bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome-wide identification and molecular characterization of the AP2/ERF superfamily members in sand pear (Pyrus pyrifolia)
Authors: Xu Yue , Li Xiaona , Yang Xiong , Wassie Misganaw , Shi Haiyan 
Published: January 2023

Abstract
Background
‘Whangkeumbae’ (Pyrus pyrifolia) is a typical climacteric fruit variety of sand pear with excellent taste. However, the rapid postharvest ethylene production limits the shelf life of ‘Whangkeumbae’ fruit. AP2/ERF superfamily is a large family of transcription factors involved in plant growth and development, including fruit ripening and senescence through the ethylene signaling pathway. The numbers and functions of AP2/ERF superfamily members in sand pear remain largely unknown.

Results
In this study, a total of 234 AP2/ERF family members were identified through the transcriptome of Pyrus pyrifolia ‘Whangkeumbae’ (17 genes) and Pyrus pyrifolia genome (223 genes) analyses. Six genes (Accession: EVM0023062.1, EVM0034833.1, EVM0027049.1, EVM0034047.1, EVM0028755.1, EVM0015862.1) identified via genome analysis shared 100% identity with PpERF14-L, PpERF5-L, PpERF3a, PpERF3, PpERF017 and PpERF098, respectively, which were identified from transcriptome sequencing. Further, the AP2/ERF superfamily members were divided into AP2, ERF, and RAV subfamilies, each comprising 38, 188, and 8 members, respectively. Tissue-specific expression analysis showed that PpERF061, PpERF113, PpERF51L-B, PpERF5-L, and PpERF017 were predominantly expressed in fruits than in other tissues. Additionally, PpERF5-L and PpERF017 showed higher expressions at the early stage of fruit development. While, PpERF51B-L exhibited higher expression during the fruit ripening stage. Besides, PpERF061 and PpERF113 had pronounced expressions during fruit senescence.

Conclusion
These results indicate that PpERF061, PpERF113, PpERF51L-B, PpERF5-L, and PpERF017 could play crucial roles in sand pear fruit development, ripening, and senescence. Overall, this study provides valuable information for further functional analysis of the AP2/ERF genes during fruit ripening and senescence in sand pear.
Deciphering key genomic regions controlling flag leaf size in wheat via integration of meta-QTL and in silico transcriptome assessment
Authors: Kong Binxue , Ma Jingfu , Zhang Peipei , Chen Tao , Liu Yuan , Che Zhuo , Shahinnia Fahimeh , Yang Delong 
Published: January 2023

AbstractBackgroundGrain yield is a complex and polygenic trait influenced by the photosynthetic source-sink relationship in wheat. The top three leaves, especially the flag leaf, are considered the major sources of photo-assimilates accumulated in the grain. Determination of significant genomic regions and candidate genes affecting flag leaf size can be used in breeding for grain yield improvement.ResultsWith the final purpose of understanding key genomic regions for flag leaf size, a meta-analysis of 521 initial quantitative trait loci (QTLs) from 31 independent QTL mapping studies over the past decades was performed, where 333 loci eventually were refined into 64 meta-QTLs (MQTLs). The average confidence interval (CI) of these MQTLs was 5.28 times less than that of the initial QTLs. Thirty-three MQTLs overlapped the marker trait associations (MTAs) previously reported in genome-wide association studies (GWAS) for flag leaf traits in wheat. A total of 2262 candidate genes for flag leaf size, which were involved in the peroxisome, basal transcription factor, and tyrosine metabolism pathways were identified in MQTL regions by the in silico transcriptome assessment. Of these, the expression analysis of the available genes revealed that 134 genes with > 2 transcripts per million (TPM) were highly and specifically expressed in the leaf. These candidate genes could be critical to affect flag leaf size in wheat.ConclusionsThe findings will make further insight into the genetic determinants of flag leaf size and provide some reliable MQTLs and putative candidate genes for the genetic improvement of flag leaf size in wheat.
Antimicrobial activity of D-amino acid in combination with photo-sonoactivated hypericin nanoparticles against Acinetobacter baumannii
Authors: Pourhajibagher Maryam , Hosseini Nava , Bahador Abbas 
Published: January 2023

Abstract
Background
The emergence of multidrug-resistant Acinetobacter baumannii strains is increasing worldwide. To overcome these life-threatening infections, the development of new treatment approaches is critical. For this purpose, this study was conducted to determine the antimicrobial photo-sonodynamic therapy (aPSDT) using hypericin nanoparticles (HypNP) in combination with D-Tryptophan (D-Trp) against A. baumannii.

Materials and methods
HypNP was synthesized and characterized, followed by the determination of the fractional inhibitory concentration (FIC) index of HypNP and D-Trp by checkerboard assay. Next, the antimicrobial and anti-biofilm potential of HypNP@D-Trp-mediated aPSDT against A. baumannii was evaluated. Finally, the anti-virulence activity of aPSDT using HypNP@D-Trp was accessed following the characterization of HypNP@D-Trp interaction with AbaI using in silico virtual screening and molecular docking.

Results
A synergistic activity in the combination of HypNP and D-Trp against A. baumannii was observed with a FIC index value of 0.5. There was a 5.10 log10 CFU/mL reduction in the cell viability of A. baumannii when the bacterial cells were treated with 1/2 × MIC of HypNP@D-Trp and subsequently exposed to ultrasound waves and blue light (P < 0.05). Moreover, a significant biofilm degradation effect on biofilm-associated cells of A. baumannii was observed after treatment with aPSDT using 2 × MIC of HypNP@D-Trp in comparison with the control groups (P < 0.05). According to the molecular docking analysis of the protein-ligand complex, Hyp with a high affinity for AbaI showed a binding affinity of − 9.41 kcal/mol. Also, the expression level of abaI gene was significantly downregulated by 10.32-fold in A. baumannii treated with aPSDT as comprised with the control group (P < 0.05).

Conclusions
It can be concluded that HypNP@D-Trp-mediated aPSDT can be considered a promising strategy to overcome the infections caused by A. baumannii by reducing the growth of bacterial biofilm and decreasing the expression of abaI as a gene involved in A. baumannii biofilm formation.
Clinical characteristics and risk factors of organ failure and death in necrotizing pancreatitis
Authors: Yu Liqing , Xie Fengwen , Luo Lingyu , Lei Yupeng , Huang Xin , Yang Xiaoyu , Zhu Yong , He Cong , Li Nianshuang , He Wenhua , Zhu Yin , Lu Nonghua , Yu Bingjun 
Published: January 2023

Abstract
Background
Organ failure (OF) and death are considered the most significant adverse outcomes in necrotizing pancreatitis (NP). However, there are few NP-related studies describing the clinical traits of OF and aggravated outcomes.

Purpose
An improved insight into the details of OF and death will be helpful to the management of NP. Thus, in our research, we addressed the risk factors of OF and death in NP patients.

Methods
We performed a study of 432 NP patients from May 2017 to December 2021. All patients with NP were followed up for 36 months. The primary end-points were risk factors of OF and death in NP patients. The risk factors were evaluated by logistic regression analysis.

Results
NP patients with OF or death patients were generally older, had a higher APACHE II score, longer hospital stay, longer ICU stay, as well as a higher incidence of severe acute pancreatitis (SAP), shock and pancreatic necrosis. Independent risk factors related to OF included BMI, APACHE II score and SAP (P < 0.05). Age, shock and APACHE II score (P < 0.05) were the most significant factors correlated with the risk of death in NP patients. Notably, increased mortality was linked to the number of failed organs.

Conclusions
NP is a potentially fatal disease with a long hospital or ICU stay. Our study indicated that the incidence of OF and death in NP patients was 69.9% and 10.2%, respectively. BMI, SAP, APACHE II score, age and shock are potential risk factors of OF and death in NP patients. Clinicians should focus on these factors for early diagnosis and appropriate therapy.
IgG4-related eosinophilic pleural effusion: a case report
Authors: Wang Lina , Di Jiting , Huang Junfang , Guo Cuiyan 
Published: January 2023

Abstract
Background
The diagnosis of unilateral eosinophilic pleural effusion (EPE) is difficult, especially for the elderly. IgG4-related disease (IgG4-RD) is a rare cause of EPE.

Case presentation
An 81-year-old man was admitted to the hospital for dyspnea due to right pleural effusion. Laboratory examination shows elevated IgG4 and eosinophils in both serum and pleural fluid. The patient was diagnosed with IgG4-RD by video-assisted thoracoscopy and pleural biopsy. We found no evidence of other organ involvement except for the EPE and history of prurigo. He was treated with prednisolone 40 mg daily orally and pleural effusion decreased significantly.

Conclusion
IgG4-RD should be considered in the differential diagnosis of EPE in the elderly. High effusion IgG4 concentration may be an indication of IgG4-related pleural lesions.
Prevention of mother-to-child transmission of HIV in Kermanshah, west of Iran from 2014 to 2021
Authors: Lorestani Roya Chegene , Rostamian Mosayeb , Akya Alisha , Rezaeian Shahab , Afsharian Mandana , Habibi Reza , Bozorgomid Arezoo , Kazemisafa Narges , Jafari Somayeh , Yeilaghi Soliman , Salehi Mansour Mohammad , Namdari Hiva , Ghadiri Keyghobad 
Published: January 2023

AbstractBackgroundThis study aimed to evaluate the implementation of the prevention of mother-to-child transmission (PMTCT) of the HIV-PMTCT program in Kermanshah, west of Iran, from 2014 to 2021.MethodsThe data of all HIV-infected mothers and their infants who were monitored by the Kermanshah behavioral diseases counseling center was extracted and recorded in a checklist.ResultsOut of 95 included infant, 45 (47.4%) were girls and 50 (52.6%) were boys. The mothers were mostly infected with HIV via their infected spouse. The pregnancies of 77 cases (82.1%) were in accordance with the national guideline. The average length of treatment for this group was 185 days. Of the 18 mothers who did not receive treatment, nine were diagnosed during childbirth and nine had no available information. All infants born from infected mothers underwent after-birth-antiretroviral prophylaxis, and all remained healthy. There was no statistically significant relationship between the birth weight and height of neonates with maternal age, maternal last viral load, disease stage, education, and maternal CD4 levels. Only a statistically significant relationship was observed between the duration of treatment and the infants’ weight.ConclusionThe results suggest the feasibility and effectiveness of the PMTCT program for HIV-positive mothers in Kermanshah. It seems that if pregnant HIV-positive women are diagnosed early and covered by a good prevention program on time, the risk of HIV to their babies will be reduced, significantly.
Use of the Strengths and Difficulties Questionnaire in child and school health services among children aged 4 and 6 years in Southern Norway: clinical considerations
Authors: Mølland Eirin , Haraldstad Kristin , Abildsnes Eirik , Håland Åshild Tellefsen , Köpp Unni Mette Stamnes , Fegran Liv , Westergren Thomas 
Published: January 2023

AbstractBackgroundParent reported mental health can be assessed by the Strengths and Difficulties Questionnaire (SDQ). Currently, Norwegian norms for parent-reported SDQ do not exist, whereas Swedish, Danish, and United Kingdom (UK) norms have been published. We aimed to (1) describe parent-reported SDQ among children aged 4 and 6 years in Southern Norway, (2) evaluate empirical cutoff values within the context of the Starting RightTMproject in relation to the Swedish, Danish, and UK cutoffs, and (3) evaluate the representativeness of the study sample with regard to parental socioeconomic status.MethodsThis study included parent-reported observations for 665 children (63% consent rate). Means and standard deviations were calculated for the domains of SDQ, and gender differences were assessed. Based on the Swedish, Danish, and UK cutoffs and the 80thand 90thpercentile cutoff values within the study, we calculated the total number of children with borderline and abnormal scores.ResultsBoys had higher mean total difficulties (7.3 vs 5.6) and impact scores (0.3 vs 0.1) and lower prosocial scores (8.3 vs 8.8) than girls. The differences in means were largest in the case of externalizing symptoms (5.0 vs 3.6) and hyperactivity subscore (3.2 vs 2.3). Using the UK cutoff values, 28 and 25 children had borderline and abnormal total difficulties scores, respectively. The corresponding numbers using the within study or Scandinavian cutoff values were 84–99 and 54–79, respectively. Overall, our study sample was well representative of the target population.ConclusionsOur findings consistently indicated that girls had better SDQ scores than boys among children aged 4 and 6 years. Fewer children would be identified as having mental health difficulties using the UK cutoff values than using the Scandinavian age- and gender-relevant cutoff values.
Efficacy of three sputum specimens for the diagnosis of Mycobacterium avium complex pulmonary disease
Authors: Urabe Naohisa , Sakamoto Susumu , Masuoka Marie , Kato Chiaki , Yamaguchi Asuka , Tokita Nozomi , Homma Sakae , Kishi Kazuma 
Published: January 2023

Abstract
Background
In Mycobacterium avium complex pulmonary disease (MAC-PD), diagnosis requires a positive culture from at least two separate expectorated sputum specimens. The optimal number of sputum examinations remains unclear.

Objective
This study sought to elucidate the diagnostic yield of acid-fast bacilli in MAC-PD using 3 sputum specimens and to clarify the clinical characteristics of patients with MAC-PD diagnosed using 3 sputum specimens. Furthermore, we investigated the correlation between increased number of sputum specimens and diagnostic yield.

Methods
We reviewed the medical records of 139 patients with MAC-PD diagnosed at Toho University Omori Medical Center for whom at least three sputum specimens were examined before treatment from November 2014 through June 2021. Patients were classified into the 3-sputum diagnosed and the non-3 sputum diagnosed groups based on diagnostic procedure; clinical and radiological characteristics were compared. We also assessed diagnostic yield with the increased number of sputum specimens.

Results
Diagnostic yield with 3 sputum specimens was 16.5% (23/139). The 3-sputum diagnosed group had a lower body mass index [18.6(17–19.5) vs. 19.5(18–21.5); p = 0.014], and higher chest CT score [9(6.5–13) vs. 6(4–9); p = 0.011] including cavitary lesions (39.1% vs. 19%; p = 0.037) compared with the non-3 sputum diagnosed group. When the number of sputum specimens was increased to 6, the diagnostic yield increased to 23.7% (33/139).

Conclusion
Diagnostic yield with 3 sputum specimens was 16.5%. Patients diagnosed using 3 sputum specimens had more severe chest CT findings including cavitary lesions. Increasing the number of sputum specimens to 6 improved diagnostic yield by 7.2%.
The classification of flash visual evoked potential based on deep learning
Authors: Liang Na , Wang Chengliang , Li Shiying , Xie Xin , Lin Jun , Zhong Wen 
Published: January 2023

Abstract
Background
Visual electrophysiology is an objective visual function examination widely used in clinical work and medical identification that can objectively evaluate visual function and locate lesions according to waveform changes. However, in visual electrophysiological examinations, the flash visual evoked potential (FVEP) varies greatly among individuals, resulting in different waveforms in different normal subjects. Moreover, most of the FVEP wave labelling is performed automatically by a machine, and manually corrected by professional clinical technicians. These labels may have biases due to the individual variations in subjects, incomplete clinical examination data, different professional skills, personal habits and other factors. Through the retrospective study of big data, an artificial intelligence algorithm is used to maintain high generalization abilities in complex situations and improve the accuracy of prescreening.

Methods
A novel multi-input neural network based on convolution and confidence branching (MCAC-Net) for retinitis pigmentosa RP recognition and out-of-distribution detection is proposed. The MCAC-Net with global and local feature extraction is designed for the FVEP signal that has different local and global information, and a confidence branch is added for out-of-distribution sample detection. For the proposed manual features,a new input layer is added.

Results
The model is verified by a clinically collected FVEP dataset, and an accuracy of 90.7% is achieved in the classification task and 93.3% in the out-of-distribution detection task.

Conclusion
We built a deep learning-based FVEP classification algorithm that promises to be an excellent tool for screening RP diseases by using FVEP signals.
Evaluation the efficacy of oral immunization of broiler chickens with a recombinant Lactobacillus casei vaccine vector expressing the Carboxy-terminal fragment of α-toxin from Clostridium perfringens
Authors: Shamshirgaran Mohammad Ali , Golchin Mehdi , Salehi Mahmoud , Kheirandish Reza 
Published: January 2023

Abstract
Background
Clostridium perfringens (C. perfringens) is a serious anaerobic enteric pathogen causing necrotic enteritis (NE) in broiler chickens. Following the ban on antibiotics as growth promoters in animal feedstuffs, there has been a remarkable rise in occurrence of NE which resulted in considering alternative approaches, particularly vaccination. The objective of this work was to evaluate the recombinant Lactobacillus casei (L. casei) expressing the C-terminal domain of α-toxin from C. perfringens as a potential probiotic-based vaccine candidate to immunize the broiler chickens against NE.

Results
The broiler chickens immunized orally with recombinant vaccine strain were significantly protected against experimental NE challenge, and developed specific serum anti-α antibodies. Additionally, the immunized birds showed higher body weight gains compared with control groups during the challenge experiment.

Conclusions
The current study showed that oral immunization of broiler chickens with a safe probiotic-based vector vaccine expressing α-toxin from C. perfringens could provide protective immunity against NE in birds.
Accumulated hypertension burden on atrial fibrillation risk in diabetes mellitus: a nationwide population study
Authors: Choi JungMin , Lee So‑Ryoung , Choi Eue‑Keun , Lee HuiJin , Han MinJu , Ahn Hyo-Jeong , Kwon Soonil , Lee Seung-Woo , Han Kyung‑Do , Oh Seil , Lip Gregory Y. H. 
Published: January 2023

Abstract
Background
Patients with diabetes mellitus have an increased risk of incident atrial fibrillation (AF). The effect of accumulated hypertension burden is a less well-known modifiable risk factor. We explored the relationship between accumulated hypertension burden and incident AF in these patients.

Methods
We evaluated data for 526,384 patients with diabetes who underwent three consecutive health examinations, between 2009 and 2012, from the Korean National Health Insurance Service. Hypertension burden was calculated by assigning points to each stage of hypertension in each health examination: 1 for stage 1 hypertension (systolic blood pressure [SBP] 130–139 mmHg; diastolic blood pressure [DBP] 80–89 mmHg); 2 for stage 2 (SBP 140–159 mmHg and DBP 90–99 mmHg); and 3 for stage 3 (SBP ≥ 160 mmHg or DBP ≥ 100 mmHg). Patients were categorized into 10 hypertensive burden groups (0–9). Groups 1–9 were then clustered into 1–3, 4–6, and 7–9.

Results
During a mean follow-up duration of 6.7 ± 1.7 years, AF was newly diagnosed in 18,561 (3.5%) patients. Compared to patients with hypertension burden 0, those with burden 1 to 9 showed a progressively increasing risk of incident AF: 6%, 11%, 16%, 24%, 28%, 41%, 46%, 57%, and 67% respectively. Clusters 1–3, 4–6, and 7–9 showed increased risks by 10%, 26%, and 45%, respectively, when compared to a hypertension burden of 0.

Conclusions
Accumulated hypertension burden was associated with an increased risk of incident AF in patients with diabetes. Strict BP control should be emphasized for these patients.
The effect of physician density on colorectal cancer stage at diagnosis: causal inference methods for spatial data applied on regional-level data
Authors: Draganic Dajana , Wangen Knut Reidar 
Published: January 2023

Abstract
Background
The early detection of colorectal cancer (CRC) through regular screening decreases its incidence and mortality rates and improves survival rates. Norway has an extremely high percentage of CRC cases diagnosed at late stages, with large variations across municipalities and hospital catchment areas. This study examined whether the availability of physicians related to CRC primary diagnosis and preoperative investigations, or physician density, contributes to the observed geographical differences in late-stage incidence rates.

Method
Municipality-level data on CRC stage at diagnosis were obtained from the Cancer Registry of Norway for the period 2012–2020. Physician density was calculated as the number of physicians related to CRC investigations, general practitioners (GPs) and specialists per 10,000 people, using physician counts per municipality and hospital areas from Statistics Norway. The relationship was examined using a novel causal inference method for spatial data—neighbourhood adjustment method via spatial smoothing (NA approach)—which allowed for studying the region-level effect of physician supply on CRC outcome by using spatially referenced data and still providing causal relationships.

Results
According to the NA approach, an increase in one general practitioner per 10,000 people will result in a 3.6% (CI −0.064 to −0.008) decrease in late-stage CRC rates. For specialists, there was no evidence of a significant correlation with late-stage CRC distribution, while for both groups, GPs and specialists combined, an increase of 1 physician per 10,000 people would be equal to an average decrease in late-stage incidence rates by 2.79% (CI −0.055 to −0.001).

Conclusion
The study confirmed previous findings that an increase in GP supply will significantly improve CRC outcomes. In contrast to previous research, this study identified the importance of accessibility to both groups of physicians—GPs and specialists. If GPs encounter insufficient workforces in hospitals and long delays in colonoscopy scheduling, they will less often recommend colonoscopy examinations to patients. This study also highlighted the efficiency of the novel methodology for spatially referenced data, which allowed us to study the effect of physician density on cancer outcomes within a causal inference framework.