bluuebunny/crossref_metadata_2025_split huggingface dataset:
MOFormer: Multi-Objective Antimicrobial Peptide Generation through Conditional Transformer with Multi-Fusion Descriptors
Authors: Wang Li , Fu Xiangzheng , Yang Jiahao , Zhang Xinyi , Ye Xiucai , Sakurai Tetsuya , Zeng Xiangxiang , Liu Yiping 
Published: September 2024

Abstract

Deep learning offers considerable potential for designing peptides with desirable properties, essential for expediting drug discovery. Despite recent advances in generating antimicrobial peptides (AMPs), the simultaneous production of AMPs with multiple desired properties remains a formidable challenge. We introduce MOFormer, a multi-objective AMP design pipeline that optimizes several AMP properties concurrently. This model leverages a condition Transformer to refine the AMP sequence-property landscape for multi-objective generation, while multi-fusion descriptors improve the capture of intricate sequence details. Regularization techniques enable the model to uphold a highly structured latent space, facilitating the generation of more effective and potent new AMPs. Comparative analyses highlight that MOFormer outperforms existing methods in the dual-objective generation tasks of enhancing antimicrobial activity and minimizing hemolysis. Furthermore, we apply a Pareto-based non-dominated sorting algorithm and deep-learning surrogate models for hierarchical candidate screening. MOFormer's high efficacy is verified through two aspects: (1) elucidating candidates' structure and functions using molecular simulations and interpretable analysis, and (2) improving known AMPs towards additional dual-objective and triple-objective scenarios.
Evolution of Perianal Pathology in Patients Undergoing Bariatric Surgery. A Prospective, Multicentre Study With 12-month Follow-up.
Authors: Ferrer-Márquez Manuel , García-Redondo Manuel , Fernández-Alonso Ana Maria , Rubio-Gil Francisco , Acín-Gándara Débora , Vidaña-Marquez Elisabet , Belda-Lozano Ricardo , Reina-Duarte Ángel José 
Published: September 2024

Abstract

Introduction: Bariatric surgery provides good weight-loss results over the medium to long term, improving a significant number of comorbidities. Benign anal pathology is common; in addition, obesity is part of the pathophysiology of some of these diseases.
Objectives: The aim of this study is to describe and analyse benign anal pathology in patients affected by obesity who are candidates for bariatric surgery, as well as to assess its evolution after 12 months following weight-loss surgery.
Methodology: A descriptive, prospective, multicentre study was designed. Seventy patients who were candidates for bariatric surgery were included. At first contact, initial descriptive variables (weight, BMI, etc.) were collected, a perianal examination was performed, and quality-of-life questionnaires (SF12v2, HEMO-FISS-QoL) were completed. The second contact took place 12 months after surgery, in which the variables and questionnaires were again recorded.
Results: At 12 months from the intervention, a significant decrease in both the prevalence of symptomatic internal haemorrhoids and external haemorrhoids (p<0.001) was observed. The mean number of acute hidradenitis suppurativa flare-ups decreased significantly, to 0.22 over the preceding 6 months (p<0.001). Quality of life improved significantly, both generally and in relation to perianal pathology.
Conclusion: Patients who underwent bariatric surgery using restrictive and hypoabsorptive techniques showed an improvement in their perianal pathology, as well as a significant improvement in their quality of life. To consolidate these results more studies are required that encompass a larger number of patients and a longer evolution period.
Boiling Histotripsy Combined with Anti-SIRPα Ab Enhances Immunomodulation in YUMM1.7 Melanoma
Authors: Chandrasekar Sri Vidhya , Singh Akansha , Chamani Faraz , Ranjan Ashish 
Published: September 2024

Abstract

Focused ultrasound-based histotripsy (HT) rapidly lyses tumor cells and releases antigens, stimulating anti-tumor immunity. However, SIRPα-CD47 interactions inhibit macrophage-mediated phagocytosis, reducing efficacy. We hypothesized that combining HT with an anti-SIRPα antibody (anti-SIRPα Ab) would enhance immune response and treatment efficacy. In mice with poorly immunogenic YUMM1.7 tumors, the combination of HT and anti-SIRPα Ab significantly reduced tumor growth compared to monotherapies, increased antigen-presenting cells, enhanced CD8 T cell infiltration, and decreased immunosuppressive cells in tumor-draining lymph nodes. These findings suggest HT combined with anti-SIRPα Ab could improve outcomes against poorly immunogenic tumors.
Patterns of extinction across Hawaiian Lepidoptera offer lessons from a diverse, neglected, and vulnerable endemic fauna
Authors: Austin Kyhl , Rubinoff Daniel 
Published: September 2024

Abstract

Although insects make up the overwhelming majority of the described life on Earth, virtually nothing is known about the conservation status for all but the most charismatic taxa (i.e., butterflies, dragonflies) and many are at risk of imminent extinction. Given that island faunas are particularly vulnerable to extinction, we examined the conservation status of all 935 described species of native Lepidoptera in Hawaiʻi as a model to better understand levels of threat in poorly-known groups and how their rates of extinction might warrant actions to conserve them and inform future management. Using 100- and 50-year cut-offs for the time since each species was last recorded, we consider 269 species (28.8%) to be “presumed extinct,” 85 species (9.1%) to be “possibly extinct,” and 581 species (62.1%) to be “extant” or “likely extant,” giving an extinction rate of 37.9%. Baseline data such as these are crucial in establishing which taxa persist and which lineages may be most vulnerable to extinction in the immediate future. Continued field surveys and identification of museum specimens are critical to more precisely quantify extinction rates, focusing on taxa requiring the most immediate conservation action, and may result in the rediscovery of some “extinct” species. We discuss discrepancies in extinction rates across taxa and between islands as well as summarizing major threats and obstacles to protecting the Hawaiian Lepidoptera fauna going forward. Conservation specifically geared towards Hawaiian Lepidoptera is almost non-existent, which is inconsistent with the extreme rarity and high rates of extinction across many lineages.
Accelerometry-measured Physical Activity and Determinants in PE classes of Fourth-Grade Primary school students in China
Authors: Li Meibing , Qian Zhangzhi , Tian Chong , Han XiaoYan , Guo Haonan , Guo Haixia , Li Hongjuan 
Published: September 2024

Abstract

Purpose
Physical education (PE) classes provide opportunities for students to meet recommended daily moderate-to-vigorous physical activity (MVPA). This study aimed to explore PA levels and determinants in PE among Chinese fourth-grade primary school students.
Methods
This cross-sectional study recruited 195 Grade 4 children (49.2% boys; aged 12 to 13 years). Accelerometers (ActiGraph GT3X) were used to measure PA in PE. Physical fitness (PF) was measured by professional PE teachers during PE lessons from October 10 to October 20, 2020, following the Chinese National Student Physical Fitness Standard (CNSPFS) guidelines, as established by the Ministry of Education. Students' body mass index (BMI) and fitness scores were calculated and evaluated from their PF test. We observed 10 PE lessons and recorded lesson contents. Independent samples t-tests and analysis of variance (ANOVA) were applied to compare the differences in PA between genders, weight statuses, and PF scores among the students. The multiple linear regression model (MLR) was developed to identify the influencing factors that influence the PA levels of boys and girls enrolled in PE classes.
Results
Within 40 minutes of each PE class, children averagely accumulated 6.69 ± 4.05 minutes MVPA, equaling 16.73% of PE time. Boys were more active than girls (%MVPA: Boys 18.95%, Girls 14.56%; %Sedentary Behaviour: Boys 42.44%, Girls 49.29%; P < 0.01). MVPA was significantly affected by teaching content (Boys β = 0.613, P < 0.001; Girls β = 0.837, P < 0.001). PF (Boys β = 0.113, P = 0.246; Girls β = 0.093, P = 0.196) and BMI (Boys β=-0.069, P = 0.474; Girls β=-0.029, P = 0.690) did not significantly affect MVPA in PE.
Conclusion
The percentage of MVPA in PE was much lower than the proposed standards (50%). Teaching content significantly affects the MVPA level of elementary school students, especially for girls. PF and BMI did not significantly affect MVPA in PE. In China, there is an urgent need to design contents for improving MVPA in PE.
Mitochondrial genomes of Meghimatium pictum and Succinea arundinetorum provide insight into the gene order rearrangement within Stylommatophora (Gastropoda, Panpulmonata)
Authors: Wang Gang , Yin Chijie , Zhu Ying , Ji Qiuting , Tang Jun , Sun Xiaoli , Chen Hao , Sun Zijun , Liu Qiuning , Tang Boping , Chen Lianfu , Zhang Daizheng 
Published: September 2024

Abstract

In this study, we report the whole mitochondrial genomes of two species, Meghimatium pictum and Succinea arundinetorum, which belong to Stylommatophora, one of the most abundant orders of Gastropoda. The total sizes of M. pictum and S. arundinetorum mitogenomes are 14,352 bp and 15,282 bp, with surprisingly biased proportions of A + T contents that reach to 72.1% and 76.78%, respectively. The protein coding genes (PCGs) in two mitogenomes show negative AT skew values and evolved primarily under purifying selection. Compared with the ancestor of stylommatophora, the mitochondrial genes of M. pictum exhibited multiple rearrangement events while the mitochondrial genes of S. arundinetorum showed only minor differences. Moreover, the order of PCGs were conserved while the tRNA genes showed high frequency of rearrangement among the stylommatophoran species, suggesting that the latter could be one of the major driving forces of mitogenomic evolution in terrestrial molluska species. Our research lays a theoretical foundation for investigating the evolution and divergence of mitochondrial genes and provides valuable resources for studying evolutionary genetics in stylommatophoran species.
Association of Socio-demographic and Decision Making Factors with the unmet need of family planning among Married Women in Madi Municipality, Chitwan, Nepal
Authors: Ghimire Rochana , Shah Rajani , Baral Yojana , Malla Dinesh Kumar , Thapa Kanchan 
Published: September 2024

Abstract

Background
Sustainable Development Goal of Nepal targets universal access to family planning (FP) services and increasing the contraceptive prevalence rate to 75% by 2030. Despite continuous efforts from the government of Nepal in the FP sector, the prevalence of unmet need for FP is high. This study aimed to identify sociodemographic and decision-making factors associated with the unmet need for FP among married women of reproductive age.
Methods
This is a community-based cross-sectional study conducted in Madi municipality, Chitwan, Nepal. Face-to-face interviews were conducted with 218 married women of reproductive age using a semi-structured questionnaire. Descriptive statistics, chi-square tests and multivariable logistic regression were used to analyse the data.
Results
Nearly half (47%) were age group 25–34, 58% lived in nuclear families, 76% belonged to advantaged ethnic groups, majority of respondents (67%) and their husbands (75%) had at least secondary education. Most women (59%) were involved in agriculture, while most husbands (44%) were in foreign employment. Participants (91.3%) have heard about Depo-Provera. The overall unmet need for FP was 38%. Respondents whose husbands were involved in foreign employment were more likely [aOR: 4.408; CI: 2.068–9.399] to have an unmet need for FP than those employed within the country. The likelihood of the unmet need was higher [aOR: 3.212; CI: 1.368–8.135] among couples who did not discuss using FP methods compared to those who discussed three or more times. Women with up to two children [aOR: 5.212; CI: 1.163–23.363] and three or more children [aOR: 8.758; CI: 1.691–45.355] were more likely to have a higher unmet need for FP than women without a child.
Conclusion
A significant proportion of women had an unmet need for FP. Intervention should focus on addressing the FP needs of migrants and their spouses, promoting spousal discussion on FP and counselling on the treatment as well as side effects of contraceptives. Furthermore, empowering women would enable them in the decision-making process and in accessing FP services.
Responses of rhizosphere microbial communities and resource competition to soil amendment in saline and alkaline soils
Authors: Chang Doudou , Lu Xiaoyu , Sun Yan , Fan Hua , Wang Kaiyong 
Published: September 2024

Abstract

Background and aims
Soil amendments have been widely applied in the remediation of saline soil and the improvement of crops resistance to external stresses. However, the responses of soil microbial community composition, structure, function, and resource competition strategy to soil amendment in saline and alkaline soil remain unclear.
Methods
A barrel experiment was performed in a cotton field to explore the effects of soil amendment on soil microbial life history strategies under simulated saline and alkali stresses during cotton flowering stage.
Results
The results showed that saline and alkali stresses disrupted soil microbial succession and altered rhizosphere soil micro-environment. However, after the application of amendment in saline soil, the abundance of dominant bacteria (Subgroup_17) and fungi (Mortierella, Chaetomium), soil metabolic functions (biosynthesis of amino acids and fatty acid), soil K+ content and Si/N ratio significantly increased, while soil Na+ content and electrical conductivity (EC) significantly reduced. After the application of amendment in alkaline soil, the abundance of dominant soil bacteria (Aeromicronium, Rokubacteriales, RB41) and fungi (Mycosphaeralla, Aspergillus), phenylalanine metabolise and fatty acid biosynthesis pathways soil K+/Na+ ratio, organic carbon content, total nitrogen, and Si/N ratio significantly increased, while soil Na+ content, pH, and Si/C ratio significantly decreased.
Conclusions
Application of soil amendment could significantly increased soil nutrient content,the formation of different life cycle strategies of soil microorganisms, so as to alleviate the saline stress and alkali stress. This study provides reference for alleviating the saline and alkaline stresses to cotton by influencing key soil microorganisms using soil amendment.
Unlocking the Walnut Genetic Resources in Northeastern Iran for Late-Leafing and Nut Quality
Authors: Hamidirad Maryam , Nikpendar Amirhossein , Sheikhi Abdollatif , Sarikhani Saadat , Vahdati Kourosh , Roozban Mahmoud Reza , Ghahramanzadeh Sara 
Published: September 2024

Abstract

This study aimed to exploit the genetic diversity of walnut populations in Joveyn region, Northeastern Iran. Phenological and pomological characteristics of 135 out of 500 genotypes were evaluated for two consecutive years (2021–2022) based on UPOV and IPGRI descriptors. The results showed that nut and kernel weight and kernel percentage ranged between 6.81–17.29 g, 3.06–8.24 g, and 38–59%, respectively. The highest nut weight belonged to genotype 21KH-JC14 with an average of 16.88 g, while the lowest belonged to genotype 21KH-A88 with an average of 6.99 g, over two years. The highest kernel weight was recorded for genotype 21KH-JC16 with an average of 8.78 g over two years, while the lowest kernel weight with an average weight of 2.3 g belonged to genotype 21KH-A88. The budbreak date of the earliest and the latest genotypes were 1 and 17 days after the reference standard, respectively. The harvest date of the earliest and the latest genotypes, were 2 and 15 days after the reference standard, respectively. Based on the results of the two-year phenotypic evaluation, according to leafing date, yield, lateral bearing, nut weight, and kernel quality, five genotypes, including 21KH-JC1, 21KH-JC9, 21KH-A94, 21KH-BK66, and 21KH-J131, were selected as the superior genotypes and were re-evaluated for phenotypic evaluation. The nut weight, kernel weight and percentage of the selected superior genotypes ranged between 14.87–16.45 (g), 7.43–8.4 (g), and 47-51.09 percent, respectively. These genotypes had desired shell thickness with large nut size and light kernel color which was easily removed from the shell. Overall, these selected superior genotypes can be used in further field trials and walnut breeding programs.
Electron acceleration via vacuum bubble field in Laguerre Gaussian laser
Authors: Wang Wenpeng , Lv Zhengxing , Sun Fengyu , Shi Zhiyong , Lu Xiaoming , Li Jinfeng , Xu Rongjie , Liang Xiaoyan , Leng Yuxin , Li Ruxin , Xu Zhizhan 
Published: September 2024

Abstract

Enhancing the flux, brightness, and density of energetic electron beams is crucial for applications such as ultrafast electron diffraction, fast ignition in confined fusion, and free-electron lasers. Laser Wakefield Acceleration (LWFA) has demonstrated potential for accelerating collimated electrons up to 10 Giga-electron volts in 'bubble-like' plasma channels. However, its reliance on the plasma environment constrains the enhancement of acceleration stability and gradients. In contrast, Direct Laser Acceleration (DLA) does not depend on plasma and can achieve efficient acceleration with traditional Gaussian lasers. Nonetheless, traditional DLA often results in uncertain and divergent electron beams due to the ponderomotive force of the Gaussian laser. To overcome these limitations, our proof-of-principle experiments achieved collimated acceleration using a left circularly polarized Laguerre Gaussian (LG) laser in a DLA mechanism. Studies revealed that a novel vacuum bubble field formed by the LG laser is critical in simultaneously concentrating and accelerating electrons. This vacuum bubble field mechanism integrates the advantages of both traditional DLA and LWFA, offering significant benefits for applications such as particle collimation, high-flux particle sources, and coherent radiation sources in new relativistic regimes.
Genetic Diversity Analysis of the Innovative Black Rice RILs Developed by Interspecific Hybridization (O. sativa x O. rufipogon) Based on Agromorphology and Grain Quality
Authors: Roy Subhas Chandra , Shil Pankaj 
Published: September 2024

Abstract

Rice (Oryza sativa L.) is an important staple grain because more than half of the world's population depends on it for their livelihood. White rice contributes to the daily caloric intake (20–40%) of Asian countries, but its nutritional quality is poor compared to that of pigmented rice. Pigmented rice varieties (black and red) are gaining popularity among consumers due to nutritional health benefits. Despite having nutritional importance, pigmented rice is usually low-yielding due to the narrow genetic base that occurred during domestication and artificial selection. Considering the potentials of wild rice, two distinct RIL populations (each 100 lines) were developed through interspecific hybridization BWF (Badshabhog x O. rufipogon) and CWF (Chenga x O. rufipogon) to break the yield plateaus. In the present study, we have created novel and inventive aromatic black lines from non-black parental lines. Significant genetic diversity prevailed in the RIL lines, which were assessed through genetic variability parameters, path coefficient, Mahalanobis D2 test, and PCA using 15 agromorphological traits. High heritability (>90%), high GA and GAM were found in RIL lines, suggesting additive gene action for the characteristics. The first four principal components together accounted for 73.74% of the variability in BWF, and the first six PCs showed 71.90% cumulative variability in CWF (eigenvalue >1). Total anthocyanin content was varying at 261 mg/100 g, 253 mg/100 g, and 259 mg/100 g in BW23, CW16, and control black, respectively. The DPPH activity was highest in BWF (78.37%) compared to control black (76.29%). Amylose content varies from 7.57 to 24.59%, and protein content was recorded at 8.76 to 8.81 g/100 g in the RIL lines. RIL lines (BW23, CW16) contain high-quality essential amino acids, including anthocyanin petunidin 3-O glucoside, quantified through HR-LCMS-QTOF. The Kala4 gene-specific PCR amplification product supports the acquired mutation with neo-functionalization activity through LINE1 insertional rearrangement near the Kala4 promoter, suggesting that the Kala4 gene is activated in black lines. Moreover, the RIL lines may provide some insight into the evolutionary and domestication history of black rice origin and can be used as important genetic resources for improving black rice for food and nutritional security.
Bioelectrochemical Intercalation for Scalable Lithium Recovery
Authors: okamoto akihiro , Shimokawa Kohei , Pham Duyen Minh , Teah Heng Yi , Long Xizi , Kikuchi Yasunori 
Published: September 2024

Abstract

The escalating demand for large-scale rechargeable batteries to achieve sustainability goals underscores the urgent need to secure Li metal from diverse sources 1-3. Intercalation materials offer promise for selective and efficient electrochemical recovery from various sources, but the requirement of electrodes in driving intercalation reactions presents challenges for scale-up 4-6. Herein, we introduce a biologically driven method for electrochemical Li recovery, utilizing a combination of intercalation nanomaterials and dissimilatory metal-reducing bacteria, specifically Shewanella oneidensis MR-1. This method couples bacterial metabolic hydrocarbon oxidation with Li intercalation into λ-MnO₂, achieving rates and selectivity comparable to electrode-based methods across different Li concentrations. Over 95% of Li was recovered from seawater within hours, with less than 1% co-intercalation of other metal ions. The efficacy of this reaction is maintained across scales by the autonomous formation of microbe/λ-MnO₂ agglomerates, in which extracellular and cell-surface cytochromes facilitate efficient electron transfer. Comprehensive techno-economic and life-cycle analyses for Li₂CO₃ production indicate that our method outperforms conventional evaporative processes, reducing on-site Li source water loss by two orders of magnitude without increasing costs. Our scalable bioelectrochemical approach could enable efficient Li recovery and offer great potential for sustainable resource management and recycling for both research and industrial applications.