bluuebunny/crossref_metadata_2025 huggingface dataset:
Physiological and Environmental Influences on Wingbeat Frequency of Oriental Armyworm,Mythimna separata(Lepidoptera: Noctuidae)
Authors: Xu Rui-Bin , Ge Shi-Shuai , Yu Wen-Hua , Li Xiao-Kang , Wu Kong-Ming
Published: November 2022

The oriental armyworm, Mythimna separata (Walker, 1865) (Lepidoptera: Noctuidae), is a serious global migratory insect pest of grain crops. Although its migratory biology has been studied for a long history, the factors affecting wingbeat frequency (WBF), which is closely related to the flight activity of the insect, remain unclear. In this study, the WBFs of both cultured and migrating moths were tested under different conditions in the laboratory using a stroboscope. The results indicated that age and mating status significantly influenced WBF. One day old adults had the lowest WBF, and unmated females had a significantly higher WBF than that of mated females. In general, the WBF of males was significantly higher than that of female individuals. The WBF decreased gradually with increasing environmental humidity, and WBF had a significant negative binomial regression relationship with temperature change. The WBF of moths that fed on hydromel was much higher than those of the controls that fed on water or without diet. However, wind speed and air pressure had no significant effects on the moth WBF in the test environments. These findings provide a deeper understanding of factors that affect flight ability in M. separata, which will be helpful for developing a regional migratory monitoring and warning system of the pest, such as identifying target insect species based on the WBF from radar observation.
Combined effects of exploitation and environmental change on life history: a comparative analysis on Atlantic herring
Authors: Beaudry-Sylvestre Manuelle , Benoît Hugues P , Hutchings Jeffrey A
Published: November 2022

The consequences of fisheries-induced evolution on stock productivity and yield depend, to a large extent, on the general prospects for growth and survival. Here, we compare the selection pressures imposed by two distinct patterns of exploitation—principally targeting spawning or non-spawning aggregations—on age at maturity among 15 Canadian stocks of Atlantic herring (Clupea harengus) that have exhibited a consistent pattern of length-at-age responses to common large-scale environmental drivers since the 1960s. In accordance with expectations for maturity-dependent harvesting, the establishment of a spawner-targeted fishery in the southern Gulf of St. Lawrence coincided with a shift towards delayed maturity in both resident stocks, whereas stocks elsewhere subject to fisheries that also exploited juveniles more commonly exhibited trends towards earlier maturity. Despite these differences, we find that environmentally driven changes in length at maturation, combined with total mortality, may overwhelmingly determine lifetime reproductive success and possibly fitness. By linking phenotypic changes experienced in the juvenile period to simple correlates of egg production in mature age classes, our study highlights the importance of managing fisheries in the context of ubiquitous but contrasting environmental constraints on life histories.
Amenability of Monomial Algebras, Minimal Subshifts, and Free Subalgebras
Authors: Bell Jason P , Greenfeld Be’eri
Published: November 2022

We give a combinatorial characterization of amenability of monomial algebras and prove the existence of monomial Følner sequences, answering a question due to Ceccherini–Silberstein and Samet–Vaillant. We then use our characterization to prove that over projectively simple monomial algebras, every module is exhaustively amenable; we conclude that convolution algebras of minimal subshifts admit the same property. We deduce that any minimal subshift of positive entropy gives rise to a graded algebra, which does not satisfy an extension of Vershik’s conjecture on amenable groups, proposed by Bartholdi. Finally, we show that non-amenable monomial algebras must contain noncommutative free subalgebras. Examples are given to emphasize the sharpness and necessity of the assumptions in our results.
Evaluation of supplemental fat sources and pre-farrow essential fatty acid intake on lactating sow performance and essential fatty acid composition of colostrum, milk, and adipose tissue
Authors: Holen Julia P , Woodworth Jason C , Tokach Mike D , Goodband Robert D , DeRouchey Joel M , Gebhardt Jordan T
Published: November 2022

A total of 91 sows (Line 241, DNA Genetics) were used to evaluate the effects of supplemental fat sources and essential fatty acid intake on sow farrowing performance, litter growth performance, and essential fatty acid composition of colostrum, milk, and adipose tissue. At approximatelyday 107 of gestation, sows were blocked by body weight and parity, then allotted to 1 of 5 experimental treatments as part of a 2 × 2 + 1 factorial arrangement. Experimental diets were corn-soybean meal-based with a control diet that contained no added fat or diets with 3% added fat as either beef tallow or soybean oil, with consumption of the added fat diets starting on day 107 or 112 of gestation and fed until weaning. Thus, sows were provided low essential fatty acids (EFA; as linoleic and α-linolenic acid) without supplemental fat or with beef tallow or high EFA with soybean oil. Sows were provided approximately 2.8 kg/d of their assigned lactation diet pre-farrow and then provided ad libitum access after parturition. Sows consuming diets with beef tallow had greater lactation ADFI (fat source, P = 0.030), but lower daily linoleic acid (LA) and α-linolenic acid (ALA) intake than sows that consumed diets with soybean oil (fat source, P < 0.001). Supplemental fat sources providing either low or high EFA did not influence litter growth performance (fat source, P > 0.05). Sows fed diets with beef tallow did not influence the LA composition of colostrum; however, lactation diets with high EFA provided by soybean oil on day 107 of gestation increased colostrum LA concentration compared to providing diets on day 112 of gestation (fat source × time, P = 0.084; time, P < 0.001). Additionally, regardless of pre-farrow timing, ALA concentration of colostrum increased when sows consumed diets with soybean oil compared to beef tallow (fat source, P < 0.001). Both LA and ALA concentrations of milk at weaning were greater for sows that consumed diets with soybean oil compared to beef tallow (fat source, P < 0.001). Furthermore, concentrations of LA and ALA within adipose tissue were greater at weaning when sows consumed diets with high EFA compared to low EFA (fat source, P < 0.05). These responses suggest that providing dietary fat sources with high concentrations of EFA can increase backfat, colostrum, and milk LA and ALA. However, in this experiment, changes in colostrum and milk composition did not influence litter growth performance.
Extinction and survival of raninoid crabs (Decapoda: Brachyura: Raninoida) from the Early Cretaceous to the present
Authors: Hartzell Samantha M , Schweitzer Carrie E , Feldmann Rodney M
Published: November 2022

Faunal turnover is a pattern of diversification and extinction in taxa throughout the geologic record. Patterns of repeated faunal turnovers are referred to as faunal progression, demonstrated by Decapoda in clawed lobsters and podotrematous and heterotrematous crabs. The transition between podotrematous and heterotrematous crabs is the most recent. Among these, section Raninoida Ahyong, Lai, Sharkey, Colgan & Ng, 2007, commonly called “frog crabs,” constitutes a major monophyletic group with podotrematous body forms, and the focus of our study. Declines in raninoidan diversity were aligned with mass extinction events and major climate shifts, especially cooling. Likewise, diversification within Raninoida occurred in warm, greenhouse climates. Thus, a major factor in patterns of faunal turnover in Decapoda is shown to be environmental conditions. Raninoidan families exhibiting adaptations facilitating back-burrowing preferentially survived the end-Cretaceous mass extinction event, whereas raninoidans lacking such adaptions did not go completely extinct at the end-Cretaceous but failed to recover diversity. Given the diversification of heterotrematous crabs into a wide variety of ecological niches throughout the Cenozoic, competition may be a secondary, but still crucial, factor in this faunal turnover.
The impact of habitat loss on molecular signatures of coevolution between an iconic butterfly (Alcon blue) and its host plant (Marsh gentian)
Authors: Warson Jonas , Baguette Michel , Stevens Virginie M , Honnay Olivier , De Kort Hanne
Published: November 2022

Habitat loss is threatening natural communities worldwide. Small and isolated populations suffer from inbreeding and genetic drift, which jeopardize their long-term survival and adaptive capacities. However, the consequences of habitat loss for reciprocal coevolutionary interactions remain poorly studied. In this study, we investigated the effects of decreasing habitat patch size and connectivity associated with habitat loss on molecular signatures of coevolution in the Alcon blue butterfly (Phengaris alcon) and its most limited host, the marsh gentian (Gentiana pneumonanthe). Because reciprocal coevolution is characterized by negative frequency-dependent selection as a particular type of balancing selection, we investigated how signatures of balancing selection vary along a gradient of patch size and connectivity, using single nucleotide polymorphisms (SNPs). We found that signatures of coevolution were unaffected by patch characteristics in the host plants. On the other hand, more pronounced signatures of coevolution were observed in both spatially isolated and in large Alcon populations, together with pronounced spatial variation in SNPs that are putatively involved in coevolution. These findings suggest that habitat loss can facilitate coevolution in large butterfly populations through limiting swamping of locally beneficial alleles by maladaptive ones. We also found that allelic richness (Ar) of the coevolutionary SNPs is decoupled from neutral Ar in the butterfly, indicating that habitat loss has different effects on coevolutionary as compared with neutral processes. We conclude that this specialized coevolutionary system requires particular conservation interventions aiming at generating a spatial mosaic of both connected and of isolated habitat to maintain coevolutionary dynamics.
Successful treatment of a patient with Takayasu’s arteritis complicated with Crohn’s disease with ustekinumab: A case report
Authors: Suga Takeshi , Hidaka Yukiko , Hori Maisa , Yamasaki Hiroshi , Wakasugi Daisuke , Yamasaki Satoshi , Yamaguchi Rin , Ida Hiroaki , Nakashima Munetoshi
Published: November 2022

A 17-year-old woman was referred to our department with fever, general malaise, and weight loss. She was diagnosed with Takayasu arteritis (TAK) and Crohn’s disease (CD) following positron emission tomography-computed tomography (PET-CT) and colonoscopy, respectively. Serological human leukocyte antigen (HLA) typing revealed HLA-B52 positivity. Initial treatment with prednisolone (PSL) (0.5 mg/kg) was insufficient; therefore, ustekinumab and 5-aminosalicylic acid were added. This treatment achieved PSL-free remission for both diseases, as confirmed by PET-CT and colonoscopy. Although treatment guidelines for TAK and CD have been previously established, treatment of patients with TAK with coexisting CD is controversial. Our case suggests that ustekinumab has the ability to achieve TAK remission in addition to its therapeutic effect on CD.
NPASS database update 2023: quantitative natural product activity and species source database for biomedical research
Authors: Zhao Hui , Yang Yuan , Wang Shuaiqi , Yang Xue , Zhou Kaicheng , Xu Caili , Zhang Xuyao , Fan Jiajun , Hou Dongyue , Li Xingxiu , Lin Hanbo , Tan Ying , Wang Shanshan , Chu Xin-Yi , Zhuoma Dongzhi , Zhang Fengying , Ju Dianwen , Zeng Xian , Chen Yu Zong
Published: November 2022

Quantitative activity and species source data of natural products (NPs) are important for drug discovery, medicinal plant research, and microbial investigations. Activity values of NPs against specific targets are useful for discovering targeted therapeutic agents and investigating the mechanism of medicinal plants. Composition/concentration values of NPs in individual species facilitate the assessments and investigations of the therapeutic quality of herbs and phenotypes of microbes. Here, we describe an update of the NPASS natural product activity and species source database previously featured in NAR. This update includes: (i) new data of ∼95 000 records of the composition/concentration values of ∼1 490 NPs/NP clusters in ∼390 species, (ii) extended data of activity values of ∼43 200 NPs against ∼7 700 targets (∼40% and ∼32% increase, respectively), (iii) extended data of ∼31 600 species sources of ∼94 400 NPs (∼26% and ∼32% increase, respectively), (iv) new species types of ∼440 co-cultured microbes and ∼420 engineered microbes, (v) new data of ∼66 600 NPs without experimental activity values but with estimated activity profiles from the established chemical similarity tool Chemical Checker, (vi) new data of the computed drug-likeness properties and the absorption, distribution, metabolism, excretion and toxicity (ADMET) properties for all NPs. NPASS update version is freely accessible at http://bidd.group/NPASS.
Gene co-expression analyses of health(span) across multiple species
Authors: Möller Steffen , Saul Nadine , Projahn Elias , Barrantes Israel , Gézsi András , Walter Michael , Antal Péter , Fuellen Georg
Published: November 2022

Health(span)-related gene clusters/modules were recently identified based on knowledge about the cross-species genetic basis of health, to interpret transcriptomic datasets describing health-related interventions. However, the cross-species comparison of health-related observations reveals a lot of heterogeneity, not least due to widely varying health(span) definitions and study designs, posing a challenge for the exploration of conserved healthspan modules and, specifically, their transfer across species. To improve the identification and exploration of conserved/transferable healthspan modules, here we apply an established workflow based on gene co-expression network analyses employing GEO/ArrayExpress data for human and animal models, and perform a comprehensive meta-study of the resulting modules related to health(span), yielding a small set of literature backed health(span) candidate genes. For each experiment, WGCNA (weighted gene correlation network analysis) was used to infer modules of genes which correlate in their expression with a ‘health phenotype score’ and to determine the most-connected (hub) genes (and their interactions) for each such module. After mapping these hub genes to their human orthologs, 12 health(span) genes were identified in at least two species (ACTN3, ANK1, MRPL18, MYL1, PAXIP1, PPP1CA, SCN3B, SDCBP, SKIV2L, TUBG1, TYROBP, WIPF1), for which enrichment analysis by g:profiler found an association with actin filament-based movement and associated organelles, as well as muscular structures. We conclude that a meta-study of hub genes from co-expression network analyses for the complex phenotype health(span), across multiple species, can yield molecular-mechanistic insights and can direct experimentalists to further investigate the contribution of individual genes and their interactions to health(span).
Caveats of Using Bacterial Type Three Secretion Assays for Validating Fungal Avirulence Effectors in Wheat
Authors: Jensen Cassandra , Korolev Andrey , Corredor-Moreno Pilar , Minter Francesca , Dodds Peter N. , Saunders Diane G. O.
Published: November 2022

Functional characterization of effector proteins of fungal obligate biotrophic pathogens, especially confirmation of avirulence (Avr) properties, has been notoriously difficult, due to the experimental intractability of many of these organisms. Previous studies in wheat have shown promising data suggesting the type III secretion system (T3SS) of bacteria may be a suitable surrogate for delivery and detection of Avr properties of fungal effectors. However, these delivery systems were tested in the absence of confirmed Avr effectors. Here, we tested two previously described T3SS-mediated delivery systems for their suitability when delivering two confirmed Avr effectors from two fungal pathogens of wheat, Puccinia graminis f. sp. tritici and Magnaporthe oryzae pathotype tritici. We showed that both effectors (AvrSr50 and AvrRmg8) were unable to elicit a hypersensitive response on wheat seedlings with the corresponding resistance gene when expressed by the Pseudomonas fluorescens “Effector to Host Analyser” (EtHAn) system. Furthermore, we found the utility of Burkholderia glumae for screening Avr phenotypes is severely limited, as the wild-type strain elicits nonhost cell death in multiple wheat accessions. These results provide valuable insight into the suitability of these systems for screening fungal effectors for Avr properties that may help guide further development of surrogate bacterial delivery systems in wheat.

[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Outcome of bracing vs. surgical treatment in adolescents with idiopathic scoliosis based on device measured daily physical activity: a prospective pilot study
Authors: Chopra Swati , Larson A. Noelle , Milbrandt Todd A. , Kaufman Kenton R.
Published: November 2022

Adolescent idiopathic scoliosis (AIS) can be treated with bracing or surgery, which may affect patient’s physical activity (PA). However, there are limited objective assessments of PA in patients with AIS. This study aims to compare the outcome of spinal bracing vs. surgery in patients with AIS based on a device that measured daily PA. In total 24 patients with AIS participated, including 12 patients treated with bracing and 12 with spinal surgery. Daily PA was measured throughout 4 consecutive days using four tri-axial accelerometers and patient-reported functional status was reported using the SRS-22 questionnaire. The participants were assessed both before the treatment and after treatment at a 12-month follow-up. Patients with AIS had no significant change in their PA levels at the 12-month follow-up after surgical correction. On the contrary, patients with AIS following a year-long bracing treatment had significantly reduced time spent active (P = 0.04) with an average reduction in walking steps by 2137 steps/day (P = 0.005). There was no significant difference in function, pain, self-image and mental health domains following both treatments, as reported by the SRS-22. There was a significant improvement in satisfaction for both treatment groups (P ≤ 0.02). Significantly reduced PA and increased sedentary time are reported in patients with AIS following bracing treatment. An objective PA assessment is recommended to track the effect of scoliosis treatment on PA. Patients with AIS should be actively encouraged to achieve and maintain their recommended daily PA levels irrespective of the type of treatment. Level of evidence: Level II.
Public health services and intersectional stigma: a social sciences perspective with implications for HIV service design and delivery
Authors: Tan Rayner Kay Jin , Tang Weiming , Tucker Joseph D.
Published: November 2022

Purpose of review

Understanding stigma is important for improving HIV care services and gaps in HIV service delivery have been attributed to stigma. This review article synthesizes recent evidence on stigma and its implications for HIV service design and delivery. Given the intersectional nature of stigma, we will focus on HIV stigma as well as related forms of stigma based on one's race, sexual identity, gender identity and other identities.

Recent findings

Stigma remains a barrier to achieving equity in HIV services. Individualistic measures of stigma remain influential and are associated with barriers to accessing HIV health services. Recent work also highlights stigma measured at a structural level and its impact on HIV services contexts. Individuals situated at intersections of marginalized identities continue to face greatest injustices, and although intersectional approaches have been adapted to design services at a micro level, few focus on structural change. Recent evidence for mitigating stigma indicates some success for psychosocial interventions that target internalized stigma. Furthermore, community-led approaches show promise in addressing stigma that manifests in HIV health services settings.

Interventions that address individual-level stigma and structural stigma are needed. Theoretical and applied antistigma research is needed to make HIV services more equitable.
Survey of Well-Being of Young Children (SWYC): Preliminary Norms for Screening for Developmental Delay in Brazilian Children Younger than 65 Months
Authors: Guimarães Marina Aguiar Pires , Magalhães Lívia de Castro , Moreira Rafaela Silva , Bessa Francilena Ribeiro , Alves Claudia Regina Lindgren
Published: November 2022

Objective:

The objective of this study was to investigate the reliability and validity of the Developmental Milestones Questionnaire of the Survey of Wellbeing of Young Children Brazilian version (DM-SWYC-BR) and establish the preliminary norms to identify suspected developmental delay in Brazilian children up to 65 months.

Methods:

A psychometric study was conducted on 1535 children from 3 Brazilian regions. The caregivers answered the Brazilian Portuguese cross-culturally adapted version of the DM-SWYC. We calculated the internal consistency and performed an exploratory factor analysis (EFA). The clinical threshold for the suspected developmental delay was set at 85% from the DM-SWYC-BR mean score for each age. The prevalence of suspected delay was calculated using current preliminary cutoffs and original norms.

Results:

EFA confirmed the unidimensionality of the DM-SWYC-BR items (average variance extracted = 0.78). Cronbach's alpha was 0.97. At most ages, the difference between the cutoff points in the Brazilian and North American samples was lower than or equal to 2 points, except at 18, 23, 29, 44, 45, 46, and from 54 to 58 months. There was a marked divergence in the prevalence of suspected developmental delay by age ranges using the Brazilian or North American cutoff points. However, the general mean prevalence was quite similar (27.5% vs. 28.2%, respectively).

Conclusions:

We established the cutoff points to interpret the DM-SWYC-BR results when screening for developmental delays in Brazilian children. The satisfactory psychometric properties support its use for screening developmental delays in the public health system. Reliable assessment tools are critical to promoting child development effectively, ensuring timely intervention.
New and old approaches to nutritional management of acute and chronic glomerulonephritis
Authors: Hanna Ramy M. , Ahdoot Rebecca S. , Rhee Connie M. , Tantisattamo Ekamol , Al Ammar Fawaz , Kalantar-Zadeh Kamyar
Published: November 2022

Purpose of review

It has been well published that a low protein diet (0.6–0.8 g/kg/day) is optimal for nutritional management of chronic kidney disease and with care be used without inducing protein malnutrition.

Recent findings

Though care with this approach must be demonstrated in patients with end-stage renal disease and with prominent protein energy wasting, another category of renal patient exists for whom dietary recommendations need more exploration. The Kidney Disease Improving Global Outcomes consortium, actually identifies renal disease as those patients with reduced filtration and those with excessive proteinuria excretion. Proteinuria, indeed, has proven to be a serious marker predisposing renal patients to atherosclerotic heart disease, venous thromboembolism, cerebrovascular accidents, and overall mortality. We discuss what is known about nutritional strategies to curb proteinuria and control inflammation in the setting of glomerulonephritis.

While this area of management of a set of conditions maybe nascent, it has the potential to provide incredible breakthroughs in nutritional management of auto immune diseases of the kidney specifically and the body writ large.
IMPELLA VERSUS EXTRACORPOREAL MEMBRANE OXYGENATION IN CARDIOGENIC SHOCK: A SYSTEMATIC REVIEW AND META-ANALYSIS
Authors: Abusnina Waiel , Ismayl Mahmoud , Al-abdouh Ahmad , Ganesan Vaishnavi , Mostafa Mostafa Reda , Hallak Osama , Peterson Emily , Abdou Mahmoud , Goldsweig Andrew M. , Aboeata Ahmed , Dahal Khagendra
Published: November 2022

Background: Cardiogenic shock (CS) carries high mortality. The roles of specific mechanical circulatory support (MCS) systems are unclear. We compared the clinical outcomes of Impella versus extracorporal membrane oxygenation (ECMO) in patients with CS. Methods: This is a systematic review and meta-analysis that was conducted in accordance with Preferred Reporting Items for Systematic Reviews and Meta Analyses guidelines. We searched PubMed, Cochrane Central Register, Embase, Web of Science, Google Scholar, and ClinicalTrials.gov (inception through May 10, 2022) for studies comparing the outcomes of Impella versus ECMO in CS. We used random-effects models to calculate risk ratios (RRs) with 95% confidence interval (CIs). End points included in-hospital, 30-day, and 12-month all-cause mortality, successful weaning from MCS, bridge to transplant, all reported bleeding, stroke, and acute kidney injury. Results: A total of 10 studies consisting of 1,827 CS patients treated with MCS were included in the analysis. The risk of in-hospital all-cause mortality was significantly lower with Impella compared with ECMO (RR, 0.80; 95% CI, 0.65–1.00; P = 0.05), whereas there was no statistically significant difference in 30-day (RR, 0.97, 95% CI, 0.82–1.16; P = 0.77) and 12-month mortality (RR, 0.90; 95% CI, 0.74–1.11; P = 0.32). There were no significant differences between the two groups in terms of successful weaning (RR, 0.97; 95% CI, 0.81–1.15; P = 0.70) and bridging to transplant (RR, 0.88; 95% CI, 0.58–1.35; P = 0.56). There was less risk of bleeding and stroke in the Impella group compared with the ECMO group. Conclusions: In patients with CS, the use of Impella is associated with lower rates of in-hospital mortality, bleeding, and stroke than ECMO. Future randomized studies with adequate sample sizes are needed to confirm these findings.
LATE POSTPANCREATICODUODENECTOMY HEMORRHAGE: INCIDENCE, RISK FACTORS, MANAGEMENT AND OUTCOME
Authors: Jacquemin Mathieu , Mokart Djamel , Faucher Marion , Ewald Jacques , Tourret Maxime , Brun Clément , Tezier Marie , Mallet Damien , Nguyen Duong Lam , Cambon Sylvie , Pouliquen Camille , Ettori Florence , Sannini Antoine , Gonzalez Frédéric , Bisbal Magali , Chow-Chine Laurent , Servan Luca , de Guibert Jean Manuel , Boher Jean Marie , Turrini Olivier , Garnier Jonathan
Published: November 2022

Background:Postpancreaticoduodenectomy (PD) hemorrhage (PPH) is a life-threatening complication after PD. The main objective of this study was to evaluate incidence and factors associated with late PPH as well as the management strategy and outcomes. Methods: Between May 2017 and March 2020, clinical data from 192 patients undergoing PD were collected prospectively in the CHIRPAN Database (NCT02871336) and retrospectively analyzed. In our institution, all patients scheduled for a PD are routinely admitted for monitoring and management in intensive/intermediate care unit (ICU/IMC). Results: The incidence of late PPH was 17% (32 of 192), whereas the 90-day mortality rate of late PPH was 19% (6 of 32). Late PPH was associated with 90-day mortality (P = 0.001). Using multivariate analysis, independent risk factors for late PPH were postoperative sepsis (P = 0.036), and on day 3, creatinine (P = 0.025), drain fluid amylase concentration (P = 0.023), lipase concentration (P < 0.001), and C-reactive protein (CRP) concentration (P < 0.001). We developed two predictive scores for PPH occurrence, the PANCRHEMO scores. Score 1 was associated with 68.8% sensitivity, 85.6% specificity, 48.8% predictive positive value, 93.2% negative predictive value, and an area under the receiver operating characteristic curves of 0.841. Score 2 was associated with 81.2% sensitivity, 76.9% specificity, 41.3% predictive positive value, 95.3% negative predictive value, and an area under the receiver operating characteristic curve of 0.859. Conclusions: Routine ICU/IMC monitoring might contribute to a better management of these complications. Some predicting factors such as postoperative sepsis and biological markers on day 3 should help physicians to determine patients requiring a prolonged ICU/IMC monitoring.
Evaluation of five commercial DNA extraction kits using Salmonella as a model for implementation of rapid Nanopore sequencing in routine diagnostic laboratories
Authors: Eagle Shannon H.C. , Robertson James , Bastedo D. Patrick , Liu Kira , Nash John H.E.
Published: November 2022

Oxford Nanopore long-read sequencing offers advantages over Illumina short-reads for the identification and characterization of bacterial pathogens for outbreak detection and surveillance activities within a diagnostic public health laboratory context. Compared to Illumina, Nanopore is more cost-effective for small batches, has a lower capital cost, and has a faster turnaround time, in addition to the ability to assemble complete bacterial genomes. The quantity and quality of DNA required for Nanopore sequencing is higher than Illumina, and DNA extraction methods recommended for obtaining high molecular weight DNA are different from those typically used in diagnostic laboratories. Using a Salmonella isolate with a previously closed PacBio genome as a model Enterobacteriaceae organism, we evaluated the quantity, quality, and fragmentation of five commercial DNA extraction kits. Nanopore sequencing performance was evaluated for the top three methods: Qiagen EZ1 DNA Tissue, Qiagen DNeasy Blood and Tissue, and a modified, in-house version of the MasterPure Complete DNA and RNA purification. To evaluate the effect of post-extraction DNA purification methods, we subjected extracted DNA from the three selected extraction methods to purification by AMPure beads or ethanol precipitation and compared these outputs with untreated DNA as a control. All methods are suitable for routine Whole Genome Sequencing (WGS), since all 60 replicates had very high genome recovery rates, with ≥ 98% of the reference genome covered by mapped Nanopore reads. For 85% of the replicates, assembly was able to produce a complete, circular chromosome using either Flye or Canu. In most cases, it is recommended to move directly from extraction to sequencing as untreated DNA had the highest rates of genome closure regardless of extraction method. Using our evaluation criteria, the Qiagen DNeasy Blood and Tissue kit was found to be the best overall method due to its low-cost, ability to scale from single tube to 96-well plates, and high consistency in yield and sequencing performance.
Rhizopus homothallicus, an emerging pathogen causing cavitary lung lesions
Authors: Taneja juhi , Chatterjee Kuhu , Sachdeva Ruchi Arora , Abbas S Zafar , Sen MK
Published: November 2022

Introduction:  Rhizopus homothallicus is a new emerging pathogen causing Mucormycosis.
Case Presentation: We report a case of pneumonia caused by Rhizopus homothallicus in a 54 year old type 2 diabetic patient. The organism was isolated from bronchoalveolar lavage fluid and preliminary identified by fungal morphology and finally by sequencing of the internal transcribed spacer region.
Conclusion: Mucormycosis may be associated with cavitary lung lesions in the backdrop of poorly controlled diabetes or other immunosuppressed states. Pulmonary mucormycosis may have variable clinical and radiological presentations. Therefore, strong clinical suspicion and prompt management can prevent high fatality associated with the disease.
Preliminary exploration of facial electromyographic indices of pain in people undergoing hand surgery
Authors: Panchevski Filip , Mavridou Ifigeneia , Gjoreski Hristijan , Gjoreski Martin , Kiprijanovska Ivana , Stankoski Simon , Nduka Charles , Broulidakis John
Published: November 2022

Assessing pain levels in real-world conditions, such as during active surgery, can be challenging. Self-reports, often considered globally as ‘ground-truth’ can be unreliable, episodic and ill-suited to routine monitoring or use with non-verbal patients. Lately, physiological measurements have been explored as an objective method for assessing the symptoms of pain increase on the body. We investigated the effects of pain (high pain) using facial mask – emteqPRO, equipped with seven facial electromyographic (fEMG) sensors.

Our aims were to: (i) investigate the efficacy of continuous physiological monitoring within surgery at a hospital environment, and (ii) to produce initial findings and show how pain increase affects the data from fEMG sensors.
Video-driven simulation of lower limb mechanical loading during aquatic exercises
Authors: Lauer Jessy
Published: November 2022

Understanding the mechanical demands of an exercise on the musculoskeletal system is crucial to prescribe effective training or therapeutic interventions. Yet, that knowledge is currently limited in water, mostly because of the difficulty in evaluating external resistance. Here I reconcile recent advances in 3D markerless pose and mesh estimation, biomechanical simulations, and hydrodynamic modeling, to predict lower limb mechanical loading during aquatic exercises. Simulations are driven exclusively from a single video. In silico hip and knee joint forces agreed well with in vivo instrumented implant recordings downloaded from the OrthoLoad database, both in magnitude and direction. New insights into individual muscle contributions to joint loading were gained. This noninvasive method has the potential to standardize the reporting of exercise intensity, inform the design of rehabilitation protocols and improve their reproducibility.
Public perceptions, knowledge and factors associated with the acceptability of genetically modified foods in Kampala city, Uganda
Authors: Nowamukama Miria
Published: November 2022

Food is a basic human need important for the survival of all human beings. The rapidly growing world population puts pressure on food sources, inviting the need to devise mechanisms to sustain it. Biotechnology has developed important measures for improving plants and livestock as a remedy for food security with aim to achieve the Sustainable Development goal two (2). Globally, the adoption and use of genetically modified foods (GMFs) has been controversial as it is in Uganda today due to concerns related to the risk uncertainties. This study was therefore conducted to assess the public perceptions, knowledge and factors that influence the acceptability of genetically modified foods in Kampala City.

This was a cross sectional quantitative study that involved one hundred and ninety-eight participants. The data were collected using a survey tool and summarized using descriptive and linear regression analysis.

The findings of this study showed that almost two-thirds of participants (129/198, 65%) had some basic knowledge on genetically modified foods. About 45.3% (90/198) of the participants perceived genetically modified foods as being unsafe for human consumption. Eighty-eight participants (44.3%) perceived them as being associated with major human health and environmental safety concerns. The acceptability of these foods was significantly associated with gender, education level, nutritional value and health effects. Female participants were more likely to accept genetically modified foods (OR.4.84 95% CI: 1.37 - 7.68). Those who perceived genetically modified foods as being of high nutrition value were more likely to accept them (OR. 3.07, 95% CI: 1.27 - 7.37).

The public is predominantly aware of genetical modified foods since a big proportion had basic knowledge about them although with a lot of misinformation. People with a higher education level had positive perceptions on the use of these foods hence a need to educate the public to dispel misinformation that influences their acceptability
Multivalent Human Cytomegalovirus Glycoprotein B Nucleoside-Modified mRNA Vaccines Demonstrate a Greater Breadth in T cell but not Antibody Responses
Authors: Wang Hsuan-Yuan (Sherry) , Li Leike , Nelson Cody S. , Barfield Richard , Valencia Sarah , Chan Cliburn , Muramatsu Hiromi , Lin Paulo J.C. , Pardi Norbert , An Zhiqiang , Weissman Drew , Permar Sallie R.
Published: November 2022

Human cytomegalovirus (HCMV) remains the most common congenital infection and infectious complication in immunocompromised patients. The most successful HCMV vaccine to-date, an HCMV glycoprotein B (gB) subunit vaccine adjuvanted with MF59, achieved 50% efficacy against primary HCMV infection. A previous study demonstrated that gB/MF59 vaccinees were less frequently infected with HCMV gB genotype strains most similar to the vaccine strain than strains encoding genetically distinct gB genotypes, suggesting strain-specific immunity accounted for the limited efficacy. To determine whether vaccination with multiple HCMV gB genotypes could increase the breadth of anti-HCMV gB humoral and cellular responses, we immunized 18 female rabbits with monovalent (gB-1), bivalent (gB-1+gB-3), or pentavalent (gB-1+gB-2+gB-3+gB-4+gB-5) gB lipid nanoparticle-encapsulated nucleoside-modified RNA (mRNA-LNP) vaccines. The multivalent vaccine groups did not demonstrate higher magnitude or breadth of the IgG response to the gB ectodomain or cell-associated gB compared to that of monovalent vaccine. Also, the multivalent vaccines did not show an increase in the breadth of neutralization activity and antibody-dependent cellular phagocytosis against HCMV strains encoding distinct gB genotypes. Yet, peripheral blood mononuclear cell-derived T cell responses elicited by multivalent vaccines were of a higher magnitude compared to that of monovalent vaccinated animals against a vaccine-mismatched gB genotype at peak immunogenicity. Our data suggests that inclusion of multivalent gB antigens is beneficial to increase the magnitude of T cell response but not an effective strategy to increase the breadth of anti-HCMV gB antibody responses. Further studies are required to validate whether the multivalent gB mRNA vaccines could effectively increase the T cell response breadth.
Multi-omics integration in Esophageal Adenocarcinoma reveals therapeutic targets and EAC-specific regulation of protein abundances
Authors: O’Neill J Robert , Mayordomo Marcos Yébenes , Mitulović Goran , Al Shboul Sofian , Bedran Georges , Faktor Jakub , Hernychova Lenka , Uhrik Lukas , Gomez-Herranz Maria , Kocikowski Mikołaj , Save Vicki , Vojtěšek Bořivoj , Arends Mark ,   OCCAMS consortium, Hupp Ted , Alfaro Javier
Published: November 2022

Background

Efforts to address the poor prognosis associated with esophageal adenocarcinoma (EAC) have been hampered by a lack of biomarkers to identify early disease and therapeutic targets. Despite extensive efforts to understand the somatic mutations associated with EAC over the past decade, a gap remains in understanding how the atlas of genomic aberrations in this cancer impacts the proteome. Differences in transcript and the corresponding protein abundances remain under-explored, leaving gaps in our understanding of the mechanisms underlying the disease.

Methods

We performed a quantitative proteomic analysis of 23 EACs and matched adjacent normal esophageal and gastric tissues. We explored the correlation of transcript and protein abundance used tissue-matched RNAseq and proteomic data from 7 patients and further integrated these data with a cohort of EAC RNA-seq data (n=264 patients), whole-genome sequencing (n=454 patients) and external published datasets.

Results

We quantified protein expression from 5897 genes in EAC and patient-matched normal tissues. Several biomarker candidates with EAC-specific expression were identified including the transmembrane protein GPA33. We further verified the EAC-enriched expression of GPA33 in an external cohort of 115 patients and confirm this as an attractive diagnostic and therapeutic target. To further extend the insights gained from our proteomic data, an integrated analysis of protein and RNA expression in EAC and normal tissues revealed several genes with poorly correlated Protein and RNA abundance, suggesting post-transcriptional regulation of protein expression. These outlier genes including SLC25A30, TAOK2, and AGMAT, only rarely demonstrated somatic mutation suggesting post-transcriptional drivers for this EAC-specific phenotype. AGMAT was demonstrated to be over-expressed at the protein level in EAC compared to adjacent normal tissues with an EAC-specific post-transcriptional mechanism of regulation of protein expression proposed.

Conclusions

By quantitative proteomic analysis we have identified GPA33 as an EAC-specific biomarker. Integrated analysis of proteome, transcriptome, and genome in EAC has revealed several genes with tumor-specific post-transcriptional regulation of protein expression which may be an exploitable vulnerability.
High-resolution African HLA resource uncoversHLA-DRB1expression effects underlying vaccine response
Authors: Mentzer Alexander J. , Dilthey Alexander T. , Pollard Martin , Gurdasani Deepti , Karakoc Emre , Carstensen Tommy , Muhwezi Allan , Cutland Clare , Diarra Amidou , Antunes Ricardo da Silva , Paul Sinu , Smits Gaby , Wareing Susan , Kim HwaRan , Pomilla Cristina , Chong Amanda Y. , Brandt Debora Y.C. , Nielsen Rasmus , Neaves Samuel , Timpson Nicolas , Crinklaw Austin , Lindestam Arlehamn Cecilia S. , Rautanen Anna , Kizito Dennison , Parks Tom , Auckland Kathryn , Elliott Kate E. , Mills Tara , Ewer Katie , Edwards Nick , Fatumo Segun , Peacock Sarah , Jeffery Katie , van der Klis Fiona R.M. , Kaleebu Pontiano , Vijayanand Pandurangan , Peters Bjorn , Sette Alessandro , Cereb Nezih , Sirima Sodiomon , Madhi Shabir A. , Elliott Alison M. , McVean Gil , Hill Adrian V.S. , Sandhu Manjinder S.
Published: November 2022

How human genetic variation contributes to vaccine immunogenicity and effectiveness is unclear, particularly in infants from Africa. We undertook genome-wide association analyses of eight vaccine antibody responses in 2,499 infants from three African countries and identified significant associations across the human leukocyte antigen (HLA) locus for five antigens spanning pertussis, diphtheria and hepatitis B vaccines. Using high-resolution HLA typing in 1,706 individuals from 11 African populations we constructed a continental imputation resource to fine-map signals of association across the class II HLA observing genetic variation explaining up to 10% of the observed variance in antibody responses. Using follicular helper T-cell assays,in silicobinding, and immune cell eQTL datasets we find evidence ofHLA-DRB1expression correlating with serological response and inferred protection from pertussis following vaccination. This work improves our understanding of molecular mechanisms underlying HLA associations that should support vaccine design and development across Africa with wider global relevance.

Teaser

High-resolution typing of HLA diversity provides mechanistic insights into differential potency and inferred effectiveness of vaccines across Africa.
Long-term, multi-event surprise enhances autobiographical memory
Authors: Antony James W. , Van Dam Jacob , Massey Jarett R. , Barnett Alexander J. , Bennion Kelly A.
Published: November 2022

Neurobiological and psychological models of learning emphasize the importance of prediction errors (surprises) for memory formation. These effects have focused on memory for information surrounding a momentary surprising event; however, it is less clear whether surprise that unfolds across multiple events and timescales impacts memory. We asked basketball fans about their most positive and negative autobiographical memories of individual plays, games, and seasons, allowing surprise measurements spanning seconds, hours, and months. We used advanced analytics on National Basketball Association play-by-play data and betting odds spanning 17 seasons, >22K games, >5.6M plays to compute and align the estimated surprise values of each memory. We found that surprising events biased positive memories on the scale of seconds and months and negative memories across all three timescales. Critically, game and season memories could not be explained by surprise at shorter timescales, suggesting that long-term, multi-event surprise influences memory. These results expand the role of surprise in models of learning and reinforce its relevance in real-world domains.
Profound impact of hippocampal output on the interpretation of tactile input patterns in SI neurons
Authors: Etemadi Leila , Enander Jonas M.D. , Jörntell Henrik
Published: November 2022

Due to continuous state variations in neocortical circuits, individual SI neuronsin vivodisplay a variety of intracellular response types to repeated presentations of the exact same tactile input pattern. The specific intracellular response obtained depends on a time-evolving combination of the specific input with the current neocortical state. To manipulate the internal cortical state, we here used brief electrical stimulation of the output region of the hippocampus, which preceded the delivery of specific tactile afferent input patterns to digit 2 of the anesthetized rat. We find that hippocampal output had a diversified and remarkably strong impact on the specific set of intracellular response types each SI neuron displays to each given tactile input pattern. The findings show that hippocampal output can profoundly impact the state-dependent interpretation of tactile inputs in SI neurons and hence influence their perception, potentially with affective and semantic components.
Fcγ receptor-dependent antibody effector functions are required for vaccine protection against infection by antigenic variants of SARS-CoV-2
Authors: Mackin Samantha R. , Desai Pritesh , Whitener Bradley M. , Karl Courtney E. , Liu Meizi , Baric Ralph S. , Edwards Darin K. , Chicz Taras M. , McNamara Ryan P. , Alter Galit , Diamond Michael S.
Published: November 2022

Emerging SARS-CoV-2 variants with antigenic changes in the spike protein are neutralized less efficiently by serum antibodies elicited by legacy vaccines against the ancestral Wuhan-1 virus. Nonetheless, these vaccines, including mRNA-1273 and BNT162b2, retained their ability to protect against severe disease and death, suggesting that other aspects of immunity control infection in the lung. Although vaccine-elicited antibodies can bind Fc gamma receptors (FcγRs) and mediate effector functions against SARS-CoV-2 variants, and this property correlates with improved clinical COVID-19 outcome, a causal relationship between Fc effector functions and vaccine-mediated protection against infection has not been established. Here, using passive and active immunization approaches in wild-type and Fc-gamma receptor (FcγR) KO mice, we determined the requirement for Fc effector functions to protect against SARS-CoV-2 infection. The antiviral activity of passively transferred immune serum was lost against multiple SARS-CoV-2 strains in mice lacking expression of activating FcγRs, especially murine FcγR III (CD16), or depleted of alveolar macrophages. After immunization with the preclinical mRNA-1273 vaccine, protection against Omicron BA.5 infection in the respiratory tract also was lost in mice lacking FcγR III. Our passive and active immunization studies in mice suggest that Fc-FcγR engagement and alveolar macrophages are required for vaccine-induced antibody-mediated protection against infection by antigenically changed SARS-CoV-2 variants, including Omicron strains.