bluuebunny/crossref_metadata_2025 huggingface dataset:
Association of Speech Recognition Thresholds With Brain Volumes and White Matter Microstructure: The Rotterdam Study
Authors: Armstrong Nicole M. , Croll Pauline H. , Oosterloo Berthe C. , Lin Frank R. , Ikram M. Arfan , Goedegebure André , Vernooij Meike W.
Published: June 2020

Objectives:

Brain volumetric declines may underlie the association between hearing loss and dementia. While much is known about the peripheral auditory function and brain volumetric declines, poorer central auditory speech processing may also be associated with decreases in brain volumes.

Methods:

Central auditory speech processing, measured by the speech recognition threshold (SRT) from the Digits-in-Noise task, and neuroimaging assessments (structural magnetic resonance imaging [MRI] and fractional anisotropy and mean diffusivity from diffusion tensor imaging), were assessed cross-sectionally in 2,368 Rotterdam Study participants aged 51.8 to 97.8 years. SRTs were defined continuously and categorically by degrees of auditory performance (normal, insufficient, and poor). Brain volumes from structural MRI were assessed on a global and lobar level, as well as for specific dementia-related structures (hippocampus, entorhinal cortex, parahippocampal gyrus). Multivariable linear regression models adjusted by age, age-squared, sex, educational level, alcohol consumption, intracranial volume (MRI only), cardiovascular risk factors (hypertension, diabetes, obesity, current smoking), and pure-tone average were used to determine associations between SRT and brain structure.

Results:

Poorer central auditory speech processing was associated with larger parietal lobe volume (difference in mL per dB increase= 0.24, 95% CI: 0.05, 0.42), but not with diffusion tensor imaging measures. Degrees of auditory performance were not associated with brain volumes and white matter microstructure.

Conclusions:

Central auditory speech processing in the presence of both vascular burden and pure-tone average may not be related to brain volumes and white matter microstructure. Longitudinal follow-up is needed to explore these relationships thoroughly.
Oral preexposure prophylaxis continuation, measurement and reporting
Authors: Stankevitz Kayla , Grant Hannah , Lloyd Josie , Gomez Gabriela B. , Kripke Katharine , Torjesen Kristine , Ong Jason J. , Terris-Prestholt Fern
Published: June 2020

Objective:

The aim of this study was to appropriately plan for rollout and monitor impact of oral preexposure prophylaxis (PrEP). It is important to understand PrEP continuation and come to a consensus on how best to measure PrEP continuation. This study reviews data on PrEP continuation to document how it is reported, and to compare continuation over time and across populations.

Design:

A systematic review and meta-analysis.

Methods:

We searched MEDLINE, Embase and Global Health and reviewed abstracts from HIV conferences from 2017 to 2018 for studies reporting primary data on PrEP continuation. Findings were summarized along a PrEP cascade and continuation was presented by population at months 1, 6 and 12, with random-effects meta-analysis.

Results:

Of 2578 articles and 596 abstracts identified, 41 studies were eligible covering 22 034 individuals. Continuation data were measured and reported inconsistently. Results showed high discontinuation at month 1 and persistent discontinuation at later time points in many studies. Pooled continuation estimates were 66% at month 1 [n = 5348; 95% confidence interval (95% CI): 48–82], 63% at month 6 (n = 13 629; 95% CI: 48–77) and 71% at month 12 (n = 14 933; 95% CI: 60–81; higher estimate than previous timepoints due to inclusion of different studies). Adequate data were not available to reliably compare estimates across populations.

Conclusion:

This review found that discontinuation at one month was high, suggesting PrEP initiations may be a poor measure of effectiveness. Continuation declined further over time in many studies, indicating existing cross-sectional indicators may not be adequate to understand PrEP use patterns. Studies do not measure continuation consistently, and consensus is needed.
Association Between CD4 Count and Chemoradiation Therapy Outcomes Among Cervical Cancer Patients With HIV
Authors: Grover Surbhi , Mehta Priyanka , Wang Qiao , Bhatia Rohini , Bvochora-Nsingo Memory , Davey Sonya , Iyengar Meera , Shah Sidrah , Shin Sanghyuk S. , Zetola Nicola M.
Published: June 2020

Background:

In Botswana, nearly two-thirds of cervical cancer patients are HIV-positive. This study examined the relationship between CD4 count and chemoradiation therapy outcomes among cervical cancer patients with HIV.

Setting:

A prospective cohort study of 231 HIV-positive women with locally invasive cervical cancer was conducted in Gaborone, Botswana from January 2015 to February 2018.

Methods:

Primary outcome was survival, defined as time from scheduled end of chemoradiation therapy to death or last contact with patient. Nadir CD4 count was defined as lowest CD4 available before cancer diagnosis. Delta CD4 count was defined as improvement from nadir CD4 to CD4 at cancer diagnosis. Hazard ratio (HR) analyses were adjusted for presenting variables (age, baseline hemoglobin, cancer stage, and performance status) and treatment variables (chemotherapy cycles and radiation dose).

Results:

Two hundred thirty-one patients were included in nadir CD4 analysis; 139 were included in delta CD4 analysis. Higher delta CD4 was significantly associated with reduced mortality after adjusting for presenting and treatment variables (CD4 100–249: HR 0.45, 95% CI: 0.21 to 0.95; CD4 ≥250: HR 0.45, 95% CI: 0.20 to 1.02). Higher nadir CD4 showed a trend toward reduced mortality after adjusting for presenting and treatment variables (HR 0.94, 95% CI: 0.84 to 1.06).

Conclusions:

Higher delta CD4 (greater improvement from nadir CD4 to CD4 at cervical cancer diagnosis) is significantly associated with lower mortality. Although not statistically significant, data suggest that higher nadir CD4 may reduce mortality. These results reinforce the importance of early HIV diagnosis and antiretroviral therapy initiation, as their effects influence cervical cancer outcomes years later.
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

Rapid 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

Motivation

Genomic 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.

Implementation

MeltingPlot was developed in R. The web tool and the standalone versions are available.

General features

The 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.

Availability

The 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

Aim

To evaluate the four-year outcome of intravitreal anti-vascular endothelial growth factor (anti-VEGF) therapy in an eye unit in sub-Saharan Africa.

Methodology

This 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.

Results

The 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.

Conclusion

Visual 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

Cochlear 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

Hue 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

Metaplasia 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

A 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

Despite 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

Focal 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.
Agonists of orally expressed TRP channels stimulate salivary secretion and modify the salivary proteome
Authors: Houghton Jack William , Carpenter Guy , Hans Joachim , Pesaro Manuel , Lynham Steven , Proctor Gordon
Published: June 2020

Natural compounds that can stimulate salivary secretion are of interest in developing treatments for xerostomia, the perception of a dry mouth, that affects between 10 and 30% of the adult and elderly population. Chemesthetic transient receptor potential (TRP) channels are expressed in the surface of the oral mucosa. The TRPV1 agonists capsaicin and piperine have been shown to increase salivary flow when introduced into the oral cavity but the sialogogic properties of other TRP channel agonists have not been investigated. In this study we have determined the influence of different TRP channel agonists on the flow and protein composition of saliva.

Mouth rinsing with the TRPV1 agonist nonivamide or menthol, a TRPM8 agonist, increased whole mouth saliva (WMS) flow and total protein secretion compared to unstimulated saliva, the vehicle control mouth rinse or cinnamaldehyde, a TRPA1 agonist. Nonivamide also increased the flow of labial minor gland saliva but parotid saliva flow rate was not increased. The influence of TRP channel agonists on the composition and function of the salivary proteome was investigated using a multi-batch quantitative mass spectrometry method novel to salivary proteomics. Inter-personal and inter-mouth rinse variation was observed in the secreted proteomes and, using a novel bioinformatics method, inter-day variation was identified with some of the mouth rinses. Significant changes in specific salivary proteins were identified after all mouth rinses. In the case of nonivamide, these changes were attributed to functional shifts in the WMS secreted, primarily the over representation of salivary and non-salivary cystatins which was confirmed by immunoassay.

This study provides new evidence of the impact of TRP channel agonists on the salivary proteome and the stimulation of salivary secretion by a TRPM8 channel agonist, which suggests that TRP channel agonists are potential candidates for developing treatments for sufferers of xerostomia.
Molecular determinants of MED1 interaction with the DNA bound VDR-RXR heterodimer
Authors: Belorusova Anna Y. , Bourguet Maxime , Hessmann Steve , Chalhoub Sandra , Kieffer Bruno , Cianférani Sarah , Rochel Natacha
Published: June 2020

The MED1 subunit of the Mediator complex is an essential coactivator of nuclear receptor-mediated transcriptional activation. While structural requirements for ligand-dependent binding of classical coactivator motifs of MED1 to numerous nuclear receptor ligand-binding domains have been fully elucidated, the recognition of the full-length or truncated coactivator by full nuclear receptor complexes remain unknown. Here we present structural details of the interaction between a large part of MED1 comprising its structured N-terminal and the flexible receptor-interacting domains and the mutual heterodimer of the vitamin D receptor (VDR) and the retinoid X receptor (RXR) bound to their cognate DNA response element. Using a combination of structural and biophysical methods we show that the ligand-dependent interaction between VDR and the second coactivator motif of MED1 is crucial for complex formation and we identify additional, previously unseen, interaction details. In particular, we identified RXR regions involved in the interaction with structured N-terminal domain of MED1, as well as VDR regions outside the classical coactivator binding cleft affected by coactivator recruitment. These findings highlight important roles of each receptor within the heterodimer in selective recognition of MED1 and contribute to our understanding of the nuclear receptor-coregulator complexes.
A new (old) approach to genotype-based phylogenomic inference within species, with an example from the saguaro cactus (Carnegiea gigantea)
Authors: Sanderson Michael J. , Búrquez Alberto , Copetti Dario , McMahon Michelle M. , Zeng Yichao , Wojciechowski Martin F.
Published: June 2020

Abstract

Genome sequence data are routinely being used to infer phylogenetic history within and between closely related diploid species, but few tree inference methods are specifically tailored to diploid genotype data. Here we re-examine the method of “polymorphism parsimony” (Inger 1967; Farris 1978; Felsenstein 1979), originally introduced to study morphological characters and chromosome inversion polymorphisms, to evaluate its utility for unphased diploid genotype data in large scale phylogenomic data sets. We show that it is equivalent to inferring species trees by minimizing deep coalescences—assuming an infinite sites model. Two potential advantages of this approach are scalability and estimation of a rooted tree. As with some other single nucleotide polymorphism (SNP) based methods, it requires thinning of data sets to statistically independent sites, and we describe a genotype-based test for phylogenetic independence. To evaluate this approach in genome scale data, we construct intraspecific phylogenies for 10 populations of the saguaro cactus using 200 Gbp of resequencing data, and then use these methods to test whether the population with highest genetic diversity corresponds to the root of the genotype trees. Results were highly congruent with the (unrooted) trees obtained using SVDquartets, a scalable alternative method of phylogenomic inference.
Genome ofSolanum pimpinellifoliumprovides insights into structural variants during tomato breeding
Authors: Wang Xin , Gao Lei , Jiao Chen , Stravoravdis Stefanos , Hosmani Prashant S. , Saha Surya , Zhang Jing , Mainiero Samantha , Strickler Susan R. , Catala Carmen , Martin Gregory B. , Mueller Lukas A. , Vrebalov Julia , Giovannoni James J. , Wu Shan , Fei Zhangjun
Published: June 2020

Solanum pimpinellifolium(SP) is the wild progenitor of cultivated tomato. Because of its remarkable stress tolerance and intense flavor, SP has been used as an important germplasm donor in modern breeding of tomato. Here we present a high-quality chromosome-scale genome sequence of SP LA2093. Genome comparison identifies more than 92,000 high-confidence structural variants (SVs) between LA2093 and the modern cultivar, Heinz 1706. Genotyping these SVs in ~600 representative tomato accessions unravels alleles under selection during tomato domestication, improvement and modern breeding, and discovers numerous novel SVs underlying genes known to regulate important breeding traits such as fruit weight and lycopene content. Expression quantitative trait locus (eQTL) analysis detects hotspots harboring master regulators controlling important fruit quality traits, including cuticular wax accumulation and flavonoid biosynthesis, and novel SVs contributing to these complex regulatory networks. The LA2093 genome sequence and the identified SVs provide rich resources for future research and biodiversity-based breeding.
Sorghum bicolorcultivars have divergent and dynamic gene regulatory networks that control the temporal expression of genes in stem tissue
Authors: Arachchilage Madara Hetti , Mullet John E. , Marshall-Colon Amy
Published: June 2020

The genetic engineering of value-added traits such as the accumulation of bioproducts in high biomass C4 grass stems is one promising strategy to make plant-derived biofuels more economical for industrial use. A first step toward achieving this goal is to identify stem-specific promoters that can drive the expression of genes of interest with good temporal and spatial specificity. However, a comprehensive characterization of the spatial-temporal regulatory elements of stem tissue-specific promoters for C4 grasses has not been reported. Therefore, we performed anin-silicoanalysis onSorghum bicolor cv BTx623transcriptomes from multiple tissues over development to identify stem-expressed genes. The analysis identified 10 genes that are “Always-On-Stem-Specific,” 59 genes that are “Temporally-Stem-Specific during early development,” and 21 genes that are “Temporally-Stem-Specific during late development.” Promoter analysis revealed common and/or unique cis-regulatory elements in promoters of genes within each of the three categories. Subsequent gene regulatory network (GRN) analysis revealed that different transcriptional regulatory programs are responsible for the temporal activation of the stem-expressed genes. The analysis of temporal stem GRNs between sweet (cv Della) and grain (cv BTx623) sorghum varieties revealed genetic variation that could influence the regulatory landscape. This study provides new insights about sorghum stem biology, and information for future genetic engineering efforts to fine-tune the spatial-temporal expression of transgenes in C4 grass stems.
Extracellular matrix protein composition dynamically changes during murine forelimb development
Authors: Jacobson Kathryn R. , Saleh Aya M. , Lipp Sarah N. , Ocken Alexander R. , Kinzer-Ursem Tamara L. , Calve Sarah
Published: June 2020

The extracellular matrix (ECM) is an integral part of multicellular organisms, connecting different cell layers and tissue types. During morphogenesis and growth, tissues undergo substantial reorganization involving cellular proliferation, migration, and differentiation. While it is intuitive that the ECM remodels in concert, little is known regarding how matrix composition and organization change during development. We utilized tissue fractionation and mass spectrometry to define ECM protein (matrisome) dynamics during murine forelimb development and resolved significant differences in ECM composition as a function of development, disease and tissue type. Additionally, we used bioorthogonal non-canonical amino acid tagging (BONCAT) to label newly synthesized ECM within the developing forelimb. We demonstrate the feasibility of using BONCAT to enrich for newly synthesized matrisome components and identified differences in ECM synthesis between morphogenesis and growth. This resource will guide future research investigating the role of the matrisome during complex tissue development.
Ten Genetic Loci Identified for Milk Yield, Fat, and Protein in Holstein Cattle
Authors: Liu Liyuan , Zhou Jinghang , Chen Chunpeng James , Zhang Juan , Wen Wan , Tian Jia , Zhang Zhiwu , Gu Yaling
Published: June 2020

High-yield and high-quality of milk are the primary goals of dairy production. Understanding the genetic architecture underlying these milk production traits is beneficial so that genetic variants can be targeted toward the genetic improvement. In this study, we measured five milk production traits in Holstein cattle population from China. These traits included milk yield, protein yield, fat yields; fat percentage and protein percentages. We used the estimated breeding values as dependent variables to conduct the genome-wide association studies (GWAS). Breeding values were estimated through pedigree relationships by using a mixed linear model for individuals with and without phenotypic data. Genotyping was carried out on the individuals with phenotypes by using the Illumina BovineSNP150 BeadChip. The association analyses were conducted by using the Fixed and random model Circulating Probability Unification (FarmCPU) method. A total of ten SNPs was detected above the genome-wide significant threshold, including six located in previously reported QTL regions. We found eight candidate genes within distances of 120 kb upstream or downstream to the associated SNPs. The most significant SNP is onDGAT1gene affecting milk fat and protein percentage. These genetic variants and candidate genes would be valuable resources to enhance dairy cattle breeding.
Neural correlates of temporal presentness in the precuneus: a crosslinguistic fMRI study based on speech stimuli
Authors: Tang Long , Takahashi Toshimitsu , Shimada Tamami , Komachi Masayuki , Imanishi Noriko , Nishiyama Yuji , Iida Takashi , Otsu Yukio , Kitazawa Shigeru
Published: June 2020

Abstracts

The position of any event in time could be either present, past, or future. This temporal discrimination is vitally important in our daily conversations, but it remains elusive how the human brain distinguishes among the past, present, and future. To address this issue, we searched for neural correlates of presentness, pastness, and futurity, each of which is automatically evoked when we hear sentences such as ‘it is raining now’, ‘it rained yesterday’, or ‘it will rain tomorrow’. Here, we show that sentences that evoked ‘presentness’ activated the bilateral precuneus more strongly than those that evoked ‘pastness’ or ‘futurity’. Interestingly, this contrast was shared across native speakers of Japanese, English, and Chinese, languages which vary considerably in their verb tense systems. The results suggest that the precuneus serves as a key region that provides the origin, the Now, to our time perception irrespective of differences in tense systems across languages.
Molecular mode of action of an Acyl Protein thioesterase
Authors: Abrami Laurence , Audagnotto Martina , Ho Sylvia , Marcaida Maria Jose , Mesquita Francisco S. , Anwar Muhammad U. , Sandoz Patrick A. , Fonti Giulia , Pojer Florence , Peraro Matteo Dal , van der Goot F. Gisou
Published: June 2020

Many biochemical reactions occur at the membrane interfaces. The proper control of these reactions requires spatially and temporally controlled recruitment of protein complexes. These assemblies are largely regulated by post-translational modifications and a frequent one is S-acylation, which consists of the addition of medium length acyl chains. Reversibility of this modification is ensured by acyl protein thioesterases (APTs), which are poorly understood enzymes. Using a combination of computational, structural, biochemical, and cellular approaches, we dissect the mode of action of a major cellular thioesterase, APT2 (LYPLA2). We show that for APT2 to encounter its targets, it must interact with membranes by two consecutive steps, the insertion of a hydrophobic loop and subsequent S-acylation by the ZDHHC3 or ZDHHC7 palmitoyltransferases. Once bound, APT2 deforms the lipid bilayer to extract the acyl chain bound to its substrate, capturing it in a hydrophobic pocket and allowing hydrolysis. Deacylation releases APT2, allowing it to bind to other membranes, but also renders it vulnerable to ubiquitination and proteasomal degradation. This molecular understanding of APT2 paves the way to understand the dynamics of APT2-mediated depalmitoylation throughout the endomembrane system.
Comparison of human and mouse fetal intestinal tissues reveals differential maturation timelines
Authors: Lim A.A. , Nadkarni R.R. , Courteau B.C. , Draper J.S.
Published: June 2020

Maturation of the intestinal epithelium is a necessary step for development of a fully functioning gastrointestinal tract. Studies of rodent gastrointestinal development and maturation have long been used to guide understanding of human intestinal maturation, in part because accessing human gestational stage intestinal tissues to perform equivalent human studies can be difficult. Notable differences have already been described in the timing of key stages in intestinal development between rodents and humans, but the conservation of intestinal maturation events between the two species is poorly understood. We hypothesized that species-related differences in intestinal development would alter the timing of key maturation events between human and mouse. We tested our hypothesis by performing a detailed comparison of hallmarks of intestinal maturation in human and mouse gestational intestine, including markers that describe the emergence of intestinal cell types, functionality and structural integrity. Our study demonstrates clear timing differences between maturation stages in mouse and human, with the majority of human maturation hallmarks acquired post-partum, in contrast to their gestational emergence in mouse. Our work suggests caution when translating murine intestinal maturation observations to the human, and provides a maturation road map that will be helpful to those seeking to produce mature intestine fromin vitrostem cell sources.
Bcr-Abl tyrosine kinase inhibitor imatinib as a potential drug for COVID-19
Authors: Mulgaonkar Nirmitee , Wang Haoqi , Mallawarachchi Samavath , Fernando Sandun , Martina Byron , Ruzek Daniel
Published: June 2020

The rapid geographic expansion of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the infectious agent of Coronavirus Disease 2019 (COVID-19) pandemic, poses an immediate need for potent drugs. Enveloped viruses infect the host cell by cellular membrane fusion, a crucial mechanism required for virus replication. The SARS-CoV-2 spike glycoprotein, due to its primary interaction with the human angiotensin-converting enzyme 2 (ACE2) cell-surface receptor, is considered as a potential target for drug development. Based onin silicoscreening followed byin vitrostudies, here we report that the existing FDA-approved Bcr-Abl tyrosine kinase inhibitor, imatinib, inhibits SARS-CoV-2 with an IC50of 130 nM. We provide evidence that although imatinib binds to the receptor-binding domain (RBD) of SARS-CoV-2 spike protein with an affinity at micromolar, i.e., 2.32 ± 0.9 μM levels, imatinib does not directly inhibit the spike RBD:ACE2 interaction – suggesting a Bcr-Abl kinase-mediated fusion inhibition mechanism is responsible for the inhibitory action. We also show that imatinib inhibits other coronaviruses, SARS-CoV, and MERS-CoV via fusion inhibition. Based on promisingin vitroresults, we propose the Abl tyrosine kinase inhibitor (ATKI), imatinib, to be a viable repurposable drug against COVID-19.
Accessory ESCRT-III proteins selectively regulate Rab11-exosome biogenesis inDrosophilasecondary cells
Authors: Marie Pauline P. , Fan Shih-Jung , Mendes Claudia C. , Wainwright S. Mark , Harris Adrian L. , Goberdhan Deborah C. I. , Wilson Clive
Published: June 2020

Exosomes are secreted nanovesicles with potent signalling activity that are initially formed as intraluminal vesicles (ILVs) in multivesicular endosomes, which subsequently fuse with the plasma membrane. These ILVs are made in both late endosomes and recycling endosomes, the latter marked by the small GTPase Rab11 and generating exosomes with different cargos and functions. Core proteins within four Endosomal Sorting Complex Required for Transport (ESCRT) assemblies (0-III) play key sequential roles in late endosomal exosome biogenesis and ILV-mediated destruction of ubiquitinylated cargos through the endolysosomal system. They also control additional cellular processes, such as cytokinesis and other vesicle budding. By contrast, the functions of several accessory ESCRTs are not well defined. Here we assess the ESCRT-dependency of Rab11-exosomes, using RNA knockdown inDrosophilasecondary cells (SCs) of the male accessory gland, which have unusually enlarged Rab11-positive compartments. Unexpectedly, not only are core proteins in all four ESCRT complexes required for Rab11-exosome formation, but also accessory ESCRT-III proteins, CHMP1, CHMP5 and IST1. Suppressing expression of these accessory proteins does not affect other aspects of cell morphology, unlike most core ESCRT knockdowns, and does not lead to accumulation of ubiquitinylated cargos. We conclude that accessory ESCRT-III components have a specific and potentially ubiquitin-independent role in Rab11-exosome generation, which might provide a target for blocking the pro-tumorigenic activities of these vesicles in cancer.