bluuebunny/crossref_metadata_2025_split huggingface dataset:
Protein–protein interaction site prediction by model ensembling with hybrid feature and self-attention
Authors: Cong Hanhan , Liu Hong , Cao Yi , Liang Cheng , Chen Yuehui 
Published: December 2023

Abstract
Background
Protein–protein interactions (PPIs) are crucial in various biological functions and cellular processes. Thus, many computational approaches have been proposed to predict PPI sites. Although significant progress has been made, these methods still have limitations in encoding the characteristics of each amino acid in sequences. Many feature extraction methods rely on the sliding window technique, which simply merges all the features of residues into a vector. The importance of some key residues may be weakened in the feature vector, leading to poor performance.

Results
We propose a novel sequence-based method for PPI sites prediction. The new network model, PPINet, contains multiple feature processing paths. For a residue, the PPINet extracts the features of the targeted residue and its context separately. These two types of features are processed by two paths in the network and combined to form a protein representation, where the two types of features are of relatively equal importance. The model ensembling technique is applied to make use of more features. The base models are trained with different features and then ensembled via stacking. In addition, a data balancing strategy is presented, by which our model can get significant improvement on highly unbalanced data.

Conclusion
The proposed method is evaluated on a fused dataset constructed from Dset186, Dset_72, and PDBset_164, as well as the public Dset_448 dataset. Compared with current state-of-the-art methods, the performance of our method is better than the others. In the most important metrics, such as AUPRC and recall, it surpasses the second-best programmer on the latter dataset by 6.9% and 4.7%, respectively. We also demonstrated that the improvement is essentially due to using the ensemble model, especially, the hybrid feature. We share our code for reproducibility and future research at https://github.com/CandiceCong/StackingPPINet.
Exploring the mechanism of artificial selection signature in Chinese indigenous pigs by leveraging multiple bioinformatics database tools
Authors: Feng Xueyan , Diao Shuqi , Liu Yuqiang , Xu Zhiting , Li Guangzhen , Ma Ye , Su Zhanqin , Liu Xiaohong , Li Jiaqi , Zhang Zhe 
Published: December 2023

Abstract
Background
Chinese indigenous pigs in Yunnan exhibit considerable phenotypic diversity, but their population structure and the biological interpretation of signatures of artificial selection require further investigation. To uncover population genetic diversity, migration events, and artificial selection signatures in Chinese domestic pigs, we sampled 111 Yunnan pigs from four breeds in Yunnan which is considered to be one of the centres of livestock domestication in China, and genotyped them using Illumina Porcine SNP60K BeadChip. We then leveraged multiple bioinformatics database tools to further investigate the signatures and associated complex traits.

Results
Population structure and migration analyses showed that Diannanxiaoer pigs had different genetic backgrounds from other Yunnan pigs, and Gaoligongshan may undergone the migration events from Baoshan and Saba pigs. Intriguingly, we identified a possible common target of sharing artificial selection on a 265.09 kb region on chromosome 5 in Yunnan indigenous pigs, and the genes on this region were associated with cardiovascular and immune systems. We also detected several candidate genes correlated with dietary adaptation, body size (e.g., PASCIN1, GRM4, ITPR2), and reproductive performance. In addition, the breed-sharing gene MMP16 was identified to be a human-mediated gene. Multiple lines of evidence at the mammalian genome, transcriptome, and phenome levels further supported the evidence for the causality between MMP16 variants and the metabolic diseases, brain development, and cartilage tissues in Chinese pigs. Our results suggested that the suppression of MMP16 would directly lead to inactivity and insensitivity of neuronal activity and skeletal development in Chinese indigenous pigs.

Conclusion
In this study, the population genetic analyses and identification of artificial selection signatures of Yunnan indigenous pigs help to build an understanding of the effect of human-mediated selection mechanisms on phenotypic traits in Chinese indigenous pigs. Further studies are needed to fully characterize the process of human-mediated genes and biological mechanisms.
Evaluation of potassium-enriched biochar and GA3 effectiveness for Improving wheat growth under drought stress
Authors: Sarwar Ghulam , Anwar Tauseef , Malik Mehvish , Rehman Haseeb ur , Danish Subhan , Alahmadi Tahani Awad , Ansari Mohammad Javed 
Published: December 2023

AbstractOsmotic stress is a significant concern in agricultural crop production as it can harm crop growth, development, and productivity. Agriculture crops are particularly vulnerable to osmotic stress due to their reliance on water availability for various physiological processes. Organic amendments like activated carbon biochar and growth hormone gibberellic acid (GA3) can play a vital role. However, the time needed is to modify the established amendment to achieve better results. That’s why the current study used potassium-enriched biochar (KBC = 0.75%) with and without GA3 (15 mg/L) as amendments under no osmotic stress and osmotic stress in wheat. Results showed that GA3 + KBC caused significant enhancement in germination (9.44%), shoot length (29.30%), root length (21.85%), shoot fresh weight (13.56%), shoot dry weight (68.38), root fresh weight (32.68%) and root dry weight (28.79%) of wheat over control under osmotic stress (OS). A significant enhancement in chlorophyll a, chlorophyll b and total chlorophyll, while the decline in electrolyte leakage of wheat, also validated the effectiveness of GA3 + KBC over control in OS. In conclusion, GA3 + KBC is the most effective among all applied treatments for improving wheat growth attributes under no osmotic and osmotic stress. Further research is needed at the field level, focusing on various cereal crops, to establish GA3 + KBC as the optimal treatment for effectively mitigating the impacts of osmotic stress.
3 L split-dose polyethylene glycol is superior to 2 L polyethylene glycol in colonoscopic bowel preparation in relatively high-BMI (≥ 24 kg/m2) individuals: a multicenter randomized controlled trial
Authors: Yan Hailin , Huang Hongyu , Yang Dailan , Chen Zonghua , Liu Chao , Huang Zhong , Zhao Rui , Shan Jing , Yang Li , Yang Jinlin , Deng Kai 
Published: December 2023

Abstract
Background
Whether body mass index (BMI) is a risk factor for poor bowel preparation is controversial, and the optimal bowel preparation regimen for people with a high BMI is unclear.

Methods
We prospectively included 710 individuals with high BMIs (≥ 24 kg/m2) who were scheduled to undergo colonoscopy from January to November 2021 at 7 hospitals. Participants were randomly allocated into 3 L split-dose polyethylene glycol (PEG) group (n=353) and 2 L PEG group (n=357). The primary outcome was the rate of adequate bowel preparation, and the secondary outcomes included Boston Bowel Preparation Scale (BBPS) score, polyp detection rate, cecal intubation rate, and adverse reactions during bowel preparation. Furthermore, we did exploratory subgroup analyses for adequate bowel preparation.

Results
After enrollment, 15 individuals didn’t undergo colonoscopy, finally 345 participants took 3 L split-dose PEG regimen, and 350 participants took 2 L PEG regimen for colonoscopic bowel preparation. 3 L split-dose PEG regimen was superior to 2 L PEG regimen in the rate of adequate bowel preparation (81.2% vs. 74.9%, P = 0.045), BBPS score (6.71±1.15 vs. 6.37±1.31, P < 0.001), and the rate of polyp detection (62.0% vs. 52.9%, P = 0.015). The cecal intubation rate was similar in both groups (99.7%). Regarding adverse reactions, individuals were more likely to feel nausea in the 3 L PEG group (30.9% vs. 19.3%; P = 0.001); however, the degree was mild. In the subgroup analysis for adequate bowel preparation, 3 L split-dose PEG regimen performed better than 2 L PEG regimen in the overweight (BMI 25-29.9 kg/m2 ) (P = 0.006) and individuals with constipation (P = 0.044), while no significant differences were observed in relatively normal (BMI 24-24.9 kg/m2) (P = 0.593) and obese individuals (BMI ≥ 30 kg/m2) (P = 0.715).

Conclusions
3 L split-dose PEG regimen is superior to 2 L PEG regimen for colonoscopic Bowel Preparation in relatively high-BMI individuals, especially overweight individuals (BMI 25-29.9 kg/m2 ).

Trial Registration
This trial was registered in the Chinese Clinical Trials Registry (ChiCTR2000039068). The date of first registration, 15/10/2020, http://www.chictr.org.cn
Patience with foster children as a major problem for grandparents in the role of kinship carers aged 60 + and the psychosocial determinants of this deficit
Authors: Giezek Marta , Wojtkowska Anna , Zabielska Paulina , Karakiewicz Beata 
Published: December 2023

AbstractKinship care represents the most prevalent form of foster care in Poland. Most commonly, the role of kinship carers is taken on by grandparents, who may struggle with various problems, needs and deficits in this role. The aim of this study was to investigate the problem of patience in kinship carers aged 60 + and its impact on deficits in the performance of roles and duties.Methods Seventy-five foster grandparents (63 female, 84%) aged from 61 to 97 years (M = 69,12; SD = 6.22) were investigated in north-western Poland in 2018 and 2019. The study was based on the diagnostic survey method.Results Psychological disposition, functioning, health problems and parental needs and deficits were assessed using standardised psychometric scales and tools self-constructed for this research study. A lack of patience with foster children was reported by 46.7% (n = 35) of the respondents. Patience deficits corresponded with a significantly lower sense of coherence, especially in the manageability domain (p < 0.001) and such stress coping strategies as lower positive reappraisal (p = 0.016) and seeking of emotional support (p = 0.025), as well as a greater tendency for suppression of activities (p = 0.014) and venting of emotions (p = 0.035). Relatively permanent personality traits and general self-efficacy were not differentiated by patience with children.Conclusions The results suggest that patience – so important for biological and foster parents – is related to psychological competencies that can be improved through psychoeducation and skills-training, which may be beneficial for improving foster carers’ effectiveness.
Cross-cultural adaption and inter-rater reliability of the Swedish version of the updated clinical frailty scale 2.0
Authors: Olsson Henrik , Åhlund Kristina , Alfredsson Joakim , Andersson David , Boström Anne-Marie , Guidetti Susanne , Prytz Mattias , Ekerstad Niklas 
Published: December 2023

Abstract
Background
Worldwide, there is a large and growing group of older adults. Frailty is known as an important discriminatory factor for poor outcomes. The Clinical Frailty Scale (CFS) has become a frequently used frailty instrument in different clinical settings and health care sectors, and it has shown good predictive validity. The aims of this study were to describe and validate the translation and cultural adaptation of the CFS into Swedish (CFS-SWE), and to test the inter-rater reliability (IRR) for registered nurses using the CFS-SWE.

Methods
An observational study design was employed. The ISPOR principles were used for the translation, linguistic validation and cultural adaptation of the scale. To test the IRR, 12 participants were asked to rate 10 clinical case vignettes using the CFS-SWE. The IRR was assessed using intraclass correlation and Krippendorff’s alpha agreement coefficient test.

Results
The Clinical Frailty Scale was translated and culturally adapted into Swedish and is presented in its final form. The IRR for all raters, measured by an intraclass correlation test, resulted in an absolute agreement value among the raters of 0.969 (95% CI: 0.929–0.991) and a consistency value of 0.979 (95% CI: 0.953–0.994), which indicates excellent reliability. Krippendorff’s alpha agreement coefficient for all raters was 0.969 (95% CI: 0.917–0.988), indicating near-perfect agreement. The sensitivity of the reliability was examined by separately testing the IRR of the group of specialised registered nurses and non-specialised registered nurses respectively, with consistent and similar results.

Conclusion
The Clinical Frailty Scale was translated, linguistically validated and culturally adapted into Swedish following a well-established standard technique. The IRR was excellent, judged by two established, separately used, reliability tests. The reliability test results did not differ between non-specialised and specialised registered nurses. However, the use of case vignettes might reduce the generalisability of the reliability findings to real-life settings. The CFS has the potential to be a common reference tool, especially when older adults are treated and rehabilitated in different care sectors.
Fibronectin glomerulopathy in a kidney allograft biopsy
Authors: Klair Nathaniel , Mahmood Salman B. , El-Rifai Rasha , Nast Cynthia C. , Bu Lihong , Bregman Adam 
Published: December 2023

Abstract
Background
Fibronectin glomerulopathy is a rare genetic nephropathy with only a few cases of post-transplant recurrence being reported previously. We highlight a case that was initially misdiagnosed and emphasize the importance of full immunofluorescence and electron microscopy evaluation in allograft biopsies.

Case presentation
A 36-year-old male with a history of end-stage kidney disease secondary to biopsy-proven type 1 membranoproliferative glomerulonephritis (MPGN) status-post living unrelated donor kidney transplant 12 years prior, presented with increasing creatinine and proteinuria. Biopsy was performed and was consistent with fibronectin glomerulopathy. Subsequent genetic testing revealed an FN1 mutation, the primary gene associated with this condition.

Conclusions
Full histologic evaluation of the allograft biopsy corrected the diagnosis and additionally suggested that the patient's mother, who had expired in her 30s and had received a diagnosis of type 1 MPGN on autopsy, likely also had fibronectin glomerulopathy, enabling appropriate genetic counseling for the family.
Associations of elevated glucose levels at each time point during OGTT with fetal congenital heart diseases: a cohort study of 72,236 births
Authors: Zhang Qian , Lai Shuhua , Zhang Yulong , Ye Xu , Wu Yi , Lin Tinghua , Huang Huiyun , Zhang Wenhui , Lin Hai , Yan Jianying 
Published: December 2023

AbstractBackgroundIt remains unclear how the condition of glucose metabolism during pregnancy affects fetal outcomes. This study aimed to investigate the associations of gestational diabetes mellitus (GDM) and elevated glucose levels at each time point during oral glucose tolerance test (OGTT) with congenital heart disease (CHD) risk in offspring.MethodsWe conducted a retrospective cohort study of mothers with singleton pregnancies of 20 weeks or more registered at Maternal and Child Health Centers in Fujian Province, China. The OGTT results and offspring CHD occurrence were collected. We used logistic regression to analyse the association between elevated blood glucose at each time point during OGTT and CHD.ResultsA total of 71,703 normal and 533 CHD fetuses were included. Compared to the corresponding normal group, women with GDM, elevated blood glucose at different time points in OGTT (0 h ≥ 5.1 mmol/L, 1 h ≥ 10 mmol/L, and 2 h ≥ 8.5 mmol/L) showed an increased risk of CHD in offspring (adjusted OR = 1.41, 1.36, 1.37, and 1.41, allP < 0.05, respectively). Compared to group 1 (normal OGTT 0 h, 1 h and 2 h), the risk of CHD was higher in group 3 (normal OGTT 0 h and abnormal OGTT 1 h or 2 h) and group 4 (abnormal OGTT 0 h, 1 h and 2 h), OR = 1.53 and 2.21, allP < 0.05, respectively. Moreover, we divided participants by advanced maternal age, multipara, assisted reproduction, fetal sex, and others, similar associations were observed in the subgroup analyses.ConclusionElevated blood glucose at different time points during OGTT was associated with CHD in offspring. Fetuses of pregnant women with GDM should be screened for a high risk of CHD.
A systematic review with meta-analysis of the relation of aflatoxin B1 to growth impairment in infants/children
Authors: Nejad Behnam Ghorbani , Mostafaei Zahra , Rezaabad Ali Balouchi , Mehravar Fatemeh , Zarei Mahtab , Dehghani Azadeh , Estabragh Mohammad Amin Raeisi , Karami-Mohajeri Somayyeh , Alizadeh Hamzeh 
Published: December 2023

Abstract
Background
Aflatoxins are regarded as the most potent genotoxic and carcinogenic type of mycotoxins. This meta-analysis was performed to investigate a the relation of aflatoxin B1 (AFB1) to growth measurements of infants/children, including wasting, underweight, stunting, as well as weight-for-age (WAZ), height-for-age (HAZ), and weight-for-height (WHZ) z-scores.

Methods
Electronic databases of PubMed, Web of Science, and Scopus were searched to identify related publications. Effect sizes for associations were pooled using the random effects analysis. Subgroup analysis by study design, method used to assess AFB1, and adjustment for covariateswas performed to detect possible sources of heterogeneity.

Results
Pooled analysis of available data showed that AFB1 exposure was negatively associated growth z-scores, including WHZ (β = -0.02, 95%CI = -0.07 to 0.03), with WAZ (β = -0.18, 95%CI = -0.33 to -0.02), and HAZ (β = -0.17, 95%CI = -0.30 to -0.03) in infants/children. There was a remarkable heterogeneity among studies on WAZ and HAZ (P ≤ 0.001). In prospective cohort studies, AFB1 exposure was found to be significantly associated with the elevated risk of underweight (OR = 1.20, 95%CI = 1.03 to 1.40) and stunting (OR = 1.21, 95%CI = 1.11 to 1.33).

Conclusions
This meta-analysis highlighted the importance of AFB1 exposure as a potential risk factor for growth impairment in infants/children.
Effects of different therapy regimens to increase final adult height in males at advanced bone age with idiopathic short stature
Authors: Wang Wei , Wang Yan , Xiao Ya , Cao Niuniu , Wang Yifan 
Published: December 2023

Abstract
Background
This retrospective study explored the effect on adult height of a combination of recombinant human growth hormone (rhGH) and aromatase inhibitors (AIs), or rhGH and a gonadotropin-releasing hormone analog (GnRHa), and compared their effects with rhGH alone in males at advanced bone age with idiopathic short stature (ISS).

Methods
In this retrospective study, rhGH or rhGH combined with GnRHa or rhGH combined with AI therapy was given to males with advanced bone age (13–15 years) and diagnosed with ISS. The patients were followed to assess their adult height.

Results
(1) A total of 68 patients were reviewed; 22 males were treated with rhGH for 24.9 ± 4.47 months, 22 males were treated with GnRHa + rhGH for 34.1 ± 3.36 months, and 24 males were treated with AI + RHGH for 22.7 ± 2.49 months. (2) Before treatment, the HtSDS-CA for the three groups were -1.04 ± 0.95, -1.23 ± 1.06, and -0.85 ± 0.98, respectively, and the HtSDS-BA were -2.14 ± 0.29, -2.14 ± 0.21, and-2.26 ± 0.31, respectively. The target heights for each group were 169.7 ± 4.0 cm, 169.7 ± 3.9 cm, and 169.1 ± 3.9 cm, respectively. The predicted adult heights were 161.7 ± 3.35 cm, 162.3 ± 1.75 cm, and 161.6 ± 2.89 cm, respectively. (3) After treatment, the HtSDS-CA for the rhGH group increased by 1.30 ± 0.58, and the HtSDS-BA increased by 2.00 ± 0.27. For the GnRHa + rhGH group, the HtSDS-CA and HtSDS-BA increased by1.42 ± 0.73and 2.74 ± 0.28, respectively. The AI + RHGH group increased by1.39 ± 0.64 and 2.76 ± 0.31, respectively. (4) There was no significant difference between the adult height (170.9 ± 0.7 cm) and target height for the rhGH group (P > 0.05), but the adult heights for the GnRHa + rhGH and AI + RHGH groups (173.2 ± 1.5 cm and 173.5 ± 1.0 cm, respectively, P > 0.05) were higher than the target height (P < 0.05). (5) Compared with the predicted adult height, the adult heights for the three groups improved significantly (P < 0.05). (6) No severe adverse reactions during the treatment occurred in any of the children. However, the total incidence of side effects in the three groups was significant (χ2 = 20.433, P = 0.00).

Conclusion
Different therapeutic approaches have been investigated to improve the final adult height of males at advanced bone ages with ISS, and the optimal strategy remains controversial. In children at advanced bone ages with ISS, clinicians should carefully consider the advantages and disadvantages prior to treatment.
Psychometric validation of the Hospital Anxiety and Depression Scale (HADS) in community-dwelling older adults
Authors: Sivertsen Heidi Emly , Helvik Anne-Sofie , Gjøra Linda , Haugan Gørill 
Published: December 2023

Abstract
Objectives
The Hospital Anxiety and Depression Scale (HADS) is commonly used to measure anxiety and depression, but the number of studies validating psychometric properties in older adults are limited. To our knowledge, no previous studies have utilized confirmative factor analyses in community-dwelling older adults, regardless of health conditions. Thus, this study aimed to examine the psychometric properties of HADS in older adults 70 + living at home in a large Norwegian city.

Methods
In total, 1190 inhabitants ≥ 70 (range 70 – 96) years completed the HADS inventory in the population-based Trøndelag Health Study (HUNT), termed “HUNT4 70 + ” in Trondheim, Norway. Confirmatory factor analyses were performed to test the dimensionality, reliability, and construct validity.

Results
The original two-factor-solution (Model-1) revealed only partly a good fit to the present data; however, including a cross-loading for item 6D (“I feel cheerful”) along with a correlated error term between item 2D (“I still enjoy the things I used to enjoy”) and 12D (“I look forward with enjoyment to things”) improved the fit substantially. Good to acceptable measurement reliability was demonstrated, and the construct validity was acceptable.

Conclusions
The HADS involves some items that are not reliable and valid indicators for the depression construct in this population, especially item 6 is problematic. To improve the reliability and validity of the Norwegian version of HADS, we recommend that essential aspects of depression in older adults should be included.