bluuebunny/crossref_metadata_2025 huggingface dataset:
Single-cell RNA sequencing reveals mRNA splice isoform switching during kidney development
Authors: Wineberg Yishay , Bar-Lev Tali Hana , Futorian Anna , Ben-Haim Nissim , Armon Leah , Ickowicz Debby , Oriel Sarit , Bucris Efrat , Yehuda Yishai , Pode-Shakked Naomi , Gilad Shlomit , Benjamin Sima , Hohenstein Peter , Dekel Benjamin , Urbach Achia , Kalisky Tomer
Published: July 2019

During mammalian kidney development, nephron progenitors undergo a mesenchymal to epithelial transition and eventually differentiate into the various tubular segments of the nephron. Recently, the different cell types in the developing kidney were characterized using the Dropseq single cell RNA sequencing technology for measuring gene expression from thousands of individual cells. However, many genes can also be alternatively spliced and this creates an additional layer of heterogeneity. We therefore used full transcript length single-cell RNA sequencing to obtain the transcriptomes of 544 individual cells from mouse embryonic kidneys. We first used gene expression levels to identify each cell type. Then, we comprehensively characterized the splice isoform switching that occurs during the transition between mesenchymal and epithelial cellular states and identified several putative splicing regulators, including the genes Esrp1/2 and Rbfox1/2. We anticipate that these results will improve our understanding of the molecular mechanisms involved in kidney development.
Functional analysis of KIT gene structural mutations causing porcine dominant white phenotype by using genome edited mouse models
Authors: Sun Guangjie , Liang Xinyu , Qin Ke , Qin Yufeng , Shi Xuan , Cong Peiqing , Mo Deling , Liu Xiaohong , Chen Yaosheng , He Zuyong
Published: July 2019

Dominant white phenotype in pigs is considered to be caused by two structural mutations inKITgene, including a 450-kb duplication encompassing the entireKITgene, and a splice mutation (G > A) at the first base in intron 17, which leads to the deletion of exon 17 in matureKITmRNA, and the production of KIT protein lacking a critical catalytic domain of kinase. However, this speculation has not yet been validated by functional studies. Here, by using CRISPR/Cas9 technology, we created two mouse models mimicing the structural mutations ofKITgene in dominant white pigs, including the splice mutation mouse modelKITD17/+with exon 17 of one allele ofKITgene deleted, and duplication mutation mouse modelKITDup/+with one allele ofKITgene coding sequence (CDS) duplicated. We found that each mutation individually can not cause dominant white phenotype. Splice mutation homozygote is lethal and heterozygous mice present piebald coat. Inconsistent with previous speculation, we foundKITgene duplication mutation did not confer the patched phenotype, and had no obvious impact on coat color. Interestingly, combination of these two mutations lead to dominant white phenotype. Further molecular analysis revealed that combination of these two structural mutations could inhibit the kinase activity of the KIT protein, thus reduce the phosphorylation level of PI3K and MAPK pathway associated proteins, which may be related to the observed impaired migration of melanoblasts during embryonic development, and eventually lead to dominant white phenotype. Our study provides a further insight into the underlying genetic mechanisms of porcine dominant white coat colour.

Author summary

KIT plays a critical role in control of coat colour in mammals. Two mutation coexistence inKITare considered to be the cause of theDominant whitephenotype in pigs. One mutation is a 450-kb large duplication encompassing the entireKITgene, another mutation is a splice mutation causing the skipping of KIT exon 17. The mechanism of these two mutations of KIT on coat color formation has not yet been validated. In this study, by using genome edited mouse models, we found each structural mutation individual does not lead dominant white phenotype, but combination of these two mutations could lead to a nearly complete white coat colour similar to pig dominant white phenotype, possibly due to the inhibition of the kinase activity of the KIT protein, thus its signalling function on PI3K and MAPK pathways, leading to impaired migration of melanoblasts during embryonic development, and eventually lead to dominant white phenotype. Our study provides a further insight into the underlying genetic mechanisms of porcine dominant white coat colour.
A dynamic cell recruitment process drives growth of the Drosophila wing by overscaling the Vestigial expression pattern
Authors: Muñoz-Nava Luis Manuel , Alvarez Hugo Ariel , Flores-Flores Marycruz , Chara Osvaldo , Nahmad Marcos
Published: July 2019

Organs mainly attain their size by cell growth and proliferation, but sometimes also grow through recruitment of undifferentiated cells. Here we investigate the participation of cell recruitment in establishing the pattern of Vestigial (Vg), the product of the wing selector gene in Drosophila. We find that the Vg pattern overscales along the dorsal-ventral (DV) axis of the wing imaginal disc,i.e., it expands faster than the DV length of the pouch. The overscaling of the Vg pattern cannot be explained by differential proliferation, apoptosis, or oriented-cell divisions, but can be recapitulated by a mathematical model that explicitly considers cell recruitment. By impairing cell recruitment genetically, we find that the Vg pattern almost perfectly scales and adult wings are approximately 20% smaller. Furthermore, using fluorescent reporter tools, we provide direct evidence that cell recruitment takes place in a specific time between early and mid third-instar larval development. Altogether, our work quantitatively shows when, how, and by how much cell recruitment shapes the Vg pattern and drives growth of the Drosophila wing.
Predicting long-term Type 2 Diabetes with Support Vector Machine using Oral Glucose Tolerance Test
Authors: Abbas Hasan , Alic Lejla , Erraguntla Madhav , Ji Jim , Abdul-Ghani Muhammad , Abbasi Qammer , Qaraqe Marwa
Published: July 2019

Diabetes is a large healthcare burden worldwide. There is substantial evidence that lifestyle modifications and drug intervention can prevent diabetes, therefore, an early identification of high risk individuals is important to design targeted prevention strategies. In this paper, we present an automatic tool that uses machine learning techniques to predict the development of type 2 diabetes mellitus (T2DM). Data generated from an oral glucose tolerance test (OGTT) was used to develop a predictive model based on the support vector machine (SVM). We trained and validated the models using the OGTT and demographic data of 1,492 healthy individuals collected during the San Antonio Heart Study. This study collected plasma glucose and insulin concentrations before glucose intake and at three time-points thereafter (30, 60 and 120 min). Furthermore, personal information such as age, ethnicity and body-mass index was also a part of the dataset. Using 11 oral glucose tolerance test (OGTT) measurements, we have deduced 61 features, which are then assigned a rank and the top ten features are shortlisted using Minimum Redundancy Maximum Relevance feature selection algorithm. All possible combinations of the 10 best ranked features were used to generate SVM based prediction models. This research shows that an individual’s plasma glucose levels, and the information derived therefrom have the strongest predictive performance for the future development of T2DM. Significantly, insulin and demographic features do not provide additional performance improvement for diabetes prediction. The results of this work identify the parsimonious clinical data needed to be collected for an efficient prediction of T2DM. Our approach shows an average accuracy of 96.80 % and a sensitivity of 80.09 % obtained on a holdout set.
Tissue-specific changes in size and shape of the ligaments and tendons of the porcine knee during post-natal growth
Authors: Cone Stephanie G. , Piercy Hope E. , Lambeth Emily P. , Ru Hongyu , Piedrahita Jorge A. , Spang Jeffrey T. , Fordham Lynn A. , Fisher Matthew B.
Published: July 2019

Prior studies have analyzed growth of musculoskeletal tissues between species or across body segments; however, little research has assessed the differences in similar tissues within a single joint. Here we studied changes in the length and cross-sectional area of four ligaments and tendons, (anterior cruciate ligament, patellar tendon, medial collateral ligament, lateral collateral ligament) in the tibiofemoral joint of female Yorkshire pigs through high-field magnetic resonance imaging throughout growth. Tissue lengths increased by 4-to 5-fold from birth to late adolescence across the tissues while tissue cross-sectional area increased by 10-20-fold. The anterior cruciate ligament and lateral collateral ligament showed allometric growth favoring change in length over change in cross-sectional area while the patellar tendon and medial collateral ligament grow in an isometric manner. Additionally, changes in the length and cross-sectional area of the anterior cruciate ligament did not increase as much as in the other ligaments and tendon of interest. Overall, these findings suggest that musculoskeletal soft tissue morphometry can vary within tissues of similar structure and within a single joint during post-natal growth.
Reducing expression of dynamin-related protein 1 increases radiation sensitivity of glioblastoma cells
Authors: Cheng Wen-Yu , Chow Kuan-Chih , Chiao Ming-Tsang , Yang Yi-Chin , Shen Chiung-Chyi
Published: July 2019

Background

Dynamin-related protein 1 (DRP1) is a GTPase involved in mitochondrial fission, mitochondrial protein imports, and drug sensitivity, suggesting an association with cancer progression. This study is to evaluate the prognostic significance of DRP1 in glioblastoma multiforme (GBM).

Material and Methods

DRP1 expression was measured by immunohistochemistry and Western blotting. Correlations between DRP1 expression and clinicopathological parameters were analyzed by statistical analysis. Differences in survival were compared by a log-rank test.

Results

DRP1 expression was detected in 87.2% (41/47) patients with GBM. Patients with higher DRP1 levels had worse survival (p = 0.0398). In vitro, silencing of DRP1 reduced cell proliferation, metastatic potential, and radiation resistance. The addition of shikonin inhibited DRP1 expression and increased drug uptake. Moreover, shikonin reduced the nuclear entry of DNA repair-associated enzymes and increased radiation sensitivity, suggesting that to reduce DRP1 expression could inhibit DNA repair and increase the radiation sensitivity of GBM cells.

Conclusion

Our results indicate that DRP1 overexpression is a prospective radio-resistant phenotype in GBM. Therefore, DRP1 could be a potential target for improving the effectiveness of radiation therapy.

Abbreviations used are: ATAD3A, the ATPase family, AAA domain containing 3A; CIM, confocal immunofluorescence microscopy; DRP1, dynamin-related protein 1; ER, endoplasmic reticulum; GBM, glioblastoma multiforme; hHR23A, human homolog of yeast Rad23 protein A; IDH1, isocitrate dehydrogenase 1; MAM, mitochondria-associated membrane; MGMT, O6-methylguanine-DNA-methyltransferase; SAHA, suberoylanilide hydroxamic acid (vorinostat); TMZ, temozolomide

Translational Relevance

This study shows that dynamin-related protein 1 (DRP1), an essential 80-kDa GTPase, which is involved in mitochondrial fission, and mitochondrial protein imports, is highly expressed in glioblastoma multiforme (GBM). Moreover, we demonstrate that DRP1 expression is closely associated with radiation sensitivity, cancer progression, and patients’ cumulative survival. In vitro, inhibition of DRP1 expression reduced the nuclear entry of DNA repair-associated enzymes, such as ATM, but increased radiation sensitivity and nuclear drug uptakes of glioblastoma cells. More importantly, the silencing of DRP1 induced cellular autophagy. These results indicate that DRP1 overexpression could be a prospective radio-resistant phenotype in GBM and a clinically important target for improving the effectiveness of radiation therapy.
Computational fluid dynamics simulation of changes in the morphology and airflow dynamics of the upper airways in OSAHS patients after treatment with oral appliances
Authors: Baolong Song , Yibo Li , Jianwei Sun , Yizhe Qi , Peng Li , Yongming Li , Zexu Gu
Published: July 2019

Objectives

To explore the changes of morphology and internal airflow in upper airways (UA) after the use of oral appliances (OAs) in patients with obstructive sleep apnea hypopnea syndrome (OSAHS), and investigate the mechanisms by which OAs function as a therapy for OSAHS.

Methods

Eight OSAHS patients (all male, aged 37-58, mean age 46.25) underwent CT scans before and after OA use. Then, computational fluid dynamics(CFD) models were built on the base of the CT scans using Mimics and ANSYS ICEM CFD software. The internal airflow of the upper airways was simulated using ANSYS-FLUENT and the results were analyzed using ANSYS-CFD-Post. The data were analyzed to identify the most important changes of biomechanical properties between patients with and without OA intervention. Upper airway morphology and the internal airflow changes were compared using t-tests and Spearman correlation coefficient analysis.

Results

The narrowest area of upper airways was found to be located in the lower bound of velopharynx, where the volume and pressure were statistically significantly increased (P<0.05) and the air velocity was statistically significantly decreased (P<0.05) in the presence of the OA(P<0.05). After wearing OA, pharyngeal resistance was significantly decreased (P<0.05), from 290.63 to 186.25Pa/L, and the airflow resistance of the pharynx has reduced by 35.9%.

Conclusion

The enlargement of the upper airway after wearing the OA changed its airflow dynamics, which decreased the negative pressure and resistance in narrow areas of the upper airways. Thus, the collapsibility of the upper airways was reduced and patency was sustained.
Impact of Rigid Gas Permeable Contact Lenses Removal on Anterior and Posterior Corneal Surfaces in Keratoconus Patients
Authors: Itoi Motohiro , Kitazawa Koji , Higashihara Hisayo , Sotozono Chie
Published: July 2019

Purpose

To evaluate the impact of removal of rigid gas-permeable (RGP) contact lenses on the anterior and posterior cornea surfaces of eyes with keratoconus.

Methods

Eight eyes of 8 patients with keratoconus (KC) (age 34.3 ± 15.3 years; range 19–60 years) were enrolled. Anterior segment optical coherence tomography (AS-OCT) was performed at 1, 5, 10, 20, and 60 minutes after the patients removed their RGP contact lenses. Measurements included anterior and posterior best-fit sphere (BFS); elevation values and corneal surface areas; corneal thickness at the thinnest point; and the anterior-posterior ratio of the corneal surface (As/Ps) between 1 minute and 60 minutes after RGP contact lens removal.

Results

Anterior and posterior elevation values and corneal surface areas showed significant increases, whereas anterior and posterior BFS and central corneal thickness decreased significantly (P < 0.01) between 1 minute and 60 minutes after RGP contact lens removal. No statistically significant differences were found in the As/Ps ratio during the first hour after suspending RGP contact lens wear.

Conclusions

We found that the patients with keratoconus experienced significant changes in both the anterior and posterior corneal shape for 60 minutes after removal of RGP contact lenses.
A geometric approach to human stress based on stress-related surrogate measures
Authors: Kloucek Petr , von Gunten Armin
Published: July 2019

We present a predictive Geometric Stress Index (pGSI) and its relation to behavioural Entropy (b𝔼).b𝔼 is a measure of the complexity of an organism’s reactivity to stressors yielding patterns based on different behavioural and physiological variables selected as surrogate markers of stress (SMS). We present a relationship between pGSI andb𝔼 in terms of a power law model. This nonlinear relationship describes congruences in complexity derived from analyses of observable and measurable SMS patterns interpreted as stress. The adjective geometric refers to subdivision(s) of the domain derived from two SMS (heart rate variability and steps frequency) with respect to a positive/negative binary perceptron based on a third SMS (blood oxygenation). The presented power law allows for both quantitative and qualitative evaluations of the consequences of stress measured by pGSI. In particular, we show that elevated stress levels in terms of pGSI leads to a decrease of theb𝔼 of the blood oxygenation as a model of SMS.
Factors associated with unsuppressed viremia in women living with HIV on lifelong ART in a multi-country cohort study: US-PEPFAR PROMOTE study
Authors: Atuhaire Patience , Hanley Sherika , Yende-Zuma Nonhlanhla , Aizire Jim , Stranix-Chibanda Lynda , Makanani Bonus , Milala Beteniko , Cassim Haseena , Taha Taha , Fowler Mary Glenn
Published: July 2019

Background

Despite recent efforts to scale-up lifelong combination antiretroviral therapy (cART) in sub-Saharan Africa, high rates of unsuppressed viremia persist among cART users, and many countries in the region fall short of the UNAIDS 2020 target to have 90% virally suppressed. We sought to determine the factors associated with unsuppressed viremia (defined for the purpose of this study as >200 copies/ml) among African women on lifelong cART.

Methods

This analysis was based on baseline data of the PROMOTE longitudinal cohort study at 8 sites in Uganda, Malawi, Zimbabwe and South Africa. The study enrolled 1987 women living with HIV who initiated lifelong cART at least 1 year previously to assesses long-term safety and effectiveness of cART. Socio-demographic, clinical, and cART adherence data were collected. We used multivariable Poisson regression with robust variance to identify factors associated with unsuppressed viremia.

Results

At enrolment, 1947/1987 (98%) women reported taking cART. Of these, HIV-1 remained detectable in 293/1934 (15%), while 216/1934 (11.2%) were considered unsuppressed (>200 copies/ml). The following factors were associated with an increased risk of unsuppressed viremia: not having household electricity (adjusted prevalence rate ratio (aPRR) 1.74, 95% confidence interval (CI) 1.28-2.36, p<0.001); self-reported missed cART doses (aPRR 1.63, 95% CI 1.24-2.13, p<0.001); recent hospitalization (aPRR 2.48, 95% CI 1.28-4.80, p=0.007) and experiencing abnormal vaginal discharge in the last three months (aPRR 1.88; 95% CI 1.16-3.04, p=0.010). Longer time on cART (aPRR 0.75, 95% CI 0.64-0.88, p<0.001) and being older (aPRR 0.77, 95% CI 0.76-0.88, p<0.001) were associated with reduced risk of unsuppressed viremia.

Conclusion

Socioeconomic barriers such as poverty, not being married, young age, and self-reported missed doses remain key predictors of unsuppressed viremia. Targeted interventions are needed to improve cART adherence among women living with HIV with this risk factor profile.
Assessment of the optimum fertilizer rates and planting density for soybean production in China
Authors: Lv Jilong , He Ping , Wei Dan , Xu Xinpeng , Qiu Shaojun , Zhao Shicheng
Published: July 2019

Fertilization rate and planting density are important factors affecting crop yield. A large number of soybean [Glycine max (L.) Merr] field experimental data (1998-2017) were collected through different database sources to evaluate the optimum fertilizer rate and planting density for high yield of spring and summer soybean in China. The yield of spring and summer soybean gradually increased over year, with their average yields were 2610 and 2724 kg ha−1, respectively. Based on the fitted quadratic curve, the optimal rate of nitrogen (N), phosphorus (P), and potassium (K) fertilizers for high yield of summer soybean was 96 kg N ha−1, 80 kg P2O5 ha−1, and 126 kg K2O ha−1, and the corresponding yields were 3038, 2801 and 2305 kg ha−1, respectively. The optimal rate of N, P and K fertilizers for spring soybean was 71 kg N ha-1, 108 kg P2O5 ha-1 and 74 kg K2O ha−1, and the corresponding yields were 2932, 2834 and 2678 kg ha−1, respectively. The optimum density was 27×104 and 34×104 plants ha−1 under high yield for summer and spring soybean, respectively. Stepwise regression analysis showed that the P fertilizer had the greatest influence on the spring soybean yield followed by K fertilizer and planting density. For summer soybean, population density had the major effect on yield followed by P fertilizer. Overall, the P fertilization and planting density should be payed attention to increase soybean yield in different regions of China.
Drone-based effective counting and ageing of hippopotamus (Hippopotamus amphibius) in the Okavango Delta in Botswana
Authors: Inman Victoria L. , Kingsford Richard T. , Chase Michael J. , Leggett Keith E. A.
Published: July 2019

Accurately estimating hippopotamus (Hippopotamus amphibius) numbers is difficult due to their aggressive nature, amphibious lifestyle, and habit of diving and surfacing. Traditionally, hippos are counted using aerial surveys and land/boat surveys. We compared estimates of numbers of hippos in a lagoon in the Okavango Delta, counted from land and video taken from a DJI Phantom 4™ drone, testing for effectiveness at three heights (40 m, 80 m, and 120 m) and four times of day (early morning, late morning, early afternoon, and late afternoon). In addition, we determined effectiveness for differentiating age classes (juvenile, subadult, and adult), based on visual assessment and measurements from drone images, at different times and heights. Estimates in the pool averaged 9.18 (± 0.25SE, range 1 – 14, n = 112 counts). Drone counts at 40 m produced the highest counts of hippos, 10.6% higher than land counts and drone counts at 80 m, and 17.6% higher than drone counts at 120 m. Fewer hippos were counted in the early morning, when the hippos were active and most likely submerged, compared to all other times of day, when they tended to rest in shallow water with their bodies exposed. We were able to assign age classes to similar numbers of hippos from land counts and counts at 40 m, although land counts were better at identifying juveniles and subadults. Early morning was the least effective time to age hippos given their active behaviour, increasingly problematic with increasing height. Use of a relatively low-cost drone provided a rigorous and repeatable method for estimating numbers and ages of hippos, but not in the early morning.
Beyond rRNA and snRNA: tRNA as a 2′-O-methylation target for nucleolar and Cajal body box C/D RNPs
Authors: Nostramo Regina T. , Hopper Anita K.
Published: July 2019

Box C/D small nucleolar RNAs (snoRNAs) and small Cajal body (CB) RNAs (scaRNAs) form ribonucleoprotein (RNP) complexes to mediate 2′-O-methylation of rRNAs and small nuclear RNAs (snRNAs), respectively. The site of methylation is determined by antisense elements in the box C/D RNAs that are complementary to sequences in target RNAs. However, numerous box C/D RNAs in mammalian cells lack antisense elements to rRNAs or snRNAs; thus, their targets remain unknown. In this issue of Genes & Development, Vitali and Kiss (pp. 741–746) demonstrate that “orphan” nucleolar box C/D snoRNA SNORD97 and CB box C/D scaRNA SCARNA97 contain antisense elements that target the wobble cytidine at position 34 of human elongator tRNAMet(CAT) for 2′-O-methylation (C34m). C34m is jointly mediated by SNORD97 and SCARNA97 despite their apparently different intranuclear locations. Furthermore, the investigators demonstrate that C34m prohibits site-specific cleavage of tRNAMet (CAT) into tRNA fragments (tRFs) by the stress-responsive endoribonuclease angiogenin, thereby uncovering a role for SNORD97 and SCARNA97 in the biogenesis of tRFs, which modulate a diverse set of cellular functions in human health and disease.
Analysis of Phosphorylation Status of Ectopically Expressed Proteins in Early Xenopus Embryos
Authors: Hardwick Laura J.A. , Philpott Anna
Published: July 2019

Xenopus embryos provide a rapid and accessible in vivo model, expressing a plethora of endogenous kinase and phosphatase enzymes that control protein phosphorylation and, in turn, affect physiological function. Traditionally, the detection of protein phosphorylation has been achieved by radioisotope phosphate labeling of proteins, sometimes with in vitro assays using recombinant proteins or with site-specific phospho-antibodies. However, the target phospho-sites and kinases responsible are often unknown, and the use of radioactive isotopes is not always desirable. Therefore, as a first step in determining the functional significance of potential phosphorylation, it is useful to show that a protein can be phosphorylated in vivo in Xenopus eggs and/or embryos. This protocol describes a nonradioactive method to visualize protein phosphorylation by exposing the protein to the egg/embryo kinase environment and then observing a difference in protein migration (as assessed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis [SDS-PAGE] and western blot analysis) with and without treatment with the lambda phosphatase enzyme. Subsequent investigation of the ability of site-specific phospho-mutant proteins to recapitulate the effect of phosphatase treatment can be used to explore the identity of the phosphorylated sites. Moreover, the detection of multiple bands of the protein of interest even after phosphatase treatment points to the presence of other types of posttranslational modifications.
Farmers’ constraints, governmental support and climate change adaptation: Evidence from Guangdong Province, China
Authors: Xu Ying , Findlay Christopher
Published: July 2019

While climate change is widely acknowledged, the role of government support in adaptation is less understood. We narrow this knowledge gap by modelling adaptation as a three‐stage process where a farmer sequentially decides: (i) whether there is a need for adaptation; (ii) whether there are constraints that prevent adaptation; and (iii) whether such constraints are removed through government support. We develop a triple‐hurdle model to describe this decision‐making process and empirically estimate the impact of government support using a rural household survey from Guangdong Province, China. It is found that government support is positively associated with raising the odds of adaptation by about one quarter. This magnitude is larger than the estimates in recent literature, suggesting government support is more effective for farmers bound by constraints. Therefore, for cost‐effective policy outcomes there is a need to identify the constraints and the farmers facing them.
Effectiveness of a counselling intervention implemented in antenatal setting for pregnant women facing domestic violence: a pre‐experimental study
Authors: Arora S , Deosthali PB , Rege S
Published: July 2019

Objective

To assess the effectiveness of a counselling intervention in antenatal care settings for pregnant women who report domestic violence.

Design

Pre‐experimental study with pretest‐posttest design.

Settings

Two public hospitals in Mumbai, India.

Sample

In all, 2778 pregnant women accessing antenatal care (ANC) in the hospitals from February to November 2016 were approached for study participation; 2515 women consented. These women were screened by trained counsellors for domestic violence during pregnancy (domestic violence during pregnancy). Domestic violence during pregnancy was reported by 16.2% (408) of women. Of these, 155 women sought counselling services. Post‐intervention analyses were carried out with 142 women at 6 weeks post‐delivery; 13 women were not contactable.

Methods

The 442 women who reported domestic violence during pregnancy were provided a minimum of two counselling sessions by trained counsellors during their ANC visits. A counselling intake form was used to collect pre‐ and post‐intervention data.

Main outcome measures

Prevalence of domestic violence during pregnancy, change in women's ability to cope, safety, and health.

Results

Prevalence of domestic violence during pregnancy (16.1%) was comparable to those of common obstetric complications routinely screened for during ANC. In all, 60–65% women reported cognitive changes such as recognising impact of violence and need to speak out against it. In all, 50.7% women took action at the individual level to address domestic violence during pregnancy. This change was not statistically significant (P‐value 0.193). Of the women studied, 35.9% adopted at least one safety measure, and 84% of the women reported better health status post‐intervention.

Conclusions

Routine enquiry and counselling for domestic violence during pregnancy are effective in improving women's ability to cope, safety, and health.

Funding

This study was funded by The John D. and Catherine T. MacArthur Foundation.

Tweetable abstract

Improving coping strategies, safety and health of pregnant women who reported domestic violence by providing counselling in antenatal care setting.
Review article: Interventions for people presenting to emergency departments with a mental health problem: A systematic scoping review
Authors: Johnston Amy NB , Spencer Melinda , Wallis Marianne , Kinner Stuart A , Broadbent Marc , Young Jesse T , Heffernan Ed , Fitzgerald Gerry , Bosley Emma , Keijzers Gerben , Scuffham Paul , Zhang Ping , Martin‐Khan Melinda , Crilly Julia
Published: July 2019

The number of people presenting to EDs with mental health problems is increasing. To enhance and promote the delivery of safe and efficient healthcare to this group, there is a need to identify evidence‐based, best‐practice models of care. This scoping review aims to identify and evaluate current research on interventions commenced or delivered in the ED for people presenting with a mental health problem. A systematic search of eight databases using search terms including emergency department, mental health, psyc* and interventions, with additional reference chaining, was undertaken. For included studies, level of evidence was assessed using the NHMRC research guidelines and existing knowledge was synthesised to map key concepts and identify current research gaps. A total of 277 papers met the inclusion criteria. These were grouped thematically into seven domains based on primary intervention type: pharmacological (n = 43), psychological/behavioural (n = 25), triage/assessment/screening (n = 28), educational/informational (n = 12), case management (n = 28), referral/follow up (n = 36) and mixed interventions (n = 105). There was large heterogeneity observed as to the level of evidence within each intervention group. The interventions varied widely from pharmacological to behavioural. Interventions were focused on either staff, patient or institutional process domains. Few interventions focused on multiple domains (n = 64) and/or included the patient's family (n = 1). The effectiveness of interventions varied. There is considerable, yet disconnected, evidence around ED interventions to support people with mental health problems. A lack of integrated, multifaceted, person‐centred interventions is an important barrier to providing effective care for this vulnerable population who present to the ED.
The shape is more important than we ever thought: Plant to plant interactions in a high mountain community
Authors: Pescador David S. , de la Cruz Marcelino , Chacón‐Labella Julia , Escudero Adrián
Published: July 2019

Plant to plant interactions are probably the most important driver of species coexistence at fine spatial scales, but their detection represents a challenge in Ecology. Spatial point pattern analysis (SPPA) is likely the approach most used to identify them, however, it suffers from some limitations related to the over‐simplification of individuals to points.

Here, we propose a new approach called Overlapping Area Analysis (OAA) to test whether the consideration of the shape and orientation of the individuals reveal signs of interactions between species that would remain undetected with SPPA. We used this approach to analyse a fully mapped cryophilic grassland in the Sierra de Guadarrama National Park (Spain), where the crown of each individual plant (i.e. the species canopy) was approximated by a polygon. We then computed and compared the total overlapping area between the canopy of a focal species and that of any other species in the community with the expectations of a null model of random rotation of each plant around its centroid. We complemented the results of our new approach by comparing with that of SPPA of plants’ centroids.

Results of OAA showed that up to 41% of species pairs had less canopy overlap than expected, suggesting that many interspecific canopy associations in this plant community were significantly negative at the finest spatial scale. Contrarily, SPPA estimated that 12% of species pairs were positively associated at spatial scales up to 20 cm, confirming the facilitative effect displayed by the main engineer in the community (Festuca curvifolia Lag.) and by some other dominant species.

Our new approach quantifying canopy associations provides new insights into the processes guiding community assembly. While the results of SPPA suggested the prevalence of traditional ‘stress gradient hypothesis’ (i.e. prevalence of positive interactions under stressful abiotic conditions), OAA revealed that many interspecific canopy associations were significantly negative. Overall, most facilitated species optimized this positive effect by placing their centroids as close to the benefactor species as their foraging behaviour allowed while avoiding crown overlap. The method proposed is available in a dedicated r‐package that will facilitate its application by other ecologists.
BA3‐SNPs: Contemporary migration reconfigured in BayesAss for next‐generation sequence data
Authors: Mussmann Steven M. , Douglas Marlis R. , Chafin Tyler K. , Douglas Michael E.
Published: July 2019

Quantifying “demographic independence” is a vital step in establishing potential conservation units for a species in that it effectively distinguishes migration from within‐population reproduction. This is an important aspect because it allows for an accurate estimate of recruitment. For example, populations may be designated as 'management units' (=MUs) if indeed population growth results from local demography rather than immigration. Of additional interest is the calculation of immigrant ancestry and ascertainment of the temporal context over which immigration occurred. This is because MUs depend largely upon local (self‐sustaining) birth and death rates, and the quantification of ancestry is necessary to validate demographic independence. Dispersal rate is also of immediate interest to conservation biologists, and can be assessed by quantifying genetic divergence among populations. The capacity with which to gauge these benchmarks has now been extended herein to genome‐wide molecular data, in an attempt to adjust an analytical tool that was until now intractable for the next generation sequencing data.

In this study, a popular legacy program for migrant detection (i.e. BayesAss3) has been modified to accept SNP (single nucleotide polymorphism) data. We validated BA3‐SNPs using empirical data to demonstrate its suitability for both high‐performance and desktop computing environments. We also facilitate high analytical throughput by presenting a binary search algorithm that automates MCMC (Markov chain Monte Carlo) parameter tuning.

Our BA3‐SNPs‐autotune program required five or fewer rounds of optimization for 99% of input files, with acceptable mixing parameters derived in 100% of our test cases. Runtime for BA3‐SNPs is a function of the number of loci analysed. Benchmarking yielded an average runtime <32 hr (10 million MCMC generations) for datasets containing thousands of SNPs.

The BA3 algorithm remains a viable option for analysing modern SNP datasets. Source code (C++ and Python) is released publicly under the GNU General Public License v3.0, and is available for download (Linux and Mac OSX) from the following URL: https://github.com/stevemussmann/.
Comparative transcriptome analysis reveals genes related to the yolk ratio of duck eggs
Authors: Du X. , Ren J. D. , Xu X. Q. , Chen G. H. , Huang Y. , Du J. P. , Tao Z. R. , Cai Z. X. , Lu L. Z. , Yang H.
Published: July 2019

Yolk ratio is an important production index in the salted duck egg industry. Yolk constituents are deposited during development of follicles. However, the molecular mechanism responsible for different yolk ratios in laying ducks remains elusive. In this study, Shaoxing ducks laying eggs with different yolk ratios were chosen for an analysis of liver and ovary transcriptome information. Twelve libraries were constructed and generated an average of 58.5 million clean reads per library, of which 69% of clean reads from liver and 65% of clean reads from ovary were mapped to a reference genome. Between cross‐phenotype groups, a total of 250 and 230 differently expressed genes (DEGs) were identified in liver and ovary respectively, of which 101 and 50 DEGs respectively were characterized. Several DEGs were detected, among which HMGCS1, HMGCR, FDFT1, (DHCR7), (STARD4), CYP46A1 and LPIN3 are involved in cholesterol metabolism‐related pathways; KIAA0319, STARD4, AP1S3, SH3GL2 and CAV2 are involved in vesicular transport in the liver; and ELOVL2 and PSD2 are involved in fatty acid elongation and endocytosis in the ovary. High yolk‐ratio ducks had higher activity for cholesterol synthesis and molecular trafficking. The identification of candidate genes greatly advances the understanding of the genetic basis of the formation of different yolk ratios.
Pigmentation of the aortic and pulmonary valves in C57BL/6J x Balb/cByJ hybrid mice of different coat colours
Authors: Sánchez‐Piña Jaira , Lorenzale Miguel , Fernández María Carmen , Durán Ana C. , Sans‐Coma Valentín , Fernández Borja
Published: July 2019

Neural crest‐derived melanocytes have been recorded in several parts of the mammalian heart but not in the pulmonary valve. We report here the presence of melanin‐containing cells in the leaflets (cusps) of both the aortic and pulmonary valves. A total of 158 C57BL/6J x Balb/cByJ hybrid mice exhibiting four coat colours, namely black, white, agouti and non‐agouti brown, were examined. We sought for any relationship between the presence of melanocytes in the valves and the coat colour of the animals. The pigmentation levels of the leaflets were accomplished using a scale of five pigment intensities. White mice lacked pigment in the heart. In 10.5% of the remaining animals, there were melanocytes in the pulmonary valve leaflets. Thus, this is the first study to report the presence of such cells in the pulmonary valve of mammals. Melanocytes occurred in the leaflets of the aortic valves of 87.2% of mice. The incidence of melanocytes and the pigmentation level of the leaflets did not statistically differ according to the coat colours of the animals. This disagrees with previous observations, indicating that the amount of melanocytes in the heart reflects that of the skin. The incidence and distribution of melanocytes in aortic and pulmonary valves are consistent with the notion that the formation of the arterial valves is mediated by specific subpopulations of neural crest cells. We hypothesize that melanocytes, even not producing melanin, may be more frequent in the heart than previously thought, exerting presumably an immunological function.
Hidradenitis suppurativa and polycystic ovarian syndrome: Systematic review and meta‐analysis
Authors: Phan Kevin , Charlton Olivia , Smith Saxon D
Published: July 2019

Background/Objectives

Hidradenitis suppurativa has been associated with a number of pathologies, including various endocrine and autoimmune disorders. Although signs of hyperandrogenism are common in hidradenitis suppurativa, few formal studies have assessed the relationship between hidradenitis suppurativa and polycystic ovarian syndrome. Therefore, we performed a systematic review and meta‐analysis to assess the association between hidradenitis suppurativa and polycystic ovarian syndrome.

Methods

We performed a systematic review and meta‐analysis according to PRISMA guidelines. Odds ratio was used as the effect size, with random‐effects meta‐analysis.

Results

We identified five case‐control studies for inclusion. From pooled data, we found a significantly higher proportion of polycystic ovarian syndrome in hidradenitis suppurativa cases compared with controls (OR 2.64; 95% CI 1.69–4.11; P < 0.00001). There was significant heterogeneity noted (I2 = 88%, P < 0.00001). Limitations included that studies reviewed were observational by design which are susceptible to bias, and lack of randomisation.

Conclusions

In summary, pooled analysis of existing case‐control studies supports a significant association between hidradenitis suppurativa and polycystic ovarian syndrome. Our results imply that hidradenitis suppurativa patients with signs of hyperandrogenism may benefit from screening for polycystic ovarian syndrome, and may potentially benefit from anti‐androgen therapy.
Hyperhomocysteinaemia and the risk of recurrent venous thrombosis: results from the MEGA follow‐up study
Authors: Hensen Annefleur D. O. , Lijfering Willem M. , Cannegieter Suzanne C. , Rosendaal Frits R. , van Hylckama Vlieg Astrid
Published: July 2019

The measurement of homocysteine is still part of routine thrombosis or thrombophilia work‐up in many thrombosis centres in the world. Previous observational studies have shown that hyperhomocysteinaemia is associated with an increased risk of first and recurrent venous thrombosis (VT). Randomised trials, however, showed no benefit of homocysteine‐lowering therapy on the risk of first or recurrent VT. This discrepancy could be explained by incomplete adjustment for confounders in the observational studies. We investigated in a large population‐based follow‐up study whether if the levels of homocysteine and its metabolites, methionine and cysteine, were associated with recurrent VT. Approximately three months after discontinuation of anticoagulant treatment, homocysteine, methionine and cysteine concentrations were measured in 2210 patients with VT. During a median follow‐up of 6·9 years, 340 patients developed a recurrence (incidence rate, 2·8/100 patient‐years). We found that elevated homocysteine concentrations were not associated with an increased risk of recurrent VT, neither as a continuous variable per 5 μmol/l increase (hazard ratio [HR] 0·98 (95% confidence interval [CI], 0·90–1·04)) nor when levels were >95th (>23·0 μmol/l) percentile (HR 1·03 (95% CI, 0·65–1·64)). Similar results were obtained for cysteine and methionine values. We conclude that hyperhomocysteinaemia is not associated with an increased risk of recurrent VT.
Evidence for altered configural body processing in women at risk of disorders characterized by body image disturbance
Authors: Groves Katie , Kennett Steffan , Gillmeister Helge
Published: July 2019

Two studies were conducted to assess appearance‐related visual processing mechanisms in populations at risk of disorders characterized by body image disturbance. Using inverted stimuli, Experiment 1 assessed visual processing mechanisms associated with body, face, and house viewing in adolescents. Experiment 2 applied the same protocol to assess appearance‐related configural processing in high‐ and low‐risk adolescent women, and women recovering from disorders characterized by body image disturbance. Experiment 1 found evidence for typical configural face and body processing, although adolescent women reported higher levels of body image concern (BIC) and self‐objectified to a greater extent than adolescent men. In Experiment 2, typical body inversion effects were seen in the low‐risk group, whilst there was some evidence to suggest a disruption to the configural processing of body stimuli in high‐risk adolescents and in women recovering from body image disorders. Women in recovery were also quicker to respond to all stimuli, whilst high‐risk adolescents took longer to respond to bodies than to other stimuli. Configural face processing was intact in all groups, and effects did not directly relate to BIC or self‐objectification. These findings have implications for future research looking to inform early interventions and treatment, suggesting that there could be a tendency to visually process individual body parts at the expense of the whole‐body form in women at risk of developing body image disorders, as well as those in recovery.
MWCNT‐7 administered to the lung by intratracheal instillation induces development of pleural mesothelioma in F344 rats
Authors: Numano Takamasa , Higuchi Hitomi , Alexander David B. , Alexander William T. , Abdelgied Mohamed , El‐Gazzar Ahmed M. , Saleh Dina , Takase Hiroshi , Hirose Akihiko , Naiki‐Ito Aya , Suzuki Shugo , Takahashi Satoru , Tsuda Hiroyuki
Published: July 2019

Multi‐walled carbon nanotube‐7 (MWCNT‐7) fibers are biopersistent and have a structure similar to asbestos. MWCNT‐7 has been shown to induce malignant mesothelioma when administered by intrascrotal or intraperitoneal injection in rats and mice, and an inhalation study demonstrated that rats exposed to respirable MWCNT‐7 developed lung tumors. MWCNT‐N, which is similar to MWCNT‐7, was shown to induce both lung tumors and malignant mesothelioma in rats when administered by trans‐tracheal intrapulmonary spraying (TIPS). The present study was performed to investigate the carcinogenicity of MWCNT‐7 when administered by the TIPS method. Ten‐week‐old male F344/Crj rats were divided into 3 groups and administered 0.5 mL vehicle, 0.250 μg/mL MWCNT‐7 or 0.250 μg/mL crocidolite once a week for 12 weeks (total doses of 1.5 mg/rat) and then observed for up to 104 weeks. Rats in the MWCNT‐7 group began to die from pathologies associated with the development of malignant mesothelioma 35 weeks after the final TIPS administration. Overall, the incidence of malignant mesothelioma in the MWCNT‐7 group was significantly higher than in the vehicle or crocidolite groups.
Muscle spindle reinnervation using transplanted embryonic dorsal root ganglion cells after peripheral nerve transection in rats
Authors: Asano Kenichi , Nakano Tomonori , Tokutake Katsuhiro , Ishii Hisao , Nishizuka Takanobu , Iwatsuki Katsuyuki , Onishi Tetsuro , Kurimoto Shigeru , Yamamoto Michiro , Tatebe Masahiro , Hirata Hitoshi
Published: July 2019

Objectives

Muscle spindles are proprioceptive receptors in the skeletal muscle. Peripheral nerve injury results in a decreased number of muscle spindles and their morphologic deterioration. However, the muscle spindles recover when skeletal muscles are reinnervated with surgical procedures, such as nerve suture or nerve transfer. Morphological changes in muscle spindles by cell transplantation procedure have not been reported so far. Therefore, we hypothesized that transplantation of embryonic sensory neurons may improve sensory neurons in the skeletal muscle and reinnervate the muscle spindles.

Materials and methods

We collected sensory neurons from dorsal root ganglions of 14‐day‐old rat embryos and prepared a rat model of peripheral nerve injury by performing sciatic nerve transection and allowing for a period of one week before which we performed the cell transplantations. Six months later, the morphological changes of muscle spindles in the cell transplantation group were compared with the naïve control and surgical control groups.

Results

Our results demonstrated that transplantation of embryonic dorsal root ganglion cells induced regeneration of sensory nerve fibre and reinnervation of muscle spindles in the skeletal muscle. Moreover, calbindin D‐28k immunoreactivity in intrafusal muscle fibres was maintained for six months after denervation in the cell transplantation group, whereas it disappeared in the surgical control group.

Conclusions

Cell transplantation therapies could serve as selective targets to modulate mechanosensory function in the skeletal muscle.