bluuebunny/crossref_metadata_2025_split huggingface dataset:
TNFR2 expression by CD4 effector T cells is required to induce full-fledged experimental colitis
Authors: Chen Xin , Nie Yingjie , Xiao Haitao , Bian Zhaoxiang , Scarzello Anthony J. , Song Na-Young , Trivett Anna L. , Yang De , Oppenheim Joost J. 
Published: September 2016

AbstractThere is now compelling evidence that TNFR2 is constitutively expressed on CD4+ Foxp3+ regulatory T cells (Tregs) and TNF-TNFR2 interaction is critical for the activation, expansion and functional stability of Tregs. However, we showed that the expression of TNFR2 was also up-regulated on CD4+ Foxp3− effector T cells (Teffs) upon TCR stimulation. In order to define the role of TNFR2 in the pathogenic CD4 T cells, we compared the effect of transferred naïve CD4 cells from WT mice and TNFR2−/− mice into Rag 1−/− recipients. Transfer of TNFR2-deficient Teff cells failed to induce full-fledged colitis, unlike WT Teffs. This was due to defective proliferative expansion of TNFR2-deficient Teff cells in the lymphopenic mice, as well as their reduced capacity to express proinflammatory Th1 cytokine on a per cell basis. In vitro, the proliferative response of TNFR2 deficient naïve CD4 cells to anti-CD3 stimulation was markedly decreased as compared with that of WT naïve CD4 cells. The hypoproliferative response of TNFR2-deficient Teff cells to TCR stimulation was associated with an increased ratio of p100/p52, providing a mechanistic basis for our findings. Therefore, this study clearly indicates that TNFR2 is important for the proliferative expansion of pathogenic Teff cells.
Glimpsing Speech in the Presence of Nonsimultaneous Amplitude Modulations From a Competing Talker: Effect of Modulation Rate, Age, and Hearing Loss
Authors: Fogerty Daniel , Ahlstrom Jayne B. , Bologna William J. , Dubno Judy R. 
Published: September 2016

Purpose
This study investigated how listeners process acoustic cues preserved during sentences interrupted by nonsimultaneous noise that was amplitude modulated by a competing talker.

Method
Younger adults with normal hearing and older adults with normal or impaired hearing listened to sentences with consonants or vowels replaced with noise amplitude modulated by a competing talker. Sentences were spectrally shaped according to individual audiograms or to the mean audiogram from the listeners with hearing impairment for a younger spectrally shaped control group. The modulation spectrum of the noise was low-pass filtered at different modulation cutoff frequencies. The effect of noise level was also examined.

Results
Performance declined when nonsimultaneous masker modulation included faster rates and was maximized when masker modulation matched the preserved primary speech modulation. Vowels resulted in better performance compared with consonants at slower modulation cutoff rates, likely due to suprasegmental features. Poorer overall performance was observed with increased age or hearing loss, and for listeners who received spectrally shaped speech.

Conclusions
Nonsimultaneous amplitude modulations from a competing talker significantly interacted with the preserved speech segment, and additional listener factors were observed for age and hearing loss. Importantly, listeners may obtain benefit from nonsimultaneous competing modulations when they match the preserved modulations of the sentence.
Record 34.2% efficient mm‐wave N‐polar AlGaN/GaN MISHEMT at 87 GHz
Authors: Romanczyk B. , Guidry M. , Wienecke S. , Li H. , Ahmadi E. , Zheng X. , Keller S. , Mishra U.K. 
Published: September 2016

A novel device technology has been developed to enable the fabrication of high performance mm‐wave GaN high electron mobility transistors (HEMTs) for solid‐state power amplifiers operating in W‐band. By utilising the reverse polarisation of N‐polar GaN, an in‐situ GaN cap layer added in the device access regions acts to improve the channel conductivity and reduces the impact of surface states on device performance. A low dispersion HEMT with 149 GHz peak fT and 285 GHz peak fmax demonstrated simultaneous high efficiency and output power density with 34.2% peak power‐added efficiency and an associated 2.5 W/mm output power at 87 GHz.
Phase noise coherence of two continuous wave radio frequency signals of different frequency
Authors: Rönnow Daniel , Amin Shoaib , Alizadeh Mahmoud , Zenteno Efrain 
Published: September 2016

A method is proposed for determining the correlated and uncorrelated parts of phase noise spectra (PNS) of two continuous wave radio signals of different frequencies, ω1 and ω2. The PNS of the two signals and of mixed signals are measured. The PNS are modelled as having a correlated part that is the same for both signals, except for a multiplicative factor, and uncorrelated parts, that are different for the two signals. A property of the model that the PNS of some mixing products are linear combinations of the PNS of the signals at ω1, ω2, and ω1 − ω2 is experimentally verified. The difference of the PNS at ω1 + ω2 and ω1 − ω2 is proportional to the correlated part of the PNS and is a part of auxiliary functions that are used for finding the multiplicative factor and the correlated, partly correlated, and uncorrelated phase noise at different offset frequencies. A conventional spectrum analyser was used to characterise two signal generators, a phase‐coherent and a non‐phase‐coherent one. For the phase‐coherent generator the phase noise of two signals was found to be correlated for offset frequencies below 10 Hz, partly correlated for 10 Hz–1 kHz and uncorrelated above 1 kHz.
Modelling of wire resistance effect in PCM‐based nanocrossbar memory
Authors: El‐Hassan Nemat H. , Kumar Nandha Thulasiraman , Almurib Haider Abbas F. 
Published: September 2016

At nanoscale grain boundaries and surface scattering effects lead to an increase of connecting wires electrical resistivity with decreasing wire dimensions. This increase of resistivity leads to significant power loss across connecting wires in nanocrossbars. In this study, the resistance of connecting wire as a function of material properties and feature size is calculated. Then the effect of the connecting wires resistance in phase change memory (PCM) performance in PCM‐based passive nanocrossbar was evaluated. The performance metrics tested are: programmed resistance levels, programming duration, and energy consumption. Based on the simulation results, it was found that the power consumed in connecting wires decreases the power supplied to PCM cells. This reduction in power results in higher programmed low resistive state (R ON). The effect of connecting wire resistance on PCM performance is studied as a function of the wire size, cell position on the nanocrossbar, and nanocrossbar size. Simulation results showed that the programmed R ON is inversely proportional to feature size. Moreover, it increases up to almost 40%, with decreasing feature size to 40 nm. Moreover, programmed R ON increases proportionally with increasing nanocrossbar size. Moreover, R OFF /R ON ratio drops almost 90% of targeted ratio at 1 kbit nanocrossbars. Furthermore, cells closer to supply sources are the least affected by wire resistance, while cells furthest from supply are the most affected. Finally, at the end of this study two methods are suggested to resolve the programmed R ON reliability issue caused by energy drop across connecting wires.
EFSUMB Recommendations and Guidelines for Gastrointestinal Ultrasound - Part 1: Examination Techniques and Normal Findings (Short version)
Authors: Nylund Kim , Maconi Giovanni , Hollerweger Alois , Ripolles Tomas , Pallotta Nadia , Higginson Antony , Serra Carla , Dietrich Christoph , Sporea Ioan , Saftoiu Adrian , Dirks Klaus , Hausken Trygve , Calabrese Emma , Romanini Laura , Maaser Christian , Nuernberg Dieter , Gilja Odd 
Published: September 2016

AbstractIn October 2014 the European Federation of Societies for Ultrasound in Medicine and Biology formed a Gastrointestinal Ultrasound (GIUS) task force group to promote the use of GIUS in a clinical setting. One of the main objectives of the task force group was to develop clinical recommendations and guidelines for the use of GIUS under the auspices of EFSUMB. The first part, gives an overview of the examination techniques for GIUS recommended by experts in the field. It also presents the current evidence for the interpretation of normal sonoanatomical and physiological features as examined with different ultrasound modalities.
GluA1 signal peptide determines the spatial assembly of heteromeric AMPA receptors
Authors: He Xue-Yan , Li Yan-Jun , Kalyanaraman Chakrapani , Qiu Li-Li , Chen Chen , Xiao Qi , Liu Wen-Xue , Zhang Wei , Yang Jian-Jun , Chen Guiquan , Jacobson Matthew P. , Shi Yun Stone 
Published: September 2016

Significance
In the brain, AMPA-type glutamate receptors, especially heteromeric GluA1/A2s, are the major postsynaptic receptors mediating fast excitatory neurotransmission. Recently, the crystal structure of GluA2 homomeric AMPA-type glutamate receptors (AMPARs) revealed some interesting features, such as the four subunits in each AMPAR are of two different conformations. However, what the heteromeric GluA1/A2 receptors look like is unknown. In this study, we used a biochemical technique called cysteine cross-linking assay to analyze the spatial architecture of GluA1/A2s. We determined that GluA1/GluA2s have preferred spatial assembly. Surprisingly, this spatial assembly pattern is dictated by the excisable signal peptides, but not the intrinsic sequences of the subunit proteins.
Coordinated autoinhibition of F-BAR domain membrane binding and WASp activation by Nervous Wreck
Authors: Stanishneva-Konovalova Tatiana B. , Kelley Charlotte F. , Eskin Tania L. , Messelaar Emily M. , Wasserman Steven A. , Sokolova Olga S. , Rodal Avital A. 
Published: September 2016

SignificanceMembrane-deforming proteins cooperate with the cytoskeleton to sculpt lipid bilayers into complex and dynamic geometries, but we still do not understand how their activities are temporally and spatially regulated in cells. Here we show that the neuronal membrane remodeling protein Nervous Wreck (Nwk) is autoinhibited by intramolecular interactions between its membrane binding F-BAR domain and its C-terminal SRC homology 3 (SH3) domains. These autoinhibitory interactions control Fes/Cip4 homology-Bin/Amphiphysin/Rvs167 (F-BAR)–mediated membrane remodeling and also, unexpectedly, inhibit SH3-mediated actin cytoskeleton assembly. Uncoupling these dual autoregulatory mechanisms in the fruit fly leads to excess neuronal synapse growth. Thus, coordinated autoregulation couples membrane remodeling and SH3 domain activities, and is critical for proper control of neuronal shape and size.
Variation in the molecular clock of primates
Authors: Moorjani Priya , Amorim Carlos Eduardo G. , Arndt Peter F. , Przeworski Molly 
Published: September 2016

Significance
Much of our understanding of the chronology of human evolution relies on a fixed “molecular clock”; that is, a constant rate of substitutions per unit time. To evaluate the validity of this assumption, we analyze whole-genome sequences from 10 primate species. We find that there is substantial variation in the molecular clock between apes and monkeys and that rates even differ within hominines. Importantly, not all mutation types behave similarly; notably, transitions at CpG sites exhibit a more clocklike behavior than other substitutions, presumably because of their nonreplicative origin. Thus, the mutation spectra, and not just the overall substitution rates, are changing across primates. This finding suggests that events in primate evolution are most reliably dated using CpG transitions.
Biaxial ferromagnetic liquid crystal colloids
Authors: Liu Qingkun , Ackerman Paul J. , Lubensky Tom C. , Smalyukh Ivan I. 
Published: September 2016

Significance
We introduce a soft-matter system with fluidity coexisting with long-range biaxial and ferromagnetic ordering of anisotropic molecular and magnetic colloidal building blocks. The facile polar switching of this complex fluid promises technological applications and rich physical behavior arising from the properties of solid magnetic nanoparticles and their long-range ordering prompted by interactions with the host medium.
Gene-expression profiling of different arms of lymphatic vasculature identifies candidates for manipulation of cell traffic
Authors: Iftakhar-E-Khuda Imtiaz , Fair-Mäkelä Ruth , Kukkonen-Macchi Anu , Elima Kati , Karikoski Marika , Rantakari Pia , Miyasaka Masayuki , Salmi Marko , Jalkanen Sirpa 
Published: September 2016

SignificanceThis paper elucidates one of the enigmas in immunology: What determines the discriminative traffic via afferent and efferent lymphatics? We report so far unrecognized and vastly distinct molecular profiles of lymphatic endothelial cells (LECs) in the afferent and efferent arms of the lymphatic system in the lymph nodes. Moreover, the work takes three of the hit molecules to more detailed analyses regarding their expression and function, and presents a previously unknown function in regulation of the lymphocyte traffic for macrophage scavenger receptor on LECs of the subcapsular sinus. Importantly, the findings of this work may potentially be exploitable in drug design when searching for new targets to manipulate immune response or cancer spread.
TRiC subunits enhance BDNF axonal transport and rescue striatal atrophy in Huntington’s disease
Authors: Zhao Xiaobei , Chen Xu-Qiao , Han Eugene , Hu Yue , Paik Paul , Ding Zhiyong , Overman Julia , Lau Alice L. , Shahmoradian Sarah H. , Chiu Wah , Thompson Leslie M. , Wu Chengbiao , Mobley William C. 
Published: September 2016

Significance
Degeneration of the corticostriatal circuit is a key neuropathological and clinical feature of Huntington’s disease (HD). To define disease mechanisms and explore treatments, we recreated the corticostriatal circuit in microfluidic chambers using neurons from the BACHD mouse model of HD and WT controls. We showed that expression of mutant huntingtin (mHTT) induced defects in brain-derived neurotrophic factor (BDNF) transport in BACHD cortical axons that resulted in atrophy of striatal target neurons. Introducing subunits of the cytosolic chaperonin T-complex 1 (TCP-1) ring complex (TRiC) into BACHD cortical neurons reduced mHTT, rescued defects in BDNF transport, and normalized the size of striatal neurons. These findings encourage studies to explore a role for TRiC reagents as possible treatments for HD.
Ultrafast anisotropic protein quake propagation after CO photodissociation in myoglobin
Authors: Brinkmann Levin U. L. , Hub Jochen S. 
Published: September 2016

Significance
Scattering in solution conducted at X-ray free-electron lasers in principle provides a probe for the ultrafast dynamics of proteins. However, extracting useful structural information from the experimental signals remains a major challenge. Here, we used molecular-dynamics simulations to model the ultrafast “quake-like” dissipation of energy in myoglobin. The simulations provide a detailed atomistic movie of the protein quake, and they help to translate solution scattering signals into functional protein dynamics. Remarkably, we further find that accounting for solvent dynamics is crucial to avoid misinterpretation of time-resolved solution scattering data.
Kinetic barriers to SNAREpin assembly in the regulation of membrane docking/priming and fusion
Authors: Li Feng , Tiwari Neeraj , Rothman James E. , Pincet Frederic 
Published: September 2016

Significance
Neurotransmission requires fusion of the synaptic vesicles that are closely apposed to the presynaptic membrane. This apposition is achieved through the initial association of proteins known as soluble NSF attachment protein receptors (SNAREs). After a neurotransmission event, other vesicles must be rapidly prepared for the next round of fusion. Here we find the kinetics of the initial formation of SNARE complexes are too slow to spontaneously achieve this process because of a high activation energy barrier, but can be accelerated by molecular factors. In addition, we show that a second energy barrier transiently traps the SNARE complexes in a half-zippered state. This pause provides time for the regulatory machinery that accurately controls synchronized neurotransmission to be set in place.
Synthesis and transfer of galactolipids in the chloroplast envelope membranes of
Arabidopsis thaliana
Authors: Kelly Amélie A. , Kalisch Barbara , Hölzl Georg , Schulze Sandra , Thiele Juliane , Melzer Michael , Roston Rebecca L. , Benning Christoph , Dörmann Peter 
Published: September 2016

Significance
Establishment of the progenitor of chloroplasts by the host plant cell during endosymbiosis required the integration of two sets of biological membranes, the endoplasmic reticulum and the chloroplast envelopes, participating in the synthesis of galactolipid precursors for the photosynthetic membranes. Galactolipid synthesis is unequally distributed between the two envelope membranes, necessitating lipid transfer between the envelopes and toward the thylakoids. Here we show that the N-terminal sequence of digalactosyldiacylglycerol synthase 1 is essential for the integration of the chloroplast galactolipid synthesis machinery into the host cell. This N-terminal sequence was invented at the time the endosymbiotic organelle was established, providing a basic glycosyltransferase with a neofunction essential for lipid mobilization between organelles and endomembrane systems in plants.
Minibrain and Wings apart control organ growth and tissue patterning through down-regulation of Capicua
Authors: Yang Liu , Paul Sayantanee , Trieu Kenneth G. , Dent Lucas G. , Froldi Francesca , Forés Marta , Webster Kaitlyn , Siegfried Kellee R. , Kondo Shu , Harvey Kieran , Cheng Louise , Jiménez Gerardo , Shvartsman Stanislav Y. , Veraksa Alexey 
Published: September 2016

Significance
The transcriptional repressor protein Capicua (Cic) is a conserved regulator of organ growth and tissue patterning, and mutations in the CIC gene in humans result in the brain cancer oligodendroglioma. Cic activity is controlled by the receptor tyrosine kinase (RTK) signaling pathway. Here, we identify the kinase Minibrain (Mnb) and its adaptor Wings apart (Wap) as Cic regulators. Mnb and Wap bind to and phosphorylate the Cic protein, and inhibit the ability of Cic to repress gene expression. Mnb-dependent down-regulation of Cic is necessary for the proper growth of multiple organs and correct the patterning of tissues. Our results uncover a previously unknown mechanism of Cic regulation that acts in parallel to other growth-controlling pathways.
Actinomycin D enhances killing of cancer cells by immunotoxin RG7787 through activation of the extrinsic pathway of apoptosis
Authors: Liu Xiu Fen , Xiang Laiman , Zhou Qi , Carralot Jean-Philippe , Prunotto Marco , Niederfellner Gerhard , Pastan Ira 
Published: September 2016

Significance
Because effective cancer therapy usually requires a combination of drugs, we searched for clinically used anticancer agents that would enhance the activity of immunotoxin RG7787 so they could be combined in humans. We show here that actinomycin D activates the extrinsic pathway of apoptosis and acts synergistically with RG7787 to kill a variety of cancer cell lines and cause striking tumor regression in mice. These data indicate that combining immunotoxins like RG7787 that kill cells by inhibiting protein synthesis with actinomycin D is a useful strategy to enhance their antitumor activity in humans.
Circulating microRNA signature for the diagnosis of very high-risk prostate cancer
Authors: Alhasan Ali H. , Scott Alexander W. , Wu Jia J. , Feng Gang , Meeks Joshua J. , Thaxton C. Shad , Mirkin Chad A. 
Published: September 2016

Significance
Serum microRNAs (miRNAs) have emerged as potential noninvasive biomarkers to diagnose prostate cancer (PCa), the most common noncutaneous malignancy among Western men. However, intermediate grades of PCa cannot be distinguished from aggressive forms using current miRNA signatures due to the heterogeneity of PCas. Recently, a high-throughput, spherical nucleic acid-based miRNA expression profiling platform, called the Scano-miR bioassay, was developed to measure the expression levels of miRNAs with both high sensitivity and specificity. By studying serum miRNAs of PCa using the Scano-miR bioassay, we identified a unique molecular signature specific for very high-risk aggressive PCa. This molecular signature will assist in differentiating patients who may benefit from therapy from those who can be closely monitored on active surveillance.
Broadband high-efficiency dielectric metasurfaces for the visible spectrum
Authors: Devlin Robert C. , Khorasaninejad Mohammadreza , Chen Wei Ting , Oh Jaewon , Capasso Federico 
Published: September 2016

Significance
Metasurfaces are optical elements that can mimic and expand on the functionality of refractive optics with a comparatively thin and planar profile. Transmissive metasurfaces suffer from high optical loss at visible wavelengths because of currently used materials and fabrication techniques. This work introduces metasurfaces that operate across the visible spectrum with high efficiencies. As the basis of our metasurfaces, we used a common material, titanium dioxide, and a fabrication method based an atomic layer deposition that creates highly anisotropic nanostructures. The results presented here provide an important advance for realizing optical components at visible wavelengths—e.g., lenses, holograms, and phase shifters—with orders of magnitude reduction in thickness compared with traditional refractive optics.
Exploring the zone of anisotropy and broken symmetries in DNA-mediated nanoparticle crystallization
Authors: O’Brien Matthew N. , Girard Martin , Lin Hai-Xin , Millan Jaime A. , Olvera de la Cruz Monica , Lee Byeongdu , Mirkin Chad A. 
Published: September 2016

Significance
Nanometer-sized materials (i.e., nanoparticles) can be used as building blocks to construct crystalline materials structured with high resolution. The specific arrangements that nanoparticles form can be controlled by their physical shape and size, as well as the molecules attached to their surfaces (i.e., ligands). In this work, DNA ligands are used as “bonds” whose sequence “encodes” which and how far apart nanoparticles interact with each other. Here, we study how the relative size of nanoparticles and DNA modulates the orientation and structural arrangement of nanoparticles within these crystalline materials and report the specific structural changes that occur for nanoparticles with different shapes. These results provide a roadmap to understand how to build nanoparticle-based materials with DNA.
PAXX and XLF DNA repair factors are functionally redundant in joining DNA breaks in a G1-arrested progenitor B-cell line
Authors: Kumar Vipul , Alt Frederick W. , Frock Richard L. 
Published: September 2016

Significance
Classical nonhomologous end joining (C-NHEJ) is a major mammalian DNA double–strand break (DSB) repair pathway. During V(D)J recombination in progenitor (pro)-B lymphocytes, C-NHEJ joins programmed DSBs in antibody gene loci to form complete antibody genes. C-NHEJ also protects mammalian cells from the harmful effects of exposure to ionizing radiation. We now find that the recently identified paralogue of XRCC4 and XLF (PAXX) DNA repair factor, like the related XLF repair factor, is dispensable for V(D)J recombination. However, combined loss of these two factors in pro–B-cell lines totally abrogates V(D)J recombination DSB joining and greatly sensitizes the cells to ionizing radiation. These findings show that PAXX can provide critical C-NHEJ functions that are normally masked by functional redundancy with XLF.