bluuebunny/crossref_metadata_2025_split huggingface dataset:
A prospective randomised controlled trial investigating household SARS-CoV-2 transmission in a densely populated community in Cape Town, South Africa – the transmission of COVID-19 in crowded environments (TRACE) study
Authors: Smith Philip , Little Francesca , Hermans Sabine , Davies Mary-Ann , Wood Robin , Orrell Catherine , Pike Carey , Peters Fatima , Dube Audry , Georgeu-Pepper Daniella , Curran Robyn , Fairall Lara , Bekker Linda-Gail 
Published: July 2024

Abstract
Background
South Africa’s first SARS-CoV-2 case was identified 5th March 2020 and national lockdown followed March 26th. Households are an important location for secondary SARS-CoV-2 infection. Physical distancing and sanitation – infection mitigation recommended by the World Health Organization (WHO) at the time – are difficult to implement in limited-resource settings because of overcrowded living conditions.

Methods
This study (ClinicalTrials.gov NCT05119348) was conducted from August 2020 to September 2021 in two densely populated, low socioeconomic Cape Town community sub-districts. New COVID-19 index cases (ICs) identified at public clinics were randomised to an infection mitigation intervention (STOPCOV) delivered by lay community health workers (CHWs) or standard of care group. STOPCOV mitigation measures included one initial household assessment conducted by a CHW in which face masks, sanitiser, bleach and written information on managing and preventing spread were provided. This was followed by regular telephonic follow-up from CHWs. SARS-CoV-2 PCR and IgM/IgG serology was performed at baseline, weeks 1, 2, 3 and 4 of follow-up.

Results
The study randomised 81 ICs with 245 HHCs. At baseline, no HHCs in the control and 7 (5%) in the intervention group had prevalent SARS-CoV-2. The secondary infection rate (SIR) based on SARS-CoV-2 PCR testing was 1.9% (n = 2) in control and 2.9% (n = 4) in intervention HHCs (p = 0.598). At baseline, SARS-CoV-2 antibodies were present in 15% (16/108) of control and 38% (52/137) of intervention participants. At study end incidence was 8.3% (9/108) and 8.03% (11/137) in the intervention and control groups respectively. Antibodies were present in 23% (25/108) of control HHCs over the course of the study vs. 46% (63/137) in the intervention arm. CHWs made twelve clinic and 47 food parcel referrals for individuals in intervention households in need.

Discussion
Participants had significant exposure to SARS-CoV-2 infections prior to the study. In this setting, household transmission mitigation was ineffective. However, CHWs may have facilitated other important healthcare and social referrals.
Evaluation of transfer ensemble learning-based convolutional neural network models for the identification of chronic gingivitis from oral photographs
Authors: Li Wen , Guo Enting , Zhao Hong , Li Yuyang , Miao Leiying , Liu Chao , Sun Weibin 
Published: July 2024

Abstract
Background
To evaluate the performances of several advanced deep convolutional neural network models (AlexNet, VGG, GoogLeNet, ResNet) based on ensemble learning for recognizing chronic gingivitis from screening oral images.

Methods
A total of 683 intraoral clinical images acquired from 134 volunteers were used to construct the database and evaluate the models. Four deep ConvNet models were developed using ensemble learning and outperformed a single model. The performances of the different models were evaluated by comparing the accuracy and sensitivity for recognizing the existence of gingivitis from intraoral images.

Results
The ResNet model achieved an area under the curve (AUC) value of 97%, while the AUC values for the GoogLeNet, AlexNet, and VGG models were 94%, 92%, and 89%, respectively. Although the ResNet and GoogLeNet models performed best in classifying gingivitis from images, the sensitivity outcomes were not significantly different among the ResNet, GoogLeNet, and Alexnet models (p>0.05). However, the sensitivity of the VGGNet model differed significantly from those of the other models (p < 0.001).

Conclusion
The ResNet and GoogLeNet models show promise for identifying chronic gingivitis from images. These models can help doctors diagnose periodontal diseases efficiently or based on self-examination of the oral cavity by patients.
Caries prevalence among children at public and private primary schools in Riyadh: a retrospective study
Authors: Almutairi Budur , Adam Tasneem Rashed , Bustami Rami 
Published: July 2024

AbstractDental caries is a global oral health issue, especially critical in children, affecting their growth, nutrition, and education due to school absences or distractions from dental pain. The aim of the study was to investigate the correlation between school types (indicative of socioeconomic conditions) and dental caries prevalence among primary school children in Riyadh, alongside assessing the overall caries prevalence among schoolchildren in Riyadh. Retrospective study on 28,343 first and fourth-grade students from 960 public and private schools in Riyadh, using data from the Saudi Ministry of Health (Feb-April 2019). Utilized the DMFT/dmft index for assessment and collected demographic data. Most of the schools were public (76.1%), private national (17.1%), and private international (6.8%). Overall, the mean DMFT index for permanent teeth and the dmft index for primary teeth were 1.78 and 1.94, respectively. 58% of school children had no dental caries, 25% had mild caries, and 17% had moderate to severe caries. Public school children showed a higher caries prevalence than private schools. Oral disease rates were higher in girls than in boys, and grade four students had a higher prevalence than grade one students. Saudi Arabia, a developing nation, faces challenges in addressing oral health, especially in public schools. Targeted initiatives are crucial for awareness, preventive measures, and meeting oral health needs.
Clinical features and risk factors for Sjogren’s syndrome patients suffering from oral candidiasis in Shanxi, China
Authors: Xing Yexing , Shi Honghong , Wang Caihong , Yang Ying 
Published: July 2024

Abstract
Objectives
To investigate the clinical features and risk factors of Sjogren’s Syndrome (SS) patients suffering from oral candidiasis and to provide a foundation for the prevention and treatment of oral candidiasis in SS patients.

Methods
The medical records of 479 SS patients admitted to the Second Hospital of Shanxi Medical University from 2018 to 2020 were analysed to determine the clinical characteristics and risk factors that influence the occurrence of oral candidiasis infection in SS patients.

Results
Patients with oral candidiasis were older than those without oral candidiasis (P < 0.05). Male SS patients had greater oral candidiasis rates (P < 0.05). Unstimulated whole saliva (UWS) and stimulated whole saliva (SWS) were both shown to be adversely associated with oral Candida infections (P < 0.001). Logistic regression revealed that a low UWS was an independent risk factor for oral Candida infections in SS patients (OR: 0.004, P = 0.023). Greater WBC counts (OR: 1.22, P < 0.001), lower haemoglobin levels (OR: 0.97, P = 0.007), lower serum albumin levels (OR: 0.88, P < 0.001), lower IgG levels (OR: 0.91, P = 0.011), lower IgA levels (OR: 0.75, P = 0.011), and lower IgM levels (OR: 0.91, P = 0.015) were found in patients with oral Candida infections. Patients on immunosuppressive medications (OR: 0.32, P = 0.011), particularly rapamycin (P < 0.001), had a decreased rate of oral Candida infections.

Conclusions
Patients with oral candidiasis were older than those without oral candidiasis. Male SS patients are more likely to have oral candidiasis. Individuals with lower UWS and SWS are more susceptible to oral Candida infection. Oral Candida infections in SS patients depend on their immunological status. Rapamycin may increase the abundance of Treg cells to reduce oral Candida infection in SS patients.
Cervical cancer screening by cytology and the burden of epithelial abnormalities in low resource settings: a tertiary-center 42-year study
Authors: Ezzelarab Sahar , El-Husseiny Amro , Nasreldin Magda , Ali Radwa , Nabhan Ashraf ,   Early Cervical Cancer Detection Consortium, Abdel-Razek Maya , Abdel-Salam Magda , Abdel-Salam Reem , Ahmed Rania , Alloub Amal , Alqenawy Hamdy , Alshabrawy Amal , Awad Nahla , Ayaad Sohair , El-Sallaly Hala , El-Sayed Mortada , Fahmy Ragia , Kasem Asmaa , Moubarak Ghada , Morsi Hasan , Rifaat Ragaa , Sakna Noha , Shehabeldin Zeinab , Zenhom Ahmed 
Published: July 2024

Abstract
Background
Cytological screening remains a high-impact practice, particularly in low-resource settings, for preventing cervical cancer. The examination of screening practices over time and the prevalence of epithelial abnormalities have not been investigated in longitudinal studies in one of the largest countries in the Middle East and Africa.

Methods
Routine healthcare data, between March 1981 and December 2022, were extracted from the database of the Early Cancer Detection Unit in a tertiary referral university hospital in the Greater Cairo Region, Egypt. Cervical smears were obtained using a standardized technique and sent to the cytopathology laboratory for conventional cytology examination by expert pathologists. The anonymous data were analyzed to determine the temporal trend of the number of women screened each year and the prevalence of epithelial abnormalities.

Results
Data included the results of satisfactory smears from 95120 women. The mean age (SD) of the women at the time of screening was 38.5 (10.5). None of the included women received an HPV vaccine. Abnormal epithelial cells were reported in 5174 women (5.44%). Of these epithelial abnormalities, the majority were low-grade squamous intraepithelial lesions in 4144 women (4.36%). Other abnormalities included atypical squamous cells in 378 women (0.40%), high-grade squamous intraepithelial lesions in 226 women (0.24%), atypical glandular cells not otherwise specified in 184 women (0.19%), adenocarcinoma in 165 women (0.17%), squamous cell carcinoma in 70 women (0.07%), and atypical glandular cells favoring neoplasms in 7 women (0.01%). Women who were at an early age at first intercourse, those who opted for routine cervical cytology screening, and those who were older at screening were more likely to have epithelial abnormalities. The yearly number of screened women was positively associated with the detection of low-grade squamous intraepithelial lesions (correlation coefficient [95% CI] = 0.84 [0.72, 0.91]) and negatively associated with the detection of squamous cell carcinoma (correlation coefficient [95% CI] = -0.55 [-0.73, -0.29]).

Conclusions
The small number of annually screened Egyptian women and the temporal trend in epithelial abnormalities critically demonstrate the need for establishing and scaling up a structured population-based program to achieve the goal of eliminating cervical cancer.
Macrothrombocytopenia with leukocyte inclusions in a patient with Wilson disease: a case report and literature review
Authors: Lin Shaoze , Cai Jianling , Huang Yuxuan , Chen Hongxing , Yu Meidie , Zhang Dongqing , Huang Zhanqin 
Published: July 2024

Abstract
Background
Wilson disease (WD) is an autosomal recessive disorder caused by homozygous or compound heterozygous mutations in ATP7B. Clinical manifestations primarily involve liver and nervous system lesions, with rarely observed hematologic manifestations.

Case presentation
In the present case, a patient with WD presented with thrombocytopenia, giant platelets, and Döhle-like cytoplasmic inclusions in the leukocytes. Initially, the May–Hegglin anomaly was considered; however, whole-exome sequencing did not reveal any mutation in the MYH9 gene but a heterozygous mutation was found in (C.2804 C > T, p.T935M) in the ATP7B gene. After two years, the patient developed tremors in his hands, lower limb stiffness, and foreign body sensation in the eyes. Additionally, Kayser–Fleischer rings in the corneal limbus were detected by slit-lamp examination. Copper metabolism test indicated a slight decrease in serum ceruloplasmin. Transmission electron microscopy revealed that the inclusion bodies of leukocytes were swollen mitochondria. Mass spectrometry analysis showed that the copper levels were almost 20-fold higher in the leukocytes of the patient than in those of the control group. Based on the Leipzig scoring system, a diagnosis of WD was confirmed. Zinc sulfate treatment ameliorated the patient’s symptoms and enhanced platelet, serum ceruloplasmin, and albumin levels.

Conclusions
In conclusion, this case represents the first documented instance of WD presenting as thrombocytopenia, giant platelets, and Döhle-like cytoplasmic inclusions in the leukocytes. Excessive cellular copper accumulation likely underlies these findings; however, understanding precise mechanisms warrants further investigation.
Microbiological characteristics of the lower airway in adults with bronchiectasis: a prospective cohort study
Authors: Duan Jie-lin , Li Cai-yun , Jiang Ying , Liu Chao , Huang Pan-rui , Gao Li-fen , Guan Wei-jie , Cheng Lin-Ling 
Published: July 2024

Abstract
Background
Microbial infection and colonization are frequently associated with disease progression and poor clinical outcomes in bronchiectasis. Identification of pathogen spectrum is crucial for precision treatment at exacerbation of bronchiectasis.

Methods
We conducted a prospective cohort study in patients with bronchiectasis exacerbation onset and stable state. Bronchoalveolar lavage fluid (BALF) was collected for conventional microbiological tests (CMTs) and metagenomic Next-Generation Sequencing (mNGS). Bronchiectasis patients were monitored for documenting the time to the next exacerbation during longitudinal follow-up.

Results
We recruited 168 eligible participants in the exacerbation cohorts, and 38 bronchiectasis patients at stable state at longitudinal follow-up. 141 bronchiectasis patients at exacerbation onset had definite or probable pathogens via combining CMTs with mNGS reports. We identified that Pseudomonas aeruginosa, non-tuberculous mycobacteria, Haemophilus influenzae, Nocardia spp, and Staphylococcus aureus were the top 5 pathogens with a higher detection rate in our cohorts via combination of CMTs and mNGS analysis. We also observed strong correlations of Pseudomonas aeruginosa, Haemophilus influenzae, non-tuberculous mycobacteria with disease severity, including the disease duration, Bronchiectasis Severity Index, and lung function. Moreover, the adjusted pathogenic index of potential pathogenic microorganism negatively correlated (r = -0.7280, p < 0.001) with the time to the next exacerbation in bronchiectasis.

Conclusion
We have revealed the pathogenic microbial spectrum in lower airways and the negative correlation of PPM colonization with the time to the next exacerbation in bronchiectasis. These results suggested that pathogens contribute to the progression of bronchiectasis.
Metabolic engineering of Komagataella phaffii for the efficient utilization of methanol
Authors: Wang Yuanyuan , Li Ruisi , Zhao Fengguang , Wang Shuai , Zhang Yaping , Fan Dexun , Han Shuangyan 
Published: July 2024

Abstract
Background
Komagataella phaffii, a type of methanotrophic yeast, can use methanol, a favorable non-sugar substrate in eco-friendly bio-manufacturing. The dissimilation pathway in K. phaffii leads to the loss of carbon atoms in the form of CO2. However, the ΔFLD strain, engineered to lack formaldehyde dehydrogenase—an essential enzyme in the dissimilation pathway—displayed growth defects when exposed to a methanol-containing medium.

Results
Inhibiting the dissimilation pathway triggers an excessive accumulation of formaldehyde and a decline in the intracellular NAD+/NADH ratio. Here, we designed dual-enzyme complex with the alcohol oxidase1/dihydroxyacetone synthase1 (Aox1/Das1), enhancing the regeneration of the formaldehyde receptor xylulose-5-phosphate (Xu5P). This strategy mitigated the harmful effects of formaldehyde accumulation and associated toxicity to cells. Concurrently, we elevated the NAD+/NADH ratio by overexpressing isocitrate dehydrogenase in the TCA cycle, promoting intracellular redox homeostasis. The OD600 of the optimized combination of the above strategies, strain DF02-1, was 4.28 times higher than that of the control strain DF00 (ΔFLD, HIS4+) under 1% methanol. Subsequently, the heterologous expression of methanol oxidase Mox from Hansenula polymorpha in strain DF02-1 resulted in the recombinant strain DF02-4, which displayed a growth at an OD600 4.08 times higher than that the control strain DF00 in medium containing 3% methanol.

Conclusions
The reduction of formaldehyde accumulation, the increase of NAD+/NADH ratio, and the enhancement of methanol oxidation effectively improved the efficient utilization of a high methanol concentration by strain ΔFLD strain lacking formaldehyde dehydrogenase. The modification strategies implemented in this study collectively serve as a foundational framework for advancing the efficient utilization of methanol in K. phaffii.
Mapping malaria transmission foci in Northeast Thailand from 2011 to 2021: approaching elimination in a hypoendemic area
Authors: Pongsoipetch Kulchada , Walshe Rebecca , Mukem Suwanna , Kamsri Tanong , Singkham Navarat , Sudathip Prayuth , Kitchakarn Suravadee , Maude Rapeephan Rattanawongnara , Maude Richard James 
Published: July 2024

Abstract
Background
Thailand is approaching local elimination of malaria in the eastern provinces. It has successfully reduced the number of cases over the past decade, but there are persistent transmission hot spots in and around forests. This study aimed to use data from the malaria surveillance system to describe the spatiotemporal trends of malaria in Northeast Thailand and fine-scale patterns in locally transmitted cases between 2011 and 2021.

Methods
Case data was stratified based on likely location of infection and parasite species. Annual Parasite Index per 1000 population (API) was calculated for different categories. Time series decomposition was performed to identify trends and seasonal patterns. Statistically significant clusters of high (hot spots) and low (cold spots) API were identified using the Getis-Ord Gi* statistic. The stability of those hot spots and the absolute change in the proportion of API density from baseline were compared by case type.

Results
The total number of confirmed cases experienced a non-linear decline by 96.6%, from 1061 in 2011 to 36 in 2021. There has been a decline in both Plasmodium vivax and Plasmodium falciparum case numbers, with only four confirmed P. falciparum cases over the last two years—a 98.89% drop from 180 in 2011. API was generally higher in Si Sa Ket province, which had peaks every 2–3 years. There was a large outbreak in Ubon Ratchathani in 2014–2016 which had a high proportion of P. falciparum reported. The proportion of cases classified increased over the study period, and the proportion of cases classed as indigenous to the village of residence increased from 0.2% to 33.3%. There were stable hot spots of indigenous and imported cases in the south of Si Sa Ket and southeast of Ubon Ratchathani. Plasmodium vivax hot spots were observed into recent years, while those of P. falciparum decreased to zero in Ubon in 2020 and emerged in the eastern part in 2021, the same year that P. falciparum hot spots in Si Sa Ket reached zero.

Conclusions
There has been a large, non-linear decline in the number of malaria cases reported and an increasing proportion of cases are classed as indigenous to the patient’s village of residence. Stable hot spots of ongoing transmission in the forested border areas were identified, with transmission likely persisting because of remote location and high-risk forest-going behaviours. Future efforts should include cross-border collaboration and continued targeting of high-risk behaviours to reduce the risk of imported cases seeding local transmission.
Preliminary monitoring of knockdown resistance (kdr) mutation in Anopheles stephensi: insights from a malarious area in Southeastern Iran
Authors: Sanei-Dehkordi Alireza , Paksa Azim , Gorouhi Mohammad Amin , Soleimani-Ahmadi Moussa , Jaberhashemi Seyed Aghil , Salim Abadi Yaser 
Published: July 2024

Abstract
Background
Anopheles stephensi is recognized as the main malaria vector in Iran. In recent years, resistance to several insecticide classes, including organochlorine, pyrethroids, and carbamate compounds, has been reported for this medically important malaria vector. The main objective of the present study was to evaluate the insecticide susceptibility status of An. stephensi collected from the southern part of Iran, and to clarify the mechanism of resistance, using bioassay tests and molecular methods comparing the sequence of susceptible and resistant mosquitoes.

Methods
Mosquito larvae were collected from various larval habitats across six different districts (Gabrik, Sardasht, Tidar, Dehbarez, Kishi and Bandar Abbas) in Hormozgan Provine, located in the southern part of Iran. From each district standing water areas with the highest densities of Anopheles larvae were selected for sampling, and adult mosquitoes were reared from them. Finally, the collected mosquito species were identified using valid keys. Insecticide susceptibility of An. stephensi was tested using permethrin 0.75%, lambdacyhalothrin 0.05%, deltamethrin 0.05%, and DDT 4%, following the World Health Organization (WHO) test procedures for insecticide resistance monitoring. Additionally, knockdown resistance (kdr) mutation in the voltage-gated sodium channel (vgsc) gene was sequenced and analysed among resistant populations to detect possible molecular mechanisms of observed resistance phenotypes.

Results
The susceptibility status of An. stephensi revealed that resistance to DDT and permethrin was found in all districts. Furthermore, resistance to all tested insecticides in An. stephensi was detected in Gabrik, Sardasht, Tidar, and Dehbarez. Analysis of knockdown resistance (kdr) mutations at the vgsc did not show evidence for the presence of this mutation in An. stephensi.

Conclusion
Based on the results of the current study, it appears that in An. stephensi from Hormozgan Province (Iran), other resistance mechanisms such as biochemical resistance due to detoxification enzymes may be involved due to the absence of the kdr mutation or non-target site resistance. Further investigation is warranted in the future to identify the exact resistance mechanisms in this main malaria vector across the country.