bluuebunny/crossref_metadata_2025_split huggingface dataset:
Liquid biopsy tracking during sequential chemo-radiotherapy identifies distinct prognostic phenotypes in nasopharyngeal carcinoma
Authors: Lv Jiawei , Chen Yupei , Zhou Guanqun , Qi Zhenyu , Tan Kuan Rui Lloyd , Wang Haitao , Lin Li , Chen Foping , Zhang Lulu , Huang Xiaodan , Liu Ruiqi , Xu Sisi , Chen Yue , Ma Jun , Chua Melvin L. K. , Sun Ying 
Published: September 2019

AbstractLiquid biopsies have the utility for detecting minimal residual disease in several cancer types. Here, we investigate if liquid biopsy tracking on-treatment informs on tumour phenotypes by longitudinally quantifying circulating Epstein-barr virus (EBV) DNA copy number in 673 nasopharyngeal carcinoma patients undergoing radical induction chemotherapy (IC) and chemo-radiotherapy (CRT). We observe significant inter-patient heterogeneity in viral copy number clearance that is classifiable into eight distinct patterns based on clearance kinetics and bounce occurrence, including a substantial proportion of complete responders (≈30%) to only one IC cycle. Using a supervised statistical clustering of disease relapse risks, we further bin these eight subgroups into four prognostic phenotypes (early responders, intermediate responders, late responders, and treatment resistant) that are correlated with efficacy of chemotherapy intensity. Taken together, we show that real-time monitoring of liquid biopsy response adds prognostic information, and has the potential utility for risk-adapted treatment de-intensification/intensification in nasopharyngeal carcinoma.
The molecular origin and taxonomy of mucinous ovarian carcinoma
Authors: Cheasley Dane , Wakefield Matthew J. , Ryland Georgina L. , Allan Prue E. , Alsop Kathryn , Amarasinghe Kaushalya C. , Ananda Sumitra , Anglesio Michael S. , Au-Yeung George , Böhm Maret , Bowtell David D. L. , Brand Alison , Chenevix-Trench Georgia , Christie Michael , Chiew Yoke-Eng , Churchman Michael , DeFazio Anna , Demeo Renee , Dudley Rhiannon , Fairweather Nicole , Fedele Clare G. , Fereday Sian , Fox Stephen B. , Gilks C Blake , Gourley Charlie , Hacker Neville F. , Hadley Alison M. , Hendley Joy , Ho Gwo-Yaw , Hughes Siobhan , Hunstman David G. , Hunter Sally M. , Jobling Tom W. , Kalli Kimberly R. , Kaufmann Scott H. , Kennedy Catherine J. , Köbel Martin , Le Page Cecile , Li Jason , Lupat Richard , McNally Orla M. , McAlpine Jessica N. , Mes-Masson Anne-Marie , Mileshkin Linda , Provencher Diane M. , Pyman Jan , Rahimi Kurosh , Rowley Simone M. , Salazar Carolina , Samimi Goli , Saunders Hugo , Semple Timothy , Sharma Ragwha , Sharpe Alice J. , Stephens Andrew N. , Thio Niko , Torres Michelle C. , Traficante Nadia , Xing Zhongyue , Zethoven Magnus , Antill Yoland C. , Scott Clare L. , Campbell Ian G. , Gorringe Kylie L. 
Published: September 2019

AbstractMucinous ovarian carcinoma (MOC) is a unique subtype of ovarian cancer with an uncertain etiology, including whether it genuinely arises at the ovary or is metastatic disease from other organs. In addition, the molecular drivers of invasive progression, high-grade and metastatic disease are poorly defined. We perform genetic analysis of MOC across all histological grades, including benign and borderline mucinous ovarian tumors, and compare these to tumors from other potential extra-ovarian sites of origin. Here we show that MOC is distinct from tumors from other sites and supports a progressive model of evolution from borderline precursors to high-grade invasive MOC. Key drivers of progression identified areTP53mutation and copy number aberrations, including a notable amplicon on 9p13. High copy number aberration burden is associated with worse prognosis in MOC. Our data conclusively demonstrate that MOC arise from benign and borderline precursors at the ovary and are not extra-ovarian metastases.
Auger-spectroscopy in quantum Hall edge channels and the missing energy problem
Authors: Krähenmann T. , Fischer S. G. , Röösli M. , Ihn T. , Reichl C. , Wegscheider W. , Ensslin K. , Gefen Y. , Meir Yigal 
Published: September 2019

AbstractQuantum Hall edge channels offer an efficient and controllable platform to study quantum transport in one dimension. Such channels are a prospective tool for the efficient transfer of quantum information at the nanoscale, and play a vital role in exposing intriguing physics. Electric current along the edge carries energy and heat leading to inelastic scattering, which may impede coherent transport. Several experiments attempting to probe the concomitant energy redistribution along the edge reported energy loss via unknown mechanisms of inelastic scattering. Here we employ quantum dots to inject and extract electrons at specific energies, to spectrally analyse inelastic scattering inside quantum Hall edge channels. We show that the missing energy puzzle could be untangled by incorporating non-local Auger-like processes, in which energy is redistributed between spatially separate parts of the sample. Our theoretical analysis, accounting for the experimental results, challenges common-wisdom analyses which ignore such non-local decay channels.
Emulating evolutionary processes to morph aureothin-type modular polyketide synthases and associated oxygenases
Authors: Peng Huiyun , Ishida Keishi , Sugimoto Yuki , Jenke-Kodama Holger , Hertweck Christian 
Published: September 2019

AbstractPolyketides produced by modular type I polyketide synthases (PKSs) play eminent roles in the development of medicines. Yet, the production of structural analogs by genetic engineering poses a major challenge. We report an evolution-guided morphing of modular PKSs inspired by recombination processes that lead to structural diversity in nature. By deletion and insertion of PKS modules we interconvert the assembly lines for related antibiotic and antifungal agents, aureothin (aur) and neoaureothin (nor) (aka spectinabilin), in both directions. Mutational and functional analyses of the polyketide-tailoring cytochrome P450 monooxygenases, and PKS phylogenies give contradictory clues on potential evolutionary scenarios (generalist-to-specialist enzyme evolution vs. most parsimonious ancestor). The KS-AT linker proves to be well suited as fusion site for both excision and insertion of modules, which supports a model for alternative module boundaries in some PKS systems. This study teaches important lessons on the evolution of PKSs, which may guide future engineering approaches.
Out-of-plane orientation of luminescent excitons in two-dimensional indium selenide
Authors: Brotons-Gisbert Mauro , Proux Raphaël , Picard Raphaël , Andres-Penares Daniel , Branny Artur , Molina-Sánchez Alejandro , Sánchez-Royo Juan F. , Gerardot Brian D. 
Published: September 2019

AbstractVan der Waals materials offer a wide range of atomic layers with unique properties that can be easily combined to engineer novel electronic and photonic devices. A missing ingredient of the van der Waals platform is a two-dimensional crystal with naturally occurring out-of-plane luminescent dipole orientation. Here we measure the far-field photoluminescence intensity distribution of bulk InSe and two-dimensional InSe, WSe2 and MoSe2. We demonstrate, with the support of ab-initio calculations, that layered InSe flakes sustain luminescent excitons with an intrinsic out-of-plane orientation, in contrast with the in-plane orientation of dipoles we find in two-dimensional WSe2 and MoSe2 at room-temperature. These results, combined with the high tunability of the optical response and outstanding transport properties, position layered InSe as a promising semiconductor for novel optoelectronic devices, in particular for hybrid integrated photonic chips which exploit the out-of-plane dipole orientation.
Acetyl-CoA flux regulates the proteome and acetyl-proteome to maintain intracellular metabolic crosstalk
Authors: Dieterich Inca A. , Lawton Alexis J. , Peng Yajing , Yu Qing , Rhoads Timothy W. , Overmyer Katherine A. , Cui Yusi , Armstrong Eric A. , Howell Porsha R. , Burhans Maggie S. , Li Lingjun , Denu John M. , Coon Joshua J. , Anderson Rozalyn M. , Puglielli Luigi 
Published: September 2019

AbstractAT-1/SLC33A1 is a key member of the endoplasmic reticulum (ER) acetylation machinery, transporting acetyl-CoA from the cytosol into the ER lumen where acetyl-CoA serves as the acetyl-group donor for Nε-lysine acetylation. Dysfunctional ER acetylation, as caused by heterozygous or homozygous mutations as well as gene duplication events of AT-1/SLC33A1, has been linked to both developmental and degenerative diseases. Here, we investigate two models of AT-1 dysregulation and altered acetyl-CoA flux: AT-1S113R/+ mice, a model of AT-1 haploinsufficiency, and AT-1 sTg mice, a model of AT-1 overexpression. The animals display distinct metabolic adaptation across intracellular compartments, including reprogramming of lipid metabolism and mitochondria bioenergetics. Mechanistically, the perturbations to AT-1-dependent acetyl-CoA flux result in global and specific changes in both the proteome and the acetyl-proteome (protein acetylation). Collectively, our results suggest that AT-1 acts as an important metabolic regulator that maintains acetyl-CoA homeostasis by promoting functional crosstalk between different intracellular organelles.
Misshapen coordinates protrusion restriction and actomyosin contractility during collective cell migration
Authors: Plutoni Cédric , Keil Sarah , Zeledon Carlos , Delsin Lara Elis Alberici , Decelle Barbara , Roux Philippe P. , Carréno Sébastien , Emery Gregory 
Published: September 2019

AbstractCollective cell migration is involved in development, wound healing and metastasis. In the Drosophila ovary, border cells (BC) form a small cluster that migrates collectively through the egg chamber. To achieve directed motility, the BC cluster coordinates the formation of protrusions in its leader cell and contractility at the rear. Restricting protrusions to leader cells requires the actin and plasma membrane linker Moesin. Herein, we show that the Ste20-like kinase Misshapen phosphorylates Moesin in vitro and in BC. Depletion of Misshapen disrupts protrusion restriction, thereby allowing other cells within the cluster to protrude. In addition, we show that Misshapen is critical to generate contractile forces both at the rear of the cluster and at the base of protrusions. Together, our results indicate that Misshapen is a key regulator of BC migration as it coordinates two independent pathways that restrict protrusion formation to the leader cells and induces contractile forces.
Dissociable sensitivity and bias mechanisms mediate behavioral effects of exogenous attention
Authors: Sagar Vishak , Sengupta Ranit , Sridharan Devarajan 
Published: September 2019

AbstractAttention can be directed endogenously, based on task-relevant goals, or captured exogenously, by salient stimuli. While recent studies have shown that endogenous attention can facilitate behavior through dissociable sensitivity (sensory) and choice bias (decisional) mechanisms, it is unknown if exogenous attention also operates through dissociable sensitivity and bias mechanisms. We tested human participants on a multialternative change detection task with exogenous attention cues, which preceded or followed change events in close temporal proximity. Analyzing participants’ behavior with a multidimensional signal detection model revealed clear dissociations between exogenous cueing effects on sensitivity and bias. While sensitivity was, overall, lower at the cued location compared to other locations, bias was highest at the cued location. With an appropriately designed post-cue control condition, we discovered that the attentional effect of exogenous pre-cueing was to enhance sensitivity proximal to the cue. In contrast, exogenous attention enhanced bias even for distal stimuli in the cued hemifield. Reaction time effects of exogenous cueing could be parsimoniously explained with a diffusion-decision model, in which drift rate was determined by independent contributions from sensitivity and bias at each location. The results suggest a mechanistic schema of how exogenous attention engages dissociable sensitivity and bias mechanisms to shape behavior.
A core collection of pan-schizophrenia genes allows building cohort-specific signatures of affected brain
Authors: Xie Qinglian , Shen WenWu , Li Zhixiong , Baranova Ancha , Cao Hongbao , Li Zhe 
Published: September 2019

AbstractTo investigate whether pan-schizophrenia genes could be leveraged for building cohort-specific signatures reflecting the functioning of the affected brain, we first collected 1,518 schizophrenia-related genes upon analysis of 12,316 independent peer-reviewed literature sources. More than half of these genes have been reported in at least 3 independent studies, and a majority (81.4%) were enriched within 156 functional pathways (p-values < 1e-15). Gene expression profiles of brain tissues were extracted from 14 publicly available independent datasets, and classified into “schizophrenia” and “normal” bins using dataset-specific subsets of core schizophrenia collection genes built with either a sparse representation-based variable selection (SRVS) approach or with analysis of variance (ANOVA)-based gene selection approach. Results showed that cohort-specific classifiers by both SRVS and ANOVA methods are capable of providing significantly higher accuracy in the diagnosis of schizophrenia than using the whole core genes (p < 3.38e-6), with relatively low sensitivity to the ethnic backgrounds or areas of brain biopsies. Our results suggest that the formation of consensus collection of pan-schizophrenia genes and its dissection into the functional components could be a feasible alternative to the expansion of sample size, which is needed for further in-depth studies of the pathophysiology of the human brain.
Identification and characterization of the MADS-box genes highly expressed in the laticifer cells of Hevea brasiliensis
Authors: Wang Ying , Zhan Di-Feng , Li Hui-Liang , Guo Dong , Zhu Jia-Hong , Peng Shi-Qing 
Published: September 2019

AbstractMADS-box transcription factors possess many functions in plant reproduction and development. However, few MADS-box genes related to secondary metabolites regulation have been identified. In Hevea brasiliensis, natural rubber is a representative cis-polyisoprenoids in secondary metabolism which occurs in the rubber laticifer cells, the molecular regulation basis of natural rubber biosynthesis is not clear. Here, a total of 24 MADS-box genes including 4 type I MADS-box genes and 20 type II MADS-box genes were identified in the transcriptome of rubber tree latex. The phylogenetic analysis was performed to clarify the evolutionary relationships of all the 24 rubber tree MADS-box proteins with MADS-box transcription factors from Arabidopsis thaliana and Oryza sativa. Four type I MADS-box genes were subdivided into Mα (3 genes) and Mβ (1 gene). Twenty type II MADS-box genes were subclassified into MIKC* (8 genes) and MIKCc (12 genes). Eight MADS-box genes (HblMADS3, 5, 6, 7, 9, 13, 23, 24) were predominant expression in laticifers. ABA up-regulated the expression of HblMADS9, and the expression of HblMADS3, HblMADS5, HblMADS24 were up-regulated by MeJA. The function of HblMADS24 was elucidated. HblMADS24 bound HbFPS1 promoter in yeast and HblMADS24 activated HbFPS1 promoter in tobacco plants. Moreover, we proposed that HblMADS24 is a transcription activator of HbFPS1 which taking part in natural rubber biosynthesis.
High pressure phase transitions of paracelsian BaAl2Si2O8
Authors: Gorelova Liudmila A. , Pakhomova Anna S. , Krivovichev Sergey V. , Dubrovinsky Leonid S. , Kasatkin Anatoly V. 
Published: September 2019

AbstractThree new polymorphs of aluminosilicate paracelsian, BaAl2Si2O8, have been discovered using synchrotron-based in situ high-pressure single crystal X-ray diffraction. The first isosymmetric phase transition (from paracelsian-I to paracelsian-II) occurs between 3 and 6 GPa. The phase transition is associated with the formation of pentacoordinated Al3+ and Si4+ ions, which occurs in a stepwise fashion by sequential formation of Al-O and Si-O bonds additional to those in AlO4 and SiO4 tetrahedra, respectively. The next phase transition occurs between 25 and 28 GPa and is accompanied by the symmetry change from monoclinic (P21/c) to orthorhombic (Pna21). The structure of paracelsian-III consists of SiO6 octahedra, AlO6 octahedra and distorted AlO4 tetrahedra, i.e. the transition is reconstructive and associated with the changes of Si4+ and Al3+ coordination, which show rather complex behaviour with the general tendency towards increasing coordination numbers. The third phase transition is observed between 28 and 32 GPa and results in the symmetry decreasing from Pna21 to Pn. The transition has a displacive character. In the course of the phase transformation pathway up to 32 GPa, the structure of polymorphs becomes denser: paracelsian-II is based upon elements of cubic and hexagonal close-packing arrangements of large O2− and Ba2+ ions, whereas, in the crystal structure of paracelsian-III and IV, this arrangement corresponds to 9-layer closest-packing with the layer sequence ABACACBCB.
RETRACTED ARTICLE: Childhood iron deficiency anemia leads to recurrent respiratory tract infections and gastroenteritis
Authors: Jayaweera Jayaweera Arachchige Asela Sampath , Reyes Mohammed , Joseph Anpalaham 
Published: September 2019

AbstractAnemia affects approximately 30% of children all over the world. Acute respiratory tract infections (ARTI), urinary tract infections (UTI) and gastroenteritis (GE) are common infectious entities in children. Here, we assessed the association between anemia and development of recurrent ARTI, UTI, and GE in children. This was a case-control study in hospitalized 2–5 years old children in Professorial Pediatric Unit at Teaching Hospital Anuradhapura, Sri Lanka. An 18-month follow up was done to assess the risk factors for the development of recurrent ARTI, GE, UTI, and control presented without infections. Further, 6-month follow up done after 3-month iron supplementation to assess the occurrence of recurrences. Blood Hb concentration was measured using Drabking’s reagent. Logistic regression was used to find the risk factors for the development of recurrences. In ARTI, 121/165 (73.3%), GE, 88/124 (71%), UTI 46/96 (47.9%) and control 40/100 (40%) were having anemia. Initial ARTI group, recurrent ARTI was 24 (14.5%, p = 0.03); initial GE group: recurrent GE was 14 (11.3%, p = 0.03), recurrent ARTI was 11 (8.9%, p = 0.04); initial UTI group, development of; recurrent UTI was 8 (8.3%, p = 0.04); control, recurrent ARTI was 11 (11%, p = 0.03). Following 3-month iron supplementation reduction of recurrences was significant: initial ARTI recurrent ARTI in 90%, recurrent GE in 77.7%; initial GE recurrent GE in 83.3%, recurrent ARTI in 80%; initial UTI recurrent ARTI in 71.4% and control recurrent ARTI in 88.8%. Iron deficiency is a major type of anemia and anemic children are more prone to develop recurrent ARTI and GE. Once iron deficiency being corrected the rate of recurrent ARTI and GE was reduced. This would be a boost for policy developers to implement strategies at the community level to prevent iron deficiency in children to reduce ARTI and GE recurrences.
Multiplex staining depicts the immune infiltrate in colitis-induced colon cancer model
Authors: Pivetta Eliana , Capuano Alessandra , Scanziani Eugenio , Minoli Lucia , Andreuzzi Eva , Mongiat Maurizio , Baldassarre Gustavo , Doliana Roberto , Spessotto Paola 
Published: September 2019

AbstractAssessment of the host immune response pattern is of increasing importance as highly prognostic and diagnostic, in immune-related diseases and in some types of cancer. Chronic inflammation is a major hallmark in colon cancer formation, but, despite the extent of local inflammatory infiltrate has been demonstrated to be extremely informative, its evaluation is not routinely assessed due to the complexity and limitations of classical immunohistochemistry (IHC). In the last years, technological advance helped in bypassing technical limits, setting up multiplex IHC (mIHC) based on tyramide signal amplification (TSA) method and designing software suited to aid pathologists in cell scoring analysis. Several studies verified the efficacy of this method, but they were restricted to the analysis of human samples. In the era of translational medicine the use of animal models to depict human pathologies, in a more complete and complex approach, is really crucial. Nevertheless, the optimization and validation of this method to species other than human is still poor. We took advantage of Multispectral Imaging System to identify the immunoprofile of Dextran Sulphate Sodium (DSS)-treated mouse colon. We optimized a protocol to sequentially stain formalin fixed paraffin embedded murine colon samples for CD3, CD8a, CD4, and CD4R5B0 antigens. With this approach we obtained a detailed lymphocyte profile, while preserving the morphological tissue context, generally lost with techniques like gene expression profiling or flow cytometry. This study, comparing the results obtained by mIHC with immunophenotyping performed with cytofluorimetric and standard IHC methods validates the potentiality and the applicability of this innovative approach.
Comprehension and Inference: Relationships Between Oral and Written Modalities in Good and Poor Comprehenders During Adolescence
Authors: Potocki Anna , Laval Virginie 
Published: September 2019

Purpose
We investigated the relationships between text reading comprehension and oral idiom comprehension in adolescents. We also examined the more specific relationships between inference in text comprehension and inference in idiom comprehension.

Method

We selected participants from an initial sample of 140 students aged 13–15 years to form 2 groups, according to their decoding and reading comprehension abilities: 1 group of good comprehenders/good decoders (
n
= 49) and 1 group of less skilled comprehenders but with adequate decoding skills (
n
= 20). The reading comprehension task comprised both literal and inferential (text-based and knowledge-based) questions. These 2 groups were then compared on an idiom comprehension task. In this task, idioms were presented orally, and students were placed in a situation that simulated a real-life oral interaction. The idioms were novel for the students (translated from a foreign language), either transparent or opaque, and presented either with a supportive context or without any context.

Results
Good reading comprehenders outperformed less skilled ones on the idiom task. Both groups benefited from the supportive context, especially the good comprehenders. Knowledge-based inferences in written text comprehension were related to contextual inferences for opaque idioms, while semantic inferences for transparent idioms were related to literal text comprehension, but not to text-connecting inferences.

Conclusion
These results are discussed both theoretically, in terms of cross-modal comprehension processes, and practically, in terms of implications for remediation.