bluuebunny/crossref_metadata_2025_split huggingface dataset:
Long-Term Outcomes of Women With Recurrent Vulvovaginal Candidiasis After a Course of Maintenance Antifungal Therapy
Authors: Crouss Tess , Sobel Jack D. , Smith Katharine , Nyirjesy Paul 
Published: June 2018

Objectives
Data about long-term clinical outcome after a course of maintenance fluconazole in those with recurrent vulvovaginal candidiasis (RVVC) is lacking. We aimed to determine the rate of recurrence at a minimum of 6 months after completion of maintenance therapy.

Methods
A retrospective analysis of women with Candida albicans RVVC from January 2008 to January 2017 was performed using chart review to obtain information about recurrence after maintenance therapy. Patients were considered resolved if they had no further episodes of candidiasis, sporadic with less than 3 episodes yearly and ongoing with greater than 3 episodes yearly.

Results
Approximately 1,672 patients with C. albicans vaginal isolates were identified. Of these, 201 met the criteria for RVVC. The mean age was 40.4 years; 151 (77.4%) were white, 133 (66.2%) had comorbid vulvar conditions, and 76 (37.8%) had a risk factor for vulvovaginal candidiasis. One hundred twenty complete charts were further analyzed. The mean length of follow-up after discontinuing maintenance therapy was 39.9 months. After the initial course, 23 (19.2%), 21 (17.5%), and 76 (63.3%) were resolved, sporadic and ongoing, respectively. Risk factors, comorbid vulvar conditions, obesity, menopause status, and length of therapy were not associated with relapse. Age 40 or older was associated with relapse (p = .018). Of the 201 total patients with RVVC, 22 (10.9%) of patients self-reported at least 1 adverse event. The most common was gastrointestinal symptoms (8 [4%]).

Conclusions
Although RVVC can be controlled, relapse is common after an initial course of maintenance fluconazole. Ongoing maintenance remains the most effective treatment option.
Pressure Ulcer Rate in Multidisciplinary Hospital Units After Multifactorial Intervention: A Stepped-Wedge, Cluster Randomized Controlled Trial
Authors: Jafary Mohamadreza , Adibi Hossin , Shayanfard Kamran , Zohdi Mehri , Godarzi Zahra , Yaseri Mehdi , Najafpour Zhila 
Published: June 2018

Objectives
This study was conducted to measure the effectiveness of interventions in decreasing the rates of pressure ulcer in a general hospital setting.

Methods
Sixteen units in a general hospitals in Iran participated in this stepped-wedge, cluster randomized controlled trial during a 45-week study period. This trial has a one-sided crossover design from control to intervention. The units were randomly assigned fulfilling entry criteria. After the approval by the governing board of hospital, the manipulative intervention, in addition to usual care, was implemented on patients with a Braden criterion of 14 or less. The primary outcome was ulcer specification (grade and location of ulcer), and the secondary outcome was the length of hospital stay.

Results
A total of 18,900 patients were admitted during the 45-week study period in the study units, of whom approximately 20% (3846 patients) were identified as high risk according to the items of Braden scale criteria during the admission assessment by nurses. The highest rate of PUs (80%) was in grade 2, and 16% of patients had grade 3 and 4 PUs. The ulcers of the skin overlying the sacrum and hip areas were the most common sites in the patients under study. The rates of PU in the control, training, and intervention phases were 5.49 (4.72–6.34), 5.68 (3.82–8.15), and 4.62 (3.87–5.47), respectively, per 1000 patient-days.

Conclusions
The multifaceted intervention proposed by the present study has succeeded in reducing rate of pressure ulcer. Multifaceted programs based on training are appropriate ways to provide essential information to patients and their caregivers, which result in improvement of their participation in therapeutic process. We recommend hospitals to use these findings as a quality improvement plan for decreasing the rate of pressure ulcer.
Pulmonary Emphysema Quantification on Ultra–Low-Dose Computed Tomography Using Model-Based Iterative Reconstruction With or Without Lung Setting
Authors: Hata Akinori , Yanagawa Masahiro , Kikuchi Noriko , Honda Osamu , Tomiyama Noriyuki 
Published: June 2018

Objectives
To evaluate the influence of model-based iterative reconstruction (MBIR) with lung setting and conventional setting on pulmonary emphysema quantification by ultra–low-dose computed tomography (ULDCT) compared with standard-dose CT (SDCT).

Methods
Forty-five patients who underwent ULDCT (0.18 ± 0.02 mSv) and SDCT (6.66 ± 2.69 mSv) were analyzed in this retrospective study. Images were reconstructed using filtered back projection (FBP) with smooth and sharp kernels and MBIR with conventional and lung settings. Extent of emphysema was evaluated using fully automated software. Correlation between ULDCT and SDCT was assessed by interclass correlation coefficiency (ICC) and Bland-Altman analysis.

Results
Excellent correlation was seen between MBIR with conventional setting on ULDCT and FBP with smooth kernel on SDCT (ICC, 0.97; bias, −0.31%) and between MBIR with lung setting on ULDCT and FBP with sharp kernel on SDCT (ICC, 0.82; bias, −2.10%).

Conclusion
Model-based iterative reconstruction improved the agreement between ULDCT and SDCT on emphysema quantification.
Intrahepatic Splenosis: Incidental Liver Lesion after Splenectomy
Authors: Varghese Jerrin , Bergson Jill , Yaipen Omar 
Published: June 2018

AbstractWe describe the case of a 50-year-old man with history of remote splenectomy who underwent routine lung cancer screening chest computed tomography and was incidentally found to have a liver lesion. Dedicated liver protocol computed tomography demonstrated “archiform” enhancement pattern in the arterial phase and homogenous filling-in enhancement on portal venous and delayed phases. Multiple other smaller enhancing intraperitoneal lesions were also found. These findings along with history of splenectomy confirmed a diagnosis of intrahepatic and intraperitoneal splenosis and helped avoid biopsy. Intrahepatic splenules can be challenging to diagnose owing to its unusual location and similarity in appearance to a liver neoplasm or metastasis. However, careful evaluation of enhancement pattern and review of medical history can lead to an accurate diagnosis and avoidance of invasive biopsy.
Improvement in Liver Transplant Outcomes From Older Donors
Authors: Gao Qimeng , Mulvihill Michael S. , Scheuermann Uwe , Davis Robert P. , Yerxa John , Yerokun Babatunde A. , Hartwig Matthew G. , Sudan Debra L. , Knechtle Stuart J. , Barbas Andrew S. 
Published: June 2018

Objective:
To investigate trends in long-term graft and patient outcomes following liver transplantation using grafts from donors ≥60 years old.

Summary Background Data:
The scarcity of donor livers has led to increased utilization of organs from donors ≥60 years old. However, few studies have examined how long-term transplant outcomes from older donors have evolved over time.

Methods:
The OPTN/UNOS database was queried for all first-time isolated adult liver transplants. We identified 14,796 adult liver transplant using donors ≧60-year-old suitable for analysis from 1990 to 2014. Cohorts were then developed based on 5-year intervals of transplant date. Kaplan–Meier analysis was used to compare graft and patient survival for recipients from older donor across each 5-year era.

Results:
Utilization of donor grafts ≥60 years old increased steadily for the first 15 years of the study, but has leveled off over the last 10 years. Comparison of the earliest and latest eras in the study was notable for an increase in median recipient age (51 vs. 59, P < 0.001) and reduction in median cold ischemic time (10 vs. 6 h, P = 0.001). Unadjusted 5-year graft and patient survival has improved significantly over time (P < 0.0001). More importantly, the discrepancy in survival between older and younger grafts has narrowed substantially over time (P < 0.0001).

Conclusions:
This study demonstrates significant improvement in transplant outcomes with donor grafts ≥60-years old and supports increased but judicious use of extended criteria donors liver grafts. Improved patient selection and reduction in cold ischemia time appear to be contributing factors.
Cryo-EM structure of an amyloid fibril from systemic amyloidosis
Authors: Liberta Falk , Loerch Sarah , Rennegarbe Matthies , Schierhorn Angelika , Westermark Per , Westermark Gunilla T. , Grigorieff Nikolaus , Fändrich Marcus , Schmidt Matthias 
Published: June 2018

AbstractSystemic AA amyloidosis is a worldwide occurring disease of humans and animals that arises from the misfolding of serum amyloid A protein. To provide insights into the molecular basis of this disease we used electron cryo-microscopy and determined the structure of anex vivoamyloid fibril purified from AA amyloidotic mice at 3.0 Å resolution. The fibril consists of C-terminally truncated serum amyloid A protein arranged into a compactly folded all-β conformation. The structure identifies the protein N-terminus as central for the assembly of this fibril and provides a mechanism for its prion-like replication. Our data further explain how amino acid substitutions within the tightly packed fibril core can lead to amyloid resistancein vivo.
Scuphr: A probabilistic framework for cell lineage tree reconstruction
Authors: Koptagel Hazal , Jun Seong-Hwan , Hård Joanna , Lagergren Jens 
Published: June 2018

AbstractCell lineage tree reconstruction methods are developed for various tasks, such as investigating the development, differentiation, and cancer progression. Single-cell sequencing technologies enable more thorough analysis with higher resolution. We present Scuphr, a distance-based cell lineage tree reconstruction method using bulk and single-cell DNA sequencing data from healthy tissues. Common challenges of single-cell DNA sequencing, such as allelic dropouts and amplification errors, are included in Scuphr. Scuphr computes the distance between cell pairs and reconstructs the lineage tree using the neighbor-joining algorithm. With its embarrassingly parallel design, Scuphr can do faster analysis than the state-of-the-art methods while obtaining better accuracy. The method’s robustness is investigated using various synthetic datasets and a biological dataset of 18 cells.Author summaryCell lineage tree reconstruction carries a significant potential for studies of development and medicine. The lineage tree reconstruction task is especially challenging for cells taken from healthy tissue due to the scarcity of mutations. In addition, the single-cell whole-genome sequencing technology introduces artifacts such as amplification errors, allelic dropouts, and sequencing errors. We propose Scuphr, a probabilistic framework to reconstruct cell lineage trees. We designed Scuphr for single-cell DNA sequencing data; it accounts for technological artifacts in its graphical model and uses germline heterozygous sites to improve its accuracy. Scuphr is embarrassingly parallel; the speed of the computational analysis is inversely proportional to the number of available computational nodes. We demonstrated that Scuphr is fast, robust, and more accurate than the state-of-the-art method with the synthetic data experiments. Moreover, in the biological data experiment, we showed Scuphr successfully identifies different clones and further obtains more support on closely related cells within clones.
Multiple Functional Neurosteroid Binding Sites on GABAAReceptors
Authors: Chen Zi-Wei , Bracamontes John R. , Budelier Melissa M. , Germann Allison L. , Shin Daniel J. , Kathiresan Krishnan , Qian Ming-Xing , Manion Brad , Cheng Wayland W. L. , Reichert David E. , Akk Gustav , Covey Douglas F. , Evers Alex S. 
Published: June 2018

AbstractNeurosteroids are endogenous modulators of neuronal excitability and nervous system development and are being developed as anesthetic agents and treatments for psychiatric diseases. While GABAAreceptors are the primary molecular targets of neurosteroid action, the structural details of neurosteroid binding to these proteins remain ill-defined. We synthesized neurosteroid analogue photolabeling reagents in which the photolabeling groups were placed at three positions around the neurosteroid ring structure, enabling identification of binding sites and mapping of neurosteroid orientation within these sites. Using middle-down mass spectrometry, we identified three clusters of photolabeled residues representing three distinct neurosteroid binding sites in the human α1β3GABAAreceptor. Novel intrasubunit binding sites were identified within the transmembrane helical bundles of both the α1and β3subunits, adjacent to the extracellular domains. An intersubunit site in the interface between the β3(+) and α1(-) subunits of the GABAAreceptor pentamer was also identified. Computational docking studies of neurosteroid to the three sites predicted critical residues contributing to neurosteroid interaction with the GABAAreceptors. Electrophysiological studies based on these predictions indicate that both the α1intrasubunit and β3-α1intersubunit sites are critical for neurosteroid action.
Contributions of Low- and High-Frequency Sensorineural Hearing Deficits to Speech Intelligibility in Noise
Authors: Verhulst Sarah , Warzybok Anna 
Published: June 2018

ABSTRACTThe degree to which supra-threshold hearing deficits affect speech recognition in noise is poorly understood. To clarify the role of hearing sensitivity in different stimulus frequency ranges, and to test the contribution of low- and high-pass speech information to broadband speech recognition, we collected speech reception threshold (SRTs) for low-pass (LP < 1.5 kHz), high-pass (HP > 1.6 kHz) and broadband (BB) speech-in-noise stimuli in 34 listeners. Two noise types with similar long-term spectra were considered: stationary (SSN) and temporally modulated noise (ICRA5-250). Irrespective of the tested listener group (i.e., young normal-hearing, older normal- or impaired-hearing), the BB SRT performance was strongly related to the LP SRT. The encoding of LP speech information was different for SSN and ICRA5-250 noise but similar for HP speech, suggesting a single noise-type invariant coding mechanism for HP speech. Masking release was observed for all filtered conditions and related to the ICRA5-250 SRT. Lastly, the role of hearing sensitivity to the SRT was studied using the speech intelligibility index (SII), which failed to predict the SRTs for the filtered speech conditions and for the older normal-hearing listeners. This suggests that supra-threshold hearing deficits are important contributors to the SRT of older normal-hearing listeners.
Reliability of Static and Dynamic Network Metrics in the Resting-State: A MEG-beamformed Connectivity Analysis
Authors: Dimitriadis S. I. , Routley B. , Linden D. , Singh K.D. 
Published: June 2018

AbstractThe resting activity of the brain can be described by so-called intrinsic connectivity networks (ICNs), which consist of spatially and temporally distributed, but functionally connected, nodes. The coordinated activity of the resting state can be explored via magnetoencephalography (MEG) by studying frequency-dependent functional brain networks at the source level. Although many algorithms for the analysis of brain connectivity have been proposed, the reliability of network metrics derived from both static and dynamic functional connectivity is still unknown. This is a particular problem for studies of associations between ICN metrics and personality variables or other traits, and for studies of differences between patient and control groups, which both depend critically on the reliability of the metrics used. A detailed investigation of the reliability of metrics derived from resting-state MEG repeat scans is therefore a prerequisite for the development of connectomic biomarkers.Here, we first estimated both static (SFC) and dynamic functional connectivity (DFC) after beamforming source reconstruction using the imaginary part of the phase locking index (iPLV) and the correlation of the amplitude envelope (CorEnv). Using our approach, functional network microstates (FCμstates) were derived from the DFC and chronnectomics were computed from the evolution of FCμstates across experimental time. In both temporal scales, the reliability of network metrics (SFC), the FCμstates and the related chronnectomics were evaluated for every frequency band.Chronnectomic parameters and FCμstates were generally more reliable than node-wise static network metrics. CorEnv-based network metrics were more reproducible at the static approach. This analysis encourages the analysis of MEG resting-state via DFC.
Differential regional decline in dopamine receptor availability across adulthood: Linear and nonlinear effects of age
Authors: Seaman Kendra L. , Smith Christopher T. , Juarez Eric J. , Dang Linh C. , Castrellon Jaime J. , Burgess Leah L. , Danica San Juan M. , Kundzicz Paul M. , Cowan Ronald L. , Zald David H. , Samanez-Larkin Gregory R. 
Published: June 2018

AbstractTheories of adult brain development, based on neuropsychological test results and structural neuroimaging, suggest differential rates of age-related change in function across cortical and subcortical sub-regions. However, it remains unclear if these trends also extend to the aging dopamine system. Here we examined cross-sectional adult age differences in estimates of D2-like receptor binding potential across several cortical and subcortical brain regions using PET imaging and the radiotracer [18F]fallypride in two samples of healthy human adults (combined N = 132). After accounting for regional differences in overall radioligand binding, estimated percent difference in receptor binding potential by decade (linear effects) were highest in most temporal and frontal cortical regions (∼6–16% per decade), moderate in parahippocampal gyrus, pregenual frontal cortex, fusiform gyrus, caudate, putamen, thalamus, and amygdala (∼3–5%), and weakest in subcallosal frontal cortex, ventral striatum, pallidum, and hippocampus (∼0–2%). Some regions showed linear effects of age while many showed curvilinear effects such that binding potential declined from young adulthood to middle age and then was relatively stable until old age. Overall, these data indicate that the rate and pattern of decline in D2 receptor availability is regionally heterogeneous. However, the differences across regions were challenging to organize within existing theories of brain development and did not show the same pattern of regional change that has been observed in gray matter volume, white matter integrity, or cognitive performance. This variation suggests that existing theories of adult brain development may need to be modified to better account for the spatial dynamics of dopaminergic system aging.
Imputation of Behavioral Candidate Gene Repeat Polymorphisms in 486,551 Publicly-Available UK Biobank Individuals
Authors: Border Richard , Smolen Andrew , Corley Robin P. , Stallings Michael C. , Brown Sandra A. , Conger Rand D. , Derringer Jaime , Donnellan M. Brent , Haberstick Brett C. , Hewitt John K. , Hopfer Christian , Krauter Ken , McQueen Matthew B. , Wall Tamara L. , Keller Matthew C. , Evans Luke M. 
Published: June 2018

AbstractSome of the most widely studied polymorphisms in psychiatric genetics include variable number tandem repeat polymorphisms (VNTRs) in SLC6A3, DRD4, SLC6A4, and MAOA. While initial findings suggested large effects, their importance with respect to psychiatric phenotypes is the subject of much debate with broadly conflicting results. Despite broad interest, these loci remain absent from the largest available samples, such as the UK Biobank, limiting researchers’ ability to test these contentious hypotheses rigorously in large samples. Here, using two independent reference datasets, we report out-of-sample imputation accuracy estimates of >0.96 for all four VNTR polymorphisms and one modifying SNP, depending on the reference and target dataset. We describe the imputation procedures of these candidate polymorphisms in 486,551 UK Biobank individuals, and have made the imputed polymorphism data available to UK Biobank researchers. This resource, provided to the community, will allow the most rigorous tests to-date of the roles of these polymorphisms in behavioral and psychiatric phenotypes.
Fast and Robust Deconvolution of Tumor Infiltrating Lymphocyte from Expression Profiles using Least Trimmed Squares
Authors: Hao Yuning , Yan Ming , Lei Yu L. , Xie Yuying 
Published: June 2018

ABSTRACTGene-expression deconvolution is used to quantify different types of cells in a mixed population. It provides a highly promising solution to rapidly characterize the tumor-infiltrating immune landscape and identify cold cancers. However, a major challenge is that gene-expression data are frequently contaminated by many outliers that decrease the estimation accuracy. Thus, it is imperative to develop a robust deconvolution method that automatically decontaminates data by reliably detecting and removing outliers. We developed a new machine learning tool, Fast And Robust DEconvolution of Expression Profiles (FARDEEP), to enumerate immune cell subsets from whole tumor tissue samples. To reduce noise in the tumor gene expression datasets, FARDEEP utilizes an adaptive least trimmed square to automatically detect and remove outliers before estimating the cell compositions. We show that FARDEEP is less susceptible to outliers and returns a better estimation of coefficients than the existing methods with both numerical simulations and real datasets. FARDEEP provides the absolute quantitation of each immune cell subset in addition to relative percentages. Hence, FARDEEP represents a novel robust algorithm to complement the existing toolkit for the characterization of tissue-infiltrating immune cell landscape. The source code for FARDEEP as implemented in R is available for download at https://goo.gl/SqGKuo.
Microbial coexistence through chemical-mediated interactions
Authors: Niehaus Lori , Boland Ian , Liu Minghao , Chen Kevin , Fu David , Henckel Catherine , Chaung Kaitlin , Miranda Suyen Espinoza , Dyckman Samantha , Crum Matthew , Dedrick Sandra , Shou Wenying , Momeni Babak 
Published: June 2018

AbstractMany microbial functions happen within communities of interacting species. Explaining how species with intrinsically disparate fitness can coexist is important for applications such as manipulating host-associated microbiota or engineering industrial communities. Previous coexistence studies have often neglected interaction mechanisms. Here, we formulate and experimentally constrain a model in which chemical mediators of microbial interactions (e.g. metabolites or waste-products) are explicitly incorporated. We construct many instances of coexistence by simulating community assembly through enrichment and ask how species interactions can explain coexistence. We show that growth-facilitating influences between members are favored in assembled communities. Among negative influences, self-restraint, such as production of self-inhibiting waste, contributes to coexistence, whereas inhibition of other species disrupts coexistence. Coexistence is also favored when interactions are mediated bydepletablechemicals that get consumed or degraded, rather than byreusablechemicals that are unaffected by recipients. Our model creates null predictions for coexistence driven by chemical-mediated interactions.