bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cryptic promoter activation occurs by at least two different mechanisms in the Arabidopsis genome
Authors: Kudo Hisayuki , Matsuo Mitsuhiro , Satoh Soichirou , Hata Takayuki , Hachisu Rei , Nakamura Masayuki , Yamamoto Yoshiharu Y. , Kimura Hiroshi , Matsui Minami , Obokata Junichi 
Published: July 2021

SUMMARYIn gene‐trap screening of plant genomes, promoterless reporter constructs are often expressed without trapping of annotated gene promoters. The molecular basis of this phenomenon, which has been interpreted as the trapping of cryptic promoters, is poorly understood. Here, we found that cryptic promoter activation occurs by at least two different mechanisms using Arabidopsis gene‐trap lines in which a firefly luciferase (LUC) open reading frame (ORF) without an apparent promoter sequence was expressed from intergenic regions: one mechanism is ‘cryptic promoter capturing’, in which the LUC ORF captured pre‐existing promoter‐like chromatin marked by H3K4me3 and H2A.Z, and the other is ‘promoter de novo origination’, in which the promoter chromatin was newly formed near the 5′ end of the inserted LUC ORF. The latter finding raises a question as to how the inserted LUC ORF sequence is involved in this phenomenon. To examine this, we performed a model experiment with chimeric LUC genes in transgenic plants. Using Arabidopsis psaH1 promoter–LUC constructs, we found that the functional core promoter region, where transcription start sites (TSSs) occur, cannot simply be determined by the upstream nor core promoter sequences; rather, its positioning proximal to the inserted LUC ORF sequence was more critical. This result suggests that the insertion of the coding sequence alters the local distribution of TSSs in the plant genome. The possible impact of the two types of cryptic promoter activation mechanisms on plant genome evolution and endosymbiotic gene transfer is discussed.
Genome assembly of the Chinese maize elite inbred line RP125 and its EMS mutant collection provide new resources for maize genetics research and crop improvement
Authors: Nie Shujun , Wang Bo , Ding Haiping , Lin Haijian , Zhang Li , Li Qigui , Wang Yujiao , Zhang Bin , Liang Anping , Zheng Qi , Wang Hui , Lv Huayang , Zhu Kun , Jia Minghui , Wang Xiaotong , Du Jiyuan , Zhao Runtai , Jiang Zhenzhen , Xia Caina , Qiao Zhenghao , Li Xiaohu , Liu Boyan , Zhu Hongbo , An Rong , Li Yucui , Jiang Qian , Chen Benfang , Zhang Hongkai , Wang Dening , Tang Changxiao , Yuan Yang , Dai Jie , Zhan Jing , He Weiqiang , Wang Xuebo , Shi Jian , Wang Bin , Gong Min , He Xiujing , Li Peng , Huang Li , Li Hui , Pan Chao , Huang Hong , Yuan Guangsheng , Lan Hai , Nie Yongxin , Li Xinzheng , Zhao Xiangyu , Zhang Xiansheng , Pan Guangtang , Wu Qingyu , Xu Fang , Zhang Zhiming 
Published: July 2021

SUMMARYMaize is an important crop worldwide, as well as a valuable model with vast genetic diversity. Accurate genome and annotation information for a wide range of inbred lines would provide valuable resources for crop improvement and pan‐genome characterization. In this study, we generated a high‐quality de novo genome assembly (contig N50 of 15.43 Mb) of the Chinese elite inbred line RP125 using Nanopore long‐read sequencing and Hi‐C scaffolding, which yield highly contiguous, chromosome‐length scaffolds. Global comparison of the RP125 genome with those of B73, W22, and Mo17 revealed a large number of structural variations. To create new germplasm for maize research and crop improvement, we carried out an EMS mutagenesis screen on RP125. In total, we obtained 5818 independent M2 families, with 946 mutants showing heritable phenotypes. Taking advantage of the high‐quality RP125 genome, we successfully cloned 10 mutants from the EMS library, including the novel kernel mutant qk1 (quekou: “missing a small part” in Chinese), which exhibited partial loss of endosperm and a starch accumulation defect. QK1 encodes a predicted metal tolerance protein, which is specifically required for Fe transport. Increased accumulation of Fe and reactive oxygen species as well as ferroptosis‐like cell death were detected in qk1 endosperm. Our study provides the community with a high‐quality genome sequence and a large collection of mutant germplasm.
Peri‐transfusion quality‐of‐life assessment for patients with myelodysplastic syndromes
Authors: Abel Gregory A. , Klepin Heidi D. , Magnavita Emily S. , Jaung Tim , Lu Wen , Shallis Rory M. , Hantel Andrew , Bahl Nupur E. , Dellinger‐Johnson Rebecca , Winer Eric S. , Zeidan Amer M. 
Published: July 2021

AbstractBackgroundMany patients with myelodysplastic syndromes (MDS) receive red cell transfusions to relieve symptoms associated with anemia, with transfusions triggered by hemoglobin level. It is not known if patients' quality of life (QOL) improves after transfusion, nor if peri‐transfusion QOL assessment (PTQA) can guide future transfusion decisions.Study Design and MethodsWe conducted a prospective pilot study of adults with MDS at three centers. Participants, who had to have hemoglobin ≥7.5, completed an MDS‐specific measure of QOL (the Quality of Life in Myelodysplasia Scale, [QUALMS]) 1 day before and 7 days after red cell transfusion. A report was sent to each patient and provider before the next transfusion opportunity, indicating whether there were clinically significant changes in QOL. We assessed the proportion of patients experiencing changes in QOL, and with a follow‐up questionnaire, whether they perceived their PTQA data were used for future transfusion decisions.ResultsFrom 2018 to 2020, 62 patients enrolled (mean age 73 years) and 37 completed both pre‐ and post‐transfusion QOL assessments. Of these, 35% experienced a clinically significant increase in QUALMS score 7 days after transfusion; 46% no change; and 19% a decrease. Among those completing the follow‐up questionnaire, 23% reported that PTQA results were discussed by their provider when considering repeat transfusion.ConclusionsThese data suggest PTQA is feasible for patients with MDS. Moreover, while helpful for some, for many others, red cell transfusion may not achieve its intended goal of improving QOL. PTQA offers a strategy to inform shared decision‐making regarding red cell transfusion.
Canine junctional epidermolysis bullosa due to a novel mutation in LAMA3 with severe upper respiratory involvement
Authors: Herrmann Ina , Linder Keith E. , Meurs Kathryn M. , Friedenberg Steven G. , Cullen Jonah , Olby Natasha , Bizikova Petra 
Published: July 2021

BackgroundJunctional epidermolysis bullosa (JEB) is a group of congenital blistering skin diseases characterized by clefting through the lamina lucida of the basement membrane zone.ObjectivesTo characterize the clinical and morphological features of a congenital mechanobullous disease in a litter of puppies with severe upper respiratory involvement, and to identify an associated genetic variant.AnimalsFive of eight puppies in an Australian cattle dog cross‐bred litter showed signs of skin fragility. Three were stillborn and one died at one month of age. The two surviving puppies were presented with blistering skin disease and severe respiratory distress. Additionally, one unaffected sibling was examined and blood was obtained for genetic testing.Methods and materialsPost‐mortem examination, histopathological evaluation and electron microscopy were performed. Whole genome sequencing (WGS) of one affected puppy was compared to a database of 522 dogs of 55 different breeds for variant analysis. Sanger sequencing of one additional affected and one unaffected sibling confirmed the variant.ResultsClinically, severe mucocutaneous ulcers occurred in frictional areas with claw sloughing. Histopathological results revealed subepidermal clefts and electron microscopy confirmed the split in the lamina lucida. Post‐mortem examination documented extensive pharyngeal and laryngeal lesions with granulation tissue and fibrinous exudate obscuring the airway. Moderate tracheal hypoplasia contributed. The WGS revealed a novel missense variant in the laminin α3‐chain XP_537297.2p(Asp2867Val), with an autosomal recessive mode of inheritance.Conclusions and clinical relevanceA novel variant in LAMA3 caused a generalized and severe phenotype of JEB with an unique clinical presentation of upper airway obstruction.
Computed tomography evaluation of proposed implant corridors in canine thoracic vertebrae
Authors: Schmitt Elizabeth M. , Early Peter , Bergman Robert , Riedesel Elizabeth A. , Yuan Lingnan , Mochel Jonathan P. , Kraus Karl H. 
Published: July 2021

AbstractObjectiveIdentify acceptable implant corridors in the normal canine thoracic vertebrae (T) from T1 to T9.Study DesignRetrospective study.Sample PopulationComputed tomographic (CT) studies of normal canine thoracic spines (n = 39).MethodsCT imaging studies of normal T1‐T9 canine spines were evaluated by five independent observers. Each identified a proposed corridor, measured the width, length, and angle off mid‐sagittal that the corridor occupied.ResultsCT studies were from 39 dogs weighing 3.19–60 kg (mean 10.72, SD 9.9 kg). Vertebral corridors ranged in average width from 3.8 to 5.2 mm, the widest being located at T1. They ranged in average length from 13.3 to 17.5 mm, shortest being T1 and longest being T6. The angle of corridors varied the most between individual vertebrae at T1‐T3. The average corridor angles were: T1 = 38°, T2 = 32°, T3 = 27°, T4 = 26°. T5‐T9 angle ranged from 23° to 24°.ConclusionThe average dimensions of corridors measured in dogs weighing 3.1–60 kg were consistent with those of commercially available cortical screws and pins.Clinical SignificanceCorridor trajectories identified in this population can be achieved from a dorsal approach between T5 and T9. A dorsal approach for implant placement would be challenging for T1‐T4 due to the variability found in these vertebrae as well as regional anatomical constraints.
Molecular detection and characterization of pathogenic Leptospira species in bats (Chiroptera) roosting in human habitats in Nigeria, West Africa
Authors: Kamani Joshua , Harrus Shimon , Ocholi Reuben A. , Yague Irene I. , Nyango Patrick G. , González‐Miguel Javier , Koizumi Nobuo 
Published: July 2021

AbstractLeptospirosis is a neglected zoonosis with a nearly global distribution. In order to determine the role of bats in the epidemiology of leptospirosis in Nigeria, a total of 231 bats belonging to three families, Pteropodidae (n = 117), Molossidae (n = 107) and Nycteridae (n = 17), roosting in human habitats were screened by PCR and sequencing for the detection of pathogenic Leptospira species. DNA extracted from the kidneys of bats were subjected to conventional PCR targeting the rrs1, rrs2, flaB and secY genes for the detection of pathogenic Leptospira spp. Overall, 27 out of the 231 (11.7%) of the samples screened were positive for Leptospira spp. High prevalence (>80%) of Leptospira spp. DNA was detected in Chaerophon and Nycteris bat species captures in an abandoned well located within a human habitation. Sequences generated in this study were highly identical to Leptospira borgpetersenii and Leptospira interrogans and clustered with sequences of pathogenic species in GenBank. The detection of pathogenic Leptospira spp. was significantly associated (p < .001) with the bat species, feeding habit, roosting site and study location. To the best of our knowledge, this is the first molecular detection and characterization of pathogenic Leptospira spp. in bats from Nigeria. Results show that bats in Nigeria are infected with diverse Leptospira genotypes phylogenetically related to known pathogenic, including zoonotic taxa. Together, these findings reinforce bats’ roles as potential reservoirs of Leptospira spp. and should be considered as a starting point for future comparative studies to improve our understanding of the epidemiology of this bacterial pathogen in Nigeria.
Interactions of cone cannabinoid CB1 and dopamine D4 receptors increase day/night difference in rod‐cone gap junction coupling in goldfish retina
Authors: Cao Jiexin , Mangel Stuart C. 
Published: July 2021

Key points
Although cone and rod photoreceptor cells in the retina have a type of cannabinoid receptor called a CB1 receptor, little is known about how cannabinoids, the active component in marijuana, affect retinal function.
Studies have shown that a circadian (24‐h) clock in the retina uses dopamine receptors, which are also on photoreceptors, to regulate gap junctions (a type of cell‐to‐cell communication) between rods and cones, so that they are functional (open) at night but closed in the day.
We show that CB1 receptors have opposite effects on rod‐cone gap junctions in day and night, decreasing communication in the day when dopamine receptors are active and increasing communication when dopamine receptors are inactive.
CB1 and dopamine receptors thus work together to enhance the day/night difference in rod‐cone gap junction communication.
The increased rod‐cone communication at night due to cannabinoid CB1 receptors may help improve night vision.
AbstractCannabinoid CB1 receptors and dopamine D4 receptors in the brain form receptor complexes that interact but the physiological function of these interactions in intact tissue remains unclear. In vertebrate retina, rods and cones, which are connected by gap junctions, express both CB1 and D4 receptors. Because the retinal circadian clock uses cone D4 receptors to decrease rod‐cone gap junction coupling in the day and to increase it at night, we studied whether an interaction between cone CB1 and D4 receptors increases the day/night difference in rod‐cone coupling compared to D4 receptors acting alone. Using electrical recording and injections of Neurobiotin tracer into individual cones in intact goldfish retinas, we found that SR141716A (a CB1 receptor antagonist) application alone in the day increased both the extent of rod‐cone tracer coupling and rod input to cones, which reaches cones via open gap junctions. Conversely, SR141716A application alone at night or SR141716A application in the day following 30‐min spiperone (a D4 receptor antagonist) application decreased both rod‐cone tracer coupling and rod input to cones. These results show that endogenous activation of cone CB1 receptors decreases rod‐cone coupling in the day when D4 receptors are activated but increases it at night when D4 receptors are not activated. Therefore, the D4 receptor‐dependent day/night switch in the effects of CB1 receptor activation results in an enhancement of the day/night difference in rod‐cone coupling. This synergistic interaction increases detection of very dim large objects at night and fine spatial details in the day.
Pre‐loading large volume oral electrolytes: tracing fluid and ion fluxes in horses during rest, exercise and recovery
Authors: Waller Amanda P. , Lindinger Michael I. 
Published: July 2021

Key pointsExercise results in rapid and large extracellular to intracellular fluid shifts, as well as significant sweating losses of water and ions.It is unknown whether ions within oral electrolyte supplements are taken up by muscle (and other soft tissues) and whether oral supplementation can effectively offset sweating losses.Pre‐loading with 8 L of a balanced hypotonic electrolyte supplement attenuated extracellular fluid losses, increased exercise duration and increased sweating fluid and ion losses during submaximal exercise.Supplemented electrolytes appear in skeletal muscle within 1 h after administration.Electrolyte supplementation increased exercise performance, improved maintenance of extracellular fluid volumes, and attenuated body fluid losses while maintaining sweating rates.AbstractThis study used radioactive sodium (24Na) and potassium (42K) in a balanced, hypotonic electrolyte supplement to trace their appearance in skeletal muscle, and also quantified extracellular and whole‐body fluid and ion changes during electrolyte supplementation, exercise and recovery. In a randomized crossover design, 1 h after administration of 1 to 3 L of water or electrolyte supplement with24Na, horses were exercised at 35% VO2maxto voluntary fatigue or, after administration of 8 L of water or electrolyte supplement with42K were exercised at 50% peak VO2for 45 min (n= 4 in each trial). Pre‐exercise electrolyte supplementation was associated with decreased loss of fluid and electrolytes from the extracellular fluid compartments during exercise and recovery compared with water alone. The improved fluid and ion balance during prolonged exercise was associated with increased exercise duration, despite continuing sweating losses of fluid and ions. Nasogastric administration of radiotracer24Na+and42K+showed rapid absorption into the blood with plasma levels peaking 45 min after administration, followed by distribution into the extracellular space and intracellular fluid of muscle within 1 h. Following exercise, virtually all Na+remained within the extracellular compartment, while the majority of K+underwent intracellular uptake by 2 h of recovery. It is concluded that pre‐loading with a large volume, balanced electrolyte supplement helps maintain whole‐body fluid and ion balance and support muscle function during periods of prolonged sweat ion losses.
Hybrid Reactivity-Equivalent Physical Transformation Method on Double-Heterogeneous System Containing Dispersed Fuel Particles and Burnable Poison Particles
Authors: Lou Lei , Chai Xiaoming , Yao Dong , Peng Xingjie , Li Mancang , Chen Liang , Yu Yingrui , Wang Lianjie 
Published: July 2021

Abstract
Because of the double heterogeneity of particle-dispersed fuel and particle-dispersed burnable poisons in double-heterogeneous (DH) systems, traditional software for reactor neutronics calculation cannot model and calculate them, and the volume homogenization method may bring large calculation deviations. The traditional reactivity-equivalent physical transformation (RPT) method can equivalently transform a DH system into a single-heterogeneous (SH) system which can be modeled and calculated by proven traditional software for reactor neutronic calculation. The DH system containing both particle-dispersed fuel and particle-dispersed burnable poisons can be treated by the Improved RPT (IRPT) method based on the traditional RPT method. However, when the IRPT method is used to treat the DH system containing particle-dispersed burnable poisons with large absorption cross section, large volume fraction or large particle size, there will be larger calculation deviations in the burnup. The Ring RPT (RRPT) method can not only deal with the problem of dispersed fuel particles that can be handled by the traditional RPT method, but also the problem of dispersed burnable poison particles that make the traditional RPT method invalid because of the large absorption cross section. For DH systems containing both particle-dispersed fuel and particle-dispersed burnable poisons, a two-step RRPT (TRRPT) method can be used. For DH systems containing particle-dispersed burnable poison with a large absorption cross section, a large volume fraction, or a large particle size, TRRPT method has higher calculation accuracy than the IRPT method. In this article, it was found that for DH systems containing both particle-dispersed fuel and particle-dispersed burnable poison, the TRRPT method may be invalid in some situation. Also, a new method named hybrid RPT (HRPT) method has been proposed for DH systems containing both particle-dispersed fuel and particle-dispersed burnable poisons, herein. And then the HRPT are analyzed and studied on the equivalent transformation range of DH systems comparing with the TRRPT method and the IRPT method. It was found that the HRPT method not only has a wider equivalent transformation range of DH systems than the TRRPT method, but also has higher calculation accuracy than the IRPT method. Results of depletion calculations for different types, different volume fractions, and different particle sizes of burnable poisons particles dispersed the DH systems with dispersed particle-type fuel and the comparison with Monte Carlo results of grain models have proved the effectiveness and applicability of HRPT method.
The Effect of Transient Characteristics on Optimization of Fixed-Bed Regenerators
Authors: Ramin Hadi , Krishnan Easwaran N. , Gurubalan A. , Simonson Carey J. 
Published: July 2021

Abstract
Fixed-bed regenerators (FBRs) have high sensible effectiveness, making them an energy-efficient air-to-air energy recovery exchanger (AAEE) to reduce energy consumption for ventilation in buildings. FBRs operate by alternately storing and releasing heat in fixed exchangers, which result in outlet temperature that varies with time during both heating and cooling periods. This variation in FBR's outlet temperature adds a new optimization variable that needs to be considered when designing FBRs. For example, in heating, ventilating, and air conditioning (HVAC) systems, careful design is required to prevent large variations in FBR’s outlet temperature (temperature swing (TS)), which might deteriorate occupant thermal comfort and introduce a variable load on the HVAC system. In this paper, a correlation for TS is developed as a function of FBR design parameters. FBRs optimization is performed considering TS as an additional objective to the traditional parameters of exchanger effectiveness, pressure drop, payback period (PBP), and mass. A selection procedure (decision-making procedure) is also integrated into the optimization process to select the optimized FBRs from Pareto fronts. The results show that when TS is included as an additional objective to the optimization and selection process, the selected optimized FBRs have higher mass and effectiveness.
Three-Dimensional Flow Simulation of a Twin-Screw Pump for the Analysis of Gap Flow Characteristics
Authors: Moghaddam Ali H. , Kutschelis Boris , Holz Frank , Börjesson Tomas , Skoda Romuald 
Published: July 2021

AbstractUnsteady three-dimensional flow simulations on a twin-screw pump are performed for an assessment of the radial, circumferential, and flank gap flow effect on the pump performance. By means of the overset grid technique, rigid computational grids around the counter-rotating spindles yield a high cell quality and a high spatial resolution of the gap backflow down to the viscous sublayer in terms of y+&lt;1. An optimization of the hole-cutting process is performed on a generic gap flow and transferred to the complex moving gaps in the pump. Grid independence is ensured, and conservation properties of the overset grid interpolation technique are assessed. Simulation results are validated against measured pump characteristics. Pump performance in terms of pressure build-up along the flow path through the spindles and volume flow rate is presented for a wide range of spindle speed and pump head. Flow rate fluctuations are found to depend on head but hardly on speed. By a profound assessment of the respective radial, circumferential, and flank gap contribution to the total backflow, the importance of the most complex flank gap is pointed out. Backflow rate characteristics in dependence on the pump head and the pump speed are presented.