bluuebunny/crossref_metadata_2025_split huggingface dataset:
Magnetic Resonance Rectal Enema Versus Computed Tomographic Colonography in the Diagnosis of Rectosigmoid Endometriosis
Authors: Biscaldi Ennio , Barra Fabio , Scala Carolina , Stabilini Cesare , Vellone Valerio Gaetano , Ferrero Simone 
Published: June 2020

Objectives
Rectosigmoid involvement by endometriosis causes intestinal symptoms such as constipation, diarrhea, and dyschezia. A precise diagnosis about the presence, location, and extent of bowel implants is required to plan the most appropriate treatment. The aim of the study was to compare the accuracy of magnetic resonance with distension of the rectosigmoid (MR-e) with computed colonography (CTC) for diagnosing rectosigmoid endometriosis.

Methods
This study was based on the retrospective analysis of a prospectively collected database of patients with suspicion of rectosigmoid endometriosis who underwent both MR-e and CTC, and subsequently were treated by laparoscopy. The findings of imaging techniques were compared with surgical and histological results.

Results
Of 90 women included in the study, 44 (48.9%) had rectosigmoid nodules and underwent bowel surgery. Sensitivity, specificity, positive predictive value, negative predictive value, and accuracy for the diagnosis of rectosigmoid endometriosis were 88.6%, 93.5%, 92.9%, 89.6%, and 91.1% for CTC, and 93.2%, 97.9%, 97.6%, 93.8%, and 95.6% for MR-e. There was no significant difference in the accuracy of both radiologic examinations for diagnosing rectosigmoid endometriosis (P = 0.344). However, MR-e was more accurate than CTC in estimating the largest diameter of the main rectosigmoid nodule (P < 0.001). The pain perceived by the patients was significantly lower during MR-e than during CTC (P < 0.001).

Conclusions
MR-e and CTC have similar diagnostic performance for the diagnosis of rectosigmoid involvement of endometriosis. However, MR-e is more accurate in the estimation of the largest diameter of main rectosigmoid nodule and more tolerated than CTC.
Enhanced Computed Tomography–Based Radiomics Signature Combined With Clinical Features in Evaluating Nuclear Grading of Renal Clear Cell Carcinoma
Authors: Yan Li , Chai Ning , Bao Yuanzhao , Ge Yaqiong , Cheng Qi 
Published: June 2020

Objective
The aim of the study was to explore the value of enhanced computed tomography (CT)-based radiomics signature combined with clinical features in evaluating nuclear grading of clear cell renal cell carcinoma (ccRCC).

Methods
One hundred one patients with ccRCC were classified into low- and high-grade group, and the data were divided into training set and verification set. Radiomics signatures were constructed in the training set in enhanced 3 stages and the combination of them. The predictive nomogram was constructed. The classification efficiency and the clinical practicability of the integrated radiomics model were evaluated.

Results
The classification efficiency of enhanced 3-stage integrated histology model was higher than that of each single-phase model. The predictive nomogram incorporated the best radiomics signature, and the independent clinical risk factors showed good performance. A decision curve analysis curve shows that the net benefit of the combined model.

Conclusions
It is feasible to evaluate the nuclear grading of ccRCC based on enhanced CT radiomics signature combined with clinical features.
Uterine Cervical Carcinoma: Evaluation Using Non-Gaussian Diffusion Kurtosis Imaging and Its Correlation With Histopathological Findings
Authors: Yamada Ichiro , Oshima Noriko , Wakana Kimio , Miyasaka Naoyuki , Wakabayashi Akira , Sakamoto Junichiro , Saida Yukihisa , Tateishi Ukihide , Kobayashi Daisuke 
Published: June 2020

Objective
The aim of the study was to assess non-Gaussian diffusion kurtosis imaging (DKI)'s usefulness as a noninvasive method to evaluate tumor invasion depth, histological grade, and lymph node metastasis in cervical carcinoma (CC) patients.

Methods
Twenty-two consecutive patients with histologically confirmed CC were examined by 1.5-T MRI and non-Gaussian DKI with 4 b values of 0, 500, 1000, and 2000 s/mm2. Kurtosis (K), diffusivity (D), and apparent diffusion coefficient (ADC) maps were compared with histopathological findings.

Results
Kurtosis maps revealed the fibrous stroma as a distinct high K zone (1.442 ± 0.373) that was significantly different from values of the cervical mucosa, outer stroma, and parametrium (0.648 ± 0.083, 0.715 ± 0.113, and 0.504 ± 0.060, respectively, P < 0.0001). Kurtosis (1.189 ± 0.228) and D (0.961 ± 0.198 × 10−3 mm2/s) values of all CCs were significantly different from those of all uterine cervical wall layers. Kurtosis and D values were significantly correlated with histological grades of CCs (r = 0.934, P < 0.0001, and r = −0.925, P < 0.0001, respectively), whereas no significant differences were found in ADC values between grades 2 and 3 CCs (P = 0.787). Metastatic and nonmetastatic lymph nodes showed significantly different K (P < 0.0001) and D (P < 0.0001) values; however, their ADC values did not show significant differences (P = 0.437). For differentiating grade 3 CCs from grade 1 or 2 CCs, the areas under the curve for K (0.991, P = 0.0375) and D (0.982, P = 0.0337) values were significantly higher than those for ADC values (0.759). For differentiating metastatic and nonmetastatic lymph nodes, the areas under the curve for K (0.974, P = 0.0028) and D (0.968, P = 0.0018) values were significantly higher than those for ADC (0.596).

Conclusions
Non-Gaussian DKI may be clinically useful for noninvasive evaluation of tumor invasion depth, histological grade, and lymph node metastasis in CC patients.
Computed Tomography Findings Predicting the Need for Surgery in Cases of Small Bowel Obstruction: Emphasis on Duodenal Distension
Authors: Cengel Ferhat , Gurkan Okan , Dogan Sebahat Nacar , Sayar Samed 
Published: June 2020

Objective
The aim of the study is to retrospectively evaluate the utility of computed tomography (CT) findings, especially newly defined duodenal distension, for predicting the need to operate on small bowel obstruction (SBO) cases.

Methods
During a 51-month period, 228 patients (100 women and 128 men; mean age, 55 years) were included in this study, among 438 patients who were hospitalized with a prediagnosis of SBO. The final study population was then divided into 2 groups: a surgery group (n = 76) and a conservative group (n = 152). The CT findings of the SBO patients whose treatment decisions and outcomes were unknown were examined by 2 gastrointestinal radiologists with consensus. Statistical analyses were conducted using univariate and binary logistic regression analyses.

Results
According to the univariate analysis, the degree of obstruction (P = 0.001), small bowel diameter (P = 0.014), and presence of mesenteric fluid (P < 0.001), intraperitoneal free fluid (P = 0.04), intra-abdominal free gas (P < 0.001), and duodenal distension (P < 0.001) showed statistically significant differences between the surgery and conservative groups. However, there were no statistically significant group differences regarding the presence of a transition point, small bowel feces or mesenteric congestion. According to the binary logistic regression analysis, the degree of obstruction (P = 0.012), presence of mesenteric fluid (P = 0.008), intra-abdominal free gas (P = 0.019), and duodenal distension (P < 0.001) were significant predictors of the need for surgery in SBO cases.

Conclusions
Duodenal distension as a CT finding predicted the need for surgery in SBO cases.
Evaluation of the performance of SARS-CoV-2 serological tools and their positioning in COVID-19 diagnostic strategies
Authors: Velay Aurelie , Gallais Floriane , Benotmane Ilies , Wendling Marie Josée , Danion François , Collange Olivier , De Sèze Jérôme , Schmidt-Mutter Catherine , Schneider Francis , Bilbault Pascal , Meziani Ferhat , Fafi-Kremer Samira 
Published: June 2020

ABSTRACTRapid and accurate diagnosis is crucial for successful outbreak containment. During the current coronavirus disease 2019 (COVID-19) public health emergency, the gold standard for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection diagnosis is the detection of viral RNA by reverse transcription (RT)-PCR. Additional diagnostic methods enabling the detection of current or past SARS-CoV-2 infection would be highly beneficial to ensure the timely diagnosis of all infected and recovered patients. Here, we investigated several serological tools, i.e., two immunochromatographic lateral flow assays (LFA-1 (Biosynex COVID-19 BSS) and LFA-2 (COVID-19 Sign IgM/IgG)) and two enzyme-linked immunosorbent assays (ELISAs) detecting IgA (ELISA-1 Euroimmun), IgM (ELISA-2 EDI) and/or IgG (ELISA-1 and ELISA-2) based on well-characterized panels of serum samples from patients and healthcare workers with PCR-confirmed COVID-19 and from SARS-CoV-2-negative patients. A total of 272 serum samples were used, including 62 serum samples from hospitalized patients (panel 1 and panel 3), 143 serum samples from healthcare workers (panel 2) diagnosed with COVID-19 and 67 serum samples from negative controls. Diagnostic performances of each assay were assessed according to days after symptom onset (dso) and the antigenic format used by manufacturers. We found overall sensitivities ranging from 69% to 93% on panels 1 and 2 and specificities ranging from 83% to 98%. The clinical sensitivity varied greatly according to the panel tested and the dso. The assays we tested showed poor mutual agreement. A thorough selection of serological assays for the detection of ongoing or past infections is advisable.
Software application profile: MeltingPlot, a user-friendly online tool for epidemiological investigation using High Resolution Melting data
Authors: Perini Matteo , Biffignandi Gherard Batisti , Di Carlo Domenico , Pasala Ajay Ratan , Piazza Aurora , Panelli Simona , Zuccotti Gian Vincenzo , Comandatore Francesco 
Published: June 2020

AbstractMotivationGenomic investigations show that nosocomial outbreaks can be sustained by the simultaneous spreading of multiple pathogen clones. Rapid pathogen typing and real-time clones monitoring is a key strategy to control pathogen spreading in hospital settings. A novel approach to High Resolution Melting (HRM) data analysis allows pathogen typing in less than 5 hours. MeltingPlot is the first tool specifically designed for epidemiological investigations using HRM data. The tool is suitable for large real-time surveillance and rapid outbreak reconstructions.ImplementationMeltingPlot was developed in R. The web tool and the standalone versions are available.General featuresThe tool implements a graph-based algorithm designed to discriminate pathogen clones on the basis of HRM data, producing portable typing results. MeltingPlot also merges typing information with isolates and patients metadata to create graphical and tabular outputs useful in epidemiological investigations.AvailabilityThe web interface is available at https://skynet.unimi.it/index.php/tools/meltingplot, the standalone version at https://github.com/MatteoPS/MeltingPlot.
Visual outcome of Anti-Vascular Endothelial Growth Factor Injections at the University College Hospital, Ibadan
Authors: Oluleye Tunji Sunday , Babalola Yewande Olubunmi , Majekodunmi Oluwole , Ijaduola Modupe , Adewole Adeyemi Timothy 
Published: June 2020

AbstractAimTo evaluate the four-year outcome of intravitreal anti-vascular endothelial growth factor (anti-VEGF) therapy in an eye unit in sub-Saharan Africa.MethodologyThis retrospective study included 182 eyes of 172 patients managed in the vitreoretinal unit between 2016 and 2019 who were treated with intravitreal anti-VEGF Bevacizumab (1.25 mg/0.05 ml) with at least one year of follow up. The outcome measures were change in best-corrected visual acuity (BCVA) over one year of follow-up, the number of injections taken and complications.ResultsThe mean age was 61.1 ± 16.3 years (M: F of 1:1.1) and about 62.1% were > 60 years. A total of 330 injections were given during the period audited. The mean number of injections was 1.8 ± 0.93. Ninety-four (51.7%) eyes had only one injection while 33 (18.1%), 50 (27.5%) and 5 (2.7%) had 2, 3 and 4 injections, respectively. About 78.5% had moderate-severe visual impairment at baseline and 44.5%, 16.4%,12.6% and 7.1% at 1, 3, 6- and 12-months post injections, respectively. The mean BCVA improved for all eyes from 1.67 ±0.91 logMAR at baseline to 1.50±1.27 logMAR at one year. The logMAR letters gained was 23 at 1 month and 8.25 at 1 year with a statistically significant association between increasing number of injections and improved visual outcome (p= 0.015). One patient each developed endophthalmitis (0.6%) and inferior retinal detachment (0.6%) post-injection.ConclusionVisual acuity gain was recorded in patients who had at least two intravitreal Anti-VEGF injections in 1 year.
The ATPase mechanism of myosin 15, the molecular motor mutated in DFNB3 human deafness
Authors: Jiang Fangfang , Takagi Yasuharu , Shams Arik , Heissler Sarah M. , Friedman Thomas B. , Sellers James R. , Bird Jonathan E. 
Published: June 2020

AbstractCochlear hair cells possess an exquisite bundle of actin-based stereocilia that detect sound. Unconventional myosin 15 (MYO15A) traffics and delivers critical molecules required for stereocilia development and is essential for building the mechanosensory hair bundle. Mutations in the humanMYO15Agene interfere with stereocilia trafficking and cause hereditary hearing loss, DFNB3. To understand the molecular mechanism of how MYO15A delivers proteins within stereocilia, we performed a kinetic study of the ATPase motor domain to characterize its mechano-chemical cycle. Using the baculovirus-Sf9 system, we purified a recombinant minimal motor domain (S1) by co-expressing the mouse MYO15 ATPase, essential and regulatory light chains that bind its IQ domains, and UNC45 and HSP90A chaperones required for correct folding of the ATPase. MYO15 purified with either UNC45A or UNC45B co-expression had similar ATPase activities (kcat= ~ 6 s−1at 20°C). Using stopped-flow and quenched-flow transient kinetic analyses, we measured the major rate constants describing the ATPase cycle, including ATP, ADP and actin binding, hydrolysis and phosphate release. Actin-attached ADP release was the slowest measured transition (~ 12 s−1at 20°C), although this did not rate-limit the ATPase cycle. The kinetic analysis shows the MYO15 motor domain has a moderate duty ratio (~ 0.5) and weak thermodynamic coupling between ADP and actin binding. This is consistent with MYO15 being adapted for strain sensing as a monomer, or processive motility if oligomerized into ensembles. Our kinetic characterization enables future studies into how deafness-causing mutations affect MYO15 and ultimately disrupt stereocilia trafficking necessary for normal hearing.
Temporal dynamics of the neural representation of hue and luminance polarity
Authors: Hermann Katherine L. , Singh Shridhar R. , Rosenthal Isabelle A. , Pantazis Dimitrios , Conway Bevil R. 
Published: June 2020

AbstractHue and luminance contrast are basic visual features, yet the timing of the neural computations that extract them, and whether they depend on common neural circuits, is not well established. Using multivariate analyses of magnetoencephalography data, we show that hue and luminance-contrast polarity can be decoded from MEG data and, with lower accuracy, both features can be decoded across changes in the other feature. These results are consistent with the existence of both common and separable neural mechanisms. The decoding time course is earlier and more temporally precise for luminance polarity than hue, a result that does not appear to depend on task, suggesting that luminance contrast is an updating signal that separates visual events. Meanwhile, cross-temporal generalization is slightly greater for representations of hue compared to luminance polarity, providing a neural correlate of the preeminence of hue in perceptual grouping and memory. Finally, decoding of luminance polarity varies depending on the hues used to obtain training and testing data; the pattern of results suggests that luminance contrast is mediated by both L-M and S cone sub-cortical mechanisms.
GATA4, expressed in Barrett’s esophagus and esophageal adenocarcinoma, can block squamous epithelial cell gene expression in human esophageal cells
Authors: Stavniichuk Roman , DeLaForest Ann , Thompson Cayla A. , Miller James , Souza Rhonda F. , Battle Michele A. 
Published: June 2020

ABSTRACTMetaplasia often involves a change from one cell type to another that was present during organogenesis. The embryonic esophagus is initially lined by columnar cells that are replaced by squamous cells, and metaplasia in Barrett’s esophagus (BE) involves a change from squamous to columnar cells in the setting of gastroesophageal reflux. Here, we explored the effect of ectopic expression of the essential developmental transcription factor GATA4 on squamous epithelial cell gene expression using human esophageal squamous epithelial cells. We found that GATA4 protein, although absent in mature human esophageal squamous epithelium, was present in BE and esophageal adenocarcinoma (EAC). Moreover, acid and bile inducedGATA4mRNA in esophageal squamous epithelial cells. Ectopic GATA4 expression in esophageal squamous epithelial cells generally compromised squamous cell marker gene expression, although the extent varied between cell lines studied. We observed GATA4 occupancy in thep63, KRT5, andKRT15gene promoters, suggesting that GATA4 can directly repress expression of typical squamous epithelial cell marker genes. Overall, our data suggest a mechanism whereby GATA4 expression in abnormal esophageal cells, possibly induced by reflux, supports a columnar metaplastic cell identity by repressing expression of key genes required to program stratified squamous epithelial cell identity.
Pain and itch processing by subpopulations of molecularly diverse spinal and trigeminal projection neurons
Authors: Wercberger R. , Braz J.M. , Weinrich J.A. , Basbaum A.I. 
Published: June 2020

ABSTRACTA remarkable molecular and functional heterogeneity of the primary sensory neurons and dorsal horn interneurons transmits pain- and or itch-relevant information, but the molecular signature of the projection neurons that convey the messages to the brain is unclear. Here, using retro-TRAP (translating ribosome affinity purification) and RNA-seq we reveal extensive molecular diversity of spino- and trigeminoparabrachial projection neurons, which to date are almost exclusively defined by their expression of the neurokinin 1 receptor (NK1R). Among the many genes identified, we highlight distinct subsets ofCck+,Nptx2+,Nmb+, andCrh+ expressing projection neurons. By combiningin situhybridization of retrogradely labeled neurons with Fos-based assays we also demonstrate significant functional heterogeneity, including both convergence and segregation of pain- and itch-provoking inputs onto molecularly diverse subsets of NK1R- and non-NK1R-expressing projection neurons. The current study provides the first comprehensive investigation into the molecular profiles and functional properties of projection neuron subtypes.
Single cell landscape of hypertrophic scars identifies serine proteases as key regulators of myofibroblast differentiation
Authors: Vorstandlechner Vera , Laggner Maria , Copic Dragan , Chen Yiyan , Golabi Bahar , Haslik Werner , Radtke Christine , Tschachler Erwin , Ankersmit Hendrik Jan , Mildner Michael 
Published: June 2020

AbstractDespite recent advances in understanding skin scarring, mechanisms triggering hypertrophic scar formation are still poorly understood. In the present study we performed single-cell sequencing of mature human hypertrophic scars and developing scars in mice.Compared to normal skin, we found significant differences in gene expression in most cell types present in scar tissue. Fibroblasts (FBs) showed the most prominent alterations in gene expression, displaying a distinct fibrotic signature. By comparing genes upregulated in murine FBs during scar development with genes highly expressed in mature human hypertrophic scars, we identified a group of serine proteases, tentatively involved in scar formation. Two of them, dipeptidyl-peptidase 4 (DPP4) and urokinase (PLAU), were further analyzed in functional assays, revealing a role in TGFβ1-mediated myofibroblast differentiation and over-production of components of the extracellular matrix (ECM) without interfering with the canonical TGFβ1-signaling pathway.In this study, we delineate the genetic landscape of hypertrophic scars and present new insights into mechanisms involved in hypertrophic scar formation. Our data suggest the use of serine protease inhibitors for the treatment of skin fibrosis.
Phosphorylation of pericyte FAK-Y861 affects tumour cell apoptosis and tumour blood vessel regression
Authors: Lees Delphine M. , Reynolds Louise E. , Pedrosa Ana Rita , Roy-Luzarraga Marina , Hodivala-Dilke Kairbaan M. 
Published: June 2020

AbstractFocal adhesion kinase (FAK) is a non-receptor tyrosine kinase that is overexpressed in many cancer types andin vivostudies have shown that vascular endothelial cell FAK expression and FAK-phosphorylation at tyrosine (Y) 397, and subsequently FAK-Y861, are important in tumour angiogenesis. Pericytes also play a vital role in regulating tumour blood vessel stabilisation, but the involvement of pericyte FAK-Y397 and FAK-Y861 phosphorylation in tumour blood vessels is unknown. UsingPdgfrβCre+;FAKWT/WT,PdgfrβCre+;FAKY397F/Y397FandPdgfrβCre+;FAKY861F/Y861Fmice, our data demonstrate that tumour growth, tumour blood vessel density, blood vessel perfusion and pericyte coverage were affected only in late stage tumours inPdgfrβCre+;FAKY861F/Y861Fbut notPdgfrβCre+;FAKY397F/Y397Fmice. Further examination indicates a dual role for pericyte FAK-Y861 phosphorylation in the regulation of tumour vessel regression and also in the control of a pericyte derived ‘pericrine’ signals that influence apoptosis in cancer cells. Overall this study identifies the role of pericyte FAK-Y861 in the regulation of tumour vessel regression and tumour growth control and that non-phosphorylatable FAK-Y861F in pericytes reduces tumour growth and blood vessel density.