bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evidence of population genetic structure in Ecuadorian Andean bears
Authors: Cueva Dario F. , Zug Rebecca , Pozo María José , Molina Santiago , Cisneros Rodrigo , Bustamante Martín R. , Torres María de Lourdes 
Published: February 2024

AbstractWildlife conservation in Andean countries is a global priority because of the high levels of biodiversity and endemism. Historically, these countries have had limited resources to monitor wildlife (e.g., through genetic tools) and establish conservation programs. Focusing on the study and emblematic use of a few charismatic species has been a strategic approach to direct efforts for conservation and development planning. Consequently, the Andean bear is a flagship and umbrella species for highly biodiverse Andean countries like Ecuador. The few studies exploring the population genetics of this species have concluded that it has low genetic diversity and few units for conservation as populations appear to be well connected. However, these results might be attributed to ascertainment bias as studies have been performed with heterologous molecular markers. Here, using both mtDNA sequences and species-specific microsatellite markers, we show that Andean bears in Ecuador have population structure. Additionally, we found through the study of three Ecuadorian populations that the species might have a higher genetic diversity than we previously thought. These results could support the revision of research priorities, conservation, and planning strategies to improve connectivity for this species which occurs in crucial biodiversity hotspots.
Efficiency of transcription and translation of cell-free protein synthesis systems in cell-sized lipid vesicles with changing lipid composition determined by fluorescence measurements
Authors: Miwa Akari , Wakamori Masatoshi , Ariyoshi Tetsuro , Okada Yasushi , Shirouzu Mikako , Umehara Takashi , Kamiya Koki 
Published: February 2024

AbstractTo develop artificial cell models that mimic living cells, cell-sized lipid vesicles encapsulating cell-free protein synthesis (CFPS) systems are useful for protein expressions or artificial gene circuits for vesicle–vesicle communications. Therefore, investigating the transcriptional and translational properties of CFPS systems in lipid vesicles is important for maximizing the synthesis and functions of proteins. Although transcription and translation using CFPS systems inside lipid vesicles are more important than that outside lipid vesicles, the former processes are not investigated by changing the lipid composition of lipid vesicles. Herein, we investigated changes in transcription and translation using CFPS systems inside giant lipid vesicles (approximately 5–20 μm in diameter) caused by changing the lipid composition of lipid vesicles containing neutral, positively, and negatively charged lipids. After incubating for 30 min, 1 h, 2 h, and 4 h, the transcriptional and translational activities in these lipid vesicles were determined by detecting the fluorescence intensities of the fluorogenic RNA aptamer on the 3′-untranslated region of mRNA (transcription) and the fluorescent protein sfCherry (translation), respectively. The results revealed that transcriptional and translational activities in a lipid vesicle containing positively charged lipids were high when the protein was synthesized using the CFPS system inside the lipid vesicle. Thus, the present study provides an experimental basis for constructing complex artificial cell models using bottom-up approaches.
Multi-scale habitat modeling framework for predicting the potential distribution of sheep gastrointestinal nematodes across Iran’s three distinct climatic zones: a MaxEnt machine-learning algorithm
Authors: Meshgi Behnam , Hanafi-Bojd Ahmad Ali , Fathi Saeid , Modabbernia Galia , Meshgi Kourosh , Shadman Mohammad 
Published: February 2024

AbstractEcological niche models (ENMs) serve as valuable tools in assessing the potential species distribution, identifying crucial habitat components for species associations, and facilitating conservation efforts. The current study aimed to investigate the gastrointestinal nematodes (GINs) infection in sheep, predict and analyze their ecological niches and ranges, and identify the key bioclimatic variables influencing their distribution across three distinct climatic regions in Iran. In a cross-sectional study, a total of 2140 fecal samples were collected from semi-arid (n = 800), arid (n = 500), and humid-subtropical (n = 840) climates in East Azerbaijan, Kerman, and Guilan provinces, respectively. The flotation method was employed to assess stool samples, whereby the fecal egg count (the number of parasite eggs per gram [EPG]) was ascertained for each individual specimen. Employing a presence-only approach, the multi-scale maximum entropy (MaxEnt) method was used to model GINs' habitat suitability using 93 selected points/locations. The findings revealed that Guilan (34.2%) and East Azerbaijan (19.62%) exhibited the utmost proportion of Strongyle-type eggs. East Azerbaijan province also displayed the highest proportion of Marshallagia and Nematodirus, respectively (approximately 40% and 27%), followed by Guilan and Kerman provinces, while Kerman province had the highest proportion of Trichuris (approximately 15%). Ecological niche modeling revealed that the precipitation of the driest quarter (Bio17) exerted the most significant influence on Marshallagia, Nematodirus, Trichuris, and ُSُُُtrongyle-type eggs' presence in East Azerbaijan and Kerman provinces. For Guilan province, the most influential factor defining habitat suitability for Strongyle-type eggs, Marshallagia, and Nematodirus was increasing slope. Additionally, the distribution of Trichuris was most affected by the variable Bio2 in Guilan province. The study highlights the response of GINs to climate drivers in highly suitable regions, providing insights into ecologically favorable areas for GINs. In conclusion, this study provides a better understanding of GINs and the environmental factors influencing their transmission dynamics.
Exploration capacity versus specific enzymatic activity of ectomycorrhizas in response to primary productivity and soil phosphorus availability in Bornean tropical rainforests
Authors: Okada Kei-ichi , Yokoyama Daiki , Aiba Shin-ichiro , Kitayama Kanehiro 
Published: February 2024

AbstractEctomycorrhizal (ECM) fungi are functionally important in biogeochemical cycles in tropical ecosystems. Extracellular enzymatic activity of ECM on a ground-area basis is the product of two attributes; exploration capacity (ECM surface-area) and specific enzymatic activity. Here, we elucidated which attribute better explained the ECM enzymatic activity in response to different levels of soil phosphorus (P) and Nitrogen (N) availability in five Bornean tropical rainforests. We determined the surface area of ECM root tips as well as the enzymatic activities per ECM surface area for carbon (C), N and P degrading enzymes in each site. We evaluated the relationship of ECM enzyme activities with the resource availabilities of C (Above-ground net primary production; ANPP), N, and P of ECM by a generalized linear mixed model. The ECM enzymatic activities on a ground-area basis were more significantly determined by specific enzymatic activity than by the exploration capacity. Specific enzymatic activities were generally negatively affected by C (ANPP) and soil P availability. ECM fungi enhance the specific enzyme activity rather than the exploration capacity to maintain the capacity of nutrient acquisition. The less dependence of ECM fungi on the exploration capacity in these forests may be related to the limitation of C supply from host trees. We highlighted the adaptive mechanisms of ECM fungi on nutrient acquisition in tropical ecosystems through the response of enzymatic activity to nutrient availability across the elements.
Nutrient patterns in relation to insulin resistance and endothelial dysfunction in Iranian women
Authors: Dehghani Farimah , Hajhashemy Zahra , Keshteli Ammar Hassanzadeh , Yazdannik Ahmadreza , Falahi Ebrahim , Saneei Parvane , Esmaillzadeh Ahmad 
Published: February 2024

AbstractPrior studies have mainly focused on the association of one specific nutrient with insulin resistance (IR) and endothelial dysfunction and limited studies have assessed the association with different nutrient patterns (NPs). We examined the association between various NPs and IR and endothelial dysfunction among Iranian women. This cross-sectional study was carried out on a sample of 368 female nurses. A 106-items food frequency questionnaire (FFQ) was applied for dietary assessments. Using factor analysis, the relationships between NPs and markers of insulin resistance (HOMA-IR, HOMA-β, and QUICKY), and endothelial dysfunction (E-selectin, sICAM-1, and sVCAM-1) were assessed. Mean age and body mass index of participants were respectively 35.21 years and 24.04 kg/m2. Three major NPs were identified. NP1, named as “dairy, fruits, and vegetables” had high values of potassium, folate, vitamins A and C, magnesium, and beta carotene. No significant association was observed between this NP and insulin resistance or endothelial dysfunction indices. The second NP was full of chromium, selenium, copper, vitamin B6, monounsaturated fatty acid (MUFA), thiamin, vitamin D, and iron. Adherence to NP2 (named “legumes, nuts, and protein foods”) was associated with lower values of insulin (6.8 ± 1.1 versus 8.4 ± 1.1, P = 0.01), homeostasis model assessment-Insulin resistance (HOMA-IR) (1.3 ± 0.2 versus 1.7 ± 0.2, P = 0.02), and vascular adhesion molecule 1 (VCAM-1) (444.2 ± 27.9 versus 475.8 ± 28.4, P = 0.03). However, adherence to the third NP, rich in saturated fatty acid (SFA), cholesterol, sodium, zinc, vitamin E, and B12, described as “animal fat and meat + vitamin E”, was associated with higher amounts of homeostasis model assessment-β (HOMA-β) (531.3 ± 176.2 versus 48.7 ± 179.8, P = 0.03). In conclusion, following the NP2, correlated with higher intakes of chromium, selenium, copper, vitamin B6, MUFA and thiamin was associated with lower values of insulin, HOMA-IR, and sVCAM-1. Adherence to NP3, rich in SFA, cholesterol, vitamin E, vitamin B12, and zinc was associated with higher levels of HOMA-β.
Rapid prototyping of PMMA-based microfluidic spheroid-on-a-chip models using micromilling and vapour-assisted thermal bonding
Authors: Ahmed Monieb A. M. , Jurczak Klaudia M. , Lynn N. Scott , Mulder Jean-Paul S. H. , Verpoorte Elisabeth M. J. , Nagelkerke Anika 
Published: February 2024

AbstractThe application of microfluidic devices as next-generation cell and tissue culture systems has increased impressively in the last decades. With that, a plethora of materials as well as fabrication methods for these devices have emerged. Here, we describe the rapid prototyping of microfluidic devices, using micromilling and vapour-assisted thermal bonding of polymethyl methacrylate (PMMA), to create a spheroid-on-a-chip culture system. Surface roughness of the micromilled structures was assessed using scanning electron microscopy (SEM) and atomic force microscopy (AFM), showing that the fabrication procedure can impact the surface quality of micromilled substrates with milling tracks that can be readily observed in micromilled channels. A roughness of approximately 153 nm was created. Chloroform vapour-assisted bonding was used for simultaneous surface smoothing and bonding. A 30-s treatment with chloroform-vapour was able to reduce the surface roughness and smooth it to approximately 39 nm roughness. Subsequent bonding of multilayer PMMA-based microfluidic chips created a durable assembly, as shown by tensile testing. MDA-MB-231 breast cancer cells were cultured as multicellular tumour spheroids in the device and their characteristics evaluated using immunofluorescence staining. Spheroids could be successfully maintained for at least three weeks. They consisted of a characteristic hypoxic core, along with expression of the quiescence marker, p27kip1. This core was surrounded by a ring of Ki67-positive, proliferative cells. Overall, the method described represents a versatile approach to generate microfluidic devices compatible with biological applications.
Changes in RDW according to prognostic predictors in newly diagnosed multiple myeloma
Authors: Carlisi Melania , Presti R. Lo , Plano F. , Mancuso S. , Siragusa S. , Caimi G. 
Published: February 2024

AbstractRDW is an erythrocyte index that increase in multiple myeloma, in which it appears to have an important role in predicting outcome. For this reason, we performed a retrospective analysis to evaluate the relationships of RDW with some important prognostic predictors. Specifically, in a cohort of 190 newly diagnosed multiple myeloma patients, we have examined the behaviour of RDW and its trend in relation to the ISS stage and other prognostic factors, such as albumin, beta-2 microglobulin, LDH and bone marrow plasma cell infiltration. We performed the analysis in the entire cohort of patients and in the three different disease isotypes (Light chain, IgA, and IgG multiple myeloma). The evaluation of RDW in the different isotypes was made with the Kruskal–Wallis test, integrated by the Dunn test. The comparison between the subgroups allocated above and below the median value of each prognostic factor, was made with the Mann–Whitney test. From our analysis, we observed that RDW is higher in the IgA multiple myeloma, and it increases significantly from ISS I to III. Moreover, RDW increases in the presence of lower albumin values, higher levels of beta2-microglobulin and LDH and in the presence of a greater bone marrow plasma cell infiltrate.
Giant enhancement of third harmonic generation in an array of graphene ribbons using amplification of surface plasmon polaritons by optical gain
Authors: Sedaghat Nejad Marzieh , Ghasempour Ardakani Abbas 
Published: February 2024

AbstractIn this paper, we theoretically study the enhancement of third-harmonic generation in a plasmonic structure composed of an array of trilayer graphene ribbons sandwiched between two $$CaF_{2}$$

C
a

F
2

layers. In fact, we suggest a new method for more enhancement of nonlinearity in plasmonic structures using incorporation of optical gain into graphene ribbons. As the pump intensity increases, the maximum output intensity of third harmonic generated (THG) wave versus fundamental frequency is blue-shifted while its value enhances. Our analysis indicates that the enhancement factor of THG in our proposed structure is 1.1 × 107 without occurring an electric breakdown compared to case at which an optically pumped trilayer graphene sheet sandwiched between two CaF2 layers. Therefore, only presence of optical gain is not sufficient for significant enhancement of output intensity of THG wave and excitation of SPPs through the structure is also essential. On the other hand, our results demonstrate that the output intensity of THG wave from the proposed structure under optical pumping enhances by $$10^{5}$$

10
5

times compared to the plasmonic structure without optical gain which confirms the role of optical gain for THG enhancement in the plasmonic structure. This is because the gain in graphene ribbons amplifies the SPPs waves leading to the more field enhancement along the graphene ribbons which results in significant enhancement of THG wave in the plasmonic structure in comparison with one without gain. Therefore, we reveal that both SPPs and optical gain contribute to the strong output intensity of THG in our proposed structure compared to the trilayer graphene sheet inserted between two CaF2 layers.
YOLOX target detection model can identify and classify several types of tea buds with similar characteristics
Authors: Yang Mengdao , Yuan Weihao , Xu Gaojian 
Published: February 2024

AbstractCurrently, the accuracy of tea bud identification is crucial in the intelligent development of the tea industry, and this is due to the fact that identifying tea buds is a key step in determining the quality of tea and distinguishing the categories. In this experiment, 3728 tea shoots with similar characteristics in four categories (Anji White Tea, Huangshan Seed, Longjing 43, and NongKang Early) were photographed to establish the dataset TBD (Tea Bud Dataset). In this experiment, we constructed a tea shoot recognition model. We used seven mainstream algorithms (YOLOv4, YOLOv5, YOLOX, YOLOv7, EfficientDet, Faster R-CNN and CenterNet) to conduct shoot recognition comparison experiments and found that the YOLOX algorithm performs the best with its Precision, Recall, F1 score, mAP 89.34%, 93.56%, 0.91, and 95.47%, respectively. Then the YOLOX algorithm combined with the dataset to construct the shoot recognition model, the shoots of four kinds of tea to establish a tea shoot classification model, the model to identify the Anji white tea shoots of Precision 76.19%, the yellow mountain species of Precision 90.54%, Longjing 43 Precision 80%, NongKang early to the morning of the Precision was 77.78%. The results of this experiment show that the established tea shoot classification model has achieved a better classification of the above four types of tea shoots, which can also understand the feasibility of mechanical intelligent tea picking and provide some theoretical support for the application of mechanical intelligent tea picking in practice.
Impact of KRAS mutations and co-mutations on clinical outcomes in pancreatic ductal adenocarcinoma
Authors: Yousef Abdelrahman , Yousef Mahmoud , Chowdhury Saikat , Abdilleh Kawther , Knafl Mark , Edelkamp Paul , Alfaro-Munoz Kristin , Chacko Ray , Peterson Jennifer , Smaglo Brandon G. , Wolff Robert A. , Pant Shubham , Lee Michael S. , Willis Jason , Overman Michael , Doss Sudheer , Matrisian Lynn , Hurd Mark W. , Snyder Rebecca , Katz Matthew H. G. , Wang Huamin , Maitra Anirban , Shen John Paul , Zhao Dan 
Published: February 2024

AbstractThe relevance of KRAS mutation alleles to clinical outcome remains inconclusive in pancreatic adenocarcinoma (PDAC). We conducted a retrospective study of 803 patients with PDAC (42% with metastatic disease) at MD Anderson Cancer Center. Overall survival (OS) analysis demonstrated that KRAS mutation status and subtypes were prognostic (p < 0.001). Relative to patients with KRAS wildtype tumors (median OS 38 months), patients with KRASG12R had a similar OS (median 34 months), while patients with KRASQ61 and KRASG12D mutated tumors had shorter OS (median 20 months [HR: 1.9, 95% CI 1.2–3.0, p = 0.006] and 22 months [HR: 1.7, 95% CI 1.3–2.3, p < 0.001], respectively). There was enrichment of KRASG12D mutation in metastatic tumors (34% vs 24%, OR: 1.7, 95% CI 1.2–2.4, p = 0.001) and enrichment of KRASG12R in well and moderately differentiated tumors (14% vs 9%, OR: 1.7, 95% CI 1.05–2.99, p = 0.04). Similar findings were observed in the external validation cohort (PanCAN’s Know Your Tumor® dataset, n = 408).
Artificial intelligence-driven virtual rehabilitation for people living in the community: A scoping review
Authors: Abedi Ali , Colella Tracey J. F. , Pakosh Maureen , Khan Shehroz S. 
Published: February 2024

AbstractVirtual Rehabilitation (VRehab) is a promising approach to improving the physical and mental functioning of patients living in the community. The use of VRehab technology results in the generation of multi-modal datasets collected through various devices. This presents opportunities for the development of Artificial Intelligence (AI) techniques in VRehab, namely the measurement, detection, and prediction of various patients’ health outcomes. The objective of this scoping review was to explore the applications and effectiveness of incorporating AI into home-based VRehab programs. PubMed/MEDLINE, Embase, IEEE Xplore, Web of Science databases, and Google Scholar were searched from inception until June 2023 for studies that applied AI for the delivery of VRehab programs to the homes of adult patients. After screening 2172 unique titles and abstracts and 51 full-text studies, 13 studies were included in the review. A variety of AI algorithms were applied to analyze data collected from various sensors and make inferences about patients’ health outcomes, most involving evaluating patients’ exercise quality and providing feedback to patients. The AI algorithms used in the studies were mostly fuzzy rule-based methods, template matching, and deep neural networks. Despite the growing body of literature on the use of AI in VRehab, very few studies have examined its use in patients’ homes. Current research suggests that integrating AI with home-based VRehab can lead to improved rehabilitation outcomes for patients. However, further research is required to fully assess the effectiveness of various forms of AI-driven home-based VRehab, taking into account its unique challenges and using standardized metrics.
Exploring TRF2-Dependent DNA Distortion Through Single-DNA Manipulation Studies
Authors: Zhao Xiaodan , Vogirala Vinod Kumar , Liu Meihan , Zhou Yu , Rhodes Daniela , Sandin Sara , Yan Jie 
Published: February 2024

AbstractTRF2 is a component of shelterin, a telomere-specific protein complex that protects the ends of mammalian chromosomes from DNA damage signaling and improper repair. TRF2 functions as a homodimer and its interaction with telomeric DNA has been studied, but its full-length DNA-binding properties are unknown. This study examines TRF2’s interaction with single-DNA strands and focuses on the conformation of the TRF2-DNA complex and TRF2’s preference for DNA chirality. The results show that TRF2-DNA can switch between extended and compact conformations, indicating multiple DNA-binding modes, and TRF2’s binding does not have a strong preference for DNA supercoiling chirality when DNA is under low tension. Instead, TRF2 induces DNA bending under tension. Furthermore, both the N-terminal domain of TRF2 and the Myb domain enhance its affinity for the telomere sequence, highlighting the crucial role of multivalent DNA binding in enhancing its affinity and specificity for telomere sequence. These discoveries offer unique insights into TRF2’s interaction with telomeric DNA.
Molecular and structural basis of anti-DNA antibody specificity for pyrrolated proteins
Authors: Anan Yusuke , Itakura Masanori , Shimoda Tatsuya , Yamaguchi Kosuke , Lu Peng , Nagata Koji , Dong Jinhua , Ueda Hiroshi , Uchida Koji 
Published: February 2024

AbstractAnti-DNA antibodies (Abs), serological hallmarks of systemic lupus erythematosus (SLE) and markers for diagnosis and disease activity, show a specificity for non-nucleic acid molecules, such as N-pyrrolated proteins (pyrP) containing Nε-pyrrole-L-lysine (pyrK) residues. However, the detailed mechanism for the binding of anti-DNA Abs to pyrP remains unknown. In the present study, to gain structural insights into the dual-specificity of anti-DNA Abs, we used phage display to obtain DNA-binding, single-chain variable fragments (scFvs) from SLE-prone mice and found that they also cross-reacted with pyrP. It was revealed that a variable heavy chain (VH) domain is sufficient for the recognition of DNA/pyrP. Identification of an antigenic sequence containing pyrK in pyrP suggested that the presence of both pyrK and multiple acidic amino acid residues plays important roles in the electrostatic interactions with the Abs. X-ray crystallography and computer-predicted simulations of the pyrK-containing peptide-scFv complexes identified key residues of Abs involved in the interaction with the antigens. These data provide a mechanistic insight into the molecular basis of the dual-specificity of the anti-DNA Abs and provide a basis for therapeutic intervention against SLE.