bluuebunny/crossref_metadata_2025_split huggingface dataset:
KinMod database: a tool for investigating metabolic regulation
Authors: Haddadi Kiandokht , Ahmed Barghout Rana , Mahadevan Radhakrishnan 
Published: October 2022

Abstract
The ability of current kinetic models to simulate the phenotypic behaviour of cells is limited since cell metabolism is regulated at different levels including enzyme regulation. The small molecule regulation network (SMRN) enables cells to respond rapidly to environmental fluctuations by controlling the activity of enzymes in metabolic pathways. However, SMRN is not as well studied relative to metabolic networks. The main contributor to the lack of knowledge on this regulatory system is the sparsity of experimental data and the absence of a standard framework for representing available information. In this paper, we introduce the KinMod database that encompasses more than 2 million data points on the metabolism and metabolic regulation network of 9814 organisms KinMod database employs a hierarchical data structure to: (i) signify relationships between kinetic information obtained through in-vitro experiments and proteins, with an emphasis on SMRN, (ii) provide a thorough insight into available kinetic parameters and missing experimental measurements of this regulatory network and (iii) facilitate machine learning approaches for parameter estimation and accurate kinetic model construction by providing a homogeneous list of linked omics data. The hierarchical ontology of the KinMod database allows flexible exploration of data attributes and investigation of metabolic relationships within- and cross-species. Identifying missing experimental values suggests additional experiments required for kinetic parameter estimation. Linking multi-omics data and providing data on SMRN encourages the development of novel machine learning techniques for predicting missing kinetic parameters and promotes accurate kinetic model construction of cells metabolism by providing a comprehensive list of available kinetic measurements. To illustrate the value of KinMod data, we develop six analyses to visualize associations between data classes belonging to separate sections of the metabolism. Through these analyses, we demonstrate that the KinMod database provides a unique framework for biologists and engineers to retrieve, evaluate and compare the functional metabolism of species, including the regulatory network, and discover the extent of available and missing experimental values of the metabolic regulation.
Database URL: https://lmse.utoronto.ca/kinmod/KINMOD.sql.gz
Chromosome-level genome assembly for the Aldabra giant tortoise enables insights into the genetic health of a threatened population
Authors: Çilingir F Gözde , A'Bear Luke , Hansen Dennis , Davis Leyla R , Bunbury Nancy , Ozgul Arpat , Croll Daniel , Grossen Christine 
Published: October 2022

AbstractBackgroundThe Aldabra giant tortoise (Aldabrachelys gigantea) is one of only two giant tortoise species left in the world. The species is endemic to Aldabra Atoll in Seychelles and is listed as Vulnerable on the International Union for Conservation of Nature Red List (v2.3) due to its limited distribution and threats posed by climate change. Genomic resources for A. gigantea are lacking, hampering conservation efforts for both wild and ex situpopulations. A high-quality genome would also open avenues to investigate the genetic basis of the species’ exceptionally long life span.FindingsWe produced the first chromosome-level de novo genome assembly of A. gigantea using PacBio High-Fidelity sequencing and high-throughput chromosome conformation capture. We produced a 2.37-Gbp assembly with a scaffold N50 of 148.6 Mbp and a resolution into 26 chromosomes. RNA sequencing–assisted gene model prediction identified 23,953 protein-coding genes and 1.1 Gbp of repetitive sequences. Synteny analyses among turtle genomes revealed high levels of chromosomal collinearity even among distantly related taxa. To assess the utility of the high-quality assembly for species conservation, we performed a low-coverage resequencing of 30 individuals from wild populations and two zoo individuals. Our genome-wide population structure analyses detected genetic population structure in the wild and identified the most likely origin of the zoo-housed individuals. We further identified putatively deleterious mutations to be monitored.ConclusionsWe establish a high-quality chromosome-level reference genome for A. gigantea and one of the most complete turtle genomes available. We show that low-coverage whole-genome resequencing, for which alignment to the reference genome is a necessity, is a powerful tool to assess the population structure of the wild population and reveal the geographic origins of ex situ individuals relevant for genetic diversity management and rewilding efforts.
Effect of Vegetable Host Plant Type on Halyomorpha halys (Hemiptera: Pentatomidae) Nymphal Development
Authors: Formella Adam , McIntyre Kelly , Kuhar Thomas P 
Published: October 2022

Abstract
The brown marmorated stink bug, Halyomorpha halys (Stål), is an invasive pest introduced to North America in the mid-1990’s that has caused economic losses to a wide range of commodities. In vegetables, H. halys feeding damage has been well described, but the effect of different vegetable hosts on H. halys fitness is less understood. We caged 2nd instar H. halys on different vegetable hosts (e.g., tomato, sweet corn, eggplant, bell pepper, and snap bean) and monitored their development until adulthood to compare the effects of vegetable host type on H. halys nymph survival and development time. Experiments were replicated nine times over a two-year period. Survival of 2nd instars from F1 generation (early-season) eggs was low (&lt;30%) on all vegetables resulting in no significant treatment effect. However, H. halys nymphs collected from F2 generation (late-season) eggs had higher survivorship on all vegetables except tomato. The percentage of H. halys 2nd instars that reached adulthood was greatest on corn (53%) and pepper (45%), followed by snap bean (24%), and significantly lower on eggplant (9%) and tomato (2%). Total development time from 2nd instar to adult was fastest on corn and slowest on peppers, although tomatoes were not tested due to the low survival. Trends in development rate were not seasonally-dependent. Our study compares H. halys survivability on several vegetable commodities, and provides insights into H. halys developmental success and dependence on various host plants over the season.
Protection of Potatoes and Mortality of Wireworms (Agriotes obscurus) With Various Application Methods of Broflanilide, a Novel Meta-Diamide Insecticide
Authors: van Herk Willem G , Vernon Robert S , Goudis Lindsey , Mitchell Terisha 
Published: October 2022

Abstract
Wireworms are primary pests of potatoes in Canada. Presently, the highly toxic organophosphate phorate (i.e., Thimet 20G) is the only effective insecticide in use in Canada. As such, there is an urgent need for novel alternative treatments that provide competitive tuber blemish protection and wireworm reduction with a safer human and environmental portfolio. Herein we evaluated broflanilide, a novel meta-diamide insecticide for both tuber protection and wireworm mortality. When evaluated in field trials in Agassiz, British Columbia over 6 yr, broflanilide applied as a seed piece treatment (SPT) to mother tubers at 1.5–2.0 g AI/100 kg seed (approx. 50 g AI/ha), or as an in-furrow spray (IFS) at 0.23–0.25 g AI/100 m row (approx. 25 g AI/ha) was as effective at reducing blemishes to daughter tubers by wireworms (Agriotes obscurus) as phorate (Thimet 20G at 3230 g AI/ha), bifenthrin (Capture 2EC IFS at 300 g AI/ha) and clothianidin (Titan ST at 312.5 g AI/ha). In addition, broflanilide SPT and IFS applied at the above rates reduced resident wireworms (in the field at the time of planting) by 95.4–99.0% and neonate wireworms (produced from eggs laid during the growing season) by 98.1–100%. Similar results were obtained when broflanilide IFS (nonsystemic) was paired with clothianidin SPT (systemic) for broad-spectrum potato insect pest control. Strategies for the use of broflanilide on wheat (e.g., Teraxxa F4) in rotation with potatoes (Cimegra), both registered in Canada in 2020 are discussed.
Can foundational economy save regions in crisis?
Authors: Martynovich Mikhail , Hansen Teis , Lundquist Karl-Johan 
Published: October 2022

Abstract
We perform, to our best knowledge, the first systematic mapping of the foundational economy (FE) at the sub-national level by looking at the FE employment in Swedish regions between 2007 and 2016. We show that the FE itself not only suffered less than traded activities from employment decline during the Great Recession of 2007–2009 but was also a domain of substantial job creation in the post-crisis recovery. At the same time, regions with higher dependence on foundational employment were hit harder during the crisis in terms of overall labour market performance. We demonstrate that it is specific compositions of foundational and traded activities in the regional employment mix that relate differently to regional employment growth in times of crisis and recovery. Jointly, these findings allow us to contribute to the literatures on the FE and regional resilience.
Alternatives to Pyrethroid Resistance: Combinations of Cymbopogon nardus and Ocimum americanum Essential Oils Improve the Bioefficiency Control Against the Adults’ Populations of Aedes aegypti (Diptera: Culicidae)
Authors: Balboné Mahamoudou , Diloma Soma Dieudonné , Fogné Drabo Samuel , Namountougou Moussa , Konaté Hamadou , Benson Meda Georges , Sawadogo Ignace , Romba Rahim , Bilgo Etienne , Nebié Roger C H , Bassolé Imaël H N , Dabire Roch K , Gnankine Olivier 
Published: October 2022

Abstract
Dengue vector control strategies are mostly based on chemicals use against Aedes aegypti populations. The current study aimed at investigating the insecticidal effects of essential oils (EOs) obtained from five plant species, Cymbopogon citrates (D. C.) Stapf. (Poaceae), Cymbopogon nardus (Linn.) Rendle (Poaceae), Eucalyptus camaldulensis Linn. (Myrtaceae), Lippia multiflora Moldenke (Verbenaceae), and Ocimum americanum Linn. Lamiaceae, and combinations of Cymbopogon nardus and Ocimum americanum on Ae. aegypti populations from Bobo-Dioulasso. For this purpose, adults of the susceptible and field strains of Ae. aegypti were tested in WHO tubes with EO alone and binary combinations of O. americanum (OA) and C. nardus (CN; scored from C1 to C9). The extraction of the essential oils was done by hydrodistillation, and their components were determined by GC/MS. Among the 5 EOs tested, L. multiflora essential oil was the most efficient, with KDT50 values below 60 min on all Ae. aegypti strains tested, and also with a rate of mortality up to 100 and 85% for Bora Bora and Bobo-Dioulasso strains, respectively. This efficacy may be due to its major compounds which are with major compounds as β-caryophyllene, p-cymene, thymol acetate, and 1.8 cineol. Interestingly, on all strains, C8 combination showed a synergistic effect, while C2 showed an additive effect. These combinations exhibit a rate of mortality varying from 80 to 100%. Their toxicity would be due to the major compounds and the putative combined effects of some major and minor compounds. More importanly, L. multiflora EO and combinations of C. nardus and O. americanum EO, may be used as alternatives against pyrethroid resistant of Ae. aegypti.
Addressing the Machine: Victorian Working-Class Poetry and Industrial Machinery
Authors: Blair Kirstie 
Published: October 2022

Abstract
This article explores the representation of machinery by industrial workers in the Victorian period, and argues that their writings have a qualitatively different literary approach to machinery than that found in the work of established Victorian authors. It uses little-known poems by Scottish and Northern working-class writers to investigate how they use language and form to reflect upon the place of machinery in their working lives.
A Rare Case of Hemolytic Transfusion Reaction in a Premature Infant Caused by a Passive Anti-Jka Antibody
Authors: Yang Liyan , Wang Haijuan , Jiang Yongmei , Chen Jian , Zhao Hong , Feng Jing 
Published: October 2022

Abstract
Hemolytic transfusion reaction (HTR) is an important type of transfusion-associated reaction and usually occurs after alloimmunization to red blood cell antigens. The HTRs caused by passively transferred Kidd blood group antibodies are not well documented. Here, we report about a premature infant who developed HTR owing to a passive anti-Jka antibody transfer following fresh frozen plasma transfusion. Anti-Jka antibody was detected in the infant’s plasma and was also found in the donor plasma with a titer of 1:128. We reported this case to the local blood center, and they subsequently began testing for irregular antibodies of donor plasma, which is recommended but not mandated in China. This case reveals an unusual cause of HTR and emphasizes a possible need to screen donor plasma for antibodies to minimize risks to recipients.
A Cross-Sectional Analysis of Military Physician Residency Websites
Authors: Chunn Raegan A , Clark Delaney E S , Ozcan Maj Meghan C H 
Published: October 2022

ABSTRACT

Introduction
Medical physician residency program websites often serve as the first contact for any prospective applicant. No analysis of military residency program websites has yet been conducted, in contrast to their civilian counterparts. This study evaluated all military residency programs certified by the Accreditation Council for Graduate Medical Education (ACGME) 2021-2022 to determine program website comprehensiveness and accessibility and identify areas for improvement.

Materials and Methods
A list of military residency programs in the USA was compiled using Defense Health Agency Graduate Medical Education resources together with the ACGME database. A total of 15 objective website criteria covering education and recruitment content were assessed by two independent evaluators. Accessibility was also scored. Programs’ website scores were compared by geographic location, specialty affiliation, type of institution partnership, and program size. Analysis was performed with descriptive statistics and comparison via an unpaired t-test or Kruskal–Wallis analysis, as appropriate.

Results
A total of 124 military residency program websites were evaluated with a range of scores from 0 to 15 out of 15 possible points. Six programs had no identifiable website. All three services were represented with 43% joint-service programs. Content concerning physician education and development was more widely available than content directed toward the recruitment of applicants. The number of residency program websites reporting each content criterion varied greatly, but overall, no single service had a significantly higher score across their residencies’ websites. Significant variation occurred among individual specialties (P &lt; .05) but there was no significant difference in surgical and nonsurgical specialties. Civilian-associated programs (18 programs, 14.5%) were associated with significantly greater website comprehensiveness scored best on informatics measures for recruitment and performed 64% better than military-only programs overall.

Conclusions
Program information in an accessible website platform allows prospective applicants to gain comprehensive perspectives of programs during the application process without reliance on personal visits and audition rotations. Limitations to in-person experiences, such as those caused by reductions in travel and concern for student safety during the global pandemic caused by the SARS-CoV-2 virus, may be alleviated by accessible virtual information. Our results indicate that there is opportunity for all military residency programs to improve their websites and better recruit applicants through understanding their audience and optimizing their reach online.
Miniature Inverted-repeat Transposable Elements Drive Rapid MicroRNA Diversification in Angiosperms
Authors: Guo Zhonglong , Kuang Zheng , Tao Yihan , Wang Haotian , Wan Miaomiao , Hao Chen , Shen Fei , Yang Xiaozeng , Li Lei 
Published: October 2022

Abstract
MicroRNAs (miRNAs) are fast evolving endogenous small RNAs that regulate organism function and behavior in both animals and plants. Although models for de novo miRNA biogenesis have been proposed, the genomic mechanisms driving swift diversification of the miRNA repertoires in plants remain elusive. Here, by comprehensively analyzing 21 phylogenetically representative plant species, ranging from green algae to angiosperms, we systematically identified de novo miRNA events associated with 8,649 miRNA loci. We found that 399 (4.6%), 466 (5.4%), and 1,402 (16.2%) miRNAs were derived from inverted gene duplication events, long terminal repeats of retrotransposons, and miniature inverted-repeat transposable elements (MITEs), respectively. Among the miRNAs of these origins, MITEs, especially those belonging to the Mutator, Tc1/Mariner, and PIF/Harbinger superfamilies, were the predominant genomic source for de novo miRNAs in the 15 examined angiosperms but not in the six non-angiosperms. Our data further illustrated a transposition–transcription process by which MITEs are converted into new miRNAs (termed MITE-miRNAs) whereby properly sized MITEs are transcribed and therefore become potential substrates for the miRNA processing machinery by transposing into introns of active genes. By analyzing the 58,038 putative target genes for the 8,095 miRNAs, we found that the target genes of MITE-miRNAs were preferentially associated with response to environmental stimuli such as temperature, suggesting that MITE-miRNAs are pertinent to plant adaptation. Collectively, these findings demonstrate that molecular conversion of MITEs is a genomic mechanism leading to rapid and continuous changes to the miRNA repertoires in angiosperm.
Investigation Around Cases of Crimean-Congo Hemorrhagic Fever—Mauritania, 2022
Authors: Boushab Boushab Mohamed , Yanogo Pauline K , Barry Djibril , Benane Hacen Ahmed , El Bara Ahmed , Abdellah Moussa , Basco Leonardo K , Meda Nicolas 
Published: October 2022

Abstract

Background
Crimean-Congo hemorrhagic fever (CCHF) is a zoonotic arbovirosis. Humans are infected by tick bites or contact with blood of infected animals. CCHF can be responsible for severe outbreaks due to human-to-human transmission. Our aims were to increase awareness and promote the search for risk factors and disease monitoring to prevent CCHF epidemic, capacity building, appropriate measures to treat patients, and information for the local population.

Methods
During the outbreak of hemorrhagic fever from February to May 2022, blood samples were collected from 88 patients suspected to be infected with the virus. Diagnosis was established by reverse-transcription polymerase chain reaction (RT-PCR) and/or enzyme-linked immunosorbent assay.

Results
CCHF was confirmed by RT-PCR in 7 of 88 (8%) patients. Ticks were found in cattle, sheep, or goats in the areas where the subjects resided, with the exception of 1 CCHF-positive patient in close contact with fresh animal meat. Exposure to potential risk factors was found in all patients. The interval between the onset of symptoms and hospital admission was 2–3 days. All 7 patients were admitted to our hospital and treated promptly by blood transfusion. Two patients died.

Conclusions
Mortality is high in patients with the hemorrhagic form of CCHF. Disease prevention is necessary by strengthening vector control, avoiding contact and consumption of organic products from diseased animals, and vaccinating animals in areas where the disease is endemic. Furthermore, it is essential to establish management procedures for patients infected with CCHF virus.
The role of oceanographic conditions and colony size in shaping the spatial structure ofPyrosoma atlanticumin the NW Mediterranean Sea
Authors: Pastor-Prieto Marina , SabatÉs Ana , Raya Vanesa , Canepa Antonio , Parraguez TomÁs I , Gili Josep-Maria 
Published: October 2022

AbstractThis study investigates the role of winter oceanographic conditions on the horizontal and vertical spatial structure of Pyrosoma atlanticum at different ontogenetic stages. Data were obtained on two oceanographic cruises (February 2017 and 2018) in the NW Mediterranean. Small colonies were exceptionally abundant in 2017, linked to an earlier development of spring conditions and the subsequent seasonal phytoplankton bloom. The mesoscale distribution of P. atlanticum differed depending on the colony size. Large colonies (≥7 mm) were found on the slope all along the density front, whereas small (&lt;4 mm) and medium colonies (4–6.9 mm) extended their distribution over the shelf because of instabilities of the front, and were mostly absent in the cold, low-salinity coastal waters. The analysis of their vertical distribution showed that at night colonies of all sizes remained close to the surface, where chlorophyll-a levels were high, whereas during the day they migrated to deeper layers, reaching greater depths as the colony size increased. The migratory behaviour started when colonies were 4–6.9 mm long. The relative importance of the species in the downward carbon transport is discussed. Our results highlight the need to further study the ecology of this efficient filter feeder in the Mediterranean.
ThePhytophthora sojaenuclear effector PsAvh110 targets a host transcriptional complex to modulate plant immunity
Authors: Qiu Xufang , Kong Liang , Chen Han , Lin Yachun , Tu Siqun , Wang Lei , Chen Zhiyuan , Zeng Mengzhu , Xiao Junhua , Yuan Peiguo , Qiu Min , Wang Yan , Ye Wenwu , Duan Kaixuan , Dong Suomeng , Wang Yuanchao 
Published: October 2022

AbstractPlants have evolved sophisticated immune networks to restrict pathogen colonization. In response, pathogens deploy numerous virulent effectors to circumvent plant immune responses. However, the molecular mechanisms by which pathogen-derived effectors suppress plant defenses remain elusive. Here, we report that the nucleus-localized RxLR effector PsAvh110 from the pathogen Phytophthora sojae, causing soybean (Glycine max) stem and root rot, modulates the activity of a transcriptional complex to suppress plant immunity. Soybean like-heterochromatin protein 1-2 (GmLHP1-2) and plant homeodomain finger protein 6 (GmPHD6) form a transcriptional complex with transcriptional activity that positively regulates plant immunity against Phytophthora infection. To suppress plant immunity, the nuclear effector PsAvh110 disrupts the assembly of the GmLHP1-2/GmPHD6 complex via specifically binding to GmLHP1-2, thus blocking its transcriptional activity. We further show that PsAvh110 represses the expression of a subset of immune-associated genes, including BRI1-associated receptor kinase 1-3 (GmBAK1-3) and pathogenesis-related protein 1 (GmPR1), via G-rich elements in gene promoters. Importantly, PsAvh110 is a conserved effector in different Phytophthora species, suggesting that the PsAvh110 regulatory mechanism might be widely utilized in the genus to manipulate plant immunity. Thus, our study reveals a regulatory mechanism by which pathogen effectors target a transcriptional complex to reprogram transcription.