bluuebunny/crossref_metadata_2025_split huggingface dataset:
Endometrial thickness measurements among Asherman syndrome patients prior to embryo transfer
Authors: Movilla Peter , Wang Jennifer , Chen Tammy , Morales Blanca , Wang Joyce , Williams Alexandria , Reddy Himabindu , Tavcar Jovana , Loring Megan , Morris Stephanie , Isaacson Keith 
Published: September 2020

Abstract

STUDY QUESTION
Is there an association between endometrial thickness (EMT) measurement and clinical pregnancy rate among Asherman syndrome (AS) patients utilizing IVF and embryo transfer (ET)?

SUMMARY ANSWER
EMT measurements may not be associated with successful clinical pregnancy among AS patients undergoing IVF.

WHAT IS KNOWN ALREADY
Clinical pregnancy rate after IVF is significantly lower in patients with a thin endometrium, defined as a maximum EMT of &lt;7 mm. However, AS patients often have a thin EMT measurement due to intrauterine scarring, with a paucity of data and no guidance on what EMT cutoff is appropriate when planning an ET among these patients.

STUDY DESIGN, SIZE, DURATION
This is a retrospective cohort study of 45 AS patients treated at a specialized advanced hysteroscopic clinic from 1 January 2015, to 1 March 2019.

PARTICIPANTS/MATERIALS, SETTING, METHODS
Review of EMT measurements prior to a total of 90 ETs, among 45 AS patients. The impact of the maximum EMT measurement prior to ET on clinical pregnancy rate was analyzed.

MAIN RESULTS AND THE ROLE OF CHANCE
A total of 25/45 (55.6%) AS patients ultimately went on to have ≥1 clinical pregnancy following a mean ± SD of 2.00 ± 1.26 ET attempts. There was a total of 90 ETs among the 45 AS patients, with 29/90 (32.2%) ETs resulting in a clinical pregnancy. Younger patient age (P = 0.05) and oocyte donation (P = 0.01) were the only variables identified to be significant predictors for a positive clinical pregnancy outcome on bivariate analysis. The mean EMT measurement prior to all ETs among AS patients was 7.5 ± 1.6 mm. EMT measurement prior to ET did not predict a positive clinical pregnancy on either bivariate (P = 0.84) or multivariable analysis (odds ratio 0.91, P = 0.60). 31.8% of EMT measurements measured &lt;7.0 mm. In this small cohort, no difference in the clinical pregnancy rate was detected when comparing ETs with EMT measurements of &lt;7.0 mm versus ≥7.0 mm (P = 0.83). The mean EMT measurement decreased with increasing AS disease severity; 8.0 ± 1.6 mm for mild disease, 7.0 ± 1.4 mm for moderate disease and 5.4 ± 0.1 mm for severe disease.

LIMITATIONS, REASONS FOR CAUTION
Our small sample size limits our ability to draw any definitive conclusions. In addition, patients utilized various infertility clinics. This limits our ability to evaluate the consistency of EMT measurements and the IVF care that was received.

WIDER IMPLICATIONS OF THE FINDINGS
EMT measurement cutoff values should be used with caution if canceling a scheduled ET in AS patients.

STUDY FUNDING/COMPETING INTEREST(S)
This study was not funded. K.I. reports personal fees from Karl Stroz and personal fees from Medtronics outside the submitted work. The other authors have no conflicts of interest.

TRIAL REGISTRATION NUMBER
N/A.
Epithelial Cell Biomarkers Are Predictive of Response to Biologic Agents in Crohn’s Disease
Authors: Osterman Mark T , VanDussen Kelli L , Gordon Ilyssa O , Davis Elisabeth M , Li Katherine , Simpson Kate , Ciorba Matthew , Glover Sarah C , Abraham Bincy , Guo Xueyan , Yee Eric U , Allard Felicia D , Perrigoue Jacqueline G , Claggett Brian , Shen Bo , Stappenbeck Thaddeus S , Liu Julia J 
Published: September 2020

Abstract

Background
Therapeutic efficacy of biologics has remained at about 50% for 2 decades. In Crohn’s disease (CD) patients, we examined the predictive value of an epithelial cell biomarker, ileal microvillar length (MVL), for clinical response to ustekinumab (UST) and vedolizumab (VDZ) and its relationship to another biomarker, intestinal epithelial cell (IEC) pyroptosis, with respect to response to VDZ.

Method
Ileal biopsies from the UNITI-2 randomized controlled trial were analyzed for MVL as a predictor of clinical response to UST. In a 5-center academic retrospective cohort of CD patients, ileal MVL was analyzed to determine its predictive value for response to VDZ. Correlation between ileal MVL and IEC pyroptosis was determined, and the discriminant ability of the combination of 2 biomarkers to VDZ was examined.

Results
Clinical response in UST was significantly higher than placebo (65% vs 39%; P = 0.03), with patients with normal MVL (&gt;1.7 µm) having the greatest therapeutic effect: 85% vs 20% (P = 0.02). For VDZ, clinical response with MVL of 1.35 to 1.55 µm was 82% vs 44% (&lt;1.35 µm) and 40% (&gt;1.55 µm; P = 0.038). There was no correlation between ileal MVL and IEC pyroptosis. The combination criteria of ileal pyroptosis &lt;14 positive cells/1000 IECs or MVL of 1.35 to 1.55 µm could identify 84% of responders and 67% of nonresponders (P = 0.001).

Conclusion
Ileal MVL was predictive of response to UST and VDZ in prospective and retrospective CD cohorts. It was independent of ileal IEC pyroptosis, and combination of the 2 biomarkers enhanced the discriminate ability of responders from nonresponders to VDZ.
Epigenetics of Animal Personality: DNA Methylation Cannot Explain the Heritability of Exploratory Behavior in a Songbird
Authors: van Oers Kees , Sepers Bernice , Sies William , Gawehns Fleur , Verhoeven Koen J F , Laine Veronika N 
Published: September 2020

Synopsis
The search for the hereditary mechanisms underlying quantitative traits traditionally focused on the identification of underlying genomic polymorphisms such as single-nucleotide polymorphisms. It has now become clear that epigenetic mechanisms, such as DNA methylation, can consistently alter gene expression over multiple generations. It is unclear, however, if and how DNA methylation can stably be transferred from one generation to the next and can thereby be a component of the heritable variation of a trait. In this study, we explore whether DNA methylation responds to phenotypic selection using whole-genome and genome-wide bisulfite approaches. We assessed differential erythrocyte DNA methylation patterns between extreme personality types in the Great Tit (Parus major). For this, we used individuals from a four-generation artificial bi-directional selection experiment and siblings from eight F2 inter-cross families. We find no differentially methylated sites when comparing the selected personality lines, providing no evidence for the so-called epialleles associated with exploratory behavior. Using a pair-wise sibling design in the F2 intercrosses, we show that the genome-wide DNA methylation profiles of individuals are mainly explained by family structure, indicating that the majority of variation in DNA methylation in CpG sites between individuals can be explained by genetic differences. Although we found some candidates explaining behavioral differences between F2 siblings, we could not confirm this with a whole-genome approach, thereby confirming the absence of epialleles in these F2 intercrosses. We conclude that while epigenetic variation may underlie phenotypic variation in behavioral traits, we were not able to find evidence that DNA methylation can explain heritable variation in personality traits in Great Tits.
Clinical decision support system, using expert consensus-derived logic and natural language processing, decreased sedation-type order errors for patients undergoing endoscopy
Authors: Shen Lin , Wright Adam , Lee Linda S , Jajoo Kunal , Nayor Jennifer , Landman Adam 
Published: September 2020

Abstract

Objective
Determination of appropriate endoscopy sedation strategy is an important preprocedural consideration. To address manual workflow gaps that lead to sedation-type order errors at our institution, we designed and implemented a clinical decision support system (CDSS) to review orders for patients undergoing outpatient endoscopy.

Materials and Methods
The CDSS was developed and implemented by an expert panel using an agile approach. The CDSS queried patient-specific historical endoscopy records and applied expert consensus-derived logic and natural language processing to identify possible sedation order errors for human review. A retrospective analysis was conducted to evaluate impact, comparing 4-month pre-pilot and 12-month pilot periods.

Results
22 755 endoscopy cases were included (pre-pilot 6434 cases, pilot 16 321 cases). The CDSS decreased the sedation-type order error rate on day of endoscopy (pre-pilot 0.39%, pilot 0.037%, Odds Ratio = 0.094, P-value &lt; 1e-8). There was no difference in background prevalence of erroneous orders (pre-pilot 0.39%, pilot 0.34%, P = .54).

Discussion
At our institution, low prevalence and high volume of cases prevented routine manual review to verify sedation order appropriateness. Using a cohort-enrichment strategy, a CDSS was able to reduce number of chart reviews needed per sedation-order error from 296.7 to 3.5, allowing for integration into the existing workflow to intercept rare but important ordering errors.

Conclusion
A workflow-integrated CDSS with expert consensus-derived logic rules and natural language processing significantly reduced endoscopy sedation-type order errors on day of endoscopy at our institution.
Risk Factors and Incidence of Colorectal Cancer According to Major Molecular Subtypes
Authors: Wang Liang , He Xiaosheng , Ugai Tomotaka , Haruki Koichiro , Lo Chun-Han , Hang Dong , Akimoto Naohiko , Fujiyoshi Kenji , Wang Molin , Fuchs Charles S , Meyerhardt Jeffrey A , Zhang Xuehong , Wu Kana , Chan Andrew T , Giovannucci Edward L , Ogino Shuji , Song Mingyang 
Published: September 2020

Abstract

Background
Colorectal cancer (CRC) is a heterogeneous disease that can develop via 3 major pathways: conventional, serrated, and alternate. We aimed to examine whether the risk factor profiles differ according to pathway-related molecular subtypes.

Methods
We examined the association of 24 risk factors with 4 CRC molecular subtypes based on a combinatorial status of microsatellite instability (MSI), CpG island methylator phenotype (CIMP), and BRAF and KRAS mutations by collecting data from 2 large US cohorts. We used inverse probability weighted duplication-method Cox proportional hazards regression to evaluate differential associations across subtypes.

Results
We documented 1175 CRC patients with molecular subtype data: subtype 1 (n = 498; conventional pathway; non-MSI-high, CIMP-low or negative, BRAF-wild-type, KRAS-wild-type), subtype 2 (n = 138; serrated pathway; any MSI status, CIMP-high, BRAF-mutated, KRAS-wild-type), subtype 3 (n = 367; alternate pathway; non-MSI-high, CIMP-low or negative, BRAF-wild-type, KRAS-mutated), and subtype 4 (n = 172; other marker combinations). Statistically significant heterogeneity in associations with CRC subtypes was found for age, sex, and smoking, with a higher hazard ratio (HR) observed for the subtype 2 (HR per 10 years of age = 2.64, 95% CI = 2.13 to 3.26; HR for female = 2.65, 95% CI = 1.60 to 4.39; HR per 20-pack-year of smoking = 1.29, 95% CI = 1.14 to 1.45) than other CRC subtypes (all Pheterogeneity &lt; .005). A stronger association was found for adiposity measures with subtype 1 CRC in men and subtype 3 CRC in women and for several dietary factors with subtype 1 CRC, although these differences did not achieve statistical significance at α  level of .005.

Conclusions
Risk factor profiles may differ for CRC arising from different molecular pathways.
RoadRunner: a fast and flexible exoplanet transit model
Authors: Parviainen H 
Published: September 2020

ABSTRACT
I present RoadRunner, a fast exoplanet transit model that can use any radially symmetric function to model stellar limb darkening (LD) while still being faster to evaluate than the analytical transit model for quadratic LD by Mandel & Agol. CPU and GPU implementations of the model are available in the pytransit transit modelling package, and come with platform-independent parallelization, supersampling, and support for modelling complex heterogeneous time series. The code is written in numba-accelerated python (and the GPU model in opencl) without c or fortran dependencies, which allows for the LD model to be given as any python-callable function. Finally, as an example of the flexibility of the approach, the latest version of pytransit comes with a numerical limb darkening model that uses LDTk-generated limb darkening profiles directly without approximating them by analytical models.
linestacker: a spectral line stacking tool for interferometric data
Authors: Jolly Jean-Baptiste , Knudsen Kirsten K , Stanley Flora 
Published: September 2020

ABSTRACT
linestacker is a new open access and open source tool for stacking of spectral lines in interferometric data. linestacker is an ensemble of casa tasks, and can stack both 3D cubes or already extracted spectra. The algorithm is tested on increasingly complex simulated data sets, mimicking Atacama Large Millimeter/submillimeter Array, and Karl G. Jansky Very Large Array observations of [C ii] and CO(3–2) emission lines, from z ∼ 7 and z ∼ 4 galaxies, respectively. We find that the algorithm is very robust, successfully retrieving the input parameters of the stacked lines in all cases with an accuracy ≳90 per cent. However, we distinguish some specific situations showcasing the intrinsic limitations of the method. Mainly that high uncertainties on the redshifts (Δz &gt; 0.01) can lead to poor signal-to-noise ratio improvement, due to lines being stacked on shifted central frequencies. Additionally, we give an extensive description of the embedded statistical tools included in linestacker: mainly bootstrapping, rebinning, and subsampling. Velocity rebinning is applied on the data before stacking and proves necessary when studying line profiles, in order to avoid artificial spectral features in the stack. Subsampling is useful to sort the stacked sources, allowing to find a subsample maximizing the searched parameters, while bootstrapping allows to detect inhomogeneities in the stacked sample. linestacker is a useful tool for extracting the most from spectral observations of various types.
The anatomy of a star-forming galaxy II: FUV heating via dust
Authors: Benincasa S M , Wadsley J W , Couchman H M P , Pettitt A R , Keller B W , Woods R M , Grond J J 
Published: September 2020

ABSTRACT
Far-ultraviolet (FUV) radiation greatly exceeds UV, supernovae (SNe), and winds in the energy budget of young star clusters but is poorly modelled in galaxy simulations. We present results of the first isolated galaxy disc simulations to include photoelectric heating of gas via dust grains from FUV radiation self-consistently, using a ray-tracing approach that calculates optical depths along the source–receiver sightline. This is the first science application of the TREVR radiative transfer algorithm. We find that FUV radiation alone cannot regulate star formation. However, FUV radiation produces warm neutral gas and is able to produce regulated galaxies with realistic scale heights. FUV is also a long-range feedback and is more important in the outer discs of galaxies. We also use the superbubble feedback model, which depends only on the SN energy per stellar mass, is more physically realistic than common, parameter-driven alternatives and thus better constrains SN feedback impacts. FUV and SNe together can regulate star formation without producing too much hot ionized medium and with less disruption to the interstellar medium compared to SNe alone.
Spirals, shadows, and precession in HD 100453 – I. The orbit of the binary
Authors: Gonzalez Jean-François , van der Plas Gerrit , Pinte Christophe , Cuello Nicolás , Nealon Rebecca , Ménard François , Revol Alexandre , Rodet Laetitia , Langlois Maud , Maire Anne-Lise 
Published: September 2020

ABSTRACT
In recent years, several protoplanetary discs have been observed to exhibit spirals, both in scattered light and (sub)millimetre continuum data. The HD 100453 binary star system hosts such a disc around its primary. Previous work has argued that the spirals were caused by the gravitational interaction of the secondary, which was assumed to be on a circular orbit, coplanar with the disc (meaning here the large outer disc, as opposed to the very small inner disc). However, recent observations of the CO gas emission were found incompatible with this assumption. In this paper, we run SPH simulations of the gas and dust disc for seven orbital configurations taken from astrometric fits and compute synthetic observations from their results. Comparing to high-resolution ALMA 12CO data, we find that the best agreement is obtained for an orbit with eccentricity e = 0.32 and semimajor axis a = 207 au, inclined by 61° relative to the disc plane. The large misalignment between the disc and orbit planes is compatible with the tidal evolution of a circumprimary disc in an eccentric, unequal-mass binary star.
Coronal vertical structure variations in normal branch of GX 17+2: AstroSat’s SXT and LAXPC perspective
Authors: Malu S , Sriram K , Agrawal V K 
Published: September 2020

ABSTRACT
We performed spectro-temporal analysis in the 0.8–50 keV energy band of the neutron star Z source GX 17+2 using AstroSat Soft X-ray Telescope (SXT) and Large Area X-ray Proportional Counter (LAXPC) data. The source was found to vary in the normal branch (NB) of the hardness–intensity diagram. Cross-correlation studies of LAXPC light curves in soft and hard X-ray band unveiled anticorrelated lags of the order of few hundred seconds. For the first time, cross-correlation studies were performed using SXT soft and LAXPC hard light curves and they exhibited correlated and anticorrelated lags of the order of a hundred seconds. Power density spectrum displayed normal branch oscillations (NBOs) of 6.7–7.8 Hz (quality factor 1.5–4.0). Spectral modelling resulted in inner disc radius of ∼12–16 km with Γ ∼ 2.31–2.44 indicating that disc is close to the innermost stable circular orbit and a similar value of disc radius was noticed based on the reflection model. Different methods were used to constrain the corona size in GX 17+2. Using the detected lags, corona size was found to be 27–46 km (β = 0.1, β = vcorona/vdisc) and 138–231 km (β = 0.5). Assuming the X-ray emission to be arising from the boundary layer (BL), its size was determined to be 57–71 km. Assuming that BL is ionizing the disc’s inner region, its size was constrained to ∼19–86 km. Using NBO frequency, the transition shell radius was found to be around 32 km. Observed lags and no movement of the inner disc front strongly indicate that the varying corona structure is causing the X-ray variation in the NB of Z source GX 17+2.
Spatially resolved star formation and fuelling in galaxy interactions
Authors: Moreno Jorge , Torrey Paul , Ellison Sara L , Patton David R , Bottrell Connor , Bluck Asa F L , Hani Maan H , Hayward Christopher C , Bullock James S , Hopkins Philip F , Hernquist Lars 
Published: September 2020

ABSTRACT
We investigate the spatial structure and evolution of star formation and the interstellar medium (ISM) in interacting galaxies. We use an extensive suite of parsec-scale galaxy-merger simulations (stellar mass ratio = 2.5:1), which employs the ‘Feedback In Realistic Environments-2’ model (fire-2). This framework resolves star formation, feedback processes, and the multiphase structure of the ISM. We focus on the galaxy-pair stages of interaction. We find that close encounters substantially augment cool (H i) and cold-dense (H2) gas budgets, elevating the formation of new stars as a result. This enhancement is centrally concentrated for the secondary galaxy, and more radially extended for the primary. This behaviour is weakly dependent on orbital geometry. We also find that galaxies with elevated global star formation rate (SFR) experience intense nuclear SFR enhancement, driven by high levels of either star formation efficiency (SFE) or available cold-dense gas fuel. Galaxies with suppressed global SFR also contain a nuclear cold-dense gas reservoir, but low SFE levels diminish SFR in the central region. Concretely, in the majority of cases, SFR enhancement in the central kiloparsec is fuel-driven (55 per cent for the secondary, 71 per cent for the primary) – while central SFR suppression is efficiency-driven (91 per cent for the secondary, 97 per cent for the primary). Our numerical predictions underscore the need of substantially larger, and/or merger-dedicated, spatially resolved galaxy surveys – capable of examining vast and diverse samples of interacting systems – coupled with multiwavelength campaigns aimed to capture their internal ISM structure.
A ‘head/tail’ plasmon model with a Hubble law velocity profile
Authors: Raga A C , Rodríguez-González A , Hernández-Martínez L , Cantó J , Castellanos-Ramírez A 
Published: September 2020

ABSTRACT
We present a model of a hypersonic, collimated, ‘single pulse’ outflow, produced by an event with an ejection velocity that first grows, reaches a peak, and then decreases again to zero velocity in a finite time (simultaneously, the ejection density can have an arbitrary time-variability). We obtain a flow with a leading ‘head’ and a trailing ‘tail’ that for times greater than the width of the pulse develops a linear, ‘Hubble law’ velocity versus position. We present an analytical model for a simple pulse with a parabolic ejection velocity versus time and time-independent mass-loss rate, and compare it to an axisymmetric gasdynamic simulation with parameters appropriate for fast knots in planetary nebulae. This ‘head/tail plasmon’ flow might be applicable to other high-velocity clumps with ‘Hubble law’ tails.
Asymmetrical effects of deafness-associated mitochondrial DNA 7516delA mutation on the processing of RNAs in the H-strand and L-strand polycistronic transcripts
Authors: Xiao Yun , Wang Meng , He Qiufen , Xu Lei , Zhang Qinghai , Meng Feilong , Jia Zidong , Zhang Fengguo , Wang Haibo , Guan Min-Xin 
Published: September 2020

AbstractIn this report, we investigated the molecular mechanism underlying a deafness-associated m.7516delA mutation affecting the 5′ end processing sites of mitochondrial tRNAAsp and tRNASer(UCN). An in vitro processing experiment demonstrated that m.7516delA mutation caused the aberrant 5′ end processing of tRNASer(UCN) and tRNAAsp precursors, catalyzed by RNase P. Using cytoplasmic hybrids (cybrids) derived from one hearing-impaired Chinese family bearing the m.7516delA mutation and control, we demonstrated the asymmetrical effects of m.7516delA mutation on the processing of tRNAs in the heavy (H)-strand and light (L)-strand polycistronic transcripts. Specially, the m.7516delA mutation caused the decreased levels of tRNASer(UCN) and downstream five tRNAs, including tRNATyr from the L-strand transcripts and tRNAAsp from the H-strand transcripts. Strikingly, mutant cybrids exhibited the lower level of COX2 mRNA and accumulation of longer and uncleaved precursors of COX2 from the H-strand transcripts. Aberrant RNA metabolisms yielded variable reductions in the mitochondrial proteins, especially marked reductions in the levels of ND4, ND5, CO1, CO2 and CO3. The impairment of mitochondrial translation caused the proteostasis stress and respiratory deficiency, diminished ATP production and membrane potential, increased production of reactive oxygen species and promoted apoptosis. Our findings provide new insights into the pathophysiology of deafness arising from mitochondrial tRNA processing defects.