bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exploring the ability of machine learning-based virtual screening models to identify the functional groups responsible for binding
Authors: Hadfield Thomas E. , Scantlebury Jack , Deane Charlotte M. 
Published: September 2023

AbstractMany recently proposed structure-based virtual screening models appear to be able to accurately distinguish high affinity binders from non-binders. However, several recent studies have shown that they often do so by exploiting ligand-specific biases in the dataset, rather than identifying favourable intermolecular interactions in the input protein-ligand complex. In this work we propose a novel approach for assessing the extent to which machine learning-based virtual screening models are able to identify the functional groups responsible for binding. To sidestep the difficulty in establishing the ground truth importance of each atom of a large scale set of protein-ligand complexes, we propose a protocol for generating synthetic data. Each ligand in the dataset is surrounded by a randomly sampled point cloud of pharmacophores, and the label assigned to the synthetic protein-ligand complex is determined by a 3-dimensional deterministic binding rule. This allows us to precisely quantify the ground truth importance of each atom and compare it to the model generated attributions. Using our generated datasets, we demonstrate that a recently proposed deep learning-based virtual screening model, PointVS, identified the most important functional groups with 39% more efficiency than a fingerprint-based random forest, suggesting that it would generalise more effectively to new examples. In addition, we found that ligand-specific biases, such as those present in widely used virtual screening datasets, substantially impaired the ability of all ML models to identify the most important functional groups. We have made our synthetic data generation framework available to facilitate the benchmarking of new virtual screening models. Code is available at https://github.com/tomhadfield95/synthVS.
A novel model for representing a plane target and finding the worst-case coverage in wireless sensor network based on Clifford algebra
Authors: Mahfouz Amr M. , Ismail Ahmed S. , El Sobky Wageda I. , Nasry Hany 
Published: September 2023

AbstractWireless ad hoc sensor networks have recently emerged as a premier research topic. They have great long-term economic potential and ability to transform our lives and pose many new system building challenges. Sensor networks also pose a number of new conceptual and optimization problems. Most of researches in wireless sensor networks are focused in obtaining better target coverage in order to reduce energy and cost of the network. The problem of planar target analysis is one of the crucial problems that should be considered while studying coverage problem of sensor networks. By combining computational geometry and graph theoretic techniques, specifically the Voronoi diagram and graph search algorithms, this paper introduces a novel sensor network coverage model that deals with plane target problem based on Clifford algebra which is a powerful tool that is coordinate free. Also, the calculations of the node coverage rate for the plane target in the sensor network using Clifford algebra are presented. Then, the maximum clearance path (worst-case coverage) of the sensor network for a plane target is proposed. The optimality and reliability of the proposed algorithm have been proved using simulation. Also, a comparison between the breach weight of the point target and the plane target is provided.
Mapping of nutrition policies and programs in South Asia towards achieving the Global Nutrition targets
Authors: Wali Nidhi , Agho Kingsley Emwinyore , Renzaho Andre M. N. 
Published: September 2023

Abstract
Background
South Asia continues to host the triple burden of child malnutrition with high levels of child undernutrition, hidden hunger (micronutrient deficiencies) and childhood overweight/obesity. To combat malnutrition, the international community along with the National governments have launched initiatives to track the country’s progress towards achieving the Global Nutrition targets by 2025. This review captures the country-specific efforts of nutrition-specific and nutrition-sensitive sectoral programs and policies towards achieving these targets for eight South Asian countries.

Methods
A systematic internet search was undertaken to search relevant policies and programs from Government websites and twelve International Organisations working in the region. The authors developed a template to map the policies against the following criteria: (i) enabling supportive environment; (ii) Initiatives targeted at nutrition-specific interventions; and (iii) Initiatives targeted at nutrition-specific interventions that impact child malnutrition. A narrative descriptive approach was used to present findings.

Results
All eight countries had relevant policies and programs to address child malnutrition and macronutrient deficiencies with targets for significant reductions in stunting and improved breastfeeding. However, despite the outlined there are major challenges of implementation, monitoring, evaluation and quality that persist with increased dependency on international donors and organisations for funding and/or implementation of nutrition plans.

Conclusion
There is a need to contextualise efforts designated to donors and governments to improve the tracking of efforts that impact nutrition.
The entrepreneurial ecosystem and the performance of micro and small enterprises (MSEs) in Amhara region, Ethiopia: the political–legal perspective
Authors: Wube Mulugeta Chane , Atwal Heena 
Published: September 2023

AbstractAll other parts of the entrepreneurial ecosystem in any country are commonly governed by the political and legal aspects of the entrepreneurial ecosystem. This is a novel approach that examines the integrated effect of the entrepreneurial ecosystem's political–legal subsystem on the performance of MSEs based on system theory and the mediating role of entrepreneurial competence taking a resource-based view in to account. There has been no detailed examination of the entrepreneurial ecosystem of MSEs in Africa in general, and Ethiopia in particular. A total sample of 499 MSE operators engaged in the three priority sectors: manufacturing, construction and urban agriculture was selected from the population of 4086 operators in three metropolitan cities of Amhara National Regional State, Ethiopia, using a proportional stratified sampling. Though the political–legal aspects of the entrepreneurial ecosystem have a major impact on both entrepreneurial competency and MSE’s performance, the relationship between entrepreneurial competencies and MSE performance was found to be insignificant. The role of entrepreneurial competency in mediating the relationships between policy and business performance and other business environments and business performance was shown to be insignificant. It is suggested by the study that the policies that the government designs concerning MSEs should be workable and attractive including the provision of different incentives. Lastly, other researchers in the area are suggested to further clarify the contradictions in the findings regarding the relationship between entrepreneurial competencies and the performance of SMEs.
Association between the Triglyceride–Glucose Index and Non-Alcoholic Fatty Liver Disease in patients with Atrial Fibrillation
Authors: Li Xiaozhong , Zhan Fenfang , Peng Tian , Xia Zhen , Li Juxiang 
Published: September 2023

Abstract
Background
The triglyceride and glucose index (TyG), as a surrogate of insulin resistance (IR), is closely associated with non-alcoholic fatty liver disease (NAFLD). However, the association between the TyG index and NAFLD in atrial fibrillation (AF) is unknown. Therefore, the purpose of this study is to explore the association between the TyG index and NAFLD in AF.

Methods
This retrospective study was performed at Nanchang University’s Second Affiliated Hospital. The AF patients who were hospitalized from January 2021 to December 2022 were enrolled. The association between the TyG index and NAFLD in AF patients was assessed by logistic regression and restricted cubic spline analysis. The ability of TyG index for identifying NAFLD was estimated by the area under the receiver operating characteristic (ROC).

Results
In this study, 632 people participated in the final analysis, with 176 (27.84%) having NAFLD. In the full adjustment model, there is an association between the TyG index and NAFLD [per 1 unit increment; odds ratios (ORs): 3.28; 95% confidence interval (CI) 2.14, 5.03]. Compared to the lowest tertile (TyG index < 8.29), the ORs for the highest tertile (TyG index ≥ 8.82) were 4.15 (95%CI: 2.28, 7.53). Dose–response analysis showed that the TyG index and NAFLD have a nearly linear relationship (P non-linear = 0.71). The area under the curve (AUC) of the TyG index is 0.735.

Conclusions
Our findings showed a significant association between the TyG index and NAFLD. The TyG index may be a good marker for predicting NAFLD in AF patients.
KL is a favorable prognostic factor related immune for clear cell renal cell carcinoma
Authors: Pan Ke-Hao , Yao Liqing , Chen Zhihao , Sun Jiale , Jia Zongming , Zhang Jianglei , Ling Zhixin 
Published: September 2023

Abstract
Background
Clear cell renal cell carcinoma (ccRCC) is a prevalent cancer in adult urology, often leading to metastasis and poor prognosis. Recently, advances in tumor immunology and aging research have opened up new possibilities for the treatment of kidney cancer. Therefore, the identification of potential targets and prognostic biomarkers for immunotherapy has become increasingly urgent.

Methods
Using GSE168845 data, we identified immune-aging-associated differentially expressed genes (IAR-DEGs) by intersecting differentially expressed immune-related genes and aging-related genes. The prognostic value of IAR-DEGs was determined via univariate and multivariate Cox regression analysis, revealing KL as an independent prognostic factor for ccRCC. We also investigated the correlation between KL and various immune-related factors, including immune cell infiltration, immune score, immune checkpoint, MSI, and TIED score. To confirm the expression of KL in ccRCC, we conducted qRT-PCR assays on both ccRCC cell lines and clinical tissue samples, and compared KL expression levels between normal kidney cell line (HK-2) and ACHN, a ccRCC cell line. Finally, we assessed KL protein expression levels in tissues using immunohistochemistry (IHC).

Results
In this study, we utilized Venn diagram analysis to identify 17 co-expressed immune-aging related DEGs from GSE168845, import database, and MSigDB database. GO and KEGG analysis revealed that the functions of the 17 IAR-DEGs were primarily related to “aging”. Univariate and multivariate Cox analysis validated these 17 genes, and KL was determined to be an independent prognostic factor for ccRCC. The downregulation of KL was observed in ccRCC tissues and was negatively associated with T stage, M stage, pathological stage, and histologic grade (p < 0.05). This downregulation indicated disease deterioration and a shortened overall survival period. Our calibration curves and nomogram demonstrated the excellent predictive potential of KL. GSEA analysis showed that KL gene mediated immune and aging-related pathways, and was significantly correlated with immune infiltration and MS and TIED score. More research has revealed a significant reduction in KL mRNA expression levels in human renal cancer cells, particularly in ccRCC tissues compared to adjacent normal kidney tissues. Moreover, immunohistochemistry data have demonstrated a marked decrease in KL protein expression levels in ccRCC cells when compared to adjacent normal tissues.

Conclusions
KL was a potential aging-related target for immunotherapy and valid prognostic biomarker for ccRCC patients.
Effect of JAK inhibitors on the three forms of bone damage in autoimmune arthritis: joint erosion, periarticular osteopenia, and systemic bone loss
Authors: Komagamine Masatsugu , Komatsu Noriko , Ling Rui , Okamoto Kazuo , Tianshu Shi , Matsuda Kotaro , Takeuchi Tsutomu , Kaneko Yuko , Takayanagi Hiroshi 
Published: September 2023

Abstract
Background
The types of bone damage in rheumatoid arthritis (RA) include joint erosion, periarticular osteoporosis, and systemic osteoporosis. Janus kinase (JAK) inhibitors ameliorate inflammation and joint erosion in RA, but their effect on the three types of bone loss have not been reportedly explored in depth. We aimed to clarify how JAK inhibitors influence the various types of bone loss in arthritis by modulating osteoclastic bone resorption and/or osteoblastic bone formation.

Methods
Collagen-induced arthritis (CIA) mice were treated with a JAK inhibitor after the onset of arthritis. Micro-computed tomography (μCT) and histological analyses (bone morphometric analyses) on the erosive calcaneocuboid joint, periarticular bone (distal femur or proximal tibia), and vertebrae were performed. The effect of four different JAK inhibitors on osteoclastogenesis under various conditions was examined in vitro.

Results
The JAK inhibitor ameliorated joint erosion, periarticular osteopenia and systemic bone loss. It reduced the osteoclast number in all the three types of bone damage. The JAK inhibitor enhanced osteoblastic bone formation in the calcaneus distal to inflammatory synovium in the calcaneocuboid joints, periarticular region of the tibia and vertebrae, but not the inflamed calcaneocuboid joint. All the JAK inhibitors suppressed osteoclastogenesis in vitro to a similar extent in the presence of osteoblastic cells. Most of the JAK inhibitors abrogated the suppressive effect of Th1 cells on osteoclastogenesis by inhibiting IFN-γ signaling in osteoclast precursor cells, while a JAK inhibitor did not affect this effect due to less ability to inhibit IFN-γ signaling.

Conclusions
The JAK inhibitor suppressed joint erosion mainly by inhibiting osteoclastogenesis, while it ameliorated periarticular osteopenia and systemic bone loss by both inhibiting osteoclastogenesis and promoting osteoblastogenesis. These results indicate that the effect of JAK inhibitors on osteoclastogenesis and osteoblastogenesis depends on the bone damage type and the affected bone area. In vitro studies suggest that while JAK inhibitors inhibit osteoclastic bone resorption, their effects on osteoclastogenesis in inflammatory environments vary depending on the cytokine milieu, JAK selectivity and cytokine signaling specificity. The findings reported here should contribute to the strategic use of antirheumatic drugs against structural damages in RA.
Nailfold capillaroscopy in Egyptian systemic lupus erythematosus (SLE) patients: correlation with demographic features and serum levels of IL 17A and IFNs I
Authors: Nasser Mohamed , Wadie Mary , Farid Alyaa , Amir Azza El 
Published: September 2023

Abstract
Background
In SLE patients, cytokines are linked to endothelial cell damage. Nailfold capillaroscopy (NFC) is a simple method for evaluating micro-vascular abnormalities in different connective tissue diseases (CTDs). The study aimed to detect the levels of interleukin 17A (IL 17A), type I interferons (IFNs I) in the serum, and NFC changes in Egyptian SLE patients compared to a control group and to correlate NFC findings with patients’ demographic features and serum levels of IL 17A and IFNs I.

Results
Serum levels of IL 17A, IFN α, and IFN β were significantly higher in SLE patients than in control group (P < 0.0001). About thirty nine patients (73.6%) of the 53 SLE patients showed abnormal NFC changes. Egyptian SLE patients had a high prevalence of the NFC non-specific pattern, with 32 (60.4%) patients showing non-specific changes and 7 (13.2%) patients showing scleroderma pattern, including 3 (5.6%) patients with active scleroderma pattern and 4 (7.55%) patients with late scleroderma pattern. Furthermore, Raynaud’s phenomenon (RP) was observed in 8 (15.1%) SLE patients, with 3 (5.6%) having normal NFC pattern and 5 (9.4%) having scleroderma pattern. All controls (n = 20) showed normal hairpin shape capillaries. Except for SLEDAI (P = 0.03) and the presence of RP (P < 0.0001), there were no significant differences in demographic and laboratory parameters between the three NFC patterns (normal, non-specific, and scleroderma); additionally, NFC score correlated significantly with SLEDAI (P = 0.021).

Conclusion
As a result of the high disease activity, Egyptian SLE patients had elevated serum levels of IL 17A and IFNs I. The most common NFC pattern in Egyptian SLE patients was a non-specific pattern. NFC abnormalities in Egyptian SLE patients were correlated with disease activity but not with patients’ ages, disease duration, or serum levels of IL 17A and IFNs I. SLE patients with scleroderma NFC pattern and RP should be closely followed for the possibility of appearance of anti-U1 RNP antibodies and MCTDS.
Retrospective study of acupuncture treatment for canine thoracolumbar intervertebral disc herniation
Authors: Jia Qianyu , Wang Yu , Pang Haidong , Fan Kai , Xie Huisheng , Lin Jiahao 
Published: September 2023

AbstractThoracolumbar interverbal disk herniation (TL-IVDH) is a common neurological disorder in dogs, which often affects the life quality of patients and their caregivers. Acupuncture is increasingly accepted by veterinarians and animal owners, and has been used in the treatment of neurologic disorders. This study aims to evaluate the effects of acupuncture treatment for canine TL-IVDH. Clinical cases from 2016 to 2021 were collected. According to the inclusion and exclusion criteria, 94 TL-IVDH cases that received acupuncture treatment were selected. Clinical classification and efficacy criteria were formulated based on the Frankel Score. For each case, clinical presentation, improvement, recovery and recurrence were recorded. Male dogs with TL-IVDH accounted for 64% of all cases. The average age was 7.49 years old, the predominant breed was poodle, and the incidence site was concentrated from T11 to L1. The overall recovery rate after receiving acupuncture treatment was 79.78%, which was comparable when considering only cases with grade 2, 3, or 4 spinal cord lesions (83.33% ~ 85.19%). In conclusion, canine with grade 2, 3, and 4 spinal cord lesions due to TL-IVDH receiving acupuncture had a high recovery rate, suggesting acupuncture could be a viable treatment options for canine with TL-IVDH.
Color origin and its sedimentary and paleoenvironmental significance of the Permian-Triassic strata in the Ordos Basin, China
Authors: Tan Cong , Yu Bingsong , Liu Ce , Cao Zhenglin , Bi He , Jin Hui , Yang Rongjun 
Published: September 2023

The Permian-Triassic strata in the Ordos Basin deposit a colorful set of strata. Although there have been many studies on oil and gas resources here, little attention has been paid to the genesis mechanism of its color. To analyze the color origin of the Permian-Triassic claystones and to clarify the dialectical relationship between rock color and sedimentary environment, petrological and geochemical methods such as polarization microscope, scan electron microscope, X-ray diffractometer, and inductively coupled plasma-mass spectrometer are used. The results indicate that the minerals with different colors, composition, and content serve as colorants in sedimentary rocks, with the predominant dyeing component in dark claystones being the organic matter, whereas red beds primarily acquire their color from hematite and other ferric minerals. In addition, different rock colors correspond to distinct chemical composition variations. The black-gray rocks of the Yanchang and Shihezi Formations have high total organic carbon content, Fe2+/Fe3+, V/Cr, and low CaO/(MgO × Al2O3) and Sr/Cu, whereas the red-brown rocks of the Liujiagou and Heshanggou Formations exhibit the opposite. Therefore, different colors of the rocks stem from their different mineral and chemical compositions, which in turn influenced by the changes in the paleoclimate, paleoenvironment, and tectonic movements. Comprehensive analysis of color, mineral, and chemical composition reveals the evolution process of paleoclimate and paleoenvironment in the Ordos Basin from the late Permian to Triassic, beginning with a warm humid climate characterized by a weak oxidation environment in the Shihezi and Shiqianfeng Formations, transitioning to a hot arid climate in the Liujiagou and Heshanggou Formations, and returning to a warm humid climate with a weak oxidation environment in the Zhifang and Yanchang Formations. This evolution history aligns with the global tectonic and climate evolution. Overall, systematic analysis of sedimentary rock color can provide an important basis for the study of the paleoclimate and paleoenvironment.
Quantum work statistics of controlled evolutions
Authors: Campbell Steve 
Published: September 2023

Abstract
We use the quantum work statistics to characterize the controlled dynamics governed by a counterdiabatic driving field. Focusing on the Shannon entropy of the work probability distribution, P(W), we demonstrate that the thermodynamics of a controlled evolution serves as an insightful tool for studying the non-equilibrium dynamics of complex quantum systems. In particular, we show that the entropy of P(W) recovers the expected scaling according to the Kibble-Zurek mechanism for the Landau-Zener model. Furthermore, we propose that the entropy of the work distribution provides a useful summary statistic for characterizing the need and complexity of the control fields for many-body systems.
Wettability and morphology of proboscises interweave with hawkmoth evolutionary history
Authors: Palaoro Alexandre V. , Gole Akshata R. , Sun Yueming , Puchalski Adam , Beard Charles E. , Adler Peter H. , Kornev Konstantin G. 
Published: September 2023

ABSTRACT
Hovering hawkmoths expend significant energy while feeding, which should select for greater feeding efficiency. Although increased feeding efficiency has been implicitly assumed, it has never been assessed. We hypothesized that hawkmoths have proboscises specialized for gathering nectar passively. Using contact angle and capillary pressure to evaluate capillary action of the proboscis, we conducted a comparative analysis of wetting and absorption properties for 13 species of hawkmoths. We showed that all 13 species have a hydrophilic proboscis. In contradistinction, the proboscises of all other tested lepidopteran species have a wetting dichotomy with only the distal ∼10% hydrophilic. Longer proboscises are more wettable, suggesting that species of hawkmoths with long proboscises are more efficient at acquiring nectar by the proboscis surface than are species with shorter proboscises. All hawkmoth species also show strong capillary pressure, which, together with the feeding behaviors we observed, ensures that nectar will be delivered to the food canal efficiently. The patterns we found suggest that different subfamilies of hawkmoths use different feeding strategies. Our comparative approach reveals that hawkmoths are unique among Lepidoptera and highlights the importance of considering the physical characteristics of the proboscis to understand the evolution and diversification of hawkmoths.