bluuebunny/crossref_metadata_2025_split huggingface dataset:
Intensive Outpatient Program Effects on High-need Patients’ Access, Continuity, Coordination, and Engagement
Authors: Wu Frances M. , Slightam Cindie A. , Wong Ava C. , Asch Steven M. , Zulman Donna M. 
Published: October 2017

Objective:
The intensive and varied services required by high-need patients have inspired a number of new care delivery models; however, evidence of their effectiveness is mixed. This study evaluated whether augmenting a patient-centered medical home (PCMH) with intensive outpatient management enhances high-need patients’ care processes.

Research Design:
Retrospective analysis using differences-in-differences and χ2 tests.

Subjects:
Of 545 high-need patients receiving PCMH care, 140 were previously randomly selected for the intensive outpatient management program; the remaining received usual care.

Measures:
We evaluated program effects on care continuity (proportion of primary care visits with assigned primary care physician); access (proportion of telephone visits out of all primary care encounters, missed appointment rate); care coordination (rate of follow-up after hospital discharge, new telehealth enrollment); and patient engagement (rates of online personal health record registration, advance directive completion).

Results:
Compared with patients receiving usual care, patients enrolled in intensive management experienced a 5.9% increase in proportion of primary care visits with an assigned primary care physician (P<0.001) and a 17.9% increase in proportion of telephone-based visits (P<0.001). Patients in the program had 7.5% higher rates of telehealth referral (P=0.01), 17.2% higher rates of advance directive completion (P<0.01), and 9.3% higher rates of personal health record registration (P=0.02). There was no effect on missed appointments or posthospital discharge visit rates.

Conclusions:
Augmenting a PCMH with intensive outpatient management may have positive effects on primary care processes related to continuity, access, coordination, and patient engagement.
Women Firefighters and Workplace Harassment
Authors: Hom Melanie A. , Stanley Ian H. , Spencer-Thomas Sally , Joiner Thomas E. 
Published: October 2017

Abstract
This cross-sectional study investigated the association between harassment, career suicidality, and psychiatric symptoms among women firefighters. Women firefighters (n = 290) completed self-report measures of experiences with harassment on the job, career suicidality, and various psychiatric symptoms. Logistic regression analyses and one-way analyses of variance were used to address study aims. Of the sample, 21.7% reported having experienced sexual harassment and 20.3% reported having been threatened or harassed in another way on their firefighting job. Sexual harassment and other threats/harassment on the job were both significantly associated with a greater likelihood of reporting career suicidal ideation, as well as reporting more severe psychiatric symptoms. Harassment and threats experienced on the job may be associated with increased suicide risk and more severe psychiatric symptoms among women firefighters. Efforts are needed to reduce the occurrence of harassment and threats within the fire service and provide support for women firefighters who have been harassed or threatened.
The Impact of the Endovascular Treatment of Cerebral Aneurysms on Headaches
Authors: Assadi Mitra , Binning Mandy , Liebman Kenneth , Veznedaroglu Erol 
Published: October 2017

Objective:
The co-occurrence of headaches and cerebral aneurysms is common in clinical practice, although a clear causal relationship has not been ascertained. We aimed to investigate the impact of endovascular obliteration of aneurysms on headaches using a cross-sectional, prospective, open-label protocol. We also sought to characterize the preexisting headaches in patients harboring cerebral aneurysms using the International Classification of Headache Disorders criteria.

Methods:
A total of 33 patients were recruited into the study and underwent endovascular treatment for obliteration of their aneurysms. A standardized survey was administered before and 3 to 6 months after the procedure, documenting the HIT-6 scores as well as the headache frequency.

Results:
The study cohort included 25 women and 8 men. In 61% of cases, the aneurysms were located in the posterior circulation. We achieved grade 0 or 1 obliteration of aneurysms in 100% of cases and there were no complications. The mean for HIT-6 scores were 52.3 at baseline and 49.6 postprocedure (student t test, P<0.047). The headache frequency measured as total headache days per month did not demonstrate statistical significance. Our data indicated that more than half of our cohort had preexisting headaches which fulfilled the criteria for a primary headache disorder. These individuals showed a more robust response to the intervention compared with the remainder of the group, although the P-value per se was not considered statistically significant due to the small sample size.

Conclusions:
Endovascular treatment of the aneurysms mitigates the headache-related disability.
Sustaining Teamwork Behaviors Through Reinforcement of TeamSTEPPS Principles
Authors: Lee Soo-Hoon , Khanuja Harpal S. , Blanding Renee J. , Sedgwick Jeanne , Pressimone Kathleen , Ficke James R. , Jones Lynne C. 
Published: October 2017

Background
Teamwork training improves short-term teamwork behaviors. However, improvements are often not sustained.

Question/Purpose
The purpose of this study was to explore the extent to which teamwork reinforcement activities for orthopedic surgery teams lead to sustained teamwork behaviors.

Methods
Seven months after 104 staff from an orthopedic surgical unit were trained in Team Strategies and Tools to Enhance Performance and Patient Safety principles, 4 reinforcement activities were implemented regarding leadership and communication: lectures with videos on leadership skills for nursing staff; an online self-paced learning program on communication skills for nursing staff; a 1-page summary on leadership skills e-mailed to surgical staff; and a 1-hour perioperative grand rounds on Team Strategies and Tools to Enhance Performance and Patient Safety principles for anesthesia staff and new staff. Twenty-four orthopedic surgical teams were evaluated on teamwork behaviors during surgery by 2 observers before and after the reinforcement period using the Observational Teamwork Assessment for Surgery tool.

Results
After reinforcement, leadership (P = 0.022) and communication (P = 0.044) behaviors improved compared with prereinforcement levels. Specifically, nursing staff improved in leadership (P = 0.016) and communication (P = 0.028) behaviors, surgical staff improved in leadership behaviors (P = 0.009), but anesthesia staff did not improve in any teamwork behaviors.

Conclusions
Sustained improvement in teamwork behaviors requires reinforcement.

Level of Evidence
Level III, prospective pre-post cohort study.
Learning From Morbidity and Mortality Conferences: Focus and Sustainability of Lessons for Patient Care
Authors: de Vos Marit S. , Hamming Jaap F. , Marang-van de Mheen Perla J. 
Published: October 2017

Objective
It remains unclear to what extent the morbidity and mortality conference (M&M) meets the objective of improving quality and safety of patient care. It has been suggested that M&M may be too focused on individual performance, hampering system-level improvement. The aim of this study was to assess focus and sustainability of lessons for patient care that were derived from M&M.

Methods
This is an observational study of routinely collected data on evaluated complications and identified lessons at surgical M&M for 8 years, assessing type and recurrence of lessons and cases from which these were drawn. Semistructured interviews with clinicians were qualitatively analyzed to explore factors contributing to lesson focus and recurrence.

Results
Three hundred eighteen lessons were drawn from 10,883 evaluated complications, primarily for those that were more severe, related to surgical or other treatment, and occurring in nonemergent, lower risk cases (all P < 0.001). Most lessons targeted intraoperative (43%) rather than preoperative or postoperative care as well as specifically technical (87%) and individual-level issues (74%). There were 43 recurring lessons (14%), mostly about postoperative care (47%) and medication management (50%). Interviewed clinicians attributed the intraoperative, technical focus primarily to greater appeal and control but identified an array of factors contributing to lesson recurrence, such as typical staff turnover in teaching hospitals.

Conclusions
This study provided empirical evidence that learning at M&M has a tendency to focus on intraoperative, technical performance, with challenges to sustain lessons for more system-level issues. Morbidity and mortality conference formats need to anticipate these tendencies to ensure a wide focus for learning with lasting and wide impact.
The Effects of Oxygen and Treatments in Hypoxic Conditions in SH-SY5Y Cells
Authors: Cho Young-Duck , Choi Sung-Hyuk , Yoon Young-Hoon , Kim Jung-Youn , Park Sung-Jun , Lim Chae-Seung 
Published: October 2017

ABSTRACTMany patients are admitted to the emergency department due to trauma. Patients with massive hemorrhage and respiratory failure can fall into hypovolemic shock. Thereafter, oxygen is an essential part of the treatment of trauma patients, but the mechanisms of its effects in the management of trauma patients remain unknown. Therefore, we conducted an experiment to apply hypoxia, hyperoxia, and other treatment with the goal of decreasing hypoxic neuronal cells damage, as reflected by cell survival, apoptosis, hydrogen peroxide (H2O2) production, and hypoxia-inducible factor 1α (HIF) expression in SH-SY5Y cells. Under hypoxic insults, cell survival percentages decreased and apoptosis was seen with increased necrotic cell death. High-pressure oxygen (80% O2) had no effect compared with normal-pressure oxygen (20% O2). After exposure to hypoxia, H2O2production and levels of HIF significantly increased compared with normoxia. However, when pentoxifylline (PTX), steroid, and hypertonic saline (HTS) were added after exposure to hypoxic conditions, the production of H2O2and HIF levels significantly decreased in the groups treated with PTX and HTS. That is, the neuroprotective effect of PTX and HTS alleviated the impacts of hypoxic insulted on neuronal cells.
Whole Genomes Define Concordance of Matched Primary, Xenograft, and Organoid Models of Pancreas Cancer
Authors: Gendoo Deena M.A. , Denroche Robert E. , Zhang Amy , Radulovich Nikolina , Jang Gun Ho , Lemire Mathieu , Fischer Sandra , Chadwick Dianne , Lungu Ilinca M. , Ibrahimov Emin , Cao Ping-Jiang , Stein Lincoln D. , Wilson Julie M. , Bartlett John M.S. , Tsao Ming-Sound , Dhani Neesha , Hedley David , Gallinger Steven , Haibe-Kains Benjamin 
Published: October 2017

ABSTRACTPancreatic ductal adenocarcinoma (PDAC) has the worst prognosis among solid malignancies and improved therapeutic strategies are needed to improve outcomes. Patient-derived xenografts (PDX) and patient-derived organoids (PDO) serve as promising tools to identify new drugs with therapeutic potential in PDAC. For these preclinical disease models to be effective, they should both recapitulate the molecular heterogeneity of PDAC and validate patient-specific therapeutic sensitivities. To date however, deep characterization of PDAC PDX and PDO models and comparison with matched human tumour remains largely unaddressed at the whole genome level. We conducted a comprehensive assessment of the genetic landscape of 16 whole-genome pairs of tumours and matched PDX, from primary PDAC and liver metastasis, including a unique cohort of 5 ‘trios’ of matched primary tumour, PDX, and PDO. We developed a new pipeline to score concordance between PDAC models and their paired human tumours for genomic events, including mutations, structural variations, and copy number variations. Comparison of genomic events in the tumours and matched disease models displayed single-gene concordance across major PDAC driver genes, and genome-wide similarities of copy number changes. Genome-wide and chromosome-centric analysis of structural variation (SV) events revealed high variability across tumours and disease models, but also highlighted previously unrecognized concordance across chromosomes that demonstrate clustered SV events. Our approach and results demonstrate that PDX and PDO recapitulate PDAC tumourigenesis with respect to simple somatic mutations and copy number changes, and capture major SV events that are found in both resected and metastatic tumours.
Antiferromagnetic switch in serum
Authors: Raja Sufi O. , Chatterjee Sanjay , Dasgupta Anjan Kr. 
Published: October 2017

1.AbstractFerritin contains naturally occurring iron oxide nanoparticle surrounded by a structured spherical array of peptide residues that provides tremendous stability to this iron storage protein. We use synthetic citrate coated Super Paramagnetic Iron Oxide Nanoparticles (SPIONs) and static magnetic field in exploring the Ferritin induced magnetic environment of human serum samples with varying ferritin level collected from thalassemic patients. We report anti-ferromagnetic properties of serum in patients with iron overloading. Magnetic pulling by an external magnetic field showed a cusp-like behavior with increasing concentration of serum Ferritin measured by standard ELISA based kit. A reduction in the extent of pulling after a threshold concentration of Ferritin (1500 ng/ml) suggests a Ferritin dependent magnetic switching.Negative magnetization (anti-ferromagnetization) was confirmed by Vibrating Sample Magnetometric (VSM) analysis of SPION-serum mixture containing very high level of Ferritin. Such magnetic switching may have a possible role in iron homeostasis during overloading of Ferritin.3.AbbreviationsSPIONs: Super Paramagnetic Iron Oxide Nanoparticles, VSM: Vibrating Sample Magnetometry, SQUID: Super conducting Quantum Interference Device, PCS: Photon Correlation Spectroscopy
Linked-read analysis identifies mutations in single cell DNA sequencing data
Authors: Bohrson Craig L. , Barton Allison R. , Lodato Michael A. , Rodin Rachel E. , Viswanadham Vinay , Gulhan Doga , Cortes Isidro , Sherman Maxwell A. , Luquette Lovelace J. , Kwon Minseok , Coulter Michael E. , Walsh Christopher A. , Park Peter J. 
Published: October 2017

AbstractWhole-genome sequencing of DNA from single cells has the potential to reshape our understanding of the mutational heterogeneity in normal and disease tissues. A major difficulty, however, is distinguishing artifactual mutations that arise from DNA isolation and amplification from true mutations. Here, we describelinked-readanalysis (LiRA), a method that utilizes phasing of somatic single nucleotide variants with nearby germline variants to identify true mutations, thereby allowing accurate estimation of somatic mutation rates at the single cell level.
Single-molecule tracking in liveYersinia enterocoliticareveals distinct cytosolic complexes of injectisome subunits
Authors: Rocha Julian , Richardson Charles , Zhang Mingxing , Darch Caroline , Cai Eugene , Diepold Andreas , Gahlmann Andreas 
Published: October 2017

AbstractIn bacterial type 3 secretion, substrate proteins are actively transported from the bacterial cytoplasm into the host cell cytoplasm by a large membrane-embedded machinery called the injectisome. Injectisomes transport secretion substrates in response to specific environmental signals, but the molecular details by which the cytosolic secretion substrates are selected and transported through the type 3 secretion pathway remain unclear. Secretion activity and substrate selectivity are thought to be controlled by a sorting platform consisting of the proteins SctK, SctQ, SctL, and SctN, which together localize to the cytoplasmic side of membrane-embedded injectisomes. However, recent work revealed that sorting platform proteins additionally exhibit substantial cytosolic populations and that SctQ reversibly binds to and dissociates from the cytoplasmic side of membrane-embedded injectisomes. Based on these observations, we hypothesized that dynamic molecular turnover at the injectisome and cytosolic assembly among sorting platform proteins is a critical regulatory component of type 3 secretion. To determine whether sorting platform complexes exist in the cytosol, we measured the diffusive properties of the two central sorting platform proteins, SctQ and SctL, using live cell high-throughput 3D single-molecule tracking microscopy. Single-molecule trajectories, measured in wild-type and mutantYersinia enterocoliticacells, reveal that both SctQ and SctL exist in several distinct diffusive states in the cytosol, indicating that these proteins form stable homo- and hetero-oligomeric complexes in their native environment. Our findings provide the first diffusive state-resolved insights into the dynamic regulatory network that interfaces stationary membrane-embedded injectisomes with the soluble cytosolic components of the type 3 secretion system.
Assessing and characterising the repertoire of constitutive promoter elements in soil metagenomic libraries inEscherichia coli
Authors: Westmann Cauã Antunes , de Fátima Alves Luana , Silva-Rocha Rafael , Guazzaroni María-Eugenia 
Published: October 2017

SUMMARYAlthough functional metagenomics has been widely employed for the discovery of genes relevant to biotechnology and biomedicine, its potential for assessing the diversity of transcriptional regulatory elements of microbial communities has remained poorly explored. Here, we have developed a novel framework for prospecting, characterising and estimating the accessibility of promoter sequences in metagenomic libraries by combining a bi-directional reporter vector, high-throughput fluorescence assays and predictive computational methods. Using the expression profiling of fluorescent clones from two independent libraries from soil samples, we directly analysed the regulatory dynamics of novel promoter elements, addressing the relationship between the “metaconstitutome” of a bacterial community and its environmental context. Through the construction and screening of plasmid-based metagenomic libraries followed byin silicoanalyses, we were able to provide both (i) a consensus exogenous promoter elements recognizable byEscherichia coliand (ii) an estimation of the accessible promoter sequences in a metagenomic library, which was close to 1% of the whole set of available promoters. The results presented here should provide new directions for the exploration through functional metagenomics of novel regulatory sequences in bacteria, which could expand the Synthetic Biology toolbox for novel biotechnological and biomedical applications.
Mmp10 is required for post-translational methylation of arginine at the active site of methyl-coenzyme M reductase
Authors: Lyu Zhe , Chou Chau-wen , Shi Hao , Patel Ricky , Duin Evert C. , Whitman William B. 
Published: October 2017

AbstractCatalyzing the key step for anaerobic methane production and oxidation, methyl-coenzyme M reductase or Mcr plays a key role in the global methane cycle. The McrA subunit possesses up to five post-translational modifications (PTM) at its active site. Bioinformatic analyses had previously suggested that methanogenesis marker protein 10 (Mmp10) could play an important role in methanogenesis. To examine its role, MMP1554, the gene encoding Mmp10 inMethanococcus maripaludis, was deleted with a new genetic tool, resulting in the specific loss of the 5-(S)-methylarginine PTM of residue 275 in the McrA subunit and a 40~60 % reduction in the maximal rates of methane formation by whole cells. Methylation was restored by complementations with the wild-type gene. However, the rates of methane formation of the complemented strains were not always restored to the wild type level. This study demonstrates the importance of Mmp10 and the methyl-Arg PTM on Mcr activity.
Spatial Theta Cells in Competitive Burst Synchronization Networks: Reference Frames from Phase Codes
Authors: Monaco Joseph D. , Blair Hugh T. , Zhang Kechen 
Published: October 2017

AbstractSpatial cells of the hippocampal formation are embedded in networks of theta cells. The septal theta rhythm (6–10 Hz) organizes the spatial activity of place and grid cells in time, but it remains unclear how spatial reference points organize the temporal activity of theta cells in space. We study spatial theta cells in simulations and single-unit recordings from exploring rats to ask whether temporal phase codes may anchor spatial representations to the outside world. We theorize that an experience-independent mechanism for temporal coding may combine with burst synchronization to continuously calibrate self-motion to allocentric reference frames. Subcortical recordings revealed spatial theta cells with strong rate-phase correlations related to distinct theta phases. Simulations of bursting neurons and networks explained that relationship and, with competitive learning, demonstrated flexible spatial synchronization patterns when driven by low-dimensional spatial components from the recording data. Thus temporal coding synchrony may reconcile extrinsic and intrinsic neural codes.
Whole-genome sequencing of Nicotiana glauca
Authors: Khafizova Galina , Dobrynin Pavel , Polev Dmitrii , Matveeva Tatyana 
Published: October 2017

AbstractBackgroundNicotiana glauca (tree tobacco) is a member of the Solanaceae family, which includes important crops (potato, tomato, eggplant, pepper) and many medicinal plants. This diploid plant is native to South America and is one of the first Nicotiana species with Agrobacterium cellular T-DNA (cT-DNA). Its cT-DNA is a partial, inverted repeat, called gT. Tree tobacco belongs to the section Noctiflorae. Sequencing of the genomes of N. tomentosiformis and N. otophora (section Tomentosae) and N. tabacum (section Nicotiana) allowed the detection of previously unknown multiple cT-DNAs, raising the question whether there are other T-DNA insertions in the N. glauca. NGS data can help answer this question. Besides, N. glauca contains a profile of alkaloids different from N. tabacum. The plant is used for medicinal purposes. Comparative analysis of genomic data of phylogenetically distant tobacco species will provide valuable information on the genetic basis for various traits, especially secondary metabolism.FindingsWe report a high-depth sequencing and de novo assembly of N. glauca full genome, which was obtained from 210 Gb Illumina HiSeq data. The final draft genome is 3.2 Gb, with N50 size of 31.1 kbp. T-DNA analysis confirmed the presence of the previously described gT insertion and the absence of other ones.ConclusionWe provide the first comprehensive de novo full genome assembly of three tobacco, and a cT-DNA insertion analysis. These genome data could be used in pharmacological and in phylogenetic studies.