bluuebunny/crossref_metadata_2025_split huggingface dataset:
Co-inheritance of recombined chromatids maintains heterozygosity in a parthenogenetic ant
Authors: Lacy Kip D. , Hart Taylor , Kronauer Daniel J. C. 
Published: July 2024

AbstractAccording to Mendel’s second law, chromosomes segregate randomly in meiosis. Non-random segregation is primarily known for cases of selfish meiotic drive in females, in which particular alleles bias their own transmission into the oocyte. Here we report a rare example of unselfish meiotic drive for crossover inheritance in the clonal raider ant, Ooceraea biroi, in which both alleles are co-inherited at all loci across the entire genome. This species produces diploid offspring parthenogenetically via fusion of two haploid nuclei from the same meiosis. This process should cause rapid genotypic degeneration due to loss of heterozygosity, which results if crossover recombination is followed by random (Mendelian) segregation of chromosomes. However, by comparing whole genomes of mothers and daughters, we show that loss of heterozygosity is exceedingly rare, raising the possibility that crossovers are infrequent or absent in O. biroi meiosis. Using a combination of cytology and whole-genome sequencing, we show that crossover recombination is, in fact, common but that loss of heterozygosity is avoided because crossover products are faithfully co-inherited. This results from a programmed violation of Mendel’s law of segregation, such that crossover products segregate together rather than randomly. This discovery highlights an extreme example of cellular ‘memory’ of crossovers, which could be a common yet cryptic feature of chromosomal segregation.
The Tropical Andes Biodiversity Hotspot: A Comprehensive Dataset for the Mira-Mataje Binational Basins
Authors: Yánez-Muñoz Mario H. , Jarrín-V. Pablo , Brito M. Jorge , Román-RR Roberto , Astorquiza Juranny M. , Baca Aida E. , Baker Paul A. , Bejarano-Muñoz Patricia , Cuesta R. Eric Y. , Freire Efraín , Garzón César , Gómez-Paredes Jorge , Klinger William , Lagos Luz E. , Medina Wilderson , Mena-Valenzuela Patricio , Mosquera R. Luis J. , Mosquera M. Robinson S. , Murillo Yirsela , Murillo A. Yiscar D. , Nagle R. Edsson , Narváez Germán , Pimm Stuart , Proaño Cecilia , Prieto A. Francisco J. , Quezada Zoraida , Ramírez Giovanny , Rengifo I. Reimer , Rentería M. Luis E. , Urgilés-Merchán Miguel A. , Vargas Lady , Valdospinos Carla , Valolyes Zulmary , Inclán Diego J. 
Published: July 2024

AbstractWe present a flora and fauna dataset for the Mira-Mataje binational basins. This is an area shared between southwestern Colombia and northwestern Ecuador, where both the Chocó and Tropical Andes biodiversity hotspots converge. We systematized data from 120 sources in the Darwin Core Archive (DwC-A) standard and geospatial vector data format for geographic information systems (GIS) (shapefiles). Sources included natural history museums, published literature, and citizen science repositories across 13 countries. The resulting database has 33,460 records from 6,821 species, of which 540 have been recorded as endemic, and 612 as threatened. The diversity represented in the dataset is equivalent to 10% of the total plant species and 26% of the total terrestrial vertebrate species in both hotspots. The dataset can be used to estimate and compare biodiversity patterns with environmental parameters and provide value to ecosystems, ecoregions, and protected areas. The dataset is a baseline for future assessments of biodiversity in the face of environmental degradation, climate change, and accelerated extinction processes.
Refinement of rice blast disease resistance QTLs and gene networks through meta-QTL analysis
Authors: Devanna Basavantraya Navadagi , Sucharita Sumali , Sunitha N. C. , Anilkumar C. , Singh Pankaj K. , Pramesh D. , Samantaray Sanghamitra , Behera Lambodar , Katara Jawahar Lal , Parameswaran C. , Rout Prachitara , Sabarinathan Selvaraj , Rajashekara Hosahatti , Sharma Tilak Raj 
Published: July 2024

AbstractRice blast disease is the most devastating disease constraining crop productivity. Vertical resistance to blast disease is widely studied despite its instability. Clusters of genes or QTLs conferring blast resistance that offer durable horizontal resistance are important in resistance breeding. In this study, we aimed to refine the reported QTLs and identify stable meta-QTLs (MQTLs) associated with rice blast resistance. A total of 435 QTLs were used to project 71 MQTLs across all the rice chromosomes. As many as 199 putative rice blast resistance genes were identified within 53 MQTL regions. The genes included 48 characterized resistance gene analogs and related proteins, such as NBS–LRR type, LRR receptor-like kinase, NB-ARC domain, pathogenesis-related TF/ERF domain, elicitor-induced defense and proteins involved in defense signaling. MQTL regions with clusters of RGA were also identified. Fifteen highly significant MQTLs included 29 candidate genes and genes characterized for blast resistance, such as Piz, Nbs-Pi9, pi55-1, pi55-2, Pi3/Pi5-1, Pi3/Pi5-2, Pikh, Pi54, Pik/Pikm/Pikp, Pb1 and Pb2. Furthermore, the candidate genes (42) were associated with differential expression (in silico) in compatible and incompatible reactions upon disease infection. Moreover, nearly half of the genes within the MQTL regions were orthologous to those in O. sativa indica, Z. mays and A. thaliana, which confirmed their significance. The peak markers within three significant MQTLs differentiated blast-resistant and susceptible lines and serve as potential surrogates for the selection of blast-resistant lines. These MQTLs are potential candidates for durable and broad-spectrum rice blast resistance and could be utilized in blast resistance breeding.
Magnetic field and initial stress on a rotating photothermal semiconductor medium with ramp type heating and internal heat source
Authors: Salah Doaa M. , Abd-Alla A. M. , Abo-Dahab S. M. , Alharbi F. M. , Abdelhafez M. A. 
Published: July 2024

AbstractThis manuscript addresses a significant research gap in the study by employing a mathematical model of photo thermoelastic wave propagation in a rotator semiconductor medium under the effect of a magnetic field and initial stress, as well as ramp-type heating. The considered model is formulated during the photothermal theory and in two-dimensional (2D) electronic-elastic deformation. The governing equations represent the interaction between the primary physical parameters throughout the process of photothermal transfer. Computational simulations are performed to determine the temperature, carrier density, displacement components, normal stress, and shear stress using the application of Lame’s potential and normal mode analysis. Numerical calculations are carried out and graphically displayed for an isotropic semiconductor like silicon (Si) material. Furthermore, comparisons are made with the previous results obtained by the others, as well as in the presence and absence of magnetic field, rotation, and initial stress. The obtained results illustrate that the rotation, initial stress, magnetic field, and ramp-type heating parameter all have significant effects. This investigation provides valuable insights into the synergistic dynamics among a magnetization constituent, semiconducture structures, and wave propagation, enabling advancements in nuclear reactors' construction, operation, electrical circuits, and solar cells.
Predicting pathological complete response after neoadjuvant chemotherapy in breast cancer by clinicopathological indicators and ultrasound parameters using a nomogram
Authors: Zhang Tingjian , Liu Yuyao , Tian Tian 
Published: July 2024

AbstractThe study explored the impact of pretreatment serum albumin-to-alkaline phosphatase ratio (AAPR) and changes in tumor blood supply on pathological complete response (pCR) in breast cancer (BC) patients following neoadjuvant chemotherapy (NACT). Additionally, a nomogram for predicting pCR was established and validated. The study included BC patients undergoing NACT at Yongchuan Hospital of Chongqing Medical University from January 2019 to October 2023. We analyzed the correlation between pCR and clinicopathological factors, as well as tumor ultrasound features, using chi-square or Fisher's exact test. We developed and validated a nomogram predicting pCR based on regression analysis results. The study included 176 BC patients. Logistic regression analysis identified AAPR [odds ratio (OR) 2.616, 95% confidence interval (CI) 1.140–5.998, P = 0.023], changes in tumor blood supply after two NACT cycles (OR 2.247, 95%CI 1.071–4.716, P = 0.032), tumor histological grade (OR 3.843, 95%CI 1.286–10.659, P = 0.010), and HER2 status (OR 2.776, 95%CI 1.057–7.240, P = 0.038) as independent predictors of pCR after NACT. The nomogram, based on AAPR, changes in tumor blood supply after two NACT cycles, tumor histological grade, and HER2 status, demonstrated a good predictive capability.
Improvement of Bacillus subtilis PI agarase production, hydrolysate scavenging capability assessment, and saccharification of algal biomass for green ethanol generation
Authors: Goda Doaa A. , Shalaby Nagham H. , Soliman Nadia A. 
Published: July 2024

AbstractThe goal of the current work was to optimize the growth parameters needed to manufacture agarase enzyme from a non-marine PI strain of Bacillus subtilis on an agar-based medium. Using Plackett–Burman design (PBD), nine process parameters were evaluated, and agar, peptone, and yeast-extract were identified as the most significant independent factors influencing agarase production with confidence levels more than 90%. To evaluate the optimal concentrations of the indicated process parameters on agarase production, the Box–Behnken design (BBD) was applied. After optimization, B. subtilis strain PI produced 119.8 U/ml of agarase, representing a 1.36-fold increase. In addition the agar hydrolysate fermented products contain the liberated oligosaccharide acts as strong antioxidant which has 62.4% scavenging activity. Also, the agarase yields increased (1141.12, 1350.253, 1684.854 and 1921.863 U/ml) after substitution the agar with algal biomass of Carolina officinalis at different concentrations (2, 5, 10 and 15%), respectively. After completing the saccharification process, the resulted hydrolysate was used to produce ethanol through fermentation with Pichia pastoris yeast strain as an economical method giving yields (6.68317, 7.09748, 7.75648 and 8.22332 mg/ml), that are higher than using yeast extract peptone dextrose (YPD) medium (4.461 mg/ml).
Systematic analysis of microorganisms’ metabolism for selective targeting
Authors: Dehghan Manshadi Mehdi , Setoodeh Payam , Zare Habil 
Published: July 2024

AbstractSelective drugs with a relatively narrow spectrum can reduce the side effects of treatments compared to broad-spectrum antibiotics by specifically targeting the pathogens responsible for infection. Furthermore, combating an infectious pathogen, especially a drug-resistant microorganism, is more efficient by attacking multiple targets. Here, we combined synthetic lethality with selective drug targeting to identify multi-target and organism-specific potential drug candidates by systematically analyzing the genome-scale metabolic models of six different microorganisms. By considering microorganisms as targeted or conserved in groups ranging from one to six members, we designed 665 individual case studies. For each case, we identified single essential reactions as well as double, triple, and quadruple synthetic lethal reaction sets that are lethal for targeted microorganisms and neutral for conserved ones. As expected, the number of obtained solutions for each case depends on the genomic similarity between the studied microorganisms. Mapping the identified potential drug targets to their corresponding pathways highlighted the importance of key subsystems such as cell envelope biosynthesis, glycerophospholipid metabolism, membrane lipid metabolism, and the nucleotide salvage pathway. To assist in the validation and further investigation of our proposed potential drug targets, we introduced two sets of targets that can theoretically address a substantial portion of the 665 cases. We expect that the obtained solutions provide valuable insights into designing narrow-spectrum drugs that selectively cause system-wide damage only to the target microorganisms.
CXCL9, IL2RB, and SPP1, potential diagnostic biomarkers in the co-morbidity pattern of atherosclerosis and non-alcoholic steatohepatitis
Authors: Wu Xize , Yuan Changbin , Pan Jiaxiang , Zhou Yi , Pan Xue , Kang Jian , Ren Lihong , Gong Lihong , Li Yue 
Published: July 2024

AbstractNon-alcoholic steatohepatitis (NASH) is a hepatocyte inflammation based on hepatocellular steatosis, yet there is no effective drug treatment. Atherosclerosis (AS) is caused by lipid deposition in the endothelium, which can lead to various cardiovascular diseases. NASH and AS share common risk factors, and NASH can also elevate the risk of AS, causing a higher morbidity and mortality rate for atherosclerotic heart disease. Therefore, timely detection and diagnosis of NASH and AS are particularly important. In this study, differential gene expression analysis and weighted gene co-expression network analysis were performed on the AS (GSE100927) and NASH (GSE89632) datasets to obtain common crosstalk genes, respectively. Then, candidate Hub genes were screened using four topological algorithms and externally validated in the GSE43292 and GSE63067 datasets to obtain Hub genes. Furthermore, immune infiltration analysis and gene set variation analysis were performed on the Hub genes to explore the underlying mechanisms. The DGIbd database was used to screen candidate drugs for AS and NASH. Finally, a NASH model was constructed using free fatty acid-induced human L02 cells, an AS model was constructed using lipopolysaccharide-induced HUVECs, and a co-morbidity model was constructed using L02 cells and HUVECs to verify Hub gene expression. The result showed that a total of 113 genes common to both AS and NASH were identified as crosstalk genes, and enrichment analysis indicated that these genes were mainly involved in the regulation of immune and metabolism-related pathways. 28 candidate Hub genes were screened according to four topological algorithms, and CXCL9, IL2RB, and SPP1 were identified as Hub genes after in vitro experiments and external dataset validation. The ROC curves and SVM modeling demonstrated the good diagnostic efficacy of these three Hub genes. In addition, the Hub genes are strongly associated with immune cell infiltration, especially macrophages and γ–δ T cell infiltration. Finally, five potential therapeutic drugs were identified. has-miR-185 and hsa-miR-335 were closely related to AS and NASH. This study demonstrates that CXCL9, IL2RB, and SPP1 may serve as potential biomarkers for the diagnosis of the co-morbidity patterns of AS and NASH and as potential targets for drug therapy.
A microtomographic and histopathological evaluation of dental cements as late-stage peri-implant complication in a rat model
Authors: Lakkasetter Chandrashekar Bhuvana , Biguetti Claudia C. , Arteaga Alexandra , Miramontes Andres J. , Rios Evelin , Rodrigues Danieli C. 
Published: July 2024

AbstractCement mediated peri-implantitis accounts for 1.9–75% of dental implant failures associated with peri-implant diseases. This study evaluated the biological impact of dental cements on osseointegrated implants using Lewis rats. Twenty-two rats were distributed into 6 groups: negative control (NC) soft diet (SD), and hard diet (HD); positive control SD and HD (n = 3); Implant + bio-ceramic Cement (BC) SD and HD which included contralateral Sham sites (n = 5). Titanium implants were placed on either side of the maxillae and allowed to heal for 14 days. Later, both sides of experimental groups underwent a re-entry surgery to simulate clinical cementation. The right side received 0.60 mg of BC. At 14 days post cement application, maxillae were harvested for clinical, microtomographic, and histological evaluations. Clinical and microtomographic evaluations indicated evidence of extensive inflammation and circumferential bone resorption around BC implants in comparison to NC. Histology revealed cement particles surrounded by inflammatory infiltrate in the implant area accompanied by biofilm for SD groups. Both sides of BC indicated intensive bone resorption accompanied by signs of osteolysis when compared to NC. Cemented groups depicted significantly lower bone to implant contact when compared to NC. In conclusion, residual cement extravasation negatively impacted osseointegrated implants after re-entry surgeries.
Effect of gamma irradiation on properties of the synthesized PANI-Cu nanoparticles assimilated into PS polymer for electromagnetic interference shielding application
Authors: Bekhit Mohamad , Fathy E. S. , Sharaf A. 
Published: July 2024

AbstractConductive polymer nanocomposites for electromagnetic interference (EMI) shielding are important materials that can be combat the increasingly dangerous radiation pollution arising from electronic equipment and our surrounding environment. In this work, we have synthesized polyaniline-copper nanoparticles (PANI-Cu NPs) by the copper salt based oxidative polymerization method at room temperature and then added with different concentration (0, 1, 3 and 5 wt%) in polystyrene polymer forming PS/ PANI-Cu nanocomposites films by means of the traditional solution casting technique. The formed PANI-Cu NPs were investigated by UV/Vis spectroscopy, X-ray diffraction (XRD), transmission electron microscopy (TEM) and SEM/EDX elemental mapping techniques. On the other hand, the prepared PS/PANI-Cu nanocomposites films were evaluated by UV and SEM, the mechanical properties of the nanocomposites films were evaluated and showed an improvement by added PANI-Cu NPs up to 3 wt% and 50 kGy gamma exposure dose. The PS/PANI-Cu nanocomposites films were examined as electromagnetic interference shielding material. Electromagnetic shielding effectiveness of the produced nanocomposites were tested in the X-band of the radio frequency range namely from 8 to 12 GHz using the vector network analyzer (VNA) and a proper wave guide. All samples were studied before and after 50 kGy gamma-ray irradiation under the same condition of pressure and temperature. The results showed that the nanocomposites have improved shielding properties.
Protozoan communities serve as a strong indicator of water quality in the Nile River
Authors: El-Tohamy Wael S. , Taher Mohamed E. , Ghoneim Ahmed M. , Hopcroft Russell R. 
Published: July 2024

AbstractThe relationship between the protozoan communities and environmental variables was studied in the Nile River to evaluate their potential as water quality indicators. Protozoans were sampled monthly at six sampling sites in the Nile's Damietta Branch across a spatial gradient of environmental conditions during a 1-year cycle (February 2016–January 2017). The Protozoa community was comprised of 54 species belonging to six main heterotrophic Protozoa phyla. The abundance (average, 1089 ± 576.18 individuals L−1) and biomass (average, 86.60 ± 106.13 μg L−1) were comparable between sites. Ciliates comprised the majority of protozoan species richness (30 species), abundance (79.72%), and biomass (82.90%). Cluster analysis resulted in the distribution of protozoan species into three groups, with the most dominant species being the omnivorous ciliate Paradileptus elephantinus. Aluminium, fluoride, and turbidity negatively affected abundance and biomass, while dissolved oxygen and potassium positively impacted biomass. Of the dominant species recorded over the study area, the amoebozoa Centropyxis aculeata was associated with runoff variables, while the bacterivorous ciliates Colpidium colpoda, Glaucoma scintillans, and Vorticella convallaria were related to the abundance of heterotrophic bacteria, phytoplankton biomass, and total organic carbon. Total dissolved salts, PO4, NH3, NO2, dissolved oxygen, and total organic carbon were the strongest causative factors for protozoa distribution. The α-Mesosaprobic environment at site VI confirmed a high load of agricultural runoffs compared to other sites. This study demonstrates that protozoans can be a potential bioindicator of water quality status in this subtropical freshwater river system.
Rifabutin loaded inhalable β-glucan microparticle based drug delivery system for pulmonary TB
Authors: Ahmad Firoz , Ahmad Shad , Upadhyay Tarun Kumar , Singh Sanjay , Khubaib Mohd , Singh Jyotsna , Saeed Mohd , Ahmad Irfan , Al-Keridis Lamya Ahmed , Sharma Rolee 
Published: July 2024

AbstractInhalable microparticle-based anti TB drug delivery systems are being investigated extensively for Tuberculosis [TB] treatment as they offer efficient and deep lung deposition with several advantages over conventional routes. It can reduce the drug dose, treatment duration and toxic effects and optimize the drug bioavailability. Yeast derived β-glucan is a β-[1–3/1–6] linked biocompatible polymer and used as carrier for various biomolecules. Due to presence of glucan chains, particulate glucans act as PAMP and thereby gets internalized via receptor mediated phagocytosis by the macrophages. In this study, β-glucan microparticles were prepared by adding l-leucine as excipient, and exhibited 70% drug [Rifabutin] loading efficiency. Further, the sizing and SEM data of particles revealed a size of 2–4 µm with spherical dimensions. The FTIR and HPLC data confirmed the β-glucan composition and drug encapsulations efficiency of the particles. The mass median aerodynamic diameter [MMAD] and geometric standard deviation [GSD] data indicated that these particles are inhalable in nature and have better thermal stability as per DSC thermogram. These particles were found to be non-toxic upto a concentration of 80 µg/ml and were found to be readily phagocytosed by human macrophage cells in-vitro as well as in-vivo by lung alveolar macrophage. This study provides a framework for future design of inhalable β-glucan particle based host-directed drug delivery system against pulmonary TB.
Association of dietary and lifestyle inflammation score (DLIS) with chronic migraine in women: a cross-sectional study
Authors: Bakhshimoghaddam Farnush , Shalilahmadi Davood , Mahdavi Reza , Nikniaz Zeinab , Karandish Majid , Hajjarzadeh Samaneh 
Published: July 2024

AbstractDue to more frequent and intense attacks, chronic migraine (CM) sufferers usually report more disability compared to patients with episodic migraine (EM). There is increasing evidence that points to inflammatory diet and lifestyle as a probable underlying cause of migraine. The present study investigated the association of dietary and lifestyle inflammation scores (DLIS) with the odds of CM in Iranian women. In the current study, 285 women with migraine enrolled. Migraine was diagnosed by a single neurologist based on the third edition of the International Classification of Headache Disorders (ICHD-III). The women were categorized into CM and EM groups based on their attack frequency per month. Adherence to the dietary inflammation score (DIS), Lifestyle Inflammatory Score (LIS), and DLIS (DIS + LIS) was assessed based on last year’s dietary intakes collected using a semi-quantitative food frequency questionnaire (FFQ). The Odds Ratio (OR) for CM across the DIS, LIS, and DLIS tertiles were assessed through logistic regression. Most of the participants were overweight or obese (74.4%). The percentage of women with CM was 40.7%. Women with CM had significantly higher DIS (P = 0.002) and DLIS (P = 0.04) than women with EM. There was a significant positive association between CM and DIS. Those in the third tertile of the DIS had almost two times higher chance of experiencing chronic migraine compared with those in the first tertile [OR = 2.02; 95% CI 1.06–3.82; P = 0.03]. the P-value for the trend also was significant (0.03). In terms of LIS and DLIS tertiles, no significant association was observed. Adherence to the more inflammatory diets was associated with higher chances of experiencing CM in women.