bluuebunny/crossref_metadata_2025 huggingface dataset:
Melatonin improves the first cleavage of parthenogenetic embryos from vitrified–warmed mouse oocytes potentially by promoting cell cycle progression
Authors: Pan Bo , Qazi Izhar Hyder , Guo Shichao , Yang Jingyu , Qin Jianpeng , Lv Tianyi , Zang Shengqin , Zhang Yan , Zeng Changjun , Meng Qingyong , Han Hongbing , Zhou Guangbin
Published: July 2021

Background

This study investigated the effect of melatonin (MT) on cell cycle (G1/S/G2/M) of parthenogenetic zygotes developed from vitrified-warmed mouse metaphase II (MII) oocytes and elucidated the potential mechanism of MT action in the first cleavage of embryos.

Results

After vitrification and warming, oocytes were parthenogenetically activated (PA) andin vitrocultured (IVC). Then the spindle morphology and chromosome segregation in oocytes, the maternal mRNA levels of genes includingMiss, Doc1r, Setd2andYthdf2in activated oocytes, pronuclear formation, the S phase duration in zygotes, mitochondrial function at G1 phase, reactive oxygen species (ROS) level at S phase, DNA damage at G2 phase, early apoptosis in 2-cell embryos, cleavage and blastocyst formation rates were evaluated. The results indicated that the vitrification/warming procedures led to following perturbations 1) spindle abnormalities and chromosome misalignment, alteration of maternal mRNAs and delay in pronucleus formation, 2) decreased mitochondrial membrane potential (MMP) and lower adenosine triphosphate (ATP) levels, increased ROS production and DNA damage, G1/S and S/G2 phase transition delay, and delayed first cleavage, and 3) increased early apoptosis and lower levels of cleavage and blastocyst formation. Our results further revealed that such negative impacts of oocyte cryopreservation could be alleviated by supplementation of warming, recovery, PA and IVC media with 10− 9 mol/L MT before the embryos moved into the 2-cell stage of development.

Conclusions

MT might promote cell cycle progression via regulation of MMP, ATP, ROS and maternal mRNA levels, potentially increasing the first cleavage of parthenogenetic zygotes developed from vitrified–warmed mouse oocytes and their subsequent development.
Resection and reconstruction of pancreatic artery aneurysms caused by the compression of the celiac trunk by the median arcuate ligament: a report of two cases
Authors: Uchiyama Hideaki , Kuma Sosei , Ishida Mayumi , Tsujita Eiji , Nobuto Yoshinari , Kasagi Yuta , Natsugoe Keita , Aoyagi Takehiko , Iguchi Tomohiro , Itoh Hiroyuki
Published: July 2021

Background

Some patients with the compression of the celiac trunk by the median arcuate ligament (MAL) suffer pancreatic artery aneurysms (PAAs) due to excessive blood flow from the superior mesenteric artery. These aneurysms are in peril because they are prone to rupture irrespective of size. Here, we present two cases of resection and reconstruction of PAAs caused by the compression of the celiac trunk by the MAL.

Case presentation

Patient 1 was a 44-year-old man who was first diagnosed to have a visceral artery aneurysm with a diameter of 4 cm accidentally found by ultrasound examination at a regular medical check-up. Contrast-enhanced CT revealed the compression of the celiac trunk by the MAL and a PAA originating from the first jejunal artery. First, laparoscopic excision of the MAL followed by a stent placement into the celiac trunk was performed. Although the stent was patent, the PAA still grew. The patient underwent resection and reconstruction of the PAA. Reconstruction of the pancreatic arterial arcade was needed because clamping of the inferior pancreaticoduodenal artery (IPDA) resulted in disappearance of the hepatic arterial blood flow. The follow-up CT 2 years and 9 months after the operation revealed no recurrence of aneurysms and the patent anastomosis. Patient 2 was a 68-year-old man who presented with an epigastric pain. Contrast-enhanced CT revealed the compression of the celiac trunk by the MAL and a PAA approximately 6 cm in diameter originating from the IPDA. The PAA was surrounded by a relatively low-intensity area, suggesting impending rupture of the PAA. The patient underwent resection and reconstruction of the PAA under an emergency situation. Reconstruction of the pancreatic arterial arcade was needed because clamping of the inflow IPDA resulted in disappearance of the hepatic blood flow. The follow-up CT 1 year and 8 months after the operation revealed no recurrence of aneurysms and the patent anastomosis.

Conclusions

Although long-term follow-up is needed, resection and reconstruction is one of the therapeutic choices for PAAs caused by the compression of the celiac trunk by the MAL in order to prevent catastrophic aneurysm rupture.
Identifying the research gap of zoonotic disease in displacement: a systematic review
Authors: Braam Dorien Hanneke , Jephcott Freya Louise , Wood James Lionel Norman
Published: July 2021

Background

Outbreaks of zoonotic diseases that transmit between animals and humans, against a backdrop of increasing levels of forced migration, present a major challenge to global public health. This review provides an overview of the currently available evidence of how displacement may affect zoonotic disease and pathogen transmission, with the aim to better understand how to protect health and resilience of displaced and host populations.

Methods

A systematic review was conducted aligned with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) reporting guidelines. Between December 2019 - February 2020, PubMed, Web of Science, PLoS, ProQuest, Science Direct and JSTOR were searched for literature. Studies were included based on a focus on zoonotic disease risks in displacement and/or humanitarian emergencies, and relevance in terms of livestock dependency of the displaced populations. Evidence was synthesised in form of a table and thematic analysis.

Results

Of all records, 78 papers were selected for inclusion. Among the included studies, the majority were based on secondary data, including literature reviews (n=43) and case studies (n=5), while the majority of papers covered wide geographical areas such as the Global South (n=17) and Africa (n=20). The review shows significant gaps in the literature, which is specifically lacking primary data on zoonotic diseases in displacement. Risk factors for the transmission of zoonoses in displacement are based on generic infectious disease risks, which include the loss of health services, increased population density, changes in environment, reduced quality of living conditions and socio-economic factors. Regardless of the presence of these disease drivers during forced migration however, there is little evidence of large-scale zoonotic disease outbreaks linked directly to livestock in displacement.

Conclusion

Due to the lack of primary research, the complex interlinkages of factors affecting zoonotic pathogen transmission in displacement remain unclear. While the presence of animals may increase the burden of zoonotic pathogens, maintaining access to livestock may improve livelihoods, nutrition and mental health, with the potential to reduce people’s vulnerability to disease. Further primary interdisciplinary and multi-sectoral research is urgently required to address the evidence gaps identified in this review to support policy and program development.
Uncertainty modeling of wind power frequency regulation potential considering distributed characteristics of forecast errors
Authors: Yan Cheng , Tang Yi , Dai Jianfeng , Wang Chenggen , Wu Shengjun
Published: July 2021

Large-scale integration of wind power generation decreases the equivalent inertia of a power system, and thus makes frequency stability control challenging. However, given the irregular, nonlinear, and non-stationary characteristics of wind power, significant challenges arise in making wind power generation participate in system frequency regulation. Hence, it is important to explore wind power frequency regulation potential and its uncertainty. This paper proposes an innovative uncertainty modeling method based on mixed skew generalized error distribution for wind power frequency regulation potential. The mapping relationship between wind speed and the associated frequency regulation potential is established, and key parameters of the wind turbine model are identified to predict the wind power frequency regulation potential. Furthermore, the prediction error distribution of the frequency regulation potential is obtained from the mixed skew model. Because of the characteristics of error partition, the error distribution model and predicted values at different wind speed sections are summarized to generate the uncertainty interval of wind power frequency regulation potential. Numerical experiments demonstrate that the proposed model outperforms other state-of-the-art contrastive models in terms of the refined degree of fitting error distribution characteristics. The proposed model only requires the wind speed prediction sequence to accurately model the uncertainty interval. This should be of great significance for rationally optimizing system frequency regulation resources and reducing redundant backup.
A survey: which features are required for dynamic visual simultaneous localization and mapping?
Authors: Xu Zewen , Rong Zheng , Wu Yihong
Published: July 2021

In recent years, simultaneous localization and mapping in dynamic environments (dynamic SLAM) has attracted significant attention from both academia and industry. Some pioneering work on this technique has expanded the potential of robotic applications. Compared to standard SLAM under the static world assumption, dynamic SLAM divides features into static and dynamic categories and leverages each type of feature properly. Therefore, dynamic SLAM can provide more robust localization for intelligent robots that operate in complex dynamic environments. Additionally, to meet the demands of some high-level tasks, dynamic SLAM can be integrated with multiple object tracking. This article presents a survey on dynamic SLAM from the perspective of feature choices. A discussion of the advantages and disadvantages of different visual features is provided in this article.
Bio-competitive exclusion: efficacy of non-aflatoxigenic Aspergillus section Flavi-L morphotypes in control of aflatoxigenic Aspergillus flavus in groundnuts (Arachis hypogaea L.)
Authors: Chofamba Anyway
Published: July 2021

Background

The biological control mechanism of Aspergillus flavus (aflatoxigenic) strains in groundnuts with atoxigenic strains from the same species through competitive exclusion employed the use of endemic and well-adapted strains within the agro-ecological zones of Zimbabwe. The selected elite non-aflatoxigenic isolates of A. flavus native to Zimbabwe were evaluated for their capability to reduce aflatoxin contamination in groundnuts under laboratory conditions.

Results

Average reduction percentages in aflatoxin B concentration for the 2019 and 2020 set of experiments ranged from 91.6 ± 3.4 to 95.8 ± 3.1% and 90.29 ± 3.6% to 95.29 ± 4.1%, respectively. Levels of aflatoxin in the co-inoculation research experiments administered were significantly reduced in all the experimental units carried out. Treatment efficiencies of the tested isolates in this study at 4:1 and 2:1 ranged from 1.20 to 2.52 and from 1.02 to 1.21, respectively. The efficacy of the tested non-aflatoxigenic strains against the aflatoxigenic strain native to Zimbabwe (ZMW 0127) indicates that the non-aflatoxigenic isolates of A. flavus. have sound practical applications against vast communities of aflatoxin-producing fungi across all the agro-ecological zones in Zimbabwe.

Conclusion

The recognized non-aflatoxigenic isolates will be of an incentive as dynamic active ingredients in biocontrol formulations for the decrease in aflatoxins in groundnuts grown in Zimbabwe.
Central µ-Opioid Receptor Antagonism Blocks Glucoprivic LH Pulse Suppression and Gluconeogenesis/Feeding in Female Rats
Authors: Tsuchida Hitomi , Kawai Narumi , Yamada Koki , Takizawa Marina , Inoue Naoko , Uenoyama Yoshihisa , Tsukamura Hiroko
Published: July 2021

Energetic status often affects reproductive function, glucose homeostasis, and feeding in mammals. Malnutrition suppresses pulsatile release of the gonadotropin-releasing hormone (GnRH)/luteinizing hormone (LH) and increases gluconeogenesis and feeding. The present study aims to examine whether β-endorphin-μ-opioid receptor (MOR) signaling mediates the suppression of pulsatile GnRH/LH release and an increase in gluconeogenesis/feeding induced by malnutrition. Ovariectomized female rats treated with a negative feedback level of estradiol-17β (OVX + low E2) receiving 2-deoxy-D-glucose (2DG), an inhibitor of glucose utilization, intravenously (iv) were used as a malnutrition model. An administration of D-Phe-Cys-Tyr-D-Trp-Orn-Thr-Pen-Thr-NH2 (CTOP), a selective MOR antagonist, into the third ventricle blocked the suppression of the LH pulse and increase in gluconeogenesis/feeding induced by iv 2DG administration. Histological analysis revealed that arcuate Kiss1 (kisspeptin gene)-expressing cells and preoptic Gnrh1 (GnRH gene)-expressing cells co-expressed little Oprm1 (MOR gene), while around 10% of arcuate Slc17a6 (glutamatergic marker gene)-expressing cells co-expressed Oprm1. Further, the CTOP treatment decreased the number of fos-positive cells in the paraventricular nucleus (PVN) in OVX + low E2 rats treated with iv 2DG but failed to affect the number of arcuate fos-expressing Slc17a6-positive cells. Taken together, these results suggest that the central β-endorphin-MOR signaling mediates the suppression of pulsatile LH release and that the β-endorphin may indirectly suppress the arcuate kisspeptin neurons, a master regulator for GnRH/LH pulses during malnutrition. Furthermore, the current study suggests that central β-endorphin-MOR signaling is also involved in gluconeogenesis and an increase in food intake by directly or indirectly acting on the PVN neurons during malnutrition in female rats.
Cyclic growth of dermal papilla and regeneration of follicular mesenchymal components during feather cycling
Authors: Wu Ping , Jiang Ting-Xin , Lei Mingxing , Chen Chih-Kuan , Hsieh Li Shu-Man , Widelitz Randall B. , Chuong Cheng-Ming
Published: July 2021

How dermis maintains tissue homeostasis in cyclic growth and wounding is a fundamental unsolved question. Here, we study how dermal components of feather follicles undergo physiological (molting) and plucking injury-induced regeneration in chickens. Proliferation analyses reveal quiescent, transient-amplifying (TA) and long-term label-retaining dermal cell (LRDC) states. During the growth phase, LRDCs are activated to make new dermal components with distinct cellular flows. Dermal TA cells, enriched in the proximal follicle, generate both peripheral pulp, which extends distally to expand the epithelial-mesenchymal interactive interface for barb patterning, and central pulp, which provides nutrition. Entering the resting phase, LRDCs, accompanying collar bulge epidermal label-retaining cells, descend to the apical dermal papilla. In the next cycle, these apical dermal papilla LRDCs are re-activated to become new pulp progenitor TA cells. In the growth phase, lower dermal sheath can generate dermal papilla and pulp. Transcriptome analyses identify marker genes and highlight molecular signaling associated with dermal specification. We compare the cyclic topological changes with those of the hair follicle, a convergently evolved follicle configuration. This work presents a model for analyzing homeostasis and tissue remodeling of mesenchymal progenitors.
Frequency of parasitic infections in Arachishypogaea L (groundnuts), Citrulluslanatus seeds (watermelon seeds), and Ziziphusspina-christi (nabag) sold by street vendors in Khartoum State, Sudan: a cross-sectional study
Authors: Suleiman Mohammed Arwa , Abd Alla Ahmed , Galander Ahmed , Elfaki Tayseer , Ibrahim Hashim Ahmed , N. Altayb Hisham
Published: July 2021

Background: Plant products, including seeds are an important source of vitamins, minerals, proteins, and energy. This study aimed to assess parasitic contaminations in roasted groundnuts,

nabag, and tasali (watermelon seeds) sold by street vendors in Khartoum State, Sudan.

Methods: The frequency of parasitic contaminations among all crop products was detected by washing the plants with saline, and then conducting an examination using a formal ether

concentration technique (FECT), followed by a saturated sugar floatation technique.

Results: The detected parasites belonged to two species: Entamoeba histolytica (33.3%) and Giardia lamblia (15.6%). No helminthic parasites were detected. Mixed contamination of the mentioned parasites was also observed (11.1%). The most contaminated crop was nabag, followed by groundnut, and finally tasali.

Conclusion: No relation was established between the positivity of samples for parasites and crop type, Khartoum State city, or  seller sex. FECT was more sensitive than the saturated sugar floatation technique as a detection method.
Case Report: Diabetic nephropathy aggravates the progression and prognosis of COVID-19-associated acute limb ischemia
Authors: Hertanto Decsa M. , Sutanto Henry , Adi Soebagijo
Published: July 2021

Hypercoagulation is a hallmark of both the novel coronavirus disease (COVID-19) and type 2 diabetes mellitus (T2DM). It increases the risk for vascular thrombosis, including peripheral artery diseases. Among others, acute limb ischemia (ALI) is one of most common complications that requires immediate and prompt treatments to reduce morbidity and mortality. However, the complex interplay between COVID-19, T2DM and its complications (e.g., diabetic nephropathy), and ALI creates a great challenge in the management of the disease. Here, we present a case of a 59-year-old diabetic female with progressive pain in her left leg in the last five years, which was significantly intensified following COVID-19 diagnosis. Bluish coloration, numbness and functional impairments were observed during examinations with no palpable pulsation on left posterior tibial and dorsalis pedis arteries. The patient also had diabetic nephropathy (stage III), hypoalbuminemia, anemia and a urinary tract infection that complicated the management of the disease. Due to the excruciating pain and the worsening of the limb conditions, right leg revascularization and left leg amputation were performed at day 14 after admission. Following the surgeries, no more pain was observed and patient was discharged for further follow-up at the outpatient clinic.
De la participación simbólica a la participación política de la niñez: aproximación cualitativa en estudiantes de educación primaria
Authors: Salazar Alondra , Muñiz Carlos , Saldierna Alma Rosa
Published: July 2021

La participación de niños y niñas ha planteado su reconocimiento como sujetos de derecho, proyectándolos, como ciudadanos activos dentro de la sociedad. Para ello, la legislación mexicana establece mecanismos de participación que promueven su involu­cramiento político. Pero cabe cuestionar cómo se ha desarrollado dicha participación, limitada normalmente a un ámbito simbólico (tokenismo), y cómo se manifiestan sus actitudes políticas hasta construir su ciudadanía. Para dar respuesta a estas cuestiones, se realizaron ocho grupos focales con niños y niñas de 5 ° y/o 6 ° grado de educación primaria del estado de Nuevo León, México. Más allá de una actitud pasiva, se observó un nivel elevado de interés por parte de niñas y niños para influir en la toma de decisiones sobre problemáticas de su entorno, aunque con limitaciones para su desarrollo efectivo.
Transit Planning Optimization Under Ride-Hailing Competition and Traffic Congestion
Authors: Wei Keji , Vaze Vikrant , Jacquillat Alexandre
Published: July 2021

With the soaring popularity of ride-hailing, the interdependence between transit ridership, ride-hailing ridership, and urban congestion motivates the following question: can public transit and ride-hailing coexist and thrive in a way that enhances the urban transportation ecosystem as a whole? To answer this question, we develop a mathematical and computational framework that optimizes transit schedules while explicitly accounting for their impacts on road congestion and passengers’ mode choice between transit and ride-hailing. The problem is formulated as a mixed integer nonlinear program and solved using a bilevel decomposition algorithm. Based on computational case study experiments in New York City, our optimized transit schedules consistently lead to 0.4%–3% system-wide cost reduction. This amounts to rush-hour savings of millions of dollars per day while simultaneously reducing the costs to passengers and transportation service providers. These benefits are driven by a better alignment of available transportation options with passengers’ preferences—by redistributing public transit resources to where they provide the strongest societal benefits. These results are robust to underlying assumptions about passenger demand, transit level of service, the dynamics of ride-hailing operations, and transit fare structures. Ultimately, by explicitly accounting for ride-hailing competition, passenger preferences, and traffic congestion, transit agencies can develop schedules that lower costs for passengers, operators, and the system as a whole: a rare win–win–win outcome.
Focal osteolysis and corrosion at the junction of Precice Stryde intramedullary lengthening device
Authors: Frommer Adrien , Roedl Robert , Gosheger Georg , Hasselmann Julian , Fuest Cordula , Toporowski Gregor , Laufer Andrea , Tretow Henning , Schulze Martin , Vogt Bjoern
Published: July 2021

Aims

This study aims to enhance understanding of clinical and radiological consequences and involved mechanisms that led to corrosion of the Precice Stryde (Stryde) intramedullary lengthening nail in the post market surveillance era of the device. Between 2018 and 2021 more than 2,000 Stryde nails have been implanted worldwide. However, the outcome of treatment with the Stryde system is insufficiently reported.

Methods

This is a retrospective single-centre study analyzing outcome of 57 consecutive lengthening procedures performed with the Stryde nail at the authors’ institution from February 2019 until November 2020. Macro- and microscopic metallographic analysis of four retrieved nails was conducted. To investigate observed corrosion at telescoping junction, scanning electron microscopy (SEM) and energy dispersive x-ray spectroscopy (EDX) were performed.

Results

Adjacent to the nail’s telescoping junction, osteolytic changes were observed in bi-planar radiographs of 20/57 segments (35%) after a mean of 9.5 months (95% confidence interval 7.2 to 11.9) after surgery. A total of 8/20 patients with osseous alterations (40%) reported rest and ambulation pain of the lengthened segment during consolidation. So far, 24 Stryde nails were retrieved and in 20 (83%) macroscopic corrosion was observed at the nail’s telescoping junction. Before implant removal 11/20 radiographs (55%) of lengthened segments with these 20 nails revealed osteolysis. Implant retrieval analysis by means of SEM showed pitting and crevice corrosion. EDX detected chromium as the main metallic element of corrosion.

Conclusion

Patients are exposed to the risk of implant-related osteolysis of unclear short- and long-term clinical consequences. The authors advocate in favour of an early implant removal after osseous consolidation. Cite this article: Bone Joint Res 2021;10(7):425–436.
Comparative Analysis of the Numeral Systems of Ígálà , Yoruba, German and English
Authors: Omachonu Gideon S.
Published: July 2021

This study undertakes a comparative analysis of the numeral systems of Igala, Yoruba, English and German. An essential part of data collation for the study comprises compilation of comparative wordlists of Ígálà, Yoruba, German and English numeral systems in addition to the writer's personal observation and knowledge of the systems. The investigation reveals that the complexity of deriving especially non-basic numerals in the languages involves three predominant arithmetic processes of addition, subtraction (Yoruba in particular) and multiplication in addition to certain grammatical processes, especially vowel elision, clipping, compounding and so on. In addition, the summary of the quasi constraints or derivational patterns for the languages reveals that whereas German and English maintain very similar patterns because of their very close affinity as sisters from the same parent, it is not so with Ígálà and Yoruba even though both belong to the same language family. Incorporating insights from optimality theory, the paper argues that even though numeracy and the constraints that ensure well-formedness of numerals are somewhat universal, parametric variations abound. The actual patterning of the sequences of the derivational processes in individual languages may be very similar but definitely not the same, no matter how closely related the languages concerned may be. If not, they would cease to represent core grammars of different languages.
Infrared object classification with a hybrid optical convolution neural
network
Authors: Chen Jianbo , Talley Jennifer , Kelly Kevin F.
Published: July 2021

Recent advancements in machine vision have enabled a great range of
applications from image classification to autonomous driving. However,
there is still a dilemma between the pursuit of higher-resolution
training images that require a detector array with more pixels on the
front end, and the demands on acquisition for embedded systems
restrained by power, transmission bandwidth, and storage. In this
paper, a multi-pixel hybrid optical convolutional neural network
machine vision system was designed and validated to perform high-speed
infrared object detection. The proposed system replicates the front
convolution layer in a convolutional neural network utilizing a
high-speed digital micro-mirror device to display the first layer of
kernels at a resolution greater than the subsequent detector. After
this, further convolutions are carried out in software to perform the
object recognition. An infrared vehicle dataset was used to validate
the performance of the hybrid system through simulation. We also
tested this in hardware by performing infrared classification on toy
vehicles to showcase the feasibility of such a design.
Loss ratio parameter γ to analyze transmission characteristics for optical antenna systems
Authors: He Miao , Caiyang Weinan , Jiang Ping , Zhou Miaofang , Qin Yan , Cao Biao , Yang Huajun
Published: July 2021

Analyzing optical antenna systems through geometrical optics is quite popular for its convenience, which, however, may cause remarkable errors. This paper uses both geometrical optics and diffraction theory to analyze the performance of a traditional optical antenna system, and the results calculated through the two methods are carefully compared. Based on the comparison, it shows the situations in which geometric optics will cause significant errors. In addition, a parameter

γ

is defined to quickly determine whether geometrical optics is suitable for analyzing optical antenna systems under some situations. This paper can help engineers quickly choose the proper method for designing and analyzing optical antenna systems.
Implementation of the real–virtual 3D scene-fused full-parallax holographic stereogram
Authors: Yan Xingpeng , Wang Chenqing , Liu Yunpeng , Wang Xi , Liu Xinlei , Jing Tao , Chen Song , Li Pei , Jiang Xiaoyu
Published: July 2021

This work focuses on the generation of three-dimensional (3D)-scene information as well as the fusion of real and virtual 3D scene information for the full-parallax holographic stereogram based on the effective perspective images’ segmentation and mosaicking (EPISM) method. The improved depth-image-based rendering (DIBR) method was used to generate the virtual viewpoint images of the real 3D scene, and the regularization and densification processing models of the degraded light field were established; as a result, the real sampling-light field was reconstructed. Combined with the computer-rendered virtual 3D scene information, a “real + virtual” light-field fusion method based on a pixel-affine-projection was proposed to realize the fusion of the real and virtual 3D scene. The fusion information was then processed by the EPISM encoding and was then holographically printed. The optical experiment results showed that the full-parallax holographic stereogram with the real–virtual scene-fused 3D scenes could be correctly printed and reconstructed, which validated the effectiveness of our proposed method.
Prioritizing and characterizing functionally relevant genes across human tissues
Authors: Somepalli Gowthami , Sahoo Sarthak , Singh Arashdeep , Hannenhalli Sridhar
Published: July 2021

Knowledge of genes that are critical to a tissue’s function remains difficult to ascertain and presents a major bottleneck toward a mechanistic understanding of genotype-phenotype links. Here, we present the first machine learning model–FUGUE–combining transcriptional and network features, to predict tissue-relevant genes across 30 human tissues. FUGUE achieves an average cross-validation auROC of 0.86 and auPRC of 0.50 (expected 0.09). In independent datasets, FUGUE accurately distinguishes tissue or cell type-specific genes, significantly outperforming the conventional metric based on tissue-specific expression alone. Comparison of tissue-relevant transcription factors across tissue recapitulate their developmental relationships. Interestingly, the tissue-relevant genes cluster on the genome within topologically associated domains and furthermore, are highly enriched for differentially expressed genes in the corresponding cancer type. We provide the prioritized gene lists in 30 human tissues and an open-source software to prioritize genes in a novel context given multi-sample transcriptomic data.
The selfish yeast plasmid utilizes the condensin complex and condensed chromatin for faithful partitioning
Authors: Kumar Deepanshu , Prajapati Hemant Kumar , Mahilkar Anjali , Ma Chien-Hui , Mittal Priyanka , Jayaram Makkuni , Ghosh Santanu K.
Published: July 2021

Equipartitioning by chromosome association and copy number correction by DNA amplification are at the heart of the evolutionary success of the selfish yeast 2-micron plasmid. The present analysis reveals frequent plasmid presence near telomeres (TELs) and centromeres (CENs) in mitotic cells, with a preference towards the former. Inactivation of Cdc14 causes plasmid missegregation, which is correlated to the non-disjunction of TELs (and of rDNA) under this condition. Induced missegregation of chromosome XII, one of the largest yeast chromosomes which harbors the rDNA array and is highly dependent on the condensin complex for proper disjunction, increases 2-micron plasmid missegregation. This is not the case when chromosome III, one of the smallest chromosomes, is forced to missegregate. Plasmid stability decreases when the condensin subunit Brn1 is inactivated. Brn1 is recruited to the plasmid partitioning locus (STB) with the assistance of the plasmid-coded partitioning proteins Rep1 and Rep2. Furthermore, in a dihybrid assay, Brn1 interacts with Rep1-Rep2. Taken together, these findings support a role for condensin and/or condensed chromatin in 2-micron plasmid propagation. They suggest that condensed chromosome loci are among favored sites utilized by the plasmid for its chromosome-associated segregation. By homing to condensed/quiescent chromosome locales, and not over-perturbing genome homeostasis, the plasmid may minimize fitness conflicts with its host. Analogous persistence strategies may be utilized by other extrachromosomal selfish genomes, for example, episomes of mammalian viruses that hitchhike on host chromosomes for their stable maintenance.
Transcriptomic analysis and molecular docking reveal genes involved in the response of Aedes aegypti larvae to an essential oil extracted from Eucalyptus
Authors: Sierra Ivana , Latorre-Estivalis Jose Manuel , Traverso Lucila , Gonzalez Paula V. , Aptekmann Ariel , Nadra Alejandro Daniel , Masuh Héctor , Ons Sheila
Published: July 2021

Background

Aedes aegypti (L.) is an urban mosquito, vector of several arboviruses that cause severe diseases in hundreds of million people each year. The resistance to synthetic insecticides developed by Ae. aegypti populations worldwide has contributed to failures in vector control campaigns, increasing the impact of arbovirus diseases. In this context, plant-derived essential oils with larvicidal activity could be an attractive alternative for vector control. However, the mode of action and the detoxificant response of mosquitoes to plant derived compounds have not been established, impairing the optimization of their use.

Methods and findings

Here we compare gene expression in Ae. aegypti larvae after 14 hrs of exposure to Eucalyptus camaldulensis essential oil with a control group exposed to vehicle (acetone) for the same lapse, by using RNA-Seq. We found differentially expressed genes encoding for cuticle proteins, fatty-acid synthesis, membrane transporters and detoxificant related gene families (i.e. heat shock proteins, cytochromes P450, glutathione transferases, UDP-glycosyltransferases and ABC transporters). Finally, our RNA-Seq and molecular docking results provide evidence pointing to a central involvement of chemosensory proteins in the detoxificant response in mosquitoes.

Conclusions and significance

Our work contributes to the understanding of the physiological response of Ae. aegypti larvae to an intoxication with a natural toxic distilled from Eucalyptus leafs. The results suggest an involvement of most of the gene families associated to detoxification of xenobiotics in insects. Noteworthy, this work provides important information regarding the implication of chemosensory proteins in the detoxification of a natural larvicide. Understanding the mode of detoxification of Eucalyptus distilled compounds could contribute to their implementation as a tool in mosquito control.
The rodent object-in-context task: A systematic review and meta-analysis of important variables
Authors: Sep Milou S. C. , Vellinga Marijn , Sarabdjitsingh R. Angela , Joëls Marian
Published: July 2021

Environmental information plays an important role in remembering events. Information about stable aspects of the environment (here referred to as ‘context’) and the event are combined by the hippocampal system and stored as context-dependent memory. In rodents (such as rats and mice), context-dependent memory is often investigated with the object-in-context task. However, the implementation and interpretation of this task varies considerably across studies. This variation hampers the comparison between studies and—for those who design a new experiment or carry out pilot experiments–the estimation of whether observed behavior is within the expected range. Also, it is currently unclear which of the variables critically influence the outcome of the task. To address these issues, we carried out a preregistered systematic review (PROSPERO CRD42020191340) and provide an up-to-date overview of the animal-, task-, and protocol-related variations in the object-in-context task for rodents. Using a data-driven explorative meta-analysis we next identified critical factors influencing the outcome of this task, such as sex, testbox size and the delay between the learning trials. Based on these observations we provide recommendations on sex, strain, prior arousal, context (size, walls, shape, etc.) and timing (habituation, learning, and memory phase) to create more consensus in the set-up, procedure, and interpretation of the object-in-context task for rodents. This could contribute to a more robust and evidence-based design in future animal experiments.
A deadly encounter: Alien invasive Spodoptera frugiperda in Africa and indigenous natural enemy, Cotesia icipe (Hymenoptera, Braconidae)
Authors: Mohamed Samira Abuelgasim , Wamalwa Mark , Obala Francis , Tonnang Henri E. Z. , Tefera Tadele , Calatayud Paul-Andre , Subramanian Sevgan , Ekesi Sunday
Published: July 2021

The invasion and wide spread of Spodoptera frugiperda represent real impediments to food security and the livelihood of the millions of maize and sorghum farming communities in the sub-Saharan and Sahel regions of Africa. Current management efforts for the pest are focused on the use of synthetic pesticides, which are often economically unviable and are extremely hazardous to the environment. The use of biological control offers a more economically and environmentally safer alternative. In this study, the performance of the recently described parasitoid, Cotesia icipe, against the pest was elucidated. We assessed the host stage acceptability by and suitability for C. icipe, as well as its ovigenic status. Furthermore, the habitat suitability for the parasitoid in the present and future climatic conditions was established using Maximum Entropy (MaxEnt) algorithm and the Genetic Algorithm for Rule‐set Prediction (GARP). Cotesia icipe differentially accepted the immature stages of the pest. The female acceptance of 1st and 2nd instar larvae for oviposition was significantly higher with more than 60% parasitism. No oviposition on the egg, 5th and 6th larval instars, and pupal stages was observed. Percentage of cocoons formed, and the number of emerged wasps also varied among the larval stages. At initial parasitism, parasitoid progenies, time to cocoon formation and overall developmental time were significantly affected by the larval stage. Egg-load varied significantly with wasp age, with six-day-old wasps having the highest number of mature eggs. Ovigeny index of C. icipe was 0.53. Based on the models, there is collinearity in the ecological niche of the parasitoid and the pest under current and future climate scenarios. Eastern, Central and parts of coastal areas of western Africa are highly suitable for the establishment of the parasitoid. The geographic distribution of the parasitoid would remain similar under future climatic conditions. In light of the findings of this study, we discuss the prospects for augmentative and classical biological control of S. frugiperda with C. icipe in Africa.
Landscape structure shapes the diversity of tree seedlings at multiple spatial scales in a fragmented tropical rainforest
Authors: Nicasio-Arzeta Sergio , Zermeño-Hernández Isela E. , Maza-Villalobos Susana , Benítez-Malvido Julieta
Published: July 2021

The maintenance of seedling diversity of animal-dispersed tree species is fundamental for the structure and function of forest patches in fragmented tropical rainforests. Nonetheless, the effects of landscape structure at different spatial scales on α- and β-diversity of tree seedling communities are recently explored. Using a multi-scale approach, we assessed the relative effect of landscape composition and configuration on α- and β-diversity of animal-dispersed seedlings within 16 forest patches in the Lacandona rainforest, Mexico. We assessed these effects at 13 spatial scales (from 300 to 1500 m radius, at 100 m intervals) for three metrics of effective number of species considering α- and β-diversity. We found that α-diversity was largely affected by landscape composition and β-diversity by landscape configuration. On the one hand, the amount of secondary forest influenced α-diversity. Additionally, species richness increased in landscapes with highly aggregated forest patches. On the other hand, β-diversity was affected positively by forest fragmentation and negatively by the edge contrast of forest patches with the surrounding matrix. Our findings indicate that landscape configuration is a strong driver of seedling diversity in highly deforested rainforests. Promoting forest patches and secondary forests through payment for ecosystem services’ programs, favoring matrix quality within land-sharing schemes of smallholder agriculture and secondary forest management, and identifying restoration opportunities for assisted or unassisted natural regeneration are urgently needed for conservation of seedling diversity in human-modified tropical landscapes.
Dropping out of voluntary community-based health insurance in rural Uganda: Evidence from a cross-sectional study in rural south-western Uganda
Authors: Nshakira-Rukundo Emmanuel , Mussa Essa Chanie , Cho Min Jung
Published: July 2021

Aim

Community Based Health Insurance (CBHI) schemes have become central to health systems financing as avenues of achieving universal health coverage in developing countries. Yet, while emphasis in research and policy has mainly concentrated on enrolment, very little has been apportioned to high rates of dropping out after initial enrolment. The main aim of this study is to understand the factors behind CBHI dropping out through a cross-sectional quantitative research design to gain insights into curtailing the drop out of CBHI in Uganda.

Methods

The survey for the quantitative research component took place between August 2015 and March 2016 covering 464 households with under-5 children in south-western Uganda. To understand the factors associated with dropping out of CBHI, we employ a multivariate logistic regression on a subsample of 251 households who were either currently enrolled or had enrolled at one time and later dropped out.

Results

Overall, we find that 25.1 percent of the households that had ever enrolled in insurance reported dropping out. Household socioeconomic status (wealth) was one of the key factors that associated with dropping out. Larger household sizes and distance from the hospital were significantly associated with dropping out. More socially connected households were less likely to drop out revealing the influence of community social capital in keeping households insured.

Conclusion

The findings have implications for addressing equity and inclusion concerns in community-based health insurance programmes such as one in south-western Uganda. Even when community based informal system aim for inclusion of the poorest, they are not enough and often the poorest of the poor slip into the cracks and remain uninsured or drop out. Moreover, policy interventions toward curtailing high dropout rates should be considered to ensure financial sustainability of CBHI schemes.
Genotypic analysis of the female BPH/5 mouse, a model of superimposed preeclampsia
Authors: Sones Jenny L. , Yarborough Christina C. , O’Besso Valerie , Lemenze Alexander , Douglas Nataki C.
Published: July 2021

Animal models that recapitulate human diseases and disorders are widely used to investigate etiology, diagnosis, and treatment of those conditions in people. Disorders during pregnancy are particularly difficult to explore as interventions in pregnant women are not easily performed. Therefore, models that allow for pre-conception investigations are advantageous for elucidating the mechanisms involved in adverse pregnancy outcomes that are responsible for both maternal and fetal morbidity, such as preeclampsia. The Blood Pressure High (BPH)/5 mouse model has been used extensively to study the pathogenesis of preeclampsia. The female BPH/5 mouse is obese with increased adiposity and borderline hypertension, both of which are exacerbated with pregnancy making it a model of superimposed preeclampsia. Thus, the BPH/5 model shares traits with a large majority of women with pre-existing conditions that predisposes them to preeclampsia. We sought to explore the genome of the BPH/5 female mouse and determine the genetic underpinnings that may contribute to preeclampsia-associated phenotypes in this model. Using a whole genome sequencing approach, we are the first to characterize the genetic mutations in BPH/5 female mice that make it unique from the closely related BPH/2 model and the normotensive background strain, C57Bl/6. We found the BPH/5 female mouse to be uniquely different from BPH/2 and C57Bl/6 mice with a genetically complex landscape. The majority of non-synonymous consequences within the coding region of BPH/5 females were missense mutations found most abundant on chromosome X when comparing BPH/5 and BPH/2, and on chromosome 8 when comparing BPH/5 to C57Bl/6. Genetic mutations in BPH/5 females largely belong to immune system-related processes, with overlap between BPH/5 and BPH/2 models. Further studies examining each gene mutation during pregnancy are warranted to determine key contributors to the BPH/5 preeclamptic-like phenotype and to identify genetic similarities to women that develop preeclampsia.
Belowground productivity varies by assessment technique, vegetation type, and nutrient availability in tidal freshwater forested wetlands transitioning to marsh
Authors: From Andrew S. , Krauss Ken W. , Noe Gregory B. , Cormier Nicole , Stagg Camille L. , Moss Rebecca F. , Whitbeck Julie L.
Published: July 2021

Wetlands along upper estuaries are characterized by dynamic transitions between forested and herbaceous communities (marsh) as salinity, hydroperiod, and nutrients change. The importance of belowground net primary productivity (BNPP) associated with fine and coarse root growth also changes but remains the dominant component of overall productivity in these important blue carbon wetlands. Appropriate BNPP assessment techniques to use in various tidal wetlands are not well-defined, and could make a difference in BNPP estimation. We hypothesized that different BNPP techniques applied among tidal wetlands differ in estimation of BNPP and possibly also correlate differently with porewater nutrient concentrations. We compare 6-month and 12-month root ingrowth, serial soil coring techniques utilizing two different calculations, and a mass balance approach (TBCA, Total Belowground Carbon Allocation) among four tidal wetland types along each of two river systems transitioning from freshwater forest to marsh. Median values of BNPP were 266 to 2946 g/m2/year among all techniques used, with lower BNPP estimation from root ingrowth cores and TBCA (266–416 g/m2/year), and higher BNPP estimation from serial coring of standing crop root biomass (using Smalley and Max-Min calculation methods) (2336–2946 g/m2/year). Root turnover (or longevity) to a soil depth of 30 cm was 2.2/year (1.3 years), 2.7/year (1.1 years), 4.5/year (0.9 years), and 1.2/year (2.6 years), respectively, for Upper Forest, Middle Forest, Lower Forest, and Marsh. Marsh had greater root biomass and BNPP, with slower root turnover (greater root longevity) versus forested wetlands. Soil porewater concentrations of NH3 and reactive phosphorus stimulated BNPP in the marsh when assessed with short-deployment BNPP techniques, indicating that pulses of mineralized nutrients may stimulate BNPP to facilitate marsh replacement of forested wetlands. Overall, ingrowth techniques appeared to represent forested wetland BNPP adequately, while serial coring may be necessary to represent herbaceous plant BNPP from rhizomes as marshes replace forested wetlands.