bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparing Real-Time Self-Tracking and Device-Recorded Exercise Data in Subjects with Type 1 Diabetes
Authors: Groat Danielle , Kwon Hyo , Grando Maria , Cook Curtiss , Thompson Bithika 
Published: December 2018

Background Insulin therapy, medical nutrition therapy, and physical activity are required for the treatment of type 1 diabetes (T1D). There is a lack of studies in real-life environments that characterize patient-reported data from logs, activity trackers, and medical devices (e.g., glucose sensors) in the context of exercise.
Objective The objective of this study was to compare data from continuous glucose monitor (CGM), wristband heart rate monitor (WHRM), and self-tracking with a smartphone application (app), iDECIDE, with regards to exercise behaviors and rate of change in glucose levels.
Methods Participants with T1D on insulin pump therapy tracked exercise for 1 month with the smartphone app while WHRM and CGM recorded data in real time. Exercise behaviors tracked with the app were compared against WHRM. The rate of change in glucose levels, as recorded by CGM, resulting from exercise was compared between exercise events documented with the app and recorded by the WHRM.
Results Twelve participants generated 277 exercise events. Tracking with the app aligned well with WHRM with respect to frequency, 3.0 (2.1) and 2.5 (1.8) days per week, respectively (p = 0.60). Duration had very high agreement, the mean duration from the app was 65.6 (55.2) and 64.8 (54.9) minutes from WHRM (p = 0.45). Intensity had a low concordance between the data sources (Cohen's kappa = 0.2). The mean rate of change of glucose during exercise was –0.27 mg/(dL*min) and was not significantly different between data sources or intensity (p = 0.21).
Conclusion We collated and analyzed data from three heterogeneous sources from free-living participants. Patients' perceived intensity of exercise can serve as a surrogate for exercise tracked by a WHRM when considering the glycemic impact of exercise on self-care regimens.
Basic Principle and Step-by-Step Procedure of Abdominal Hysterectomy: Part 2
Authors: Konishi Ikuo 
Published: December 2018

AbstractAbdominal hysterectomy is the ultimate standard operation among various gynecologic surgeries. However, the actual procedure for a patient varies substantially according to the morphological changes of the uterus and adnexa. Therefore, it is important to assess the deviation from standard and the difficulties in the procedure and to plan the modification of the operation at the preoperative conference. In this chapter, a standard step-by-step procedure for abdominal hysterectomy is described.
Computational approaches for alternative and transient secondary structures of ribonucleic acids
Authors: Fukunaga Tsukasa , Hamada Michiaki 
Published: December 2018

AbstractTransient and alternative structures of ribonucleic acids (RNAs) play essential roles in various regulatory processes, such as translation regulation in living cells. Because experimental analyses for RNA structures are difficult and time-consuming, computational approaches based on RNA secondary structures are promising. In this article, we review computational methods for detecting and analyzing transient/alternative secondary structures of RNAs, including static approaches based on probabilistic distributions of RNA secondary structures and dynamic approaches such as kinetic folding and folding pathway predictions.
MoMo: discovery of statistically significant post-translational modification motifs
Authors: Cheng Alice , Grant Charles E , Noble William S , Bailey Timothy L 
Published: December 2018

Abstract

Motivation
Post-translational modifications (PTMs) of proteins are associated with many significant biological functions and can be identified in high throughput using tandem mass spectrometry. Many PTMs are associated with short sequence patterns called ‘motifs’ that help localize the modifying enzyme. Accordingly, many algorithms have been designed to identify these motifs from mass spectrometry data. Accurate statistical confidence estimates for discovered motifs are critically important for proper interpretation and in the design of downstream experimental validation.

Results
We describe a method for assigning statistical confidence estimates to PTM motifs, and we demonstrate that this method provides accurate P-values on both simulated and real data. Our methods are implemented in MoMo, a software tool for discovering motifs among sets of PTMs that we make available as a web server and as downloadable source code. MoMo re-implements the two most widely used PTM motif discovery algorithms—motif-x and MoDL—while offering many enhancements. Relative to motif-x, MoMo offers improved statistical confidence estimates and more accurate calculation of motif scores. The MoMo web server offers more proteome databases, more input formats, larger inputs and longer running times than the motif-x web server. Finally, our study demonstrates that the confidence estimates produced by motif-x are inaccurate. This inaccuracy stems in part from the common practice of drawing ‘background’ peptides from an unshuffled proteome database. Our results thus suggest that many of the papers that use motif-x to find motifs may be reporting results that lack statistical support.

Availability and implementation
The MoMo web server and source code are provided at http://meme-suite.org.

Supplementary information
Supplementary data are available at Bioinformatics online.
The role of thoracic endovascular repair in elective, symptomatic and ruptured thoracic aortic diseases
Authors: Fiorucci Beatrice , Kölbel Tilo , Rohlffs Fiona , Heidemann Franziska , Carpenter Sebastian William , Debus Eike Sebastian , Tsilimparis Nikolaos 
Published: December 2018

Abstract

OBJECTIVES
Thoracic endovascular aortic repair (TEVAR) has emerged as a safe procedure in the treatment of a wide spectrum of descending thoracic aortic pathologies, with satisfactory results both in elective and urgent settings. We investigated the results of our elective, urgent and emergency TEVAR interventions.

METHODS
A single-centre retrospective analysis of all consecutive patients undergoing TEVAR from 2010 to 2016 was performed. Primary end point of the study was early mortality, whereas the secondary end points included major complications according to the urgency of the procedure. The analysis was further conducted comparing symptomatic, asymptomatic and ruptured cases.

RESULTS
Two hundred and eight patients were treated with TEVAR between January 2010 and April 2016 (mean age 67 ± 12 years, 142 men, 68.3%). Patients undergoing TEVAR as a first-stage procedure for complex thoraco-abdominal repair were excluded. The indication for treatment was a dissection in most cases (n = 92, 44.2%; acute dissection in 40 cases, 19.2%), followed by thoracic aneurysms (n = 64, 30.8%), penetrating aortic ulcers (n = 37, 17.8%), intramural haematomas (n = 8, 3.8%), traumatic ruptures (n = 3, 1.4%) and other indications (n = 4, 1.8%). One hundred and eight procedures were performed electively and 100 urgently. Forty-three patients were treated on an emergency bas for aortic rupture, 44 urgently for thoracic pain and 13 for acute ischaemic complications of aortic dissection or other indications. Ischaemic complications of dissection included 1 case of mesenteric ischaemia, 3 cases of acute renal failure, 4 cases of limb ischaemia and multiple ischaemic complications in 4 cases. Other causes of urgent TEVAR included 1 patient bleeding from a bronchial artery treated with TEVAR after several embolization attempts. In-hospital mortality was 7.7%, significantly higher in the urgent setting (14% vs 1.9%, P = 0.001). Urgent procedures were also more frequently associated with major adverse clinical events (7.4% vs 26%, P = 0.0003) and specifically with paraplegia (2.8% vs 10%, P = 0.043). Perioperative mortality was significantly higher in the ruptured group compared to the symptomatic group (25.6% vs 2.3%, P = 0.002). When the analysis was conducted to compare the symptomatic and the asymptomatic patients, no differences in terms of perioperative mortality were detected.

CONCLUSIONS
TEVAR is an effective treatment strategy in thoracic aortic disease. Though emergency repair of the ruptured thoracic aorta still shows high rates of perioperative mortality and morbidity, symptomatic non-ruptured and asymptomatic patients have comparable early outcomes.
Adipose Tissue Senescence and Inflammation in Aging is Reversed by the Young Milieu
Authors: Ghosh Amiya Kumar , O’Brien Martin , Mau Theresa , Qi Nathan , Yung Raymond 
Published: December 2018

Abstract
Visceral adipose tissue (VAT) inflammation plays a central role in longevity and multiple age-related disorders. Cellular senescence (SEN) is a fundamental aging mechanism that contributes to age-related chronic inflammation and organ dysfunction, including VAT. Recent studies using heterochronic parabiosis models strongly suggested that circulating factors in young plasma alter the aging phenotypes of old animals. Our study investigated if young plasma rescued SEN phenotypes in the VAT of aging mice. With heterochronic parabiosis model using young (3 months) and old (18 months) mice, we found significant reduction in the levels of pro-inflammatory cytokines and altered adipokine profile that are protective of SEN in the VAT of old mice. These data are indicative of protection from SEN of aging VAT by young blood circulation. Old parabionts also exhibited diminished expression of cyclin-dependent kinase inhibitors (CDKi) genes p16 (Cdkn2a) and p21 (Cdkn1a/Cip1) in the VAT. In addition, when exposed to young serum condition in an ex vivo culture system, aging adipose tissue–derived stromovascular fraction cells produced significantly lower amounts of pro-inflammatory cytokines (MCP-1 and IL-6) compared to old condition. Expressions of p16 and p21 genes were also diminished in the old stromovascular fraction cells under young serum condition. Finally, in 3T3-preadipocytes culture system, we found reduced pro-inflammatory cytokines (Mcp-1 and Il-6) and diminished expression of cyclin-dependent kinase inhibitor genes in the presence of young serum compared to old serum. In summary, this study demonstrates that young milieu is capable of protecting aging adipose tissue from SEN and thereby inflammation.
Cost-effectiveness of Hepatitis B Virus Infection Screening and Treatment or Vaccination in 6 High-risk Populations in the United States
Authors: Chahal Harinder S , Peters Marion G , Harris Aaron M , McCabe Devon , Volberding Paul , Kahn James G 
Published: December 2018

Abstract

Background
Two million individuals with chronic hepatitis B (CHB) in the United States are at risk for premature death due to liver cancer and cirrhosis. CHB can be prevented by vaccination and controlled with treatment.

Methods
We created a lifetime Markov model to estimate the cost-effectiveness of strategies to prevent or treat CHB in 6 high-risk populations: foreign-born Asian/Pacific Islanders (API), Africa-born blacks (AbB), incarcerated, refugees, persons who inject drugs (PWID), and men who have sex with men (MSM). We studied 3 strategies: (a) screen for HBV infection and treat infected (“treatment only”), (b) screen for HBV susceptibility and vaccinate susceptible (“vaccination only”), and (c) screen for both and follow-up appropriately (“inclusive”). Outcomes were expressed in incremental cost-effectiveness ratios (ICERs), clinical outcomes, and new infections.

Results
Vaccination-only and treatment-only strategies had ICERs of $6000–$21 000 per quality-adjusted life-year (QALY) gained, respectively. The inclusive strategy added minimal cost with substantial clinical benefit, with the following costs per QALY gained vs no intervention: incarcerated $3203, PWID $8514, MSM $10 954, AbB $17 089, refugees $17 432, and API $18 009. Clinical complications dropped in the short/intermediate (1%–25%) and long (0.4%–16%) term. Findings were sensitive to age, discount rate, health state utility in immune or susceptible stages, progression rate to cirrhosis or inactive disease, and tenofovir cost. The probability of an inclusive program costing &lt;$50 000 per QALY gained varied between 61% and 97% by population.

Conclusions
An inclusive strategy to screen and treat or vaccinate is cost-effective in reducing the burden of hepatitis B virus among all 6 high-risk, high-prevalence populations.
An evaluation of the coverage of theoretically based implementation factors in disseminated classroom physical activity programs
Authors: Calvert Hannah G , Lane Hannah G , Bejarano Carolina M , Snow Kelli , Hoppe Kate , Alfonsin Nicole , Turner Lindsey , Carlson Jordan A 
Published: December 2018

Abstract
Classroom-based physical activity (CBPA) is increasingly recommended as a method to support children’s physical activity, health, and academic performance. Many adoption-ready programs exist to aid in the implementation of CBPA in schools; yet, implementation rates remain low. The purpose of this study was to evaluate the extent to which resources provided by adoption-ready CBPA programs addressed theory-based implementation contextual factors to support implementation. Existing CBPA programs (N = 37) were identified through Internet searches and all materials (e.g., implementation guides) provided by each program were coded for their inclusion of 51 implementation factors based on the Consolidated Framework for Implementation Research (CFIR). Analyses were conducted to compare inclusion of implementation factors across CFIR Domains and by three program groupings: free (yes/no), research evidence (yes/no), and targeted to teacher only (vs. school). Programs covered a mean of 25.9 per cent (SD = 18.7 per cent) of the 14 Inner Setting implementation factors, 34.2 per cent (SD = 18.0 per cent) of the 6 Characteristics of Individuals implementation factors, and 34.8 per cent (SD = 24.3 per cent) of the 8 Process implementation factors. Programs with research evidence covered more implementation factors than programs without research evidence (43.7 vs. 25.9 per cent; p &lt; .05). Although numerous adoption-ready CBPA programs are available and have many strengths, their inclusion of theory-based factors that support or inhibit implementation is generally low. Consideration of such factors, including organizational climate and teacher-level behavior change, is likely critical to supporting ongoing school-wide implementation of CBPA. Research is needed to develop and test effective strategies for addressing these factors to support more widespread CBPA implementation.
Challenges and Management of Surgical Site Occurrences
Authors: Gabriel Allen , Gupta Subhas , Orgill Dennis P. 
Published: December 2018

Summary:
Postoperative complications such as surgical site infections, dehiscence, seromas, and hematomas prolong wound care and impose significant cost increases to patients and healthcare providers. Clinicians aiming to reduce the incidence of these complications should be aware of risk factors associated with surgical type, procedures used, patient characteristics, and postoperative care. Today, improved guidelines and general practices for managing surgical incisions have reduced the incidence of complications to historic lows. In addition to these standard care options, advanced wound care approaches have been extensively studied and exist as options for clinicians to provide adjunctive postoperative support and facilitate wound healing. These systems include advanced wound dressings and closed-incision negative-pressure therapy. Advanced wound care is not appropriate in all settings, and healthcare providers must assess each case for specific needs to be addressed by the available incision management plans. Emerging therapies that are intended to improve the continuum of postoperative care should continue to be evaluated in controlled clinical trials to determine their effectiveness under different circumstances and to support the creation of more robust guidelines for their use.
CBP/EP300-dependent acetylation and stabilization of HSF2 are compromised in the rare disorder, Rubinstein-Taybi syndrome
Authors: de Thonel Aurélie , Ahlskog Johanna K. , Abane Ryma , Pires Geoffrey , Dubreuil Véronique , Berthelet Jérémy , Aalto Anna L. , Naceri Sarah , Cordonnier Marion , Benasolo Carène , Sanial Matthieu , Duchateau Agathe , Vihervaara Anniina , Puustinen Mikael C. , Miozzo Federico , Henry Mathilde , Bouvier Déborah , Concordet Jean-Paul , Fergelot Patricia , Lebigot Élise , Verloes Alain , Gressens Pierre , Lacombe Didier , Gobbo Jessica , Garrido Carmen , Westerheide Sandy D. , Petitjean Michel , Taboureau Olivier , Rodrigues-Uma Fernando , Lancaster Madeline , Passemart Sandrine , Sabéran-Djoneidi Délara , Sistonen Lea , Mezger Valérie 
Published: December 2018

SUMMARYCells respond to protein-damaging insults by activating heat shock factors (HSFs), key transcription factors of proteostasis. Abnormal HSF protein levels occur in cancer and neurodegenerative disorders, highlighting the importance of the tight control of HSF expression. HSF2 is a short-lived protein, but it is abundant in the prenatal brain cortex and required for brain development. Here, we reveal that HSF2 is acetylated and co-localized with the lysine-acetyl transferases CBP and EP300 in human brain organoids. Using unbiased, biochemical, cell-imaging, and in silico approaches, we show that CBP/EP300 acetylates HSF2 at specific lysine residues, which promotes HSF2 stabilization, whereas the lysine deacetylase HDAC1 catalyzes its proteasomal degradation. The CBP KIX domain and KlX-recognizing motifs in HSF2 are critical for its interaction with acetylating enzymes. The functional importance of acetylated HSF2 is evidenced in Rubinstein-Taybi syndrome (RSTS), characterized by mutated CBP or EP300. We show that RSTS patient cells exhibit decreased HSF2 levels and impaired heat shock response. The dysregulated HSF pathway in RSTS opens new avenues for understanding the molecular basis of this multifaceted pathology.
Feedback between a retinoid-related nuclear receptor and the let-7 microRNAs controls the pace and number of molting cycles in C. elegans
Authors: Patel Ruhi , Galagali Himani , Kim John K. , Frand Alison R. 
Published: December 2018

SUMMARYAnimal development requires coordination among cyclic processes, sequential cell fate specifications, and once-a-lifetime morphogenic events, but the underlying mechanisms are not well understood. C. elegans undergo four molts at regular 8–10 h intervals. The pace of the cycle is governed by PERIOD/lin-42 and other as-yet unknown factors. Cessation of the cycle in young adults is controlled by the let-7 family of microRNAs and downstream transcription factors in the heterochronic pathway. Here, we characterize a negative feedback loop between NHR-23, the worm homolog of mammalian retinoid-related orphan receptors (RORs), and the let-7 family of microRNAs that regulates both the frequency and finite number of molts. The molting cycle is decelerated in nhr-23 knockdowns, accelerated in let-7(-) mutants, and similar to wild type animals in let-7(-) nhr-23(-) double mutants. NHR-23 binds response elements (ROREs) in the let-7 promoter and activates transcription. In turn, let-7 dampens nhr-23 expression across development via a complementary let-7 binding site (LCS) in the nhr-23 3′ UTR. The molecular interactions between NHR-23 and let-7 hold true for other let-7 family microRNAs. Either derepression of nhr-23 transcripts by LCS deletion or high gene dosage of nhr-23 leads to protracted behavioral quiescence and extra molts in adults. NHR-23 and let-7 also co-regulate scores of genes required for execution of the molts, including lin-42. In addition, ROREs and LCSs isolated from mammalian ROR and let-7 genes function in C. elegans, suggesting conservation of this feedback mechanism. We propose that this feedback loop unites the molting timer and the heterochronic gene regulatory network possibly by functioning as a cycle counter.
Sharing cells with Wolbachia: the transovarian vertical transmission of Culex pipiens densovirus
Authors: Altinli Mine , Soms Julien , Ravallec Marc , Justy Fabienne , Bonneau Manon , Weill Mylene , Gosselin‐Grenet Anne‐Sophie , Sicard Mathieu 
Published: December 2018

SummaryCulex pipiens densovirus (CpDV), a single stranded DNA virus, has been isolated from Culex pipiens mosquitoes but differs from other mosquito densoviruses in terms of genome structure and sequence identity. Its transmission from host to host, the nature of its interactions with both its host and host's endosymbiotic bacteria Wolbachia are not known. Here, we report the presence of CpDV in the ovaries and eggs of Cx. pipiens mosquitoes in close encounters with Wolbachia. In the ovaries, CpDV amount significantly differed between mosquito lines harbouring different strains of Wolbachia and these differences were not linked to variations in Wolbachia densities. CpDV was vertically transmitted in all laboratory lines to 17%–20% of the offspring. For some females, however, the vertical transmission reached 90%. Antibiotic treatment that cured the host from Wolbachia significantly decreased both CpDV quantity and vertical transmission suggesting an impact of host microbiota, including Wolbachia, on CpDV transmission. Overall our results show that CpDV is transmitted vertically via transovarian path along with Wolbachia with which it shares the same cells. Our results are primordial to understand the dynamics of densovirus infection, their persistence and spread in populations considering their potential use in the regulation of mosquito vector populations.
Transcriptomic responses of the marine cyanobacterium Prochlorococcus to viral lysis products
Authors: Fang Xiaoting , Liu Yaxin , Zhao Yao , Chen Yue , Liu Riyue , Qin Qi‐Long , Li Gang , Zhang Yu‐Zhong , Chan Wan , Hess Wolfgang R. , Zeng Qinglu 
Published: December 2018

SummaryViral infection of marine phytoplankton releases a variety of dissolved organic matter (DOM). The impact of viral DOM (vDOM) on the uninfected co‐occurring phytoplankton remains largely unknown. Here, we conducted transcriptomic analyses to study the effects of vDOM on the cyanobacterium Prochlorococcus, which is the most abundant photosynthetic organism on Earth. Using Prochlorococcus MIT9313, we showed that its growth was not affected by vDOM, but many tRNAs increased in abundance. We tested tRNA‐gly and found that its abundance increased upon addition of glycine. The decreased transcript abundances of N metabolism genes also suggested that Prochlorococcus responded to organic N compounds in vDOM. Addition of vDOM to Prochlorococcus reduced the maximum photochemical efficiency of photosystem II and CO2 fixation while increasing its respiration rate, consistent with differentially abundant transcripts related to photosynthesis and respiration. One of the highest positive fold‐changes was observed for the 6S RNA, a noncoding RNA functioning as a global transcriptional regulator in bacteria. The high level of 6S RNA might be responsible for some of the observed transcriptional responses. Taken together, our results revealed the transcriptional regulation of Prochlorococcus in response to viral lysis products and suggested its metabolic potential to utilize organic N compounds.