bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evolutionary genomics of APSE: a tailed phage that lysogenically converts the bacterium Hamiltonella defensa into a heritable protective symbiont of aphids
Authors: Boyd Bret M. , Chevignon Germain , Patel Vilas , Oliver Kerry M. , Strand Michael R. 
Published: November 2021

AbstractBackgroundMost phages infect free-living bacteria but a few have been identified that infect heritable symbionts of insects or other eukaryotes. Heritable symbionts are usually specialized and isolated from other bacteria with little known about the origins of associated phages.Hamiltonella defensais a heritable bacterial symbiont of aphids that is usually infected by a tailed, double-stranded DNA phage named APSE.MethodsWe conducted comparative genomic and phylogenetic studies to determine how APSE is related to other phages and prophages.ResultsEach APSE genome was organized into four modules and two predicted functional units. Gene content and order were near-fully conserved in modules 1 and 2, which encode predicted DNA metabolism genes, and module 4, which encodes predicted virion assembly genes. Gene content of module 3, which contains predicted toxin, holin and lysozyme genes differed among haplotypes. Comparisons to other sequenced phages suggested APSE genomes are mosaics with modules 1 and 2 sharing similarities withBordetella-Bcep-Xylostella fastidiosa-like podoviruses, module 4 sharing similarities with P22-like podoviruses, and module 3 sharing no similarities with known phages. Comparisons to other sequenced bacterial genomes identified APSE-like elements in other heritable insect symbionts (Arsenophonusspp.) and enteric bacteria in the familyMorganellaceae.ConclusionsAPSEs are most closely related to phage elements in the genusArsenophonusand other bacteria in theMorganellaceae.
The association between fat-to-muscle ratio and metabolic disorders in type 2 diabetes
Authors: Liu Dixing , Zhong Jiana , Ruan Yuting , Zhang Zhen , Sun Jia , Chen Hong 
Published: November 2021

Abstract
Background
Altered body composition is known to be related to abnormal metabolism. The aim of this study was to determine the association between the fat-to-muscle ratio (FMR) and metabolic disorders in type 2 diabetes (T2DM) population.

Method
In total, 361 T2DM participants aged ≥ 18 years were included in our research. A bioelectrical impedance analyzer was applied to measure fat mass and muscle mass. FMR was calculated as body fat mass (kg) divided by muscle mass (kg). The performance of FMR to assess metabolic disorders in T2DM was conducted using ROC curves. The independent association between FMR and metabolic syndrome (MS) was tested by logistic regression analysis.

Results
The FMR was significantly higher in patients with MS than in those without MS (p < 0.001). The optimal FMR cutoff point for identifying MS was higher in females than in males (0.465 vs. 0.296, respectively). In addition, the areas under the ROC curve (AUCs) for the evaluation of MS by FMR, fat mass, muscle mass, BMI and waist circumference were further compared, indicating that the AUC of FMR (0.843) was the largest among the five variables in females, but the AUC of waist circumference (0.837) was still the largest among other variables in males. Based on the derived FMR cutoff point, patients with a high FMR exhibited more cardiometabolic risk indicators (all p < 0.05). Using a low FMR as a reference, the relative risk of a high FMR for MS was 2.861 (95% CI 1.111–7.368, p = 0.029) in males and 9.518 (95% CI 2.615–34.638, p = 0.001) in females following adjustment for confounding factors.

Conclusions
The fat-to-muscle ratio is independently and positively associated with metabolic disorders in T2DM. FMR may serve as an optimal method for screening T2DM patients coupled with a high risk of abnormal metabolism, especially in females, providing a new perspective for the prevention and treatment of cardiovascular complications in Chinese type 2 diabetes.
Sigmoid volvulus in pregnancy: a case report
Authors: Lodhia Jay , Magoma Joachim , Tendai Joylene , Msuya David , Suleiman Jamil , Chilonga Kondo 
Published: November 2021

Abstract
Introduction
Sigmoid volvulus in pregnancy is a rare cause of intestinal obstruction with high maternal and fetal morbidity and mortality if not diagnosed and managed early.

Case presentation
A 29-year-old female (Chagga by tribe) presented with clinical features of intestinal obstruction 24 weeks into her second pregnancy. She had symptoms for one week. An emergency laparotomy was performed whereby gangrenous sigmoid volvulus was found; thus, it was resected and Hartmann’s colostomy was raised. Unfortunately, she experienced intrauterine fetal death post-operatively. She was discharged clinically stable.

Conclusion
Early diagnosis and management can prevent adverse effects such as bowel ischemia and preterm labor. Because classic clinical and radiological features may not be evident, high degree of suspicion is warranted.
Methamphetamine facilitates HIV infection of primary human monocytes through inhibiting cellular viral restriction factors
Authors: Liu Yu , Meng Feng-Zhen , Wang Xu , Wang Peng , Liu Jin-Biao , Hu Wen-Hui , Young Won-Bin , Ho Wen-Zhe 
Published: November 2021

Abstract
Background
Methamphetamine (METH), a potent addictive psychostimulant, is highly prevalent in HIV-infected individuals. Clinically, METH use is implicated in alteration of immune system and increase of HIV spread/replication. Therefore, it is of importance to examine whether METH has direct effect on HIV infection of monocytes, the major target and reservoir cells for the virus.

Results
METH-treated monocytes were more susceptible to HIV infection as evidenced by increased levels of viral proteins (p24 and Pr55Gag) and expression of viral GAG gene. In addition, using HIV Bal with luciferase reporter gene (HIV Bal-eLuc), we showed that METH-treated cells expressed higher luciferase activities than untreated monocytes. Mechanistically, METH inhibited the expression of IFN-λ1, IRF7, STAT1, and the antiviral IFN-stimulated genes (ISGs: OAS2, GBP5, ISG56, Viperin and ISG15). In addition, METH down-regulated the expression of the HIV restriction microRNAs (miR-28, miR-29a, miR-125b, miR-146a, miR-155, miR-223, and miR-382).

Conclusions
METH compromises the intracellular anti-HIV immunity and facilitates HIV replication in primary human monocytes.
The regulatory mechanism of neutrophil extracellular traps in cancer biological behavior
Authors: Wang Hui , Zhang Yiyin , Wang Qianling , Wei Xiaoli , Wang Hua , Gu Kangsheng 
Published: November 2021

AbstractAs the predominant host defense against pathogens, neutrophil extracellular traps (NETs) have attracted increasing attention due to their vital roles in infectious inflammation in the past few years. Interestingly, NETs also play important roles in noninfectious conditions, such as rheumatism and cancer. The process of NETs formation can be regulated and the form of cell death accompanied by the formation of NETs is regarded as “NETosis”. A large amount of evidence has confirmed that many stimuli can facilitate the release of NETs from neutrophils. Furthermore, it has been illustrated that NETs promote tumor growth and progression via many molecular pathways. Meanwhile, NETs also can promote metastasis in many kinds of cancers based on multiple studies. In addition, some researchs have found that NETs can promote coagulation and cancer-associated thrombosis. In the present review, it will highlight how NETosis, which is stimulated by various stimuli and signaling pathways, affects cancer biological behaviors via NETs. Given their crucial roles in cancer, NETs will become possible therapeutic targets for inhibiting proliferation, metastasis and thrombosis in cancer patients.
Association among dysmenorrhea and activity limitation and participation restrictions in adult women: a cross-sectional study, Brazil -2017
Authors: Brito dos Santos Luana , Ferreira Caroline Wanderley Souto , Gonçalves Caroline Gomes , de Oliveira Xavier Mikaela Aparecida , Dantas Jardelina Hermecina , Barbosa Isabelle Ribeiro , da Câmara Saionara Maria Aires , Dantas Diego 
Published: November 2021

Abstract
Background
The present study aims to analyse if dysmenorrhea is associated with activity limitations and participation restrictions in experencied by adult women.

Methods
This is a cross-sectional study carried out with adult women recruited from primary health services in Brazil between 2016 and 2017. Dysmenorrhea was measured via a self-report and the activity limitation and participation restrictions was assessed by the World Health Disability Assessment Schedule (WHODAS2.0). Pain and level of physical activity were assessed, respectively, by the numerical pain rating scale and International Physical Activity Questionnaire (IPAQ), short version. Associations between groups, dysmenorrhea and without dysmenorrhea (WD), were analysed by the median difference, Mann Whitney test, effect size measures and 95 % confidence interval. Statistical significance was p <0.05.

Results
The prevalence of dysmenorrhea was 54 %. The pain lasted an average of three days or more (66 %). The average pain intensity, in the crisis period, was 6.1 ± 2.6, women who presented severe pain complaints were associated with considerable difficulties in their domains of mobility (p = 0.003; 2 = 0.115), participation (p = 0.030; 2 = 0.063) and total score (p = 0.012; 2 = 0.086), with a moderate effect size for all variables.

Conclusions
Severe dysmenorrhea was associated with higher scores of disabilities assessed by the WHODAS 2.0, especially in mobility, and participation domains.
Perspectives on extended-release naltrexone induction among patients living with HIV and opioid use disorder: a qualitative analysis
Authors: Hoffman Kim A. , Baker Robin , Fanucchi Laura C. , Lum Paula J. , Kunkel Lynn E. , Ponce Terashima Javier , McCarty Dennis , Jacobs Petra , Korthuis P. Todd 
Published: November 2021

Abstract
Background
The CHOICES study randomized participants with HIV and opioid use disorder (OUD) to HIV clinic-based extended-release naltrexone (XR-NTX), which requires complete cessation of opioid use, versus treatment-as-usual (i.e., buprenorphine, methadone). Study participants randomized to XR-NTX were interviewed to assess their experiences with successful and unsuccessful XR-NTX induction.

Methods
Semi-structured qualitative interviews were completed with a convenience sample of study participants with HIV and OUD (n = 37) randomized to XR-NTX in five HIV clinics between 2018 and 2019. All participants approached agreed to be interviewed. Interviews were digitally recorded, professionally transcribed, and analyzed using thematic analysis.

Results
Participants included women (43%), African Americans (62%) and Hispanics (16%), between 27 to 69 years of age. Individuals who completed XR-NTX induction (n = 20) reported experiencing (1) readiness for change, (2) a supportive environment during withdrawal including comfort medications, and (3) caring interactions with staff. Four contrasting themes emerged among participants (n = 17) who did not complete induction: (1) concern and anxiety about withdrawal including past negative experiences, (2) ambivalence about or reluctance to stop opioids, (3) concerns about XR-NTX effects, and (4) preferences for other medications.

Conclusions
The results highlight opportunities to improve initiation of XR-NTX in high-need groups. Addressing expectations regarding induction may enhance XR-NTX initiation rates.
Trial Registration ClinicalTrials.gov: NCT03275350. Registered September 7, 2017. https://clinicaltrials.gov/ct2/show/NCT03275350?term=extended+release+naltrexone&cond=Opioid+Use.
State of the art, recent advances, and challenges in the field of fungal mycelium materials: a snapshot of the 2021 Mini Meeting
Authors: Attias Noam , Livne Achiya , Abitbol Tiffany 
Published: November 2021

AbstractMaterial development based on fungal mycelium is a fast-rising field of study as researchers, industry, and society actively search for new sustainable materials to address contemporary material challenges. The compelling potential of fungal mycelium materials is currently being explored in relation to various applications, including construction, packaging, “meatless” meat, and leather-like textiles. Here, we highlight the discussions and outcomes from a recent 1-day conference on the topic of fungal mycelium materials (“Fungal Mycelium Materials Mini Meeting”), where a group of researchers from diverse academic disciplines met to discuss the current state of the art, their visions for the future of the material, and thoughts on the challenges surrounding widescale implementation.
The role of ceRNA-mediated diagnosis and therapy in hepatocellular carcinoma
Authors: Shi Yi , Liu Ji-Bin , Deng Jing , Zou Da-Zhi , Wu Jian-Jun , Cao Ya-Hong , Yin Jie , Ma Yu-Shui , Da Fu , Li Wen 
Published: November 2021

AbstractHepatocellular carcinoma (HCC) is one of the leading causes of cancer-related death worldwide due to its high degree of malignancy, high incidence, and low survival rate. However, the underlying mechanisms of hepatocarcinogenesis remain unclear. Long non coding RNA (lncRNA) has been shown as a novel type of RNA. lncRNA by acting as ceRNA can participate in various biological processes of HCC cells, such as tumor cell proliferation, migration, invasion, apoptosis and drug resistance by regulating downstream target gene expression and cancer-related signaling pathways. Meanwhile, lncRNA can predict the efficacy of treatment strategies for HCC and serve as a potential target for the diagnosis and treatment of HCC. Therefore, lncRNA serving as ceRNA may become a vital candidate biomarker for clinical diagnosis and treatment. In this review, the epidemiology of HCC, including morbidity, mortality, regional distribution, risk factors, and current treatment advances, was briefly discussed, and some biological functions of lncRNA in HCC were summarized with emphasis on the molecular mechanism and clinical application of lncRNA-mediated ceRNA regulatory network in HCC. This paper can contribute to the better understanding of the mechanism of the influence of lncRNA-mediated ceRNA networks (ceRNETs) on HCC and provide directions and strategies for future studies.
Experimental and computational studies on activated Bambara groundnut (Vigna subterranean) hulls for the adsorptive removal of herbicides from aqueous solution
Authors: Nyijime Thomas Aondofa , Ayuba Abdullahi Muhammad , Chahul Habibat Faith 
Published: November 2021

AbstractBackgroundThe excessive usage of herbicides to control herbs by farmers has become an issue of interest to the environmentalist due to the threat posed by such act to the ecosystem, and therefore, there is the need to curb such practices.The efficiency of Bambara groundnut shell for the removal of pendimethalin (PE) and paraquat dichloride (PQ) herbicides from aqueous solution was established in this work. The activated carbon was prepared via chemical activation method using trioxonitrate (v) acid by determining its void volume, moisture content, bulk density and Fourier transform infrared (FTIR) and scanning electron microscopy (SEM) methods. Batch adsorption techniques were set to optimize the adsorption parameters such as solution pH, adsorbate concentration, contact time, adsorbent dosage and temperature in order to depict the best optimal conditions for the adsorption process. The adsorption process was examined in terms of its equilibrium data, kinetics, thermodynamics involved in the adsorption process as well as computational quantum chemical parameters evaluation.ResultsThe batch adsorption experiments revealed that the amounts of PE and PQ adsorbed were found to vary with the contact time, adsorbent dosage, pH and initial concentration. The adsorption of PE and PQ decreased with increasing adsorbent dose but increases with increasing initial concentration of the PE and PQ solution. Isotherm studies revealed that the equilibrium data fitted to both Langmuir and Freundlich model withR-squared values of 0.976, 0.993 and 0.909, 0.978 for PE and PQ, respectively, which implied that Langmuir isotherm had a better fit. This was also found to be an indication that the uptake of PE and PQ by ACBGNS occurred through monolayer adsorption on identical homogenous sites. Also, kinetic modeling results obtained showed that the pseudo-second-order model explained the adsorption kinetics of PE and PQ by ACBGNS best, which meant that chemisorption was the slowest step and, thus, the rate determining step. The positive value of ΔHand the positive value of ΔGshow the endothermic and spontaneous nature of adsorption of PE and PQ ACBGNS.ConclusionBatch adsorption experiment and characterization of the ACBGNS have indicated that Bambara ground nut shell can be used to produce activated carbon that can be applied effectively for adsorption of PE and PQ from an aqueous solution. Computational studies results obtained from quantum chemical analysis are consistent with the experimental results obtained from this study.
Seismic wave equation formulated by generalized viscoelasticity in fluid-saturated porous media
Authors: Ni Jun , Gu Hanming , Wang Yanghua 
Published: November 2021

Biot’s theory of poroelasticity describes seismic waves propagating through fluid-saturated porous media, so-called two-phase media. The classic Biot’s theory of poroelasticity considers the wave dissipation mechanism as being the friction of relative motion between the fluid in the pores and the solid rock skeleton. However, within the seismic frequency band, the friction has a major influence only on the slow P-wave and an insignificant influence on the fast P-wave. To represent the intrinsic viscoelasticity of the solid skeleton, we incorporate a generalized viscoelastic wave equation into Biot’s theory for the fluid-saturated porous media. The generalized equation that unifies the pure elastic and viscoelastic cases is constituted by a single viscoelastic parameter, presented as the fractional order of the wavefield derivative in the compact form of the wave equation. The generalized equation that includes the viscoelasticity appropriately describes the dissipation characteristics of the fast P-wave. Plane-wave analysis and numerical solutions of our wave equation reveal that (1) the viscoelasticity in the solid skeleton causes the energy attenuation on the fast P-wave and the slow P-wave at the same order of magnitude and (2) the generalized viscoelastic wave equation effectively describes the dissipation effect of the waves propagating through the fluid-saturated porous media.
Using relative geologic time to constrain convolutional neural network-based seismic interpretation and property estimation
Authors: Di Haibin , Li Zhun , Abubakar Aria 
Published: November 2021

Three-dimensional seismic interpretation and property estimation is essential for subsurface mapping and characterization, in which machine learning, particularly supervised convolutional neural network (CNN), has been extensively implemented for improved efficiency and accuracy in the past few years. However, in most seismic applications, the amount of available expert annotations often is limited, which raises the risk of overfitting a CNN, particularly when only seismic amplitudes are used for learning. In such a case, the trained CNN would have poor generalization capability, causing the interpretation and property results of obvious artifacts, limited lateral consistency, and thus restricted application to following interpretation/modeling procedures. Our study proposes addressing such an issue by using relative geologic time (RGT), which explicitly preserves the large-scale continuity of seismic patterns, to constrain a seismic interpretation and/or property estimation CNN. Such constrained learning is enforced twofold: (1) from the perspective of input, the RGT is used as an additional feature channel besides seismic amplitude, and more innovatively (2) the CNN has two output branches, with one for matching the target interpretation or properties and the other for reconstructing the RGT. In addition, multiplicative regularization is used to facilitate the simultaneous minimization of the target-matching loss and the RGT-reconstruction loss. The performance of such an RGT-constrained CNN is validated by two examples, facies identification in the Parihaka data set and property estimation in the F3 Netherlands data set. Compared with those purely from seismic amplitudes, the facies and property predictions using the proposed RGT constraint demonstrate significantly reduced artifacts and improved lateral consistency throughout a seismic survey.
“She Was Raised on Blood”
Authors: Dumas Raechel 
Published: November 2021

Abstract
Contemporary Japan has been widely identified as a scene of crisis marked by the breakdown of established sociocultural institutions and the subordination of identity and desire to ever-evolving technocapitalist whims. Japanese-horror (J-horror) media of this period reveals a collective concern with these cultural themes, routinely employing haunted technologies to elaborate the perils and possibilities of existence in a world of incertitude. This article examines Shimizu Takashi’s 2004 Marebito with attention to how the film develops a critique of the estranging forces of late capitalism and elaborates an alluring alternative, located in a return to what Derrida describes as the scene of humanity’s second trauma: “the Darwinian.” In doing so, the article traces how the drive for self-annihilation emerges in Marebito not only as a terrifying prospect but also as an occasion to forge intimate relationships with the repressed of culture.
The effect of dietary phosphorus load and food matrix on postprandial serum phosphate in hemodialysis patients: a pilot study
Authors: Byrne Fiona , Gillman Barbara , Palmer Brendan , Kiely Mairead , Eustace Joseph , Kearney Patricia , Davidson Fred , Shiely Frances 
Published: November 2021

Background: Potential dietary strategies for controlling hyperphosphataemia include the use of protein sources with lower phosphorus bioavailability such as pulses and nuts, focus on phosphorus to protein ratios and the avoidance of all phosphate additives. Methods: We conducted a controlled crossover feeding study in 8 haemodialysis (HD) patients to investigate the acute postprandial effect of a modified versus standard low phosphorus diet for one day on serum phosphate, potassium and intact parathyroid levels in prevalent HD patients. Each participant consumed the modified diet on one day and the standard diet on a second day one week apart. The modified diet included beef and less dairy, with a lower phosphorus to protein ratio, as well as plant-based protein, whole grains, pulses and nuts containing phytates which reduces phosphorus bioavailability. Both diets were tailored for each participant to provide 1.1g protein/kg ideal body weight. Participants provided fasting bloods before breakfast, a pre-prandial sample before the lunch time main meal and samples at one-hour intervals for the four hours after the lunch time main meal, for analysis of phosphate, potassium and intact parathyroid hormone (iPTH). Results: At four hours post the lunch time main meal on each study day, individuals on the modified diet had serum phosphate readings 0.30 mmol/l lower than when on the standard diet (p-value = 0.015, 95% confidence interval [CI] -0.57, -0.04). The corresponding change in serum potassium at four hours was a decrease of 0.675 mmol/l (p-value = 0.011, CI -1.25, -0.10). Conclusions: Decreases in both serum phosphate and serum potassium readings on a modified low phosphorus diet encourage further larger studies to explore the possibility of greater food choice and healthier plant-based diets in HD patients. ClinicalTrials.gov registration: NCT04845724 (15/04/2021)