bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cover Image
Authors: Eto Shotaro , Kato Daiki , Saeki Kohei , Iguchi Takaaki , Shiyu Qin , Kamoto Satoshi , Yoshitake Ryohei , Shinada Masahiro , Ikeda Namiko , Tsuboi Masaya , Chambers James , Uchida Kazuyuki , Nishimura Ryohei , Nakagawa Takayuki 
Published: November 2024

The cover image is based on the article Comprehensive Analysis of the Tumour Immune Microenvironment in Canine Urothelial Carcinoma Reveals Immunosuppressive Mechanisms Induced by the COX‐Prostanoid Cascade by Shotaro Eto et al., https://doi.org/10.1111/vco.12999.
image
Evaluation of serum protein electrophoresis and immunofixation in dogs seropositive for various vector‐borne pathogens
Authors: Jornet‐Rius Oriol , Chornarm Nida , Skeldon Niki , McGrew Ashley , Lappin Michael , Solano‐Gallego Laia , Moore A Russell 
Published: November 2024

AbstractBackgroundCanine vector‐borne diseases (VBDs) induce non‐specific dysproteinemias, detectable by serum protein electrophoresis (SPE). VBDs have been reported to induce a monoclonal gammopathy pattern. Monoclonal gammopathies are commonly the result of paraprotein (M‐protein) produced by an immunoglobulin‐secreting neoplasm.ObjectivesThe aims of this study were to characterize and compare SPE and immunofixation (IF) changes, evaluate the performance of previously identified SPE and IF interpretative criteria, and identify M‐proteins in a cohort of dogs seropositive for a VBD and with an unknown history for an immunoglobulin‐secreting neoplasm.MethodsA total of 143 serum samples from dogs that tested seropositive for different vector‐borne pathogens were assessed by SPE. Cases with abnormal globulin fractions were further characterized by IF. Protein fraction and IF labeling results were evaluated using Kruskal–Wallis with Dunn's multiple comparisons and principal component analysis (PCA).ResultsIF was performed in 112 VBD‐seropositive samples with dysproteinemia evaluated by SPE. Most (84/112, 75%) had a polyclonal expansion. Only two dogs had findings suggestive of an M‐protein when considering both SPE and immunofixation. PCA clustered E.canis/A.phagocytophilum and B.gibsoni/CM.haematoparvum groups with relatively more γ‐globulins than albumin and α‐globulins, and the B.gibsoni/CM.haematoparvum group with more prominent IgA and IgM labeling than IgG labeling. Additionally, D.immitis clustered with more prominent β‐globulins than γ‐globulins and more IgG4 than IgG‐FC.ConclusionsThe previously derived interpretative criteria suggested an M‐protein in very few VBD‐seropositive dogs. PCA identified SPE and immunofixation pattern differences between dogs seropositive for different infectious agents.
FIELD PERFORMANCE OF HOT IN-PLANT PRODUCED ASPHALTIC CONCRETE WEARING COURSE (ACWC) WITH 30% RECLAIMED ASPHALT PAVEMENT (RAP)
Authors: Yee Teh Sek , Ab Wahab Md Yunus , Yunus Nordin , Abu Haris Rino Effendy , Ayob Mohd Azli , Ramzi Mohammad Riad , Mustaffa Kamal Dini Dayana 
Published: November 2024

Hot in-plant recycling stands as an effective yet underutilized method in Malaysia for reusing pavement milling waste, resulting in insufficient established benchmarks and validated trials. The Utilization of Reclaimed Asphalt Pavement (RAP) can divert a significant amount of waste asphalt millings from landfills, while conserving energy and natural resources. This study focused on the recycled mixture, ACWC-30RAP, which integrated 30% Reclaimed Asphalt Pavement (RAP). In July 2022, a 400 m trial lay was conducted from KM413.90 to KM414.30 Southbound (SB), Section C3, along the PLUS North-South Expressway (NSE). Field tests were systematically conducted on both the ACWC-30RAP and conventional ACWC20 mixtures at different phases including month-6, month-9, and month-12 post-construction. The primary objective was to assess fundamental properties related to the structural stiffness of pavement layers as well as the pavement performance and condition for both trial sections using various field testing including Falling Weight Deflectometer (FWD) and Multi-Laser Profiler (MLP). Following the 12-month trial period, both the ACWC-30RAP and conventional ACWC20 mixtures experienced actual traffic loading and environmental conditions. Remarkably, the ACWC-30RAP demonstrated comparable field performance as the conventional ACWC20. This alignment in performance signified a promising avenue for employing the recycled mixture with high RAP content. Using ACWC-30RAP can also provide economic benefit, reducing the production cost by approximately 25%. In essence, the ACWC-30RAP had achieved an equivalent level of confidence to the conventional ACWC20 mixture, which was exclusively composed of virgin materials. cts.
DESIGN OF A 24.5 GHZ CMOS LOW NOISE AMPLIFIER USING 0.13-µM TECHNOLOGY FOR 6G WIRELESS APPLICATIONS
Authors: Zainol Murad Sohiful Anuar , Abd Manaf Asrulnizam , A. Rhaffor Nuha , Abdullah Zawawi Ruhaifi 
Published: November 2024

The need for high-performance circuit designs is growing as wireless communication technologies continue to advance and support newer generations of wireless applications. Much emphasis has been focused on the possibility of the 24 GHz frequency band in next-generation wireless networks, including 5G and beyond. Designing a low noise amplifier (LNA) operating at 24 GHz presents several challenges. The primary concerns include achieving high gain, low power consumption, low noise figure, and while maintaining good linearity and stability. This paper presents the design, simulation, and layout of a CMOS LNA optimized for operation at 24.5 GHz frequency, targeting 6G and beyond wireless communication applications. The proposed LNA employs three stages with a cascode topology at the first stage and follow by a common source stage at second and third stage. The three stages help to achieve high gain, and the source degeneration inductor at the first stage helps to improve linearity. Extensive simulations were conducted using a 0.13-µm CMOS technology, demonstrating a peak gain of 21 dB and a noise figure of 5.6 dB at 24.5 GHz. The LNA also exhibits good linearity and stability over a wide bandwidth. The performance metrics were validated through simulation and comparison, showcasing the feasibility of the designed LNA for 6G applications. This work contributes to the advancement of CMOS-based radio frequency (RF) front-end designs for next-generation wireless communication systems.
Lack of additional benefit from slow rewarming after therapeutic hypothermia for ischaemic brain injury in near‐term fetal sheep
Authors: McDouall Alice , Zhou Kelly Q. , Wassink Guido , Davies Anthony , Bennet Laura , Gunn Alistair J. , Davidson Joanne O. 
Published: November 2024

AbstractThe optimal rate of rewarming after therapeutic hypothermia is unclear. Slow rewarming may reduce cardiovascular instability and rebound seizures, but there is little controlled evidence to support this. The present study aimed to determine whether slow rewarming can improve neuroprotection after 72 h of hypothermia. Fetal sheep (0.85 gestation) received sham occlusion (n = 8) or 30 min of global cerebral ischaemia followed by normothermia (n = 7), or hypothermia from 3 to 72 h with either fast, spontaneous rewarming within 1 h (n = 8) or slow rewarming at 0.5°C h−1 over 10 h (n = 8). Hypothermia improved EEG and spectral edge recovery, with no significant difference between fast and slow rewarming. Hypothermia reduced the number of seizures, with no significant difference in seizure activity between fast and slow rewarming. Hypothermia improved neuronal survival in the cortex, CA1, CA3, CA4 and dentate gyrus regions of the hippocampus, with no significant difference between fast and slow rewarming. Hypothermia attenuated microglia counts in the cortex, with no significant difference between fast and slow rewarming. The rate of rewarming after a clinically relevant duration of hypothermia did not affect neurophysiological recovery, neuronal survival or attenuation of microglia after global cerebral ischaemia in term‐equivalent fetal sheep.
imageKey points
The rate of rewarming after 72 h of hypothermia did not affect recovery of EEG or spectral edge.
There was no difference in the occurrence of seizures as a result of the rate of rewarming after hypothermia.
The rate of rewarming after 72 h of hypothermia did not affect neuronal survival in the cortex or hippocampus.
Geo-classification of drug-resistant travel-associated
Plasmodium falciparum
using
Pfs47
and
Pfcpmp
gene sequences (USA, 2018–2021)
Authors: Pierre-Louis Edwin , Kelley Julia , Patel Dhruviben , Carlson Christina , Talundzic Eldin , Jacobson David , Barratt Joel Leonard Nicholas 
Published: November 2024

ABSTRACT

Travel-related malaria is regularly encountered in the United States, and the U.S. Centers for Disease Control and Prevention (CDC) characterizes
Plasmodium falciparum
drug-resistance genotypes routinely for travel-related cases. An important aspect of antimalarial drug resistance is understanding its geographic distribution. However, specimens submitted to CDC laboratories may have missing, incomplete, or inaccurate travel data. To complement genotyping for drug-resistance markers
Pfcrt
,
Pfmdr1
,
Pfk13
,
Pfdhps
,
Pfdhfr
, and
PfcytB
at CDC, amplicons of
Pfs47
and
Pfcpmp
are also sequenced as markers of geographic origin. Here, a bi-allele likelihood (BALK) classifier was trained using
Pfs47
and
Pfcpmp
sequences from published
P. falciparum
genomes of known geographic origin to classify clinical genotypes to a continent. Among
P. falciparum
-positive blood samples received at CDC for drug-resistance genotyping from 2018 to 2021 (
n
= 380), 240 included a travel history with the submission materials, though 6 were excluded due to low sequence quality. Classifications obtained for the remaining 234 were compared to their travel histories. Classification results were over 96% congruent with reported travel for clinical samples, and with collection sites for field isolates. Among travel-related samples, only two incongruent results occurred; a specimen submitted citing Costa Rican travel classified to Africa, and a specimen with travel referencing Sierra Leone classified to Asia. Subsequently, the classifier was applied to specimens with unreported travel histories (
n
= 140; 5 were excluded due to low sequence quality). For the remaining 135 samples, geographic classification data were paired with results generated using CDC’s Malaria Resistance Surveillance (MaRS) protocol, which detects single-nucleotide polymorphisms in and generates haplotypes for
Pfcrt
,
Pfmdr1
,
Pfk13
,
Pfdhps
,
Pfdhfr
, and
PfcytB
. Given the importance of understanding the geographic distribution of antimalarial drug resistance, this work will complement domestic surveillance efforts by expanding knowledge on the geographic origin of drug-resistant
P. falciparum
entering the USA.
Development of a simple, low-cost, blue light-emitting diode illuminator for hands-on training of DNA detection experiments using agarose gel electrophoresis
Authors: Honda Haruka , Miyajima Hisayuki , Miyamoto Noritaka , Yoshida Keigo , Tanaka Yuichi 
Published: November 2024

ABSTRACT

DNA detection by agarose gel electrophoresis (AGE) is commonly used in molecular biology. AGE is a separation method that provides opportunities for students to learn about the topology and size of DNA molecules. Recently, several fluorescent dyes have been used for DNA staining owing to their convenience, safety, reduced toxicity, and high sensitivity. A blue light-emitting diode (LED) transilluminator is required to detect DNA using fluorescent dyes; however, the associated high cost may limit its availability in classrooms or small laboratories. Therefore, we have designed a simple, low-cost blue LED illuminator to enable easy assembly for instructors and students. We evaluated the performance of the proposed illuminator by observing fluorescent dye-stained DNA markers using AGE, revealing clear DNA marker bands. Despite its limited functionality, the ease of construction and affordability of the proposed illuminator make it sufficient for hands-on molecular biology training in classrooms, thereby enhancing the learning environment and educational efficiency.
Metagenomic sequencing of cyanobacterial-dominated Lake Victoria—an African Great Lake
Authors: Zepernick Brittany N. , Hart Lauren N. , Natwora Kaela E. , Brown Katelyn M. , Obuya Julia A. , Olokotum Mark , Okech Eric O. , Keating Natalie G. , Lomeo Davide , Tebbs Emma J. ,   NSF-IRES 2022-2023 Lake Victoria Research Consortium, Sheik Cody S. , Sherman David H. , Dick Gregory J. , Wilhelm Steven W. , Drouillard Ken G. , Lawrence Theodore , Getabu Albert , Owuor Bethwell , Shitandi Anakalo , Omondi Reuben , Njiru James , Sitoki Lewis , Otiso Kefa M. , McKay R. Michael L. , Bullerjahn George S. , Achieng Dorine , Achieng Tonny , Achiya James , Abibo Adem Jack , Adhikari Anjana , Allan Trinity , Barker Katelyn B. , Barnard Malcolm A. , Basweti George M. , Beal Max , Byrne Aidan , Chepkirui Mercy , Cody William R. , Nasrin Khan Nusrat , Kiteresi Linet I. , Miruka Jared B. , Mohney Samantha , Moseti Martha , Okutoyi Pamela , Otieno Dennis , Owino Omondi A. , Owoko Winnie , Radock Lisa , Stoll Jordyn , Swaleh Mariam , Wagner Ryan S. , Varga Emily 
Published: November 2024

ABSTRACT

We report 40 metagenomic libraries collected from the Winam Gulf of Lake Victoria during May–July of 2022–2023 and an additional eight opportunistic libraries from adjacent Lakes Simbi, Naivasha, and regional river systems. The sampling period captured cyanobacterial bloom events – shedding insight onto community composition and genomic potential.
Understanding brewing trait inheritance in
de novo
Lager yeast hybrids
Authors: Zavaleta Vasni , Pérez-Través Laura , Saona Luis A. , Villarroel Carlos A. , Querol Amparo , Cubillos Francisco A. 
Published: November 2024

ABSTRACT

Hybridization between
Saccharomyces cerevisiae
and
Saccharomyces eubayanus
resulted in the emergence of
S. pastorianus
, a crucial yeast for lager fermentation. However, our understanding of hybridization success and hybrid vigor between these two species remains limited due to the scarcity of
S. eubayanus
parental strains. Here, we explore hybridization success and the impact of hybridization on fermentation performance and volatile compound profiles in newly formed lager hybrids. By selecting parental candidates spanning a diverse array of lineages from both species, we reveal that the Beer and PB-2 lineages exhibit high rates of hybridization success in
S. cerevisiae
and
S. eubayanus
, respectively. Polyploid hybrids were generated through a spontaneous diploid hybridization technique (rare-mating), revealing a prevalence of triploids and diploids over tetraploids. Despite the absence of heterosis in fermentative capacity, hybrids displayed phenotypic variability, notably influenced by maltotriose consumption. Interestingly, ploidy levels did not significantly correlate with fermentative capacity, although triploids exhibited greater phenotypic variability. The
S. cerevisiae
parental lineages primarily influenced volatile compound profiles, with significant differences in aroma production. Interestingly, hybrids emerging from the Beer
S. cerevisiae
parental lineages exhibited a volatile compound profile resembling the corresponding
S. eubayanus
parent. This pattern may result from the dominant inheritance of the
S. eubayanus
aroma profile, as suggested by the over-expression of genes related to alcohol metabolism and acetate synthesis in hybrids including the Beer
S. cerevisiae
lineage. Our findings suggest complex interactions between parental lineages and hybridization outcomes, highlighting the potential for creating yeasts with distinct brewing traits through hybridization strategies.

IMPORTANCE

Our study investigates the principles of lager yeast hybridization between
Saccharomyces cerevisiae
and
Saccharomyces eubayanus
. This process gave rise to the lager yeast
Saccharomyces pastorianus
. By examining how these novel hybrids perform during fermentation and the aromas they produce, we uncover the genetic bases of brewing trait inheritance. We successfully generated polyploid hybrids using diverse strains and lineages from both parent species, predominantly triploids and diploids. Although these hybrids did not show improved fermentation capacity, they exhibited varied traits, especially in utilizing maltotriose, a key sugar in brewing. Remarkably, the aroma profiles of these hybrids were primarily influenced by the
S. cerevisiae
parent, with Beer lineage hybrids adopting aroma characteristics from their
S. eubayanus
parent. These insights reveal the complex genetic interactions in hybrid yeasts, opening new possibilities for crafting unique brewing yeasts with desirable traits.
Genome streamlining of
Pseudomonas putida
B6-2 for bioremediation
Authors: Fan Siqing , Ren Hao , Fu Xueni , Kong Xiangyu , Wu Hao , Lu Zhenmei 
Published: November 2024

ABSTRACT

Microbial transformation is a favored approach for environmental remediation. However, the effectiveness of microbial remediation has been limited by the lack of chassis cells with satisfactory contaminant degradation performance.
Pseudomonas putida
B6-2, with a wide substrate spectrum and high solvent tolerance, is a chassis strain with great potential for application in environmental remediation. Here, guided by bioinformatic analyses and genome-scale metabolic model (GEM) predictions, we successfully optimized
P. putida
B6-2 by rationally reducing its nonessential genetic components and generating a more robust genome-streamlined strain,
P. putida
BGR4. Several improvements were observed compared with the original
P. putida
B6-2 strain, including a 1.4 × 10
5
-fold increase in electroporation efficiency, an 8.3-fold increase in conjugation efficiency, improved glycerol utilization capability, and increased phenol utilization after heterologous expression of the phenol monooxygenase encoded by
dmpKLMNOP
. Additionally,
P. putida
BGR4 exhibited enhanced tolerance to several stressors, including starvation, oxidative stress, and DNA damage. Transcriptomic analysis revealed that genome streamlining led to the upregulation of genes involved in the “carbon metabolism” and “tricarboxylic acid cycle” pathways in
P. putida
BGR4, which likely contributed to the superior phenotype of
P. putida
BGR4 in terms of carbon source utilization and contaminant degradation capabilities. Furthermore, the absence of four prophages was identified as a potential cause of the enhanced stress resistance observed in
P. putida
BGR4. Overall, we developed a combined genome-streamlining strategy involving bioinformatic analyses and GEM predictions and generated a more robust chassis strain,
P. putida
BGR4, which expands the repertoire of chassis cells for environmental remediation.

IMPORTANCE

Despite the development of many chassis cells, there is still a lack of robust chassis cells with satisfactory contaminant degradation performance. Targeted genome streamlining is an effective way to provide powerful chassis cells. However, genome streamlining does not always lead to the improved phenotypes of genome-streamlined chassis cells. In this research, a novel procedure that combined bioinformatic analyses and GEM predictions was proposed to guide genome streamlining and predict the effects of genome streamlining. This genome streamlining procedure was successfully applied to
Pseudomonas putida
B6-2, which was a chassis cell with great potential for application in environmental remediation and resulted in the generation of a more robust chassis cell,
P. putida
BGR4, thereby providing a superior chassis cell for efficient and sustainable environmental remediation and a valuable framework for guiding the genome streamlining of strains for other applications.
Doxifluridine effectively kills antibiotic-resistant
Staphylococcus aureus
in chronic obstructive pulmonary disease
Authors: Zhang Lianshen , Zhang Yingzhang , Tian Lijie , Shen Qiang , Ma Xiaolong 
Published: November 2024

ABSTRACT

Chronic obstructive pulmonary disease (COPD) is a leading cause of morbidity and mortality globally, often exacerbated by infections such as methicillin-resistant
Staphylococcus aureus
(MRSA). The rise in antibiotic-resistant strains complicates treatment and underscores the need for novel therapeutic drugs. In this paper, we further investigated the antimicrobial potential of a fluoropyrimidine anticancer drug doxifluridine against multidrug-resistant
S. aureus
. Determination of minimum inhibitory concentration (MIC) or minimum bactericidal concentration (MBC), monitoring of growth curve, time-kill assays, biofilm bactericidal assays, and chequerboard studies were conducted to evaluate the antibacterial efficacy of doxifluridine. Safety was assessed via hemolysis and cytotoxicity assays, and an
in vivo Galleria mellonella
larvae model was employed to test protective effects. Doxifluridine demonstrated significant antibacterial activity against clinical multidrug resistance (MDR)
S. aureus
isolates, with MIC and MBC values ranging from 0.5 to 2 µg/mL and 1 to 4 µg/mL, respectively. The results revealed doxifluridine’s potent bactericidal effects within 8 hours. Moreover, doxifluridine-treated bacteria showed a substantial reduction in biofilm mass and viability. Furthermore, chequerboard assays indicated synergistic interactions between doxifluridine and other antibiotics, reducing MIC values by two- to eightfold. More importantly, safety evaluations confirmed that doxifluridine did not exhibit hemolytic toxicity or cytotoxicity. Finally, doxifluridine significantly increased the survival rate of MRSA-infected
G. mellonella
larvae
in vivo
. In brief, doxifluridine exhibited promising
in vitro
and
in vivo
antibacterial activity against MRSA, suggesting its potential as a repurposed drug for treating resistant bacterial infections in COPD patients.

IMPORTANCE

The study provides robust evidence for the antibacterial efficacy of doxifluridine against Methicillin-resistant
Staphylococcus aureus
in chronic obstructive pulmonary disease (COPD) patients. Its rapid action, ability to disrupt biofilms, and synergistic effects with other antibiotics, combined with a favorable safety profile, highlight its potential as a repurposed therapeutic agent. Future clinical trials will be essential to confirm these findings and pave the way for its integration into clinical practice. This work not only provides candidate for tackling the management of bacterial infections in COPD but also exemplifies the potential of drug repurposing in combating antibiotic-resistant infections.