bluuebunny/crossref_metadata_2025_split huggingface dataset:
Applied Rapid Qualitative Analysis to Develop a Contextually Appropriate Intervention and Increase the Likelihood of Uptake
Authors: Lewinski Allison A. , Crowley Matthew J. , Miller Christopher , Bosworth Hayden B. , Jackson George L. , Steinhauser Karen , White-Clark Courtney , McCant Felicia , Zullig Leah L. 
Published: May 2021

Background:
Rapid approaches to collecting and analyzing qualitative interview data can accelerate discovery timelines and intervention development while maintaining scientific rigor. We describe the application of these methods to a program designed to improve care coordination between the Veterans Health Administration (VHA) and community providers.

Methods:
Care coordination between VHA and community providers can be challenging in rural areas. The Telehealth-based Coordination of Non-VHA Care (TECNO Care) intervention was designed to improve care coordination among VHA and community providers. To ensure contextually appropriate implementation of TECNO Care, we conducted preimplementation interviews with veterans, VHA administrators, and VHA and community providers involved in community care. Using both a rapid approach and qualitative analysis, an interviewer and 1–2 note-taker(s) conducted interviews.

Results:
Over 5 months, 18 stakeholders were interviewed and we analyzed these data to identify how best to deliver TECNO Care. Responses relevant to improving care coordination include health system characteristics; target population; metrics and outcomes; challenges with the current system; and core components. Veterans who frequently visit VHA or community providers and are referred for additional services are at risk for poor outcomes and may benefit from additional care coordination. Using these data, we designed TECNO Care to include information on VHA services and processes, assist in the timely completion of referrals, and facilitate record sharing.

Conclusion:
Rapid qualitative analysis can inform near real-time intervention development and ensure relevant content creation while setting the stage for stakeholder buy-in. Rigorous and timely analyses support the delivery of contextually appropriate, efficient, high-value patient care.
Modified Reduced Field-of-View Diffusion-Weighted Magnetic Resonance Imaging of the Prostate: Comparison With Reduced Field-of-View Imaging and Single Shot Echo-Planar Imaging
Authors: Lee Eun Ji , Hwang Jiyoung , Chang Yun-Woo , Hong Seong Sook , Oh Eunsun , Nam Bo Da , Sung Jae Kon , Thomas Benkert 
Published: May 2021

Objective
The objective of this study was to compare the image quality and apparent diffusion coefficient (ADC) of diffusion-weighted imaging (DWI) with modified reduced field of view (FOV) based on 2-dimensional (2D)-selective radiofrequency excitations by tilting the excitation plane in prostate with reduced FOV using parallel-transmit-accelerated 2D-selective radiofrequency excitation and single-shot echo planar imaging (ssEPI).

Methods
Fifty patients who underwent multiparametric magnetic resonance imaging including 3 DWIs were included. Two observers independently performed qualitative image analyses using 5-point scale. Apparent diffusion coefficient measurements were performed for quantitative analysis.

Results
Modified reduced FOV provided the highest qualitative scores for all categories compared with reduced FOV and ssEPI (P < 0.000). Both reduced FOV DWIs showed higher ADC values compared with ssEPI (P < 0.001); however, the ADC ratios between the lesion and peripheral zone were not significantly different (all P > 0.05).

Conclusions
The modified reduced FOV DWI showed better overall image quality, differentiability of anatomic regions, and lesion conspicuity with fewer artifacts compared with DWI with reduced FOV and ssEPI.
Initial Experience With Diffusion-Weighted Magnetic Resonance Imaging for the Evaluation of Endometrial Fibrosis
Authors: Feng Yongjing , Jiang Peipei , Hu Qing , Sun Shuangshuang , He Jian , Chen Weibo , Zhou Nan , Hu Yali , Zhou Zhengyang 
Published: May 2021

Objective
This study aimed to determine the feasibility of diffusion-weighted imaging for detecting endometrial fibrosis in patients with intrauterine injury.

Methods
This prospective study included 34 patients with endometrial fibrosis and 34 healthy controls. All participants underwent T2-weighted and diffusion-weighted magnetic resonance imaging with b values of 0 and 1000 s/mm2 during the periovulatory phase with a dominant follicle. The endometrial apparent diffusion coefficient (ADC) and uterine anatomical parameters (endometrial thickness [EMT], length of the uterine cavity [LUC], and junctional zone thickness [JZT]) were measured and compared. Performance of the uterine endometrial ADC and anatomical parameters in diagnosing endometrial fibrosis was evaluated.

Results
Patients with endometrial fibrosis showed a lower endometrial ADC, lower EMT, shorter LUC, and higher JZT than did healthy controls (all, P < 0.001). Endometrial ADC value and uterine anatomical parameters showed good performance in diagnosing endometrial fibrosis, with the areas under the receiver operating characteristic curves of 0.976, 0.870, 0.883, and 0.864, respectively. The area under the curve of ADC was significantly higher than those of EMT (z = 1.973, P = 0.0485), LUC (z = 2.059, P = 0.0395), and JZT (z = 2.484, P = 0.0130). Intraobserver and interobserver agreements of endometrial ADC value measurements were excellent for both patients (intraclass correlation coefficient = 0.987 and 0.983, respectively) and healthy women (intraclass correlation coefficient = 0.986 and 0.989, respectively).

Conclusions
Our preliminary results suggest that diffusion-weighted imaging has the potential to be a noninvasive imaging tool for the quantitative assessment of endometrial fibrosis.
Supratentorial Extraventricular Ependymomas: Imaging Features and the Added Value of Apparent Diffusion Coefficient
Authors: Wang Xiaoshuang , Han Fang , Lv Yi , Gao Jiahao , Du Zunguo , Zhang Jiawen 
Published: May 2021

Objective
To improve the understanding and the diagnosis of intracranial ependymal tumors.

Methods
The clinical, radiological and prognostic features of 48 supratentorial extraventricular ependymomas and 74 intraventricular ependymomas were summarized and compared.

Results
Supratentorial extraventricular ependymomas, most often located in the frontal lobe (33.3%) and classified as grade III (75.0%), had relatively large eccentric cysts (3.07 ± 2.03 cm), significant enhancement (84.8%), low apparent diffusion coefficient (ADC) values, and associated with higher mortality (41.3%). The majority of intraventricular lesions occurred in the fourth ventricle (86.5%) and classified as grade II (78.4%), had relatively small and multiple cystic changes (1.04 ± 0.87 cm), slight or moderate enhancement (76.9%), high ADC values and associated with lower mortality (20.7%). There were few significant differences between grade II and grade III tumors in these 2 groups, respectively. Young age, high grade and low ADC values are worse prognostic indicators for patients with supratentorial extraventricular ependymomas, but not for those with intraventricular ependymomas.

Conclusions
Conventional radiological features, combined with clinical manifestations and quantitative information provided by diffusion-weighted imaging, may not only enhance the diagnosis and assist in determining prognosis but also provide a better pathophysiological understanding of intracranial ependymal tumors.
MRI Changes of the Symphysis Pubis in Patients With Axial Spondyloarthritis and Association With Clinical Factors
Authors: Yan Junrong , Qiao Pengyan , Meng Jingwen , Qian Lixia 
Published: May 2021

Objective
This study aimed to evaluate the magnetic resonance imaging (MRI) changes of the symphysis pubis in patients with axial spondyloarthritis (ax-SpA) and to assess its association with clinical factors.

Methods
A retrospective analysis of 172 patients with ax-SpA was performed to assess the presence of active inflammatory and structural changes of the symphysis pubis on MRI scans, and their association with clinical factors and the SPARCC (Spondyloarthritis Research Consortium of Canada) scoring of the sacroiliac joint were evaluated.

Results
The proportions of active inflammation and structural changes of the symphysis pubis were 69/172 (40.1%) and 54/172 (31.4%), respectively. When comparing the active inflammation and no-active inflammation symphysis pubis groups, the former had higher level C-reactive protein, higher erythrocyte sedimentation rate, and younger median age of patients. Moreover, no significant correlation was noted between the active inflammation of the symphysis pubis and SPARCC score of the sacroiliac joint. When comparing the normal and abnormal symphysis pubis groups, the latter had longer symptom duration.

Conclusions
The MRI changes of the symphysis pubis were seen in 55.2% of the patients with ax-SpA and were associated with C-reactive protein, erythrocyte sedimentation rate, and symptom duration.
Dual-Energy Computed Tomography Virtual Noncalcium Technique in Diagnosing Osteoporosis: Correlation With Quantitative Computed Tomography
Authors: Liu Zhenghua , Zhang Yuting , Liu Zhou , Kong Jiangtao , Huang Dageng , Zhang Xiaoyue , Jiang Yonghong 
Published: May 2021

Objective
The aim of this study was to evaluate dual-energy computed tomography (CT) virtual noncalcium (VNCa) technique as a means of quantifying osteoporosis.

Methods
Dual-energy CT scans were obtained prospectively, targeting lumbar regions of 55 patients with chronic low back pain. A standard quantitative CT (QCT) phantom was positioned at the waist during each procedure, using proprietary software (QCT Pro; Mindways, Tex) to measure bone mineral density (BMD) in each vertebral body. Vendor dual-energy analytic software was altered with a specially modified configuration file to produce a “Virtual Non Calcium” or “VNCa” output, as such output variables were remapped to produce the following calcium values rather than iodine, yielding the following QCT parameters: CT value of calcium (originally “contrast media” [CM]), CT value of mixed energy imaging (regular CT value [rCT]), calcium density (originally “contrast agent density” [CaD]), and fat fraction (FF). Pearson test served to assess correlations between BMD and these parameters. Multiple linear regression analysis was applied to construct an equation for generating regressive BMD (rBMD) values. In gauging diagnostic accuracies, the criterion-standard BMD cutoff point (<80 mg/cm3) was adopted for QCT, whereas the rBMD threshold was defined by receiver operating characteristic curve.

Results
Contrast media, rCT, CaD, and FF values (reflecting CT value of calcium, regular CT value, calcium density, and fat fraction, respectively) significantly correlated with BMD (r values: 0.885, 0.947, 0.877, and 0.492, respectively; all P < 0.01). Contrast media, CaD, and FF showed independent associations with BMD; the regressive equation was formulated as follows: rBMD = 54.82 − 0.19 × CM + 20.03 × CaD − 1.24 × FF. The area under the curve of rBMD in diagnosing osteoporosis was 0.966 ± 0.009 (P < 0.01). At an rBMD threshold of less than 81.94 mg/cm3, sensitivity and specificity were 90.0% and 92.0%, respectively.

Conclusions
Dual-energy CT VNCa technique may constitute a valid alternative method for quantifying the mineral content and marrow fat composition of bone in diagnostic assessments of osteoporosis.
Determination of Cervical Lymph Nodes Metastasis and Extra Nodal Extension Status by Quantitative Assessment of Border Irregularity and Apparent Diffusion Coefficient in Patients With Tongue Squamous Cell Carcinoma
Authors: Yang Gongxin , Rao Min , Ren Jiliang , Yang Xing , Wang Jingbo , Wu Yingwei , Tao Xiaofeng 
Published: May 2021

Objective
The objective of this study was to determine the diagnostic value of quantitative border irregularity assessment and apparent diffusion coefficient (ADC) in patients with squamous cell carcinoma of the tongue (SCCT).

Methods
Cervical lymph nodes (n = 192) from 63 patients with SCCT were examined preoperatively by magnetic resonance imaging, including routine head and neck sequences, dynamic contrast-enhanced magnetic resonance imaging, diffusion-weighted imaging, ADC, surface regularity (S
R), and visually assessed variables, and evaluated pathologically after surgery.

Results
Necrosis, lymphatic hilum, unclear margin, higher S
R, long to short axis ratio, and ADC were associated with metastasis in cervical lymph nodes (M-cLNs) and extranodal extension (ENE), and thickened nodal rim with ENE alone. Apparent diffusion coefficient, S
R, unclear margin, and visible necrosis were strongly associated with M-cLN, whereas S
R, unclear margin, and visible necrosis were associated with ENE status on logistic regression analysis.

Conclusions
Quantitative S
R and ADC data greatly improved diagnosis of M-cLNs and ENE, relative to visible variables alone in patients with SCCT.
Ruga mechanics of soft-orifice closure under external pressure
Authors: Jin Hanxun , Landauer Alexander K. , Kim Kyung-Suk 
Published: May 2021

Here, we report the closure resistance of a soft-material bilayer orifice increases against external pressure, along with ruga-phase evolution, in contrast to the conventional predictions of the matrix-free cylindrical-shell buckling pressure. Experiments demonstrate that the generic soft-material orifice creases in a threefold symmetry at a
limit-load
pressure of
p
/
μ
≈ 1.20, where
μ
is the shear modulus. Once the creasing initiates, the triple crease wings gradually grow as the pressure increases until the orifice completely closes at
p
/
μ
≈ 3.0. By contrast, a stiff-surface bilayer orifice initially wrinkles with a multifold symmetry mode and subsequently develops ruga-phase evolution, progressively reducing the orifice cross-sectional area as pressure increases. The buckling-initiation mode is determined by the layer's thickness and stiffness, and the pressure by two types of the layer's instability modes—the surface-layer-wrinkling mode for a compliant and the ring-buckling mode for a stiff layer. The ring-buckling mode tends to set the twofold symmetry for the entire post-buckling closure process, while the high-frequency surface-layer-wrinkling mode evolves with successive symmetry breaking to a final closure configuration of two- or threefold symmetry. Finally, we found that the threefold symmetry mode for the entire closure process provides the orifice's strongest closure resistance, and human saphenous veins remarkably follow this threefold symmetry ruga evolution pathway.
Homebrew reagents for low cost RT-LAMP
Authors: Matute Tamara , Nuñez Isaac , Rivera Maira , Reyes Javiera , Blázquez-Sánchez Paula , Arce Aníbal , Brown Alexander J. , Gandini Chiara , Molloy Jennifer , Ramirez-Sarmiento César A. , Federici Fernán 
Published: May 2021

ABSTRACTRT-LAMP (reverse transcription - Loop-mediated isothermal amplification) has gained popularity for the detection of SARS-CoV-2. The high specificity, sensitivity, simple protocols and potential to deliver results without the use of expensive equipment has made it an attractive alternative to RT-PCR. However, the high cost per reaction, the centralized manufacturing of required reagents and their distribution under cold chain shipping limits RT-LAMP’s applicability in low-income settings. The preparation of assays using homebrew enzymes and buffers has emerged worldwide as a response to these limitations and potential shortages. Here, we describe the production of Moloney murine leukemia virus (M-MLV) Reverse Transcriptase and BstLF DNA polymerase for the local implementation of RT-LAMP reactions at low cost. These reagents compared favorably to commercial kits and optimum concentrations were defined in order to reduce time to threshold, increase ON/OFF range and minimize enzyme quantities per reaction. As a validation, we tested the performance of these reagents in the detection of SARS-CoV-2 from RNA extracted from clinical nasopharyngeal samples, obtaining high agreement between RT-LAMP and RT-PCR clinical results. The in-house preparation of these reactions results in an order of magnitude reduction in costs, and thus we provide protocols and DNA to enable the replication of these tests at other locations. These results contribute to the global effort of developing open and low cost diagnostics that enable technological autonomy and distributed capacities in viral surveillance.
No safe level of alcohol consumption for brain health: observational cohort study of 25,378 UK Biobank participants
Authors: Topiwala Anya , Ebmeier Klaus P. , Maullin-Sapey Thomas , Nichols Thomas E. 
Published: May 2021

AbstractObjectivesTo estimate the relationship between moderate alcohol consumption and brain health, determining the threshold intake for harm and identifying whether population subgroups are at differential risk.DesignObservational cohort study. Alcohol consumption was determined at baseline assessment visit using touchscreen questionnaire (2016-10). Multi-modal MRI brain and cognitive testing were performed subsequently (2014-20). Clinical data was extracted from linked Hospital Episode Statistics.SettingUK Biobank study. Brain imaging was performed on identical scanners with identical protocols at three UK centres (2014-20).Participants25,378 participants (mean age 54.9±7.4 years).Main outcome measuresBrain health as defined by structural and functional MRI brain measures.ResultsAlcohol consumption was negatively linearly associated with global brain grey matter volume (beta= -0.1, 95%CI= -0.11 to -0.09, p<2×10−16). The association with alcohol was stronger than other modifiable factor tested and robust to unobserved confounding. Widespread negative associations were observed with white matter microstructure (beta= -0.08, 95%CI= -0.09 to -0.06, p<2×10−16) and positive correlations with functional connectivity. Higher blood pressure and body mass index increased risk of alcohol-related harm (SBP*alcohol: beta= - 0.01, 95%CI = -0.02 to -0.004, p=0.005; BMI*alcohol: beta= -0.01, 95%CI = -0.02 to -0.002, p=0.02). Binging on alcohol had additive negative effects on brain structure on top of the absolute volume consumed (daily compared to never binging: beta= -0.19, 95%CI= -0.30 to -0.08, p<0.01). No evidence was found for differential effects of drinking wine, beer or spirits.ConclusionsNo safe dose of alcohol for the brain was found. Moderate consumption is associated with more widespread adverse effects on the brain than previously recognised. Individuals who binge drink or with high blood pressure and BMI may be more susceptible. Detrimental effects of drinking appear to be greater than other modifiable factors. Current ‘low risk’ drinking guidelines should be revisited to take account of brain effects.FundingAT is supported by a Wellcome Trust fellowship (216462/Z/19/Z). KPE is supported by the UK Medical Research Council (G1001354) and the European Commission (Horizon 2020 732592). This work was also supported by the Li Ka Shing Centre for Health Information and Discovery and NIH grant (TMS, TN: R01EB026859) and a Wellcome Trust award (TN: 100309/Z/12/Z).
A widely distributed genus of soil Acidobacteria genomically enriched in biosynthetic gene clusters
Authors: Crits-Christoph Alexander , Diamond Spencer , Al-Shayeb Basem , Valentin-Alvarado Luis , Banfield Jillian F. 
Published: May 2021

AbstractBacteria of the phylum Acidobacteria are one of the most abundant bacterial across soil ecosystems, yet they are represented by comparatively few sequenced genomes, leaving gaps in our understanding of their metabolic diversity. Recently, genomes of Acidobacteria species with unusually large repertoires of biosynthetic gene clusters (BGCs) were reconstructed from grassland soil metagenomes, but the degree to which these species are widespread is still unknown. To investigate this, we augmented a dataset of publicly available Acidobacteria genomes with 46 metagenome-assembled genomes recovered from permanently saturated organic-rich soils of a vernal (spring) pool ecosystem in Northern California. We recovered high quality genomes for three novel species from Candidatus Angelobacter (a proposed subdivision 1 Acidobacterial genus), a genus that is genomically enriched in genes for specialized metabolite biosynthesis. Acidobacteria were particularly abundant in the vernal pool sediments, and a Ca. Angelobacter species was the most abundant bacterial species detected in some samples. We identified numerous diverse biosynthetic gene clusters in these genomes, and also in additional genomes from other publicly available soil metagenomes for other related Ca. Angelobacter species. Metabolic analysis indicates that Ca. Angelobacter likely are aerobes that ferment organic carbon, with potential to contribute to carbon compound turnover in soils. Using metatranscriptomics, we identified in situ expression of specialized metabolic traits for two species from this genus. In conclusion, we expand genomic sampling of the uncultivated Ca. Angelobacter, and show that they represent common and sometimes highly abundant members of dry and saturated soil communities, with a high degree of capacity for synthesis of diverse specialized metabolites.
Retro Drug Design: From Target Properties to Molecular Structures
Authors: Wang Yuhong , Michael Sam , Huang Ruili , Zhao Jinghua , Recabo Katlin , Bougie Danielle , Shu Qiang , Shinn Paul , Sun Hongmao 
Published: May 2021

AbstractTo generate drug molecules of desired properties with computational methods is the holy grail in pharmaceutical research. Here we describe an AI strategy, retro drug design, or RDD, to generate novel small molecule drugs from scratch to meet predefined requirements, including but not limited to biological activity against a drug target, and optimal range of physicochemical and ADMET properties. Traditional predictive models were first trained over experimental data for the target properties, using an atom typing based molecular descriptor system, ATP. Monte Carlo sampling algorithm was then utilized to find the solutions in the ATP space defined by the target properties, and the deep learning model of Seq2Seq was employed to decode molecular structures from the solutions. To test feasibility of the algorithm, we challenged RDD to generate novel drugs that can activate μ opioid receptor (MOR) and penetrate blood brain barrier (BBB). Starting from vectors of random numbers, RDD generated 180,000 chemical structures, of which 78% were chemically valid. About 42,000 (31%) of the valid structures fell into the property space defined by MOR activity and BBB permeability. Out of the 42,000 structures, only 267 chemicals were commercially available, indicating a high extent of novelty of the AI-generated compounds. We purchased and assayed 96 compounds, and 25 of which were found to be MOR agonists. These compounds also have excellent BBB scores. The results presented in this paper illustrate that RDD has potential to revolutionize the current drug discovery process and create novel structures with multiple desired properties, including biological functions and ADMET properties. Availability of an AI-enabled fast track in drug discovery is essential to cope with emergent public health threat, such as pandemic of COVID-19.