bluuebunny/crossref_metadata_2025_split huggingface dataset:
Automated cervical cell segmentation using deep ensemble learning
Authors: Ji Jie , Zhang Weifeng , Dong Yuejiao , Lin Ruilin , Geng Yiqun , Hong Liangli 
Published: September 2023

Abstract
Background
Cervical cell segmentation is a fundamental step in automated cervical cancer cytology screening. The aim of this study was to develop and evaluate a deep ensemble model for cervical cell segmentation including both cytoplasm and nucleus segmentation.

Methods
The Cx22 dataset was used to develop the automated cervical cell segmentation algorithm. The U-Net, U-Net +  + , DeepLabV3, DeepLabV3Plus, Transunet, and Segformer were used as candidate model architectures, and each of the first four architectures adopted two different encoders choosing from resnet34, resnet50 and denseNet121. Models were trained under two settings: trained from scratch, encoders initialized from ImageNet pre-trained models and then all layers were fine-tuned. For every segmentation task, four models were chosen as base models, and Unweighted average was adopted as the model ensemble method.

Results
U-Net and U-Net +  + with resnet34 and denseNet121 encoders trained using transfer learning consistently performed better than other models, so they were chosen as base models. The ensemble model obtained the Dice similarity coefficient, sensitivity, specificity of 0.9535 (95% CI:0.9534–0.9536), 0.9621 (0.9619–0.9622),0.9835 (0.9834–0.9836) and 0.7863 (0.7851–0.7876), 0.9581 (0.9573–0.959), 0.9961 (0.9961–0.9962) on cytoplasm segmentation and nucleus segmentation, respectively. The Dice, sensitivity, specificity of baseline models for cytoplasm segmentation and nucleus segmentation were 0.948, 0.954, 0.9823 and 0.750, 0.713, 0.9988, respectively. Except for the specificity of cytoplasm segmentation, all metrics outperformed the best baseline models (P < 0.05) with a moderate margin.

Conclusions
The proposed algorithm achieved better performances on cervical cell segmentation than baseline models. It can be potentially used in automated cervical cancer cytology screening system.
The minimum number of examined lymph nodes was 24 for optimal survival of pathological T2-4 gastric cancer: a multi-center, hospital-based study covering 20 years of data
Authors: Zhao Lulu , Zhang Fan , Jiao Fuzhi , Zhou Xiadong , Niu Penghui , Han Xue , Wang Wanqing , Luan Xiaoyi , He Mingyan , Guan Quanlin , Li Yumin , Zhao Dongbing , Gao Jidong , Chen Yingtai 
Published: September 2023

Abstract
Introduction
The current National Comprehensive Cancer Network (NCCN) guidelines recommend that at least 16 lymph nodes should be examined for gastric cancer patients to reduce staging migration. However, there is still debate regarding the optimal management of examined lymph nodes (ELNs) for gastric cancer patients. In this study, we aimed to develop and test the minimum number of ELNs that should be retrieved during gastrectomy for optimal survival in patients with gastric cancer.

Methods
We used the restricted cubic spline (RCS) to identify the optimal threshold of ELNs that should be retrieved during gastrectomy based on the China National Cancer Center Gastric Cancer (NCCGC) database. Northwest cohort, which sourced from the highest gastric cancer incidence areas in China, was used to verify the optimal cutoff value. Survival analysis was performed via Kaplan-Meier estimates and Cox proportional hazards models.

Results
In this study, 12,670 gastrectomy patients were included in the NCCGC cohort and 4941 patients in the Northwest cohort. During 1999–2019, the average number of ELNs increased from 17.88 to 34.45 nodes in the NCCGC cohort, while the number of positive lymph nodes remained stable (5–6 nodes). The RCS model showed a U-curved association between ELNs and the risk of all-cause mortality, and the optimal threshold of ELNs was 24 [Hazard ratio (HR) = 1.00]. The ELN ≥ 24 group had a better overall survival (OS) than the ELN < 24 group clearly (P = 0.003), however, with respect to the threshold of 16 ELNs, there was no significantly difference between the two groups (P = 0.101). In the multivariate analysis, ELN ≥ 24 group was associated with improved survival outcomes in total gastrectomy patients [HR = 0.787, 95% confidence interval (CI): 0.711–0.870, P < 0.001], as well as the subgroup analysis of T2 patients (HR = 0.621, 95%CI: 0.399–0.966, P = 0.035), T3 patients (HR = 0.787, 95%CI: 0.659–0.940, P = 0.008) and T4 patients (HR = 0.775, 95%CI: 0.675–0.888, P < 0.001).

Conclusion
In conclusion, the minimum number of ELNs for optimal survival of gastric cancer with pathological T2-4 was 24.
Preoperative treatment with mFOLFIRINOX or Gemcitabine/Nab-paclitaxel +/- isotoxic high-dose stereotactic body Radiation Therapy (iHD-SBRT) for borderline resectable pancreatic adenocarcinoma (the STEREOPAC trial): study protocol for a randomised comparative multicenter phase II trial
Authors: Bouchart Christelle , Navez Julie , Borbath Ivan , Geboes Karen , Vandamme Timon , Closset Jean , Moretti Luigi , Demetter Pieter , Paesmans Marianne , Van Laethem Jean-Luc 
Published: September 2023

Abstract
Background
For patients with pancreatic ductal adenocarcinoma (PDAC), surgical resection remains the only potentially curative treatment. Surgery is generally followed by postoperative chemotherapy associated with improved survival, yet neoadjuvant therapy is a rapidly emerging concept requiring to be explored and validated in terms of treatment options and oncological outcomes. In this context, stereotactic body radiation (SBRT) appears feasible and can be safely integrated into a neoadjuvant chemotherapy regimen of modified FOLFIRINOX (mFFX) with promising benefits in terms of R0 resection, local control and survival. However, the optimal therapeutic sequence is still not known, especially for borderline resectable PDAC, and the role of adding SBRT to chemotherapy in the neoadjuvant setting needs to be evaluated in randomised controlled trials. The aim of the STEREOPAC trial is to assess the impact and efficacy of adding isotoxic high-dose SBRT (iHD-SBRT) to neoadjuvant mFFX or Gemcitabine/Nab-Paclitaxel (Gem/Nab-P) in patients with borderline resectable PDAC.

Methods
This is a randomised comparative multicentre phase II trial, planning to enrol patients (n = 256) diagnosed with a borderline resectable biopsy-confirmed PDAC. Patients will receive 4 cycles of mFFX (or 6 doses of Gem/Nab-P). After full disease restaging, non-progressive patients will be randomised for receiving either 4 additional mFFX cycles (or 6 doses of Gem/Nab-P) (Arm A), or 2 mFFX cycles (or 3 doses of Gem/Nab-P) + iHD-SBRT (35 to 55 Gy in 5 fractions) + 2 mFFX cycles (or 3 doses of Gem/Nab-P) (Arm B). Then curative surgery will be performed followed by adjuvant chemotherapy according to patient’s condition. The co-primary endpoints are R0 resection and disease-free survival after the complete sequence strategy. The secondary endpoints include resection rate, overall survival, locoregional failure / distant metastasis free interval, pathologic complete response, toxicity, postoperative complications and quality of life assessment.

Discussion
This trial will help define the best neoadjuvant treatment sequence for borderline resectable PDAC and aims to evaluate if a total neoadjuvant treatment integrating iHD-SBRT improves the patients’ oncological outcomes.

Trial registration
The study was registered at ClinicalTrails.gov (NCT05083247) on October 19th, 2021, and in the Clinical Trials Information System (CTIS) EU CT database (2022-501181-22-01) on July 2022.
Comparison between P-POSSUM and NELA risk score for patients undergoing emergency laparotomy in Egyptian patients
Authors: Alabbasy Mahmoud Magdy , Elsisy Alaa Abd Elazim , Mahmoud Adel , Alhanafy Saad Soliman 
Published: September 2023

Abstract
Background and aims
The Portsmouth-Physiological and Operative Severity Score for the enumeration of Mortality and Morbidity (P-POSSUM) is one of the scores that is used most frequently for determining the likelihood of mortality in patients undergoing emergency laparotomy. National Emergency Laparotomy Audit (NELA) presents a novel and validated score. Therefore, we aimed to compare the performance of the NELA and P-POSSUM mortality risk scores in predicting 30-day and 90-day mortality in patients undergoing emergency laparotomy.

Methods
Between August 2020 and October 2022, this cohort study was undertaken at Menoufia University Hospital. We compared the P-POSSUM, preoperative NELA, and postoperative NELA scores in patients undergoing emergency laparotomy. All variables needed to calculate the used scores were collected. The outcomes included the death rates at 30 and 90 days. By calculating the area under the curve (AUC) for every mortality instrument, the discrimination of the various methods was evaluated and compared.

Results
Data from 670 patients were included. The observed risk of 30-day and 90-day mortality was 10.3% (69/670) and 13.13% (88/670), respectively. Concerning 30-day mortality, the AUC was 0.774 for the preoperative NELA score, 0.763 for the preoperative P-POSSUM score, and 0.780 for the postoperative NELA score. Regarding 90-day mortality, the AUCs for the preoperative NELA score, preoperative P-POSSUM score, and postoperative NELA score were 0.649 (0.581–0.717), 0.782 (0.737–0.828), and 0.663 (0.608–0.718), respectively. There was noticeable difference in the three models' capacity for discrimination, according to pairwise comparisons.

Conclusions
The probability of 30-day and 90-day death across the entire population was underestimated by the NELA and P-POSSUM scores. There was discernible difference in predictive performance between the two scores.
A collision tumor of nasopharyngeal carcinoma and primary mantle cell lymphoma in the nasopharynx: a case report and review of the literature
Authors: Jiang Meng , Yuan Xiao-ping , Zhang Hong , Li Chuang-quan , Mao Yong-lin , Chen Wei-liang 
Published: September 2023

Abstract
Background
Nasopharyngeal carcinoma (NPC) is more common in men aged 40 to 59, and radiotherapy is an effective treatment. Nasopharyngeal lymphoma (NPL) is rare, and the coexistence of nasopharyngeal mantle cell lymphoma (MCL) and NPC is even rarer. A collision tumor is a rare type of tumor that refers to two or more different tumors occurring in the same organ. No reports to date have described a collision tumor of NPC and MCL occurring within the same nasopharyngeal mass. We herein report the successful treatment of a unique case of synchronous coexistence of NPC and MCL occurring in the nasopharynx of a Chinese man.

Case presentation
A 58-year-old man presented with a 5-month history of swallowing discomfort. Biopsy was performed under nasopharyngeal endoscopy, and histopathology revealed NPC. Magnetic resonance imaging revealed lesions in the nasopharynx, oropharynx, and tonsils, as well as enlarged lymph nodes in the parotid gland, posterior ear, and neck. This may be a synchronous dual primary tumor coexisting with NPC and NPL. Pathology consultation confirmed that the biopsy specimen of the nasopharynx was a collision tumor of NPC and MCL. Positron emission tomography computed tomography (PET-CT) revealed thickening of the posterior wall of the nasopharynx, which was considered NPC with lymphoma. The enlargement of the pharyngeal lymph ring and multiple hypermetabolic lymph nodes were evaluated as lymphoma infiltration. The patient received two courses of R-CHOP chemotherapy (rituximab, cyclophosphamide, doxorubicin, vincristine, and prednisone) followed by head and neck radiotherapy. At the time of this writing, he had remained alive without recurrence for 61 months since the initial treatment and was still undergoing follow-up.

Conclusions
It is very important to correctly recognize collision tumors. Magnetic resonance imaging helps identify different components of collision tumors. Pathological examination helps to confirm the diagnosis. Histological examination reveals different components, and PET-CT can help determine the extent of the lesion. Dose-adjusted chemotherapy combined with radiotherapy may have promising herapeutic effects, but additional case studies are needed to confirm.
What do I do to avoid sexually transmitted diseases? A scale development study: behavioral scale for protection from sexually transmitted diseases
Authors: Kılavuz Mustafa , Yigit Feride 
Published: September 2023

AbstractThe authors’ aim is to develop and confirm a reliable and valid measurement tool that can measure women’s behavior to prevent sexually transmitted diseases. The study data were collected from adult women aged 18–47 years (n = 505). Explanatory factor analysis (EFA) was applied to the STD scale consisting of 44 items in a 5-point Likert style. According to the results of EFA, 21 items were defined in the scale. The KMO value of the scale is 90.6%. In the study, the varimax rotation method was used to bring the factors together with the related items. As a result of varimax rotation, two factors with eigenvalues greater than 1 were found in the scale. The overall Cronbach’s alpha coefficient of the scale was calculated as 0.911, 0.941 for the first subdimension and 0.889 for the second subdimension. The validity and reliability of this study have been proven according to the results of explanatory factor analysis (EFA) and confirmatory factor analysis (CFA).
Vaccination coverage in rural Burkina Faso under the effects of COVID-19: evidence from a panel study in eight districts
Authors: Cooper Sarah , Bicaba Frank , Tiendrebeogo Cheick Oumar , Bila Alice , Bicaba Abel , Druetz Thomas 
Published: September 2023

Abstract
Background
Improving infant immunization completion and promoting equitable vaccination coverage are crucial to reducing global under-5 childhood mortality. Although there have been hypotheses that the impact of the COVID-19 pandemic would decrease the delivery of health services and immunization campaigns in low- and middle-income countries, the available evidence is still inconclusive. We conducted a study in rural Burkina Faso to assess changes in vaccination coverage during the pandemic. A secondary objective was to examine long-term trends in vaccination coverage throughout 2010–2021.

Methods
Using a quasi-experimental approach, we conducted three rounds of surveys (2019, 2020, 2021) in rural Burkina Faso that we pooled with two previous rounds of demographic and household surveys (2010, 2015) to assess trends in vaccination coverage. The study population comprised infants aged 0–13 months from a sample of 325 households randomly selected in eight districts (n = 736). We assessed vaccination coverage by directly observing the infants’ vaccination booklet. Effects of the pandemic on infant vaccination completion were analyzed using multi-level logistic regression models with random intercepts at the household and district levels.

Results
A total of 736 child-year observations were included in the analysis. The proportion of children with age-appropriate complete vaccination was 69.76% in 2010, 55.38% in 2015, 50.47% in 2019–2020, and 64.75% in 2021. Analyses assessing changes in age-appropriate full-vaccination coverage before and during the pandemic show a significant increase (OR: 1.8, 95% CI: 1.14–2.85). Our models also confirmed the presence of heterogeneity in full vaccination between health administrative districts. The pandemic could have increased inequities in infant vaccination completion between these districts. The analyses suggest no disruption in age-appropriate full vaccination due to COVID-19. Our findings from our sensitivity analyses to examine trends since 2010 did not show any steady trends.

Conclusion
Our findings in Burkina Faso do not support the predicted detrimental effects of COVID-19 on the immunization schedule for infants in low- and middle-income countries. Analyses comparing 2019 and 2021 show an improvement in age-appropriate full vaccination. Regardless of achieving and sustaining vaccination coverage levels in Burkina Faso, this should remain a priority for health systems and political agendas.
Q fever and toxoplasmosis in South African livestock and wildlife: a retrospective study on seropositivity, sporadic abortion, and stillbirth cases in livestock caused by Coxiella burnetii
Authors: Mangena Maruping L. , Gcebe Nomakorinte , Thompson Peter N. , Adesiyun Abiodun A. 
Published: September 2023

Abstract
Background
Q fever and toxoplasmosis are economically important zoonoses as they cause considerable losses in livestock (cattle, sheep and goats) and wildlife (antelopes, giraffes, lions, and cheetahs) through reproductive disorders such as abortions and stillbirths. Q fever and toxoplasmosis testing in South Africa is conducted by the Agricultural Research Council-Onderstepoort Veterinary Research (ARC-OVR). However, both zoonoses are understudied and not monitored in South Africa as they are not considered controlled or notifiable diseases in the Animal Disease Act 35 of 1984. A retrospective study was conducted on Q fever (2007–2009) and toxoplasmosis (2007–2017) using diagnostic laboratory data at the ARC-OVR. Also, we report on sporadic abortion and stillbirth cases in livestock from diagnostic tissue samples submitted for Coxiella burnetii polymerase chain reaction (PCR) detection at the ARC-OVR.

Results
During 2007 to 2009, 766 animal samples were tested for C. burnetii antibodies and seropositivity was 0.9% (95%CI: 0.3–1.7) with sheep (1.9%; 95%CI: 0.6–4.4) having the highest seropositivity followed by cattle (0.7%; 95%CI: 0.09–2.6), while all goats (0.0%; 95%CI: 0.0–4.2) and wildlife (0.0%; 95%CI: 0.0–2.5) tested were negative. From 2007 to 2017, 567 sera were tested for T. gondii antibodies; overall seropositivity was 12.2% (95%CI: 9.6–15). Wildlife had highest seropositivity to T. gondii antibodies (13.9%; 95%CI: 9.0–19.7) followed by goats (12.9%; 95%CI: 9.2–17.4) and sheep (12.3%; 95%CI: 5.1–23.8) while seropositivity in cattle was 2.4% (95%CI: 0.06–12.9). Of 11 animals tested by C. burnetii PCR detection (2021–2022), 10 (91.0%) were positive. The amplicon sequences showed similarity to Coxiella burnetii strain 54T1 transposase gene partial coding sequence.

Conclusions
We have confirmed the occurrence of the causative agents of Q fever and toxoplasmosis in livestock and wildlife in South Africa, with data limitations. These zoonoses remain of importance with limited information about them in South Africa. This study provides baseline information for future studies on Q fever and toxoplasmosis in South African livestock and wildlife, as well other African countries. Due to limited data collection experienced in this study, it is recommended that improvements in data collection samples tested should include associated factors such as sex, age, and breed of the animals.
A strategy to enhance and modify fatty acid synthesis in Corynebacterium glutamicum and Escherichia coli: overexpression of acyl-CoA thioesterases
Authors: Liu Jin , Mandlaa  , Wang Jia , Sun Ziyu , Chen Zhongjun 
Published: September 2023

Abstract
Background
Fatty acid (FA) is an important platform compound for the further synthesis of high‐value biofuels and oleochemicals, but chemical synthesis of FA has many limitations. One way to meet the future demand for FA could be to use microbial cell factories for FA biosynthesis.

Results
Thioesterase (TE; TesA, TesB, and TE9) of Corynebacterium glutamicum (CG) can potentially improve FA biosynthesis, and tesA, tesB, and te9 were overexpressed in C. glutamicum and Escherichia coli (EC), respectively, in this study. The results showed that the total fatty acid (TFA) production of CGtesB and ECtesB significantly increased to 180.52 mg/g dry cell weight (DCW) and 123.52 mg/g DCW, respectively (P < 0.05). Overexpression strains CG and EC could increase the production of C16:0, C18:1(t), C18:2, C20:1, C16:1, C18:0, and C18:1(c) (P < 0.05), respectively, and the changes of long-chain FA resulted in the enhancement of TFA production. The enzymatic properties of TesA, TesB, and TE9 in vitro were determined: they were specific for long-, broad and short-chain substrates, respectively; the optimal temperature was 30.0 °C and the optimal acid–base (pH) were 8.0, 8.0, and 9.0, respectively; they were inhibited by Fe2+, Cu2+, Zn2+, Mg2+, and K+.

Conclusion
Overexpression TE enhances and modifies FA biosynthesis with multiple productive applications, and the enzyme properties provided useful clues for optimizing FA synthesis.

Graphical Abstract
The novel oncogenic factor TET3 combines with AHR to promote thyroid cancer lymphangiogenesis via the HIF-1α/VEGF signaling pathway
Authors: Yang Liyun , Zhao Runyu , Qiao Peipei , Cui Jiaxin , Chen Xiaoping , Fan Jinping , Hu An , Huang Shuixian 
Published: September 2023

Abstract
Background
Lymphangiogenesis has been reported to play crucial roles in the metastasis of thyroid cancer (THCA), but despite the significant research on lymphangiogenesis in THCA, the precise regulatory mechanism remains unclear.

Methods
Public databases including the Cancer Genome Atlas (TCGA), TIMER, and UALCAN were used to analyze and visualize the expression of TET3 and AHR in THCA, and the correlation between these molecules were used by TIMER. Additionally, RT-PCR and Western Blot were performed to determine the mRNA and protein expression of related proteins. Plate colony formation, wound healing, cell cycle, apoptosis, angiogenesis and transwell assay were used to examine the ability of proliferation, movement, lymphangiogenesis, migration and invasion of THCA cells.

Results
Analysis of the TCGA database revealed higher expression levels of TET3 and AHR in tumor tissue compared to normal tissue in THCA. Additionally, a strong correlation was observed between TET3 and AHR. UALCAN database demonstrated that high expression of TET3 and AHR was associated with advanced THCA TNM stages in THCA patients. Furthermore, TET3 activation accelerated THCA cell proliferation by inducing G2/M phase arrest and suppressing apoptosis, while AHR inactivation reduced THCA cell proliferation by decreasing G2/M phase arrest and promoting apoptosis in vitro. Notably, both TET3 and AHR significantly enhanced THCA cell lymphangiogenesis, migration and invasion. Moreover, TET3 activation and AHR inactivation regulated HIF-1α/VEGF signaling pathway, which ultimately, blocked the HIF-1α/VEGF in THCA cells and impaired their movement, migration and invasion abilities.

Conclusions
The combined action of TET3 and AHR to promote lymphangiogenesis in THCA through the HIF-1α/VEGF signaling pathway, and targeting them might provide a potential treatment strategy for THCA.