bluuebunny/crossref_metadata_2025_split huggingface dataset:
Somatic mutation detection using various targeted detection assays in paired samples of circulating tumor DNA, primary tumor and metastases from patients undergoing resection of colorectal liver metastases
Authors: Beije Nick , Helmijr Jean C. , Weerts Marjolein J.A. , Beaufort Corine M. , Wiggin Matthew , Marziali Andre , Verhoef Cornelis , Sleijfer Stefan , Jansen Maurice P.H.M. , Martens John W.M. 
Published: October 2016

AbstractAssessing circulating tumor DNA (ctDNA) is a promising method to evaluate somatic mutations from solid tumors in a minimally‐invasive way. In a group of twelve metastatic colorectal cancer (mCRC) patients undergoing liver metastasectomy, from each patient DNA from cell‐free DNA (cfDNA), the primary tumor, metastatic liver tissue, normal tumor‐adjacent colon or liver tissue, and whole blood were obtained. Investigated was the feasibility of a targeted NGS approach to identify somatic mutations in ctDNA. This targeted NGS approach was also compared with NGS preceded by mutant allele enrichment using synchronous coefficient of drag alteration technology embodied in the OnTarget assay, and for selected mutations with digital PCR (dPCR). All tissue and cfDNA samples underwent IonPGM sequencing for a CRC‐specific 21‐gene panel, which was analyzed using a standard and a modified calling pipeline. In addition, cfDNA, whole blood and normal tissue DNA were analyzed with the OnTarget assay and with dPCR for specific mutations in cfDNA as detected in the corresponding primary and/or metastatic tumor tissue. NGS with modified calling was superior to standard calling and detected ctDNA in the cfDNA of 10 patients harboring mutations in APC, ATM, CREBBP, FBXW7, KRAS, KMT2D, PIK3CA and TP53. Using this approach, variant allele frequencies in plasma ranged predominantly from 1 to 10%, resulting in limited concordance between ctDNA and the primary tumor (39%) and the metastases (55%). Concordance between ctDNA and tissue markedly improved when ctDNA was evaluated for KRAS, PIK3CA and TP53 mutations by the OnTarget assay (80%) and digital PCR (93%). Additionally, using these techniques mutations were observed in tumor‐adjacent tissue with normal morphology in the majority of patients, which were not observed in whole blood. In conclusion, in these mCRC patients with oligometastatic disease NGS on cfDNA was feasible, but had limited sensitivity to detect all somatic mutations present in tissue. Digital PCR and mutant allele enrichment before NGS appeared to be more sensitive to detect somatic mutations.
Abnormal Joint Moment Distributions and Functional Performance During Sit‐to‐Stand in Femoroacetabular Impingement Patients
Authors: Samaan Michael A. , Schwaiger Benedikt J. , Gallo Matthew C. , Link Thomas M. , Zhang Alan L. , Majumdar Sharmila , Souza Richard B. 
Published: October 2016

AbstractBackgroundFemoroacetabular impingement (FAI) is a morphological abnormality of the hip joint that causes pain when performing a mechanically demanding activity of daily living such as the sit‐to‐stand (STS) task. Previous studies have assessed lower extremity joint mechanics during an STS task in various pathologies, yet the STS task has not been studied in FAI patients.ObjectiveThe objective of this study was to identify differences in joint kinetics and performance between FAI patients and healthy controls during a STS task. It was hypothesized that FAI patients would exhibit altered time needed to complete the STS task, as well as altered lower extremity biomechanics, when compared to healthy controls.DesignThis was a cross‐sectional cohort study.SettingThe study took place at a motion capture laboratory at an institutional orthopedic facility.ParticipantsBiomechanical analysis was performed in 17 FAI patients and 31 age‐ and body mass index (BMI)−matched healthy controls during the STS task.MethodsSagittal plane joint moments, total support moment (TSM), joint contributions to the TSM, and functional measures during the STS task were compared between groups.Main Outcome MeasurementsPeak joint moments, TSM and joint contributions to the TSM were assessed during the STS task. In addition, the time to and value of the peak vertical ground reaction force (vGRF), limb symmetry index at peak vGRF, loading rate, and total time needed to perform the STS task were determined.ResultsCompared to the control participants, the FAI patients exhibited worse Hip Disability and Osteoarthritis Outcome Score (HOOS) pain and function subscores. No group differences were observed in peak sagittal joint moments during the STS task. However, when compared to controls, the FAI patients demonstrated reduced knee joint contributions to the TSM. In addition, the FAI patients exhibited increased time needed to perform the STS task, increased time to reach peak vGRF, and reduced lower extremity loading rate during the STS task.ConclusionsFAI patients demonstrated abnormal joint contributions to TSM and altered functional performance during the STS task. These altered movement patterns during the STS task may be compensatory mechanisms used by the FAI patients to reduce pain and to improve function.Level of EvidenceNot applicable.
Visuospatial memory improvement in patients with diffuse axonal injury (DAI): a 1-year follow-up study
Authors: Zaninotto Ana Luiza , Vicentini Jessica Elias , Solla Davi Jorge Fontoura , Silva Tatiana Tateishi , Guirado Vinicius Monteiro de Paula , Feltrin Fabrício , de Lucia Mara Cristina Souza , Teixeira Manoel Jacobsen , Paiva Wellingson Silva 
Published: October 2016

ObjectiveDiffuse axonal injury (DAI) is prevalent in traumatic brain injury (TBI), and is often associated with poor outcomes and cognitive impairment, including memory deficits. Few studies have explored visual memory after TBI and its relationship to executive functioning. Executive functioning is crucial for remembering an object’s location, operating devices, driving, and route finding. We compared visual memory performance via the Rey–Osterrieth Complex Figure (ROCF) test 6 and 12 months after DAI.MethodIn total, 40 patients (mean age 28.7 years; 87.5% male) with moderate-to-severe DAI following a road traffic accident completed the 1-year follow-up. There was a three-phase prospective assessment. In phase 1 (1–3 months after trauma), patients completed the Beck Depression Inventory (BDI) and State-Trait Anxiety Inventory (STAI). In phases 2 (6 months) and 3 (12 months), they completed the BDI, STAI, and a neuropsychological battery [ROCF copy and recall, digit span forward/backward, Grooved Pegboard test, intelligence quotient (IQ) by Wechsler Adult Intelligence Scale-III (WAIS-III)].ResultsThere was an improvement in ROCF recall over time (p=0.013), but not ROCF copy (p=0.657).There was no change in executive function (Savage scores) copy (p=0.230) or recall (p=0.155). Age, years of education, severity of the trauma, and IQ did not influence ROCF recall improvement.ConclusionThere are time-dependent improvements in visual memory in patients with DAI. Neuroplasticity in the 1st months after trauma provides an opportunity for visuospatial memory learning. The present findings may be useful to formulate management plans for long-term TBI rehabilitation.
Maternal diet quality before pregnancy and risk of childhood leukaemia
Authors: Singer Amanda W. , Carmichael Suzan L. , Selvin Steve , Fu Cecilia , Block Gladys , Metayer Catherine 
Published: October 2016

AbstractPrevious studies on maternal nutrition and childhood leukaemia risk have focused on the role of specific nutrients such as folate and have not considered broader measures of diet quality, which may better capture intake of diverse nutrients known to impact fetal development. We examined the relationship between maternal diet quality before pregnancy, as summarised by a diet quality index, and risk of childhood acute lymphoblastic leukaemia (ALL) and acute myeloid leukaemia (AML) in a case–control study in California. Dietary intake in the year before pregnancy was assessed using FFQ in 681 ALL cases, 103 AML cases and 1076 matched controls. Conditional logistic regression was used to estimate OR and 95 % CI for diet quality continuous score and quartiles (Q1–Q4). Higher maternal diet quality score was associated with reduced risk of ALL (OR 0·66; 95 % CI 0·47, 0·93 for Q4v.Q1) and possibly AML (OR 0·42; 95 % CI 0·15, 1·15 for Q4v.Q1). No single index component appeared to account for the association. The association of maternal diet quality with risk of ALL was stronger in children diagnosed under the age of 5 years and in children of women who did not report using vitamin supplements before pregnancy. These findings suggest that the joint effects of many dietary components may be important in influencing childhood leukaemia risk.
Vitamin D3supplementation in healthy adults: a comparison between capsule and oral spray solution as a method of delivery in a wintertime, randomised, open-label, cross-over study
Authors: Todd Joshua J. , McSorley Emeir M. , Pourshahidi L. Kirsty , Madigan Sharon M. , Laird Eamon , Healy Martin , Magee Pamela J. 
Published: October 2016

AbstractVitamin D is typically supplied in capsule form, both in trials and in clinical practice. However, little is known regarding the efficacy of vitamin D administered via oral sprays – a method that primarily bypasses the gastrointestinal absorption route. This study aimed to compare the efficacy of vitamin D3liquid capsules and oral spray solution in increasing wintertime total 25-hydroxyvitamin D (25(OH)D) concentrations. In this randomised, open-label, cross-over trial, healthy adults (n22) received 3000 IU (75 µg) vitamin D3daily for 4 weeks in either capsule or oral spray form. Following a 10-week washout phase, participants received the opposite treatment for a final 4 weeks. Anthropometrics and fasted blood samples were obtained before and after supplementation, with samples analysed for total 25(OH)D, creatinine, intact parathyroid hormone and adjusted Ca concentrations. At baseline, vitamin D sufficiency (total 25(OH)D>50 nmol/l), insufficiency (31–49 nmol/l) and clinical deficiency (<30 nmol/l) were evident in 59, 23 and 18 % of the participants, respectively. Overall, baseline total mean 25(OH)D concentration averaged 59·76 (sd29·88) nmol/l, representing clinical sufficiency. ANCOVA revealed no significant difference in the mean and standard deviation change from baseline in total 25(OH)D concentrations between oral spray and capsule supplementation methods (26·15 (sd17·85)v. 30·38 (sd17·91) nmol/l, respectively;F=1·044, adjustedr20·493,P=0·313). Oral spray vitamin D3is an equally effective alternative to capsule supplementation in healthy adults.
ADOPTION OF RICE VARIETIES. 2. ACCELERATING UPTAKE
Authors: WITCOMBE J. R. , KHADKA K. , PURI R. R. , KHANAL N. P. , SAPKOTA A. , JOSHI K. D. 
Published: October 2016

SUMMARYPlant breeding makes genetic gains over years, so growing newer varieties generally provides greater benefits than growing older ones. However, in low-altitude districts of Nepal, a few rice varieties covered 75% of the rice area and were more than 20 years old (first paper in this series). We test here if this slow rate of adoption of new varieties could be accelerated using a participatory method, Informal Research and Development (IRD), where packets of seeds of new rice varieties are widely distributed to many farmers. From 2008 to 2011, over 117 000 IRD packets were distributed in 18 districts of the Nepal Terai, including over 70 000 of three released varieties from a client-oriented breeding (COB) programme in Nepal. The IRD significantly increased the adoption of the three COB varieties. The benefits obtained by farmers in a single growing season equal the costs of IRD, if for every 75 kits distributed an additional 1 ha is grown. This assumes that the new varieties produce a 10% increase in yield (lower than that evidenced in their release proposals). On an average, fewer than three IRD kits were distributed for each hectare of a new variety grown by farmers in 2011. Furthermore, the effectiveness of IRD could be increased 1.2 to 2.7 fold (depending on the COB variety) if the IRD distribution were to be restricted to the region where the variety was most accepted. The best comparison of IRD with extension by the conventional system was their popularity compared with similar-aged varieties that had been promoted in the two systems. The adoption of three COB varieties was about twicethat of three varieties from the National Rice Research Programme (NRRP) that were closest in release date to the COB varieties. Unlike cost effectiveness assessed by hectares grown per IRD kit distributed, this comparison can only indicate efficacy because, as well as extension method, many factors influenced the adoption rates of the COB and NRRP varieties. The costs of IRD are small, both relative to the cost of breeding new varieties and to the benefits gained; so it is one of the simplest and most cost-effective interventions to increase agricultural productivity.
BODY MASS INDEX VALUES IN THE GENTRY AND PEASANTRY IN NINETEENTH AND EARLY TWENTIETH CENTURY POLAND
Authors: Czapla Zbigniew , Liczbińska Grażyna , Piontek Janusz 
Published: October 2016

SummaryThe aim of this study was to assess the impact of social and occupational status on the BMI of the gentry and peasantry in the Kingdom of Poland at the turn of 19th and early 20th centuries. Use was made of data on the height and weight of 304 men, including 200 peasants and 104 gentlemen, and 275 women, including 200 from the peasantry and 75 from the gentry. Gentlemen were characterized by a greater body height than peasants (169.40 cm and 166.96 cm, respectively), a greater body weight (67.09 kg and 60.99 kg, respectively) and a higher BMI (23.33 kg/m2and 21.83 kg/m2, respectively). Landowners and intelligentsia had a greater BMI than peasants (23.12 kg/m2and 24.20 kg/m2vs 21.83 kg/m2, respectively). In the case of women, there were no statistically significant differences in mean height, weight and BMI by their social position, and in BMI by occupational status. Underweight occurred less frequently in the gentry and more frequently in the peasantry (0.97% and 2.04%, respectively). Overweight was five times more common in gentlemen than in peasants (26.21% and 5.10%, respectively). Differences in the BMI of gentlefolk and peasants resulted from differences in diet and lifestyle related to socioeconomic status.
Directed complete poset models of T1 spaces
Authors: ZHAO DONGSHENG , XI XIAOYONG 
Published: October 2016

AbstractA poset model of a topological space X is a poset P such that the subspace Max(P) of the Scott space ΣP is homeomorphic to X, where Max(P) is the set of all maximal points of P. Every T1 space has a (bounded complete algebraic) poset model. It was, however, not known whether every T1 space has a directed complete poset model and whether every sober T1 space has a directed complete poset model whose Scott topology is sober. In this paper we give a positive answer to each of these two problems. For each T1 space X, we shall construct a directed complete poset E that is a model of X, and prove that X is sober if and only if the Scott space Σ E is sober. One useful by-product is a method for constructing more directed complete posets whose Scott topology is not sober.
Labelled seeds and the mutation group
Authors: KING ALASTAIR , PRESSLAND MATTHEW 
Published: October 2016

AbstractWe study the set${\mathcal{S}}$of labelled seeds of a cluster algebra of rankninside a field${\mathcal{F}}$as a homogeneous space for the groupMnof (globally defined) mutations and relabellings. Regular equivalence relations on${\mathcal{S}}$are associated to subgroupsWof AutMn(${\mathcal{S}}$), and we thus obtain groupoidsW\${\mathcal{S}}$. We show that for two natural choices of equivalence relation, the corresponding groupsWcandW+act on${\mathcal{F}}$, and the groupoidsWc\${\mathcal{S}}$andW+\${\mathcal{S}}$act on the model field${\mathcal{K}}$=ℚ(x1,. . .,xn). The groupoidW+\${\mathcal{S}}$is equivalent to Fock–Goncharov's cluster modular groupoid. Moreover,Wcis isomorphic to the group of cluster automorphisms, andW+to the subgroup of direct cluster automorphisms, in the sense of Assem–Schiffler–Shramchenko.We also prove that, for mutation classes whose seeds have mutation finite quivers, the stabiliser of a labelled seed underMndetermines the quiver of the seed up to ‘similarity’, meaning up to taking opposites of some of the connected components. Consequently, the subgroupWcis the entire automorphism group of${\mathcal{S}}$in these cases.
Global fascism: geography, timing, support, and strategy
Authors: Jacoby Tim 
Published: October 2016

AbstractThis article considers four aspects for understanding the greatly over-used term ‘fascism’: its place in space and also in time, the basis of its social support, and its modus operandi. While agreement exists on where and when fascism reached its apogee, there is little concurrence of opinion over the extent to which the world wars were determinative in its birth and death, and how far beyond European boundaries it has ventured. There are also wide-ranging discussions concerning the identity and extent of its backers, with some writers pointing to the formative role of the lumpen body politic, or various class fractions, and others to that of an elite vanguard, or even individual alienation. A similar spectrum of opinion over the basis of fascism’s appeal extends from studies emphasizing, and elucidating, its ideational content to those that focus on the pragmatic value of action. Such a great diversity of analyses brings both considerable empirical richness and the challenge of fragmentation. This article responds by reflecting on fascism as both a social phenomenon and a field of study, in the hope of bringing some analytical structure to what remains a vast, and continuously developing, literature.
Democracy and institutions in postcolonial Africa
Authors: GREEN ALAN 
Published: October 2016

AbstractAfrica has seen a steady rise in democracy since the end of the Cold War. This paper investigates two possible implications of democratization in African countries: better economic growth through improved institutions and less civil conflict through increased political participation. Instrumental variables regressions are estimated with the spatial lag of democracy. This instrument varies over time, allowing for consideration of country fixed effects in IV regressions. Large positive impacts of institutions on economic growth and of political participation on reducing civil conflict are found in IV regressions with fixed effects. Further estimates show that both growth and civil violence effects may be driven by civil liberties.
Specification of haematopoietic stem cell fate via modulation of mitochondrial activity
Authors: Vannini Nicola , Girotra Mukul , Naveiras Olaia , Nikitin Gennady , Campos Vasco , Giger Sonja , Roch Aline , Auwerx Johan , Lutolf Matthias P. 
Published: October 2016

AbstractHaematopoietic stem cells (HSCs) differ from their committed progeny by relying primarily on anaerobic glycolysis rather than mitochondrial oxidative phosphorylation for energy production. However, whether this change in the metabolic program is the cause or the consequence of the unique function of HSCs remains unknown. Here we show that enforced modulation of energy metabolism impacts HSC self-renewal. Lowering the mitochondrial activity of HSCs by chemically uncoupling the electron transport chain drives self-renewal under culture conditions that normally induce rapid differentiation. We demonstrate that this metabolic specification of HSC fate occurs through the reversible decrease of mitochondrial mass by autophagy. Our data thus reveal a causal relationship between mitochondrial metabolism and fate choice of HSCs and also provide a valuable tool to expand HSCs outside of their native bone marrow niches.
Polarization of M2 macrophages requires Lamtor1 that integrates cytokine and amino-acid signals
Authors: Kimura Tetsuya , Nada Shigeyuki , Takegahara Noriko , Okuno Tatsusada , Nojima Satoshi , Kang Sujin , Ito Daisuke , Morimoto Keiko , Hosokawa Takashi , Hayama Yoshitomo , Mitsui Yuichi , Sakurai Natsuki , Sarashina-Kida Hana , Nishide Masayuki , Maeda Yohei , Takamatsu Hyota , Okuzaki Daisuke , Yamada Masaki , Okada Masato , Kumanogoh Atsushi 
Published: October 2016

AbstractMacrophages play crucial roles in host defence and tissue homoeostasis, processes in which both environmental stimuli and intracellularly generated metabolites influence activation of macrophages. Activated macrophages are classified into M1 and M2 macrophages. It remains unclear how intracellular nutrition sufficiency, especially for amino acid, influences on macrophage activation. Here we show that a lysosomal adaptor protein Lamtor1, which forms an amino-acid sensing complex with lysosomal vacuolar-type H+-ATPase (v-ATPase), and is the scaffold for amino acid-activated mTORC1 (mechanistic target of rapamycin complex 1), is critically required for M2 polarization. Lamtor1 deficiency, amino-acid starvation, or inhibition of v-ATPase and mTOR result in defective M2 polarization and enhanced M1 polarization. Furthermore, we identified liver X receptor (LXR) as the downstream target of Lamtor1 and mTORC1. Production of 25-hydroxycholesterol is dependent on Lamtor1 and mTORC1. Our findings demonstrate that Lamtor1 plays an essential role in M2 polarization, coupling immunity and metabolism.
Nicotinamide is an endogenous agonist for a C. elegans TRPV OSM-9 and OCR-4 channel
Authors: Upadhyay Awani , Pisupati Aditya , Jegla Timothy , Crook Matt , Mickolajczyk Keith J. , Shorey Matthew , Rohan Laura E. , Billings Katherine A. , Rolls Melissa M. , Hancock William O. , Hanna-Rose Wendy 
Published: October 2016

AbstractTRPV ion channels are directly activated by sensory stimuli and participate in thermo-, mechano- and chemo-sensation. They are also hypothesized to respond to endogenous agonists that would modulate sensory responses. Here, we show that the nicotinamide (NAM) form of vitamin B3 is an agonist of a Caenorhabditis elegans TRPV channel. Using heterologous expression in Xenopus oocytes, we demonstrate that NAM is a soluble agonist for a channel consisting of the well-studied OSM-9 TRPV subunit and relatively uncharacterized OCR-4 TRPV subunit as well as the orthologous Drosophila Nan-Iav TRPV channel, and we examine stoichiometry of subunit assembly. Finally, we show that behaviours mediated by these C. elegans and Drosophila channels are responsive to NAM, suggesting conservation of activity of this soluble endogenous metabolite on TRPV activity. Our results in combination with the role of NAM in NAD+ metabolism suggest an intriguing link between metabolic regulation and TRPV channel activity.
Parental vitamin deficiency affects the embryonic gene expression of immune-, lipid transport- and apolipoprotein genes
Authors: Skjærven Kaja H. , Jakt Lars Martin , Dahl John Arne , Espe Marit , Aanes Håvard , Hamre Kristin , Fernandes Jorge M. O. 
Published: October 2016

AbstractWorld Health Organization is concerned for parental vitamin deficiency and its effect on offspring health. This study examines the effect of a marginally dietary-induced parental one carbon (1-C) micronutrient deficiency on embryonic gene expression using zebrafish. Metabolic profiling revealed a reduced 1-C cycle efficiency in F0generation. Parental deficiency reduced the fecundity and a total of 364 genes were differentially expressed in the F1embryos. The upregulated genes (53%) in the deficient group were enriched in biological processes such as immune response and blood coagulation. Several genes encoding enzymes essential for the 1-C cycle and for lipid transport (especially apolipoproteins) were aberrantly expressed. We show that a parental diet deficient in micronutrients disturbs the expression in descendant embryos of genes associated with overall health and result in inherited aberrations in the 1-C cycle and lipid metabolism. This emphasises the importance of parental micronutrient status for the health of the offspring.