bluuebunny/crossref_metadata_2025_split huggingface dataset:
Associations Between Race, Perceived Psychological Stress, and the Gut Microbiota in a Sample of Generally Healthy Black and White Women: A Pilot Study on the Role of Race and Perceived Psychological Stress
Authors: Carson Tiffany L. , Wang Fuchenchu , Cui Xiangqin , Jackson Bradford E. , Van Der Pol William J. , Lefkowitz Elliot J. , Morrow Casey , Baskin Monica L. 
Published: June 2018

ABSTRACT

Objective
Racial health disparities persist among black and white women for colorectal cancer. Understanding racial differences in the gut microbiota and related covariates (e.g., stress) may yield new insight into unexplained colorectal cancer disparities.

Methods
Healthy non-Hispanic black or white women (age ≥19 years) provided survey data, anthropometrics, and stool samples. Fecal DNA was collected and isolated from a wipe. Polymerase chain reaction was used to amplify the V4 region of the 16SrRNA gene and 250 bases were sequenced using the MiSeq platform. Microbiome data were analyzed using QIIME. Operational taxonomic unit data were log transformed and normalized. Analyses were conducted using linear models in R Package “limma.”

Results
Fecal samples were analyzed for 80 women (M (SD) age = 39.9 (14.0) years, 47 black, 33 white). Blacks had greater average body mass index (33.3 versus 27.5 kg/m2, p < .01) and waist circumference (98.3 versus 86.6 cm, p = .003) than whites. Whites reported more stressful life events (p = .026) and greater distress (p = .052) than blacks. Final models accounted for these differences. There were no significant differences in dietary variables. Unadjusted comparisons revealed no racial differences in alpha diversity. Racial differences were observed in beta diversity and abundance of top 10 operational taxonomic units. Blacks had higher abundances than whites of Faecalibacterium (p = .034) and Bacteroides (p = .038). Stress was associated with abundances of Bifidobacterium. The association between race and Bacteroides (logFC = 1.72, 0 = 0.020) persisted in fully adjusted models.

Conclusions
Racial differences in the gut microbiota were observed including higher Bacteroides among blacks. Efforts to cultivate an “ideal” gut microbiota may help reduce colorectal cancer risk.
Computed Tomographic Features of Primary Small Cell Neuroendocrine Tumors of the Gallbladder
Authors: Faraoun Sid Ahmed , Guerrache Youcef , Dautry Raphael , Boudiaf Mourad , Dohan Anthony , Barral Matthias , Hoeffel Christine , Rousset Pascal , Fohlen Audrey , Soyer Philippe 
Published: June 2018

Purpose
This study aimed to report the computed tomography (CT) imaging features of primary small cell neuroendocrine tumors of the gallbladder (PSCNETGs).

Materials and Methods
The CT examinations of 9 patients (5 women, 4 men; median age, 57 years) with histopathologically proven PSCNETG were reviewed. Computed tomographic images were analyzed with respect to morphologic features of primary tumors and accompanying lymph nodes.

Results
All PSCNETGs were visible on CT, with a median largest axial diameter of 60 mm (Q1, 30 mm; Q3 mm, 82; range, 25–86 mm). These tumors presented with extraluminal growth (8/9; 89%), heterogeneous enhancement (8/9; 89%), gallbladder replacement greater than 50% (5/9; 56%), hepatic metastases (5/9; 56%), and direct liver involvement by tumor (4/9; 44%). Enlarged lymph nodes were present in all patients (9/9; 100%) with a median largest axial diameter of 39 mm (Q1, 23 mm; Q3, 48 mm; range, 12–62 mm). Vessel encasement by lymph nodes was present in 6 (67%) of 9 patients.

Conclusion
Primary small cell neuroendocrine tumors of the gallbladder predominantly presents as a large, heterogeneous gallbladder mass with extraluminal growth in association with large metastatic lymph nodes and intrahepatic metastases.
Accuracy of Automated Liver Contouring, Fat Fraction, and R2* Measurement on Gradient Multiecho Magnetic Resonance Images
Authors: Stocker Daniel , Bashir Mustafa R. , Kannengiesser Stephan A.R. , Reiner Cäcilia S. 
Published: June 2018

Objective
This study aimed to evaluate the performance of an automated workflow of volumetric liver proton density fat fraction (PDFFvol) and R2* quantification with automated inline liver volume (LV) segmentation.

Methods
Dual-echo and multiecho Dixon magnetic resonance images were evaluated in 74 consecutive patients (group A, PDFF < 10%; B, PDFF ≥ 10%; C, R2* ≥ 100 s−1; D, post-hemihepatectomy). The values of PDFFvol and R2*vol measurements across the LV were generated on multiecho images in an automated fashion based on inline liver segmentation on dual-echo images. Similar measurements were performed manually.

Results
Using the inline algorithm, the mis-segmented LV was highest in group D (80%). There were no significant differences between automated and manual measurements of PDFFvol. Automated R2*vol was significantly lower than manual R2*vol in group A (P = 0.004).

Conclusions
Inline LV segmentation performed well in patients without and with hepatic steatosis. In cases with iron overload and post-hemihepatectomy, extrahepatic areas were erroneously included to a greater extent, with a tendency toward overestimation of PDFFvol.
Phantom Validation of Spectral Detector Computed Tomography–Derived Virtual Monoenergetic, Virtual Noncontrast, and Iodine Quantification Images
Authors: Ananthakrishnan Lakshmi , Duan Xinhui , Rajiah Prabhakar , Soesbe Todd C. , Lewis Matthew A. , Xi Yin , Fielding Julia R. , Lenkinski Robert E. , Leyendecker John R. , Abbara Suhny 
Published: June 2018

Purpose
Spectral detector computed tomography (SDCT) is a new CT technology that uses a dual-layer detector to perform energy separation. We aim to assess 3 clinical concepts using a phantom model: noise profile across the virtual monoenergetic (VME) spectrum, accuracy of iodine quantification, and virtual noncontrast (VNC) reconstructions' ability to remove iodine contribution to attenuation.

Methods
Six vials containing varying concentrations of iodinated contrast (0–6 mg/mL) diluted in water were placed in a water bath and scanned on an SDCT scanner. Virtual monoenergetic (40–200 keV at 10-keV increments), iodine–no-water, and VNC reconstructions were created. Attenuation (in Hounsfield units [HU]), VME noise at each energy level, CT-derived iodine concentration, and VNC attenuation were recorded.

Results
Virtual monoenergetic noise was improved at all energies compared with conventional images (conventional, 9.8–11.2; VME, 7.5–9.5). Noise profile showed a slightly higher image noise at 40 keV, but was otherwise relatively flat across the energy spectrum. On iodine–no-water reconstructions, measured varied from actual iodine concentration by ±0.1 mg/mL (SD, 0.16–0.36). Virtual noncontrast attenuation was within 5 HU of water attenuation at all iodine concentrations.

Conclusion
Reconstructions of SDCT show lower VME image noise, accurate iodine quantification, and VNC attenuation values within 5 HU of expected in a phantom model.
The magic number: Are improved outcomes observed at trauma centers with undertriage rates below 5%?
Authors: Jammula Shreya , Bradburn Eric H. , Gross Brian W. , Cook Alan D. , Reihart Michael J. , Rogers Frederick B. 
Published: June 2018

BACKGROUND
The American College of Surgeons Committee on Trauma (ACSCOT) advises trauma centers maintain <5% undertriage rate (UTR), but provides limited rationale for this figure. We sought to determine whether patients managed at Level I/II trauma centers with a UTR less than 5% had improved outcomes compared with centers with greater than 5% UTR. We hypothesized that similar overall adjusted outcomes would be observed at trauma centers in Pennsylvania regardless of their compliance with ACSCOT undertriage recommendation.

METHODS
The Pennsylvania Trauma Outcome Study database was retrospectively queried for all trauma patients managed at accredited adult Level I/II trauma centers (n = 27) from 2003 to 2015. Patients with missing data on Injury Severity Score and/or Trauma Activation Status were excluded from the analysis. Institutional UTR were calculated for all trauma centers based on ACSCOT criteria (Injury Severity Score >15; no trauma activation) and were categorized into less than 5% or greater than 5% subgroups. A multilevel mixed-effects logistic regression model assessed the adjusted impact of management at centers with less than 5% undertriage. Statistical significance was set at p less than 0.05.

RESULTS
A total of 404,315 patients from 27 trauma centers met inclusion criteria. Institutional UTRs ranged from 0% to 20.5%, with 15 centers exhibiting UTR less than 5% and 12 centers with UTR greater than 5%. No clinically meaningful difference in unadjusted mortality rate was observed between subgroups (<5% UTR: 5.19%; >5% UTR: 5.20%; p < 0.001). In adjusted analysis, no difference in mortality was found for patients managed at centers with less than 5% UTR compared to those with greater than 5% UTR (adjusted odds ratio, 1.06; 95% confidence interval, 0.85–1.33; p = 0.608).

CONCLUSION
Achieving ACSCOT less than 5% undertriage standards appears to have limited impact on institutional mortality. Further research should seek to identify new triage criteria that can be uniformly applied to all trauma centers.

LEVEL OF EVIDENCE
Epidemiological study, level III.
Augmentation Effect of Low-Frequency Repetitive Transcranial Magnetic Stimulation Over Presupplementary Motor Area in Obsessive-Compulsive Disorder
Authors: Arumugham Shyam Sundar , VS Subhasini , HN Madhuri , B Vinay , Ravi Malvika , Sharma Eesha , Thirthalli Jagadisha , Reddy YC Janardhan 
Published: June 2018

ObjectiveThe current study investigated the efficacy of low-frequency repetitive transcranial magnetic stimulation (rTMS) over bilateral presupplementary motor area (pre-SMA) in patients suffering from obsessive-compulsive disorder (OCD) with partial/poor response to pharmacotherapy, in a double-blinded randomized sham controlled trial.MethodForty subjects with OCD, who were on stable medications with partial/poor response to pharmacotherapy were randomly divided into 2 groups (n = 20 in each group), to receive either active or sham low-frequency rTMS over bilateral pre-SMA. Thirty-six patients were eligible for intent-to-treat analysis. There was no significant difference in relevant demographic and clinical variables between the 2 groups at baseline.ResultsThere were no statistically significant differences between the 2 groups after 3 weeks of treatment in the Yale-Brown Obsessive Compulsive Scale score (time*group interaction,F2.48,84.16= 0.80,P= 0.40) and other secondary outcome measures including responder rates and depressive and anxiety symptoms.ConclusionsLow-frequency rTMS over pre-SMA may not be effective as an augmenting agent in partial/poor responders to SRIs. This study underlines the need to explore alternate rTMS protocols in OCD.
Analysis of crotonaldehyde puff-by-puff release in mainstream cigarette smoke under various smoking regimens by high-performance liquid chromatography with the modified QuEChERS method
Authors: Li Chao , Li E'xian , Zhang Jian , Tao Ying , Zhang Chengming , Shen Xiaofeng , Liu Ya , Qin Yunhua 
Published: June 2018

To study puff-by-puff release characteristics of crotonaldehyde in mainstream cigarette smoke under diverse intensive smoking regimens, we designed an RM20H smoking machine with a puff-by-puff smoke collection unit to automatically trap crotonaldehyde in the mainstream cigarette smoke. Using this process, we trapped, puff-by-puff, crotonaldehyde in mainstream smoke generated by different smoking regimens and quantitatively analysed the levels of crotonaldehyde using high-performance liquid chromatography with a modified QuEChERS sample pretreatment method. On the basis of the crotonaldehyde in each puff, we determined crotonaldehyde's puff-by-puff release characteristics. The results showed that crotonaldehyde's puff-by-puff release remained nearly constant for the International Organization for Standardization mode while increased polynomial trend was seen (
n
≥ 6) under the Massachusetts and Health Canada smoking regimens. The equation fit for various regimens was good (
R
2
> 0.9192). Release characteristics by puff were classified into four categories: (1) first, second and third puffs; (2) fourth and fifth puffs; (3) sixth puff; and (4) seventh and eighth puffs.
Nanopore sequencing of Giardia reveals widespread intra-isolate structural variation
Authors: Pollo Stephen M. J. , Reiling Sarah J. , Wit Janneke , Workentine Matthew L. , Guy Rebecca A. , Batoff G. William , Yee Janet , Dixon Brent R. , Wasmuth James D. 
Published: June 2018

AbstractBackgroundGenomes of the parasite Giardia duodenalis are relatively small for eukaryotic genomes, yet there are only six publicly available. Difficulties in assembling the tetraploid G. duodenalis genome from short read sequencing data likely contribute to this lack of genomic information. We sequenced three isolates of G. duodenalis (AWB, BGS, and beaver) on the Oxford Nanopore Technologies MinION whose long reads have the potential to address genomic areas that are problematic for short reads.ResultsUsing a hybrid approach that combines MinION long reads and Illumina short reads to take advantage of the continuity of the long reads and the accuracy of the short reads we generated reference quality genomes for each isolate. The genomes for two of the isolates were evaluated against the available reference genomes for comparison. The third genome for which there is no previous data was then assembled. The long reads were used to find structural variants in each isolate to examine heterozygosity. Consistent with previous findings based on SNPs, Giardia BGS was found to be considerably more heterozygous than the other isolates that are from Assemblage A. We also find an enrichment of variant-specific surface proteins in some of the structural variant regions.ConclusionsOur results show that the MinION can be used to generate reference quality genomes in Giardia and further be used to identify structural variant regions that are an important source of genetic variation not previously examined in these parasites.
The relationship between age, neural differentiation, and memory performance
Authors: Koen Joshua D. , Hauck Nedra , Rugg Michael D. 
Published: June 2018

AbstractHealthy aging is associated with decreased neural selectivity (dedifferentiation) in category-selective cortical regions. This finding has prompted the suggestion that dedifferentiation contributes to age-related cognitive decline. Consistent with this possibility, dedifferentiation has been reported to negatively correlate with fluid intelligence in older adults. Here, we examined whether dedifferentiation is associated with performance in another cognitive domain – episodic memory – that is also highly vulnerable to aging. Given the proposed role of differentiation in age-related cognitive decline, we predicted there would be a stronger link between dedifferentiation and episodic memory performance in older than in younger adults. Young (18-30 yrs) and older (64-75 yrs) male and female humans underwent fMRI scanning while viewing images of objects and scenes prior to a subsequent recognition memory test. We computed a differentiation index in two regions-of-interest (ROIs): parahippocampal place area (PPA) and lateral occipital complex (LOC). This index quantified the selectivity of the BOLD response to an ROI’s preferred versus non-preferred category (scenes for PPA, objects for LOC). The differentiation index in the PPA, but not the LOC, was lower in older than in younger adults. Additionally, the PPA differentiation index predicted recognition memory performance for the studied items. This relationship was independent of and not moderated by age. The PPA differentiation index also predicted performance on a latent ‘fluency’ factor derived from a neuropsychological test battery; this relationship was also age invariant. These findings suggest that two independent factors, one associated with age, and the other with cognitive performance, drive neural differentiation.Significance StatementAging is associated with neural dedifferentiation – reduced neural selectivity in ‘category selective’ cortical brain regions – which has been proposed to mediate cognitive aging. Here, we examined whether neural differentiation is predictive of episodic memory performance, and whether the relationship is moderated by age. A neural differentiation index was estimated for scene-(PPA) and object-(LOC) selective cortical regions while participants studied images for a subsequent memory test. Age related reductions were observed for the PPA, but not the LOC, differentiation index. Importantly, the PPA differentiation index demonstrated age invariant correlations with subsequent memory performance and a fluency factor derived from a neuropsychological battery. Together, these findings suggest that neural differentiation is associated with two independent factors: age and cognitive performance.
Computational investigation of protein surface polarity and pH-dependence: application to antibodies shows that antibody-antigen interfaces tend to be relatively polar
Authors: Hebditch Max , Warwicker Jim 
Published: June 2018

AbstractProtein instability leads to reversible self-association and irreversible aggregation which is a major concern for developing new biopharmaceutical leads. Protein solution behaviour is dictated by the physicochemical properties of the protein and the solution. Optimising protein solutions through experimental screens and targeted protein engineering can be a difficult and time consuming process. Here, we describe development of the protein-sol web server, which was previously restricted to protein solubility prediction from amino acid sequence. Tools are presented for calculating and mapping patches of hydrophobicity and charge on the protein surface. In addition, predictions of folded state stability and net charge are displayed as a heatmap for a range of pH and ionic strength conditions. Tools are evaluated in the context of antibodies, their fragments and interactions. Surprisingly, antibody-antigen interfaces are, on average, at least as polar as Fab surfaces. This benchmarking process provides the user with thresholds with which to assess non-polar surface patches, and possible solubility implications, in proteins of interest. Stability heatmaps compare favourably with experimental data for CH2 and CH3 domains. Display and quantification of surface polarity and pH / ionic strength dependence will be useful generally for investigation of protein biophysics.
Selective inhibition of CA IX over CA XII in breast cancer cells using benzene sulfonamides: Disconnect between CA activity and growth inhibition
Authors: Mboge Mam Y. , Chen Zhijuan , Wolff Alyssa , Mathias John V. , Tu Chingkuang , Brown Kevin D. , Bozdag Murat , Carta Fabrizio , Supuran Claudiu T. , McKenna Robert , Frost Susan C. 
Published: June 2018

AbstractCarbonic anhydrases (CAs) have been linked to tumor progression, particularly membrane-bound CA isoform IX (CA IX). The role of CA IX in the context of breast cancer is to regulate the pH of the tumor microenvironment. In contrast to CA IX, expression of CA XII, specifically in breast cancer, is associated with better outcome despite performing the same catalytic function. In this study, we have structurally modeled the orientation of bound ureido-substituted benzene sulfonamides (USBs) within the active site of CA XII, in comparison to CA IX and cytosolic off-target CA II, to understand isoform specific inhibition. This has identified specific residues within the CA active site, which differ between isoforms that are important for inhibitor binding and isoform specificity. The ability of these sulfonamides to block CA IX activity in breast cancer cells is less effective than their ability to block activity of the recombinant protein (by one to two orders of magnitude depending on the inhibitor). The same is true for CA XII activity but now they are two to three orders of magnitude less effective. Thus, there is significantly greater specificity for CA IX activity over CA XII. While the inhibitors block cell growth, without inducing cell death, this again occurs at two orders of magnitude above the Kivalues for inhibition of CA IX and CA XII activity in their respective cell types. Surprisingly, the USBs inhibited cell growth even in cells where CA IX and CA XII expression was ablated. Despite the potential for these sulfonamides as chemotherapeutic agents, these data suggest that we reconsider the role of CA activity on growth potentiation.
Assembly of chromosome-scale contigs by efficiently resolving repetitive sequences with long reads
Authors: Du Huilong , Liang Chengzhi 
Published: June 2018

AbstractDue to the large number of repetitive sequences in complex eukaryotic genomes, fragmented and incompletely assembled genomes lose value as reference sequences, often due to short contigs that cannot be anchored or mispositioned onto chromosomes. Here we report a novel method Highly Efficient Repeat Assembly (HERA), which includes a new concept called a connection graph as well as algorithms for constructing the graph. HERA resolves repeats at high efficiency with single-molecule sequencing data, and enables the assembly of chromosome-scale contigs by further integrating genome maps and Hi-C data. We tested HERA with the genomes of rice R498, maize B73, human HX1 and Tartary buckwheat Pinku1. HERA can correctly assemble most of the tandemly repetitive sequences in rice using single-molecule sequencing data only. Using the same maize and human sequencing data published by Jiao et al. (2017) and Shi et al. (2016), respectively, we dramatically improved on the sequence contiguity compared with the published assemblies, increasing the contig N50 from 1.3 Mb to 61.2 Mb in maize B73 assembly and from 8.3 Mb to 54.4 Mb in human HX1 assembly with HERA. We provided a high-quality maize reference genome with 96.9% of the gaps filled (only 76 gaps left) and several incorrectly positioned sequences fixed compared with the B73 RefGen_v4 assembly. Comparisons between the HERA assembly of HX1 and the human GRCh38 reference genome showed that many gaps in GRCh38 could be filled, and that GRCh38 contained some potential errors that could be fixed. We assembled the Pinku1 genome into 12 scaffolds with a contig N50 size of 27.85 Mb. HERA serves as a new genome assembly/phasing method to generate high quality sequences for complex genomes and as a curation tool to improve the contiguity and completeness of existing reference genomes, including the correction of assembly errors in repetitive regions.