bluuebunny/crossref_metadata_2025_split huggingface dataset:
Near-degeneracy effects on the frequencies of rotationally-split mixed modes in red giants
Authors: Deheuvels S. , Ouazzani R. M. , Basu S. 
Published: June 2017

Context. The Kepler space mission has made it possible to measure the rotational splittings of mixed modes in red giants, thereby providing an unprecedented opportunity to probe the internal rotation of these stars.
Aims. Asymmetries have been detected in the rotational multiplets of several red giants. This is unexpected since all the red giants whose rotation profiles have been measured thus far are found to rotate slowly, and low rotation, in principle, produces symmetrical multiplets. Our aim here is to explain these asymmetries and find a way of exploiting them to probe the internal rotation of red giants.
Methods. We show that in the cases where asymmetrical multiplets were detected, near-degeneracy effects are expected to occur, because of the combined effects of rotation and mode mixing. Such effects have not been taken into account so far. By using both perturbative and non-perturbative approaches, we show that near-degeneracy effects produce multiplet asymmetries that are very similar to the observations. We then propose and validate a method based on the perturbative approach to probe the internal rotation of red giants using multiplet asymmetries.
Results. We successfully apply our method to the asymmetrical l = 2 multiplets of the Kepler young red giant KIC 7341231 and obtain precise estimates of its mean rotation in the core and the envelope. The observed asymmetries are reproduced with a good statistical agreement, which confirms that near-degeneracy effects are very likely the cause of the detected multiplet asymmetries.
Conclusions. We expect near-degeneracy effects to be important for l = 2 mixed modes all along the red giant branch (RGB). For l = 1 modes, these effects can be neglected only at the base of the RGB. They must therefore be taken into account when interpreting rotational splittings and as shown here, they can bring valuable information about the internal rotation of red giants.
Vergleich von klinischem und histopathologischem Staging bei Patienten mit Oropharynxkarzinom
Authors: Knipping Stephan , Theunert Anika , Stock Karsten , Wienke Andreas 
Published: June 2017

Zusammenfassung
Hintergrund Trotz der Fortschritte in Diagnostik und Therapie ist die Prognose von Oropharynxkarzinomen weiterhin ungünstig. Deshalb ist es entscheidend, das klinische Staging weiter zu verbessern, um darauf basierend Therapiemodalitäten festzulegen.
Material und Methoden In einer retrospektiven, pseudonymisierten Untersuchung aus einem 13 Jahreszeitraum wurde bei 84 primär operierten Patienten mit einem Oropharynxkarzinom die klinische Klassifikation (cTNM) mit der histopathologischen Beurteilung (pTNM) verglichen. Auch das Vorhandensein von okkulten Metastasen sowie das Gesamtüberleben in Abhängigkeit von der histopathologischen Tumorausdehnung und des regionären Lymphknotenbefalls wurden betrachtet.
Ergebnisse Die höchste Übereinstimmung zwischen cTNM und pTNM konnte bei der Computertomografie erreicht werden. Eine definitive Bewertung mit histopathologischer Zuverlässigkeit ist durch das cTNM nicht möglich. Die MRT-Untersuchungen zeigten die Tendenz, die T- und N-Kategorien und das UICC-Tumorstadium klinisch ausgedehnter einzuschätzen als durch die definitve histopathologische Beurteilung nachgewiesen. Im Rahmen der Untersuchung des Überlebens getrennt nach Geschlecht, histopathologischer T- und N-Kategorien zeigte sich bei den höheren T- bzw. N-Kategorien ein geringeres Gesamtüberleben.
Schlussfolgerungen Trotz aller Fortschritte in der bildgebenden Diagnostik bei Patienten mit Oropharynxkarzinomen ist das cTNM im Vergleich zum pTNM nur partiell in der Lage, mit klinisch geforderter Akkuratesse die TNM-Klassifikation der Tumorerkrankung zu bestimmen. Bei tendenziell sinkenden Prognosen ist es trotz moderner Therapieverfahren entscheidend, das prätherapeutische klinische Staging weiter zu verbessern und zu optimieren.
Aktueller Stand Salvage-chirurgischer Therapiekonzepte bei Rezidivtumoren des Larynx und Pharynx
Authors: Stuck B. , Rothmeier N. , Mattheis S. , Dominas N. , Lang S. 
Published: June 2017

ZusammenfassungDie therapeutischen Konzepte bei Kopf-Hals-Malignomen haben in den letzten 20 Jahren einen erheblichen Wandel erfahren, der mit einer zunehmenden Bedeutung nicht-chirurgischer Therapieverfahren einhergeht. Auch unter den Organerhaltungsprotokollen bzw. nach primärer Radiochemotherapie kommt es jedoch in erheblichem Umfang zum Auftreten von Tumorrezidiven. In dieser Situation stellt die Salvage- bzw. Rettungschirurgie im Kopf-Hals-Bereich häufig die einzig noch verbliebene kurative Option dar. Die Etablierung plastisch-rekonstruktiver Maßnahmen vor ca. 30 Jahren hat das operative Spektrum im Kopf-Hals-Bereich signifikant erweitert und neue Möglichkeiten der Salvage-Chirurgie bei rezidivierenden Karzinomen des Pharynx und Larynx eröffnet. Die Überlebensraten nach Salvage-Chirurgie hängen hierbei im Wesentlichen von der Art der Primärtherapie, der Lokalisation und dem Tumorstadium sowohl bei Erstdiagnose als auch zum Zeitpunkt des Rezidivs ab. Zur plastisch-rekonstruktiven Deckung kommen gestielte Lappen oder mikrovaskulär-anastomosierte Transplantate zum Einsatz. Die am häufigsten angewandten gestielten Lappen sind der M. pectoralis-major- und der Latissimus-dorsi-Lappen. Als freie Transplantate kommt meist das Radialis- oder ALT-Transplantat zum Einsatz. Durch Verwendung dieser Lappen und Transplantate wird nicht-bestrahltes Gewebe in die vorgeschädigten Regionen verlagert, um neben der Wiederherstellung der ursprünglichen Organfunktion auch gefürchtete postoperative Komplikationen, wie z. B. Speichelfisteln, zu reduzieren. Die Indikation zur Salvage-Chirurgie muss auch weiterhin in jedem Einzelfall vor dem Hintergrund der zu erwartenden Morbidität und einer realistischen Einschätzung der Erfolgsaussichten abgewogen werden. Die vorliegende Publikation möchte hierzu entsprechende Empfehlungen geben.
CancerSubtypes: an R/Bioconductor package for molecular cancer subtype identification, validation and visualization
Authors: Xu Taosheng , Le Thuc Duy , Liu Lin , Su Ning , Wang Rujing , Sun Bingyu , Colaprico Antonio , Bontempi Gianluca , Li Jiuyong 
Published: June 2017

AbstractSummaryIdentifying molecular cancer subtypes from multi-omics data is an important step in the personalized medicine. We introduce CancerSubtypes, an R package for identifying cancer subtypes using multi-omics data, including gene expression, miRNA expression and DNA methylation data. CancerSubtypes integrates four main computational methods which are highly cited for cancer subtype identification and provides a standardized framework for data pre-processing, feature selection, and result follow-up analyses, including results computing, biology validation and visualization. The input and output of each step in the framework are packaged in the same data format, making it convenience to compare different methods. The package is useful for inferring cancer subtypes from an input genomic dataset, comparing the predictions from different well-known methods and testing new subtype discovery methods, as shown with different application scenarios in the Supplementary Material.Availability and implementationThe package is implemented in R and available under GPL-2 license from the Bioconductor website (http://bioconductor.org/packages/CancerSubtypes/).Supplementary informationSupplementary data are available at Bioinformatics online.
MotifHyades: expectation maximization for de novo DNA motif pair discovery on paired sequences
Authors: Wong Ka-Chun 
Published: June 2017

Abstract

Motivation
In higher eukaryotes, protein–DNA binding interactions are the central activities in gene regulation. In particular, DNA motifs such as transcription factor binding sites are the key components in gene transcription. Harnessing the recently available chromatin interaction data, computational methods are desired for identifying the coupling DNA motif pairs enriched on long-range chromatin-interacting sequence pairs (e.g. promoter–enhancer pairs) systematically.

Results
To fill the void, a novel probabilistic model (namely, MotifHyades) is proposed and developed for de novo DNA motif pair discovery on paired sequences. In particular, two expectation maximization algorithms are derived for efficient model training with linear computational complexity. Under diverse scenarios, MotifHyades is demonstrated faster and more accurate than the existing ad hoc computational pipeline. In addition, MotifHyades is applied to discover thousands of DNA motif pairs with higher gold standard motif matching ratio, higher DNase accessibility and higher evolutionary conservation than the previous ones in the human K562 cell line. Lastly, it has been run on five other human cell lines (i.e. GM12878, HeLa-S3, HUVEC, IMR90, and NHEK), revealing another thousands of novel DNA motif pairs which are characterized across a broad spectrum of genomic features on long-range promoter–enhancer pairs.

Availability and implementation
The matrix-algebra-optimized versions of MotifHyades and the discovered DNA motif pairs can be found in http://bioinfo.cs.cityu.edu.hk/MotifHyades.

Supplementary information
Supplementary data are available at Bioinformatics online.
A combined meta-barcoding and shotgun metagenomic analysis of spontaneous wine fermentation
Authors: Sternes Peter R. , Lee Danna , Kutyna Dariusz R. , Borneman Anthony R. 
Published: June 2017

Abstract
Wine is a complex beverage, comprising hundreds of metabolites produced through the action of yeasts and bacteria in fermenting grape must. Commercially, there is now a growing trend away from using wine yeast (Saccharomyces) starter cultures, toward the historic practice of uninoculated or “wild” fermentation, where the yeasts and bacteria associated with the grapes and/or winery perform the fermentation. It is the varied metabolic contributions of these numerous non-Saccharomyces species that are thought to impart complexity and desirable taste and aroma attributes to wild ferments in comparison to their inoculated counterparts. To map the microflora of spontaneous fermentation, metagenomic techniques were employed to characterize and monitor the progression of fungal species in 5 different wild fermentations. Both amplicon-based ribosomal DNA internal transcribed spacer (ITS) phylotyping and shotgun metagenomics were used to assess community structure across different stages of fermentation. While providing a sensitive and highly accurate means of characterizing the wine microbiome, the shotgun metagenomic data also uncovered a significant overabundance bias in the ITS phylotyping abundance estimations for the common non-Saccharomyces wine yeast genus Metschnikowia. By identifying biases such as that observed for Metschnikowia, abundance measurements from future ITS phylotyping datasets can be corrected to provide more accurate species representation. Ultimately, as more shotgun metagenomic and single-strain de novo assemblies for key wine species become available, the accuracy of both ITS-amplicon and shotgun studies will greatly increase, providing a powerful methodology for deciphering the influence of the microbial community on the wine flavor and aroma.
Trust Busting: The Effect of Fraud on Investor Behavior
Authors: Gurun Umit G , Stoffman Noah , Yonker Scott E 
Published: June 2017

AbstractWe study the importance of trust in the investment advisory industry by exploiting the geographic dispersion of victims of the Madoff Ponzi scheme. Residents of communities that were exposed to the fraud subsequently withdrew assets from investment advisers and increased deposits at banks. Additionally, exposed advisers were more likely to close. Advisers who provided services that can build trust, such as financial planning advice, experienced fewer withdrawals. Our evidence suggests that the trust shock was transmitted through social networks. Taken together, our results show that trust plays a critical role in the financial intermediation industry.Received April 18, 2016; editorial decision March 8, 2017 by Editor Robin Greenwood.
Surgical Pain After Transobturator and Retropubic Midurethral Sling Placement
Authors: Thomas Tonya N. , Siff Lauren N. , Jelovsek J. Eric , Barber Matthew 
Published: June 2017

OBJECTIVE:
To compare prevalence and severity of any surgical pain between transobturator and retropubic slings; secondary aims were to compare pain at anatomic locations, pain medication use, and pain resolution between transobturator and retropubic slings and to compare pain between types of transobturator slings.

METHODS:
This is a secondary analysis of the Trial of Mid-Urethral Slings, which compared retropubic and transobturator sling outcomes and included 597 participants from 2006 to 2008. Postoperative assessments included body maps, visual analog scales, Surgical Pain Scales, and medication inventories for 30 days, at 6 weeks, and 6, 12, and 24 months. Postoperative pain prevalence and severity were compared. Mixed models compared pain resolution and severity over time. Regression models compared pain prevalence and severity between types of transobturator slings. Eighty percent power was provided for the primary outcome pain prevalence and 95% power was provided for the primary outcome pain severity.

RESULTS:
Postoperative prevalence of any surgical pain, pain severity, and pain medication was not different between retropubic and transobturator slings. Retropubic sling was associated with greater prevalence of suprapubic pain at 2 weeks (proportion difference 10.6%; 95% confidence interval [CI] 4.6–16.4%; P<.001). Transobturator sling was associated with greater prevalence of groin pain at 2 weeks (proportion difference 12.0%; 95% CI 7.1–16.8%; P<.001). There was no difference in pain resolution (odds ratio [OR] 1.11, 95% CI 0.88–1.40; P=.38). Between types of transobturator slings, the odds of surgical pain were similar at 2 (OR 2.39, 95% CI 0.51–11.31; P=.27) and 6 weeks (OR 0.46, 95% CI 0.02–9.20; P=.61).

CONCLUSION:
Transobturator and retropubic slings are associated with low prevalence of any surgical pain. Transobturator sling was associated with greater prevalence of groin pain at 2 weeks, and retropubic sling was associated with greater prevalence of suprapubic pain at 2 weeks. Surgical pain resolved quickly in both groups.
Placental Abruption With Delayed Fetal Compromise in Maternal Acetaminophen Toxicity
Authors: Taney Juliana , Anastasio Hannah , Paternostro Amanda , Berghella Vincenzo , Roman Amanda 
Published: June 2017

BACKGROUND:
After maternal acetaminophen overdose, fetal fulminant liver failure, stillbirth, neonatal death, or preterm delivery may occur.

CASE:
A 27-year-old woman, gravida 2 para 1, presented at 28 weeks of gestation after unintentional acetaminophen overdose. Four days after ingestion, her laboratory values worsened, including serum aspartate aminotransferase of 5,460 units/L, alanine aminotransferase of 4,936 units/L, and international normalized ratio of 2.9. On day 6 after ingestion, fetal monitoring showed minimal variability with repetitive variable and late decelerations, which prompted cesarean delivery when a hematoma was noted on the maternal placental surface, consistent with placental abruption. The neonate showed no evidence of hepatic dysfunction. Review of the literature suggests that maternal acetaminophen overdose in the second and third trimester is associated with a 5% incidence of fetal compromise (mostly the result of nonreassuring fetal status leading to delivery or stillbirth) occurring within 6 days of ingestion.

CONCLUSION:
Maternal acetaminophen overdose can be associated with delayed fetal compromise, suggesting the importance of continued fetal surveillance several days after ingestion.
Long-term Risk of Urinary Adverse Events in Curatively Treated Patients With Rectal Cancer: A Population-Based Analysis
Authors: Kwaan Mary R. , Fan Yunhua , Jarosek Stephanie , Elliott Sean P. 
Published: June 2017

BACKGROUND:
Treatment modalities for rectal cancer, including radiation, are associated with urinary adverse effects.

OBJECTIVE:
The purpose of this study was to determine the influence of surgery and radiation therapy for rectal cancer on long-term urinary complications.

DESIGN:
Using the Surveillance Epidemiology and End Results–Medicare data set from the United States, patients with rectal cancer older than 66 years of age who underwent rectal resection between 1992 and 2007 were stratified into treatment groups that accounted for surgical resection and the timing of radiation therapy, if used. A control group of patients who did not have rectal cancer were matched by age, sex, demographics, and comorbidities. The primary outcome was a urinary adverse event defined as a relevant urinary diagnosis with an associated procedure. Patients with rectal cancer in different treatment groups were compared with control patients using a propensity-adjusted, multivariable Cox regression analysis.

SETTINGS:
The study was conducted with the Surveillance Epidemiology and End Results–Medicare data set from the United States at our institution.

RESULTS:
Of the 11,068 patients with rectal cancer, 56.2% had surgical resection alone, 21.7% received preoperative radiation, and 22.1% received postoperative radiation. The median follow-up for all of the groups of patients was >2 years. All of the groups of patients with rectal cancer were more likely to develop a urinary adverse event compared with control subjects. Adjusted HRs were 2.28 (95% CI, 2.02–2.57) for abdominoperineal resection alone, 2.24 (95% CI, 1.79–2.80) for preoperative radiation and surgical resection, 2.04 (95% CI, 1.70–2.44) for surgical resection and postoperative radiation, and 1.69 (95% CI, 1.52–1.89) for low anterior resection alone.

LIMITATIONS:
Treatment patterns are somewhat outdated, with a large proportion of patients receiving postoperative radiation. The data did not allow for accurate assessment of urinary tract infections or mild urinary retention that is not managed with a procedure.

CONCLUSIONS:
Rectal cancer surgery with or without radiation is associated with a higher risk of urinary complications requiring procedures. Patients who undergo low anterior resection without radiation tend toward the lowest risk for a urinary adverse event.
Clinical Relevance of a Grading System for Anastomotic Leakage After Low Anterior Resection: Analysis From a National Cohort Database
Authors: Frouws Martine A. , Snijders Heleen S. , Malm Steve H. , Liefers Gerrit-Jan , Van de Velde Cornelis J.H. , Neijenhuis Peter A. , Kroon Hidde M. 
Published: June 2017

BACKGROUND:Anastomotic leakage is a severe complication after low anterior resection for rectal cancer. With a global increase in registration initiatives, adapting uniform definitions and grading systems is highly relevant.OBJECTIVE:This study aimed to provide clinical parameters to categorize anastomotic leakage into subcategories according to the International Study Group of Rectal Cancer.DESIGN:All of the patients who underwent a low anterior resection in the Netherlands with primary anastomosis were included using the population-based Dutch Surgical Colorectal Audit.SETTINGS:Data were derived from the Dutch Surgical Colorectal Audit.MAIN OUTCOME MEASURES:The development of grade B anastomotic leakage (requiring invasive treatment but no surgery) versus grade C anastomotic leakage (requiring reoperation) was measured.RESULTS:Overall, 4287 patients underwent low anterior resection with primary anastomosis. A total of 159 patients (4%) were diagnosed with grade B anastomotic leakage versus 259 (6%) with grade C. Hospital stay and intensive care unit visits were significantly higher in patients with grade C anastomotic leakage compared with patients with grade B leakage. Mortality in patients with grade C leakage was higher compared with grade B leakage, although nonsignificant (5.8% vs 2.5%;p= 0.12). Multivariate analysis showed that patients with diverting stomas (n = 2866) had a decreased risk of developing grade C leakage compared with grade B (OR = 0.17 (95% CI, 0.10–0.29)). Male patients had an increased risk of developing grade C anastomotic leakage, and patients receiving neoadjuvant treatment before surgery had an increased risk of developing grade B anastomotic leakage.LIMITATIONS:Some possibly relevant variables, such as smoking and nutritional status, were not recorded in the database.CONCLUSIONS:Anastomotic leakage after low anterior resection for rectal cancer was a frequent observed complication in this cohort. Differences in clinical outcome suggest that grade B and C leakage should be considered separate entities in future registrations. In patients with a diverting stoma, the chances of experiencing grade C anastomotic leakage were reduced.See Video Abstractat http://links.lww.com/DCR/A315.
Mesenteric Lymphadenectomy in Well-Differentiated Appendiceal Neuroendocrine Tumors
Authors: Raoof Mustafa , Dumitra Sinziana , O’Leary Michael P. , Singh Gagandeep , Fong Yuman , Lee Byrne 
Published: June 2017

BACKGROUND:
Surgical resection is the primary therapy for local and locally advanced appendiceal neuroendocrine tumors. The role of mesenteric lymphadenectomy in these patients is undefined.

OBJECTIVE:
The purpose of this study was to define the role and prognostic significance of mesenteric lymphadenectomy.

DESIGN:
This was a retrospective, observational study.

SETTINGS:
A population-based cohort from the National Cancer Institute Surveillance, Epidemiology, and End Results registry (January 1988 to November 2013) was used.

PATIENTS:
Patients with well-differentiated neuroendocrine tumors and nonmixed histologies undergoing surgical resection were included.

MAIN OUTCOME MEASURES:
The risk of lymph node metastases as a function of tumor size and overall survival with respect to lymph node count and tumor size was measured. Lymph node cut-point was determined using the Contal and O’Quigely method.

RESULTS:
Of the 573 patients who met the inclusion criteria, 64% were women, 79% were white, and 76% were <60 years of age. Seventy percent of the tumors were ≤2 cm, and 77% were lymph node negative. Median lymph nodes retrieved were 0 (interquartile range, 0–14). The probability of nodal metastases was 2.7% in tumors ≤1.0 cm, 31.0% in tumors 1.1 to 2.0 cm, and 64.0% in tumors >2.0 cm. The probability of a positive lymph node increased with increasing lymph node count up to 26 lymph nodes. An ideal cut-point of 12 lymph nodes was identified by statistical modeling. After adjustment in the multivariable model, the group with 12 or fewer lymph nodes examined had significantly worse overall survival (HR = 4.33 (95% CI, 1.54–12.15); p = 0.005; 5-year survival, 88% versus 96%) than the group with more than 12 lymph nodes examined.

LIMITATIONS:
Analysis was limited by the variables available in the database.

CONCLUSIONS:
This is the largest study to date that looks at prognostic significance of lymph node count for well-differentiated appendiceal neuroendocrine tumors. Overall survival was worse where 12 or fewer lymph nodes were identified for tumors >1 cm. See Video Abstract at http://links.lww.com/DCR/A352.
Lymphaticovenous Bypass: Adaptations and Lessons Learned
Authors: Baltzer Heather L. , Winocour Sebastian , Harless Christin , Saint-Cyr Michel 
Published: June 2017

Summary:
Advances in microsurgical instruments and techniques have allowed for introduction of lymphaticovenous anastomosis as a potential surgical treatment for patients with upper and lower extremity lymphedema. This article reviews the approach to lymphaticovenous anastomosis patient selection and technical modifications that improve the ease and efficiency of the procedure.