bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Sorghum bicolor reference genome: improved assembly, gene annotations, a transcriptome atlas, and signatures of genome organization
Authors: McCormick Ryan F. , Truong Sandra K. , Sreedasyam Avinash , Jenkins Jerry , Shu Shengqiang , Sims David , Kennedy Megan , Amirebrahimi Mojgan , Weers Brock D. , McKinley Brian , Mattison Ashley , Morishige Daryl T. , Grimwood Jane , Schmutz Jeremy , Mullet John E. 
Published: November 2017

SummarySorghum bicolor is a drought tolerant C4 grass used for the production of grain, forage, sugar, and lignocellulosic biomass and a genetic model for C4 grasses due to its relatively small genome (approximately 800 Mbp), diploid genetics, diverse germplasm, and colinearity with other C4 grass genomes. In this study, deep sequencing, genetic linkage analysis, and transcriptome data were used to produce and annotate a high‐quality reference genome sequence. Reference genome sequence order was improved, 29.6 Mbp of additional sequence was incorporated, the number of genes annotated increased 24% to 34 211, average gene length and N50 increased, and error frequency was reduced 10‐fold to 1 per 100 kbp. Subtelomeric repeats with characteristics of Tandem Repeats in Miniature (TRIM) elements were identified at the termini of most chromosomes. Nucleosome occupancy predictions identified nucleosomes positioned immediately downstream of transcription start sites and at different densities across chromosomes. Alignment of more than 50 resequenced genomes from diverse sorghum genotypes to the reference genome identified approximately 7.4 M single nucleotide polymorphisms (SNPs) and 1.9 M indels. Large‐scale variant features in euchromatin were identified with periodicities of approximately 25 kbp. A transcriptome atlas of gene expression was constructed from 47 RNA‐seq profiles of growing and developed tissues of the major plant organs (roots, leaves, stems, panicles, and seed) collected during the juvenile, vegetative and reproductive phases. Analysis of the transcriptome data indicated that tissue type and protein kinase expression had large influences on transcriptional profile clustering. The updated assembly, annotation, and transcriptome data represent a resource for C4 grass research and crop improvement.
Leading components in forward elastic hadron scattering: Derivative dispersion relations and asymptotic uniqueness
Authors: Fagundes D. A. , Menon M. J. , Silva P. V. R. G. 
Published: November 2017

Forward amplitude analyses constitute an important approach in the investigation of the energy dependence of the total hadronic cross-section [Formula: see text] and the [Formula: see text] parameter. The standard picture indicates for [Formula: see text] a leading log-squared dependence at the highest c.m. energies, in accordance with the Froissart–Lukaszuk–Martin bound and as predicted by the COMPETE Collaboration in 2002. Beyond this log-squared (L2) leading dependence, other amplitude analyses have considered a log-raised-to-gamma form [Formula: see text], with [Formula: see text] as a real free fit parameter. In this case, analytic connections with [Formula: see text] can be obtained either through dispersion relations (derivative forms), or asymptotic uniqueness (Phragmén–Lindelöff theorems). In this work, we present a detailed discussion on the similarities and mainly the differences between the Derivative Dispersion Relation (DDR) and Asymptotic Uniqueness (AU) approaches and results, with focus on the [Formula: see text] and L2 leading terms. We also develop new Regge–Gribov fits with updated dataset on [Formula: see text] and [Formula: see text] from [Formula: see text] and [Formula: see text] scattering, including all available data in the region 5 GeV–8 TeV. The recent tension between the TOTEM and ATLAS results at 7 TeV and mainly at 8 TeV is discussed and considered in the data reductions. Our main conclusions are the following: (1) all fit results present agreement with the experimental data analyzed and the goodness-of-fit is slightly better in case of the DDR approach; (2) by considering only the TOTEM data at the LHC region, the fits with L[Formula: see text] indicate [Formula: see text] (AU approach) and [Formula: see text] (DDR approach); (3) by including the ATLAS data the fits provide [Formula: see text] (AU) and [Formula: see text] (DDR); (4) in the formal and practical contexts, the DDR approach is more adequate for the energy interval investigated than the AU approach. A pedagogical and detailed review on the analytic results for [Formula: see text] and [Formula: see text] from the Regge–Gribov, DDR and AU approaches is presented. Formal and practical aspects related to forward amplitude analyses are also critically discussed.
Precision Oncology: Between Vaguely Right and Precisely Wrong
Authors: Brock Amy , Huang Sui 
Published: November 2017

Abstract
Precision Oncology seeks to identify and target the mutation that drives a tumor. Despite its straightforward rationale, concerns about its effectiveness are mounting. What is the biological explanation for the "imprecision?" First, Precision Oncology relies on indiscriminate sequencing of genomes in biopsies that barely represent the heterogeneous mix of tumor cells. Second, findings that defy the orthodoxy of oncogenic "driver mutations" are now accumulating: the ubiquitous presence of oncogenic mutations in silent premalignancies or the dynamic switching without mutations between various cell phenotypes that promote progression. Most troublesome is the observation that cancer cells that survive treatment still will have suffered cytotoxic stress and thereby enter a stem cell–like state, the seeds for recurrence. The benefit of “precision targeting” of mutations is inherently limited by this counterproductive effect. These findings confirm that there is no precise linear causal relationship between tumor genotype and phenotype, a reminder of logician Carveth Read's caution that being vaguely right may be preferable to being precisely wrong. An open-minded embrace of the latest inconvenient findings indicating nongenetic and "imprecise" phenotype dynamics of tumors as summarized in this review will be paramount if Precision Oncology is ultimately to lead to clinical benefits. Cancer Res; 77(23); 6473–9. ©2017 AACR.
NKG2D-Dependent Antitumor Effects of Chemotherapy and Radiotherapy against Glioblastoma
Authors: Weiss Tobias , Schneider Hannah , Silginer Manuela , Steinle Alexander , Pruschy Martin , Polić Bojan , Weller Michael , Roth Patrick 
Published: November 2017

Abstract
Purpose: NKG2D is a potent activating immune cell receptor, and glioma cells express the cognate ligands (NKG2DL). These ligands are inducible by cellular stress and temozolomide (TMZ) or irradiation (IR), the standard treatment of glioblastoma, could affect their expression. However, a role of NKG2DL for the efficacy of TMZ and IR has never been addressed.
Experimental Design: We assessed the effect of TMZ and IR on NKG2DL in vitro and in vivo in a variety of murine and human glioblastoma models, including glioma-initiating cells, and a cohort of paired glioblastoma samples from patients before and after therapy. Functional effects were studied with immune cell assays. The relevance of the NKG2D system for the efficacy of TMZ and IR was assessed in vivo in syngeneic orthotopic glioblastoma models with blocking antibodies and NKG2D knockout mice.
Results: TMZ or IR induced NKG2DL in vitro and in vivo in all glioblastoma models, and glioblastoma patient samples had increased levels of NKG2DL after therapy with TMZ and IR. This enhanced the immunogenicity of glioma cells in a NGK2D-dependent manner, was independent from cytotoxic or growth inhibitory effects, attenuated by O6-methylguanine-DNA-methyltransferase (MGMT), and required the DNA damage response. The survival benefit afforded by TMZ or IR relied on an intact NKG2D system and was decreased upon inhibition of the NKG2D pathway.
Conclusions: The immune system may influence the activity of convential cancer treatments with particular importance of the NKG2D pathway in glioblastoma. Our data provide a rationale to combine NKG2D-based immunotherapies with TMZ and IR. Clin Cancer Res; 24(4); 882–95. ©2017 AACR.
Effects of Black Raspberry on Dibenzo[a,l]Pyrene Diol Epoxide Induced DNA Adducts, Mutagenesis, and Tumorigenesis in the Mouse Oral Cavity
Authors: Chen Kun-Ming , Guttenplan Joseph B. , Sun Yuan-Wan , Cooper Timothy , Shalaby Nora A.E. , Kosinska Wieslawa , Benitez Gabrielle , Aliaga Cesar , Zhu Junjia , Liao Jason , Gowda Krishne , Amin Shantu , Stoner Gary , El-Bayoumy Karam 
Published: November 2017

Abstract
We previously showed that metabolic activation of the environmental and tobacco smoke constituent dibenzo[a,l]pyrene (DB[a,l]P) to its active fjord region diol epoxide (DB[a,l]PDE) is required to induce DNA damage, mutagenesis, and squamous cell carcinoma (SCC) in the mouse oral cavity. In contrast to procarcinogens, which were employed previously to induce SCC, DB[a,l]PDE does not require metabolic activation to exert its biological effects, and thus, this study was initiated to examine, for the first time, whether black raspberry powder (BRB) inhibits postmetabolic processes, such as DNA damage, mutagenesis, and tumorigenesis. Prior to long-term chemoprevention studies, we initially examined the effect of BRB (5% added to AIN-93M diet) on DNA damage in B6C3F1 mice using LC/MS-MS and on mutagenesis in the lacI gene in the mouse oral cavity. We showed that BRB inhibited DB[a,l]PDE-induced DNA damage (P &lt; 0.05) and mutagenesis (P = 0.053) in the oral cavity. Tumor incidence in the oral cavity (oral mucosa and tongue) of mice fed diet containing 5% BRB was significantly (P &lt; 0.05) reduced from 93% to 66%. Specifically, the incidence of benign tumor was significantly (P &lt; 0.001) reduced from 90% to 31% (62% to 28% in the oral cavity and 28% to 2% in the tongue), a nonsignificant reduction of malignant tumors from 52% to 45%. Our preclinical findings demonstrate for the first time that the chemopreventive efficacy of BRB can be extended to direct-acting carcinogens that do not require phase I enzymes and is not just limited to procarcinogens. Cancer Prev Res; 11(3); 157–64. ©2017 AACR.
Traços da cultura nacional e da cultura de inovação: uma análise dos códigos de ética de empresas brasileiras
Authors: Gasparindo Leila , Grohs Ana Cristina Da Costa Piletti 
Published: November 2017

O objetivo do artigo é identificar os traços da cultura nacional e da cultura de inovação nos códigos de ética de empresas brasileiras consideradas como as mais inovadoras pelo ranking Forbes 2013. Foi uma pesquisa exploratória a partir de um estudo bibliográfico e de análise documental dos códigos de éticas de três empresas brasileiras. Como comunicadores organizacionais, verificamos que os códigos de ética podem contribuir para a formação da cultura de inovação. Identificamos que as empresas que mais incentivam os aspectos da cultura de inovação são também àquelas com melhor colocação no ranking Forbes. Consideramos que o estudo contribuiu para a sistematização de um quadro comparativo dos traços da cultura nacional e da cultura de inovação estabelecendo categorias que podem ser utilizadas em novas pesquisas e com uma amostra mais representativa do universo de organizações brasileiras.
Back to the Future: Reading the Abraham Narratives as Prequel
Authors: Warner Megan 
Published: November 2017

This paper proposes envisaging the ancestral narratives (with a special focus on the Abraham cycle) as Persian period ‘prequel’ as a fruitful approach to exploring relationship between Genesis and the Moses and monarchic traditions. The literary capacity of a prequel to influence and alter its audience’s perceptions of an earlier, principal, work means that understanding the ancestral narratives as ‘prequel’ may highlight matters not immediately apparent when the ancestral narratives are envisaged as ‘introduction’, ‘prelude’ or ‘prologue.’ Recent insights associated with the so-called ‘Death of the Yahwist,’ including Konrad Schmid’s argument about the lack of a pre-P literary source spanning Genesis and Exodus, have been important, but remain largely unexplored from the point-of-view of the ancestral narratives. This paper proposes the application of the literary category of ‘prequel’ to the ancestral narratives as one means of exploring the issues, both synchronic and diachronic, raised by these insights.
Shallow and additional records of a rare mantis shrimp, Lysiosquilla manningi Boyko, 2000 (Stomatopoda, Lysiosquillidae), in western Mexico
Authors: Hendrickx Michel E. , Salgado-Barragán José 
Published: November 2017

New records for the mantis shrimp Lysiosquilla manningi Boyko, 2000, are presented for western Mexico. They include the shallowest sampling depth on record (1.5 m) and the largest male specimen known to date (175 mm total length). The shallowest record of L. manningi came from a coastal lagoon in Mazatlán, Mexico, where Cloridopsis dubia (H. Milne Edwards, 1837) has been collected on several occasions in similar depths. This finding is intriguing considering that the type material of L. desaussurei (Stimpson, 1857) proved to be a specimen of C. dubia originally from the same locality.
Delimitation of European Crepidotus stenocystis as different from the North American species C. brunnescens (Inocybaceae, Agaricales)
Authors: JANČOVIČOVÁ SOŇA , ADAMČÍK SLAVOMÍR , LOONEY BRIAN P. , CABOŇ MIROSLAV , ČAPLOVIČOVÁ MÁRIA , KOPÁNI MARTIN , PENNYCOOK SHAUN R. , ADAMČÍKOVÁ KATARÍNA 
Published: November 2017

Crepidotus stenocystis and C. brunnescens are morphologically similar species defined by globose to subglobose spores, the presence of clamp connections in all tissues and bottle-like or flask-like cheilocystidia. They are also similar in the pileal aspect which is hygrophanous, glabrous or white-fibrillose, at first white but becoming brownish with age. Each are described from separate continents and have only been reported from their respective continents, C. stenocystis from Europe and C. brunnescens from North America. The phylogenetic analysis of ITS and LSU nrDNA regions from original type material confirms the existence of two distinct species, C. brunnescens that is more closely related to C. malachioides, and C. stenocystis that is more closely related to C. applanatus. Crepidotus stenocystis differs from C. brunnescens by its more prominent spore ornamentation and longer cheilocystidia that are frequently narrowly utriform. Based on the studied material and published data, it seems that C. stenocystis is distributed throughout all of Europe and does not occur in North America, whereas C. brunnescens is only known from Michigan in the USA.
Results of the First Arctic Heat Open Science Experiment
Authors: Wood Kevin R. , Jayne Steven R. , Mordy Calvin W. , Bond Nicholas , Overland James E. , Ladd Carol , Stabeno Phyllis J. , Ekholm Alexander K. , Robbins Pelle E. , Schreck Mary-Beth , Heim Rebecca , Intrieri Janet 
Published: November 2017

Abstract
Seasonally ice-covered marginal seas are among the most difficult regions in the Arctic to study. Physical constraints imposed by the variable presence of sea ice in all stages of growth and melt make the upper water column and air–sea ice interface especially challenging to observe. At the same time, the flow of solar energy through Alaska’s marginal seas is one of the most important regulators of their weather and climate, sea ice cover, and ecosystems. The deficiency of observing systems in these areas hampers forecast services in the region and is a major contributor to large uncertainties in modeling and related climate projections. The Arctic Heat Open Science Experiment strives to fill this observation gap with an array of innovative autonomous floats and other near-real-time weather and ocean sensing systems. These capabilities allow continuous monitoring of the seasonally evolving state of the Chukchi Sea, including its heat content. Data collected by this project are distributed in near–real time on project websites and on the Global Telecommunications System (GTS), with the objectives of (i) providing timely delivery of observations for use in weather and sea ice forecasts, for model, and for reanalysis applications and (ii) supporting ongoing research activities across disciplines. This research supports improved forecast services that protect and enhance the safety and economic viability of maritime and coastal community activities in Alaska. Data are free and open to all (see www.pmel.noaa.gov/arctic-heat/).
Voice and Swallowing Dysfunction in Neurofibromatosis 2
Authors: Best Simon R. , Ahn Julie , Langmead Shannon , Dhillon Vaninder , Hillel Alexander T. , Akst Lee M. , Blakeley Jaishri O. 
Published: November 2017

ObjectiveNeurofibromatosis 2 (NF2) is a neuro‐oncologic condition that presents with bilateral vestibular schwannomas of the cerebellopontine angle (CPA). Voice and swallowing impairment can occur from direct involvement or compression of the vagus nerve or as the result of surgical excision of CPA tumors. The objectives in this study are to (1) assess the prevalence of voice and swallowing impairments and (2) analyze the effects of vagal dysfunction in patients with NF2.Study DesignCross‐sectional.SettingAcademic tertiary care center.Subjects and MethodsPatients at a neurofibromatosis center were mailed Voice Handicap Index and Sydney Swallow Questionnaire surveys. Stroboscopic, voice, and swallowing evaluations were performed for patients who elected to participate in screening exams.ResultsThere were high rates of self‐assessed and objective voice and swallowing handicaps in this population. Fourteen of 40 (35%) patients had a self‐assessed voice handicap, and 20 of 40 (50%) patients had a self‐assessed swallow handicap. Vocal fold motion impairment (VFMI) was observed in 22 of 31 (71%) patients examined, with 27 of 62 (44%) possible vocal cords affected. Velopharyngeal insufficiency (45%) and piriform sinus pooling or residue (39%) were seen in a significant percentage of patients. There was a significant relationship between vocal cord motion impairment and CPA surgical intervention ipsilateral to the impairment (P =. 002). The presence of VFMI was strongly associated with voice (P =. 002) and swallowing (P =. 01) impact on quality of life.ConclusionSpeech and swallowing impairments are highly prevalent in patients with NF2, cause significant impact on quality of life, and are most commonly related to surgical interventions in the CPA region.
Management of transient ischemic attacks diagnosed by early-career general practitioners: A cross-sectional study
Authors: Davey Andrew R , Lasserson Daniel S , Levi Christopher R , Tapley Amanda , Morgan Simon , Henderson Kim , Holliday Elizabeth G , Ball Jean , van Driel Mieke L , McArthur Lawrie , Spike Neil A , Magin Parker J 
Published: November 2017

Background Transient ischemic attack incurs a risk of recurrent stroke that can be dramatically reduced by urgent guideline-recommended management at the point of first medical contact. Aims This study describes the prevalence and associations of new transient ischemic attack presentations to general practice registrars and the management undertaken. Methods A cross-sectional analysis of the Registrar Clinical Encounters in Training cohort study. General practice registrars from five Australian states (urban to very remote practices) collected data on 60 consecutive patient encounters during each of their three six-month training terms. The proportion of problems managed being new transient ischemic attacks and proportion of transient ischemic attacks with guideline-recommended management were calculated. Univariate and multivariable logistic regression established associations of patient, registrar, and practice factors with a problem being a new transient ischemic attack. Results A total 1331 general practice registrars contributed data (response rate 95.8%). Of the 250,625 problems, there were 65 new transient ischemic attacks diagnosed (0.03% [95% confidence interval: 0.02–0.03%]). General practice registrars were more likely to seek help, generate learning goals, and spend more time for a new transient ischemic attack compared to other problems. Compliance with management guidelines was modest: 15.4% ordered brain and arterial imaging, 36.9% prescribed antiplatelet medication, and 3.1% prescribed antihypertensive medication. Conclusions Transient ischemic attack is a very infrequent presentation for general practice registrars, giving little clinical opportunity to reinforce training program education regarding guideline-recommended management. General practice registrars found transient ischemic attacks challenging and management was not ideal. Since most transient ischemic attacks first present to general practice and urgent management is essential, an enhanced model of care utilizing rapid access to specialist transient ischemic attack support and follow-up could improve guideline compliance.
Poor glycaemic control is associated with reduced exercise performance and oxygen economy during cardio-pulmonary exercise testing in people with type 1 diabetes
Authors: Moser Othmar , Eckstein Max L. , McCarthy Olivia , Deere Rachel , Bain Stephen C. , Haahr Hanne L. , Zijlstra Eric , Bracken Richard M. 
Published: November 2017

Abstract
Background
To explore the impact of glycaemic control (HbA1c) on functional capacity during cardio-pulmonary exercise testing in people with type 1 diabetes.

Methods
Sixty-four individuals with type 1 diabetes (age: 34 ± 8 years; 13 females, HbA1c: 7.8 ± 1% (62 ± 13 mmol/mol), duration of diabetes: 17 ± 9 years) performed a cardio-pulmonary cycle ergometer exercise test until volitional exhaustion. Stepwise linear regression was used to explore relationships between HbA1c and cardio-respiratory data with p ≤ 0.05. Furthermore, participants were divided into quartiles based on HbA1c levels and cardio-respiratory data were analysed by one-way ANOVA. Multiple regression analysis was performed to explore the relationships between changes in time to exhaustion and cardio-respiratory data. Data were adjusted for confounder.

Results
HbA1c was related to time to exhaustion and oxygen consumption at the power output elicited at the sub-maximal threshold of the heart rate turn point (r = 0.47, R2 = 0.22, p = 0.03). Significant differences were found at time to exhaustion between QI vs. QIV and at oxygen consumption at the power output elicited at the heart rate turn point between QI vs. QII and QI vs. QIV (p < 0.05). Changes in oxygen uptake, power output and in oxygen consumption at the power output elicited at the heart rate turn point and at maximum power output explained 55% of the variance in time to exhaustion (r = 0.74, R2 = 0.55, p < 0.01).

Conclusions
Poor glycaemic control is related to less economical use of oxygen at sub-maximal work rates and an earlier time to exhaustion during cardio-pulmonary exercise testing. However, exercise training could have the same potential to counteract the influence of poor glycaemic control on functional capacity.
Trial registration NCT01704417. Date of registration: October 11, 2012