bluuebunny/crossref_metadata_2025_split huggingface dataset:
Organometallic ruthenium anticancer complexes inhibit human peroxiredoxin I activity by binding to and inducing oxidation of its catalytic cysteine residue
Authors: Lin Yu , Wang Jie , Zheng Wei , Luo Qun , Wu Kui , Du Jun , Zhao Yao , Wang Fuyi 
Published: January 2019

Abstract
Peroxiredoxins (Prxs) are a family of ubiquitous antioxidant proteins and the inhibition of Prxs would elevate the reactive oxygen species level so as to induce cancer cell death. The interactions of organometallic ruthenium arene anticancer complexes with proteins play important roles in their mechanisms of action. Herein, we demonstrate that Ru complexes [(η6-arene)Ru(en)Cl]+ (en = ethylenediamine, arene = p-cymene (1), biphenyl (2) and 9,10-dihydrophenanthrene (3)) can inhibit the enzymatic activity of human peroxiredoxin I (Prx-I) in an order of 1 &gt; 3 &gt; 2. Mass spectrometric (MS) analysis revealed that 1–3 coordinated to the catalytic site Cys173 of Prx-I, and partially induced the oxidation of the thiolate to sulfenate. Quantitative MS analysis demonstrated that the higher level of the ruthenation of Cys173 is correlated with the higher inhibitory potency of the Ru complexes against Prx-I, suggesting their binding to Cys173 accounts for their inhibition towards Prx-I.
Designating ligand specificities to metal uptake ABC transporters in Thermus thermophilus HB8
Authors: Mandal Suraj Kumar , Adhikari Rahi , Sharma Anjaney , Chandravanshi Monika , Gogoi Prerana , Kanaujia Shankar Prasad 
Published: January 2019

Abstract
Micronutrients such as metal ions are indispensable for the growth and survival of microorganisms in assorted environmental niches. However, change in cellular concentration of metal ions is pernicious for an organism; thus metal ion homeostasis is crucial for their survival and growth. An eminent mechanism for maintaining metal ion homeostasis in microorganisms is ATP-binding cassette (ABC) transporters, which transport metal ions in their ionic/complex forms across the cell membrane. For the uptake, metals are sequestered by substrate-binding proteins (SBPs) and transferred to transmembrane domains (TMDs) for their transport. In this work, a high-throughput data mining analysis has been performed to identify open reading frames (ORFs) encoding metal-specific ABC transporters in a thermophilic bacterium Thermus thermophilus HB8. In total, 22 ORFs resulting in eight ABC transport systems were identified, which are potentially involved in the uptake of metal ions. This study suggests that three out of eight metal-specific ABC import systems are specific to iron ions. Among the remaining five, two are particular to divalent metal ions such as Mg2+ and Zn2+/Mn2+, another two are for tetrahedral oxyanions such as MoO42− and WO42− and the remaining one imports cyanocobalamin (vitamin B12). Besides these, the results of this study demonstrate the existence of a mechanism where TMD and NBD components are shared among different ABC transport systems hinting that multiple substrates can be imported via a single transporter. This study thus provides the first ever preliminary glimpse into the entire repertoire of metal uptake ABC transporters in a thermophilic organism.
VU limit pre‐assessment for high‐speed railway considering a grid connection scheme
Authors: Chen Yinyu , Chen Minwu , Tian Zhongbei , Liu Yuanli , Hillmansen Stuart 
Published: January 2019

Single‐phase 25 kV AC traction power supply systems (TPSSs) are widely used in high‐speed railways, leading to an increasingly prominent problem of voltage unbalance (VU) in the power grid. To fairly regulate the system VU level, implementing VU limit pre‐assessment is an urgent need. A grid connection scheme including traction transformer selection and exchange phase connection design is a vital part of TPSS design that obviously affects the VU factor of power systems. A uniform mathematical model is established using Thevenin's theorem, which reveals the impact of multiple grid connection schemes on the VU propagation behaviour of a three‐phase grid. Afterwards, under the requirements of IEC/TR 61000‐3‐13, an improved VU limit pre‐assessment process is proposed, which correlates mapping between the grid connection scheme and VU limit. The unbalance compensation calculation is given, adopting the allocation limit; furthermore, the optimal design of the grid connection scheme with minimised compensation capacity as an object is presented. The correctness of the model and the rationality of the pre‐assessment process are verified by a case study.
Frame-based Stereotactic Biopsy: Description and Association of Anatomical, Radiologic, and Surgical Variables with Diagnostic Yield in a Series of 407 Cases
Authors: Lara-Almunia Monica , Hernandez-Vicente Javier 
Published: January 2019

Background and Study Aims Stereotactic biopsy is a versatile, minimally invasive technique to obtain tissue safely from intracranial lesions for their histologic diagnosis and therapeutic management. Our objective was to determine the anatomical, radiologic, and technical factors that can affect the diagnostic yield of this technique. We suggest recommendations to improve its use in clinical practice.
Methods This retrospective study evaluated 407 patients who underwent stereotactic biopsies in the past 34 years. The surgical methodology changed through time, distinguished by three distinct periods. Different stereotactic frames (Todd-Wells, CRW, Leksell), neuroimaging tests, and planning programs were used. Using SPSS software v.23, we analyzed a total of 50 variables for each case.
Results The series included 265 men (65.1%) and 142 women (34.9%) (average age 53.8 years). The diagnostic yield was 90.4%, morbidity was 5.65% (n = 17), and mortality was 0.98% (n = 4). Intraoperative biopsy improved accuracy (p = 0.024). Biopsies of deep lesions (p = 0.043), without contrast enhancement (p = 0.004), edema (p = 0.036), extensive necrosis (p = 0.028), or a large cystic component (p = 0.023) resulted in a worse diagnostic yield. Neurosurgeons inexperienced in stereotactic techniques obtained more nondiagnostic biopsies (p = 0.043). Experience was the clearest predictive factor of diagnostic yield (odds ratio: 4.049).
Conclusions Increased experience in stereotactic techniques, use of the most suitable magnetic resonance imaging sequences during biopsy planning, and intraoperative evaluation of the sample before finalizing the collection are recommended features and ways to improve the diagnostic yield of this technique.
Carpal Kinematics following Sequential Scapholunate Ligament Sectioning
Authors: Padmore Clare , Stoesser Helen , Langohr G. Daniel , Johnson James , Suh Nina 
Published: January 2019

Background The scapholunate ligament (SLL) is the most commonly injured intercarpal ligament of the wrist. It is the primary stabilizer of the scapholunate (SL) joint, but the scaphotrapeziotrapezoid (STT) and radioscaphocapitate (RSC) ligaments may also contribute to SL stability. The contributions of SL joint stabilizers have been reported previously; however, this study aims to examine their contributions to SL stability using a different methodology than previous studies.
Purpose The purpose of this in vitro biomechanical study was to quantify changes in SL kinematics during wrist flexion and extension following a previously untested sequential sectioning series of the SL ligament and secondary stabilizers.
Methods Eight cadaveric upper extremities underwent active wrist flexion and extension in a custom motion wrist simulator. SL kinematics were captured with respect to the distal radius. A five-stage sequential sectioning protocol was performed, with data analyzed from 45-degree wrist flexion to 45-degree wrist extension.
Results Wrist flexion and extension caused the lunate to adopt a more extended posture following sectioning of the SLL and secondary stabilizers compared with the intact state (p < 0.009). The isolated disruption to the dorsal portion of the SLL did not result in significant change in lunate kinematics compared with the intact state (p > 0.05). Scaphoid kinematics were altered in wrist flexion following sequential sectioning (p = 0.013). Additionally, disruption of the primary and secondary stabilizers caused significant change to SL motion in both wrist flexion and wrist extension (p < 0.03).
Conclusions The SLL is the primary stabilizer of the SL articulation, with the STT and RSC ligaments playing secondary stabilization roles.
Clinical Relevance Understanding the role primary and secondary SL joint stabilizers may assist in the development of more effective treatment strategies and patient outcomes following SLL injuries.
Future Challenges in Pediatric and Neonatal Sepsis: Emerging Pathogens and Antimicrobial Resistance
Authors: Folgori Laura , Bielicki Julia 
Published: January 2019

AbstractThe incidence of severe infections caused by multidrug-resistant (MDR) pathogens is currently rising worldwide, and increasing numbers of neonates and children with serious bloodstream infections due to resistant bacteria are being reported. Severe sepsis and septic shock due to gram-negative bacteria represent a significant cause of morbidity and mortality, and contribute to high health care costs. Antimicrobial resistance among Enterobacteriaceae represents a major problem in both health care-associated and community-acquired infections, with extended-spectrum β-lactamases (ESBLs) and carbapenem-resistant Enterobacteriaceae (CRE) now presenting the main threat. These infections in adult populations have been associated with poor clinical outcomes, but very limited data have been published so far about risk factors and clinical outcome of ESBL-associated and CRE sepsis in the pediatric population. The treatment of these infections in neonates and children is particularly challenging due to the limited number of available effective antimicrobials. Evidence-based use of new and older antibiotics based on both strategic and regulatory clinical trials is paramount to improve management of these severe infections in neonates and children.
Relationship of Sociodemographic Factors and Outcomes in Functional Rhinoplasty
Authors: Spataro Emily , Olds Cristen , Kandathil Cherian , Most Sam , Nuyen Brian 
Published: January 2019

AbstractThe objective of this article was to compare the effect of such sociodemographic factors as gender, age, marital status, employment status, race, and income on short- and long-term rhinoplasty outcomes using a validated disease-specific instrument—Nasal Obstruction Symptom Evaluation (NOSE) scale, as well as complication and revision rates. Patients who underwent a functional (+/− cosmetic) rhinoplasty with the senior author between January, 1 2012, and September 9, 2017, and had both a preoperative and at least one postoperative NOSE score, were included in the study. Sociodemographic variables of binary gender, age, marital status, employment status, race, and income based on zip code were collected. The primary outcomes were the differences between the preoperative and postoperative NOSE scores with short-term (less than 3 months) and longer-term (greater than 3 months) follow-up. Secondary outcomes were general complications and specifically revision surgery. Standard descriptive statistics, as well as univariable linear and logistic regressions, were conducted with each outcome measure. A total of 341 patients were included in this study. No individual patient-level variables were found to significantly affect the short- or longer-term average change in NOSE scores, although older age trended toward significance in longer-term average change in NOSE scores (p = 0.07). No factors significantly affected the rate of complications or revision surgery in this cohort. The authors found improvement in NOSE scores after rhinoplasty was not related to factors of age, gender, race, employment status, income, and marital status. This cohort also did not demonstrate differential rates in complications or revision surgery based on sociodemographic variables.
Citation analysis
Authors: Bruhn Mark J. 
Published: January 2019

AbstractThis paper presents series of historiometric studies that exemplify the value of “citation analysis” as an empirical approach to professional literary-critical interpretation, especially with respect to the question of the “literariness” of literary texts. Specifically, the studies show that professional interpreters of Wordsworth’s poetry, across more than a century of time and despite widely varying critical approaches, tend to pay more attention to and therefore more frequently cite lines that involve prospective enjambments. Lines involving nominative noun phrase and retrospective enjambments, however, did not reveal the same correlation with frequency of citation. The studies thus suggest that literariness does indeed have a relatively stable textual component that may be discriminated through citation analysis of professional interpretations of individual literary texts by authors writing in distinct genres of literature and in different periods in literary history.
Living metaphor as the site of bidirectional literary engagement
Authors: Kuiken Don , Douglas Shawn 
Published: January 2019

Abstract
Articulation of an interactive model of literariness calls for separate specification of (a) a text’s perceptible
mode of representation, (b) a reader’s mode of engagement with a text so perceived, and (c) the generative (e.g., creative,
expressive) effects of the interaction between this mode of representation and mode of reader engagement. We present a model that
identifies two aspects of metaphoric textual representation: structured sequences of nominal metaphors and quasi-metaphoric
structures with optional metaphoric construal. This model also distinguishes two modes of reader engagement: expressive enactment
and integrative comprehension (Kuiken & Douglas, 2017). The generativity of
literary reading is located especially within the interplay between expressive enactment and sequences of metaphoric (and
quasi-metaphoric) modes of representation. Evidence suggests that readers reporting expressive enactment also report inexpressible
realizations and a temporal progression leading through epistemic tensions that comprise “living metaphor” (Ricoeur, 1981). Thus the generativity – and aesthetic effects – of literary reading are found within the
departures from conventionality that comprise the emergent meanings of complex metaphoric structures.
Understandability, actionability, and readability of online patient education materials about diabetes mellitus
Authors: Lipari Melissa , Berlie Helen , Saleh Yasmin , Hang Pang , Moser Lynette 
Published: January 2019

Abstract

Purpose
The purpose of this study was to assess the understandability, actionability, and readability of online diabetes education materials.

Summary
This was a descriptive study that identified printable diabetes education materials through an online search. Materials were included from the following sources: national organizations with materials approved by expert panels, corporations with materials subject to FDA approval, and not-for-profit organizations with inter-professional advisory boards to approve materials. Topics included were basic knowledge of diabetes, hypoglycemia, insulin, and blood sugar goals. Materials were excluded if they were non-printable, contained active links, had a publication date prior to January 2011, were greater than 2 pages in length, or were pediatric focused. Understandability and actionability of the patient education materials were evaluated using the Patient Education Materials Assessment Tool (PEMAT). Descriptive statistics and inter-rater reliability analysis using the kappa statistic were utilized. Readability was assessed using the Flesch-Kincaid Grade Level and Simple Measure of Gobbledygook (SMOG) formula. Pearson correlation coefficient was calculated to assess the relationship between reading grade level and PEMAT scores. In total, 25 websites were identified, 5 of which met the inclusion criteria; 13 patient education materials were included, PEMAT scoring revealed that 4 of these met the criteria for understandability and only 1 met the criteria for actionability. There was no correlation found between PEMAT scores and reading grade levels (Pearson correlation coefficient = −0.30, p = 0.325).

Conclusion
The majority of diabetes patient education materials reviewed scored poorly using the PEMAT. Future development of diabetes patient education materials should be designed with the goal of increasing understandability and actionability.
Resource allocation trade-offs and the loss of chemical defences during apple domestication
Authors: Whitehead Susan R , Poveda Katja 
Published: January 2019

AbstractBackground and AimsMost crops have been dramatically altered from their wild ancestors with the primary goal of increasing harvestable yield. A long-held hypothesis is that increased allocation to yield has reduced plant investment in defence and resulted in crops that are highly susceptible to pests. However, clear demonstrations of these trade-offs have been elusive due to the many selective pressures that occur concurrently during crop domestication.MethodsTo provide a robust test of whether increased allocation to yield can alter plant investment in defence, this study examined fruit chemical defence traits and herbivore resistance across 52 wild and 56 domesticated genotypes of apples that vary &gt;26-fold in fruit size. Ninety-six phenolic metabolites were quantified in apple skin, pulp and seeds, and resistance to the codling moth was assessed with a series of bioassays.Key ResultsThe results show that wild apples have higher total phenolic concentrations and a higher diversity of metabolites than domesticated apples in skin, pulp and seeds. A negative phenotypic relationship between fruit size and phenolics indicates that this pattern is driven in part by allocation-based trade-offs between yield and defence. There were no clear differences in codling moth performance between wild and domesticated apples and no overall effects of total phenolic concentration on codling moth performance, but the results did show that codling moth resistance was increased in apples with higher phenolic diversity. The concentrations of a few individual compounds (primarily flavan-3-ols) also correlated with increased resistance, primarily driven by a reduction in pupal mass of female moths.ConclusionsThe negative phenotypic relationship between fruit size and phenolic content, observed across a large number of wild and domesticated genotypes, supports the hypothesis of yield–defence trade-offs in crops. However, the limited effects of phenolics on codling moth highlight the complexity of consequences that domestication has for plant–herbivore interactions. Continued studies of crop domestication can further our understanding of the multiple trade-offs involved in plant defence, while simultaneously leading to novel discoveries that can improve the sustainability of crop production.
admixr—R package for reproducible analyses using ADMIXTOOLS
Authors: Petr Martin , Vernot Benjamin , Kelso Janet 
Published: January 2019

Abstract

Summary
We present a new R package admixr, which provides a convenient interface for performing reproducible population genetic analyses (f3, D, f4, f4-ratio, qpWave and qpAdm), as implemented by command-line programs in the ADMIXTOOLS software suite. In a traditional ADMIXTOOLS workflow, the user must first generate a set of text configuration files tailored to each individual analysis, often using a combination of shell scripting and manual text editing. The non-tabular output files then need to be parsed to extract values of interest prior to further analyses. Our package simplifies this process by automating all low-level configuration and parsing steps, making analyses as simple as running a single R command. Furthermore, we provide a set of R functions for processing, filtering and manipulating datasets in the EIGENSTRAT format. By unifying all steps of the workflow under a single R framework, this package enables the automation of analytic pipelines, significantly improving the reproducibility of population genetic studies.

Availability and implementation
The source code of the R package is available under the MIT license. Installation instructions, reference manual and a tutorial can be found on the package website at https://bioinf.eva.mpg.de/admixr.

Supplementary information
Supplementary data are available at Bioinformatics online.
multiHiCcompare: joint normalization and comparative analysis of complex Hi-C experiments
Authors: Stansfield John C , Cresswell Kellen G , Dozmorov Mikhail G 
Published: January 2019

Abstract

Motivation
With the development of chromatin conformation capture technology and its high-throughput derivative Hi-C sequencing, studies of the three-dimensional interactome of the genome that involve multiple Hi-C datasets are becoming available. To account for the technology-driven biases unique to each dataset, there is a distinct need for methods to jointly normalize multiple Hi-C datasets. Previous attempts at removing biases from Hi-C data have made use of techniques which normalize individual Hi-C datasets, or, at best, jointly normalize two datasets.

Results
Here, we present multiHiCcompare, a cyclic loess regression-based joint normalization technique for removing biases across multiple Hi-C datasets. In contrast to other normalization techniques, it properly handles the Hi-C-specific decay of chromatin interaction frequencies with the increasing distance between interacting regions. multiHiCcompare uses the general linear model framework for comparative analysis of multiple Hi-C datasets, adapted for the Hi-C-specific decay of chromatin interaction frequencies. multiHiCcompare outperforms other methods when detecting a priori known chromatin interaction differences from jointly normalized datasets. Applied to the analysis of auxin-treated versus untreated experiments, and CTCF depletion experiments, multiHiCcompare was able to recover the expected epigenetic and gene expression signatures of loss of chromatin interactions and reveal novel insights.

Availability and implementation
multiHiCcompare is freely available on GitHub and as a Bioconductor R package https://bioconductor.org/packages/multiHiCcompare.

Supplementary information
Supplementary data are available at Bioinformatics online.