bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome-wide transcriptional profiling for elucidating the effects of brassinosteroids on Glycine max during early vegetative development
Authors: Song Li , Chen Wei , Yao Qiuming , Guo Binhui , Valliyodan Babu , Wang Zhiyong , Nguyen Henry T. 
Published: November 2019

AbstractSoybean is a widely grown grain legume and one of the most important economic crop species. Brassinosteroids play a crucial role in plant vegetative growth and reproductive development. However, it remains unclear how BRs regulate the developmental processes in soybean, and the molecular mechanism underlying soybean early development is largely unexplored. In this study, we first characterized how soybean early vegetative growth was specifically regulated by the BR biosynthesis inhibitor propiconazole; this characterization included shortened root and shoot lengths, reduced leaf area, and decreased chlorophyll content. In addition, the growth inhibition induced by Pcz could be rescued by exogenous brassinolide application. The RNA-seq technique was employed to investigate the BR regulatory networks during soybean early vegetative development. Identification and analysis of differentially expressed genes indicated that BRs orchestrate a wide range of cellular activities and biological processes in soybean under various BR concentrations. The regulatory networks between BRs and multiple hormones or stress-related pathways were investigated. The results provide a comprehensive view of the physiological functions of BRs and new insights into the molecular mechanisms at the transcriptional level of BR regulation of soybean early development.
Variation of Burkholderia cenocepacia cell wall morphology and mechanical properties during cystic fibrosis lung infection, assessed by atomic force microscopy
Authors: Hassan A. Amir , Vitorino Miguel V. , Robalo Tiago , Rodrigues Mário S. , Sá-Correia Isabel 
Published: November 2019

AbstractThe influence that Burkholderia cenocepacia adaptive evolution during long-term infection in cystic fibrosis (CF) patients has on cell wall morphology and mechanical properties is poorly understood despite their crucial role in cell physiology, persistent infection and pathogenesis. Cell wall morphology and physical properties of three B. cenocepacia isolates collected from a CF patient over a period of 3.5 years were compared using atomic force microscopy (AFM). These serial clonal variants include the first isolate retrieved from the patient and two late isolates obtained after three years of infection and before the patient’s death with cepacia syndrome. A consistent and progressive decrease of cell height and a cell shape evolution during infection, from the typical rods to morphology closer to cocci, were observed. The images of cells grown in biofilms showed an identical cell size reduction pattern. Additionally, the apparent elasticity modulus significantly decreases from the early isolate to the last clonal variant retrieved from the patient but the intermediary highly antibiotic resistant clonal isolate showed the highest elasticity values. Concerning the adhesion of bacteria surface to the AFM tip, the first isolate was found to adhere better than the late isolates whose lipopolysaccharide (LPS) structure loss the O-antigen (OAg) during CF infection. The OAg is known to influence Gram-negative bacteria adhesion and be an important factor in B. cenocepacia adaptation to chronic infection. Results reinforce the concept of the occurrence of phenotypic heterogeneity and adaptive evolution, also at the level of cell size, form, envelope topography and physical properties during long-term infection.
Empirical design of a variant quality control pipeline for whole genome sequencing data using replicate discordance
Authors: Adelson Robert P. , Renton Alan E. , Li Wentian , Barzilai Nir , Atzmon Gil , Goate Alison M. , Davies Peter , Freudenberg-Hua Yun 
Published: November 2019

AbstractThe success of next-generation sequencing depends on the accuracy of variant calls. Few objective protocols exist for QC following variant calling from whole genome sequencing (WGS) data. After applying QC filtering based on Genome Analysis Tool Kit (GATK) best practices, we used genotype discordance of eight samples that were sequenced twice each to evaluate the proportion of potentially inaccurate variant calls. We designed a QC pipeline involving hard filters to improve replicate genotype concordance, which indicates improved accuracy of genotype calls. Our pipeline analyzes the efficacy of each filtering step. We initially applied this strategy to well-characterized variants from the ClinVar database, and subsequently to the full WGS dataset. The genome-wide biallelic pipeline removed 82.11% of discordant and 14.89% of concordant genotypes, and improved the concordance rate from 98.53% to 99.69%. The variant-level read depth filter most improved the genome-wide biallelic concordance rate. We also adapted this pipeline for triallelic sites, given the increasing proportion of multiallelic sites as sample sizes increase. For triallelic sites containing only SNVs, the concordance rate improved from 97.68% to 99.80%. Our QC pipeline removes many potentially false positive calls that pass in GATK, and may inform future WGS studies prior to variant effect analysis.
Evaluating differential nanoparticle accumulation and retention kinetics in a mouse model of traumatic brain injury via Ktrans mapping with MRI
Authors: Miller Hunter A. , Magsam Alexander W. , Tarudji Aria W. , Romanova Svetlana , Weber Laura , Gee Connor C. , Madsen Gary L. , Bronich Tatiana K. , Kievit Forrest M. 
Published: November 2019

AbstractTraumatic brain injury (TBI) is a leading cause of injury-related death worldwide, yet there are no approved neuroprotective therapies that improve neurological outcome post-injury. Transient opening of the blood-brain barrier following injury provides an opportunity for passive accumulation of intravenously administered nanoparticles through an enhanced permeation and retention-like effect. However, a thorough understanding of physicochemical properties that promote optimal uptake and retention kinetics in TBI is still needed. In this study, we present a robust method for magnetic resonance imaging of nanoparticle uptake and retention kinetics following intravenous injection in a controlled cortical impact mouse model of TBI. Three contrast-enhancing nanoparticles with different hydrodynamic sizes and relaxivity properties were compared. Accumulation and retention were monitored by modelling the permeability coefficient, Ktrans, for each nanoparticle within the reproducible mouse model. Quantification of Ktrans for different nanoparticles allowed for non-invasive, multi-time point assessment of both accumulation and retention kinetics in the injured tissue. Using this method, we found that 80 nm poly(lactic-co-glycolic acid) nanoparticles had maximal Ktrans in a TBI when injected 3 hours post-injury, showing significantly higher accumulation kinetics than the small molecule, Gd-DTPA. This robust method will enable optimization of administration time and nanoparticle physicochemical properties to achieve maximum delivery.
Geothermal sweetspots identified in a volcanic lake integrating bathymetry and fluid chemistry
Authors: Brehme Maren , Giese Ronny , Suherlina Lily , Kamah Yustin 
Published: November 2019

AbstractWe investigate fluid pathways beneath volcanic lakes using bathymetry and geochemical measurements to locate best-possible drilling sites. Highly permeable structures, such as faults, provide fluid channels that are the most suitable access points to the geothermal resource. Accurate mapping of these structures therefore guides the successful targeting of wells. Lakes, rivers or ocean, can hide surface footprints of these permeable structures, such as in our case beneath Lake Linau. High-resolution bathymetry identifies linear and conical discontinuities, which are linked to offshore tectonic structures as confirmed by surrounding outcrops and hot springs. Geochemical measurements document inflow of hot saline acidic water into the lake verifying bathymetry-located highly permeable structures. Integrating onshore well data, our bathymetry and chemical results locates an ideal drilling site into the geothermal reservoir beneath the western shore line of Lake Linau.
Phytoplankton community and algal toxicity at a recurring bloom in Sullivan Bay, Kabetogama Lake, Minnesota, USA
Authors: Christensen Victoria G. , Maki Ryan P. , Stelzer Erin A. , Norland Jack E. , Khan Eakalak 
Published: November 2019

AbstractKabetogama Lake in Voyageurs National Park, Minnesota, USA suffers from recurring late summer algal blooms that often contain toxin-producing cyanobacteria. Previous research identified the toxin microcystin in blooms, but we wanted to better understand how the algal and cyanobacterial community changed throughout an open water season and how changes in community structure were related to toxin production. Therefore, we sampled one recurring bloom location throughout the entire open water season. The uniqueness of this study is the absence of urban and agricultural nutrient sources, the remote location, and the collection of samples before any visible blooms were present. Through quantitative polymerase chain reaction (qPCR), we discovered that toxin-forming cyanobacteria were present before visible blooms and toxins not previously detected in this region (anatoxin-a and saxitoxin) were present, indicating that sampling for additional toxins and sampling earlier in the season may be necessary to assess ecosystems and human health risk.
Novel insights into transketolase activation by cofactor binding identifies two native species subpopulations
Authors: Wilkinson Henry C. , Dalby Paul A. 
Published: November 2019

AbstractTransketolase (TK) cofactor binding has been studied extensively over many years, yet certain mysteries remain, such as a lack of consensus on the cooperativity of thiamine pyrophosphate (TPP) binding into the two active sites, in the presence and absence of the divalent cation, Mg2+. Using a novel fluorescence-based assay, we determined directly the dissociation constants and cooperativity of TPP binding and provide the first comprehensive study over a broad range of cofactor concentrations. We confirmed the high-affinity dissociation constants and revealed a dependence of both the affinity and cooperativity of binding on [Mg2+], which explained the previous lack of consensus. A second, discrete and previously uncharacterised low-affinity TPP binding-site was also observed, and hence indicated the existence of two forms of TK with high- (TKhigh) and low-affinity (TKlow). The relative proportions of each dimer were independent of the monomer-dimer transition, as probed by analytical ultracentrifugation at various [TK]. Mass spectrometry revealed that chemical oxidation of TKlow led to the formation of TKhigh, which was 22-fold more active than TKlow. Finally, we propose a two-species model of transketolase activation that describes the interconversions between apo-/holo-TKhigh and TKlow, and the potential to significantly improve biocatalytic activity by populating only the most active form.
Protective effects of seaweed supplemented diet on antioxidant and immune responses in European seabass (Dicentrarchus labrax) subjected to bacterial infection
Authors: Peixoto Maria J. , Ferraz Renato , Magnoni Leonardo J. , Pereira Rui , Gonçalves José F. , Calduch-Giner Josep , Pérez-Sánchez Jaume , Ozório Rodrigo O. A. 
Published: November 2019

AbstractEuropean seabass (Dicentrarchus labrax) production is often hampered by bacterial infections such as photobacteriosis caused by Photobacterium damselae subsp. piscicida (Phdp). Since diet can impact fish immunity, this work investigated the effect of dietary supplementation of 5% Gracilaria sp. aqueous extract (GRA) on seabass antioxidant capacity and resistance against Phdp. After infection, mortality was delayed in fish fed GRA, which also revealed increased lysozyme activity levels, as well as decreased lipid peroxidation, suggesting higher antioxidant capacity than in fish fed a control diet. Dietary GRA induced a down-regulation of hepatic stress-responsive heat shock proteins (grp-78, grp-170, grp-94, grp-75), while bacterial infection caused a down-regulation in antioxidant genes (prdx4 and mn-sod). Diet and infection interaction down-regulated the transcription levels of genes associated with oxidative stress response (prdx5 and gpx4) in liver. In head-kidney, GRA led to an up-regulation of genes associated with inflammation (il34, ccr9, cd33) and a down-regulation of genes related to cytokine signalling (mif, il1b, defb, a2m, myd88). Additionally, bacterial infection up-regulated immunoglobulins production (IgMs) and down-regulated the transcription of the antimicrobial peptide leap2 in head kidney. Overall, we found that GRA supplementation modulated seabass resistance to Phdp infection.
Redox chemistry of π-extended tellurophenes
Authors: Shida Naoki , Nishiyama Hiroki , Zheng Feng , Ye Shuyang , Seferos Dwight S. , Tomita Ikuyoshi , Inagi Shinsuke 
Published: November 2019

AbstractIn the past decade, the incorporation of tellurophene motifs into organic devices has been a promising strategy for the design of advanced materials. However, fundamental redox behavior of tellurophene-containing materials have never been comprehensively explored. Here, we report unique redox behavior of π-extended tellurophenes. The facile coordination of solvent molecules and/or anions becomes evident, in addition to the attachment of nucleophilic halides. This indicates that the tellurium center in oxidized 2,5-diphenyltellurophene is highly electron-deficient and easily yields coordinated structures. This coordination appears to trap the positive charge on the tellurium center rather than delocalizing it over the π-system. When no coordinating counter ion is present, however, oxidation appears to be delocalized over the entire π-system. Additionally, by using more delocalized structures, we show that coordination and charge-delocalization can co-exist. These results provide important insights to understand the properties of tellurophene-containing molecules and materials with extended π-systems.
Concurrent Validity and Reliability of the Core Lexicon Measure as a Measure of Word Retrieval Ability in Aphasia Narratives
Authors: Kim Hana , Wright Heather Harris 
Published: November 2019

Purpose
General agreement exists in the literature that clinicians struggle with quantifying discourse-level performance in clinical settings. Core lexicon analysis has gained recent attention as an alternative tool that may address difficulties that clinicians face. Although previous studies have demonstrated that core lexicon measures are an efficient means of assessing discourse in persons with aphasia (PWAs), the psychometric properties of core lexicon measures have yet to be investigated. The purpose of this study was (a) to examine the concurrent validity by using microlinguistic and macrolinguistic measures and (b) to demonstrate interrater reliability without transcription by raters with minimal training.

Method
Eleven language samples collected from PWAs were used in this study. Concurrent validity was assessed by correlating performance on the core lexicon measure with microlinguistic and macrolinguistic measures. For interrater reliability, 4 raters used the core lexicon checklists to score audio-recorded discourse samples from 10 PWAs.

Results
The core lexicon measures significantly correlated with microlinguistic and macrolinguistic measures. Acceptable interrater reliability was obtained among the 4 raters.

Conclusions
Core lexicon analysis is potentially useful for measuring word retrieval impairments at the discourse level. It may also be a feasible solution because it reduces the amount of preparatory work for discourse assessment.
Langzeitbetrachtung – Krankheitskosten im Verlauf der Alzheimer-Krankheit
Authors: Fietz Cornelia 
Published: November 2019

Sopina E et al. Long-term medical costs of Alzheimer’s disease: matched cohort analysis. Eur J Health Econ 2019; 20: 333–342
Je nach Perspektive, Umfeld und angewandter Methode variieren Schätzungen der Krankheitskosten der Alzheimer-Krankheit dramatisch. Oft werden diese nur über eine kurze Zeitspanne und nicht über den kompletten Verlauf der Erkrankung berichtet und nur selten mit denen eines gesunden Kollektivs verglichen. Da solche Daten für entscheidungsanalytische Modellierungen nicht präzise genug sind, ermitteln die Autoren die medizinischen Langzeitkosten im Verlauf der Alzheimer-Krankheit.
Multiples Myelom – Evaluation der Kosten für Kombinationstherapien
Authors: Thiem Helena 
Published: November 2019

Ailawadhi S et al. Cost offsets in the treatment journeys of patients with relapsed/refractory multiple myeloma. Clin Ther 2019: 41(3): 477–493
Die Therapiemöglichkeiten für das Multiple Myelom, insbesondere das rezidivierende/refraktäre Multiple Myelom, haben sich in den letzten Jahren weiterentwickelt und mehrere neue Wirkstoffe haben die Zulassung erhalten. Vor diesem Hintergrund erscheint eine Betrachtung der durch die unterschiedlichen Therapiemöglichkeiten entstehenden Kosten wichtig. Ailawadhi et al. analysierten die im Rahmen der Behandlung dieses Krankheitsbildes anfallenden Gesamtkosten.
Neurological Dashboards and Consultation Turnaround Time at an Academic Medical Center
Authors: Kummer Benjamin R. , Willey Joshua Z. , Zelenetz Michael J. , Hu Yiping , Sengupta Soumitra , Elkind Mitchell S. V. , Hripcsak George 
Published: November 2019

Abstract
Background Neurologists perform a significant amount of consultative work. Aggregative electronic health record (EHR) dashboards may help to reduce consultation turnaround time (TAT) which may reflect time spent interfacing with the EHR.
Objectives This study was aimed to measure the difference in TAT before and after the implementation of a neurological dashboard.
Methods We retrospectively studied a neurological dashboard in a read-only, web-based, clinical data review platform at an academic medical center that was separate from our institutional EHR. Using our EHR, we identified all distinct initial neurological consultations at our institution that were completed in the 5 months before, 5 months after, and 12 months after the dashboard go-live in December 2017. Using log data, we determined total dashboard users, unique page hits, patient-chart accesses, and user departments at 5 months after go-live. We calculated TAT as the difference in time between the placement of the consultation order and completion of the consultation note in the EHR.
Results By April 30th in 2018, we identified 269 unique users, 684 dashboard page hits (median hits/user 1.0, interquartile range [IQR] = 1.0), and 510 unique patient-chart accesses. In 5 months before the go-live, 1,434 neurology consultations were completed with a median TAT of 2.0 hours (IQR = 2.5) which was significantly longer than during 5 months after the go-live, with 1,672 neurology consultations completed with a median TAT of 1.8 hours (IQR = 2.2; p = 0.001). Over the following 7 months, 2,160 consultations were completed and median TAT remained unchanged at 1.8 hours (IQR = 2.5).
Conclusion At a large academic institution, we found a significant decrease in inpatient consult TAT 5 and 12 months after the implementation of a neurological dashboard. Further study is necessary to investigate the cognitive and operational effects of aggregative dashboards in neurology and to optimize their use.
Endoscopic-Assisted Lateral Corridor to the Infratemporal Fossa: Proposal and Quantitative Comparison to the Endoscopic Transpterygoid Approach
Authors: Yacoub Abraam , Schneider Daniel , Ali Ahmed , Wimmer Wilhelm , Caversaccio Marco , Anschuetz Lukas 
Published: November 2019

Abstract
Objective This study was aimed to propose an expanded endoscopic-assisted lateral approach to the infratemporal fossa (ITF) and compare its area of exposure and surgical freedom with the endoscopic endonasal transptergyoid approach (EETA).
Methods Anatomical dissections were performed in five cadaver heads (10 sides). The ITF was first examined through the endoscopically assisted lateral corridor, herein referred to as the endoscopic-assisted transtemporal fossa approach (TTFA). After that, the EETA was performed and coupled with two sequential maxillary procedures (medial maxillectomy [MM], and endoscopic-assisted Denker's approach [DA]). Using the stereotactic neuronavigation, measurements of the area of exposure and surgical freedom at the foramen ovale were determined for the previously mentioned approaches.
Results Bimanual exploration of the ITF through the endoscopic-assisted lateral approach was achieved in all specimens. The DA (729 ± 49 mm2) provided a larger area of exposure than MM (568 ± 46 mm2; p < 0.0001). However, areas of exposure were similar between the DA and the TTFA (677 ± 35 mm2; p = 0.09). The surgical freedom offered by the TTFA (109.3 ± 19 cm2) was much greater than the DA (24.7 ± 4.8 cm2; p < 0.0001), and the MM (15.2 ± 3.2 cm2, p < 0.0001).
Conclusion The study demonstrates the feasibility of the proposed approach to provide direct access to the extreme extensions of the ITF. The lateral corridor offers an ideal working area in the posterior compartment of the ITF without crossing over important neurovascular structures. The new technique may be used alone in selected primary ITF lesions or in combination with endonasal approaches in pathologies spreading laterally from the nose or nasopharynx.
Effects of single ingestion of rice cracker and cooked rice with high resistant starch on postprandial glucose and insulin responses in healthy adults: two randomized, single-blind, cross-over trials
Authors: Saito Yuhi , Watanabe Toshiyuki , Sasaki Toshiyuki , Watanabe Kenichi , Hirayama Masao , Fujita Naoko 
Published: November 2019

ABSTRACT
Rice with double mutation of starch synthase IIIa and branching enzyme IIb (ss3a/be2b) has much higher amounts of apparent amylose and resistant starch (RS) than usual varieties. In this study, we conducted two randomized, single-blind, crossover trials to investigate the effect of single ingestion of two processed foods composed of ss3a/be2b mutant rice on postprandial blood glucose and insulin response in healthy adults, compared to those of usual cultivar. In trial 1, of ingestion of rice crackers, the incremental area under the curves of glucose (IAUCglc) and insulin (IAUCins) in RS group was significantly lower than in the control group. In trial 2, of the ingestion of cooked rice, IAUCglc in the RS group was significantly lower than in the control group. These results showed that the ss3a/be2b-mutant rice cracker and cooked rice having high RS can attenuate postprandial blood glucose and insulin response.