bluuebunny/crossref_metadata_2025 huggingface dataset:
Analysis of Denosumab by a Validated CZE Method and Determination of Sialic Acids by the RP–HPLC Method
Authors: Dumoncel Rafaela Ferreira Perobelli , Xavier Bruna , Cardoso Júnior Clóvis Dervil Appratto , da Silva Francielle Santos , Motta Luís Gustavo Jung , Cavalheiro Thaís Neuhaus , Dalmora Sérgio Luiz
Published: February 2022

A capillary zone electrophoresis (CZE) method was developed and validated to quantitate the monoclonal antibody denosumab (DmAb) and its charge variants in pharmaceutical products, demonstrating excellent precision, linearity and accuracy. Separations were obtained with migration times of 11.3 min for DmAb and the calibration curve was linear in the range of 0.95–20 mg/mL. The analytical comparability of seven batches of Prolia® showed mean differences of the estimated content/potencies of 1.87% lower, and 0.84 and 1.21% higher compared with the size-exclusion and reversed-phase liquid chromatography (SE–HPLC and RP–HPLC) methods and the osteoclast antiproliferative bioassay, respectively, with non-significant differences (P > 0.05). An RP–HPLC method with fluorescence detection (RP–HPLC–F), performed on a Kinetex® EVO C18 column (5 μm, 100 Å, 250 mm × 4.6 mm), was optimized to determine the levels of sialic acids of DmAb biomolecules, giving mean concentrations of 0.16 and 0.17 μg N-acetylneuraminic acid/mg DmAb for Prolia® and Xgeva® pharmaceutical products, respectively. The results demonstrated the capability of each one of the methods, and their use in combination constitutes a strategy to monitor instability, thereby assuring the quality and the batch-to-batch consistency of the biotechnology-derived medicine.
A review on antimicrobial peptides databases and the computational tools
Authors: Ramazi Shahin , Mohammadi Neda , Allahverdi Abdollah , Khalili Elham , Abdolmaleki Parviz
Published: February 2022

Antimicrobial Peptides (AMPs) have been considered as potential alternatives for infection therapeutics since antibiotic resistance has been raised as a global problem. The AMPs are a group of natural peptides that play a crucial role in the immune system in various organisms AMPs have features such as a short length and efficiency against microbes. Importantly, they have represented low toxicity in mammals which makes them potential candidates for peptide-based drugs. Nevertheless, the discovery of AMPs is accompanied by several issues which are associated with labour-intensive and time-consuming wet-lab experiments. During the last decades, numerous studies have been conducted on the investigation of AMPs, either natural or synthetic type, and relevant data are recently available in many databases. Through the advancement of computational methods, a great number of AMP data are obtained from publicly accessible databanks, which are valuable resources for mining patterns to design new models for AMP prediction. However, due to the current flaws in assessing computational methods, more interrogations are warranted for accurate evaluation/analysis. Considering the diversity of AMPs and newly reported ones, an improvement in Machine Learning algorithms are crucial. In this review, we aim to provide valuable information about different types of AMPs, their mechanism of action and a landscape of current databases and computational tools as resources to collect AMPs and beneficial tools for the prediction and design of a computational model for new active AMPs.
Impacts of Winter Annual Cover Crops and Neonicotinoid Seed Treatments on Arthropod Diversity in Mississippi Soybean
Authors: Whalen D A , Catchot A L , Gore J , Cook D R , Barton B T , Brown R L , Irby J T , Speights C J
Published: February 2022

Winter annual cover crops can be planted before soybean in Mississippi for many agronomic reasons. Incorporating winter annual cover crops into soybean production changes the seasonal hosts within fields. Some studies suggest that reducing tillage and using diverse species of cover crops can increase arthropod diversity and predator activity. Neonicotinoid seed treatments are often implemented to combat early season insect pests in soybean that follow cover crops, but negative effects on the environment such as reductions in biodiversity are often attributed to these compounds. We conducted an experiment to measure the effects on the diversity of the soybean epigeal and foliar communities when incorporating cover crops as well as insecticidal seed treatments into Mississippi soybean growing systems. Our results showed that legume cover crops had significant impacts on the epigeal community diversity of soybean planted behind them. These cover crops, especially hairy vetch, supported a more diverse foliar community before termination. To prevent increases in herbivorous arthropods, neonicotinoid seed treatments can be used without affecting epigeal predators such as beetles, ants, and spiders. The neonicotinoid seed treatments affected arthropod diversity, but the reductions were mainly caused by decreases in herbivorous pest insects that fed on treated soybean plants.
Craniofacial changes from 13 to 62 years of age
Authors: Al-Taai Nameer , Persson Maurits , Ransjö Maria , Levring Jäghagen Eva , Fors Ronny , Westerlund Anna
Published: February 2022

Background

In long-term studies of orthodontic, orthognathic, and prosthodontic treatments, control subjects are needed for comparison.

Objectives

To study the craniofacial (skeletal, soft tissue, and dental) changes that occur in untreated subjects with normal occlusion between 13 and 62 years of age.

Materials/Methods

Thirty subjects with a Class I normal occlusion and harmonious facial profile were studied. X-ray examinations were performed at 13 (T1), 16 (T2), 31 (T3), and 62 (T4) years of age, and data were obtained from cephalograms. In total, 53 angular and linear parameters were measured using superimposition-based and conventional cephalometric methods to describe the craniofacial changes.

Results

The jaws showed significant anterior growth from T1 to T2, and significant retrognathism from T3 to T4. The anterior face height and jaw dimensions increased significantly until T3. Significant posterior rotation of the mandible and opening of the vertical jaw relation, in addition to significant retroclination of the incisors and straightening of the facial profile, were found from T3 to T4.

Limitations

Given the small sample size at T4, it was not possible to analyse the gender dimension.

Conclusions/Implications

Craniofacial changes continue up to the sixth decade of life. These changes are consistent, albeit to a lesser extent, with the adolescent growth patterns for most of the studied parameters, with the exceptions of incisor inclination, sagittal jaw position, vertical jaw relation and inclination, and posterior face height.
Quantifying the Value of Log Sorting Based on the Location of Timber Harvest Sites Across Wisconsin
Authors: Wysocki Adam , Gautam Shuva , Rijal Baburam , Doruska Paul , Burns Kevin
Published: February 2022

It is generally understood that sorting logs based on grade generates maximum value for all stakeholders. However, the benefits of sorting logs may depend on the location of a timber sale and distances to manufacturing mills. The objective is to quantify the potential value of log sorting through scenario-based analysis in different areas with divergent forest and mill types. An optimization model was developed to allocate logs from the timber sale to the highest profit-yielding mills. Factors considered by the model included logging and transportation cost, timber sale tract-to-mill distances, mills’ acceptance criteria, and price at the mill gate. Four timber sales from across Wisconsin were selected for the study. Three scenarios were tested, with each scenario yielding different proportions of log sorts. The results showed that log sorting increased profit by up to $41.10 per cord in certain locations but was not profitable in other locations.

Study Implications

The methods proposed in this study can help foresters and landowners increase the value of harvested timber. Practitioners can use the proposed method to systematically assess the gain or loss in profit associated with log sorting at each timber sale. It also provides directives on the best mill for each log sort to be sent. The proposed method should be adopted to minimize underutilization of timber, especially in areas where profits are marginal.
Characterizing the gene–environment interaction underlying natural morphological variation in Neurospora crassa conidiophores using high-throughput phenomics and transcriptomics
Authors: Krach Emily K , Skaro Michael , Wu Yue , Arnold Jonathan
Published: February 2022

Neurospora crassa propagates through dissemination of conidia, which develop through specialized structures called conidiophores. Recent work has identified striking variation in conidiophore morphology, using a wild population collection from Louisiana, United States of America to classify 3 distinct phenotypes: Wild-Type, Wrap, and Bulky. Little is known about the impact of these phenotypes on sporulation or germination later in the N. crassa life cycle, or about the genetic variation that underlies them. In this study, we show that conidiophore morphology likely affects colonization capacity of wild N. crassa isolates through both sporulation distance and germination on different carbon sources. We generated and crossed homokaryotic strains belonging to each phenotypic group to more robustly fit a model for and estimate heritability of the complex trait, conidiophore architecture. Our fitted model suggests at least 3 genes and 2 epistatic interactions contribute to conidiophore phenotype, which has an estimated heritability of 0.47. To uncover genes contributing to these phenotypes, we performed RNA-sequencing on mycelia and conidiophores of strains representing each of the 3 phenotypes. Our results show that the Bulky strain had a distinct transcriptional profile from that of Wild-Type and Wrap, exhibiting differential expression patterns in clock-controlled genes (ccgs), the conidiation-specific gene con-6, and genes implicated in metabolism and communication. Combined, these results present novel ecological impacts of and differential gene expression underlying natural conidiophore morphological variation, a complex trait that has not yet been thoroughly explored.
Genome-scale patterns in the loss of heterozygosity incidence in Saccharomyces cerevisiae
Authors: Tutaj Hanna , Pirog Adrian , Tomala Katarzyna , Korona Ryszard
Published: February 2022

Former studies have established that loss of heterozygosity can be a key driver of sequence evolution in unicellular eukaryotes and tissues of metazoans. However, little is known about whether the distribution of loss of heterozygosity events is largely random or forms discernible patterns across genomes. To initiate our experiments, we introduced selectable markers to both arms of all chromosomes of the budding yeast. Subsequent extensive assays, repeated over several genetic backgrounds and environments, provided a wealth of information on the genetic and environmental determinants of loss of heterozygosity. Three findings stand out. First, the number of loss of heterozygosity events per unit time was more than 25 times higher for growing than starving cells. Second, loss of heterozygosity was most frequent when regions of homology around a recombination site were identical, about a half-% sequence divergence was sufficient to reduce its incidence. Finally, the density of loss of heterozygosity events was highly dependent on the genome’s physical architecture. It was several-fold higher on short chromosomal arms than on long ones. Comparably large differences were seen within a single arm where regions close to a centromere were visibly less affected than regions close, though usually not strictly adjacent, to a telomere. We suggest that the observed uneven distribution of loss of heterozygosity events could have been caused not only by an uneven density of initial DNA damages. Location-depended differences in the mode of DNA repair, or its effect on fitness, were likely to operate as well.
Hearing and Mobility in Aging—The Moderating Role of Neuropsychological Function
Authors: Pupo Daniel A , Small Brent J , Deal Jennifer A , Armstrong Nicole M , Simonsick Eleanor M , Resnick Susan M , Lin Frank R , Ferrucci Luigi , Tian Qu
Published: February 2022

Background

In older persons, neuropsychological function, especially sensorimotor function, is strongly associated with mobility. Hearing impairment is related to poor mobility, and we hypothesize that such relationships would be stronger in persons with compromised sensorimotor function than those with preserved sensorimotor function.

Methods

We analyzed 601 cognitively normal (Mini-Mental State Examination ≥24 or free of cognitive impairment/dementia) Baltimore Longitudinal Study of Aging participants aged 50 or older with concurrent data on hearing (better ear pure-tone average [PTA]), mobility (6 m usual gait, 400 m endurance walk), and neuropsychological function including attention via Trail Making Test (TMT)-A, executive function via the difference between TMT-A and B, and Digit Symbol Substitution Test, and manual dexterity via Pegboard performance. We examined the association of PTA, each cognitive measure, and their interaction with mobility using multivariable linear regression, adjusted for covariates.

Results

After covariate adjustment, there were significant interactions between PTA and all cognitive measures in the association with 400 m endurance walking speed as the outcome. There was also a significant interaction between PTA and pegboard nondominant hand performance in the association with 6 m gait as the outcome. In all these cases, the PTA–mobility relationship was stronger among participants with lower cognition.

Conclusion

Impaired hearing more strongly relates to poor mobility among those with compromised neuropsychological performance, especially manual dexterity reflecting the motor–cognitive interface and sensorimotor function, than those with preserved neuropsychological performance. Future longitudinal studies are needed to test whether hearing impairment more strongly predicts mobility decline over time in older persons with compromised neuropsychological function.
Multi-ancestry genome-wide association study of gestational diabetes mellitus highlights genetic links with type 2 diabetes
Authors: Pervjakova Natalia , Moen Gunn-Helen , Borges Maria-Carolina , Ferreira Teresa , Cook James P , Allard Catherine , Beaumont Robin N , Canouil Mickaël , Hatem Gad , Heiskala Anni , Joensuu Anni , Karhunen Ville , Kwak Soo Heon , Lin Frederick T J , Liu Jun , Rifas-Shiman Sheryl , Tam Claudia H , Tam Wing Hung , Thorleifsson Gudmar , Andrew Toby , Auvinen Juha , Bhowmik Bishwajit , Bonnefond Amélie , Delahaye Fabien , Demirkan Ayse , Froguel Philippe , Haller-Kikkatalo Kadri , Hardardottir Hildur , Hummel Sandra , Hussain Akhtar , Kajantie Eero , Keikkala Elina , Khamis Amna , Lahti Jari , Lekva Tove , Mustaniemi Sanna , Sommer Christine , Tagoma Aili , Tzala Evangelia , Uibo Raivo , Vääräsmäki Marja , Villa Pia M , Birkeland Kåre I , Bouchard Luigi , Duijn Cornelia M , Finer Sarah , Groop Leif , Hämäläinen Esa , Hayes Geoffrey M , Hitman Graham A , Jang Hak C , Järvelin Marjo-Riitta , Jenum Anne Karen , Laivuori Hannele , Ma Ronald C , Melander Olle , Oken Emily , Park Kyong Soo , Perron Patrice , Prasad Rashmi B , Qvigstad Elisabeth , Sebert Sylvain , Stefansson Kari , Steinthorsdottir Valgerdur , Tuomi Tiinamaija , Hivert Marie-France , Franks Paul W , McCarthy Mark I , Lindgren Cecilia M , Freathy Rachel M , Lawlor Deborah A , Morris Andrew P , Mägi Reedik
Published: February 2022

Gestational diabetes mellitus (GDM) is associated with increased risk of pregnancy complications and adverse perinatal outcomes. GDM often reoccurs and is associated with increased risk of subsequent diagnosis of type 2 diabetes (T2D). To improve our understanding of the aetiological factors and molecular processes driving the occurrence of GDM, including the extent to which these overlap with T2D pathophysiology, the GENetics of Diabetes In Pregnancy Consortium assembled genome-wide association studies of diverse ancestry in a total of 5485 women with GDM and 347 856 without GDM. Through multi-ancestry meta-analysis, we identified five loci with genome-wide significant association (P < 5 × 10−8) with GDM, mapping to/near MTNR1B (P = 4.3 × 10−54), TCF7L2 (P = 4.0 × 10−16), CDKAL1 (P = 1.6 × 10−14), CDKN2A-CDKN2B (P = 4.1 × 10−9) and HKDC1 (P = 2.9 × 10−8). Multiple lines of evidence pointed to the shared pathophysiology of GDM and T2D: (i) four of the five GDM loci (not HKDC1) have been previously reported at genome-wide significance for T2D; (ii) significant enrichment for associations with GDM at previously reported T2D loci; (iii) strong genetic correlation between GDM and T2D and (iv) enrichment of GDM associations mapping to genomic annotations in diabetes-relevant tissues and transcription factor binding sites. Mendelian randomization analyses demonstrated significant causal association (5% false discovery rate) of higher body mass index on increased GDM risk. Our results provide support for the hypothesis that GDM and T2D are part of the same underlying pathology but that, as exemplified by the HKDC1 locus, there are genetic determinants of GDM that are specific to glucose regulation in pregnancy.
Thyroid function, pernicious anemia and erythropoiesis: a two-sample Mendelian randomization study
Authors: Kjaergaard Alisa D , Teumer Alexander , Marouli Eirini , Deloukas Panos , Kuś Aleksander , Sterenborg Rosalie , Åsvold Bjørn O , Medici Marco , Ellervik Christina
Published: February 2022

Autoimmune thyroid disease (AITD) and pernicious anemia (PA) often coexist, but the directionality is unknown. In a two-sample Mendelian randomization (MR) analysis, using summary statistics from large genome-wide association studies (GWASs) in Europeans (N = 49 269–755 406), we examined the genetic associations between thyroid function, PA and markers of erythropoiesis. We performed inverse variance weighted random-effects MR, several sensitivity MR analyses, and bidirectional MR and MR Steiger for directionality. AITD and PA were associated bidirectionally (P ≤ 8 × 10−6). Neither euthyroid thyroid stimulating hormone (TSH) nor free thyroxine (FT4) were causally associated with PA. One standard deviation (SD) increase in euthyroid FT4 regulated by genetic variants in deiodinases 1 and 2 genes (DIO1/DIO2), corresponding to low-normal free triiodothyronine (FT3) levels, was causally associated with a pernicious/macrocytic anemia pattern, i.e. decreased erythrocyte counts (rank-based inverse normal transformed β = −0,064 [95% confidence interval: −0,085, −0,044], P = 8 × 10−10) and hemoglobin (−0.028 [−0.051, −0.005], P = 0.02) and increased mean corpuscular hemoglobin (0.058 [0.025, 0.091], P = 5 × 10−4) and mean corpuscular volume levels (0.075 [0.052, 0.098], P = 1 × 10−8). Meanwhile, subclinical hyperthyroidism mirrored that pattern. AITD was causally associated with increased erythrocyte distribution width (P = 0.007) and decreased reticulocyte counts (P ≤ 0.02), whereas high-normal FT4 regulated by DIO1/DIO2 variants was causally associated with decreased bilirubin (−0.039 (−0.064, −0.013), P = 0.003). In conclusion, the bidirectional association between AITD and PA suggests a shared heritability for these two autoimmune diseases. AITD was causally associated with impaired erythropoiesis and not autoimmune hemolysis. Additionally, in euthyroid individuals, local regulation of thyroid hormones by deiodinases likely plays a role in erythropoiesis.
Grafting: a potential method to reveal the differential accumulation mechanism of secondary metabolites
Authors: Dong Ding , Shi Ya-Na , Mou Zong-Min , Chen Sui-Yun , Zhao Da-Ke
Published: February 2022

Plant secondary metabolites make a great contribution to the agricultural and pharmaceutical industries. Their accumulation is determined by the integrated transport of target compounds and their biosynthesis-related RNA, protein, or DNA. However, it is hard to track the movement of these biomolecules in vivo. Grafting may be an ideal method to solve this problem. The differences in genetic and metabolic backgrounds between rootstock and scion, coupled with multiple omics approaches and other molecular tools, make it feasible to determine the movement of target compounds, RNAs, proteins, and DNAs. In this review, we will introduce methods of using the grafting technique, together with molecular biological tools, to reveal the differential accumulation mechanism of plant secondary metabolites at different levels. Details of the case of the transport of one diterpene alkaloid, fuziline, will be further illustrated to clarify how the specific accumulation model is shaped with the help of grafting and multiple molecular biological tools.
Utility of Therapeutic Drug Monitoring for Tumor Necrosis Factor Antagonists and Ustekinumab in Postoperative Crohn’s Disease
Authors: Pan Yushan , Ahmed Waseem , Mahtani Prerna , Wong Rochelle , Longman Randy , Jeremy Lukin Dana , Scherl Ellen J , Battat Robert
Published: February 2022

Background

In postoperative Crohn’s disease (POCD), data are lacking on relationships between serum biologic concentrations and treatment outcomes. We assessed if established threshold concentrations of infliximab (IFX), adalimumab (ADA), and ustekinumab (UST) impact outcomes in POCD.

Methods

Data were extracted from POCD patients with serum biologic concentration measurements using Weill Cornell Medicine biobanks. The primary outcome compared rates of deep remission (achieving both objective [endoscopic or biomarker] and clinical [Harvey-Bradshaw index or Crohn’s Disease Patient Reported Outcome-2] remission), using established serum drug level cutoffs of IFX ≥3 µg/mL, ADA ≥7.5 µg/mL, and UST ≥4.5 µg/mL.

Results

In 130 patients, median IFX, ADA, and UST concentrations were 10 (interquartile range [IQR], 2.9-26.9) µg/mL, 10.5 (IQR, 4.9-14.9) µg/mL, and 6.9 (IQR, 5.1-10.2) µg/mL, respectively. In patients with IFX ≥3 µg/mL, higher rates of deep remission (39% vs 0%; P = .02) existed compared with those with IFX <3 µg/mL. Similar differences existed for clinical (44% vs 9%; P = .04) and objective (83% vs 62%; P = .1) remission. In patients with ADA ≥7.5 µg/mL, rates of deep (42% vs 0%; P = .02), clinical (42% vs 0%; P = .02), and objective (88% vs 40%; P = .007) remission were higher than patients with lower concentrations. For UST, rates of deep (28% vs 17%; P = 1.0), clinical (33% vs 33%; P = 1.0), and objective (70% vs 67%; P = 1.0) remission were similar between patients regardless of drug concentration.

Conclusions

In POCD, established anti-tumor necrosis factor concentrations were associated with improved outcomes. No relationship between UST concentrations and postoperative outcomes existed.
Multi-method approach shows stock structure inLoligo forbesiisquid
Authors: Sheerin Edel , Barnwall Leigh , Abad Esther , Larivain Angela , Oesterwind Daniel , Petroni Michael , Perales-Raya Catalina , Robin Jean-Paul , Sobrino Ignacio , Valeiras Julio , O'Meara Denise , Pierce Graham J , Allcock A Louise , Power Anne Marie
Published: February 2022

Knowledge of stock structure is a priority for effective assessment of commercially-fished cephalopods. Loligo forbesii squid are thought to migrate inshore for breeding and offshore for feeding and long-range movements are implied from past studies showing genetic homogeneity in the entire neritic population. Only offshore populations (Faroe and Rockall Bank) were considered distinct. The present study applied mitchondrial and microsatellite markers (nine loci) to samples from Rockall Bank, north Scotland, North Sea, various shelf locations in Ireland, English Channel, northern Bay of Biscay, north Spain, and Bay of Cadiz. No statistically significant genetic sub-structure was found, although some non-significant trends involving Rockall were seen using microsatellite markers. Differences in L. forbesii statolith shape were apparent at a subset of locations, with most locations showing pairwise differences and statoliths from north Ireland being highly distinct. This suggests that (i) statolith shape is highly sensitive to local conditions and (ii) L. forbesii forms distinguishable groups (based on shape statistics), maintaining these groups over sufficiently long periods for local conditions to affect the shape of the statolith. Overall evidence suggests that L. forbesii forms separable (ecological) groups over short timescales with a semi-isolated breeding group at Rockall whose distinctiveness varies over time.
Validation of the CompactDry “Nissui” YMR for Enumeration of Yeasts and Molds in a Variety of Foods: AOAC Performance Tested MethodSM 092002
Authors: Mizuochi Shingo , Betts Gail
Published: February 2022

Background

The CompactDry “Nissui” YMR is a ready-to-use dry media sheet using a chromogenic medium with selective agents for the detection and enumeration of yeasts and molds in products after incubation at 25 ± 1°C for 3 days.

Objective

The CompactDry “Nissui” YMR method was validated in order to achieve AOAC Performance Tested MethodsSM certification.

Method

The performance of the CompactDry “Nissui” YMR was compared to that of ISO 21527-1:2008 for 10 matrixes including cooked prawns, deli vegetable salad, tuna pâté, fermented yogurt drink, spinach and ricotta quiche, egg custard tarts, fruit and vegetable smoothie, cream cheese, egg salad sandwich, and deli pasta salad. Performance indicators included repeatability, difference of means (DOM), and inclusivity/exclusivity.

Results

After log10 transformation of the data, the relative standard deviation of repeatability (RSDr) was <10% for all 30 materials (10 matrixes each at 3 levels) analyzed by the CompactDry “Nissui” YMR method and for 29 of the 30 matrix/level combinations analyzed by the reference method. The DOM ranged from −0.284 (−0.310, −0.257) log10 CFU/g to 0.307 (−0.013, 0.627) log10 CFU/g. Method equivalence was demonstrated in 29 of the 30 matrix/level combinations based on the 90% confidence interval of the DOM being within (–0.5, 0.5). All 51 inclusivity strains showed expected or atypical results, and all 32 exclusivity organisms showed no growth on the medium. The method was shown to be robust to changes in sample volume, incubation temperature, and incubation time, and data are presented supporting product consistency and a 24-month shelf life.

Conclusions

The CompactDry “Nissui” YMR method is validated for the determination of yeasts and molds in a variety of matrixes.

Highlights

The CompactDry “Nissui” YMR method is equivalent to the ISO 21527-1:2008 reference method and is suitable for Performance Tested MethodsSM certification for the matrixes tested.
Independent Study for the Detectx Combined Assay for the Detection of Aspergillus, Salmonella, and STEC (stx1 and/or 2) in Dried Cannabis Flower and Dried Hemp Flower: Level 3 Modification Study 012201
Authors: Katchman Benjamin A , Tomchaney Michael , Bueschel Dawn , Ulrich Peaches , Freeman Shayla , O’Brian Kevin , Eggers Rick , May Melissa , Hogan Mike , Thompson Wesley , Benzinger M Joseph , Bastin Benjamin
Published: February 2022

Background

The PathogenDx family of assays uses microarray technology to simultaneously detect the presence of bacterial and fungal pathogens in food products, environmental surfaces, and cannabis products.

Objective

The Detectx Combined assay was validated for the detection of Aspergillus, (Aspergillus flavus, Aspergillus fumigatus, Aspergillus niger, and Aspergillus terreus), Salmonella, and a broad range of STEC (stx1 and/or 2) species. The validation consisted of two matrix studies in dried hemp flower and dried cannabis flower (>0.3% delta-9 tetrahydrocannabinol) flower, product consistency, stability, robustness, and inclusivity and exclusivity for two targets: Aspergillus and STEC.

Method

The PathogenDx Detectx Combined assay was evaluated with 30 replicates in each matrix and confirmed according to the instructions outlined in this study.

Results

Results of the validation study met the requirements of AOAC Standard Method Performance Requirement (SMPR®) 2020.002 and 2020.012. In the inclusivity and exclusivity study, all target isolates (Aspergillus and STEC) were correctly detected. For the exclusivity study, 26 out of 30 Aspergillus and 30 out of 30 STEC non-target strains were correctly excluded. In the matrix study, the PathogenDx Detectx Combined assay showed no significant statistical differences between confirmed results for dried hemp and cannabis flower. Robustness testing indicated that small changes to the method parameters did not impact the performance of the assay. Stability and consistency studies verified that the assay’s shelf-life claims were appropriate, and manufacturing of the assay was consistent.

Conclusions

The validation study indicated that the PathogenDx DetectX Combined assay was successful in detection of the new target analytes (Aspergillus flavus, Aspergillus fumigatus, Aspergillus niger, and Aspergillus terreus and STEC containing stx1 and/or 2) and could successfully recover these organisms and Salmonella from dried hemp flower and dried cannabis flower (>0.3% delta-9 tetrahydrocannabinol).

Highlights

The PathogenDx DetectX Combined Assay will be the first PTM approved multiplex assay for Aspergillus, E. coli and Salmonella that does not require an enrichment step.
Brand Morphogenesis: The Role of Heterogeneous Consumer Sub-Assemblages in the Change and Continuity of a Brand
Authors: Molander Susanna , Ostberg Jacob , Peñaloza Lisa
Published: February 2022

How do brands change in environments defined by increasing consumer heterogeneity? Drawing on assemblage theory, this research develops the concepts of brand morphogenesis and consumer sub-assemblage to explain how heterogeneous consumer groups instigate, reinforce and hinder the evolution of a brand. This longitudinal case study of a Swedish fashion brand delineates the role of heterogeneous consumer sub-assemblages in the continual process of emergence and transformation of a brand assemblage through space and time—a process defined as brand morphogenesis. The findings detail brand morphogenesis in the sub-assemblage dynamics of exploration, actualization, and habituation of value, as heterogeneous consumer groups form consumer sub-assemblages in interaction with other brand components and interact in patterns of coexisting with, coopting, and contesting other sub-assemblages. By charting consumers’ value negotiations as they play out within and among consumer sub-assemblages, this research contributes to understanding continuity and change for brands that face increasing consumer heterogeneity.
Environmental Policy in Good and Bad Times: The Countercyclical Effects of Carbon Taxes and Cap-and-Trade
Authors: Dominioni Goran , Faure Michael
Published: February 2022

‘Green recovery’ is one of the key themes of the stimulus packages implemented around the world in response to the Covid-19-related economic downturn. Recent research points to the potential role of regulation that becomes less stringent during recessions (ie countercyclical regulation) as an instrument to stimulate a quicker recovery. When this argument is put in the context of a green recovery, two key questions arise: should we implement countercyclical environmental regulation? If yes, what environmental instruments are better suited to stimulate the economy in periods of economic downturn? This article addresses these questions by discussing the risks of countercyclical environmental regulation and comparing the countercyclical effects of two critical environmental instruments: carbon taxes and cap-and-trade. The article argues that policymakers should be cautious in implementing countercyclical environmental regulation because the benefits of this practice are uncertain and it entails various risks. The article also challenges the belief common among academics and policymakers that cap-and-trade is inherently more countercyclical than carbon taxes by showing that whether this is true depends on the design of these instruments and other contingent factors.
Mesenteric venous thrombosis: a rare complication of small bowel neuroendocrine tumor presenting with gangrenous appendicitis
Authors: Bachelani Arshad M
Published: February 2022

A 61-year-old woman presented to the hospital with a clinical picture consistent with acute appendicitis. During surgery, the appendix was found to be gangrenous and involved the appendiceal base, so an ileocecectomy was performed. Pathology revealed an incidental neuroendocrine tumor of the terminal ileum involving five of nine lymph nodes. The patient later developed mesenteric venous thrombosis but was diagnosed and treated promptly, and she is now doing well. There have been previous reports of small bowel neuroendocrine tumor resulting in bowel ischemia, usually due to fibrosis which can result in obstruction of the mesenteric vessels. However, this is the first known report of a small bowel neuroendocrine tumor presenting with appendicitis, which most likely was from an ischemic etiology. This case also demonstrates the importance of a high index of suspicion for mesenteric ischemia in patients with small bowel neuroendocrine tumor who present with acute abdominal pain.
Appendix diverticulosis in a patient diagnosed on pathology after laparoscopic appendectomy for appendicular mucinous mass—case report and literature review
Authors: Alghamdi Wejdan A , Roublah Alaa A , Almaghrabi Jaudah , Alabbas Haytham H
Published: February 2022

Diverticulum of the appendix is uncommon cause of right iliac fossa pain and inflammation with delayed diagnosis and high risk of complications, as it mimics acute appendicitis. Here we present a case of an elderly male patient who had lung cancer post-treatment. During the follow-up, appendicle lesion was discovered and suspected to be mucinous appendix. The pathology reported after appendectomy as appendicular diverticulosis without evidence of malignancy. As appendicular diverticulum is best confirmed by pathology, still its clinical presentation is difficult to be distinguished from other appendicular diseases. It is frequently linked to increased risk of cancer, particularly carcinoid tumors and mucinous adenomas.
Salinity, waterlogging, and elevated [CO2] interact to induce complex responses in cultivated and wild tomato
Authors: Zhou Rong , Yu Xiaqing , Song Xiaoming , Rosenqvist Eva , Wan Hongjian , Ottosen Carl-Otto
Published: February 2022

The effects of individual climatic factors on crops are well documented, whereas the interaction of such factors in combination has received less attention. The frequency of salinity and waterlogging stress is increasing with climate change, accompanied by elevated CO2 concentration (e[CO2]). This study explored how these three variables interacted and affected two tomato genotypes. Cultivated and wild tomato (Solanum lycopersicum and Solanum pimpinellifolium) were grown at ambient [CO2] and e[CO2], and subjected to salinity, waterlogging, and combined stress. Leaf photosynthesis, chlorophyll fluorescence, quenching analysis, pigment, and plant growth were analyzed. The response of tomatoes depended on both genotype and stress type. In cultivated tomato, photosynthesis was inhibited by salinity and combined stress, whereas in wild tomato, both salinity and waterlogging stress, alone and in combination, decreased photosynthesis. e[CO2] increased photosynthesis and biomass of cultivated tomato under salinity and combined stress compared with ambient [CO2]. Differences between tomato genotypes in response to individual and combined stress were observed in key photosynthetic and growth parameters. Hierarchical clustering and principal component analysis revealed genetic variations of tomatoes responding to the three climatic factors. Understanding the interacting effects of salinity and waterlogging with e[CO2] in tomato will facilitate improvement of crop resilience to climate change.
Creating in Conflict
Authors: Gussak David E.
Published: February 2022

This chapter emerged from the premise that making art has been used to react to, respond to, and regain a sense of power and resilience within a hostile environment that foments powerlessness. While it does not always deter violence, art may provide an oasis. The psychobiographies of six artists—Goya, Beckmann, Nussbaum, Vann Nath, Traylor, and Rockwell—are recounted to examine how their art emerged from their experiences of social and environmental upheaval. Each in their way was impacted by conflict and used art to maintain a semblance of control and resistance. They are divided among three categories: witnesses to global conflict, victims of war, and artists responding to civil unrest. Angry and reactive but ineffectual to what was going on around them, it wasn’t until they picked up a brush and redirected the energy that they found a weapon through which they could fight back.
Low-frequency wideband timing of InPTA pulsars observed with the uGMRT
Authors: Nobleson K , Agarwal Nikita , Girgaonkar Raghav , Pandian Arul , Joshi Bhal Chandra , Krishnakumar M A , Susobhanan Abhimanyu , Desai Shantanu , Prabu T , Bathula Adarsh , Pennucci Timothy T , Banik Sarmistha , Bagchi Manjari , Dhanda Batra Neelam , Choudhary Arpita , Dandapat Subhajit , Dey Lankeswar , Gupta Yashwant , Hisano Shinnosuke , Kato Ryo , Kharbanda Divyansh , Kikunaga Tomonosuke , Kolhe Neel , Maan Yogesh , Marmat Piyush , Arumugam P , Manoharan P K , Pathak Dhruv , Singha Jaikhomba , Surnis Mayuresh P , Susarla Sai Chaitanya , Takahashi Keitaro
Published: February 2022

High-precision measurements of the pulsar dispersion measure (DM) are possible using telescopes with low-frequency wideband receivers. We present an initial study of the application of the wideband timing technique, which can simultaneously measure the pulsar times of arrivals (ToAs) and DMs, for a set of five pulsars observed with the upgraded Giant Metrewave Radio Telescope (uGMRT) as part of the Indian Pulsar Timing Array (InPTA) campaign. We have used the observations with the 300–500 MHz band of the uGMRT for this purpose. We obtain high precision in DM measurements with precisions of the order 10−6 cm−3 pc. The ToAs obtained have sub-μs precision and the rms of the post-fit ToA residuals are in the sub-μs range. We find that the uncertainties in the DMs and ToAs obtained with this wideband technique, applied to low-frequency data, are consistent with the results obtained with traditional pulsar timing techniques and comparable to high-frequency results from other PTAs. This work opens up an interesting possibility of using low-frequency wideband observations for precision pulsar timing and gravitational wave detection with similar precision as high-frequency observations used conventionally.
ALMA’s view of the M-dwarf GSC 07396-00759’s edge-on debris disc: AU Mic’s coeval twin
Authors: Cronin-Coltsmann Patrick F , Kennedy Grant M , Adam Christian , Kral Quentin , Lestrade Jean-François , Marino Sebastian , Matrà Luca , Murphy Simon J , Olofsson Johan , Wyatt Mark C
Published: February 2022

We present new ALMA Band 7 observations of the edge-on debris disc around the M1V star GSC 07396-00759. At ∼20 Myr old and in the β Pictoris Moving Group along with AU Mic, GSC 07396-00759 joins it in the handful of low-mass M-dwarf discs to be resolved in the sub-mm. With previous VLT/SPHERE scattered light observations, we present a multiwavelength view of the dust distribution within the system under the effects of stellar wind forces. We find the mm dust grains to be well described by a Gaussian torus at 70 au with a full width at half-maximum of 48 au and we do not detect the presence of CO in the system. Our ALMA model radius is significantly smaller than the radius derived from polarimetric scattered light observations, implying complex behaviour in the scattering phase function. The brightness asymmetry in the disc observed in scattered light is not recovered in the ALMA observations, implying that the physical mechanism only affects smaller grain sizes. High-resolution follow-up observations of the system would allow investigation into its unique dust features as well as provide a true coeval comparison for its smaller sibling AU Mic, singularly well-observed amongst M-dwarfs systems.
Testing the reliability of X-rays as a tool for constraining mass-loss rates of hot stars
Authors: Gunderson Sean J , Gayley Kenneth G , Pradhan Pragati , Huenemoerder David P , Miller Nathan A
Published: February 2022

We fit a new line shape model to Chandra X-ray spectra of the O supergiant ζ Puppis to test the robustness of mass-loss rates derived from X-ray wind line profiles against different assumed heating models. Our goal is to track the hot gas by replacing the common assumption that it is proportional to the cool gas emission measure. Instead of assuming a turn-on radius for the hot gas (as appropriate for the line-deshadowing instability internal to the wind), we parametrize the hot gas in terms of a mean-free path for accelerated low-density gas to encounter slower high-density material. This alternative model is equally successful as previous approaches at fitting X-ray spectral lines in the 5–17 Å wavelength range. We find that the characteristic radius where the hottest gas appears is inversely proportional to line-formation temperature, suggesting that stronger shocks appear generally closer to the surface. This picture is more consistent with pockets of low density, rapid acceleration at the lower boundary than with an internally generated wind instability. We also infer an overall wind mass-loss rate from the profile shapes with a technique used previously in the literature. In doing so, we find evidence that the mass-loss rate derived from X-ray wind line profiles is not robust with respect to changes in the specific heating picture used.
G-quadruplexes in helminth parasites
Authors: Cantara Alessio , Luo Yu , Dobrovolná Michaela , Bohalova Natalia , Fojta Miroslav , Verga Daniela , Guittat Lionel , Cucchiarini Anne , Savrimoutou Solène , Häberli Cécile , Guillon Jean , Keiser Jennifer , Brázda Václav , Mergny Jean Louis
Published: February 2022

Parasitic helminths infecting humans are highly prevalent infecting ∼2 billion people worldwide, causing inflammatory responses, malnutrition and anemia that are the primary cause of morbidity. In addition, helminth infections of cattle have a significant economic impact on livestock production, milk yield and fertility. The etiological agents of helminth infections are mainly Nematodes (roundworms) and Platyhelminths (flatworms). G-quadruplexes (G4) are unusual nucleic acid structures formed by G-rich sequences that can be recognized by specific G4 ligands. Here we used the G4Hunter Web Tool to identify and compare potential G4 sequences (PQS) in the nuclear and mitochondrial genomes of various helminths to identify G4 ligand targets. PQS are nonrandomly distributed in these genomes and often located in the proximity of genes. Unexpectedly, a Nematode, Ascaris lumbricoides, was found to be highly enriched in stable PQS. This species can tolerate high-stability G4 structures, which are not counter selected at all, in stark contrast to most other species. We experimentally confirmed G4 formation for sequences found in four different parasitic helminths. Small molecules able to selectively recognize G4 were found to bind to Schistosoma mansoni G4 motifs. Two of these ligands demonstrated potent activity both against larval and adult stages of this parasite.
The Diversity and Abundance of Soft Rot Pectobacteriaceae Along the Durance River Stream in the Southeast of France Revealed by Multiple Seasonal Surveys
Authors: Ben Moussa Hajar , Bertrand Claire , Rochelle-Newall Emma , Fiorini Sarah , Pédron Jacques , Barny Marie-Anne
Published: February 2022

Although irrigation water is frequently assessed for the presence of plant pathogens, large spatial and temporal surveys that provide clues on the diversity and circulation of pathogens are missing. We evaluate the diversity of soft rot Pectobacteriaceae (SRP) of the genera Dickeya and Pectobacterium over 2 years in a temperate, mixed-use watershed. The abundance of isolated strains correlates with the agricultural gradient along the watershed with a positive correlation found with temperature, nitrate, and dissolved organic carbon water concentration. We characterized 582 strains by amplification and sequencing of the gapA gene. Multilocus sequence analysis, performed with three housekeeping genes for 99 strains, and core genome analysis of 38 sequenced strains, confirmed for all the strains but one, the taxonomic assignation obtained with the sole gapA sequence. Pectobacterium spp. (549 isolates) were far more abundant than Dickeya spp. (33 isolates). Dickeya spp. were only observed in the lower part of the river when water temperature was >19°C, and we experimentally confirmed a decreased fitness of several Dickeya spp. at 8°C in river water. D. oryzae dominates the Dickeya spp. and P. versatile and P. aquaticum dominate the Pectobacterium spp., but their repartition along the watershed was different, with P. versatile being the only species regularly recovered all along the watershed. Excepting P. versatile, the Dickeya and Pectobacterium spp. responsible for disease outbreak on crops were less abundant or rarely detected. This work sheds light on the various ecological behaviors of different SRP types in stream water and indicates that SRP occupation is geographically structured.
Quality improvement engagement
Authors: Blok Amanda C. , Alexander Catherine C. , Tschannen Dana , Milner Kerry A.
Published: February 2022

A comparison of frontline nurses, advanced practice nurses, and nurse leaders