bluuebunny/crossref_metadata_2025_split huggingface dataset:
A high-throughput microscopy method for single-cell analysis of event-time correlations in nanoparticle-induced cell death
Authors: Murschhauser Alexandra , Röttgermann Peter J. F. , Woschée Daniel , Ober Martina F. , Yan Yan , Dawson Kenneth A. , Rädler Joachim O. 
Published: January 2019

AbstractThe temporal context of cell death decisions remains generally hidden in ensemble measurements with endpoint readouts. Here, we describe a method to extract event times from fluorescence time traces of cell death-related markers in automated live-cell imaging on single-cell arrays (LISCA) using epithelial A549 lung and Huh7 liver cancer cells as a model system. In pairwise marker combinations, we assess the chronological sequence and delay times of the events lysosomal membrane permeabilization, mitochondrial outer membrane permeabilization and oxidative burst after exposure to 58 nm amino-functionalized polystyrene nanoparticles (PS-NH2 nanoparticles). From two-dimensional event-time scatter plots we infer a lysosomal signal pathway at a low dose of nanoparticles (25 µg mL−1) for both cell lines, while at a higher dose (100 µg mL−1) a mitochondrial pathway coexists in A549 cells, but not in Huh7. In general, event-time correlations provide detailed insights into heterogeneity and interdependencies in signal transmission pathways.
Biocatalytic production of bicyclic β-lactams with three contiguous chiral centres using engineered crotonases
Authors: Hamed Refaat B. , Gomez-Castellanos J. Ruben , Henry Luc , Warhaut Sven , Claridge Timothy D. W. , Schofield Christopher J. 
Published: January 2019

AbstractThere is a need to develop asymmetric routes to functionalised β-lactams, which remain the most important group of antibacterials. Here we describe biocatalytic and protein engineering studies concerning carbapenem biosynthesis enzymes, aiming to enable stereoselective production of functionalised carbapenams with three contiguous chiral centres. Structurally-guided substitutions of wildtype carboxymethylproline synthases enable tuning of their C-N and C-C bond forming capacity to produce 5-carboxymethylproline derivatives substituted at C-4 and C-6, from amino acid aldehyde and malonyl-CoA derivatives. Use of tandem enzyme incubations comprising an engineered carboxymethylproline synthase and an alkylmalonyl-CoA forming enzyme (i.e. malonyl-CoA synthetase or crotonyl-CoA carboxylase reductase) can improve stereocontrol and expand the product range. Some of the prepared 4,6-disubstituted-5-carboxymethylproline derivatives are converted to bicyclic β-lactams by carbapenam synthetase catalysis. The results illustrate the utility of tandem enzyme systems involving engineered crotonases for asymmetric bicyclic β-lactam synthesis.
Global properties of the light curves of magnetic, chemically peculiar stars as a testbed for the existence of dipole-like symmetry in surface structures
Authors: Jagelka M. , Mikulášek Z. , Hümmerich S. , Paunzen E. 
Published: January 2019

Context. Magnetic, chemically peculiar stars are known for exhibiting surface abundance inhomogeneities (chemical spots) that lead to photometric and spectroscopic variability with the rotation period. It is commonly assumed that the surface structures are causally connected with the global magnetic field that dominates the photospheric and subphotospheric layers of these stars. As a rule, the observed magnetic fields show a simple dipole-like geometry, with the magnetic axis being noncollinear to the rotational one.
Aims. The present study aims at detecting underlying patterns in the distribution of photometric spots in a sample of 650 magnetic, chemically peculiar stars and examines their link to the magnetic field topology.
Methods. Photometric time-series observations from the ASAS-3 archive were employed to inspect the light-curve morphology of our sample stars and divide them into representative classes described using a principal component analysis. Theoretical light curves were derived from numerous simulations assuming different spot parameters and following the symmetry of a simple dipole magnetic field. These were subsequently compared with the observed light curves.
Results. The results from our simulations are in contradiction with the observations and predict a much higher percentage of double-wave light curves than is actually observed. We thereby conclude that the distribution of the chemical spots does not follow the magnetic field topology, which indicates that the role of the magnetic field in the creation and maintenance of the surface structures may be more subsidiary than what is predicted by theoretical studies.
Homogeneous internal structure of CM-like asteroid (41) Daphne
Authors: Carry B. , Vachier F. , Berthier J. , Marsset M. , Vernazza P. , Grice J. , Merline W. J. , Lagadec E. , Fienga A. , Conrad A. , Podlewska-Gaca E. , Santana-Ros T. , Viikinkoski M. , Hanuš J. , Dumas C. , Drummond J. D. , Tamblyn P. M. , Chapman C. R. , Behrend R. , Bernasconi L. , Bartczak P. , Benkhaldoun Z. , Birlan M. , Castillo-Rogez J. , Cipriani F. , Colas F. , Drouard A. , Ďurech J. , Enke B. L. , Fauvaud S. , Ferrais M. , Fetick R. , Fusco T. , Gillon M. , Jehin E. , Jorda L. , Kaasalainen M. , Keppler M. , Kryszczynska A. , Lamy P. , Marchis F. , Marciniak A. , Michalowski T. , Michel P. , Pajuelo M. , Tanga P. , Vigan A. , Warner B. , Witasse O. , Yang B. , Zurlo A. 
Published: January 2019

Context.CM-like asteroids (Ch and Cgh classes) are a major population within the broader C-complex, encompassing about 10% of the mass of the main asteroid belt. Their internal structure has been predicted to be homogeneous, based on their compositional similarity as inferred from spectroscopy and numerical modeling of their early thermal evolution.Aims.Here we aim to test this hypothesis by deriving the density of the CM-like asteroid (41) Daphne from detailed modeling of its shape and the orbit of its small satellite.Methods.We observed Daphne and its satellite within our imaging survey with the Very Large Telescope extreme adaptive-optics SPHERE/ZIMPOL camera and complemented this data set with earlier Keck/NIRC2 and VLT/NACO observations. We analyzed the dynamics of the satellite with ourGenoidmeta-heuristic algorithm. Combining our high-angular resolution images with optical lightcurves and stellar occultations, we determine the spin period, orientation, and 3D shape, using ourADAMshape modeling algorithm.Results.The satellite orbits Daphne on an equatorial, quasi-circular, prograde orbit, like the satellites of many other large main-belt asteroids. The shape model of Daphne reveals several large flat areas that could be large impact craters. The mass determined from this orbit combined with the volume computed from the shape model implies a density for Daphne of 1.77 ± 0.26 g cm−3(3σ). This densityis consistent with a primordial CM-like homogeneous internal structure with some level of macroporosity (≈ 17%).Conclusions.Based on our analysis of the density of Daphne and 75 other Ch/Cgh-type asteroids gathered from the literature, we conclude that the primordial internal structure of the CM parent bodies was homogeneous.
Endoscopic ultrasound-guided needle-based confocal laser endomicroscopy for diagnosis of gastric subepithelial tumors: a pilot study
Authors: Zhang Ming-Ming , Zhong Ning , Wang Xiao , Li Chang-Qing , Ji Rui , Li Zhen , Gu Xiang , Yu Yan-Bo , Li Li-Xiang , Zuo Xiu-Li , Li Yan-Qing 
Published: January 2019

Abstract
Background The diagnostic yield of current techniques for gastric subepithelial tumors (SETs) is suboptimal. This prospective study aimed to develop diagnostic criteria for needle-based confocal laser endomicroscopy (nCLE) of gastric SETs, and to evaluate the diagnostic efficacy, feasibility, and safety of endoscopic ultrasound-guided nCLE (EUS-nCLE).
Methods Eligible patients were prospectively recruited to undergo EUS-nCLE. Four unblinded investigators evaluated nCLE videos and corresponding histopathology to develop the nCLE criteria. The recorded nCLE videos were reviewed off-line by one endoscopist 3 months later. Image quality (five-point scale, 1 = poor and 5 = very good) and the interobserver agreements were assessed.
Results All 33 patients underwent successful EUS-nCLE procedures. The nCLE criteria for gastric SETs were established. Overall accuracy of off-line nCLE was significantly higher than that of EUS alone (87.9 % vs. 63.6 %; P = 0.02). The mean image quality score was 3.9. The kappa values of the interobserver agreements were 0.66 for gastrointestinal stromal tumor, 0.89 for ectopic pancreas, 0.58 for leiomyoma, and 0.72 for carcinoma.
Conclusions EUS-nCLE was feasible and safe to accurately diagnose gastric SETs.
VIS-IT: Visualizing the Injured Tibia—A Cadaveric Study of Limb Positioning for Posterolateral Tibial Plateau Fracture Visualization
Authors: Kendal Joseph K. , Clark Damian , Longino David , Marion Travis E. , Buckley Richard , Schneider Prism S. , Martin Ryan 
Published: January 2019

AbstractPosterolateral tibial plateau (PLTP) fractures are often associated with anterior cruciate ligament (ACL) incompetence, such as tibial eminence fractures. Both occur from a pivot shift like mechanism. Malreductions of the tibial plateau most frequently occur in the posterolateral quadrant. Acquiring adequate intraoperative visualization of the PLTP poses a challenge. We hypothesized that visualization of PLTP could be improved by positioning the knee at 110 degrees of flexion with the addition of a varus anterolateral rotatory vector. This position and maneuver take advantage of both the nonisometric nature of the lateral soft tissues and, when present, ACL incompetence. In this cadaveric study, we digitally quantified the percentage of the lateral tibial plateau visualized under different conditions after performing an anterolateral surgical approach with submeniscal arthrotomy. Four conditions were assessed for articular visualization: (1) 30 degrees of knee flexion, (2) 110 degrees of knee flexion, (3) 110-degrees of knee flexion plus varus anterolateral rotatory vector, (4) 110-degrees of knee flexion plus varus anterolateral rotatory vector with ACL sacrifice (ACL incompetence model). In the ACL competent models, maximal lateral tibial plateau exposure was obtained with the knee positioned at 110 degrees of flexion with a varus anterolateral rotatory vector (58.2%, range: 52.9–63.4%). Articular visualization was further improved with the ACL incompetent model (82.4%, range: 77.1–87.7%), modeling a tibial eminence fracture.
Microsurgical and Endoscope Assisted Resection of a Right Intracanalicular Vestibular Schwannoma Two-Dimensional Operative Video
Authors: Cheng Chun-Yu , Qazi Zeeshan , Sekhar Laligam N. 
Published: January 2019

A 36-year-old lady presented with tinnitus and hearing loss for 1 year which was progressively worsening. A hearing test revealed pure tone average (PTA) between 48 to 65 dB and speech discrimination of 56% at 95 dB. Brain magnetic resonance imaging (MRI) showed a right vestibular schwannoma 5 × 8 mm (Fig. 1) which extended far laterally to the fundus of internal auditory canal (IAC). A translabyrinthine approach was suggested by another neurosurgeon/neurotologist team, but the patient decided to undergo operation by retrosigmoid approach with attempted hearing preservation.She underwent a right retrosigmoid craniotomy, craniectomy, and mastoidectomy with far lateral approach. We performed petrous transcanalicular microsurgical approach with the assistance of neuroendoscope. Intraoperatively, the internal auditory artery was looping into the IAC between cranial nerves VII and VIII, and coming out inferiorly. The IAC was opened by the diamond drill, ultrasonic bone curette, and fine rongeurs. The tumor was grayish in color with filling the lateral aspect of the IAC. After circumferential dissection of the tumor capsule, the tumor was removed completely. It was arising from the inferior vestibular nerve which was stretched. The patient had vertigo and nausea postoperatively but it is steadily improving. Her hearing test has improved to a PTA of 22 dB and speech discrimination of 100% at 70 dB at 6 weeks. The postoperative MRI showed total resection.This two-dimensional video shows the technical nuances of microsurgical retrosigmoid approach and endoscopic assisted resection of an intracanalicular vestibular schwannoma and the value of attempting hearing preservation in all vestibular schwannomas (Fig. 2).The link to the video can be found at: https://youtu.be/KHrO_iDI2tw.
Nonlinear excitations in magnetic lattices with long-range interactions
Authors: Molerón Miguel , Chong C , Martínez Alejandro J , Porter Mason A , Kevrekidis P G , Daraio Chiara 
Published: January 2019

Abstract
We study—experimentally, theoretically, and numerically—nonlinear excitations in lattices of magnets with long-range interactions. We examine breather solutions, which are spatially localized and periodic in time, in a chain with algebraically-decaying interactions. It was established two decades ago (Flach 1998 Phys. Rev. E 58 R4116) that lattices with long-range interactions can have breather solutions in which the spatial decay of the tails has a crossover from exponential to algebraic decay. In this article, we revisit this problem in the setting of a chain of repelling magnets with a mass defect and verify, both numerically and experimentally, the existence of breathers with such a crossover.
Lewis on the way
Authors: Como James 
Published: January 2019

Abstract
‘Lewis on the way’ describes the many images of C. S. Lewis—the author and the man. He was a Christian writer, religious and social philosopher, teacher, conversationalist, and general man of letters; he was imaginative and rational, authoritative and familiar, witty though intellectually severe, combative and mild, certain yet somehow restrained, defiant and unfashionable while also gregarious, good-humoured, and popular to the point of being charismatic. It concludes that his personal influence upon millions of people is deep, significant, and abiding, and his personality and life continue to arouse interest. His many voices have produced a trenchant body of work that includes hallmarks of its many types, remains relevant, and invites commentary.
Fame
Authors: Como James 
Published: January 2019

Abstract
‘Fame’ discusses C. S. Lewis’s work through the 1940s and the rise of his vocation as an apologist. It considers The Screwtape Letters (1942) and his vastly popular BBC talks (which were all to be consolidated and edited by Lewis as Mere Christianity, 1952). Amid prodigious letter writing, he continues the tradition of walking tours with Warren and others from the 1930s and converses with the Inklings. His thoughts on Milton’s Paradise Lost are discussed along with his ideas on the difference between primary and secondary epics. The Abolition of Man, The Great Divorce, and his cosmic mythological fiction—Out of the Silent Planet, Perelandra, and That Hideous Strength—are also considered.
Identifying Aesthetically Appealing Upper Eyelid Topographic Proportions
Authors: Vaca Elbert E , Bricker Jonathan T , Helenowski Irene , Park Eugene D , Alghoul Mohammed S 
Published: January 2019

Abstract

Background
The goal of upper eyelid procedures is to restore or create the ideal proportions between the pretarsal space and the upper lid fold.

Objectives
The aim of this study was to define the topographic features of the attractive upper lid.

Methods
Caucasian female frontal facial photographs were obtained from public media and periorbital areas were cropped. A total of 294 photographs of eyes were rated by 6 evaluators using a 4-point Likert scale. Eyes rating an average ≥3.5 were defined as “attractive,” whereas those rated ≤2.0 were defined as “unattractive” and analyzed using Adobe Illustrator.

Results
Fifty-one and 19 eyes were included in the attractive and unattractive cohorts, respectively. (Upper lid foldPretarsal) shows ratios averaged between 1.8 and 3.0 among attractive eyes, and larger ratios were observed laterally. These ratios were significantly larger laterally among attractive vs unattractive eyes (P ≤ 0.003). The lash line peak (P &lt; 10–4), lid crease peak (P &lt; 10–3), and brow peak (P &lt; 0.05) were significantly more lateralized in attractive eyes.

Conclusions
Attractive eyes tend to exhibit decreased pretarsal show. However, there is pronounced variability in these ratios among attractive eyes, suggesting the importance of other features. Interestingly, progressive lateralization of the lash line, lid crease, and brow peaks appears to be an undescribed feature common to attractive eyes. Knowledge of attractive eyelid features may be an important consideration for planning and optimization of upper lid rejuvenation procedures.
Rapid alignment-free phylogenetic identification of metagenomic sequences
Authors: Linard Benjamin , Swenson Krister , Pardi Fabio 
Published: January 2019

Abstract

Motivation
Taxonomic classification is at the core of environmental DNA analysis. When a phylogenetic tree can be built as a prior hypothesis to such classification, phylogenetic placement (PP) provides the most informative type of classification because each query sequence is assigned to its putative origin in the tree. This is useful whenever precision is sought (e.g. in diagnostics). However, likelihood-based PP algorithms struggle to scale with the ever-increasing throughput of DNA sequencing.

Results
We have developed RAPPAS (Rapid Alignment-free Phylogenetic Placement via Ancestral Sequences) which uses an alignment-free approach, removing the hurdle of query sequence alignment as a preliminary step to PP. Our approach relies on the precomputation of a database of k-mers that may be present with non-negligible probability in relatives of the reference sequences. The placement is performed by inspecting the stored phylogenetic origins of the k-mers in the query, and their probabilities. The database can be reused for the analysis of several different metagenomes. Experiments show that the first implementation of RAPPAS is already faster than competing likelihood-based PP algorithms, while keeping similar accuracy for short reads. RAPPAS scales PP for the era of routine metagenomic diagnostics.

Availability and implementation
Program and sources freely available for download at https://github.com/blinard-BIOINFO/RAPPAS.

Supplementary information
Supplementary data are available at Bioinformatics online.
Hippocampal Interaction With Area 25, but not Area 32, Regulates Marmoset Approach–Avoidance Behavior
Authors: Wallis Chloe U , Cockcroft Gemma J , Cardinal Rudolf N , Roberts Angela C , Clarke Hannah F 
Published: January 2019

AbstractAffective disorders are associated with increased sensitivity to negative feedback that influences approach–avoidance decision making. Although neuroimaging studies of these disorders reveal dysregulation in primate cingulate areas 25 and 32 and the anterior hippocampus (aHipp), the causal involvement of these structures and their interaction in the primate brain is unknown. We therefore investigated the effects of localized pharmacological manipulations of areas 25 and 32 and/or the aHipp of the marmoset monkey on performance of an anxiolytic-sensitive instrumental decision-making task in which an approach–avoidance conflict is created by pairing a response with reward and punishment. During control infusions animals avoided punishment, but this bias was reduced by increasing glutamate release within the aHipp or area 32, and inactivation or 5-HT1a antagonism within area 25. Conversely, increasing glutamate release in area 25 enhanced punishment avoidance but, in contrast to previous reports, area 32 and aHipp inactivations had no effect. Simultaneous inactivation or 5-HT1a antagonism within area 25, but not area 32, abolished the reduced punishment avoidance seen after increasing aHipp glutamate. Besides providing causal evidence that these primate areas differentially regulate negative feedback sensitivity, this study links the decision-making deficits in affective disorders to aberrant aHipp–area 25 circuit activity.
The Increasing Prevalence of Obesity in Residents of U.S. Nursing Homes: 2005–2015
Authors: Zhang Ning , Field Terry , Mazor Kathleen M , Zhou Yanhua , Lapane Kate L , Gurwitz Jerry H 
Published: January 2019

Abstract

Background
Obesity prevalence has been increasing over decades among the U.S. population. This study analyzed trends in obesity prevalence among long-stay nursing home residents from 2005 to 2015.

Methods
Data came from the Minimum Data Sets (2005–2015). The study population was limited to long-stay residents (ie, those residing in a nursing home ≥100 days in a year). Residents were stratified into body mass index (BMI)-based groups: underweight (BMI < 18.5), normal weight (18.5 ≤ BMI < 25), overweight (25 ≤ BMI < 30), and obese (BMI ≥ 30); residents with obesity were further categorized as having Class I (30 ≤ BMI < 35), Class II (35 ≤ BMI < 40), or Class III (BMI ≥ 40) obesity. Minimum Data Sets assessments for 2015 were used to compare clinical and functional characteristics across these groups.

Results
Obesity prevalence increased from 22.4% in 2005 to 28.0% in 2015. The prevalence of Class III obesity increased from 4.0% to 6.2%. The prevalence of underweight, normal weight, and overweight decreased from 8.5% to 7.2%, from 40.3% to 37.1%, and from 28.9% to 27.8%, respectively. In 2015, compared with residents with normal weight, residents with obesity were younger, were less likely to be cognitively impaired, had high levels of mobility impairment, and were more likely to have important medical morbidities.

Conclusions and Relevance
There was a steady upward trend in obesity prevalence among nursing home residents for 2005–2015. Medical and functional characteristics of these residents may affect the type and level of care required, putting financial and staffing pressure on nursing homes.
Gender differences in relationships between sociodemographic factors and e-cigarette use with smoking cessation: 2014–15 current population survey tobacco use supplement
Authors: Abrams Leah R , Kalousova Lucie , Fleischer Nancy L 
Published: January 2019

Abstract

Background
There is conflicting evidence regarding whether men and women are equally likely to quit smoking. We assessed whether gender differences in smoking cessation varied between different sociodemographic groups and across e-cigarette use.

Methods
The 2014–15 cross-section of the Current Population Survey Tobacco Use Supplement was weighted to represent the US adult population of current/former smokers (N = 16 040). Log binomial models tested whether gender modified the relationships between race/ethnicity, education, income or e-cigarette use and 90-day smoking cessation in the past year.

Results
Gender was not associated with cessation in adjusted models (RR = 0.97, CI: 0.85, 1.11). There were no statistically significant interactions between gender and sociodemographic covariates. Current e-cigarette use was associated with higher cessation (RR = 1.53, CI: 1.30, 1.81), and the association varied by gender (Interaction P = 0.013). While male e-cigarette users had a 15% predicted cessation in the past year (CI: 12, 18%), female users had a 9% predicted cessation (95% CI: 7, 11%). Probability of cessation for female e-cigarette users was not different from non-users.

Conclusions
These findings suggest that there are no gender differences in smoking cessation in the USA overall, or by sociodemographic groups. Current e-cigarette use is associated with higher likelihood of recent successful smoking cessation, particularly for men.