bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exploring Collagen Parameters in Pure Special Types of Invasive Breast Cancer
Authors: Natal Rodrigo de Andrade , Paiva Geisilene R. , Pelegati Vitor B. , Marenco Ludwing , Alvarenga César A. , Vargas Renato F. , Derchain Sophie F. , Sarian Luis O. , Franchet Camille , Cesar Carlos L. , Schmitt Fernando C. , Weigelt Britta , Vassallo José 
Published: May 2019

AbstractOne of the promising tools to evaluate collagen in the extracellular matrix is the second-harmonic generation microscopy (SHG). This approach may shed light on the biological behavior of cancers and their taxonomy, but has not yet been applied to characterize collagen fibers in cases diagnosed as invasive breast carcinoma (BC) of histological special types (IBC-ST). Tissue sections from 99 patients with IBC-ST and 21 of invasive breast carcinoma of no special type (IBC-NST) were submitted to evaluation of collagen parameters by SHG. Tissue microarray was performed to evaluate immunohistochemical-based molecular subtype. In intratumoral areas, fSHG and bSHG (forward-SHG and backward-SHG) collagen parameters achieved their lowest values in mucinous, papillary and medullary carcinomas, whereas the highest values were found in classic invasive lobular and tubular carcinomas. Unsupervised hierarchical cluster analysis and minimal spanning tree using intratumoral collagen parameters allowed the identification of three main groups of breast cancer: group A (classic invasive lobular and tubular carcinomas); group B (IBC-NST, metaplastic, invasive apocrine and micropapillary carcinomas); and group C (medullary, mucinous and papillary carcinomas). Our findings provide further characterization of the tumor microenvironment of IBC-ST. This understanding may add information to build more consistent tumor categorization and to refine prognostication.
Potential protective effects of bilirubin following the treatment of neonatal hypoxic-ischemic encephalopathy with hypothermia therapy
Authors: Zou Liangyan , Yuan Hao , Liu Qing , Lu Chunmei , Wang Laishuan 
Published: May 2019

Abstract
Background: Therapeutic hypothermia (TH) is the standard therapy for hypoxic-ischemic encephalopathy (HIE) and is associated with a wide range of physiological changes. Objective: We re-evaluated the effects of HIE and TH on bilirubin measurements following HIE in a center involved in the China cooling randomized controlled trial (RCT). Methods: Serial serum bilirubin concentrations measured during the first week of life were compared among the HIE + NT (normothermia) group, HIE + TH treatment group and control group (without HIE). Survivors of HIE were followed and assessed at approximately 2 years of age, and the results were correlated with peak bilirubin levels during the first week of life. Results: One hundred and thirty-eight infants were available for analysis. Significantly lower bilirubin levels were recorded in the HIE + NT group than in the controls (P&lt;0.05). Significant differences were not observed among the patients in the HIE + NT group (mild to severe) or between the HIE + TH group and the HIE + NT group at any time point (P&gt;0.05). The peak serum bilirubin concentrations recorded at 96 h of age showed a good correlation with the results of the Bayley Scales of Infant and Toddler Development, third edition (BSID-III) (P=0.02). Conclusion: Bilirubin potentially exerts a neuroprotective effect during the first week of life, and low temperature does not affect the possible antioxidant function of bilirubin during TH following HIE.
Evolution of the gravity offset of mixed modes in RGB stars
Authors: Pinçon C. , Takata M. , Mosser B. 
Published: May 2019

Context.Observations of mixed modes in evolved low-mass stars enable us to probe the properties of not only the outer envelope of these stars, but also their deep layers. Among the seismic parameters associated with mixed modes, the gravity offset, denoted withεg, is expected to reveal information on the boundaries of the inner buoyancy resonant cavity. This parameter was recently measured for hundreds of stars observed by theKeplersatellite and its value was shown to change during evolution.Aims.In this article, we theoretically investigate the reasons for such a variation in terms of structure properties, focusing only on the red giant branch.Methods.Using available asymptotic analyses and a simple model of the Brunt–Väisälä and Lamb frequencies in the upper part of the radiative zone, we derived an analytical expression ofεgfor dipolar modes and compared its predictions to observations.Results.First, we show that the asymptotic value ofεgwell agrees with the mean value observed at the beginning of the ascent of the red giant branch, which results from the high density contrast between the helium core and the base of the convective envelope. Second, we demonstrate that the predicted value also explains the sharp decrease inεgobserved for the more luminous red giant stars of the sample. This rapid drop turns out to occur just before the luminosity bump and results from the kink of the Brunt–Väisälä frequency near the upper turning point associated with the buoyancy cavity as stars evolve and this latter nears the base of the convective envelope. The potential ofεgto probe the value and slope of the Brunt–Väisälä frequency below the base of the convective region is clearly highlighted.Conclusions.The observed variation inεgand its link with the internal properties on the red giant branch are now globally understood. This work motivates further analyses of the potential of this parameter as a seismic diagnosis of the region located between the hydrogen-burning shell and the base of the convective envelope, and of the local dynamical processes associated for instance with core contraction, the migration of the convective boundary, or overshooting.
Outcomes of hip arthroscopy for femoroacetabular impingement: The effect of morphological type and chondrolabral damage
Authors: Said Hatem Galal , Masoud Mohammad A. , Morsi Mohamed Mohamed Abdel-Hamid , El-Assal Maher A. 
Published: May 2019

Introduction: Hip arthroscopy for treatment of femoroacetabular impingement (FAI) has shown significant pain and functional improvement. However, the differential outcome of each of the FAI morphological types in contrast to one another remains largely unknown. This study was conducted to detect a possible difference in outcome among different FAI types treated using hip arthroscopy.Methods: In this prospective non randomized comparative study, after exclusion of non-FAI cases and cases with advanced arthritic changes, 90 hips in 85 patients that had hip arthroscopy for the treatment of FAI between 2011 and 2015 in our center were analyzed. The collected patient reported outcome measures (PROMs) included visual analog scale (VAS) of pain, the modified Harris hip score (mHHS), and the non arthritic hip score (NAHS) both preoperatively and at final follow-up. Patient satisfaction was collected at final follow-up. Postoperative PROMs were subjected to three main comparisons based on each of FAI type, labral procedure, and extent of cartilage damage. Repeat comparison based on FAI type after matching of exact chondrolabral condition was also attempted.Results: Mean follow-up was 32.8 months (five patients lost from follow-up). There was a significant improvement in the overall PROMs. This improvement was significantly higher in the cam group in contrast to the mixed group. After matching for chondrolabral condition, this difference was consistent and more evident.Discussion: The outcome of arthroscopic treatment of pure cam FAI is significantly better than that of mixed FAI. Matching of the same chondrolabral condition and repeating the comparison yields similar results.
Prävention des Typ-2-Diabetes nach Schwangerschaftsdiabetes
Authors: Potzel Anne , Fritsche Andreas , Fritsche Louise , Müssig Karsten , van Gemert Theresa , Seißler Jochen , Lechner Andreas 
Published: May 2019

ZusammenfassungEin Schwangerschaftsdiabetes zeigt ein deutlich erhöhtes Risiko für die spätere Entwicklung eines Typ-2-Diabetes an 1. Eine gesundheitsfördernde Lebensweise kann dieses Risiko senken 2,3 ist aber für junge Mütter schwierig umzusetzen. Traditionelle Lebensstilberatung bleibt in dieser Gruppe meist erfolglos 4. Die Präventions-App TRIANGLE soll diese Versorgungslücke schließen.
Vom Risikotest zur Risikowahrnehmung
Authors: Schiborn Catarina , Mühlenbruch Kristin , Schulze Matthias B. 
Published: May 2019

ZusammenfassungMit dem Online-Tool des Deutschen Institutes für Ernährungsforschung Potsdam-Rehbrücke (DIfE) können interessierte Personen zur Selbstinformation ihr 5-Jahres-Risiko für Typ-2-Diabetes berechnen 1,2. Es ist bekannt, dass kommunizierte Gesundheitsrisiken abhängig von der verwendeten Darstellungsform zu unterschiedlichen Risikowahrnehmungen führen können. Das kann in Kombination mit anderen Einflussfaktoren zu einer Überschätzung oder auch Unterschätzung des tatsächlichen Risikos führen, was wiederum Auswirkungen auf die Aufnahme von möglicherweise notwendigen Präventionsmaßnahmen hat. Um das Risikoverständnis von Nutzern des Risiko-Tests systematisch zu untersuchen und die bisherige Ergebnisdarstellung mit einer alternativen erweiterten Darstellung, die den Risikoverlauf zeigt, zu vergleichen, wurde die DIRIKO-Studie entwickelt. Dabei werden Daten zur Risikowahrnehmung und möglichen Einflussfaktoren in Form eines anonymen Online-Fragebogens erhoben.
clustermq enables efficient parallelization of genomic analyses
Authors: Schubert Michael 
Published: May 2019

AbstractMotivationHigh performance computing (HPC) clusters play a pivotal role in large-scale bioinformatics analysis and modeling. For the statistical computing language R, packages exist to enable a user to submit their analyses as jobs on HPC schedulers. However, these packages do not scale well to high numbers of tasks, and their processing overhead quickly becomes a prohibitive bottleneck.ResultsHere we present clustermq, an R package that can process analyses up to three orders of magnitude faster than previously published alternatives. We show this for investigating genomic associations of drug sensitivity in cancer cell lines, but it can be applied to any kind of parallelizable workflow.Availability and implementationThe package is available on CRAN and https://github.com/mschubert/clustermq. Code for performance testing is available at https://github.com/mschubert/clustermq-performance.Supplementary informationSupplementary data are available at Bioinformatics online.
Progressive agrammatic aphasia without apraxia of speech as a distinct syndrome
Authors: Tetzloff Katerina A , Duffy Joseph R , Clark Heather M , Utianski Rene L , Strand Edythe A , Machulda Mary M , Botha Hugo , Martin Peter R , Schwarz Christopher G , Senjem Matthew L , Reid Robert I , Gunter Jeffrey L , Spychalla Anthony J , Knopman David S , Petersen Ronald C , Jack Clifford R , Lowe Val J , Josephs Keith A , Whitwell Jennifer L 
Published: May 2019

Abstract
Agrammatic aphasia affects grammatical language production and can result from a neurodegenerative disease. Although it typically presents with concomitant apraxia of speech, this is not always the case. Little is known about the clinical course and imaging features of patients that present with agrammatism in the absence of apraxia of speech, which we will refer to as progressive agrammatic aphasia. We aimed to make a detailed description of the longitudinal clinical, linguistic, and neuroimaging features of a cohort of 11 patients with progressive agrammatic aphasia to provide a complete picture of this syndrome. All patients underwent detailed speech and language, neurological and neuropsychological assessments, 3 T structural and diffusion tensor imaging MRI, 18F-fluorodeoxyglucose and Pittsburgh compound B PET. The 11 patients were matched by age and gender to 22 patients who had mixed apraxia of speech and agrammatism. The progressive agrammatic aphasia patients performed abnormally on tests of language, general cognition, executive function, and functional ability at baseline and declined in these measures over time. Only two patients eventually developed apraxia of speech, while parkinsonism was absent-to-mild throughout all visits for all patients. When compared to the patients with mixed apraxia of speech and agrammatism, the patients with progressive agrammatic aphasia performed better on tests of motor speech and parkinsonism but more poorly, and declined faster over time, on tests of general aphasia severity, agrammatism, and naming. The patients with progressive agrammatic aphasia also showed different neuroimaging abnormalities, with greater atrophy, hypometabolism and white matter tract degeneration in the prefrontal and anterior temporal lobes compared to patients with mixed apraxia of speech and agrammatism. These differences were more pronounced as the disease progressed. These results demonstrate that progressive agrammatic aphasia has a different clinical disease course and different underlying neuroanatomical abnormalities than patients with the more common syndrome of mixed agrammatism and apraxia of speech. This supports the distinction of progressive agrammatic aphasia and has implications for the classification of patients with agrammatic aphasia.
Markers of kidney tubule function and risk of cardiovascular disease events and mortality in the SPRINT trial
Authors: Garimella Pranav S , Lee Alexandra K , Ambrosius Walter T , Bhatt Udayan , Cheung Alfred K , Chonchol Michel , Craven Timothy , Hawfield Amret T , Jotwani Vasantha , Killeen Anthony , Punzi Henry , Sarnak Mark J , Wall Barry M , Ix Joachim H , Shlipak Michael G 
Published: May 2019

Abstract

Aims
Biomarkers of kidney tubule injury, inflammation and fibrosis have been studied extensively and established as risk markers of adverse kidney and cardiovascular disease (CVD) outcomes. However, associations of markers of kidney tubular function with adverse clinical events have not been well studied, especially in persons with chronic kidney disease (CKD).

Methods and results
Using a sample of 2377 persons with CKD at the baseline Systolic Blood Pressure Intervention Trial (SPRINT) visit, we evaluated the association of three urine tubular function markers, alpha-1 microglobulin (α1m), beta-2 microglobulin (β2m), and uromodulin, with a composite CVD endpoint (myocardial infarction, acute coronary syndrome, stroke, acute decompensated heart failure, or death from cardiovascular causes) and mortality using Cox proportional hazards regression, adjusted for baseline estimated glomerular filtration rate (eGFR), albuminuria, and CVD risk factors. In unadjusted analysis, over a median follow-up of 3.8 years, α1m and β2m had positive associations with composite CVD events and mortality, whereas uromodulin had an inverse association with risk for both outcomes. In multivariable analysis including eGFR and albuminuria, a two-fold higher baseline concentration of α1m was associated with higher risk of CVD [hazard ratio (HR) 1.25; 95% confidence interval (CI): 1.10–1.45] and mortality (HR 1.25; 95% CI: 1.10–1.46), whereas β2m had no association with either outcome. A two-fold higher uromodulin concentration was associated with lower CVD risk (HR 0.79; 95% CI: 0.68–0.90) but not mortality (HR 0.86; 95% CI: 0.73–1.01) after adjusting for similar confounders.

Conclusion
Among non-diabetic persons with CKD, biomarkers of tubular function are associated with CVD events and mortality independent of glomerular function and albuminuria.
Real-life outcome of implantable cardioverter-defibrillator and cardiac resynchronization defibrillator replacement/upgrade in a contemporary population: observations from the multicentre DECODE registry
Authors: Biffi Mauro , Ammendola Ernesto , Menardi Endrj , Parisi Quintino , Narducci Maria Lucia , De Filippo Paolo , Manzo Michele , Stabile Giuseppe , Potenza Domenico Rosario , Zanon Francesco , Quartieri Fabio , Rillo Mariano , Saporito Davide , Zacà Valerio , Berisso Massimo Zoni , Bertini Matteo , Tumietto Fabio , Malacrida Maurizio , Diemberger Igor 
Published: May 2019

Abstract

Aims
The benefit of prolonged implantable cardioverter-defibrillator (ICD)/cardiac resynchronization therapy defibrillator (CRT-D) therapy following device replacement is hindered by clinical and procedure-related adverse events (AEs). Adverse events rate is highest in more complex devices and at upgrades, as per the REPLACE registry experience, but is changing owing to the improvement in device technology and medical care. We aimed at understanding the extent and type of AEs in a contemporary Italian population.

Methods and results
Detect long-term complications after ICD replacement (DECODE) was a prospective, single-arm, multicentre cohort study aimed at estimating medium- to long-term AEs in a large population of patients undergoing ICD/cardiac resynchronization defibrillator replacement/upgrade from 2013 to 2015. We prospectively analysed all clinical and device-related AEs at 12-month follow-up (FU) of 983 consecutive patients (median age 71 years, 76% male, 55% ischaemic, 47% CRT-D) followed for 353 ± 49 days. Seven percent of the patients died (60.6% for cardiovascular reasons), whereas 104 AEs occurred; 43 (4.4%) patients needed at least one surgical action to treat the AE. Adverse events rates were 3.3/100 years lead-related, 3.4/100 years bleedings, and 1.6/100 years infective. The primary endpoint was predicted by hospitalization in the month prior to the procedure [hazard ratio (HR) = 2.23, 1.16–4.29; 0.0169] and by upgrade (HR = 1.75, 1.02–2.99, 0.0441). One hundred and twelve (11.4%) patients met the combined endpoint of death from any cause, cardiac implantable electronic device (CIED)-related infection, and surgical action/hospitalization required to treat the AE. Hospitalization within 30 days prior to the procedure (HR = 2.07, 1.13–3.81; 0.0199), anticoagulation (HR = 1.97, 1.26–3.07; 0.003), and ischaemic cardiomyopathy (HR = 1.67, 95% confidence interval 1.06–2.63; P = 0.0276) were associated with the combined endpoint during FU.

Conclusions
Adverse events following CIED replacement/upgrade are lower than previously reported, possibly owing to improved patients care. Hospitalization in the month prior to the procedure, upgrade, and clinical profile (anticoagulation, ischaemic cardiomyopathy) hint to increased risk, suggesting an individualized planning of the procedure to minimize overall AEs.

Clinical trial registration
URL: http://clinicaltrials.gov/ Identifier: NCT02076789.
The impact of the scope of technological search on path-dependence in export specialization: evidence for European countries
Authors: Reinstaller Andreas , Reschenhofer Peter 
Published: May 2019

Abstract
This paper examines how product relatedness and the breadth of technological search affect the path-dependent development of export specializations across countries documented in prior research. The results of the econometric analysis in this paper show that broader technological search in an industry has a positive impact on the development of comparative advantages in the product lines it exports. The interplay between product relatedness and the scope of technological search has a two-edged character. On the one hand, broader technological search supports adjustments and consolidations of the export baskets on the extensive margin. This contributes to weaken path-dependency. On the other hand, it fosters the competitiveness of products that are related to current export specializations, and thereby promotes path-dependency on the intensive margin of trade. These results differ across countries with different levels of technological capabilities.
CRISPR’d babies: human germline genome editing in the ‘He Jiankui affair’*
Authors: Greely Henry T 
Published: May 2019

Abstract
The world was shocked in Nov. 25, 2018 by the revelation that He Jiankui had used clustered regularly interspaced short palindromic repeats (‘CRISPR’) to edit embryos—two of which had, sometime in October, become living babies. This article is an effort to provide some deep context for the He Jiankui affair and to begin analyzing it. It focuses on He's experiment, without delving into the broader ethical issues around ‘human germline genome editing’ in the abstract. It begins by carefully defining ‘human germline genome editing’. It then describes the little we know about the experiment before providing background on CRISPR, the pre-He ethical and legal status of human germline genome editing, and on He himself. The fourth, and longest, section provides a detailed narrative of the revelation of the He experiment and its fallout. The fifth section critiques the experiment, which I believe merits unequivocal condemnation on several grounds. The last section suggests some important immediate reactions, by ‘Science’ and by China.
Depth-correlated backscattered electron signal intensity for 3D-profile measurement of high aspect ratio holes
Authors: Sun Wei , Ohta Hiroya , Ninomiya Taku , Goto Yasunori , Sohta Yasunari 
Published: May 2019

Abstract
In-line metrology for measuring 3D features of the high aspect ratio (HAR) holes is becoming more challenging due to the progressing semiconductor technology, particularly in memory devices. Measurements of the bottom critical dimension (CD), taper angles and 3D profiles of the HAR holes require new imaging capabilities. In this work, we explored the characteristics of high-energy backscattered electron (BSE) signals and demonstrated their promising application to 3D metrology. From Monte Carlo simulation results, it is worth noting that BSE signal intensity emitted from an irradiated location in the depth of the hole decreases exponentially with the increase of the depth from the top surface (perpendicular depth) of the hole. Furthermore, the influences of various factors including the electron energy, the depth and the sidewall angle (SWA) of the hole on the attenuation of the BSE signal intensity were investigated. The simulation results show that the attenuation of the BSE signal intensity depends on the electron energy, the depth and the density of the hole but is independent of the SWA and the incident angle of the primary electron beam. Based on the characteristics of the BSE signal intensity, an algorithm was proposed for the 3D metrology of the HAR holes. Finally, the differences in CDs between the measured value and the target value of HAR holes with various geometries were examined. A maximum measurement bias within ±2.0 nm for various holes with different depths, densities and SWA values shows great potential of depth-correlated BSE signals in 3D metrology.