −0.41, P = .04). This effect persisted in regression models adjusted for the percentage of residents with diabetes (β = −0.73, P = .04), skin lesions (β = −1.17, P = .002), or invasive devices (β = −1.4, P = .0006).Conclusions.The inverse association between MRSA and MSSA point prevalence and minimal association on admission prevalence suggest MSSA carriage may protect against MRSA acquisition in nursing homes. The minimal association on admission prevalence further suggests competition may occur during nursing home stays.Infect Control Hosp Epidemiol 2014;35(10):1257–1262
RCSB PDB
Mobile
: iOS and Android mobile apps to provide data access and visualization to the RCSB Protein Data Bank
Authors: Quinn Gregory B. , Bi Chunxiao , Christie Cole H. , Pang Kyle , Prlić Andreas , Nakane Takanori , Zardecki Christine , Voigt Maria , Berman Helen M. , Bourne Philip E. , Rose Peter W. 
Published: September 2014

Abstract
Summary: The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) resource provides tools for query, analysis and visualization of the 3D structures in the PDB archive. As the mobile Web is starting to surpass desktop and laptop usage, scientists and educators are beginning to integrate mobile devices into their research and teaching. In response, we have developed the RCSB PDB Mobile app for the iOS and Android mobile platforms to enable fast and convenient access to RCSB PDB data and services. Using the app, users from the general public to expert researchers can quickly search and visualize biomolecules, and add personal annotations via the RCSB PDB’s integrated MyPDB service.
Availability and implementation: RCSB PDB Mobile is freely available from the Apple App Store and Google Play ( http://www.rcsb.org ).
Contact: pwrose@ucsd.edu
Sports and childhood brain tumors: Can I play?
Authors: Perreault Sébastien , Lober Robert M. , Davis Carissa , Stave Christopher , Partap Sonia , Fisher Paul G. 
Published: September 2014

AbstractBackgroundIt is unknown whether children with brain tumors have a higher risk of complications while participating in sports. We sought to estimate the prevalence of such events by conducting a systematic review of the literature, and we surveyed providers involved with pediatric central nervous system (CNS) tumor patients.MethodsA systematic review of the literature in the PubMed, Scopus, and Cochrane databases was conducted for original articles addressing sport-related complications in the brain-tumor population. An online questionnaire was created to survey providers involved with pediatric CNS tumor patients about their current recommendations and experience regarding sports and brain tumors.ResultsWe retrieved 32 subjects, including 19 pediatric cases from the literature. Most lesions associated with sport complications were arachnoid cysts (n = 21), followed by glioma (n = 5). The sports in which symptom onset most commonly occurred were soccer (n = 7), football (n = 5), and running (n = 5). We surveyed 111 pediatric neuro-oncology providers. Sport restriction varied greatly from none to 14 sports. Time to return to play in sports with contact also varied considerably between providers. Rationales for limiting sports activities were partly related to subspecialty. Responders reported 9 sport-related adverse events in patients with brain tumor.ConclusionsSport-related complications are uncommon in children with brain tumors. Patients might not be at a significantly higher risk and should not need to be excluded from most sports activities.
Magnitude of Anemia at Discharge Increases 30-Day Hospital Readmissions
Authors: Koch Colleen G. , Li Liang , Sun Zhiyuan , Hixson Eric D. , Tang Anne , Chagin Kevin , Kattan Michael , Phillips Shannon C. , Blackstone Eugene H. , Henderson J. Michael 
Published: September 2014

Background
Anemia during hospitalization is associated with poor health outcomes. Does anemia at discharge place patients at risk for hospital readmission within 30 days of discharge? Our objectives were to examine the prevalence and magnitude of anemia at hospital discharge and determine whether anemia at discharge was associated with 30-day readmissions among a cohort of hospitalizations in a single health care system.

Methods
From January 1, 2009, to August 31, 2011, there were 152,757 eligible hospitalizations within a single health care system. The endpoint was any hospitalization within 30 days of discharge. The University HealthSystem Consortium's clinical database was used for demographics and comorbidities; hemoglobin values are from the hospitals' electronic medical records, and readmission status was obtained from the University HealthSystem Consortium administrative data systems. Mild anemia was defined as hemoglobin of greater than 11 to less than 12 g/dl in women and greater than 11 to less than 13 g/dl in men; moderate, greater than 9 to less than or equal to 11 g/dl; and severe, less than or equal to 9 g/dl. Logistic regression was used to assess the association of anemia and 30-day readmissions adjusted for demographics, comorbidity, and hospitalization type.

Results
Among 152,757 hospitalizations, 72% of patients were discharged with anemia: 31,903 (21%), mild; 52,971 (35%), moderate; and 25,522 (17%), severe. Discharge anemia was associated with severity-dependent increased odds for 30-day hospital readmission compared with those without anemia: for mild anemia, 1.74 (1.65–1.82); moderate anemia, 2.76 (2.64–2.89); and severe anemia, 3.47 (3.30–3.65), P < 0.001.

Conclusions
Anemia at discharge is associated with a severity-dependent increased risk for 30-day readmission. A strategy focusing on anemia treatment care paths during index hospitalization offers an opportunity to influence subsequent readmissions.
Dimorphic development inStreblospio benedicti:genetic analysis of morphological differences between larval types
Authors: Zakas Christina , Rockman Matthew V. 
Published: September 2014

AbstractThe marine polychaeteStreblospio benedictiexhibits two distinct larval types, making it a model for the study of developmental evolution. Females produce either large eggs or small ones, which develop into distinct lecithotrophic or planktotrophic larvae with concomitant morphological and life-history differences. Here, we investigate the inheritance of key morphological traits that distinguish the larval types. We use genetic crosses to establish the influence of maternal and zygotic differences on larval phenotypes. We find a large maternal effect on larval size and the number of larval chaetae, while the number and length of these chaetae are also strongly influenced by zygotic genotype. Interestingly, the distribution of larval phenotypes produced by these crosses suggests traits intermediate to the two parental types should not be uncommon. Yet, despite gene flow between the types in natural populations, such intermediates are rarely found in nature, suggesting that selection may be maintaining distinct larval modes.
Neofunctionalization of DuplicatedTic40Genes Caused a Gain-of-Function Variation Related to Male Fertility inBrassica oleraceaLineages
Authors: Dun Xiaoling , Shen Wenhao , Hu Kaining , Zhou Zhengfu , Xia Shengqian , Wen Jing , Yi Bin , Shen Jinxiong , Ma Chaozhi , Tu Jinxing , Fu Tingdong , Lagercrantz Ulf 
Published: September 2014

AbstractGene duplication followed by functional divergence in the event of polyploidization is a major contributor to evolutionary novelties. The Brassica genus evolved from a common ancestor after whole-genome triplication. Here, we studied the evolutionary and functional features of Brassica spp. homologs to Tic40 (for translocon at the inner membrane of chloroplasts with 40 kDa). Four Tic40 loci were identified in allotetraploid Brassica napus and two loci in each of three basic diploid Brassica spp. Although these Tic40 homologs share high sequence identities and similar expression patterns, they exhibit altered functional features. Complementation assays conducted on Arabidopsis thaliana tic40 and the B. napus male-sterile line 7365A suggested that all Brassica spp. Tic40 homologs retain an ancestral function similar to that of AtTic40, whereas BolC9.Tic40 in Brassica oleracea and its ortholog in B. napus, BnaC9.Tic40, in addition, evolved a novel function that can rescue the fertility of 7365A. A homologous chromosomal rearrangement placed bnac9.tic40 originating from the A genome (BraA10.Tic40) as an allele of BnaC9.Tic40 in the C genome, resulting in phenotypic variation for male sterility in the B. napus near-isogenic two-type line 7365AB. Assessment of the complementation activity of chimeric B. napus Tic40 domain-swapping constructs in 7365A suggested that amino acid replacements in the carboxyl terminus of BnaC9.Tic40 cause this functional divergence. The distribution of these amino acid replacements in 59 diverse Brassica spp. accessions demonstrated that the neofunctionalization of Tic40 is restricted to B. oleracea and its derivatives and thus occurred after the divergence of the Brassica spp. A, B, and C genomes.
Arabidopsis Triphosphate Tunnel Metalloenzyme2 Is a Negative Regulator of the Salicylic Acid-Mediated Feedback Amplification Loop for Defense Responses
Authors: Ung Huoi , Moeder Wolfgang , Yoshioka Keiko 
Published: September 2014

AbstractThe triphosphate tunnel metalloenzyme (TTM) superfamily represents a group of enzymes that is characterized by their ability to hydrolyze a range of tripolyphosphate substrates. Arabidopsis (Arabidopsis thaliana) encodes three TTM genes, AtTTM1, AtTTM2, and AtTTM3. Although AtTTM3 has previously been reported to have tripolyphosphatase activity, recombinantly expressed AtTTM2 unexpectedly exhibited pyrophosphatase activity. AtTTM2 knockout mutant plants exhibit an enhanced hypersensitive response, elevated pathogen resistance against both virulent and avirulent pathogens, and elevated accumulation of salicylic acid (SA) upon infection. In addition, stronger systemic acquired resistance compared with wild-type plants was observed. These enhanced defense responses are dependent on SA, PHYTOALEXIN-DEFICIENT4, and NONEXPRESSOR OF PATHOGENESIS-RELATED GENES1. Despite their enhanced pathogen resistance, ttm2 plants did not display constitutively active defense responses, suggesting that AtTTM2 is not a conventional negative regulator but a negative regulator of the amplification of defense responses. The transcriptional suppression of AtTTM2 by pathogen infection or treatment with SA or the systemic acquired resistance activator benzothiadiazole further supports this notion. Such transcriptional regulation is conserved among TTM2 orthologs in the crop plants soybean (Glycine max) and canola (Brassica napus), suggesting that TTM2 is involved in immunity in a wide variety of plant species. This indicates the possible usage of TTM2 knockout mutants for agricultural applications to generate pathogen-resistant crop plants.
Case of allergic contact dermatitis due to 1,3‐butylene glycol
Authors: Aizawa Atsuko , Ito Akiko , Masui Yukiko , Ito Masaaki 
Published: September 2014

Abstract1,3‐Butylene glycol (1,3‐BG) is widely used in cosmetics, including low‐irritant skin care products and topical medicaments, as an excellent and low‐irritation humectant. We report a case of allergic contact dermatitis caused by 1,3‐BG. A 28‐year‐old woman suffered from an itchy erythematous eruption on her face. By 2 days of closed patch testing, her own cosmetics and many of the hypo‐irritant skin care products showed positive results. A second patch testing showed positive reaction to 1,3‐BG (1% and 5%). 1,3‐BG was a common component in most of the products that had elicited a positive reaction in the first patch testing. Although allergic contact dermatitis due to 1,3‐BG is not so common, we have to consider 1,3‐BG as a possible contact allergen in the patients presenting with allergic contact dermatitis due to various cosmetics.
A first look at the Oxford Nanopore MinION sequencer
Authors: Mikheyev Alexander S. , Tin Mandy M. Y. 
Published: September 2014

AbstractOxford Nanopore's third‐generation single‐molecule sequencing platform promises to decrease costs for reagents and instrumentation. After a 2‐year hiatus following the initial announcement, the first devices have been released as part of an early access program. We explore the performance of this platform by resequencing the lambda phage genome, and amplicons from a snake venom gland transcriptome. Although the handheld MinION sequencer can generate more than 150 megabases of raw data in one run, at most a quarter of the resulting reads map to the reference, with less than average 10% identity. Much of the sequence consists of insertion/deletion errors, or is seemingly without similarity to the template. Using the lambda phage data as an example, although the reads are long, averaging 5 kb, at best 890 ± 1932 bases per mapped read could be matched to the reference without soft clipping. In the course of a 36 h run on the MinION, it was possible to resequence the 48 kb lambda phage reference at 16× coverage. Currently, substantially larger projects would not be feasible using the MinION. Without increases in accuracy, which would be required for applications such as genome scaffolding and phasing, the current utility of the MinION appears limited. Library preparation requires access to a molecular laboratory, and is of similar complexity and cost to that of other next‐generation sequencing platforms. The MinION is an exciting step in a new direction for single‐molecule sequencing, though it will require dramatic decreases in error rates before it lives up to its promise.