bluuebunny/crossref_metadata_2025_split huggingface dataset:
Amplification and sequencing of entire tick mitochondrial genomes for a phylogenomic analysis
Authors: Kneubehl Alexander R. , Muñoz-Leal Sebastián , Filatov Serhii , de Klerk Daniel G. , Pienaar Ronel , Lohmeyer Kimberly H. , Bermúdez Sergio E. , Suriyamongkol Thanchira , Mali Ivana , Kanduma Esther , Latif Abdalla A. , Sarih M’hammed , Bouattour Ali , de León Adalberto A. Pérez , Teel Pete D. , Labruna Marcelo B. , Mans Ben J. , Lopez Job E. 
Published: November 2022

AbstractThe mitochondrial genome (mitogenome) has proven to be important for the taxonomy, systematics, and population genetics of ticks. However, current methods to generate mitogenomes can be cost-prohibitive at scale. To address this issue, we developed a cost-effective approach to amplify and sequence the whole mitogenome of individual tick specimens. Using two different primer sites, this approach generated two full-length mitogenome amplicons that were sequenced using the Oxford Nanopore Technologies’ Mk1B sequencer. We used this approach to generate 85 individual tick mitogenomes from samples comprised of the three tick families, 11 genera, and 57 species. Twenty-six of these species did not have a complete mitogenome available on GenBank prior to this work. We benchmarked the accuracy of this approach using a subset of samples that had been previously sequenced by low-coverage Illumina genome skimming. We found our assemblies were comparable or exceeded the Illumina method, achieving a median sequence concordance of 99.98%. We further analyzed our mitogenome dataset in a mitophylogenomic analysis in the context of all three tick families. We were able to sequence 72 samples in one run and achieved a cost/sample of ~ $10 USD. This cost-effective strategy is applicable for sample identification, taxonomy, systematics, and population genetics for not only ticks but likely other metazoans; thus, making mitogenome sequencing equitable for the wider scientific community.
Mixtures of genotypes increase disease resistance in a coral nursery
Authors: Brown Anya L. , Anastasiou Dagny-Elise , Schul Monica , MacVittie Sophia , Spiers Lindsay J. , Meyer Julie L. , Manfrino Carrie , Frazer Thomas K. 
Published: November 2022

AbstractMarine infectious diseases are a leading cause of population declines globally due, in large part, to challenges in diagnosis and limited treatment options. Mitigating disease spread is particularly important for species targeted for conservation. In some systems, strategic arrangement of organisms in space can constrain disease outbreaks, however, this approach has not been used in marine restoration. Reef building corals have been particularly devastated by disease and continue to experience catastrophic population declines. We show that mixtures of genotypes (i.e., diversity) increased disease resistance in the critically endangered Acropora cervicornis, a species that is frequently targeted for restoration of degraded reefs in the broader Caribbean region. This finding suggests a more generalized relationship between diversity and disease and offers a viable strategy for mitigating the spread of infectious diseases in corals that likely applies to other foundation species targeted for restoration.
Simulation of nerve fiber based on anti-resonant reflecting optical waveguide
Authors: Omidi Marzieh , Zibaii Mohammad Ismail , Granpayeh Nosrat 
Published: November 2022

AbstractLight and optical techniques are widely used for the diagnosis and treatment of neurological diseases as advanced methods. Understanding the optical properties of nervous tissue and nerve cells is vital. Using light sources in these methods raises significant challenges, such as finding the place of light transmission in nerve fibers that could be an appropriate substrate for neural signaling. The myelinated axons are a promising candidate for transmitting neural signals and light due to their waveguide structures. On the other hand, with the emergence of diseases such as multiple sclerosis and disorders within the production and transmission of nerve signals, because of the demyelination, understanding the properties of the myelinated axon as a waveguide is obtaining additional necessity. The present study aims to show that the myelinated axon’s refractive index (RI) profile plays an essential role in transmitting the beams in it. According to the nerve fiber, RI profile and its similarity to depressed core fiber with lower RI of the core compared to the cladding, the behaviors of the nerve fiber based on anti-resonant reflecting optical waveguide structure are investigated by taking into account the realistic optical imperfections. Light launching to the myelin sheath and axon is shown by introducing the axon and myelin sheath as a waveguide in the presence of both axon and myelin with bends, myelin sheath variation, and node of Ranvier.
Discovery of pathway-independent protein signatures associated with clinical outcome in human cancer cohorts
Authors: Konaté Mariam M. , Li Ming-Chung , McShane Lisa M. , Zhao Yingdong 
Published: November 2022

AbstractProteomic data provide a direct readout of protein function, thus constituting an information-rich resource for prognostic and predictive modeling. However, protein array data may not fully capture pathway activity due to the limited number of molecules and incomplete pathway coverage compared to other high-throughput technologies. For the present study, our aim was to improve clinical outcome prediction compared to published pathway-dependent prognostic signatures for The Cancer Genome Atlas (TCGA) cohorts using the least absolute shrinkage and selection operator (LASSO). RPPA data is particularly well-suited to the LASSO due to the relatively low number of predictors compared to larger genomic data matrices. Our approach selected predictors regardless of their pathway membership and optimally combined their RPPA measurements into a weighted risk score. Performance was assessed and compared to that of the published signatures using two unbiased approaches: 1) 10 iterations of threefold cross-validation for unbiased estimation of hazard ratio and difference in 5-year survival (by Kaplan–Meier method) between predictor-defined high and low risk groups; and 2) a permutation test to evaluate the statistical significance of the cross-validated log-rank statistic. Here, we demonstrate strong stratification of 445 renal clear cell carcinoma tumors from The Cancer Genome Atlas (TCGA) into high and low risk groups using LASSO regression on RPPA data. Median cross-validated difference in 5-year overall survival was 32.8%, compared to 25.2% using a published receptor tyrosine kinase (RTK) prognostic signature (median hazard ratios of 3.3 and 2.4, respectively). Applicability and performance of our approach was demonstrated in three additional TCGA cohorts: ovarian serous cystadenocarcinoma (OVCA), sarcoma (SARC), and cutaneous melanoma (SKCM). The data-driven LASSO-based approach is versatile and well-suited for discovery of new protein/disease associations.
Valorization of spent double substituted Co–Ni–Zn–Fe LDH wastewater nanoadsorbent as methanol electro-oxidation catalyst
Authors: Mahmoud Rehab , Mohamed Hamdy F. M. , Hafez Sarah H. M. , Gadelhak Yasser M. , Abdel-Hady E. E. 
Published: November 2022

AbstractFinding suitable non-expensive electrocatalyst materials for methanol oxidation is a significant challenge. Waste valorization of spent wastewater nanoadsorbents is a promising route toward achieving circular economy guidelines. In this study, the residual of layered double hydroxide (LDH) can be used as an electrocatalyst in direct methanol fuel cells as a novel approach. The Co–Ni–Zn–Fe LDH was prepared by the co-precipitation method followed by the adsorption of methyl orange (MO). Moreover, the spent adsorbent was calcined at different temperatures (200, 400, and 600 °C) to be converted to the corresponding mixed metal oxides (MMO). The prepared samples were characterized using XRD, FTIR, HRTEM, zeta potential, and hydrodynamic size measurements. The spent adsorbent was tested as an electro-catalyst for direct methanol electro-oxidation. The spent LDH/MO adsorbent showed a maximum current density of 6.66 mA/cm2 at a 50 mV/s scan rate and a 1 M methanol concentration. The spent MMO/MO adsorbent showed a maximum current density of 8.40 mA/cm2 at a 200 °C calcination temperature, 50 mV/s scan rate, and a 3 M methanol concentration. Both samples show reasonable stability over time, as indicated by the chronoamperometric response. Further nanoengineering of used nanoadsorbents could be a promising path to repurposing these wastes as electro-oxidation catalysts.
Near-infrared quantum cutting luminescence in Pr3+/Yb3+ doped lead bismuth borate glass
Authors: Seshadri Meruva , Santos Ilza T. C. , Bell Maria Jose V. , Lapointe Jerome , Messaddeq Younes , Anjos Virgilio 
Published: November 2022

AbstractIn this paper, thermally stable lead-bismuth-borate glasses were doped with 0.5 mol% of Pr3+ ions at several concentration levels of Yb3+ ions. Structural characterizations were performed via Raman, differential scanning calorimetry, optical absorption and fluorescence spectra. The Judd–Ofelt intensity parameter, $${\Omega }_2$$

Ω
2

, of Pr3+ doped glass was comparatively higher than those from reported ones, which reflects the increase of co-valency and asymmetry of chemical bonds in the local environment of Pr3+. Near-infrared emission in 900–2200 nm wavelength range was recorded through 443 nm blue laser pumping. Visible to near-IR quantum cutting and concentration quenching mechanisms were discussed to understand the luminescent behaviour. Intense IR emission ($$\sim 1.0\,\upmu {\text {m}})$$

∼
1.0

μ
m
)

features generated by absorbing one visible photon leads to quantum efficiencies close to 128% in Pr3+/Yb3+ co-doped samples which may improve the solar spectrum absorption and accordingly, increase the efficiency of c-Si solar cells. Emission cross-section, lifetime, figure of merit and gain bandwidth corresponding to Pr3+: $$^3F_2 \rightarrow ^3H_4$$

3

F
2

→
3

H
4

($$\sim 2.0\,\upmu$$

∼
2.0

μ

m) were comparatively reported suggesting that the glass with molar composition 0.5Pr3+/0.1Yb3+ might be a potential candidate for $$\sim 2.0\,\upmu$$

∼
2.0

μ

m laser operation with low pump threshold.
Decreased PPARgamma in the trigeminal spinal subnucleus caudalis due to neonatal injury contributes to incision-induced mechanical allodynia in female rats
Authors: Otsuji Jo , Hayashi Yoshinori , Hitomi Suzuro , Soma Chihiro , Soma Kumi , Shibuta Ikuko , Iwata Koichi , Shirakawa Tetsuo , Shinoda Masamichi 
Published: November 2022

AbstractWhisker pad skin incision in infancy causes the prolongation of mechanical allodynia after re-incision in adulthood. A recent study also proposed the importance of sex differences in pain signaling in the spinal cord. However, the sex difference in re-incision-induced mechanical allodynia in the orofacial region is not fully understood. In the rats that experienced neonatal injury in the whisker pad skin, the mechanical allodynia in the whisker pad was significantly prolonged after re-incision in adulthood compared to sham injury in infancy. No significant sex differences were observed in the duration of mechanical allodynia. The duration of mechanical allodynia in male rats was shortened by intracisternal administration of minocycline. However, minocycline had no effects on the duration of mechanical allodynia in female rats. In contrast, intracisternal administration of pioglitazone markedly suppressed mechanical allodynia in female rats after re-incision. Following re-incision, the number of peroxisome proliferator-activated receptor gamma (PPARgamma)-positive cells were reduced in the trigeminal spinal subnucleus caudalis (Vc) in female rats that experienced neonatal injury. Immunohistochemical analyses revealed that PPARgamma was predominantly expressed in Vc neurons. Pioglitazone increased the number of PPARgamma-positive Vc neurons in female rats whose whisker pad skin was incised in both infancy and adulthood stages. Pioglitazone also upregulated heme oxygenase 1 and downregulated NR1 subunit in the Vc in female rats after re-incision. Together, PPARgamma signaling in Vc neurons is a female-specific pathway for whisker pad skin incision-induced mechanical allodynia.
Diversity of soil faunal community as influenced by crop straw combined with different synthetic fertilizers in upland purple soil
Authors: Xie Xiuhong , Wang Xuefeng , Dong Zhixin , Zhu Bo 
Published: November 2022

AbstractSoil fauna play a crucial role in sustaining agro-ecosystem functions. Crop straw is recommended for application to agricultural fields to improve soil quality. However, the effects of crop straw combined with different synthetic fertilizers on the soil faunal community remain unclear, and knowledge regarding purple soil is limited. Using the conserved cytochrome c oxidase I (COI) gene as markers, we examined the responses of the soil faunal community to different fertilization in upland purple soil of southwestern China. The accuracy of the morphological and molecular methods in characterizing soil nematodes was compared. Our results showed that different fertilization treatments significantly changed the soil faunal community structure (Adonis test,R2 = 0.43,P = 0.011). Sixteen biomarkers were identified according to LEfSe (linear discriminant analysis effect size). The diversity and species number of soil fauna were closely related to soil organic matter (SOM) and total phosphorus (TP) (P < 0.05). This study indicates that crop straw return can improve the soil fertility and diversity of soil fauna in purple soil. Additionally, the morphological approach and molecular method based on the COI gene can be considered as complementary approaches in characterizing soil nematode community.
Riboflavin attenuates tartrazine toxicity in the cerebellar cortex of adult albino rat
Authors: Ismail Omnia I. , Rashed Noha A. 
Published: November 2022

AbstractTartrazine is a synthetic yellowish dye considered one of the most common food colorants. Extensive usage of tartrazine in humans led to harmful health impacts. To investigate the impact of tartrazine administration on the cerebellum and to assess the potential role of riboflavin co-administration in the adult male albino rat. Four groups of adult albino rats were included in this study. Group I was supplied with distilled water. Group II was supplied tartrazine orally at a dose of 7.5 mg/kg BW dissolved in distilled water. Group III was supplied with tartrazine at the same previously mentioned dose and riboflavin orally at a dose of 25 mg/kg BW dissolved in distilled water. Group IV was supplied with riboflavin at the same previously mentioned dose. The study was conducted for 30 days then rats were sacrificed, weighted and the cerebella extracted and handled for light, ultrastructural and immunohistochemical evaluation. It was found with tartrazine treatment focal areas of Purkinje cell loss leaving empty spaces, a broad spread of neuronal affection to the degree of the disappearance of some of the granular cells, reduced the thickness of the molecular and granular layers, and strong positive GFAP immunoreactions. With riboflavin coadministration restored continuous Purkinje layer with normal appeared Purkinje cells, but some cells were still shrunken and vacuolated as well as the molecular and granular cell layers appeared normal. Tartrazine had deleterious effects on the cerebellar cytoarchitecture, and riboflavin co-administration alleviated these neurotoxic effects.
High throughput method of 16S rRNA gene sequencing library preparation for plant root microbial community profiling
Authors: Kumaishi Kie , Usui Erika , Suzuki Kenta , Kobori Shungo , Sato Takumi , Toda Yusuke , Takanashi Hideki , Shinozaki Satoshi , Noda Munehiro , Takakura Akiko , Matsumoto Kayoko , Yamasaki Yuji , Tsujimoto Hisashi , Iwata Hiroyoshi , Ichihashi Yasunori 
Published: November 2022

AbstractMicrobiota are a major component of agroecosystems. Root microbiota, which inhabit the inside and surface of plant roots, play a significant role in plant growth and health. As next-generation sequencing technology allows the capture of microbial profiles without culturing the microbes, profiling of plant microbiota has become a staple tool in plant science and agriculture. Here, we have increased sample handling efficiency in a two-step PCR amplification protocol for 16S rRNA gene sequencing of plant root microbiota, improving DNA extraction using AMPure XP magnetic beads and PCR purification using exonuclease. These modifications reduce sample handling and capture microbial diversity comparable to that obtained by the manual method. We found a buffer with AMPure XP magnetic beads enabled efficient extraction of microbial DNA directly from plant roots. We also demonstrated that purification using exonuclease before the second PCR step enabled the capture of higher degrees of microbial diversity, thus allowing for the detection of minor bacteria compared with the purification using magnetic beads in this step. In addition, our method generated comparable microbiome profile data in plant roots and soils to that of using common commercially available DNA extraction kits, such as DNeasy PowerSoil Pro Kit and FastDNA SPIN Kit for Soil. Our method offers a simple and high-throughput option for maintaining the quality of plant root microbial community profiling.
Providing curb availability information to delivery drivers reduces cruising for parking
Authors: Dalla Chiara Giacomo , Krutein Klaas Fiete , Ranjbari Andisheh , Goodchild Anne 
Published: November 2022

AbstractDelivery vehicle drivers are experiencing increasing challenges in finding available curb space to park in urban areas, which increases instances of cruising for parking and parking in unauthorized spaces. Policies traditionally used to reduce cruising for parking for passenger vehicles, such as parking fees and congestion pricing, are not effective at changing delivery drivers’ travel and parking behaviors. Intelligent parking systems that use real-time curb availability information to better route and park vehicles can reduce cruising for parking, but they have never been tested for delivery vehicle drivers. The current study tested whether providing real-time curb availability information to delivery drivers reduces the travel time and distance spent cruising for parking. A curb parking information system deployed in a study area in Seattle, Wash., displayed real-time curb availabilities on a mobile app called OpenPark. A controlled experiment assigned drivers’ deliveries in the study area with and without access to OpenPark. The data collected showed that when curb availability information was provided to drivers, their cruising for parking time significantly decreased by 27.9 percent, and their cruising distance decreased by 12.4 percent. These results demonstrate the potential for implementing intelligent parking systems to improve the efficiency of urban logistics systems.
Development of wearable multi-lead ECG measurement device using cubic flocked electrode
Authors: Takeshita Toshihiro , Yoshida Manabu , Takei Yusuke , Ouchi Atsushi , Hinoki Akinari , Uchida Hiroo , Kobayashi Takeshi 
Published: November 2022

AbstractThis paper describes the fabrication and fundamental evaluation of the cubic flocked electrode (CFE), which is a dry electrode that is fabricated using electrostatic flocking technology. The development of a wearable multi-lead electrocardiogram (ECG) measurement device using the CFE is also reported. To enable the measurement of ECG signals with sufficient quality for medical applications, the occurrence of motion artifacts (MAs) is the most important problem to be overcome. Therefore, it is necessary to stabilize the contact between the patient’s skin and the dry electrode. Because the CFE developed in this work offers both contact stability and flexibility, it is expected to enable ECG measurements with low MA levels. In this study, it is demonstrated that the number of MAs caused by respiration can be reduced when the CFE contact is made at a contact pressure of approximately 500 Pa using MA evaluation equipment that was developed in-house. Additionally, a wearable multi-lead ECG is designed and fabricated based on this contact pressure (500 Pa). The results of the demonstration experiment show that the ECG measurements are successful to the same extent as a conventional medical device.
Characterization of the Dahl salt-sensitive rat as a rodent model of inherited, widespread, persistent pain
Authors: Ferrari Luiz F. , Rey Charles , Ramirez Anna , Dziuba Adam , Zickella Jacqueline , Zickella Michael , Raff Hershel , Taylor Norman E. 
Published: November 2022

AbstractAnimal models are essential for studying the pathophysiology of chronic pain disorders and as screening tools for new therapies. However, most models available do not reproduce key characteristics of clinical persistent pain. This has limited their ability to accurately predict which new medicines will be clinically effective. Here, we characterize the Dahl salt-sensitive (SS) rat strain as the first rodent model of inherited widespread hyperalgesia. We show that this strain exhibits physiological phenotypes known to contribute to chronic pain, such as neuroinflammation, defective endogenous pain modulation, dysfunctional hypothalamic–pituitary–adrenal axis, increased oxidative stress and immune cell activation. When compared with Sprague Dawley and Brown Norway rats, SS rats have lower nociceptive thresholds due to increased inflammatory mediator concentrations, lower corticosterone levels, and high oxidative stress. Treatment with dexamethasone, the reactive oxygen species scavenger tempol, or the glial inhibitor minocycline attenuated the pain sensitivity in SS rats without affecting the other strains while indomethacin and gabapentin provided less robust pain relief. Moreover, SS rats presented impaired diffuse noxious inhibitory controls and an exacerbated response to the proalgesic mediator PGE2, features of generalized pain conditions. These data establish this strain as a novel model of spontaneous, widespread hyperalgesia that can be used to identify biomarkers for chronic pain diagnosis and treatment.
Empagliflozin protects against renal ischemia/reperfusion injury in mice
Authors: Wang Qifeng , Ju Feng , Li Jiaxue , Liu Ting , Zuo Yunxia , Abbott Geoffrey W. , Hu Zhaoyang 
Published: November 2022

AbstractRenal ischemia/reperfusion (I/R) can induce acute kidney injury. Empagliflozin is a newly developed inhibitor of sodium-glucose cotransporter-2 (SGLT2) approved as an antidiabetic medication for patients with type 2 diabetes mellitus. Despite the established cardioprotective functions of empagliflozin, its protective role in renal I/R is unclear. Here, the present study evaluated the renoprotective effects of empagliflozin in a mouse model of renal I/R injury. Male C57/BL6 mice were allocated to sham-operated, I/R, and empagliflozin groups. Kidney pedicles on both sides were clamped for 45 min and were reperfused for 24 h. Empagliflozin (1 mg/kg) was administered to the mice for 2 days preischemia. The GSK-3β inhibitor SB216763 was administered intravenously at the beginning of reperfusion (0.1 mg/kg). Renal function and histological scores were evaluated. The kidneys were taken for immunohistochemical analysis, western blotting and apoptosis measurements. We found that empagliflozin decreased serum levels of creatinine and urea, reduced the average kidney weight-to-tibia length ratio, attenuated tubular damage, reduced renal proinflammatory cytokine expression and inhibited apoptosis in injured kidneys. Furthermore, empagliflozin increased renal glycogen synthase kinase 3β (GSK-3β) phosphorylation post I/R. Pharmacological inhibition of GSK-3β activity mimicked the renal protective effects offered by empagliflozin. In summary, these results support a protective role of empagliflozin against renal I/R injury.