bluuebunny/crossref_metadata_2025_split huggingface dataset:
Interrogating the protein interactomes of RAS isoforms identifies PIP5K1A as a KRAS-specific vulnerability
Authors: Adhikari Hema , Counter Christopher M. 
Published: September 2018

AbstractIn human cancers, oncogenic mutations commonly occur in the RAS genes KRAS, NRAS, or HRAS, but there are no clinical RAS inhibitors. Mutations are more prevalent in KRAS, possibly suggesting a unique oncogenic activity mediated by KRAS-specific interaction partners, which might be targeted. Here, we determine the specific protein interactomes of each RAS isoform by BirA proximity-dependent biotin identification. The combined interactomes are screened by CRISPR-Cas9 loss-of-function assays for proteins required for oncogenic KRAS-dependent, NRAS-dependent, or HRAS-dependent proliferation and censored for druggable proteins. Using this strategy, we identify phosphatidylinositol phosphate kinase PIP5K1A as a KRAS-specific interactor and show that PIP5K1A binds to a unique region in KRAS. Furthermore, PIP5K1A depletion specifically reduces oncogenic KRAS signaling and proliferation, and sensitizes pancreatic cancer cell lines to a MAPK inhibitor. These results suggest PIP5K1A as a potential target in KRAS signaling for the treatment of KRAS-mutant cancers.
Passive sensing around the corner using spatial coherence
Authors: Batarseh M. , Sukhov S. , Shen Z. , Gemar H. , Rezvani R. , Dogariu A. 
Published: September 2018

AbstractWhen direct vision is obstructed, detecting an object usually involves either using mirrors or actively controlling some of the properties of light used for illumination. In our paradigm, we show that a highly scattering wall can transfer certain statistical properties of light, which, in turn, can assist in detecting objects even in non-line-of-sight conditions. We experimentally demonstrate that the transformation of spatial coherence during the reflection of light from a diffusing wall can be used to retrieve geometric information about objects hidden around a corner and assess their location. This sensing approach is completely passive, assumes no control over the source of light, and relies solely on natural broadband illumination.
USP4 positively regulates RLR-induced NF-κB activation by targeting TRAF6 for K48-linked deubiquitination and inhibits enterovirus 71 replication
Authors: Xu Chao , Peng Yang , Zhang Qin , Xu Xiao-Peng , Kong Xiang-Min , Shi Wei-Feng 
Published: September 2018

AbstractRetinoic acid-inducible gene I-like receptor (RLR) is one of the most important pattern recognition receptors of the innate immune system that detects positive and/or negative stranded RNA viruses. Subsequently, it stimulates downstream transcription of interferon regulatory factor 3 (IRF3) and nuclear factor κB (NF-κB) inducing the production of interferons (IFNs) and inflammatory cytokines. Tumour necrosis factor receptor associated factor 6 (TRAF6) is a key protein involved in the RLR-mediated antiviral signalling pathway, recruiting additional proteins to form a multiprotein complex capable of activating the NF-κB inflammatory pathway. Despite TRAF6 playing an important role in regulating host immunity and viral infection, the deubiquitination of TRAF6 induced by viral infection remains elusive. In this study, we found that enterovirus 71 (EV71) infection attenuated the expression of Ubiquitin-specific protease 4 (USP4) in vitro and in vivo, while overexpression of USP4 significantly suppressed EV71 replication. Furthermore, it was found that EV71 infection reduced the RLR signalling pathway and enhanced the degradation of TRAF6. USP4 was also found to interact with TRAF6 and positively regulate the RLR-induced NF-κB signalling pathway, inhibiting the replication of EV71. Therefore, as a novel positive regulator of TRAF6, USP4 plays an essential role in EV71 infection by deubiquitinating K48-linked ubiquitin chains.
Questionable Use of “Nonorganic” in Norrix et al. (2017), “Estimating Nonorganic Hearing Thresholds”
Authors: Peck James E. 
Published: September 2018

Purpose

The author of this letter to the editor expresses concern about the use of the word “nonorganic” as a source of confusion in terminology. Specifically, this is in response to the December 2017
American Journal of Audiology
article, “Estimating Nonorganic Hearing Thresholds Using Binaural Auditory Stimuli” (Norrix, Rubiano, & Mueller, 2017). “Nonorganic” is a source of confusion in terminology, because it can be used in two different ways. One way can mean to say there is no hearing loss. When used in this sense, it is illogical because it is qualifying a hearing loss believed not to exist. The second usage means there is a real disorder of function, but the organs themselves are not damaged and the basis is unknown. In the place of “nonorganic,” I have proposed “false hearing loss.” “Nonorganic” might carry a negative connotation that “false” might not. Many instances of false hearing loss stem from physical–mental health disturbances. Audiologists must stay alert to signs of psychosocial difficulty and refer for further evaluation accordingly.

Conclusion
“False” hearing loss is a more appropriate term than “nonorganic” hearing loss.
Pairing New Words With Unfamiliar Objects: Comparing Children With and Without Cochlear Implants
Authors: Lund Emily 
Published: September 2018

PurposeThis study investigates differences between preschool children with cochlear implants and age-matched children with normal hearing during an initial stage in word learning to evaluate whether they (a) match novel words to unfamiliar objects and (b) solicit information about unfamiliar objects during play.MethodTwelve preschool children with cochlear implants and 12 children with normal hearing matched for age completed 2 experimental tasks. In the 1st task, children were asked to point to a picture that matched either a known word or a novel word. In the 2nd task, children were presented with unfamiliar objects during play and were given the opportunity to ask questions about those objects.ResultsIn Task 1, children with cochlear implants paired novel words with unfamiliar pictures in fewer trials than children with normal hearing. In Task 2, children with cochlear implants were less likely to solicit information about new objects than children with normal hearing. Performance on the 1st task, but not the 2nd, significantly correlated with expressive vocabulary standard scores of children with cochlear implants.ConclusionThis study provides preliminary evidence that children with cochlear implants approach mapping novel words to and soliciting information about unfamiliar objects differently than children with normal hearing.
Autonome Störungen
Authors: Haensch Carl-Abrecht , Lührs Anke 
Published: September 2018

ZusammenfassungDas autonome Nervensystem steuert unwillkürlich zahlreiche Vorgänge im menschlichen Körper. Erkrankungen des peripheren und/oder zentralen autonomen Netzwerks können daher mit einer großen Breite autonomer Dysfunktionen symptomatisch werden. Im Mittelpunkt autonomer Funktionsdiagnostik steht dabei besonders häufig die Diagnostik eines passageren Bewusstseinsverlustes oder einer orthostatischen Intoleranz auf Grund einer neurokardiogenen Synkope, orthostatischen Hypotonie oder eines Posturalen Tachykardiesyndroms.
Sonografie peripherer Nerven: Sonografische Anatomie
Authors: Schminke Ulf , von Sarnowski Bettina 
Published: September 2018

ZusammenfassungEine qualitativ hochwertige Ultraschalldiagnostik erfordert neben Kenntnissen der methodischen und technischen Grundlagen v. a. umfangreiche Kenntnisse der sonografischen Anatomie. Der folgende Artikel hat zum Ziel, die sonografische Anatomie der wichtigsten peripheren Nerven sowie deren Identifizierung mithilfe von anatomischen Landmarken wie Blutgefäßen, Muskelbäuchen und Knochenvorsprüngen zu illustrieren. Anhand von Abbildungen und Videos werden die komplexen Topografien der Nerven in der Regio cervicalis lateralis, der Regio axillaris und der Regio inguinalis sowie der Nerven der oberen und unteren Extremitäten dargestellt.
Ultrasound of Thyroid Nodules
Authors: Bojunga Jörg 
Published: September 2018

AbstractThyroid nodules are a common finding in the general population. Ultrasonography is the most sensitive imaging tool for diagnosing thyroid nodules. However, sonographic differentiation of hormonally active versus inactive nodules, and in particular benign versus malignant nodules, remains unreliable. In this context, thyroid scintigraphy has its clinical significance predominantly in diagnosing hormonal activity of thyroid nodules. However, most nodules are benign and a significant number of patients undergo surgery for diagnostic rather than for therapeutic reasons. Efforts of the past years aimed to improve sonographic risk stratification, to predict malignancy of thyroid nodules through standardized diagnostic assessment of validated risk factors, in order to select patients who require further diagnostic workup. In the last years, several imaging and reporting systems, giving standardized categories with rates of malignancy, were evaluated as a basis for further clinical management. Recent technological developments, such as elastography, also show promising data and might be implemented into clinical practice. Ultrasound-guided fine needle aspiration is the key element in the diagnosis of sonographically suspicious thyroid nodules and significantly contributes to the diagnosis of malignancy versus benignity.
Epilepsy Surgery in Antibody-Associated Autoimmune Encephalitis and Epilepsies: Review of Literature
Authors: Luat Aimee 
Published: September 2018

AbstractThere is lack of studies that explore the role of epilepsy surgery in the treatment of drug-refractory antibody-associated autoimmune encephalitis and epilepsies. Some case reports and series suggest that surgical treatment may still be an option, but compared with other etiologies, its surgical outcome seems to be less favorable. The following review summarizes the existing experience on the surgical treatment of drug-refractory seizures associated with antibody-associated autoimmune encephalitis and epilepsies.
Grundlagen und Praxis der Neuroanästhesie
Authors: Mölders Patrick , Alders Jörg 
Published: September 2018

ZusammenfassungZentrale Aspekte der Anästhesieführung bei neurochirurgischen Operationen sind das Aufrechterhalten der zerebralen Homöostase sowie die Vermeidung sekundärer Hirnschäden. Die wichtigsten Variablen sind zerebraler Metabolismus, zerebraler Blutfluss, zerebraler Perfusionsdruck, zerebrales Blutvolumen und ihr Einfluss auf den intrakraniellen Druck. Die Ausgewogenheit dieser Faktoren ist Ziel bei jeder neurochirurgischen Operation oder Intervention.
Pluralism and the problem of purity
Authors: Builes David 
Published: September 2018

AbstractOntological Pluralism is the thesis that there are different ways of being. In his recent paper, ‘The only way to be’, Trenton Merricks has presented an important challenge to Pluralism in the form of a dilemma. The purpose of this paper is two-fold. First, I argue that Merricks’s argument against Pluralism, as stated, is unsound. I will argue that one horn of the dilemma is unproblematic for contemporary versions of Pluralism, defended by Jason Turner and Kris McDaniel, that are formulated in the framework of Ted Sider. However, my second task is to provide a new dilemma against Pluralism, which, when combined with Merricks’s arguments, constitutes a sound argument against all forms of Pluralism. The new dilemma will reveal that the real problem with Ontological Pluralism is its conflict with Ted Sider’s principle of Purity.
De novo construction of polyploid linkage maps using discrete graphical models
Authors: Behrouzi Pariya , Wit Ernst C 
Published: September 2018

Abstract

Motivation
Linkage maps are used to identify the location of genes responsible for traits and diseases. New sequencing techniques have created opportunities to substantially increase the density of genetic markers. Such revolutionary advances in technology have given rise to new challenges, such as creating high-density linkage maps. Current multiple testing approaches based on pairwise recombination fractions are underpowered in the high-dimensional setting and do not extend easily to polyploid species. To remedy these issues, we propose to construct linkage maps using graphical models either via a sparse Gaussian copula or a non-paranormal skeptic approach.

Results
We determine linkage groups, typically chromosomes, and the order of markers in each linkage group by inferring the conditional independence relationships among large numbers of markers in the genome. Through simulations, we illustrate the utility of our map construction method and compare its performance with other available methods, both when the data are clean and contain no missing observations and when data contain genotyping errors. Our comprehensive map construction method makes full use of the dosage SNP data to reconstruct linkage map for any bi-parental diploid and polyploid species. We apply the proposed method to three genotype datasets: barley, peanut and potato from diploid and polyploid populations.

Availability and implementation
The method is implemented in the R package netgwas which is freely available at https://cran.r-project.org/web/packages/netgwas.

Supplementary information
Supplementary data are available at Bioinformatics online.
The English Aristocracy and Mesne Feudalism in the Late Middle Ages
Authors: Ross James 
Published: September 2018

Abstract
Historians have generally argued that the feudal system in the later Middle Ages in England had declined into obsolescence, at least as far as the aristocracy were concerned, and little has been written in the last half-century on the subject. Yet not only were the greater landowners assiduous in keeping records of tenants holding land from them by knight’s service, serjeanty and socage, but evidence from these sources suggests that feudal rights and duties remained important. Revenues from feudal incidents (honorial courts, escheats, wardships and feudal aids) were fluctuating but often lucrative sources of income, though they had declined from thirteenth-century heights and were subject in the later fourteenth and fifteenth century to both political fluctuations and variability in quality of lordship. Lords also continued to insist on the personal performance of homage; the numbers involved, the high-status buildings in which the ceremony was performed (usually before important witnesses) and the solemnity of the ceremony itself suggest that homage was more important in the later Middle Ages than is generally acknowledged. Feudal tenants, indeed, played a significant part in aristocratic affinities. Defined in narrow terms as a system of relationships, feudalism was not moribund.
Pediatric Loss-of-Control Eating and Anxiety in Relation to Components of Metabolic Syndrome
Authors: Byrne Meghan E , Tanofsky-Kraff Marian , Kelly Nichole R , Grammer Anne Claire , Jaramillo Manuela , Mi Sarah J , Stojek Monika M , Shank Lisa M , Burke Natasha L , Cassidy Omni , Schvey Natasha A , Brady Sheila M , Demidowich Andrew P , Broadney Miranda M , Yanovski Susan Z , Yanovski Jack A 
Published: September 2018

Abstract

Objective
Pediatric loss-of-control (LOC) eating is associated with, and predictive of, gains in adiposity and adverse metabolic outcomes. In addition, some preliminary data suggest that anxiety may exacerbate the relationship of LOC eating with weight and metabolic syndrome (MetS)-related measures. We therefore examined whether anxiety moderated the relationship between LOC eating and body mass index z (BMIz), adiposity, and MetS-related measures in youth.

Methods
A convenience sample of non-treatment-seeking boys and girls of varying weight strata were interviewed to determine the presence of LOC eating and completed a questionnaire assessing trait anxiety. BMIz and MetS-related measures (blood pressure, triglycerides, high-density lipoprotein cholesterol, low-density lipoprotein cholesterol, glucose, and insulin) were measured after an overnight fast. Adiposity was assessed by air displacement plethysmography or dual-energy x-ray absorptiometry. Analyses adjusted for age, sex, race, height, fat mass, and depressive symptoms, as appropriate.

Results
In all, 379 youths (13.0 ± 2.8 years; 53% female; BMIz = 0.8 ± 1.1; 22% with LOC eating) were studied. Anxiety was not significantly related to BMIz, adiposity, or MetS-related measures. However, anxiety and LOC eating interacted such that only among youth with LOC eating, anxiety was positively associated with fasting insulin (p = .02) and insulin resistance (p = .01). The interaction of anxiety and LOC eating was not significantly related to BMIz, adiposity, or any other MetS-related measure (ps = ns).

Conclusions
Only among non-treatment-seeking youth with LOC eating, anxiety may be associated with increased insulin secretion and insulin resistance. Longitudinal studies are required to confirm these findings and explore mechanisms for these relationships.
“All the Progress to Be Made Will Be Made by Maladjusted Negroes”: Mae Mallory, Black Women’s Activism, and the Making of the Black Radical Tradition
Authors: Farmer Ashley D 
Published: September 2018

Abstract
Mae Mallory (1927–2007) was a radical political activist and a self-proclaimed “maladjusted Negro.” She played a foundational role in developing and sustaining the black freedom movement through her school desegregation protests in the 1950s, Black Power advocacy in the 1960s, and Pan-African and prisoner’s rights organizing in the 1970s and 1980s. She also espoused a politics defined by her commitment to a black, community-centered, working-class, gender-conscious, and anti-imperialist worldview. Mallory’s multifaceted organizing, intellectual production, and women-centered approach to radical politics have made her an outlier in traditional historical frameworks. However, her alternative intellectual and activist path is also generative in that it illuminates different aspects of black women’s political activism. This article examines Mallory’s organizing and intellectual production through the lens of “maladjustment.” It argues that her unconventional identifications, politics, and organizing trajectory not only showcase Mallory’s unique influence on the black radical tradition, they also offer an opportunity to rethink existing approaches to the study of black women’s activism. The essay offers one of the first overviews of Mallory’s life, organizing, and theorizing, in order to foreground her role in shaping multiple facets of black organizing. In doing so, it offers a larger commentary on how “maladjusted” women like Mallory challenge conventional narratives about the periodization, strategies, and legacies of the black freedom movement.
millepattesmicropeptides are an ancient developmental switch required for embryonic patterning
Authors: Ray Suparna , Rosenberg Miriam I , Chanut-Delalande Hélène , Decaras Amelie , Schwertner Barbara , Toubiana William , Auman Tzach , Schnellhammer Irene , Teuscher Matthias , Khila Abderrahman , Klingler Martin , Payre François 
Published: September 2018

SummarySmall open reading frames (smORFs) that code for “micropeptides” (10-100 amino acids) exhibit remarkable evolutionary complexity. Conserved micropeptides encoded by themillepattes (mlpt)gene are essential inTriboliumfor embryogenesis but inDrosophila,function only in leg and cuticle differentiation. We find that a module identified inDrosophilatrichome patterning, comprising Mlpt, UBR3, and Shaven-baby (Svb), coordinates early embryo patterning in several insect orders. Intriguingly, Mlpt segmentation function can be re-awakened in theDrosophilablastoderm, demonstrating the potency of an ancestral developmental switch retained despite evolving embryonic patterning modes. smORFs likemillepattesthus illustrate plasticity of micropeptide functions despite constraints of essential genetic networks.One sentence summaryA module comprising the small ORFs mlpt/pri/tal, the transcription factor Svb, and the ubiquitin ligase UBR3, possesses an ancestral function in insect embryo patterning which is lost in flies but reactivated when Svb expression is restored.
Two key events associated with a transposable element burst occurred during rice domestication
Authors: Chen Jinfeng , Lu Lu , Benjamin Jazmine , Diaz Stephanie , Hancock C. Nathan , Stajich Jason E. , Wessler Susan R. 
Published: September 2018

AbstractTransposable elements shape genome evolution through periodic bursts of amplification. In this study we exploited knowledge of the components of themPing/Ping/PongTE family in four rice strains undergoingmPingbursts to track their copy numbers and distribution in a large collection of genomes from the wild progenitorOryza rufipogonand domesticatedOryza sativa(rice). We characterized two events that occurred to the autonomousPingelement and appear to be critical formPinghyperactivity. First, a point mutation near the end of the element created aPingvariant (Ping16A) with reduced transposition. The proportion of strains withPing16Ahas increased during domestication while the originalPing (Ping16G)has been dramatically reduced. Second, transposition ofPing16Ainto aStowawayelement generated a locus (Ping16A_Stow) whose presence correlates with strains that have highmPingcopies. Finally, demonstration thatPongelements have been stably silenced in all strains analyzed indicates that sustained activity of themPing/Pingfamily during domestication produced the components necessary for themPingburst, not the loss of epigenetic regulation.
Soil health pilot study in England: outcomes from an on- farm earthworm survey
Authors: Stroud Jacqueline L. 
Published: September 2018

AbstractEarthworms are primary candidates for national soil health monitoring as they are ecosystem engineers that benefit both food production and ecosystem services associated with soil security. Supporting farmers to monitor soil health could help to achieve the policy aspiration of sustainable soils by 2030 in England; however, little is known about how to overcome participation barriers, appropriate methodologies (practical, cost-effective, usefulness) or training needs. This paper presents the results from a pilot #60minworms study which mobilised farmers to assess over >1300 ha farmland soils in spring 2018. The results interpretation framework is based on the presence of earthworms from each of the three ecological groups at each observation (20cm3pit) and spatially across a field (10 soil pits). Results showed that most fields have basic earthworm biodiversity, but 42 % fields may be at risk of over-cultivation as indicated by absence/rarity of epigeic and/or anecic earthworms; and earthworm counting is not a reliable indicator of earthworm biodiversity. Tillage had a negative impact (p < 0.05) on earthworm populations and organic matter management did not mitigate tillage impacts. In terms of farmer participation, Twitter and Farmers Weekly magazine were highly effective channels for recruitment. Direct feedback from participants included excellent scores in trust, value and satisfaction of the protocol (e.g. 100 % would do the test again) and 57 % would use their worm survey results to change their soil management practices. A key training need in terms of earthworm identification skills was reported. The trade-off between data quality, participation rates and fieldwork costs suggests there is potential to streamline the protocol further to #30minuteworms (5 pits), incurring farmer fieldwork costs of approximately £1.48 ha-1. At national scales, £14 million pounds across 4.7 M ha-1 in fieldwork costs per survey could be saved by farmer participation.