bluuebunny/crossref_metadata_2025 huggingface dataset:
Typical trident sign and cardiac involvement in a patient suspected to Sarcoidosis despite negative whole-body FDG-PET: a case report
Authors: Shahmohammdi Abootorab , Heidari Hora , Kohandel Kosar , Dousti Soheil , Doosti Rozita , Azimi Amir Reza , Shajari Zahra , Rabiei Parham , Shahmohammdi Sareh
Published: November 2023

Background

Sarcoidosis is a systemic inflammatory disease histologically defined by the non-caseation granulomas formation in different organs, most commonly lungs, liver, skin, gastrointestinal system, eyes, neurologic and cardiac system

Case presentation

We report the case of a 42-year-old Gilaks woman who presented with myelopathy with characteristic MRI finding called trident sign. By finding this view in axial spinal Magnetic Resonance Imaging (MRI) imaging, a systemic evaluation was performed on the patient, which led to the diagnosis of cardiac involvement in Sarcoidosis with the specific appearance of this disease in cardiac MRI despite the negative Fluorodeoxyglucose (FDG)-positron emission tomography (PET) scan.

Conclusions

Sometimes characteristic findings such as the trident sign prompt the physician to high suspicion and wide evaluation of the patient to reveal important organ involvement that changes the treatment decision and saves the patient.
Unraveling the 2,3-diketo-l-gulonic acid-dependent and -independent impacts of l-ascorbic acid on somatic cell reprogramming
Authors: Liang Lining , He Meiai , Zhang Yixin , Wang Chenchen , Qin Zhaohui , Li Qian , Yang Tingting , Meng Fei , Zhou Yusheng , Ge Haofei , Song Weining , Chen Shiyu , Dong Linna , Ren Qiwen , Li Changpeng , Guo Lin , Sun Hao , Zhang Wei , Pei Duanqing , Zheng Hui
Published: November 2023

Background

l-ascorbic acid (Asc) plays a pivotal role in regulating various biological processes, including somatic cell reprogramming, through multiple pathways. However, it remains unclear whether Asc regulates reprogramming directly or functions through its metabolites.

Results

Asc exhibited dual capabilities in promoting reprogramming through both 2,3-diketo-l-gulonic acid (DKG), a key metabolite during Asc degradation, dependent and independent routes. On the one hand, Asc facilitated reprogramming by promoting cell proliferation and inducing the conversion from pre-induced pluripotent stem cells (pre-iPSCs) to iPSCs through DKG-independent pathways. Additionally, Asc triggered mesenchymal-epithelial transition (MET) and activated glycolysis via DKG-dependent mechanisms. Notably, DKG alone activated a non-canonical tricarboxylic acid cycle characterized by increased succinate, fumarate, and malate. Consequently, this shift redirected oxidative phosphorylation toward glycolysis and induced MET. Moreover, owing to its antioxidant capabilities, Asc directly inhibited glycolysis, thereby preventing positive feedback between glycolysis and epithelial-mesenchymal transition, ultimately resulting in a higher level of MET.

Conclusion

These findings unveil the intricate functions of Asc in the context of reprogramming. This study sheds light on the DKG-dependent and -independent activities of Asc during reprogramming, offering novel insights that may extend the application of Asc to other biological processes.
mTOR hypoactivity leads to trophectoderm cell failure by enhancing lysosomal activation and disrupting the cytoskeleton in preimplantation embryo
Authors: Ma Chiyuan , Li Qin , Yang Yuxin , Ge Lei , Cai Jiaxuan , Wang Juan , Zhu Maoxian , Xiong Yue , Zhang Wenya , Xie Jingtong , Cao Yujing , Zhao Huashan , Wei Qing , Huang Chen , Shi Junchao , Zhang Jian V. , Duan Enkui , Lei Xiaohua
Published: November 2023

Background

Metabolic homeostasis is closely related to early impairment of cell fate determination and embryo development. The protein kinase mechanistic target of rapamycin (mTOR) is a key regulator of cellular metabolism in the body. Inhibition of mTOR signaling in early embryo causes postimplantation development failure, yet the mechanisms are still poorly understood.

Methods

Pregnancy mice and preimplantation mouse embryo were treated with mTOR inhibitor in vivo and in vitro respectively, and subsequently examined the blastocyst formation, implantation, and post-implantation development. We used immunofluorescence staining, RNA-Seq smart2, and genome-wide bisulfite sequencing technologies to investigate the impact of mTOR inhibitors on the quality, cell fate determination, and molecular alterations in developing embryos.

Results

We showed mTOR suppression during preimplantation decreases the rate of blastocyst formation and the competency of implantation, impairs the post implantation embryonic development. We discovered that blocking mTOR signaling negatively affected the transformation of 8-cell embryos into blastocysts and caused various deficiencies in blastocyst quality. These included problems with compromised trophectoderm cell differentiation, as well as disruptions in cell fate specification. mTOR suppression significantly affected the transcription and DNA methylation of embryos. Treatment with mTOR inhibitors increase lysosomal activation and disrupts the organization and dynamics of the actin cytoskeleton in blastocysts.

Conclusions

These results demonstrate that mTOR plays a crucial role in 8-cell to blastocyst transition and safeguards embryo quality during early embryo development.
Salivary microbiome changes distinguish response to chemoradiotherapy in patients with oral cancer
Authors: Medeiros Marcell Costa de , The Stephanie , Bellile Emily , Russo Nickole , Schmitd Ligia , Danella Erika , Singh Priyanka , Banerjee Rajat , Bassis Christine , Murphy George R. , Sartor Maureen A. , Lombaert Isabelle , Schmidt Thomas M. , Eisbruch Avi , Murdoch-Kinch Carol Anne , Rozek Laura , Wolf Gregory T. , Li Gen , Chen Grace Y. , D’Silva Nisha J.
Published: November 2023

Background

Oral squamous cell carcinoma (SCC) is associated with oral microbial dysbiosis. In this unique study, we compared pre- to post-treatment salivary microbiome in patients with SCC by 16S rRNA gene sequencing and examined how microbiome changes correlated with the expression of an anti-microbial protein.

Results

Treatment of SCC was associated with a reduction in overall bacterial richness and diversity. There were significant changes in the microbial community structure, including a decrease in the abundance of Porphyromonaceae and Prevotellaceae and an increase in Lactobacillaceae. There were also significant changes in the microbial community structure before and after treatment with chemoradiotherapy, but not with surgery alone. In patients treated with chemoradiotherapy alone, several bacterial populations were differentially abundant between responders and non-responders before and after therapy. Microbiome changes were associated with a change in the expression of DMBT1, an anti-microbial protein in human saliva. Additionally, we found that salivary DMBT1, which increases after treatment, could serve as a post-treatment salivary biomarker that links to microbial changes. Specifically, post-treatment increases in human salivary DMBT1 correlated with increased abundance of Gemella spp., Pasteurellaceae spp., Lactobacillus spp., and Oribacterium spp. This is the first longitudinal study to investigate treatment-associated changes (chemoradiotherapy and surgery) in the oral microbiome in patients with SCC along with changes in expression of an anti-microbial protein in saliva.

Conclusions

The composition of the oral microbiota may predict treatment responses; salivary DMBT1 may have a role in modulating the oral microbiome in patients with SCC.

Graphical Abstract

After completion of treatment, 6 months after diagnosis, patients had a less diverse and less rich oral microbiome. Leptotrichia was a highly prevalent bacteria genus associated with disease. Expression of DMBT1 was higher after treatment and associated with microbiome changes, the most prominent genus being Gemella
Udział możnowładztwa polskiego w wyprawie Władysława Jagiellończyka po koronę czeską w 1471 r.
Authors: Szybkowski Sobiesław
Published: November 2023

W niniejszym tekście omówiono problematykę dotyczącą stosunku polskiego możnowładztwa do zabiegów dynastii mających na celu objęcie przez Władysława Jagiellończyka, syna króla Kazimierza Jagiellończyka, tronu czeskiego w 1471 r. Dokonano analizy prozopograficznej grupy osób wywodzących się z możnowładztwa, które osobiście towarzyszył królewiczowi Władysławowi w wyprawie wojennej do Pragi w 1471 r. Jej wyniki wskazują na to, że w wydarzeniach tych uczestniczyli doświadczeni doradcy króla Kazimierza: Stanisław z Ostroroga i Mikołaj z Kutna oraz grupa możnowładczej młodzieży wraz z pocztami konnych zbrojnych. Pod względem pochodzenia terytorialnego wśród możnowładców zaangażowanych w wyprawę po koronę czeską przeważali mieszkańcy Wielkopolski (11), nad możnymi małopolskimi (7).
Las palabras de la calle
Authors: Galiana L. , Aparicio A. , Gavira Carmen
Published: November 2023

Este artículo se propone analizar a través de «las palabras de la calle», -términos, definiciones y topónimos- las permanencias y cambios de los contenidos y valores percibidos en la producción del espacio de la realidad española.
Megaciudades e hyperedificios: el impacto de la globalización sobre la estructura espacial y social.
Authors: Trachana Angelique
Published: November 2023

La autora analiza la tendencia hacia la creación de megaciudades definiendo sus características y explorando su «razón».
La confusión de los monumentos.
Authors: Melot Michel
Published: November 2023

Antaño, los monumentos remitían a un mensaje, con frecuencia a acontecimientos memorables. Marcaban el lugar de un culto o de una ceremonia. Estelas, columnas, arcadas, muros contra los cuales se rezaba, cruces alzadas después de una conquista, estatuas de personajes ilustres. Los monumentos transformaban del duelo en homenaje y la tragedia en triunfo. Pero desde hace tiempo los bustos han pasado de moda y ya no se graban máximas en los frontones.
Peculiarity of autoimmune hepatitis triggered by SARS-CoV-2 infection
Authors: Gallo Antonella , Ibba Francesca , Massaro Maria Grazia , Rognoni Fiammetta , Giustiniani Maria Cristina , Ponziani Francesca Romana , Montalto Massimo
Published: November 2023

Introduction: Recently, medical interest has been growing in SARS-CoV-2 infection and its multiorgan involvement, including the liver. Up until now, a few reports have described autoimmune hepatitis (AIH) triggered by SARS-CoV-2 infection, but no data are available about the specific liver inflammatory infiltrate and cluster of differentiation. We report a case of AIH triggered by SARS-CoV-2 infection, with a particular focus on its histological and mainly immunohistochemical features. Case description: A 60-year-old man, with a history of paucisymptomatic SARS-CoV-2 infection that occurred one month earlier, was admitted for alterations of hepatocellular necrosis and cholestasis indexes. He completed vaccination for SARS-CoV-2 a year earlier. The serologies for hepatotropic viruses were negative. The anti- smooth muscle antibodies (ASMA) and antinuclear antibodies (ANA) results were positive. Anti-liver kidney microsome (anti-LKM) antibodies and antimitochondrial (AMA) were negative. By liver biopsy, haematoxylin-eosin staining highlighted severe portal inflammation with a rich CD38+ plasma cell component, while immunohistochemical staining showed low cell CD4+ count and prevalence of CD8+ and CD3+. After biopsy, the patient started an immunosuppressant regimen, with benefit. Discussion: We can conclude that the patient developed a type 1 AIH triggered by SARS-CoV-2 infection. The presence of CD8 T-cells at immunohistochemical examination suggests different mechanisms from classic AIH. Similar cases are described after AIH triggered by SARS-CoV-2 vaccination. Conclusion: The AIH after SARS-CoV-2 infection developed by the patient showed a histological picture similar to a classic AIH for the abundant presence of plasma cells, and immunohistochemical features similar to those described after SARS-CoV-2-vaccination.
Is access to NHS tongue tie services equitable for mothers and babies in the UK?
Authors: Carter Elizabeth , Armstrong Louise , Kindred-Spalding Elaine , Gale Cathy , Wilson Deb
Published: November 2023

Background/Aims

NHS tongue tie service provision throughout the UK has previously been described as a ‘post code lottery’. A 2021 survey was conducted, with the aim to provide an update to a 2016 survey of tongue tie services in the UK.

Methods

A total of 179 trusts or health boards were approached with similar survey questions to a 2016 survey and achieved a response rate of 72% (n=130).

Results

There were similarities to the findings of the previous National Childbirth Trust survey, although there was an overall increase in NHS services provided. There is still variation in terms of the lead professional involved in delivering tongue tie services at the point of contact with the mother and baby, the criteria used for referral, the waiting time for assessment and treatment and the follow-up processes. Evidence supporting most aspects of care is limited, which causes much professional discussion.

Conclusions

The provision of NHS tongue tie services is still a ‘post code lottery’ and inequitable for mothers and babies.
A midwife's reflective writing in lactation and grief
Authors: Blanco Laura Segura
Published: November 2023

Midwifery is not just about life and joy; unfortunately, at times it also involves death, sorrow and grief. The death of a baby and subsequent grief is complex, and involves grieving the baby's life as well as the life that parents have imagined with their child, including their role as parents. Pregnancy and baby loss have devastating effects on women and their families; expecting life and meeting death leave a profound emptiness. Perinatal death can include miscarriage, stillbirth and neonatal death. Lactation in these circumstances has been described by bereaved mothers as a healing therapy, and although there is some published evidence on this topic, further research will be necessary. This article was written based on the author's personal and professional experience, combined with current evidence, following Gibbs' reflective cycle, which provides a structured approach to learning from experiences. The aim is to create awareness of the importance of giving women the opportunity to decide how to manage their lactation and to speak about a topic that, unfortunately, is still taboo.
Aeneas's Trousseau: Gender(ed) Exchange in Aeneid 1
Authors: Love Rachel Lilley
Published: November 2023

abstract: Dido's gifts to the shipwrecked Trojans in book 1 of the Aeneid resemble suitors' gifts (ἕδνα) recorded in the Hesiodic Catalogue of Women . Reading Dido against a Hesiodic rather than Homeric model casts her as a suitor of Aeneas, which in turn lends further coloring to the composition of Aeneas's reciprocating gifts of a palla ("dress"), uelamen ("veil"), corona ("crown"), and jewelry, gifts associated in Greek tragedy with the bridal trousseau (φερναί). The (imperfect) recasting of Dido and Aeneas as suitor and bride, respectively, only becomes legible when better attention is paid to the gendered dynamics of exchange and modes of female communication within the Aeneid .
The Early Years of the Hemingway Review (1981–1992): An Interview with Charles M. (“Tod”) Oliver Reprinted from the Spring 2016 issue of The Hemingway Review
Authors: Curnutt Kirk
Published: November 2023

Abstract: We are reprinting this interview with Tod Oliver, which appeared in the Spring 2016 issue of The Hemingway Review to commemorate the thirty-fifth anniversary of the Review . In this interview, Tod reminisces about the early years of the journal. He recalls its evolution from Hemingway notes , the “technologies” available for producing an issue, the founding of the Hemingway Society, and important relationships and issues along the way.
Inner Workings: John Lydgate's Kalendare at the Nexus of Time, Craft, and Devotion
Authors: Murdoch Joanna
Published: November 2023

Abstract: This article proposes that fifteenth-century English poet John Lydgate transforms the medieval tradition of calendrical verse from a mnemonic aid to a site for readers to practice interpretive agency. Building on studies of the metrical calendar genre by Michael Lapidge and Jessica Brantley, I show how Lydgate's solutions to representing time in poetic meter in fact open up new possibilities for interpretive practice within late medieval penitential devotion. Lydgate's Kalendare is a poetic prayer composed for, and received on, the material page, yet whose proper reading works on, in, and through the reader's "answere," an unfolding process of discovery drawing on a blend of interior assent and commitment to mutual aid. Rather than shutting down readers' personal agency or threatening isolation, the working parts of Lydgate's Kalendare—diction, syntax, meter, and calendar frame—construct and invite an open-ended, socially connective exploration of meaning over time.
Ocelots in the moonlight: Influence of lunar phase on habitat selection and movement of two sympatric felids
Authors: Sergeyev Maksim , Lombardi Jason V. , Tewes Michael E. , Campbell Tyler A.
Published: November 2023

Various landscape and environmental factors influence animal movement and habitat selection. Lunar illumination affects nocturnal visual perception of many species and, consequently, may influence animal activity and habitat selection. However, the effects of varying moon stage may differ across taxa. Prey species often reduce activity during highly visible periods of night while predators may increase activity or alter their habitat use. Ocelots (Leopardus pardalis) and bobcats (Lynx rufus), two nocturnal predatory felids that coexist in southern Texas, may also alter their behavior in response to the phase of the moon. To evaluate the effects of lunar phase on habitat selection of ocelots and bobcats, we executed a step selection analysis using high-frequency GPS-telemetry data collected on each species (ocelot, N = 8; bobcat, N = 13) in southern Texas during 2017–2021 and compared step length during new versus full moons. We predicted that ocelots would increase use of dense thornshrub to reduce their visibility during a full moon. However, as bobcats are habitat generalists and are more active during crepuscular periods, we predicted less influence of moon phase on activity. Ocelots did not alter habitat selection in response to lunar phase but moved shorter distances during full moon phases. Conversely, bobcats selected for greater vegetation cover during full moons, possibly to facilitate hunting during brighter periods, but exhibited no difference in movement across lunar phase. We provide, to our knowledge, the first example of habitat selection by predators in relation to lunar phase and show differences across new versus full moons by ocelots and bobcats such that ocelots alter step length but not habitat selection while bobcats altered habitat selection but not step length in response to shifting lunar phase. Further, we suggest the high potential for ocelot-vehicle collisions on darker nights due to increased movement by ocelots and poor visibility for drivers.
Diversity and plant growth promoting ability of rice root-associated bacteria in Burkina-Faso and cross-comparison with metabarcoding data
Authors: Sondo Moussa , Wonni Issa , Koïta Kadidia , Rimbault Isabelle , Barro Mariam , Tollenaere Charlotte , Moulin Lionel , Klonowska Agnieszka
Published: November 2023

Plant-associated bacteria are essential partners in plant health and development. In addition to taking advantage of the rapid advances recently achieved in high-throughput sequencing approaches, studies on plant-microbiome interactions require experiments with culturable bacteria. A study on the rice root microbiome was recently initiated in Burkina Faso. As a follow up, the aim of the present study was to develop a collection of corresponding rice root-associated bacteria covering maximum diversity, to assess the diversity of the obtained isolates based on the culture medium used, and to describe the taxonomy, phenotype and abundance of selected isolates in the rice microbiome. More than 3,000 isolates were obtained using five culture media (TSA, NGN, NFb, PCAT, Baz). The 16S rRNA fragment sequencing of 1,013 selected isolates showed that our working collection covered four bacterial phyla (Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes) and represented 33% of the previously described diversity of the rice root microbiome at the order level. Phenotypic in vitro analysis of the plant growth promoting capacity of the isolates revealed an overall ammonium production and auxin biosynthesis capacity, while siderophore production and phosphate solubilisation were enriched in Burkholderia, Ralstonia, Acinetobacter and Pseudomonas species. Of 45 representative isolates screened for growth promotion on seedlings of two rice cultivars, five showed an ability to improve the growth of both cultivars, while five others were effective on only one cultivar. The best results were obtained with Pseudomonas taiwanensis ABIP 2315 and Azorhizobium caulinodans ABIP 1219, which increased seedling growth by 158% and 47%, respectively. Among the 14 best performing isolates, eight appeared to be abundant in the rice root microbiome dataset from previous study. The findings of this research contribute to the in vitro and in planta PGP capacities description of rice root-associated bacteria and their potential importance for plants by providing, for the first time, insight into their prevalence in the rice root microbiome.
Type 2 diabetes linked FTO gene variant rs8050136 is significantly associated with gravidity in gestational diabetes in a sample of Bangladeshi women: Meta-analysis and case-control study
Authors: Amin U. S. Mahzabin , Rahman Tahia Anan , Hasan Mashfiqul , Tofail Tania , Hasanat Muhammad Abul , Seraj Zeba I. , Salimullah Md
Published: November 2023

Objective

Gestational diabetes mellitus (GDM) is a growing public health concern that has not been extensively studied. Numerous studies have indicated that a variant (rs8050136) of the fat mass-associated gene, FTO, is associated with both GDM and Type 2 diabetes mellitus(T2DM). We conducted a meta-analysis on the association between the FTO single nucleotide polymorphism (SNP) rs8050136 and T2DM, followed by a case-control study on the association of the said SNP and GDM in a sample of Bangladeshi women.

Method

A total of 25 studies were selected after exploring various databases and search engines, which were assessed using the Newcastle-Ottawa Scale (NOS). The MetaGenyo web tool was used to conduct this meta-analysis. A case-control study was performed on 218 GDM patients and 284 controls to observe any association between FTO rs8050136 and GDM. Genotyping was performed using the tetra-primer amplification refractory mutation system-polymerase chain reaction (T-ARMS) method, and statistical analyses were performed using various statistical softwares.

Results

In the meta-analysis 26231 cases and 43839 controls were examined. Pooled association analyses revealed a statistically significant relationship between the FTO rs8050136 polymorphism and an elevated risk of T2DM under all genetic models (P<0.05). In the case-control study, synergistic analyses of the SNP and gravida with GDM revealed a significant (P<0.01) association with an increase in odds by 1.6 to 2.4 folds in multigravida and decrease in odds by 2 folds in primigravida. A positive family history of diabetes and the minor allele of this SNP collectively increased the risk of developing GDM by many-fold (1.8 to 2.7 folds). However, after accounting for family history of diabetes and gravidity, analyses showed no significant association with GDM.

Conclusion

Our meta-analysis revealed a significant association between SNP rs8050136 of FTO with T2DM, and this variant was substantially associated with an increased risk of GDM in a sample of Bangladeshi multigravida women.
Analyzing drama metadata through machine learning to gain insights into social information dissemination patterns
Authors: Lo Chung-Ming , Syu Zih-Sin
Published: November 2023

TV drama, through synchronization with social phenomena, allows the audience to resonate with the characters and desire to watch the next episode. In particular, drama ratings can be the criterion for advertisers to invest in ad placement and a predictor of subsequent economic efficiency in the surrounding areas. To identify the dissemination patterns of social information about dramas, this study used machine learning to predict drama ratings and the contribution of various drama metadata, including broadcast year, broadcast season, TV stations, day of the week, broadcast time slot, genre, screenwriters, status as an original work or sequel, actors and facial features on posters. A total of 800 Japanese TV dramas broadcast during prime time between 2003 and 2020 were collected for analysis. Four machine learning classifiers, including naïve Bayes, artificial neural network, support vector machine, and random forest, were used to combine the metadata. With facial features, the accuracy of the random forest model increased from 75.80% to 77.10%, which shows that poster information can improve the accuracy of the overall predicted ratings. Using only posters to predict ratings with a convolutional neural network still obtained an accuracy rate of 71.70%. More insights about the correlations between drama metadata and social information dissemination patterns were explored.
Role of the redox state of the Pirin-bound cofactor on interaction with the master regulators of inflammation and other pathways
Authors: Ahsan Tamim , Shoily Sabrina Samad , Ahmed Tasnim , Sajib Abu Ashfaqur
Published: November 2023

Persistent cellular stress induced perpetuation and uncontrolled amplification of inflammatory response results in a shift from tissue repair toward collateral damage, significant alterations of tissue functions, and derangements of homeostasis which in turn can lead to a large number of acute and chronic pathological conditions, such as chronic heart failure, atherosclerosis, myocardial infarction, neurodegenerative diseases, diabetes, rheumatoid arthritis, and cancer. Keeping the vital role of balanced inflammation in maintaining tissue integrity in mind, the way to combating inflammatory diseases may be through identification and characterization of mediators of inflammation that can be targeted without hampering normal body function. Pirin (PIR) is a non-heme iron containing protein having two different conformations depending on the oxidation state of the iron. Through exploration of the Pirin interactome and using molecular docking approaches, we identified that the Fe2+-bound Pirin directly interacts with BCL3, NFKBIA, NFIX and SMAD9 with more resemblance to the native binding pose and higher affinity than the Fe3+-bound form. In addition, Pirin appears to have a function in the regulation of inflammation, the transition between the canonical and non-canonical NF-κB pathways, and the remodeling of the actin cytoskeleton. Moreover, Pirin signaling appears to have a critical role in tumor invasion and metastasis, as well as metabolic and neuro-pathological complications. There are regulatory variants in PIR that can influence expression of not only PIR but also other genes, including VEGFD and ACE2. Disparity exists between South Asian and European populations in the frequencies of variant alleles at some of these regulatory loci that may lead to differential occurrence of Pirin-mediated pathogenic conditions.
Portable BLAST-like algorithm library and its implementations for command line, Python, and R
Authors: Schmid Steven , Jeevannavar Aditya , Julian Timothy R. , Tamminen Manu
Published: November 2023

Basic local-alignment search tool (BLAST) is a versatile and commonly used sequence analysis tool in bioinformatics. BLAST permits fast and flexible sequence similarity searches across nucleotide and amino acid sequences, leading to diverse applications such as protein domain identification, orthology searches, and phylogenetic annotation. Most BLAST implementations are command line tools which produce output as comma-separated values files. However, a portable, modular and embeddable implementation of a BLAST-like algorithm, is still missing from our toolbox. Here we present nsearch, a command line tool and C++11 library which provides BLAST-like functionality that can easily be embedded in any application. As an example of this portability we present Blaster which leverages nsearch to provide native BLAST-like functionality for the R programming language, as well as npysearch which provides similar functionality for Python. These packages permit embedding BLAST-like functionality into larger frameworks such as Shiny or Django applications. Benchmarks show that nsearch, npysearch, and Blaster are comparable in speed and accuracy to other commonly used modern BLAST implementations such as VSEARCH and BLAST+. We envision similar implementations of nsearch for other languages commonly used in data science such as Julia to facilitate sequence similarity comparisons. Nsearch, Blaster and npysearch are free to use under the BSD 3.0 license and available on Github Conda, CRAN (Blaster) and PyPi (npysearch).
Detection and identification of oil spill species based on polarization information
Authors: Sun Hongyu , Zhao Zhehao , Fu Qiang , Shi Haodong , Li Yingchao , Yang Di , Liu Jianan , Wang Chao , Jiang Huilin
Published: November 2023

Aiming at the problem of poor oil identification accuracy in existing oil spill detection technologies, the polarization degree model of oil spill on rough sea surface under different azimuths and zenith angles was established based on Fresnel theory. The analytical expressions of visible light polarization degree in calm and fluctuating water surface were derived respectively, and the polarization degree model of oil spill in reflection space was constructed. The effectiveness of the method and its influence on the polarization distribution of oil spill were analyzed by simulation. A portable turntable was designed to test the polarization characteristics of the experiment, and the visible light polarization detection experiment was carried out. The visible light polarization images of five typical oil spills at different observation azimuth and zenth angles were obtained. The differences in the polarization degrees of different oil species were analyzed, and the correctness of the theoretical model was proved by experiments. The polarization detection experiment of visible light pBRDF was completed, which more intuitively showed the variation law of the polarization characteristics of light reflected by different oil spills in different spatial positions. Using polarization information to distinguish oil species is a useful supplement to the traditional oil spill detection method and has important significance to improve the marine pollution control ability.
A hybrid Cycle GAN-based lightweight road perception pipeline for road dataset generation for Urban mobility
Authors: Rajagopal Balaji Ganesh , Kumar Manish , Alshehri Abdulaziz H. , Alanazi Fayez , Deifalla Ahmed farouk , Yosri Ahmed M. , Azam Abdelhalim
Published: November 2023

One of the major problems that cause continual trouble in deep learning networks is that training a large network requires massive labelled datasets. The preparation of a massive labelled dataset is a cumbersome task and requires lot of human interventions. This paper proposes a novel generator network ‘Sim2Real’ transfer is a recent and fast-developing field in machine learning used to bridge the gap between simulated and real data. Training with simulated datasets often converges due to its size but fails to generalize real-world applications. Simulated datasets can be used to train and test deep learning models, enables the development and evaluation of new algorithms and architectures. By simulating road dataset, researchers can generate large amounts of realistic road-traffic dataset that can be used to study and understand several problems such as vehicular object tracking and classification, traffic situation analysis etc. The main advantage of such a transfer algorithm is to use the abundance of a simulated dataset to generate huge realistic-looking datasets to solve data-intense tasks. This work presents a novel, robust sim2real algorithm that converts the labels of a semantic segmentation map to a realistic-looking street view using the Cityscapes dataset and aims to achieve robust urban mobility for smart cities. Further, the generalizability of the Cycle Generative Adversarial Network (CycleGAN) architecture was tested by using an origami robot dataset for sim2real transfer. We show that the results were found to be qualitatively satisfactory for different traffic analysis applications. In addition, road perception was done using a lightweight SVM pipeline and evaluated on the KITTI dataset. We have incorporated Cycle Consistency Loss and Identity Loss as the metrics to evaluate the performance of the proposed Cycle GAN model. We inferred that the proposed Cycle GAN model provides an Identity loss of less than 0.2 in both the Cityscapes dataset and KITTI datasets. Also, we understand that the super-pixel resolution has a good impact on the quantitative results of the proposed Cycle GAN models.
Bacterial amidohydrolases and modified 5-fluorocytidine compounds: Novel enzyme-prodrug pairs
Authors: Preitakaitė Viktorija , Barasa Povilas , Aučynaitė Agota , Plakys Gediminas , Koplūnaitė Martyna , Zubavičiūtė Simona , Meškys Rolandas
Published: November 2023

Gene-directed enzyme prodrug therapy is an emerging strategy for cancer treatment based on the delivery of a gene that encodes an enzyme that is able to convert a prodrug into a potent cytotoxin exclusively in target cancer cells. However, it is limited by the lack of suitable enzyme variants and a scarce choice of chemical bonds that could be activated. Therefore, this study is aimed to determine the capability of bacterial amidohydrolases YqfB and D8_RL to activate novel prodrugs and the effect such system has on the viability of eukaryotic cancer cells. We have established cancer cell lines that stably express the bacterial amidohydrolase genes and selected several N4-acylated cytidine derivatives as potential prodrugs. A significant decrease in the viability of HCT116 human colon cancer cell lines expressing either the YqfB or the D8_RL was observed after exposure to the novel prodrugs. The data we acquired suggests that bacterial YqfB and D8_RL amidohydrolases, together with the modified cytidine-based prodrugs, may serve as a promising enzyme-prodrug system for gene-directed enzyme prodrug therapy.
MORA and EnsembleTFpredictor: An ensemble approach to reveal functional transcription factor regulatory networks
Authors: Boyer Kevin , Li Louis , Li Tiandao , Zhang Bo , Zhao Guoyan
Published: November 2023

Motivation

Our study aimed to identify biologically relevant transcription factors (TFs) that control the expression of a set of co-expressed or co-regulated genes.

Results

We developed a fully automated pipeline, Motif Over Representation Analysis (MORA), to detect enrichment of known TF binding motifs in any query sequences. MORA performed better than or comparable to five other TF-prediction tools as evaluated using hundreds of differentially expressed gene sets and ChIP-seq datasets derived from known TFs. Additionally, we developed EnsembleTFpredictor to harness the power of multiple TF-prediction tools to provide a list of functional TFs ranked by prediction confidence. When applied to the test datasets, EnsembleTFpredictor not only identified the target TF but also revealed many TFs known to cooperate with the target TF in the corresponding biological systems. MORA and EnsembleTFpredictor have been used in two publications, demonstrating their power in guiding experimental design and in revealing novel biological insights.
Unmasking hidden risks: The surprising link between PDE5 inhibitors and seizure susceptibility
Authors: Silva Alex Luiz Menezes da , Nascimento Chirlene Pinheiro , Azevedo Julianne Elba Cunha , Vieira Luana Rodrigues , Hamoy Akira Otake , Tiago Allan Carlos da Silva , Martins Rodrigues João Cleiton , de Araujo Daniella Bastos , Favacho Lopes Dielly Catrina , de Mello Vanessa Jóia , Hamoy Moisés
Published: November 2023

Background

Phosphodiesterase 5 inhibitors (PDE5i) are the first line treatment for erectile dysfunction; however, several articles and case reports have shown central nervous system effects, that can cause seizures in susceptible patients. This study aims to describe the changes caused by the use of Sildenafil and Tadalafil through the analysis of abnormalities expressed in the electrocorticogram (ECoG) of rats and evaluate the seizure threshold response and treatment of seizures with anticonvulsants.

Materials and methods

The study used 108 rats (Wistar). Before surgery for electrode placement in dura mater, the animals were randomly separated into 3 experiments for electrocorticogram analysis. Experiment 1: ECoG response to using PD5i (Sildenafil 20mg/kg and Tadalafil 2.6mg/kg p.o.). Experiment 2: ECoG response to the use of PD5i in association with Pentylenetetrazole (PTZ—30 mg/kg i.p.), a convulsive model. Experiment 3: ECoG response to anticonvulsant treatment (Phenytoin, Phenobarbital and Diazepam) of seizures induced by association IPDE5 + PTZ. All recordings were made thirty minutes after administration of the medication and analyzed for ten minutes, only once. We considered statistical significance level of *p<0.05, **p<0.01 and ***p < 0.001.

Results

After administration of Sildenafil and Tadalafil, there were increases in the power of recordings in the frequency bands in oscillations in alpha (p = 0.0920) and beta (p = 0.602) when compared to the control group (p<0.001). After the use of Sildenafil and Tadalafil associated with PTZ, greater potency was observed in the recordings during seizures (p<0.001), however, the Sildenafil group showed greater potency when compared to Tadalafil (p<0.05). Phenobarbital and Diazepam showed a better response in controlling discharges triggered by the association between proconvulsant drugs.

Conclusions

PDE5i altered the ECoG recordings in the rats’ motor cortexes, demonstrating cerebral asynchrony and potentiating the action of PTZ. These findings demonstrate that PDE5i can lower the seizure threshold.
A novel, benchtop model for quantitative analysis of resistance in ventricular catheters
Authors: Gopalakrishnan Pranav , Faryami Ahmad , Harris Carolyn A.
Published: November 2023

Introduction

The mechanisms of catheter obstruction are still poorly understood, but the literature suggests that resistance to fluid flow plays a significant role. We developed and assessed a gravity-driven device that measures flow through ventricular catheters. We used this device to quantitatively analyze the resistances of unused ventricular catheters used in the treatment of hydrocephalus; failed hydrocephalus catheters from our catheter biorepository were also evaluated quantitatively.

Methods

Catheters of three manufacturing companies were inserted into the benchtop model, which records time, flow rate, and pressure data using sensors. The relative resistances of catheters across six design models were evaluated. Experiments were performed to evaluate changes in the relative resistance of a catheter when the catheter’s holes were progressively closed. The relative resistance of explanted catheters from our catheter biorepository was also measured.

Results

Experimental results showed significant differences (P<0.05) between the relative resistances of different catheter models just after being removed from their packaging. A non-linear trend of increasing resistance was observed in experiments on catheters with artificially obstructed holes. Data from five individual benchtop models were compared, and the differences in measured data between the models were found to be negligible. A significant increase (P < 0.05) in relative resistance was observed in explanted catheters.

Conclusion

The current study sought to propose a novel in-vitro model and use it to examine data on differences in relative resistance among catheter models. From these experiments, we can rapidly correlate clinical patient cohorts to identify mechanisms of luminal shunt obstruction.
Competitiveness analysis of fresh tomatoes in Indonesia: Turning comparative advantage into competitive advantage
Authors: Saptana  , Sukmaya Syahrul Ganda , Perwita Atika Dyah , Malihah Fadhila Dhia , Wardhana Irwanda Wisnu , Pitaloka Atika Dian , Ghaisani Shabrina Austin , Sayaka Bambang , Ilham Nyak , Karmawati Elna , Ariani Mewa , Susilowati Sri Hery , Sumaryanto  , Saliem Handewi Purwati
Published: November 2023

Tomato commodity ranks fifth regarding vegetable export volume and value in Indonesia. The main issues with tomato production in Indonesia are seemingly its lack of variations, quantity, quality, and supply continuity. This study aimed to analyze the comparative and the competitive advantages of tomato farming, evaluate the government policy on inputs, outputs, and input-output sectors, and formulate strategic for transforming the comparative advantage into a competitive advantage. Policy Analysis Matrix (PAM) and sensitivity analysis were employed as the method with the 75 farmers as the respondents and their Focus Group Discussion (FGD) involving farmer groups, agricultural extension workers, traders, and the Agricultural Service Offices in the respective regencies. The results showed that tomato farming has both its comparative and competitive advantages. Its comparative advantage was higher than its competitive advantage in both dry and wet seasons. In general, tomato farming’s comparative and competitive advantages outside Java were higher than those in Java. Meanwhile, the divergence effects of tomato agribusiness were more beneficial to consumers than producers. It indicates that improving domestic tomato production was more profitable for Indonesia than importing this commodity in terms of domestic resource use. The sensitivity analysis shows that tomato farming was relatively stable regarding productivity and price changes. The suggested strategic policies to apply are transforming tomato farming’s comparative advantage into competitive advantage through productivity enhancement, improvement of distribution efficiency, less market distortion, and government incentives.
Women’s self-care for Coronavirus prevention and the related factors in Iran: A cross-sectional study
Authors: Nazarpour Soheila , Simbar Masoumeh , Rashidi Fakari Farzaneh , Khorrami Mobina , Dodel Andarvar Khadijeh , Jafari Torkamani Zahra , Keyvanfar Sepideh , Alavi Majd Hamid
Published: November 2023

Promoting self-care can be an effective way to decrease the rate of transmission and expansion of the infection. However, there seem to be different related factors to self-care by gender. This study aims to assess women’s self-care for COVID-19 prevention and some related factors in Tehran-Iran in 2021. This was a descriptive cross-sectional study that was performed on 403 women living in Tehran in 2021. Subjects of the study were recruited using a multi-stage sampling method. Data was collected using a socio-demographic questionnaire as well as a valid and reliable questionnaire to assess women’s self-care for COVID-19 prevention (SCVP-38). The questionnaires were sent on the Google platform to the eligible participants. After completion of the forms, the created data in the Excel software in Google Drive were converted to SPSS 24 and then analyzed by using t-test, ANOVA, Pearson correlation, and multiple linear regression tests. The overall mean score of self-care was 71.84±17.81 percent. The highest and lowest scores were respectively related to using masks in public vehicles and not touching the face. Significant negative correlations were shown between the women’s self-care on Corona prevention with stress, anxiety, concerns, and fear (P<0.001). Linear multiple regression showed two factors including women’s age (p = 0.033) and their number of children (p = 0.042) predict the self-care, so that, for increasing each year to women’s age, SCVP increases by 0.463 units, and with increasing each child, SCVP decreases by 3.608 units. We concluded that in the COVID-19 pandemic, women in Tehran are performing more than 70% of measures of self-care. Also, education about self-care is recommended for younger women with more children. Moreover, promoting the self-care program can improve women’s mental health during the COVID-19 pandemic.
The effect of experiential learning interventions on physical activity outcomes in children: A systematic review
Authors: Varman Sumantla D. , Jones Rachel A. , Kelly Bridget , Hammersley Megan L. , Parrish Anne-Maree , Stanley Rebecca , Cliff Dylan P.
Published: November 2023

Background

This systematic review examined the effectiveness of experiential learning interventions for improving children’s physical activity knowledge, attitudes, and behaviours. It also aimed to identify intervention characteristics that resulted in the greatest impact.

Methods

Four databases: Education Research Complete, Scopus, Web of Science and PsychINFO were searched from database inception to January 2023. Eligible studies: (1) included children 0–12 years; (2) assessed the effect of physical activity outcomes on children’s physical activity knowledge, attitudes or behaviour and (3) were randomised controlled trials conducted in any setting. Study risk of bias was assessed by two independent reviewers using the Cochrane risk of bias tool. Intervention approaches were categorised, and effect sizes were compared across studies for each outcome.

Results

Twelve studies were included in the review: ten in school age and two in below five years. For behavioural outcomes, six of eight studies showed medium to large effects (effects size (ES) range: 0.3–0.9), two of the three studies that assessed attitudinal outcomes displayed medium effects (ES range: 0.4–0.5) and both studies that assessed knowledge outcomes displayed medium to large effects (ES range: 0.4–1.3). The two experiential learning interventions among children < 5 years demonstrated small to medium effects on behaviour change (ES range: 0.2–0.5). Effective interventions combined enjoyable practical activities (fitness activities, games and challenges), with behaviour change techniques (goal setting, and self-monitoring), were underpinned by a behaviour change theory, and were often of short duration (< 4 months) but intense (several sessions/week). Moderate to high statistical heterogeneity was observed for behaviour outcomes and risk of bias across studies was generally high.

Conclusions

This review provides some evidence supporting the effectiveness of experiential learning interventions in improving physical activity outcomes in school-aged children. Additional evidence is needed in children <5 years old. Future experiential learning interventions need to strengthen the evidence with rigorous methodological quality and clear reporting of the experiential learning components.