bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantitative proteomics identify Tenascin-C as a promoter of lung cancer progression and contributor to a signature prognostic of patient survival
Authors: Gocheva Vasilena , Naba Alexandra , Bhutkar Arjun , Guardia Talia , Miller Kathryn M. , Li Carman Man-Chung , Dayton Talya L. , Sanchez-Rivera Francisco J. , Kim-Kiselak Caroline , Jailkhani Noor , Winslow Monte M. , Del Rosario Amanda , Hynes Richard O. , Jacks Tyler 
Published: June 2017

SignificanceQuantitative mass spectrometric profiling of the extracellular matrix composition of normal lung, fibrotic lung, primary lung tumors, and lung metastases to the lymph nodes uncovered specific signatures distinguishing these tissues. CRISPR/Cas9-mediated gene activation of one of the identified factors, Tenascin-C (Tnc), showed that this protein plays a role in mediating lung adenocarcinoma metastasis. Tnc expression is repressed, directly or indirectly, by the transcription factor Nkx2-1. Bioinformatic analysis shows that expression of three matrisome factors (TNC,S100A10, andS100A11) can predict survival in patients with lung adenocarcinoma. These factors could serve as disease markers that could be exploited for better diagnosis of lung cancer, and their future study could be used to inform the design of more potent treatments for patients.
CRISPR-Cas9 conformational activation as elucidated from enhanced molecular simulations
Authors: Palermo Giulia , Miao Yinglong , Walker Ross C. , Jinek Martin , McCammon J. Andrew 
Published: June 2017

Significance
The CRISPR-Cas9 (clustered regularly interspaced short palindromic repeats–CRISPR-associated protein 9) system recently emerged as a transformative genome editing technology that is innovating life science, with cutting-edge impact in biomedicine, pharmaceutics, and agriculture. Nevertheless, the molecular mechanism underlying CRISPR-Cas9 function is still incompletely understood. Here, enhanced molecular dynamics (MD) simulations, probing displacements over long timescales, capture at atomic level specific features that are difficult to reach via conventional MD simulations and via the currently available experimental techniques, clarifying the molecular mechanism of CRISPR-Cas9, with understanding of its activation process. The insights obtained from our molecular simulations provide key reference points for future experimental studies of CRISPR-Cas9 and its applications as a genome editing tool.
Reconstruction from limited single-particle diffraction data via simultaneous determination of state, orientation, intensity, and phase
Authors: Donatelli Jeffrey J. , Sethian James A. , Zwart Peter H. 
Published: June 2017

Significance
Single-particle diffraction is an emerging technique in which diffraction images are collected from individual particles, and is used to study molecular structure from multiple conformational states that may be inaccessible through other methods. However, determining structure from these experiments is challenging, since orientations and states of imaged particles are unknown and images are highly contaminated with noise. Furthermore, the number of useful images is often limited by achievable single-particle hit rates, currently around 0.1%. We introduce an iterative projection framework to simultaneously determine orientations, states, and molecular structure from limited single-particle data by leveraging structural constraints throughout the reconstruction. This framework offers a potential pathway to increasing the amount of information that can be extracted from single-particle diffraction.
Online retellings and the viral transformation of a twitter breakup story
Authors: De Fina Anna , Gore Brittany Toscano 
Published: June 2017

Abstract
The retelling and sharing of stories is not a new phenomenon. Many narrative analysts have devoted research to these processes. But the culture of participation (Jenkins 2006) in the digital world has brought sharing to a completely new level by allowing users not only to broadcast their opinions and evaluations of a story but also to reappropriate it and recontextualize it in infinite recursions. We focus on such process of transformation of a narrative in different media and social media outlets through the analysis of the viral spread of a story posted by an individual Twitter user in 2015. Specifically, we illustrate how participation frameworks change from one retelling to another and how the original story becomes "nested" into a new meta-story centered on the twitter user as a character and on the viral spread of the story.
Recontextualizing racialized stories on YouTube
Authors: Perrino Sabina 
Published: June 2017

AbstractWhen stories (re)appear in YouTube videos, they are recontextualized not only by their titling and editing, but especially by chains of online comments. This article explores how a Northern Italian politician’s racialized story, which was first recontextualized by a TV news reporter on a YouTube video, is further recontextualized for different ends by commenters on that video. I show how these commenters negotiate and reframe the racial aspects of digital discourse and its sociocultural meanings through their various responses and across different temporal and spatial scales. By applying linguistic anthropological and sociolinguistic theories and narrative analytical tools to digital storytelling, this study emphasizes how racialized language is neither stable nor unidirectional, but is rather constantly negotiated discursively among various groups of virtual audience members. Besides investigating the pragmatics of narrative interaction in the digital realm, this article speaks to methodological challenges that surround the study of online storytelling.
Sharing the moment as small stories
Authors: Georgakopoulou Alexandra 
Published: June 2017

Abstract
Sharing the moment live, a built-in logic of many social networking sites, is, I claim, an invitation for creating plots, which has led to systematic practices. I single out taking a narrative stance on Facebook as such a practice and show the interplay between key-norms and evolving media affordances for pre-selection of story ingredients, localization, visualization of the experience, and audience selection. These contribute to showing the moment as opposed to telling it, with selected friends serving as knowing co-narrators and with story-linking allowing for allusive, transmedia links. I review these practices in the context of increased story facilities that notably bring together several social media apps. I argue that although this curation promises a move beyond the moment, it ultimately serves to consolidate sharing-lives-in-the-moment. I reflect on the implications of this for the direction of travel in relation to stories on many social media platforms.
Inferring transcriptional logic from multiple dynamic experiments
Authors: Minas Giorgos , Jenkins Dafyd J , Rand David A , Finkenstädt Bärbel 
Published: June 2017

Abstract

Motivation
The availability of more data of dynamic gene expression under multiple experimental conditions provides new information that makes the key goal of identifying not only the transcriptional regulators of a gene but also the underlying logical structure attainable.

Results
We propose a novel method for inferring transcriptional regulation using a simple, yet biologically interpretable, model to find the logic by which a set of candidate genes and their associated transcription factors (TFs) regulate the transcriptional process of a gene of interest. Our dynamic model links the mRNA transcription rate of the target gene to the activation states of the TFs assuming that these interactions are consistent across multiple experiments and over time. A trans-dimensional Markov Chain Monte Carlo (MCMC) algorithm is used to efficiently sample the regulatory logic under different combinations of parents and rank the estimated models by their posterior probabilities. We demonstrate and compare our methodology with other methods using simulation examples and apply it to a study of transcriptional regulation of selected target genes of Arabidopsis Thaliana from microarray time series data obtained under multiple biotic stresses. We show that our method is able to detect complex regulatory interactions that are consistent under multiple experimental conditions.

Availability and implementation
Programs are written in MATLAB and Statistics Toolbox Release 2016b, The MathWorks, Inc., Natick, Massachusetts, United States and are available on GitHub https://github.com/giorgosminas/TRS and at http://www2.warwick.ac.uk/fac/sci/systemsbiology/research/software.

Supplementary information
Supplementary data are available at Bioinformatics online.
Primary Prevention in the 21st Century
Authors: Bloom Martin 
Published: June 2017

The 19th century saw the beginnings of prevention, focused primarily on specific issues, like Dr. John Snow’s (b. 1813–d. 1858) intuitive epidemiology that led to the prevention of a mysterious disease (cholera) by removing the water pump handle (of a contaminated public water source); or Pasteur’s (b. 1822–d. 1895) solid research leading to the pasteurization of milk (thus preventing illness from contaminated milk, among his many achievements). The 20th century expanded this vision through the work of large numbers of workers all over the world, and eventually came to include the prevention of predictable untoward events, the protection of existing states of health and healthy functioning, and the promotion of desired events for populations of individuals or groups relative to given physical environments and sociocultural settings. As illustrated here, many professional and nonprofessional people involved in topics on health and well-being in the 21st century are beginning to see these issues in more complex terms: to see more systemic interrelationships among helping modalities—prevention, protection, promotion, treatment, rehabilitation, and palliative care—and more cooperative ventures among social agencies, governments, universities and citizens’ groups. Tadmor (2014) in the chapter “Cancer: Multiple Services for Children Dying of Cancer and for Their Families” (in Gullotta and Bloom 2014, cited under Theories Used in Primary Prevention), Ciporah S. Tadmor illustrates why it is no longer possible to provide palliative care solely to a dying teenager without considering related health issues that might arise within his or her family, which may also need help in reconstituting (rehabilitating) the family without its lost member, all of which involve protecting existing healthy functioning of members, promotion of desired goals (to help move the family members forward in their lives), and prevention of any predictable issues that might interfere with their functioning.
Buddhism and Sexuality
Authors: Langenberg Amy 
Published: June 2017

Because of its high regard for celibate monasticism and incisive critique of desire as a root cause of suffering, Buddhism is widely assumed to be a sex-negative religion. In fact, as a growing body of scholarship has demonstrated, the sexual landscape of Buddhist traditions across time and place is varied, complex, and at times transgressive. The beginnings of Buddhism and sexuality as a research subfield can arguably be traced to the 1998 publication of Bernard Faure’s The Red Thread, a work that attempts to identity major themes and lines of tension in Buddhists’ imaginative encounters with, efforts to discipline, and philosophical understandings of human sexuality. Faure’s monograph was, however, preceded by L. P. N. Perera study of sexuality in ancient Buddhist India (Sexuality in Ancient India); see Perera 1993, cited under Seminal Monographs), Miranda Shaw’s monograph on women and Tantra (Passionate Enlightenment); see Shaw 1994, cited under Sexuality in Indo-Tibetan Tantra), and Liz Wilson’s book on disgust and the female body in early Buddhism (Charming Cadavers); see Wilson 1996, cited under Seminal Monographs). Since Faure, specialists in various Asian traditions have focused on sexuality with ever increasing levels of historical detail and theoretical sophistication. Examples include Sarah Jacoby’s work, Love and Liberation (Jacoby 2014, cited under Seminal Monographs), Richard Jaffe’s monograph, Neither Monk nor Layman (Jaffe 2001, cited under Non-celibate Monasticisms), John Power’s 2009 book A Bull of a Man (Powers 2009, cited under Seminal Monographs), and José Ignacio Cabezón’s Sexuality and Classical South Asian Buddhism (Cabezón 2017, cited under Seminal Monographs). In the meantime, scholars of tantra, yoga, and consort traditions such as Holly Gayley, David Gray, Janet Gyatso, and Christian Wedemeyer have moved past the orientalist judgements of early Indology and the phenomenology of Mircea Eliade in their treatments of Tantric sexuality; advances in Vinaya studies by Shayne Clarke, Alice Collett, Anālayo, and others have deepened understanding of early monastic negotiations with Indian sexual concepts and social mores; and queer and LGBT studies by Richard Corless and Hsiao-lan Hu have generated new research angles. The subfield of Buddhist ethics has also produced a small literature on Buddhist sexual ethics to complement its already substantial work on related topics like human rights and abortion. Additionally, specialists in Buddhist modernisms such as Ann Gleig and Stephanie Kaza have enriched the literature on Buddhism and sexuality by addressing issues such as sexual expression, sexual identity, and sexual abuse in contemporary Buddhist communities in the West.
Intramedullary Implant Choice and Cost in the Treatment of Pediatric Diaphyseal Forearm Fractures
Authors: Heare Austin , Goral Dawn , Belton Matthew , Beebe Corey , Trizno Anastasiya , Stoneback Jason 
Published: June 2017

Objectives:
To compare outcomes and costs between titanium elastic nails (TENs), stainless steel elastic nails (SENs), and Kirschner wires (K-wires) in the treatment of pediatric diaphyseal forearm fractures with intramedullary fixation.

Design:
Retrospective cohort study.

Setting:
Level 1 Pediatric Trauma Center.

Patients/Participants:
A total of 100 patients (65 male and 35 female) younger than 18 years with diaphyseal forearm fractures treated with intramedullary fixation were included in the study.

Intervention:
Patients received single or both bone intramedullary fixation with either TENs, SENs, or K-wires.

Main Outcome Measurements:
Time to radiographic union, complication rate, surgical time, and average cost per implant.

Results:
One hundred patients were included in the study. Thirty-one patients were treated with TENs, 30 with SENs, and 39 with K-wires. No significant difference in time to radiographic union, complication rate, or surgical time was found between the 3 types of fixation. Average time to union was 9.4 ± 5.4 weeks, and complication rate was 12.9% for TENs, 10.0% for SENs, and 12.8% for K-wires. There was a significant difference in cost per implant, with an average cost of $639, $172, and $24 for TENs, SENs, and K-wires, respectively (P < 0.001).

Conclusions:
This study demonstrates no difference between TENs, SENs, and K-wires in the treatment of pediatric diaphyseal forearm fractures with regards to outcome, time to union, surgical time, or complication rates. Given the significant cost difference between these implants, we recommend that surgeons consider modifying their implant selection to help mitigate cost.

Level of Evidence:
Therapeutic Level III. See Instructions for Authors for a complete description of levels of evidence.
Intramedullary Fixation With Minimally Invasive Clamp-Assisted Reduction for the Treatment of Ipsilateral Femoral Neck and Subtrochanteric Fractures: A Technical Trick
Authors: Sun Qi , Ge Wei , Li RenLong , Li ShaoHua , Cai Ming 
Published: June 2017

Summary:
The purpose of this study is to describe a surgical technique for intramedullary fixation and minimally invasive clamp-assisted reduction with selective cerclage wiring for the management of combined ipsilateral femoral neck and subtrochanteric fractures and to present the clinical outcomes in 17 patients after treatment using this technique.
Surgical Fixation of Periprosthetic Humerus Fractures Using an Extension Plate: Surgical Technique and Report of 5 Cases
Authors: Schoch Bradley , Mehta Samir , Namdari Surena 
Published: June 2017

Summary:
Periprosthetic fractures after shoulder arthroplasty occur in up to 2% of patients. In patients with stable components who fail or cannot undergo nonoperative management, stable fixation is required. We present a new technique to obtain proximal fixation around the humeral component using a 4.5-mm large fragment plate and a 3.5-mm attachment plate.
Quantifying Decreased Radiation Exposure From Modern CT Scan Technology and Surveillance Programs of Germ Cell Tumors
Authors: Howard Stephanie A. , Rosenthal Michael H. , Qin Lei , Matalon Shanna A. , Bernard Brandon D. , Beard Clair J. , Sweeney Christopher J. 
Published: June 2017

Introduction:
Upgrading computerized tomography (CT) scanners to iterative reconstruction techniques (IRT) decreases radiation dose. This reduction, combined with changes in surveillance protocols in clinical stage I testicular cancer (CS1TC) measurably decrease the lifetime attributable risk (LAR) of dying of radiation-associated cancer.

Materials and Methods:
This IRB-approved study enrolled 24 CS1TC patients who had CT scans on the same Toshiba Aquilion 64 CT before and after IRT software installation. Dose-length product and CT dose index volume were recorded. A physicist calculated effective doses. Radiation doses were compared using the Wilcoxon signed rank test. Median effective dose per scan was multiplied by scan number based on 16 versus 7 scans in 5-year AS protocols to calculate estimated cumulative dose (ECD). LAR of dying of radiation-associated solid tumor was estimated using ECD for a single exposure at age 35 with the excess absolute risk transport model from the BEIR VII analysis of long-term atomic bomb survivors.

Results:
Median preupgrade and postupgrade effective doses were 12.5 and 7.7 mSv, respectively (P<0.0001). A linear regression model with a constrained zero intercept fit to the data found that IRT dose was estimated as 61% of filtered back projection dose (95% confidence interval, 0.56-0.66). The IRT upgrade reduced the LAR of the 16-scan protocol 35%. Combination of IRT upgrade and 7-scan protocol reduced surveillance LAR 72%.

Conclusions:
Modern CT technology combined with reduced scanning strategies can markedly decrease lifetime radiation exposure, further lowering the already small potential mortality of imaging-associated cancers.
High-Velocity Paint Gun Injuries
Authors: Wohltmann Wendi E. , Wisell Joshua A. , Lafrades Celina M. C. , Cramer Daniel M. , Ragsdale Bruce D. 
Published: June 2017

Abstract:
Cutaneous injuries due to industrial high-pressure paint guns are well-documented in the literature; however, the histologic characteristics are uncommonly described, and facial involvement has not been previously reported. Histopathologic features of paint gun injuries vary depending on the time since injection and type of material. Early lesions display an acute neutrophilic infiltrate, edema, and thrombosis, with varying degrees of skin, fat, and muscle necrosis. More developed lesions (120–192 hours after injury) have prominent histiocytes and fibrosis around necrotic foci, possibly with the pitfall of muscle regenerative giant cells that could be mistaken for sarcoma. Continuing inflammation, swelling, and resultant vascular compression could explain ongoing necrosis months after the accident. The histopathologic differential diagnosis in the absence of clinical history includes paint in an abrasion, foreign body reaction to tattoo, giant cell tumor of tendon sheath, and various neoplasms. If available, radiologic studies can substitute for clinical photographs to indicate the extent of injury. The radiologic differential, uninformed by history, may include calcific periarthritis, gouty tophus, and tumoral calcinosis. Seven cases of injury due to high-velocity paint guns are presented with 4 additional cases mimicking paint gun injury and with review of the literature.
Mohs Mapping Fidelity: Optimizing Orientation, Accuracy, and Tissue Identification in Mohs Surgery
Authors: Li Janet Y. , Silapunt Sirunya , Migden Michael R. , McGinness Jamie L. , Nguyen Tri H. 
Published: June 2017

BACKGROUND
Mohs micrographic surgery (MMS) is a highly effective process that requires consistent accuracy in resection, mapping, and histologic interpretation. Although the general sequence in MMS is similar, there are numerous variations among Mohs surgeons as to how this process is performed.

OBJECTIVE
This article aims to review the process of MMS, with the intent to identify and mitigate the potential errors at each step. Existing variations will be discussed and protocols offered to minimize error and optimize accuracy.

METHODS
A Pubmed search was performed for publications on methods of tissue mapping, orienting, and processing in MMS.

RESULTS
Our literature review highlights various techniques for tissue orientation, transfer, flattening, inking, mapping, and processing of later stages and multiple specimens. We discuss our system, which reduces error during tissue transfer, tissue identification in vivo and ex vivo, and tissue flattening. Furthermore, we discuss adaptations to increase the accuracy during reexcisions of subsequent Mohs layers.

CONCLUSION
Variations in MMS reflects the diverse training and creativity among Mohs surgeons. Unless potential errors are addressed, however, false negatives will occur and undermine the superior cure rate of MMS.
Hot flush frequency and severity at baseline as predictors of time to transient and stable treatment success: pooled analysis of two CE/BZA studies
Authors: Pinkerton JoAnn V. , Bushmakin Andrew G. , Bobula Joel , Lavenberg Joanne , Komm Barry S. , Abraham Lucy 
Published: June 2017

Abstract

Objective:
To evaluate the impact of baseline hot flush frequency and severity on time to symptom improvement during treatment with conjugated estrogens/bazedoxifene (CE/BZA).

Methods:
Data were pooled through week 12 from two randomized placebo-controlled trials (SMART-1 and SMART-2) of nonhysterectomized postmenopausal women with hot flushes treated with CE 0.45 mg/BZA 20 mg or CE 0.625 mg/BZA 20 mg. Time to transient and stable improvement (≥ 50% reduction in hot flush frequency/severity) was estimated using nonparametric models.

Results:
Transient improvement in hot flush frequency occurred earlier in women treated with CE 0.45 mg/BZA 20 mg with less frequent versus more frequent baseline hot flushes per day: median time to transient improvement was 2, 7, and 11 days for women with < 3, 3 to < 8, and ≥ 8 hot flushes per day at baseline, respectively (P = 0.0009). Transient improvement in severity occurred earlier for women with less severe versus more severe baseline hot flushes: median time to transient improvement was 2, 6, and 16 days for women with mild, moderate, and severe hot flushes at baseline, respectively (P < 0.0001). Stable improvement typically occurred 2 to 3 days after the transient event and was less influenced by baseline status. A similar pattern was observed with CE 0.625 mg/BZA 20 mg treatment, though improvement occurred a few days earlier than with CE 0.45 mg/BZA 20 mg.

Conclusion:
Women with more frequent/severe hot flushes take longer to achieve transient improvements with CE/BZA and should be encouraged to continue treatment, as it may take longer than a few weeks to achieve significant improvement.