bluuebunny/crossref_metadata_2025_split huggingface dataset:
FactorialHMM: fast and exact inference in factorial hidden Markov models
Authors: Schweiger Regev , Erlich Yaniv , Carmi Shai 
Published: November 2018

Abstract

Motivation
Hidden Markov models (HMMs) are powerful tools for modeling processes along the genome. In a standard genomic HMM, observations are drawn, at each genomic position, from a distribution whose parameters depend on a hidden state, and the hidden states evolve along the genome as a Markov chain. Often, the hidden state is the Cartesian product of multiple processes, each evolving independently along the genome. Inference in these so-called Factorial HMMs has a naïve running time that scales as the square of the number of possible states, which by itself increases exponentially with the number of sub-chains; such a running time scaling is impractical for many applications. While faster algorithms exist, there is no available implementation suitable for developing bioinformatics applications.

Results
We developed FactorialHMM, a Python package for fast exact inference in Factorial HMMs. Our package allows simulating either directly from the model or from the posterior distribution of states given the observations. Additionally, we allow the inference of all key quantities related to HMMs: (i) the (Viterbi) sequence of states with the highest posterior probability; (ii) the likelihood of the data and (iii) the posterior probability (given all observations) of the marginal and pairwise state probabilities. The running time and space requirement of all procedures is linearithmic in the number of possible states. Our package is highly modular, providing the user with maximal flexibility for developing downstream applications.

Availability and implementation
https://github.com/regevs/factorial_hmm

Supplementary information
Supplementary data are available at Bioinformatics online.
Valve-in-valve-prosthesis embolization and aortic dissection: single procedure, double complication
Authors: Szlapka Michal , Michel Eriberto , Ricciardi Mark J , Malaisrie S Christopher 
Published: November 2018

Abstract
Transcatheter aortic valve implantation (TAVI) is a recognized treatment method for high-risk patients with aortic stenosis. TAVI is also recommended for structural valve degeneration of a biological valve prosthesis. TAVI-specific complications, such as prosthesis embolization and aortic dissection, are uncommon but potential concerns. A 73-year-old woman presented with structural valve degeneration 14 years after aortic root replacement with a bioprosthetic valved conduit. The patient underwent TAVI valve-in-valve under monitored anaesthesia care. Intraoperatively, the self-expandable prosthesis was difficult to deploy within the valved conduit and ultimately migrated distally. During the technically difficult passage of the prosthesis delivery system through the tortuous aorta, the patient started reporting symptoms suggestive of aortic dissection. An emergency computed tomography scan confirmed type B dissection. Thoracic endovascular aortic repair followed by deployment of a balloon-expandable prosthesis below the self-expandable implant was performed. Careful prosthesis selection in valve-in-valve patients after aortic root replacement is crucial for procedural success.
Sparsity/undersampling tradeoffs in anisotropic undersampling, with applications in MR imaging/spectroscopy
Authors: Monajemi Hatef , Donoho David L 
Published: November 2018

Abstract
We study anisotropic undersampling schemes like those used in multi-dimensional magnetic resonance (MR) spectroscopy and imaging, which sample exhaustively in certain time dimensions and randomly in others. Our analysis shows that anisotropic undersampling schemes are equivalent to certain block-diagonal measurement systems. We develop novel exact formulas for the sparsity/undersampling tradeoffs in such measurement systems, assuming uniform sparsity fractions in each column. Our formulas predict finite-$N$ phase transition behavior differing substantially from the well-known asymptotic phase transitions for classical Gaussian undersampling. Extensive empirical work shows that our formulas accurately describe observed finite-$N$ behavior, while the usual formulas based on universality are substantially inaccurate at the moderate $N$ involved in realistic applications. We also vary the anisotropy, keeping the total number of samples fixed, and for each variation we determine the precise sparsity/undersampling tradeoff (phase transition). We show that, other things being equal, the ability to recover a sparse object decreases with an increasing number of exhaustively sampled dimensions.
Metabolic regulation of T cell development by Sin1–mTORC2 is mediated by pyruvate kinase M2
Authors: Ouyang Xinxing , Han Yuheng , Qu Guojun , Li Man , Wu Ningbo , Liu Hongzhi , Arojo Omotooke , Sun Hongxiang , Liu Xiaobo , Liu Dou , Chen Lei , Zou Qiang , Su Bing 
Published: November 2018

Abstract
Glucose metabolism plays a key role in thymocyte development. The mammalian target of rapamycin complex 2 (mTORC2) is a critical regulator of cell growth and metabolism, but its role in early thymocyte development and metabolism has not been fully studied. We show here that genetic ablation of Sin1, an essential component of mTORC2, in T lineage cells results in severely impaired thymocyte development at the CD4−CD8− double negative (DN) stages but not at the CD4+CD8+ double positive (DP) or later stages. Notably, Sin1-deficient DN thymocytes show markedly reduced proliferation and glycolysis. Importantly, we discover that the M2 isoform of pyruvate kinase (PKM2) is a novel and crucial Sin1 effector in promoting DN thymocyte development and metabolism. At the molecular level, we show that Sin1–mTORC2 controls PKM2 expression through an AKT-dependent PPAR-γ nuclear translocation. Together, our study unravels a novel mTORC2−PPAR-γ−PKM2 pathway in immune-metabolic regulation of early thymocyte development.
Zebrafish hhex-null mutant develops an intrahepatic intestinal tube due to de-repression of cdx1b and pdx1
Authors: Gao Ce , Huang Weidong , Gao Yuqi , Lo Li Jan , Luo Lingfei , Huang Honghui , Chen Jun , Peng Jinrong 
Published: November 2018

Abstract
The hepatopancreatic duct (HPD) system links the liver and pancreas to the intestinal tube and is composed of the extrahepatic biliary duct, gallbladder, and pancreatic duct. Haematopoietically expressed-homeobox (Hhex) protein plays an essential role in the establishment of HPD; however, the molecular mechanism remains elusive. Here, we show that zebrafish hhex-null mutants fail to develop the HPD system characterized by lacking the biliary marker Annexin A4 and the HPD marker sox9b. The hepatobiliary duct part of the mutant HPD system is replaced by an intrahepatic intestinal tube characterized by expressing the intestinal marker fatty acid-binding protein 2a (fabp2a). Cell lineage analysis showed that this intrahepatic intestinal tube is not originated from hepatocytes or cholangiocytes. Further analysis revealed that cdx1b and pdx1 are expressed ectopically in the intrahepatic intestinal tube and knockdown of cdx1b and pdx1 could restore the expression of sox9b in the mutant. Chromatin-immunoprecipitation analysis showed that Hhex binds to the promoters of pdx1 and cdx1b genes to repress their expression. We therefore propose that Hhex, Cdx1b, Pdx1, and Sox9b form a genetic network governing the patterning and morphogenesis of the HPD and digestive tract systems in zebrafish.
Suicide in the Military: Understanding Rates and Risk Factors Across the United States’ Armed Forces
Authors: Pruitt Larry D , Smolenski Derek J , Bush Nigel E , Tucker Jennifer , Issa Fuad , Hoyt Timothy V , Reger Mark A 
Published: November 2018

Abstract
This paper presents data from the United States Department of Defense Suicide Event Report System for years 2012–2015 to detail descriptive, longitudinal rate data and risk factor profiles associated with military suicide. The annual findings were aggregated from all U.S. military suicide deaths and suicide attempts. Data elements included the most common method of suicide (firearms), most common behavioral health diagnoses (substance abuse/dependence), common life stressors (failed intimate–partner relationships), and an individual’s history of operational deployment. Age- and sex-adjusted rates for the Services were compared with rates for the U.S. adult population. Results showed that the current reporting period (2015) is similar to patterns that have been observed over the preceding years and to patterns reported in the overall U.S. adult population. Suicide rates remain elevated but stable for both the Active and Reserve Components of the Military Services compared to historical levels observed prior to 2003. Finally, we discuss common errors and misinterpretations that can occur when analyzing surveillance data.
Programmable time-domain digital-coding metasurface for non-linear harmonic manipulation and new wireless communication systems
Authors: Zhao Jie , Yang Xi , Dai Jun Yan , Cheng Qiang , Li Xiang , Qi Ning Hua , Ke Jun Chen , Bai Guo Dong , Liu Shuo , Jin Shi , Alù Andrea , Cui Tie Jun 
Published: November 2018

Abstract
Optical non-linear phenomena are typically observed in natural materials interacting with light at high intensities, and they benefit a diverse range of applications from communication to sensing. However, controlling harmonic conversion with high efficiency and flexibility remains a major issue in modern optical and radio-frequency systems. Here, we introduce a dynamic time-domain digital-coding metasurface that enables efficient manipulation of spectral harmonic distribution. By dynamically modulating the local phase of the surface reflectivity, we achieve accurate control of different harmonics in a highly programmable and dynamic fashion, enabling unusual responses, such as velocity illusion. As a relevant application, we propose and realize a novel architecture for wireless communication systems based on the time-domain digital-coding metasurface, which largely simplifies the architecture of modern communication systems, at the same time yielding excellent performance for real-time signal transmission. The presented work, from new concept to new system, opens new pathways in the application of metamaterials to practical technology.
The Value of Systemic Unimportance: The Case of MetLife*
Authors: Naubert Christopher , Tesar Linda L 
Published: November 2018

Abstract
We use an event study approach to estimate the burden of the financial regulations associated with Systemically Important Financial Institution (SIFI) designation. On March 30, 2016, the US District Court determined that MetLife’s SIFI designation was arbitrary and capricious because the Financial Stability Oversight Council (FSOC) failed to weigh the economic cost of the financial regulation on MetLife against the benefits of increased financial stability. We find significant positive abnormal returns for MetLife and AIG on the date of the ruling. We estimate that the lifting of the SIFI designation created $1.4 billion in corporate wealth for MetLife, suggesting that MetLife would be 3.4% more profitable as a non-SIFI. These gains fall short of the $8 billion stipulated by MetLife in its complaint. We also find significant abnormal returns to SIFI institutions on the day following the US Presidential election.
Finding Jobs, Forming Families, and Stressing Out? Work, Family, and Stress among Young Adult Women in the United States
Authors: Lippert Adam M , Damaske Sarah 
Published: November 2018

AbstractThe transition to adulthood is increasingly characterized by complex paths into the world of work and family, especially for young women. Yet how work and family combine to influence stress among young adult women is not well understood. Using data from the National Longitudinal Study of Adolescent to Adult Health, we leverage new extensions to latent class analysis (LCA) to identify common combinations of work and family circumstances among young adult women, their earlier life and contemporaneous correlates, and associations with two stress measures: a multi-item Perceived Stress Scale (PSS) and Epstein–Barr Viral (EBV) antibody titers, a well-validated biomarker of stress-related immunity impairments. We identify seven different common combinations of latent work–family combinations among young adult women ranging from well-compensated professional workers with and without children, mothers without paid employment, and delayed transitions to work and family. Completing a college degree was associated with a higher likelihood of membership in classes marked by professional work irrespective of motherhood, while being raised in a community with greater female labor opportunities was generally associated with membership in child-free classes. Mothers and child-free women in “pink-collar” work with low wages and decision-marking freedom reported higher stress compared to women in “white-collar” work with higher wages and decision-making freedom. These differences are mostly attenuated following adjustments for poverty-related stressors and work–family conflict. While prior work has emphasized the health benefits for women of combining work and family, our research suggests these benefits may be limited to women of higher socioeconomic status with flexible, well-compensated jobs.
Decitabine attenuates nociceptive behavior in a murine model of bone cancer pain
Authors: Appel Camilla Kristine , Scheff Nicole Newell , Viet Chi Tonglien , Schmidt Brian Lee , Heegaard Anne-Marie 
Published: November 2018

Abstract
Bone cancer metastasis is extremely painful and decreases the quality of life of the affected patients. Available pharmacological treatments are not able to sufficiently ameliorate the pain, and as patients with cancer are living longer, new treatments for pain management are needed. Decitabine (5-aza-2′-deoxycytidine), a DNA methyltransferases inhibitor, has analgesic properties in preclinical models of postsurgical and soft-tissue oral cancer pain by inducing an upregulation of endogenous opioids. In this study, we report that daily treatment with decitabine (2 µg/g, intraperitoneally) attenuated nociceptive behavior in the 4T1-luc2 mouse model of bone cancer pain. We hypothesized that the analgesic mechanism of decitabine involved activation of the endogenous opioid system through demethylation and reexpression of the transcriptionally silenced endothelin B receptor gene, Ednrb. Indeed, Ednrb was hypermethylated and transcriptionally silenced in the mouse model of bone cancer pain. We demonstrated that expression of Ednrb in the cancer cells lead to release of β-endorphin in the cell supernatant, which reduced the number of responsive dorsal root ganglia neurons in an opioid-dependent manner. Our study supports a role of demethylating drugs, such as decitabine, as unique pharmacological agents targeting the pain in the cancer microenvironment.
Lung cancer screening: Practice guidelines and insurance coverage are not enough
Authors: McDonnell Karen Kane , Estrada Robin Dawson , Dievendorf Amy Clark , Blew Lauren , Sercy Erica , Khan Samira , Hardin James W. , Warden Deborah , Eberth Jan M. 
Published: November 2018

ABSTRACT

Background and purpose:
Low-dose computed tomography (LDCT) is expected to increase early detection of lung cancer and improve survival. The growth in the number of advanced nurse practitioners (NPs) in primary care settings increases the likelihood that an NP will serve as a patient’s provider. This study's purpose was to examine knowledge, attitudes, and practices regarding LDCT among NPs who work in primary care settings.

Methods:
An explanatory, sequential, mixed-method design used a 32-item questionnaire, followed by a semi-structured telephone interview. The development of the survey and interview questions were guided by a conceptual framework representing a temporal sequence for behavior change and potential barriers to guideline adherence.

Conclusions:
Nurse practitioners believe that shared decision making with their high-risk patients about LDCT is within their scope of their practice. Working in time-constrained primary care settings, NPs have limited abilities to improve the uptake of LDCT. Substantial patient barriers exist that deter follow through on providers' recommendation. Disseminating guidelines and authorizing health insurance reimbursement is insufficient.

Implications for practice:
Research is needed that investigates the screening process so that barriers can be closely studied. Culture change is needed where early detection has greater value for insurers, providers, and patients.
The one-minute preceptor model: A systematic review
Authors: Gatewood Elizabeth , De Gagne Jennie C. 
Published: November 2018

ABSTRACT

Background and purpose:
Teaching models provide a systemic framework for didactic and clinical teaching. The One-Minute Preceptor (OMP) is one teaching model, providing five microskills to organize a learning experience for students in the clinical environment. This review aims to integrate the literature on the OMP model by highlighting potential use for nurse practitioners while identifying directions for future research.

Methods:
Electronic databases were searched from December 2017 to January 2018 for articles published in English. The databases included PubMed, CINAHL, and MEDLINE using terms including “preceptor,” “clinical teaching,” “time-efficient teaching,” and “precepting.” Of 32 articles in the final search, only 12 experimental quantitative studies were included in the synthesis and 20 descriptive studies in the discussion.

Conclusions:
The OMP model is supported by literature for its effectiveness as a teaching model and preference by students and preceptors. It has been shown to increase teaching techniques including feedback and assessment of students' clinical reasoning.

Implications for practice:
The OMP model has the potential to overcome clinicians' barriers to precepting nurse practitioner students. Future research may evaluate the use of this model specific to nurse practitioner preceptors and students, perceived time benefits in clinical teaching, overall improvement in clinical teaching, and use in interprofessional precepting.
Efficacy of vitamin D in treatment of inflammatory bowel disease
Authors: Li Jinzhong , Chen Ning , Wang Dan , Zhang Jie , Gong Xiaobing 
Published: November 2018

Abstract

Background:
Vitamin D (VitD) deficiency is prevalent in patient with inflammatory bowel disease (IBD). Recent studies have found that VitD can induce and maintain IBD remission through antibiosis, anti-inflammatory, and repair of intestinal mucosal barriers, thus improving the patient's disease activity and quality-of-life. The purpose of this meta-analysis is to evaluate the therapeutic effect and safety of VitD in the treatment of IBD.

Methods:
Published randomized controlled trials (RCTs) were included from electronic databases (PubMed, Embase, Cochrane library, Web of Science, and so forth). Cochrane handbook was applied to evaluate the methodological quality. The levels of 25(OH)D3, relapse rate, inflammation index, and adverse events were compared between the experimental group and the control group (placebo group). All statistical analyses were directed by Revman 5.3 software and statistical significance was defined as P < .05.

Results:
Eighteen RCTs involved 908 patients were included. Meta-analysis showed that VitD improved the 25(OH)D3 levels more significantly than the control group (ng/mL, weighted mean deviation [WMD] = 7.85, 95% CI (5.52, 10.18), P < .000001), and compared with lower doses, there were significant differences increasing 25(OH)D3 levels (WMD = 11.19, 95% CI [4.73, 17.65], P = .0007) in high-dose VitD treatment while there was no significant difference in the adverse events between 2 groups (WMD = 1.56, 95% CI [0.74, 3.29], P = .24). VitD reduced the relapse rate more significantly than the control group, but there were no significant differences between the low-dose and high-dose vitamin D treatment. The erythrocyte sedimentation rate (ESR) and high-sensitivity C-reactive protein (hsCRP) of the VitD and the control group showed no statistically significant difference (ESR [mm/h]: WMD = –0.22, 95% CI [–5.73, 5.29], P = .94; hsCRP (mg/dL): WMD = −0.53, 95% CI [–1.68, 0.62], P = .37).

Conclusions:
The treatment of VitD in patients with IBD can improve the level of 25(OH)D3 and control the relapse rate of the disease, whose clinical curative effect is more accurate. Thus VitD should be recommended for the treatment of IBD, at least as an adjunctive treatment.
WNT6 is an effective marker for osteosarcoma diagnosis and prognosis
Authors: Jiang Kai , Li Sha , Li Lu , Wang Xiaohua , Gu Yuanjie , Jin Zhiqiang 
Published: November 2018

Abstract
Wingless-Type MMTV Integration Site Family, Member 6 (WNT6) is a member of the Wnt family and its expression is abnormal in different human cancer cell lines. The purpose of this study was to investigate the clinical significance of WNT6 in osteosarcoma.
The levels of WNT6 mRNA and protein in tissue and serum were detected through quantitative real-time polymorperase chain reaction (qRT-PCR) and Enzyme Lined Immunosorbent Assay (ELISA), respectively. Chi-square test was performed to estimate the association of WNT6 expression with clinical parameters among osteosarcoma patients. Receiver operation characteristic (ROC) curve was plotted to determine diagnostic performance of serum WNT6 in osteosarcoma. Survival analysis was performed using Kaplan–Meier method. Cox regression analysis was adopted to evaluate prognostic significance of WNT6 expression among osteosarcoma patients.
Compared with the controls, WNT6 mRNA and protein levels were significantly elevated in patients with osteosarcoma (P > .05 for all). Furthermore, WNT6 upregulation showed positive correlation with patients’ age (P < .001), tumor grade (P < .001) and distant metastasis (P = .001). WNT6 might be a diagnostic marker for osteosarcoma with an AUC of 0.854 combining a specificity of 88.4% and a sensitivity of 77.8%. Survival analysis result indicated that high WNT6 expression predicted poor survival (log rank test, P = .001). WNT6 might be a potential prognostic biomarker for osteosarcoma (HR = 2.227, 95%CI = 1.061–10.842, P = .027).

WNT6 may be a diagnostic and prognostic marker in osteosarcoma.