bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pretransplant NPM1 MRD levels predict outcome after allogeneic hematopoietic stem cell transplantation in patients with acute myeloid leukemia
Authors: Kayser S , Benner A , Thiede C , Martens U , Huber J , Stadtherr P , Janssen J W G , Röllig C , Uppenkamp M J , Bochtler T , Hegenbart U , Ehninger G , Ho A D , Dreger P , Krämer A 
Published: July 2016

AbstractThe objective was to evaluate the prognostic impact of pre-transplant minimal residual disease (MRD) as determined by real-time quantitative polymerase chain reaction in 67 adultNPM1-mutated acute myeloid leukemia patients receiving allogeneic hematopoietic stem cell transplantation (HSCT). Twenty-eight of the 67 patients had aFLT3-ITD (42%). Median age at transplantation was 54.7 years, median follow-up for survival from time of allografting was 4.9 years. At transplantation, 31 patients were in first, 20 in second complete remission (CR) and 16 had refractory disease (RD). Pre-transplantNPM1MRD levels were measured in 39 CR patients. Overall survival (OS) for patients transplanted in CR was significantly longer as compared to patients with RD (P=0.004), irrespective of whether the patients were transplanted in first or second CR (P=0.74). There was a highly significant difference in OS after allogeneic HSCT between pre-transplant MRD-positive and MRD-negative patients (estimated 5-year OS rates of 40 vs 89%;P=0.007). Multivariable analyses on time to relapse and OS revealed pre-transplantNPM1MRD levels >1% as an independent prognostic factor for poor survival after allogeneic HSCT, whereasFLT3-ITD had no impact. Notably, outcome of patients with pre-transplantNPM1MRD positivity >1% was as poor as that of patients transplanted with RD.
First-line therapy of peripheral T-cell lymphoma: extension and long-term follow-up of a study investigating the role of autologous stem cell transplantation
Authors: Wilhelm M , Smetak M , Reimer P , Geissinger E , Ruediger T , Metzner B , Schmitz N , Engert A , Schaefer-Eckart K , Birkmann J 
Published: July 2016

AbstractCurrent guidelines recommend consolidation with autologous stem cell transplantation (autoSCT) after induction chemotherapy for most patients with peripheral T-cell lymphoma (PTCL). This assumption is based on five prospective phase II studies, three of which included <50 patients with limited follow-up. Here we present the final analysis of the prospective German study. The treatment regimen consisted of four to six cycles of CHOP chemotherapy followed by mobilizing therapy and stem cell collection. Patients in complete remission (CR) or partial remission (PR) underwent myeloablative chemo(radio)therapy and autoSCT. From January 2001 to July 2010, 111 patients were enrolled in the study. The main subgroups were PTCL not specified (n=42) and angioimmunoblastic T-cell lymphoma (n=37). Seventy-five (68%) of the 111 patients received transplantation. The main reason for not receiving autoSCT was progressive disease. In an intent-to-treat analysis, the complete response rate after myeloablative therapy was 59%. The estimated 5-year overall survival, disease-free survival and progression-free survival rates were 44%, 54% and 39%, respectively. The results of this study confirm that upfront autoSCT can result in long-term remissions in patients with all major subtypes of PTCL and therefore should be part of first-line therapy whenever possible.
Dose-dense and less dose-intense Total Therapy 5 for gene expression profiling-defined high-risk multiple myeloma
Authors: Jethava Y , Mitchell A , Zangari M , Waheed S , Schinke C , Thanendrarajan S , Sawyer J , Alapat D , Tian E , Stein C , Khan R , Heuck C J , Petty N , Avery D , Steward D , Smith R , Bailey C , Epstein J , Yaccoby S , Hoering A , Crowley J , Morgan G , Barlogie B , van Rhee F 
Published: July 2016

AbstractMultiple myeloma (MM) is a heterogeneous disease with high-risk patients progressing rapidly despite treatment. Various definitions of high-risk MM are used and we reported that gene expression profile (GEP)-defined high risk was a major predictor of relapse. In spite of our best efforts, the majority of GEP70 high-risk patients relapse and we have noted higher relapse rates during drug-free intervals. This prompted us to explore the concept of less intense drug dosing with shorter intervals between courses with the aim of preventing inter-course relapse. Here we report the outcome of the Total Therapy 5 trial, where this concept was tested. This regimen effectively reduced early mortality and relapse but failed to improve progression-free survival and overall survival due to relapse early during maintenance.
Evolving changes in disease biomarkers and risk of early progression in smoldering multiple myeloma
Authors: Ravi P , Kumar S , Larsen J T , Gonsalves W , Buadi F , Lacy M Q , Go R , Dispenzieri A , Kapoor P , Lust J A , Dingli D , Lin Y , Russell S J , Leung N , Gertz M A , Kyle R A , Bergsagel P L , Rajkumar S V 
Published: July 2016

AbstractWe studied 190 patients with smoldering multiple myeloma (SMM) at our institution between 1973 and 2014. Evolving change in monoclonal protein level (eMP) was defined as ⩾10% increase in serum monoclonal protein (M) and/or immunoglobulin (Ig) (M/Ig) within the first 6 months of diagnosis (only if M-protein ⩾3 g/dl) and/or ⩾25% increase in M/Ig within the first 12 months, with a minimum required increase of 0.5 g/dl in M-protein and/or 500 mg/dl in Ig. Evolving change in hemoglobin (eHb) was defined as ⩾0.5 g/dl decrease within 12 months of diagnosis. A total of 134 patients (70.5%) progressed to MM over a median follow-up of 10.4 years. On multivariable analysis adjusting for factors known to predict for progression to MM, bone marrow plasma cells ⩾20% (odds ratio (OR)=3.37 (1.30–8.77), P=0.013), eMP (OR=8.20 (3.19–21.05), P<0.001) and eHb (OR=5.86 (2.12–16.21), P=0.001) were independent predictors of progression within 2 years of SMM diagnosis. A risk model comprising these variables was constructed, with median time to progression of 12.3, 5.1, 2.0 and 1.0 years among patients with 0–3 risk factors respectively. The 2-year progression risk was 81.5% in individuals who demonstrated both eMP and eHb, and 90.5% in those with all three risk factors.
Rapid construction of metabolite biosensors using domain-insertion profiling
Authors: Nadler Dana C. , Morgan Stacy-Anne , Flamholz Avi , Kortright Kaitlyn E. , Savage David F. 
Published: July 2016

AbstractSingle-fluorescent protein biosensors (SFPBs) are an important class of probes that enable the single-cell quantification of analytes in vivo. Despite advantages over other detection technologies, their use has been limited by the inherent challenges of their construction. Specifically, the rational design of green fluorescent protein (GFP) insertion into a ligand-binding domain, generating the requisite allosteric coupling, remains a rate-limiting step. Here, we describe an unbiased approach, termed domain-insertion profiling with DNA sequencing (DIP-seq), that combines the rapid creation of diverse libraries of potential SFPBs and high-throughput activity assays to identify functional biosensors. As a proof of concept, we construct an SFPB for the important regulatory sugar trehalose. DIP-seq analysis of a trehalose-binding-protein reveals allosteric hotspots for GFP insertion and results in high-dynamic range biosensors that function robustly in vivo. Taken together, DIP-seq simultaneously accelerates metabolite biosensor construction and provides a novel tool for interrogating protein allostery.
Controlling nanowire growth through electric field-induced deformation of the catalyst droplet
Authors: Panciera Federico , Norton Michael M. , Alam Sardar B. , Hofmann Stephan , Mølhave Kristian , Ross Frances M. 
Published: July 2016

AbstractSemiconductor nanowires with precisely controlled structure, and hence well-defined electronic and optical properties, can be grown by self-assembly using the vapour–liquid–solid process. The structure and chemical composition of the growing nanowire is typically determined by global parameters such as source gas pressure, gas composition and growth temperature. Here we describe a more local approach to the control of nanowire structure. We apply an electric field during growth to control nanowire diameter and growth direction. Growth experiments carried out while imaging within an in situ transmission electron microscope show that the electric field modifies growth by changing the shape, position and contact angle of the catalytic droplet. This droplet engineering can be used to modify nanowires into three dimensional structures, relevant to a range of applications, and also to measure the droplet surface tension, important for quantitative development of strategies to control nanowire growth.
EphrinB2 repression through ZEB2 mediates tumour invasion and anti-angiogenic resistance
Authors: Depner C. , zum Buttel H. , Böğürcü N. , Cuesta A. M. , Aburto M. R. , Seidel S. , Finkelmeier F. , Foss F. , Hofmann J. , Kaulich K. , Barbus S. , Segarra M. , Reifenberger G. , Garvalov B. K. , Acker T. , Acker-Palmer A. 
Published: July 2016

AbstractDiffuse invasion of the surrounding brain parenchyma is a major obstacle in the treatment of gliomas with various therapeutics, including anti-angiogenic agents. Here we identify the epi-/genetic and microenvironmental downregulation of ephrinB2 as a crucial step that promotes tumour invasion by abrogation of repulsive signals. We demonstrate that ephrinB2 is downregulated in human gliomas as a consequence of promoter hypermethylation and gene deletion. Consistently, genetic deletion of ephrinB2 in a murine high-grade glioma model increases invasion. Importantly, ephrinB2 gene silencing is complemented by a hypoxia-induced transcriptional repression. Mechanistically, hypoxia-inducible factor (HIF)-1α induces the EMT repressor ZEB2, which directly downregulates ephrinB2 through promoter binding to enhance tumour invasiveness. This mechanism is activated following anti-angiogenic treatment of gliomas and is efficiently blocked by disrupting ZEB2 activity. Taken together, our results identify ZEB2 as an attractive therapeutic target to inhibit tumour invasion and counteract tumour resistance mechanisms induced by anti-angiogenic treatment strategies.
Antimicrobial peptides trigger a division block in Escherichia coli through stimulation of a signalling system
Authors: Yadavalli Srujana S. , Carey Jeffrey N. , Leibman Rachel S. , Chen Annie I. , Stern Andrew M. , Roggiani Manuela , Lippa Andrew M. , Goulian Mark 
Published: July 2016

AbstractAntimicrobial peptides are an important component of the molecular arsenal employed by hosts against bacteria. Many bacteria in turn possess pathways that provide protection against these compounds. In Escherichia coli and related bacteria, the PhoQ/PhoP signalling system is a key regulator of this antimicrobial peptide defence. Here we show that treating E. coli with sublethal concentrations of antimicrobial peptides causes cells to filament, and that this division block is controlled by the PhoQ/PhoP system. The filamentation results from increased expression of QueE, an enzyme that is part of a tRNA modification pathway but that, as we show here, also affects cell division. We also find that a functional YFP–QueE fusion localizes to the division septum in filamentous cells, suggesting QueE blocks septation through interaction with the divisome. Regulation of septation by PhoQ/PhoP may protect cells from antimicrobial peptide-induced stress or other conditions associated with high-level stimulation of this signalling system.
Species interactions in occurrence data for a community of tick-transmitted pathogens
Authors: Estrada-Peña Agustín , de la Fuente José 
Published: July 2016

AbstractInteractions between tick species, their realized range of hosts, the pathogens they carry and transmit, and the geographic distribution of species in the Western Palearctic were determined based on evidence published between 1970–2014. These relationships were linked to remotely sensed features of temperature and vegetation and used to extract the network of interactions among the organisms. The resulting datasets focused on niche overlap among ticks and hosts, species interactions, and the fraction of the environmental niche in which tick-borne pathogens may circulate as a result of interactions and overlapping environmental traits. The resulting datasets provide a valuable resource for researchers interested in tick-borne pathogens, as they conciliate the abiotic and biotic sides of their niche, allowing exploration of the importance of each host species acting as a vertebrate reservoir in the circulation of tick-transmitted pathogens in the environmental niche.
Open data set of live cyanobacterial cells imaged using an X-ray laser
Authors: van der Schot Gijs , Svenda Martin , Maia Filipe R.N.C. , Hantke Max F. , DePonte Daniel P. , Seibert M. Marvin , Aquila Andrew , Schulz Joachim , Kirian Richard A. , Liang Mengning , Stellato Francesco , Bari Sadia , Iwan Bianca , Andreasson Jakob , Timneanu Nicusor , Bielecki Johan , Westphal Daniel , Nunes de Almeida Francisca , Odić Duško , Hasse Dirk , Carlsson Gunilla H. , Larsson Daniel S.D. , Barty Anton , Martin Andrew V. , Schorb Sebastian , Bostedt Christoph , Bozek John D. , Carron Sebastian , Ferguson Ken , Rolles Daniel , Rudenko Artem , Epp Sascha W. , Foucar Lutz , Rudek Benedikt , Erk Benjamin , Hartmann Robert , Kimmel Nils , Holl Peter , Englert Lars , Loh N. Duane , Chapman Henry N. , Andersson Inger , Hajdu Janos , Ekeberg Tomas 
Published: July 2016

AbstractStructural studies on living cells by conventional methods are limited to low resolution because radiation damage kills cells long before the necessary dose for high resolution can be delivered. X-ray free-electron lasers circumvent this problem by outrunning key damage processes with an ultra-short and extremely bright coherent X-ray pulse. Diffraction-before-destruction experiments provide high-resolution data from cells that are alive when the femtosecond X-ray pulse traverses the sample. This paper presents two data sets from micron-sized cyanobacteria obtained at the Linac Coherent Light Source, containing a total of 199,000 diffraction patterns. Utilizing this type of diffraction data will require the development of new analysis methods and algorithms for studying structure and structural variability in large populations of cells and to create abstract models. Such studies will allow us to understand living cells and populations of cells in new ways. New X-ray lasers, like the European XFEL, will produce billions of pulses per day, and could open new areas in structural sciences.
Global positioning system survey data for active seismic and volcanic areas of eastern Sicily, 1994 to 2013
Authors: Bonforte Alessandro , Fagone Sonia , Giardina Carmelo , Genovese Simone , Aiesi Gianpiero , Calvagna Francesco , Cantarero Massimo , Consoli Orazio , Consoli Salvatore , Guglielmino Francesco , Puglisi Biagio , Puglisi Giuseppe , Saraceno Benedetto 
Published: July 2016

AbstractThis work presents and describes a 20-year long database of GPS data collected by geodetic surveys over the seismically and volcanically active eastern Sicily, for a total of more than 6300 measurements. Raw data were initially collected from the various archives at the Istituto Nazionale di Geofisica e Vulcanologia, Sezione di Catania—Osservatorio Etneo and organized in a single repository. Here, quality and completeness checks were performed, while all necessary supplementary information were searched, collected, validated and organized together with the relevant data. Once all data and information collections were completed, raw binary data were converted into the universal ASCII RINEX format; all data are provided in this format with the necessary information for precise processing. In order to make the data archive readily consultable, we developed software allowing the user to easily search and obtain the needed data by simple alphanumeric and geographic queries.
Coherent diffraction of single Rice Dwarf virus particles using hard X-rays at the Linac Coherent Light Source
Authors: Munke Anna , Andreasson Jakob , Aquila Andrew , Awel Salah , Ayyer Kartik , Barty Anton , Bean Richard J. , Berntsen Peter , Bielecki Johan , Boutet Sébastien , Bucher Maximilian , Chapman Henry N. , Daurer Benedikt J. , DeMirci Hasan , Elser Veit , Fromme Petra , Hajdu Janos , Hantke Max F. , Higashiura Akifumi , Hogue Brenda G. , Hosseinizadeh Ahmad , Kim Yoonhee , Kirian Richard A. , Reddy Hemanth K.N. , Lan Ti-Yen , Larsson Daniel S.D. , Liu Haiguang , Loh N. Duane , Maia Filipe R.N.C. , Mancuso Adrian P. , Mühlig Kerstin , Nakagawa Atsushi , Nam Daewoong , Nelson Garrett , Nettelblad Carl , Okamoto Kenta , Ourmazd Abbas , Rose Max , van der Schot Gijs , Schwander Peter , Seibert M. Marvin , Sellberg Jonas A. , Sierra Raymond G. , Song Changyong , Svenda Martin , Timneanu Nicusor , Vartanyants Ivan A. , Westphal Daniel , Wiedorn Max O. , Williams Garth J. , Xavier Paulraj Lourdu , Yoon Chun Hong , Zook James 
Published: July 2016

AbstractSingle particle diffractive imaging data from Rice Dwarf Virus (RDV) were recorded using the Coherent X-ray Imaging (CXI) instrument at the Linac Coherent Light Source (LCLS). RDV was chosen as it is a well-characterized model system, useful for proof-of-principle experiments, system optimization and algorithm development. RDV, an icosahedral virus of about 70 nm in diameter, was aerosolized and injected into the approximately 0.1 μm diameter focused hard X-ray beam at the CXI instrument of LCLS. Diffraction patterns from RDV with signal to 5.9 Ångström were recorded. The diffraction data are available through the Coherent X-ray Imaging Data Bank (CXIDB) as a resource for algorithm development, the contents of which are described here.
Rapid Brownian Motion Primes Ultrafast Reconstruction of Intrinsically Disordered Phe-Gly Repeats Inside the Nuclear Pore Complex
Authors: Moussavi-Baygi R. , Mofrad M. R. K. 
Published: July 2016

AbstractConformational behavior of intrinsically disordered proteins, such as Phe-Gly repeat domains, alters drastically when they are confined in and tethered to, nan channels. This has challenged our understanding of how they serve to selectively facilitate translocation of nuclear transport receptor (NTR)-bearing macromolecules. Heterogeneous FG-repeats, tethered to the NPC interior, nonuniformly fill the channel in a diameter-dependent manner and adopt a rapid Brownian motion, thereby forming a porous and highly dynamic polymeric meshwork that percolates in radial and axial directions and features two distinguishable zones: a dense hydrophobic rod-like zone located in the center and a peripheral low-density shell-like zone. The FG-meshwork is locally disrupted upon interacting with NTR-bearing macromolecules, but immediately reconstructs itself between 0.44 μs and 7.0 μs, depending on cargo size and shape. This confers a perpetually-sealed state to the NPC and is solely due to rapid Brownian motion of FG-repeats, not FG-repeat hydrophobic bonds. Elongated-shaped macromolecules, both in the presence and absence of NTRs, penetrate more readily into the FG-meshwork compared to their globular counterparts of identical volume and surface chemistry, highlighting the importance of the shape effects in nucleocytoplasmic transport. These results can help our understanding of geometrical effects in and the design of, intelligent and responsive biopolymer-based materials in nanofiltration and artificial nanopores.
Rapid detection of talcum powder in tea using FT-IR spectroscopy coupled with chemometrics
Authors: Li Xiaoli , Zhang Yuying , He Yong 
Published: July 2016

AbstractThis paper investigated the feasibility of Fourier transform infrared transmission (FT-IR) spectroscopy to detect talcum powder illegally added in tea based on chemometric methods. Firstly, 210 samples of tea powder with 13 dose levels of talcum powder were prepared for FT-IR spectra acquirement. In order to highlight the slight variations in FT-IR spectra, smoothing, normalize and standard normal variate (SNV) were employed to preprocess the raw spectra. Among them, SNV preprocessing had the best performance with high correlation of prediction (RP = 0.948) and low root mean square error of prediction (RMSEP = 0.108) of partial least squares (PLS) model. Then 18 characteristic wavenumbers were selected based on a hybrid of backward interval partial least squares (biPLS) regression, competitive adaptive reweighted sampling (CARS) algorithm and successive projections algorithm (SPA). These characteristic wavenumbers only accounted for 0.64% of the full wavenumbers. Following that, 18 characteristic wavenumbers were used to build linear and nonlinear determination models by PLS regression and extreme learning machine (ELM), respectively. The optimal model with RP = 0.963 and RMSEP = 0.137 was achieved by ELM algorithm. These results demonstrated that FT-IR spectroscopy with chemometrics could be used successfully to detect talcum powder in tea.
Phenotypic and functional characteristics of IL-21-expressing CD8+ T cells in human nasal polyps
Authors: Xiao Li , Jia Lei , Bai Lu , He Long , Yang Binyan , Wu Changyou , Li Huabin 
Published: July 2016

AbstractAlthough CD4+ T cells are recognized to play an important role in the inflammatory response of nasal polyps (NPs), the biological functions of CD8+ T cells in polypogenesis remain unclear. In this study, we analyzed cell markers, cytokine expression and transcription factors in IL-21-expressing CD8+ T cells in polyp tissues of NP patients. The results showed that the majority of IL-21-producing CD8+ T cells were effector memory cells and they co-expressed IFN-γ. IL-21-expressing CD8+ T cells in polyp tissues expressed higher CXCR5, PD-1 and ICOS levels than cells in control tissues and showed significantly higher T-bet and Bcl-6 expression levels compared with IL-21−CD8+ T cells. Purified polyp CD8+ T cells promoted IgG production from isolated polyp B cells in vitro and recombinant IL-12 modulated the expression of IL-21, IFN-γ and CD40L in purified polyp CD8+ T cells. Moreover, the percentage of IL-21+CD8+ T cells in polyp tissues was positively correlated with endoscopic and CT scan scores in NP patients. These findings indicated that polyp CD8+ T cells, by co-expressing IL-21 and IFN-γ and other markers, display a Tfh cell functionality, which is associated with the clinical severity of NP patients.
Nut intake and stroke risk: A dose-response meta-analysis of prospective cohort studies
Authors: Shao Chuan , Tang Hui , Zhao Wei , He Jianquan 
Published: July 2016

AbstractWe aim to quantify the effects of nut intake on risk of stroke by a dose-response meta-analysis with a random-effects model. Two databases (PubMed and Emabse) were searched for prospective cohort studies regarding nut intake and stroke risk. Studies were included if they fulfilled the predefined criteria. Eleven articles encompassing fourteen cohort studies were included in final analysis. The pooled relative risk (RR) of stroke for the highest versus (vs.) lowest category of nut intake was 0.88 (95% confidence interval [CI] 0.80-0.97). The power to detect a RR of 0.88 for the highest versus vs. lowest category of nut intake was 86.2%. In multiple subset analyses by gender, location and stroke subtype, the inverse association was only found in women (RR = 0.84, 95% CI 0.73–0.96) and Asia (RR = 0.79, 95% CI 0.67–0.93). In the dose-response meta-analysis, evidence for a nonlinear association between nut intake and stroke risk was observed and a RR of 0.86 was conferred for 12 g/day. Based on the Grading of Recommendations Assessment, Development and Evaluation (GRADE) system, the quality of evidence was moderate. In conclusions, finding from current meta-analysis of fourteen cohort studies indicates that nut intake may be related to decreased risk of stroke.