bluuebunny/crossref_metadata_2025_split huggingface dataset:
Survey of the high resolution infrared spectrum of methane (12CH4 and 13CH4): Partial vibrational assignment extended towards 12 000 cm−1
Authors: Ulenikov O. N. , Bekhtereva E. S. , Albert S. , Bauerecker S. , Niederer H. M. , Quack M. 
Published: December 2014

We have recorded the complete infrared spectrum of methane 12CH4 and its second most abundant isotopomer 13CH4 extending from the fundamental range starting at 1000 cm−1 up to the overtone region near 12 000 cm−1 in the near infrared at the limit towards the visible range, at temperatures of about 80 K and also at 298 K with Doppler limited resolution in the gas phase by means of interferometric Fourier transform spectroscopy using the Bruker IFS 125 HR prototype (ZP 2001) of the ETH Zürich laboratory. This provides the so far most complete data set on methane spectra in this range at high resolution. In the present work we report in particular those results, where the partial rovibrational analysis allows for the direct assignment of pure (J = 0) vibrational levels including high excitation. These results substantially extend the accurate knowledge of vibrational band centers to higher energies and provide a benchmark for both the comparison with theoretical results on the one hand and atmospheric spectroscopy on the other hand. We also present a simple effective Hamiltonian analysis, which is discussed in terms of vibrational level assignments and 13C isotope effects.
Large-scale topology and the default mode network in the mouse connectome
Authors: Stafford James M. , Jarrett Benjamin R. , Miranda-Dominguez Oscar , Mills Brian D. , Cain Nicholas , Mihalas Stefan , Lahvis Garet P. , Lattal K. Matthew , Mitchell Suzanne H. , David Stephen V. , Fryer John D. , Nigg Joel T. , Fair Damien A. 
Published: December 2014

SignificanceNoninvasive brain imaging holds great promise for expanding our capabilities of treating human neurologic and psychiatric disorders. However, key limitations exist in human-only studies, and the ability to use animal models would greatly advance our understanding of human brain function. Mice offer sophisticated genetic and molecular methodology, but correlating these data to functional brain imaging in the mouse brain has remained a major hurdle. This study is the first, to our knowledge, to use whole-brain functional imaging to show large-scale functional architecture with structural correlates in the mouse. Perhaps more important is the finding of conservation in brain topology and default network among rodents and primates, thereby clearing the way for a bridge measurement between human and mouse models.
Interspecific introgressive origin of genomic diversity in the house mouse
Authors: Liu Kevin J. , Steinberg Ethan , Yozzo Alexander , Song Ying , Kohn Michael H. , Nakhleh Luay 
Published: December 2014

SignificanceThe mouse has been one of the main mammalian model organisms used for genetic and biomedical research. Understanding the evolution of house mouse genomes would shed light not only on genetic interactions and their interplay with traits in the mouse but would also have significant implications for human genetics and health. Analysis using a recently developed statistical method shows that the house mouse genome is a mosaic that contains previously unrecognized contributions from a different mouse species. We traced these contributions to ancient and recent interbreeding events. Our findings reveal the extent of introgression in an important mammalian genome and provide an approach for genome-wide scans of introgression in other eukaryotic genomes.
Bifurcation analysis of single-cell gene expression data reveals epigenetic landscape
Authors: Marco Eugenio , Karp Robert L. , Guo Guoji , Robson Paul , Hart Adam H. , Trippa Lorenzo , Yuan Guo-Cheng 
Published: December 2014

Significance
Characterization of cellular heterogeneity and hierarchy are important tasks in developmental biology and may help overcome drug resistance in treatment of cancer and other diseases. Single-cell technologies provide a powerful tool for detecting rare cell types and cell-fate transition events, whereas traditional gene expression profiling methods can be used only to measure the average behavior of a cell population. However, the lack of suitable computational methods for single-cell data analysis has become a bottleneck. Here we present a method with the focuses on automatically detecting multilineage transitions and on modeling the associated changes in gene expression patterns. We show that our method is generally applicable and that its applications provide biological insights into developmental processes.
The role of self-interest in elite bargaining
Authors: LeVeck Brad L. , Hughes D. Alex , Fowler James H. , Hafner-Burton Emilie , Victor David G. 
Published: December 2014

SignificanceHumans frequently act contrary to their self-interest and reject low offers in bargaining games. Some evidence suggests that elites, however, are much more rational and self-interested, but this hypothesis has never been directly tested in bargaining games. Using a unique sample of US policy and business elites, we find the opposite. Compared with typical convenience samples, elites are even more prone to act contrary to self-interest by rejecting low offers when bargaining. Appearing to anticipate this fact, elites also make higher offers. This may help to explain why policy elites, such as the diplomats who negotiate treaties on topics like global warming, pay close attention to distributional concerns even though such concerns have been a perennial source of policy gridlock.
Nonredundant protective properties of FPR2/ALX in polymicrobial murine sepsis
Authors: Gobbetti Thomas , Coldewey Sina M. , Chen Jianmin , McArthur Simon , le Faouder Pauline , Cenac Nicolas , Flower Roderick J. , Thiemermann Christoph , Perretti Mauro 
Published: December 2014

Significance
Sepsis defines a syndrome with poor clinical management characterized by overlapping phases of excessive inflammation temporally aligned with an immunosuppressed state. We define an endogenous pathway centered on formyl-peptide receptor 2/3 (Fpr2/3)—ortholog to human FPR2/ALX (receptor for lipoxin A4)—that protects the host against polymicrobial sepsis. Using null mice and proof-of-concept experiments with a peptide–agonist, we demonstrate how engagement of Fpr2/3 is crucial to enact nonredundant functions that span from control of cell recruitment and phagocytosis, modulation of soluble mediator generation, to containment of bacteremia, thus preventing spreading to vital organs and opening new opportunities to manipulate the host response in sepsis.
Licensed human natural killer cells aid dendritic cell maturation via TNFSF14/LIGHT
Authors: Holmes Tim D. , Wilson Erica B. , Black Emma V. I. , Benest Andrew V. , Vaz Candida , Tan Betty , Tanavde Vivek M. , Cook Graham P. 
Published: December 2014

SignificanceAs well as having potent cytotoxic activity, natural killer (NK) cells have a regulatory role and interactions between NK cells and dendritic cells (DCs) aid DC maturation and adaptive immunity. However, the mechanisms underpinning NK–DC cross-talk are poorly defined. We show that tumor cells induce rapid production of the cytokine TNF superfamily member 14 (TNFSF14) in human NK cells and that these NK cells induce DC maturation in a TNFSF14-dependent manner. The synergistic activity of NK cell activation receptors in licensed NK cells couples the release of cytotoxic granules to TNFSF14 production. Thus, NK cell activation by tumor cells is linked to the initiation of adaptive immunity via TNFSF14-mediated NK–DC cross-talk.
Laser altimetry reveals complex pattern of Greenland Ice Sheet dynamics
Authors: Csatho Beata M. , Schenk Anton F. , van der Veen Cornelis J. , Babonis Gregory , Duncan Kyle , Rezvanbehbahani Soroush , van den Broeke Michiel R. , Simonsen Sebastian B. , Nagarajan Sudhagar , van Angelen Jan H. 
Published: December 2014

SignificanceWe present the first detailed reconstruction of surface elevation changes of the Greenland Ice Sheet from NASA’s laser altimetry data. Time series at nearly 100,000 locations allow the characterization of ice sheet changes at scales ranging from individual outlet glaciers to larger drainage basins and the entire ice sheet. Our record shows that continuing dynamic thinning provides a substantial contribution to Greenland mass loss. The large spatial and temporal variations of dynamic mass loss and widespread intermittent thinning indicate the complexity of ice sheet response to climate forcing, strongly enforcing the need for continued monitoring at high spatial resolution and for improving numerical ice sheet models.
TSPAN12 is a critical factor for cancer–fibroblast cell contact-mediated cancer invasion
Authors: Otomo Ryo , Otsubo Chihiro , Matsushima-Hibiya Yuko , Miyazaki Makoto , Tashiro Fumio , Ichikawa Hitoshi , Kohno Takashi , Ochiya Takahiro , Yokota Jun , Nakagama Hitoshi , Taya Yoichi , Enari Masato 
Published: December 2014

Significance
Cancer-associated fibroblasts (CAFs) are abundant and promote cancer proliferation, invasion, and metastasis. Mutations in the p53 gene and decreased p53 expression are often detected in CAFs, and a dysfunction in p53 in CAFs contributes to cancer progression. However, how host-derived p53 influences cancer cells remains unclear. We herein established coculture systems to monitor enhancements in invasiveness and proliferation elicited by p53-depleted fibroblasts and demonstrated that tetraspanin 12 (TSPAN12), identified as a p53-regulated gene, was required for these processes through the contact of cancer cells with stromal fibroblasts and β-catenin–mediated CXC chemokine ligand 6 (CXCL6) secretion. These results suggest that antibodies against TSPAN12 and CXCL6 may be effective therapeutic agents for cancer.
PTEN signaling through RAF1 proto-oncogene serine/threonine kinase (RAF1)/ERK in the epididymis is essential for male fertility
Authors: Xu Bingfang , Washington Angela M. , Hinton Barry T. 
Published: December 2014

Significance
Without a fully developed and functioning initial segment, the most proximal region of the epididymis, spermatozoa do not undergo maturation, resulting in male infertility. The tumor suppressor phosphatase and tensin homolog (PTEN) was deleted from the initial segment, which resulted in changes in the activity of downstream signaling components that led to epithelial dedifferentiation and male infertility. Spermatozoa were normal upon leaving the testis, but as they progressed through the duct of the dedifferentiated initial segment, they developed angled flagella and a decrease in motility. These changes prevented spermatozoa from reaching and fertilizing an egg in the female reproductive tract. PTEN plays an essential role in maintaining normal initial-segment differentiation and function and, therefore, male fertility.
Revealing bacterial targets of growth inhibitors encoded by bacteriophage T7
Authors: Molshanski-Mor Shahar , Yosef Ido , Kiro Ruth , Edgar Rotem , Manor Miriam , Gershovits Michael , Laserson Mia , Pupko Tal , Qimron Udi 
Published: December 2014

Significance
Antibiotic resistance of pathogens is a growing threat to human health, requiring immediate action. Identifying new gene products of bacterial viruses and their bacterial targets may provide potent tools for fighting antibiotic-resistant strains. We show that a significant number of phage proteins are inhibitory to their bacterial host. DNA sequencing was used to map the targets of these proteins. One particular target was a key cytoskeleton protein whose function is impaired following the phage protein’s expression, resulting in bacterial death. Strikingly, in over 70 y of extensive research into the tested bacteriophage, this inhibition had never been characterized. We believe that the presented approach may be broadened to identify novel, clinically relevant bacteriophage growth inhibitors and to characterize their targets.
Identification of a pheromone that increases anxiety in rats
Authors: Inagaki Hideaki , Kiyokawa Yasushi , Tamogami Shigeyuki , Watanabe Hidenori , Takeuchi Yukari , Mori Yuji 
Published: December 2014

Significance
Animals communicate with other members of the same species by using pheromones. Rats release a specific odor into the air when they are stressed. Because this stress-related odor increases anxiety in the other rats, it is likely that there are some anxiogenic molecules in this odor. In this study, we have tried to identify these molecules. We discovered that a combination of two molecules, 4-methylpentanal and hexanal, increased anxiety in rats. We concluded that the mixture is a pheromone in rats that can increase anxiety in conspecifics. Furthermore, we proposed that the neural circuit relating to anxiety was only activated when the two molecules were simultaneously perceived by two separate olfactory systems.
Hedgehog-induced phosphorylation by CK1 sustains the activity of Ci/Gli activator
Authors: Shi Qing , Li Shuang , Li Shuangxi , Jiang Alice , Chen Yongbin , Jiang Jin 
Published: December 2014

Significance
Hedgehog (Hh) signaling controls development and tissue homeostasis through the Cubitus interruptus (Ci)/glioma-associated oncogene homolog (Gli) transcription factors, and abnormal Gli activity causes congenital diseases and cancers. Here we show that Ci/Gli phosphorylation by Casein kinase 1 positively regulates Hh pathway activity, providing insights into the regulation of Ci/Gli activity. By showing that phosphorylation protects the Ci/Gli activator from premature degradation, our study not only sheds lights on how the production and degradation of Ci/Gli activator are delicately balanced to achieve optimal pathway activity but also provides the first evidence (to our knowledge) that protein degradation by the Cullin 3 family of E3 ubiquitin ligases is negatively regulated by phosphorylation.
GDM-associated insulin deficiency hinders the dissociation of SERT from ERp44 and down-regulates placental 5-HT uptake
Authors: Li Yicong , Hadden Coedy , Singh Preeti , Mercado Charles P. , Murphy Pamela , Dajani Nafisa K. , Lowery Curtis L. , Roberts Drucilla J. , Maroteaux Luc , Kilic Fusun 
Published: December 2014

Significance
Our findings provide insight on the molecular mechanism in which insulin regulates the dissociation of ERp44, an endoplasmic reticulum chaperon, from the serotonin (5-HT) transporter (SERT) following the completion of disulfide bond formation. Furthermore, our data show that gestational diabetes mellitus-associated defects in insulin signaling tethers SERT with ERp44, at the intracellular compartment which down-regulates 5-HT uptake rates of the placental trophoblast. All the trophoblast used in these studies were isolated and purified directly from healthy or GDM placentas in our laboratories.
Soil surface acidity plays a determining role in the atmospheric-terrestrial exchange of nitrous acid
Authors: Donaldson Melissa A. , Bish David L. , Raff Jonathan D. 
Published: December 2014

Significance
Nitrous acid (HONO) emitted from soil plays an important role in regulating the oxidizing capacity of the atmosphere. Unexpectedly high emissions of HONO are observed from soils with close to neutral pH, where aqueous acid–base and Henry’s law equilibria would predict that nitrite is the dominant nitrogen species. We show that surface acidity of soil minerals rather than aqueous acid–base equilibria controls nitrite speciation in soil, implying that up to 70% of global soils are capable of emitting HONO due to their acidic or close to neutral pH; this suggests that soil nitrite, whether microbially derived or otherwise deposited, likely plays a more widespread role in terrestrial–atmospheric cycling of nitrogen affecting air pollution and climate than previously thought.
Structural basis for the auxin-induced transcriptional regulation by Aux/IAA17
Authors: Han Mookyoung , Park Yangshin , Kim Iktae , Kim Eun-Hee , Yu Tae-Kyung , Rhee Sangkee , Suh Jeong-Yong 
Published: December 2014

Significance
Auxin is the central hormone that governs diverse developmental processes in plants. Auxin response is regulated by auxin response transcription factor (ARF) and Aux/IAA transcriptional repressor. ARF and Aux/IAA form homo-oligomers and also hetero-oligomers for transcriptional regulation of auxin-response genes. Mechanistic understanding of how ARF and Aux/IAA change their association states is not well established. This work reports, to our knowledge, the first structure of the oligomerization domain of IAA17, and describes the key determinant that dictates the switch between homo- and hetero-oligomers. While Aux/IAA and ARF use a common scaffold and interface for homotypic and heterotypic associations, the charge composition at the interface determines the affinity and the oligomerization states. Based on the results, we propose a refined model of auxin-induced transcriptional regulation.
Thermotropic liquid crystals from biomacromolecules
Authors: Liu Kai , Chen Dong , Marcozzi Alessio , Zheng Lifei , Su Juanjuan , Pesce Diego , Zajaczkowski Wojciech , Kolbe Anke , Pisula Wojciech , Müllen Klaus , Clark Noel A. , Herrmann Andreas 
Published: December 2014

Significance
Liquid crystals (LCs) found in biology are usually dispersed in a solvent, typically water, and are therefore classified as lyotropic. However, from a technological perspective, thermotropic LCs (TLCs), typically based on small rod- or disc-shaped organic molecules, have been of much greater importance. In this contribution, we show that thermotropic liquid crystal phases and materials can also be made from biomolecules, demonstrating a simple generic method to form thermotropic phases from biosystems ranging from nucleic acids and proteins to even whole viruses, spanning a size from only a few nanometers to 1 μm.
Glutamatergic regulation prevents hippocampal-dependent age-related cognitive decline through dendritic spine clustering
Authors: Pereira Ana C. , Lambert Hilary K. , Grossman Yael S. , Dumitriu Dani , Waldman Rachel , Jannetty Sophia K. , Calakos Katina , Janssen William G. , McEwen Bruce S. , Morrison John H. 
Published: December 2014

Significance
Aging is often accompanied by cognitive decline. It is of critical importance to understand the synaptic susceptibilities of the glutamatergic neural circuits to age-related cognitive decline and to intervene in this process. Maintenance of synaptic health in the face of aging is a crucially important therapeutic goal. We show that the glutamate modulator, riluzole, prevents age-related memory loss and induces clustering of dendritic spines. Clustering is a critical element of synaptic plasticity that has been previously demonstrated to increase synaptic strength. This study further elucidates neuroplastic changes in the neurocircuits vulnerable to aging and advances therapeutic development to prevent and treat age-related cognitive decline.
Hepatocyte circadian clock controls acetaminophen bioactivation through NADPH-cytochrome P450 oxidoreductase
Authors: Johnson Brian P. , Walisser Jacqueline A. , Liu Yan , Shen Anna L. , McDearmon Erin L. , Moran Susan M. , McIntosh Brian E. , Vollrath Aaron L. , Schook Andrew C. , Takahashi Joseph S. , Bradfield Christopher A. 
Published: December 2014

Significance
Acetaminophen toxicity is significantly influenced by the hepatocyte circadian clock through its control of xenobiotic metabolizing systems. We have found that, although the central circadian clock can influence detoxification through glutathione biosynthesis, the autonomous hepatocyte circadian clock also controls major aspects of acetaminophen (APAP) bioactivation. One mechanism by which APAP bioactivation is controlled is through the clock’s regulation of cytochrome P450-dependent activity through NADPH-cytochrome P450 oxidoreductase.
In silico selection of therapeutic antibodies for development: Viscosity, clearance, and chemical stability
Authors: Sharma Vikas K. , Patapoff Thomas W. , Kabakoff Bruce , Pai Satyan , Hilario Eric , Zhang Boyan , Li Charlene , Borisov Oleg , Kelley Robert F. , Chorny Ilya , Zhou Joe Z. , Dill Ken A. , Swartz Trevor E. 
Published: December 2014

Significance
mAbs are increasingly being used for treatment of chronic diseases wherein the subcutaneous delivery route is preferred to enable self-administration and at-home use. To deliver high doses (several hundred milligrams) through a small volume (∼1 mL) into the subcutaneous space, mAb solutions need to have low viscosity. Concomitantly, acceptable chemical stability is required for adequate shelf life, and normal in vivo clearance is needed for less frequent dosing. We propose in silico tools that provide rapid assessment of atypical behavior of mAbs (high viscosity, chemical degradation, and fast plasma clearance), which are simply predicted from sequence and/or structure-derived parameters. Such analysis will greatly improve the probability of success to move mAb-based therapeutics efficiently into clinical development and ultimately benefit patients.
Expression and prognostic impact of lncRNAs in acute myeloid leukemia
Authors: Garzon Ramiro , Volinia Stefano , Papaioannou Dimitrios , Nicolet Deedra , Kohlschmidt Jessica , Yan Pearlly S. , Mrózek Krzysztof , Bucci Donna , Carroll Andrew J. , Baer Maria R. , Wetzler Meir , Carter Thomas H. , Powell Bayard L. , Kolitz Jonathan E. , Moore Joseph O. , Eisfeld Ann-Kathrin , Blachly James S. , Blum William , Caligiuri Michael A. , Stone Richard M. , Marcucci Guido , Croce Carlo M. , Byrd John C. , Bloomfield Clara D. 
Published: December 2014

Significance
Long noncoding RNAs (lncRNAs) are involved in numerous biological roles including epigenetic regulation, apoptosis, and cell cycle. Whereas lncRNAs contribute to epigenetic gene regulation, metastasis, and prognosis in solid tumors, their role in acute myeloid leukemia (AML) has not been hitherto reported. Here, we show that lncRNA expression profiles are associated with recurrent mutations, clinical features, and outcome in AML. A fraction of these lncRNAs may have a functional role in leukemogenesis. Furthermore, lncRNAs could be used as biomarkers for outcome in AML. The identification of patients likely to achieve complete remission with standard therapy alone, based on lncRNA expression, is a significant advance potentially sparing such patients from other toxicities and focusing investigational approaches on postremission studies.
Discriminant Score for Celiac Disease Based on Immunohistochemical Analysis of Duodenal Biopsies
Authors: Tosco Antonella , Maglio Mariantonia , Paparo Francesco , Greco Luigi , Troncone Riccardo , Auricchio Renata 
Published: December 2014

ABSTRACTObjectives:Celiac disease (CD) represents a spectrum, which includes cases with minor histological abnormalities (potential CD). The aim of this work is to evaluate the contribution of immunohistochemical analysis of duodenal biopsies to the diagnosis of gluten‐related minor enteropathy.Methods:Duodenal biopsies from 56 patients with untreated CD and 56 controls were analyzed for CD3 and γδ intraepithelial lymphocyte number, γδ/CD3 ratio, and density of CD25+ lamina propria cells. A discriminant equation was obtained by which 61 more biopsies with normal villous architecture were blindly evaluated.Results:All of the immunohistochemical parameters were significantly different between patients with CD and controls. None of the single parameters showed sufficient specificity for CD. The combination of all of the 4 markers resulted in the following discriminant equation: discriminant score (Dscore) = (CD3 × 0.06) − (γδ × 0.119) + (CD25 × 0.012) + (γδ/CD3 × 0.131) − 4.709. Using this Dscore, patients were correctly classified as celiac or controls in 97.3% of the cases. When this equation was applied to a validation set of 61 patients with normal villous architecture and unknown diagnosis, 92.9% of those with a positive score turned out to be patients with potential CD. A normal score, however, did not exclude this condition.Conclusions:Immunohistochemistry represents a specific tool for the diagnosis of CD, but does lack sensitivity in detecting all of the potential CD cases.