bluuebunny/crossref_metadata_2025_split huggingface dataset:
Association between anthraquinone laxatives and colorectal cancer: protocol for a systematic review and meta-analysis
Authors: Lombardi Niccolò , Bettiol Alessandra , Crescioli Giada , Maggini Valentina , Gallo Eugenia , Sivelli Francesco , Sofi Francesco , Gensini Gian Franco , Vannacci Alfredo , Firenzuoli Fabio 
Published: January 2020

Abstract
Introduction
Products containing anthraquinones (AQ) are mainly used as laxatives and have several biological effects. Long-term use of AQ laxatives is associated with an increased risk of serious adverse events (AEs), such as colorectal cancer (CRC). We will systematically synthesize the evidence on the potential association between the use of AQ laxatives and the risk of CRC.

Methods and analysis
We will search MEDLINE, Embase, Scopus, the Cochrane Library, Google Scholar, and Clinicaltrials.gov. To avoid missing any relevant studies, we will search the bibliographies of retrieved papers and recent reviews in the field. Interventions will include products containing oral AQ laxatives, in particular, those derived from rhubarb, senna, cascara, buckhorn, and aloe. Two review authors will independently screen title, abstract, and full texts and will independently extract data from included studies. The primary outcome is the number of participants diagnosed with CRC, while the secondary outcome will be cases of melanosis coli. We will also consider all other AEs reported in the included studies, in particular, intestinal bleeding, alterations of gastrointestinal motility, and potential for dependence. When possible and appropriate, for each outcome, a meta-analysis will be performed.

Discussion
This protocol is prepared in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses Protocols guidelines. The protocol gives an insight into the scope and parameters for the systematic review to be carried out.

Systematic review registration
PROSPERO CRD42019125414
Extended Tension Chord Model for Boundary Elements of RC Walls Accounting for Anchorage Slip and Lap Splices Presence
Authors: Tarquini Danilo , de Almeida João Pacheco , Beyer Katrin 
Published: January 2020

AbstractThis paper presents a mechanical model for the simulation of reinforced concrete (RC) wall boundary elements with lap splices, which builds on the tension chord model. The model is composed of an assembly of components, each one accounting for a different source of deformation. Namely: (i) an anchorage-slip element accounting for the strain penetration of the longitudinal reinforcement into the foundation; (ii) a basic tension chord element evaluating the response outside the lap splice zone; and (iii) a lap splice element describing the behaviour within the lap splice region. For an imposed global displacement, the model provides the steel and concrete stress and strain distributions, the crack distribution and opening, as well as the global resisting axial force. For spliced members, the ultimate displacement is computed through a semi-empirical relationship providing the average lap splice strain at failure. Validation is carried out against a series of uniaxial cyclic tests on RC wall boundary elements featuring both continuous and spliced reinforcement; different lap splice lengths and confining reinforcement are considered. Overall, a good match is obtained between numerical and experimental results in terms of crack width, rebar strain distribution along the splices and ultimate displacement.
Dietary effects on gut microbiota of the mesquite lizard Sceloporus grammicus (Wiegmann, 1828) across different altitudes
Authors: Montoya-Ciriaco Nina , Gómez-Acata Selene , Muñoz-Arenas Ligia Catalina , Dendooven Luc , Estrada-Torres Arturo , Díaz de la Vega-Pérez Aníbal H. , Navarro-Noya Yendi E. 
Published: January 2020

AbstractBackgroundHigh-altitude ecosystems are extreme environments that generate specific physiological, morphological, and behavioral adaptations in ectotherms. The shifts in gut microbiota of the ectothermic hosts as an adaptation to environmental changes are still largely unknown. We investigated the food ingested and the bacterial, fungal, and protistan communities in feces of the lizardSceloporus grammicusinhabiting an altitudinal range using metabarcoding approaches.ResultsThe bacterial phylaBacteroidetesandFirmicutes, and the generaBacteroidesandParabacteroidesdominated the core fecal bacteriome, whileZygomycotaandAscomycota, and the speciesBasidiobolus ranarumandBasidiobolus magnusdominated the core fecal mycobiome. The diet ofS.grammicusincluded 29 invertebrate families belonging toArachnida,Chilopoda, andInsecta. The diversity and abundance of its diet decreased sharply at high altitudes, while the abundance of plant material andAgaricomyceteswas significantly higher at the highest site. The composition of the fecal microbiota ofS.grammicuswas different at the three altitudes, but not between females and males. Dietary restriction inS.grammicusat 4150 m might explain the high fecal abundance ofAkkermansiaandOscillopira, bacteria characteristic of long fasting periods, while low temperature favoredB.magnus. A high proportion of bacterial functions were digestive inS.grammicusat 2600 and 3100, while metabolism of aminoacids, vitamins, and key intermediates of metabolic pathways were higher at 4150 m. Different assemblages of fungal species in the lizard reflect differences in the environments at different elevations. Pathogens were more prevalent at high elevations than at the low ones.ConclusionsLimiting food resources at high elevations might obligeS.grammicusto exploit other food resources and its intestinal microbiota have degradative and detoxifying capacities.Sceloporus grammicusmight have acquiredB.ranarumfrom the insects infected by the fungus, but its commensal relationship might be established by the quitinolytic capacities ofB.ranarum.The mycobiome participate mainly in digestive and degradative functions while the bacteriome in digestive and metabolic functions.
Increased replication of dissimilatory nitrate-reducing bacteria leads to decreased anammox bioreactor performance
Authors: Keren Ray , Lawrence Jennifer E. , Zhuang Weiqin , Jenkins David , Banfield Jillian F. , Alvarez-Cohen Lisa , Zhou Lijie , Yu Ke 
Published: January 2020

Abstract
Background
Anaerobic ammonium oxidation (anammox) is a biological process employed to remove reactive nitrogen from wastewater. While a substantial body of literature describes the performance of anammox bioreactors under various operational conditions and perturbations, few studies have resolved the metabolic roles of their core microbial community members.

Results
Here, we used metagenomics to study the microbial community of a laboratory-scale anammox bioreactor from inoculation, through a performance destabilization event, to robust steady-state performance. Metabolic analyses revealed that nutrient acquisition from the environment is selected for in the anammox community. Dissimilatory nitrate reduction to ammonium (DNRA) was the primary nitrogen removal pathway that competed with anammox. Increased replication of bacteria capable of DNRA led to the out-competition of anammox bacteria, and the loss of the bioreactor’s nitrogen removal capacity. These bacteria were highly associated with the anammox bacterium and considered part of the core microbial community.

Conclusions
Our findings highlight the importance of metabolic interdependencies related to nitrogen- and carbon-cycling within anammox bioreactors and the potentially detrimental effects of bacteria that are otherwise considered core microbial community members.
Towards a new school’s role in the Italian contemporary city
Authors: Nucci Lucia , Galimberti Laura 
Published: January 2020

AbstractIn Italy there is a considerable amount of experience in school constructions from the 60s that have anticipated the Italian national school’s standards with a fair level of quality. Like in other countries this historical patrimony is now obsolete for several reasons of which: prefabrication, asbestos-containing materials, artificial glass fibres. The paper examines the activities carried out by the Italian Mission Structure for School Buildings Struttura di Missione per l’Edilizia Scolastica (SMES) for the coordination and boost in the implementation of the school buildings’ regeneration projects. The SMES was an office led by the Presidency of the Council of Ministers, engaged in regenerating and improving school building’s safety between 2014 and 2018.
Morphological characteristics of local entomopathogenic protozoan strains isolated from insect cadavers of certain stored-grain pests in Egypt
Authors: Alfazairy Ahlam Ahmed , El-Abed Yasien Mohamed Gamal , Karam Hedaya Hamza , Ramadan Hanan Mohamed 
Published: January 2020

AbstractThe present study has documented, for the first time in Egypt, the natural occurrence of four entomopathogenic protozoans (EPP) among five of the most abundant and damaging insect pests of stored grains or their products. These insect pests (Laemophloeus (Cryptolestes) turcicus (Grouvelle), Rhyzopertha dominica (Fabricius), Sitophilus zeamais (Motschulsky), Tribolium castaneum (Herbst), and Plodia interpunctella (Hobner) were infesting lots of crushed-maize grains, wheat grains, and wheat flour, brought, in 2015, from El-Behera Governorate, Egypt. The morphological characteristics, including spore size, of the entomopathogen infective units, spores, of the isolated entomopathogenic protozoans, were closely fit with the description to the following genera: Mattesia, Farinocystis, Adelina, and Nosema. The prevalence of these entomopathogens ranged between 9 and 89%. This study seems to be the first report of Mattesia sp. on S. zeamais; Adelina sp. on L. turcicus or R. dominica, and the second report of Nosema sp. on R. dominica. The rate of natural infection by the neogregarine, Mattesia sp. (tentatively, M. dispora), was the highest in L. turcicus beetles (89%) followed by that in P. interpunctella moths (48%), larvae (40%), and pupae (32%) and then in S. zeamais weevils (42%) and R. dominica beetles with a low rate of infection (9%). The microsporidian entomopathogen, Nosema sp., (tentatively, N. whitei) was naturally occurred in 11% of the examined adult cadavers of R. dominica. The coccidian entomopathogen, Adelina sp., was found, respectively, in 60% and 27% of larval and adult cadavers of T.castaneum, while the Adelina-natural infection rates in R. dominica and L. turcicus adult cadavers were 34% and 14%, respectively. A high rate of natural infection with another neogregarine, Farinocystis sp. (tentatively, F. tribolii), has also been recorded in T. castaneum adult (50%) or larval cadavers (36%).
Randomized, Multicenter, Phase II Trial of Gemcitabine and Cisplatin With or Without Veliparib in Patients With Pancreas Adenocarcinoma and a Germline BRCA/PALB2 Mutation
Authors: O’Reilly Eileen M. , Lee Jonathan W. , Zalupski Mark , Capanu Marinela , Park Jennifer , Golan Talia , Tahover Esther , Lowery Maeve A. , Chou Joanne F. , Sahai Vaibhav , Brenner Robin , Kindler Hedy L. , Yu Kenneth H. , Zervoudakis Alice , Vemuri Shreya , Stadler Zsofia K. , Do Richard K. G. , Dhani Neesha , Chen Alice P. , Kelsen David P. 
Published: January 2020

PURPOSE Five percent to 9% of pancreatic ductal adenocarcinomas (PDACs) develop in patients with a germline BRCA1/2 or PALB2 (g BRCA/PALB2+) mutation. Phase IB data from a trial that used cisplatin, gemcitabine, and veliparib treatment demonstrated a high response rate (RR), disease control rate (DCR), and overall survival (OS) in this population. We designed an open-label, randomized, multicenter, two-arm phase II trial to investigate cisplatin and gemcitabine with or without veliparib in g BRCA/PALB2+ PDAC. PATIENTS AND METHODS Eligible patients had untreated g BRCA/PALB2+ PDAC with measurable stage III to IV disease and Eastern Cooperative Oncology Group performance status of 0 to 1. Treatment for patients in arm A consisted of cisplatin 25 mg/m2 and gemcitabine 600 mg/m2 intravenously on days 3 and 10; treatment for patients in arm B was the same as that for patients in arm A, and arm A also received veliparib 80 mg orally twice per day on days 1 to 12 cycled every 3 weeks. The primary end point was RRs of arm A and arm B evaluated separately using a Simon two-stage design. Secondary end points were progression-free survival, DCR, OS, safety, and correlative analyses. RESULTS Fifty patients were evaluated by modified intention-to-treat analysis. The RR for arm A was 74.1% and 65.2% for arm B ( P = .55); both arms exceeded the prespecified activity threshold. DCR was 100% for arm A and 78.3% for arm B ( P = .02). Median progression-free survival was 10.1 months for arm A (95% CI, 6.7 to 11.5 months) and 9.7 months for arm B (95% CI, 4.2 to 13.6 months; P = .73). Median OS for arm A was 15.5 months (95% CI, 12.2 to 24.3 months) and 16.4 months for arm B (95% CI, 11.7 to 23.4 months; P = .6). Two-year OS rate for the entire cohort was 30.6% (95% CI, 17.8% to 44.4%), and 3-year OS rate was 17.8% (95% CI, 8.1% to 30.7%). Grade 3 to 4 hematologic toxicities for arm A versus arm B were 13 (48%) versus seven (30%) for neutropenia, 15 (55%) versus two (9%) for thrombocytopenia, and 14 (52%) versus eight (35%) for anemia. CONCLUSION Cisplatin and gemcitabine is an effective regimen in advanced g BRCA/PALB2+ PDAC. Concurrent veliparib did not improve RR. These data establish cisplatin and gemcitabine as a standard approach in g BRCA/ PALB2+ PDAC.
Diffusion in crowded colloids of particles cyclically changing their shapes
Authors: Koyano Y. , Kitahata H. , Mikhailov A. S. 
Published: January 2020

Abstract
A simple model of an active colloid consisting of dumbbell-shaped particles that cyclically change their length without propelling themselves is proposed and analyzed. At nanoscales, it represents an idealization for bacterial cytoplasm or for a biomembrane with active protein inclusions. Our numerical simulations demonstrate that non-equilibrium conformational activity of particles can strongly affect diffusion and structural relaxation: while a passive colloid behaves as a glass, it gets progressively fluidized when the activity is turned on. Qualitatively, this agrees with experimental results on optical tracking of probe particles in bacterial and yeast cells where metabolism-induced fluidization of cytoplasm was observed.
An insertion mutation of ERBB2 enhances breast cancer cell growth and confers resistance to lapatinib through AKT signaling pathway
Authors: Yang Zi-Yan , Yang Liu , Xu Chun-Wei , Wang Xiao-Jia , Lei Lei 
Published: January 2020

ABSTRACT
In clinical practice, some breast cancer (BC) patients carry a rare ERBB2 in-frame insertion (p. Pro780_Tyr781insGlySerPro) and are resistant to anti-ERBB2 therapy. To explore the potential procarcinogenic role of this ERBB2 mutation, we conducted the present study using BC cells overexpressing wild-type (WT) ERBB2 or P780-Y781 ERBB2 [mutated (MT)]. MDA-MB-231 and MCF-7 cells were transfected with the following plasmids using a lentivirus system: negative control (ERBB2-NC), WT ERBB2 overexpression (ERBB2-WT), and P780-Y781 ERBB2 overexpression (ERBB2-MT). P780-Y781 ERBB2 conferred significant resistance to lapatinib, as assessed by cell viability and colony counts. Analysis of the cell cycle showed that the P780-Y781 ERBB2 group showed an elevated proportion of cells in S, G2, and M phases compared with WT ERBB2 when exposed to lapatinib. Following lapatinib treatment, phosphorylated AKT (p-AKT) was strongly upregulated in the P780-Y781 ERBB2 group. Among ERBB2+ patients, the P780-Y781 ERBB2 group showed increased levels of p-AKT. Furthermore, the AKT inhibitor perifosine effectively suppressed lapatinib resistance, as indicated by the lapatinib inhibition curve and results of the colony formation assay, and decreased AKT phosphorylation. Altogether, we discovered a procarcinogenic mutation of ERBB2 that enhances BC cell growth through AKT signaling and causes resistance to lapatinib. Patients with this in-frame insertion mutation of ERBB2 should be recommended other therapeutic strategies apart from ERBB2 tyrosine kinase inhibitors, in particular lapatinib.
Cellular diversity and lineage trajectory: insights from mouse single cell transcriptomes
Authors: Tam Patrick P. L. , Ho Joshua W. K. 
Published: January 2020

ABSTRACT
Single cell RNA-sequencing (scRNA-seq) technology has matured to the point that it is possible to generate large single cell atlases of developing mouse embryos. These atlases allow the dissection of developmental cell lineages and molecular changes during embryogenesis. When coupled with single cell technologies for profiling the chromatin landscape, epigenome, proteome and metabolome, and spatial tissue organisation, these scRNA-seq approaches can now collect a large volume of multi-omic data about mouse embryogenesis. In addition, advances in computational techniques have enabled the inference of developmental lineages of differentiating cells, even without explicitly introduced genetic markers. This Spotlight discusses recent advent of single cell experimental and computational methods, and key insights from applying these methods to the study of mouse embryonic development. We highlight challenges in analysing and interpreting these data to complement and expand our knowledge from traditional developmental biology studies in relation to cell identity, diversity and lineage differentiation.
Six1 proteins with human branchio-oto-renal mutations differentially affect cranial gene expression and otic development
Authors: Shah Ankita M. , Krohn Patrick , Baxi Aparna B. , Tavares Andre L. P. , Sullivan Charles H. , Chillakuru Yeshwant R. , Majumdar Himani D. , Neilson Karen M. , Moody Sally A. 
Published: January 2020

ABSTRACT
Single-nucleotide mutations in human SIX1 result in amino acid substitutions in either the protein-protein interaction domain or the homeodomain, and cause ∼4% of branchio-otic (BOS) and branchio-oto-renal (BOR) cases. The phenotypic variation between patients with the same mutation, even within affected members of the same family, make it difficult to functionally distinguish between the different SIX1 mutations. We made four of the BOS/BOR substitutions in the Xenopus Six1 protein (V17E, R110W, W122R, Y129C), which is 100% identical to human in both the protein-protein interaction domain and the homeodomain, and expressed them in embryos to determine whether they cause differential changes in early craniofacial gene expression, otic gene expression or otic morphology. We confirmed that, similar to the human mutants, all four mutant Xenopus Six1 proteins access the nucleus but are transcriptionally deficient. Analysis of craniofacial gene expression showed that each mutant causes specific, often different and highly variable disruptions in the size of the domains of neural border zone, neural crest and pre-placodal ectoderm genes. Each mutant also had differential effects on genes that pattern the otic vesicle. Assessment of the tadpole inner ear demonstrated that while the auditory and vestibular structures formed, the volume of the otic cartilaginous capsule, otoliths, lumen and a subset of the hair cell-containing sensory patches were reduced. This detailed description of the effects of BOS/BOR-associated SIX1 mutations in the embryo indicates that each causes subtle changes in gene expression in the embryonic ectoderm and otocyst, leading to inner ear morphological anomalies.
Carbon-Based Nanomaterials for Separation Media
Authors: Kanao Eisuke , Kubo Takuya , Otsuka Koji 
Published: January 2020

Abstract
In the recent decades, separation technologies have been significantly furthered by the development of a variety of new separation media. Especially, carbon-based nanomaterials (CNMs), including graphene, carbon nanotubes, and fullerenes, have been applied for effective separations and sensitive detections in recent years. Here, the fundamental preparation protocols of new separation media consisting of CNMs and a great number of their applications summarize the fundamental preparation protocols of new separation media consisting of CNMs and a great number of their applications are summarized.
Assessment of robustness against setup uncertainties using probabilistic scenarios in lung cancer: a comparison of proton with photon therapy
Authors: Teoh Suliana , George Ben , Fiorini Francesca , Vallis Katherine A , Van den Heuvel Frank 
Published: January 2020

Objective:
We compared the sensitivity of intensity modulated proton therapy (IMPT) and photon volumetric modulated arc therapy (VMAT) plans to setup uncertainties in locally advanced non-small cell lung cancer (NSCLC) using probabilistic scenarios.

Methods:
Minimax robust (MM) and planning target volume (PTV) optimised IMPT and VMAT nominal plans were created with physical dose of 70 Gy in 35 fractions in 10 representative patients. Using population data of setup errors, a fractionated treatment course was simulated, summed (Dsum) and compared to the nominal plan. Three treatment-course simulations were done for each plan. Target robustness criteria were: dose deviation of ≤5% to clinical target volume (CTV) D98% and CTV V95% ≥ 99.9%. Voxelwise simulation repeatability was analysed using Bland–Altman plots. Acceptable limits of agreement were 2% of the prescription dose.

Results:
All Dsum met target robustness criteria. While fraction VMAT and MM-IMPT doses were excellent, simulated fraction doses in PTV-IMPT were suboptimal. Almost all (&gt;99%) of VMAT and MM-IMPT fraction doses met both target robustness criteria. For PTV-IMPT, only 96.9 and 80.3% of fractions met CTVD98% and V95% criteria respectively. Simulation repeatability was excellent (limits of agreement range: 0.41–1.1 Gy) with strong positive correlations.

Conclusion:
When considering the whole treatment course, setup errors do not influence robustness irrespective of planning techniques used. However, on a fraction level, VMAT and MM-IMPT plans are superior compared to PTV-IMPT plans.

Advances in knowledge:
Probabilistic analysis provides a fast and practical method for evaluating VMAT and IMPT plan sensitivity against setup uncertainty. VMAT and robust-optimised IMPT plans have comparable sensitivity to setup uncertainties in conventionally fractionated treatment for NSCLC.