bluuebunny/crossref_metadata_2025_split huggingface dataset:
Single-cell omics traces the heterogeneity of prostate cancer cells and the tumor microenvironment
Authors: Yu Xudong , Liu Ruijia , Gao Wenfeng , Wang Xuyun , Zhang Yaosheng 
Published: May 2023

AbstractProstate cancer is one of the more heterogeneous tumour types. In recent years, with the rapid development of single-cell sequencing and spatial transcriptome technologies, researchers have gained a more intuitive and comprehensive understanding of the heterogeneity of prostate cancer. Tumour-associated epithelial cells; cancer-associated fibroblasts; the complexity of the immune microenvironment, and the heterogeneity of the spatial distribution of tumour cells and other cancer-promoting molecules play a crucial role in the growth, invasion, and metastasis of prostate cancer. Single-cell multi-omics biotechnology, especially single-cell transcriptome sequencing, reveals the expression level of single cells with higher resolution and finely dissects the molecular characteristics of different tumour cells. We reviewed the recent literature on prostate cancer cells, focusing on single-cell RNA sequencing. And we analysed the heterogeneity and spatial distribution differences of different tumour cell types. We discussed the impact of novel single-cell omics technologies, such as rich omics exploration strategies, multi-omics joint analysis modes, and deep learning models, on future prostate cancer research. In this review, we have constructed a comprehensive catalogue of single-cell omics studies in prostate cancer. This article aimed to provide a more thorough understanding of the diagnosis and treatment of prostate cancer. We summarised and proposed several key issues and directions on applying single-cell multi-omics and spatial transcriptomics to understand the heterogeneity of prostate cancer. Finally, we discussed single-cell omics trends and future directions in prostate cancer.
Mitigation of Greenhouse Gas Emissions from Rice via Manipulation of Key Root Traits
Authors: Jiménez Juan de la Cruz , Pedersen Ole 
Published: May 2023

AbstractRice production worldwide represents a major anthropogenic source of greenhouse gas emissions. Nitrogen fertilization and irrigation practices have been fundamental to achieve optimal rice yields, but these agricultural practices together with by-products from plants and microorganisms, facilitate the production, accumulation and venting of vast amounts of CO2, CH4 and N2O. We propose that the development of elite rice varieties should target root traits enabling an effective internal O2 diffusion, via enlarged aerenchyma channels. Moreover, gas tight barriers impeding radial O2 loss in basal parts of the roots will increase O2 diffusion to the root apex where molecular O2 diffuses into the rhizosphere. These developments result in plants with roots penetrating deeper into the flooded anoxic soils, producing higher volumes of oxic conditions in the interface between roots and rhizosphere. Molecular O2 in these zones promotes CH4 oxidation into CO2 by methanotrophs and nitrification (conversion of NH4+ into NO3-), reducing greenhouse gas production and at the same time improving plant nutrition. Moreover, roots with tight barriers to radial O2 loss will have restricted diffusional entry of CH4 produced in the anoxic parts of the rhizosphere and therefore plant-mediated diffusion will be reduced. In this review, we describe how the exploitation of these key root traits in rice can potentially reduce greenhouse gas emissions from paddy fields.
Effects of a realistic pesticide spraying sequence for apple crop on stream communities in mesocosms: negligible or notable?
Authors: Mohr Silvia , Meinecke Stefan , Feibicke Michael , Duquesne Sabine , Frische Tobias , Sahm René 
Published: May 2023

Abstract
Background
Several large-scale studies revealed impacts and risks for aquatic communities of small rural lakes and streams due to pesticides in agricultural landscapes. It appears that pesticide risk assessment based on single products does not offer sufficient protection for non-target organisms, which are exposed repeatedly to pesticide mixtures in the environment. Therefore, a comprehensive stream mesocosm study was conducted in order to investigate the potential effects of a realistic spraying sequence for conventional orchard farmed apples on a stream community using pesticides at their regulatory acceptable concentrations (RACs). Eight 74-m-long stream mesocosms were established with water, sand, sediment, macrophytes, plankton and benthic macroinvertebrates. In total, nine fungicidal, four herbicidal and four insecticidal pesticides were applied in four of the eight stream mesocosms on 19 spraying event days in the period from April to July while the remaining four stream mesocosms served as controls. The community composition, the abundance of benthos, periphyton and macrophytes, the emergence of insects, physico-chemical water parameters, and drift measurements of aquatic invertebrates were measured.

Results
The pesticide spraying sequence induced significant effects on invertebrates, periphyton, and macrophytes as well as on the water ion composition especially in the second half of the experiment. It was not possible to relate the observed effects on the community to specific pesticides applied at certain time points and their associated toxic pressure using the toxic unit approach. The most striking result was the statistically significant increase in variation of population response parameters of some taxa in the treated mesocosms compared to the controls. This inter-individual variation can be seen as a general disturbance measure for the ecosystem.

Conclusions
The pesticide spraying sequence simulated by using RAC values had notable effects on the aquatic stream community in the conducted mesocosm study. The results indicate that the current risk assessment for pesticides may not ensure a sufficient level of protection to the field communities facing multiple pesticide entries due to spraying sequences and other combined stress. Hence, there is still room for improvement regarding the prospective risk assessment of pesticides to further reduce negative effects on the environment.
SIMplyBee: an R package to simulate honeybee populations and breeding programs
Authors: Obšteter Jana , Strachan Laura K. , Bubnič Jernej , Prešern Janez , Gorjanc Gregor 
Published: May 2023

Abstract
Background
The Western honeybee is an economically important species globally, but has been experiencing colony losses that lead to economical damage and decreased genetic variability. This situation is spurring additional interest in honeybee breeding and conservation programs. Stochastic simulators are essential tools for rapid and low-cost testing of breeding programs and methods, yet no existing simulator allows for a detailed simulation of honeybee populations. Here we describe SIMplyBee, a holistic simulator of honeybee populations and breeding programs. SIMplyBee is an R package and hence freely available for installation from CRAN http://cran.r-project.org/package=SIMplyBee.

Implementation
SIMplyBee builds upon the stochastic simulator AlphaSimR that simulates individuals with their corresponding genomes and quantitative genetic values. To enable honeybee-specific simulations, we extended AlphaSimR by developing classes for global simulation parameters, , for a honeybee colony, , and multiple colonies, . We also developed functions to address major honeybee specificities: honeybee genome, haplodiploid inheritance, social organisation, complementary sex determination, polyandry, colony events, and quantitative genetics at the individual- and colony-levels.

Results
We describe its implementation for simulating a honeybee genome, creating a honeybee colony and its members, addressing haplodiploid inheritance and complementary sex determination, simulating colony events, creating and managing multiple colonies at the same time, and obtaining genomic data and honeybee quantitative genetics. Further documentation, available at http://www.SIMplyBee.info, provides details on these operations and describes additional operations related to genomics, quantitative genetics, and other functionalities.

Discussion
SIMplyBee is a holistic simulator of honeybee populations and breeding programs. It simulates individual honeybees with their genomes, colonies with colony events, and individual- and colony-level genetic and breeding values. Regarding the latter, SIMplyBee takes a user-defined function to combine individual- into colony-level values and hence allows for modeling any type of interaction within a colony. SIMplyBee provides a research platform for testing breeding and conservation strategies and their effect on future genetic gain and genetic variability. Future developments of SIMplyBee will focus on improving the simulation of honeybee genomes, optimizing the simulator’s performance, and including spatial awareness in mating functions and phenotype simulation. We invite the honeybee genetics and breeding community to join us in the future development of SIMplyBee.
Campylobacter prevalence from food, animals, human and environmental samples in Iran: a systematic review and meta-analysis
Authors: Ansarifar Elham , Riahi Seyed Mohamad , Tasara Taurai , Sadighara Parisa , Zeinali Tayebeh 
Published: May 2023

AbstractBackgroundCampylobacterregarded as a major cause of foodborne gastroenteritis in humans. The present study aimed to determine the prevalence ofcampylobacterin food, animal and human samples of Iran.ResultsQuantitative synthesis was performed from 119 articles. White meat had the highest pooled prevalence ofCampylobacterspp. (43.9%). Pooled prevalence of 7.9% and 5.5% forCampylobacter, respectively, were determined for red meat and eggs from Iran.Campylobacterwas seen in 14.9% of environmental samples and 8.4% of human samples. In most of the samplesC. jejunihad higher frequency thanC. coli.Most of the isolatedCampylobacterharbored several of the known virulence related genes of this pathogen.ConclusionChicken was identified as theCampylobacterreservoir. As such preventive strategies in all stages of poultry production until consumption are necessary to control foodborne human infection with Campylobacter in Iran.
Neurophysiological visual assessment in patients with idiopathic intracranial hypertension: visual evoked potential and multifocal field electroretinography
Authors: Elgaly Marwa A. , Hosny Hanan , El Habashy Hala R. , Hussein Mona , Magdy Rehab , Elanwar Rehab 
Published: May 2023

Abstract
Background
Determining the cause of visual deterioration in idiopathic intracranial hypertension (IIH) patients is of clinical necessity. This study aimed to study the effect of chronic increased ICP on the retina and optic nerve through objective electrophysiological measures in chronic IIH patients.

Methods
Thirty patients with chronic IIH and thirty age and sex-matched healthy controls were included in this study. Papilledema grade and CSF pressure were evaluated in the patients’ group. Both groups were submitted to visual evoked potentials (VEP) and multifocal electroretinogram (mfERG).

Result
The mean value of P100 latencies of the right and left on two check sizes, 1 deg and 15ṁ in chronic IIH patients, was significantly delayed than controls (P-value < 0.001 for each). Chronic IIH patients showed a significantly lower amplitude of the right and left R1, R2, R3, R4 & R5 compared to controls (P-value < 0.001, < 0.001) (P-value < 0.001, < 0.001) (P-value < 0.001, < 0.001) (P-value < 0.001, = 0.001) (P-value = 0.002, < 0.001), respectively. Also, patients showed a significantly delayed peak time of the right and left R1 and R2 compared to controls (P-value < 0.001, < 0.001) (P-value = 0.001, = 0.009), respectively. There was a significant positive correlation between each of CSF pressure and papilledema grade with right and left PVEP latencies. In contrast, there was no statistically significant correlation between either CSF pressure or papilledema grade and PVEP amplitudes in both eyes.

Conclusion
In chronic IIH patients, both optic nerve dysfunction and central retinal changes were identified, supported by VEP and the mfERG findings.
Effect of low-molecular-weight heparin in women undergoing frozen-thawed embryo transfer cycles: a retrospective cohort study
Authors: Sun Bo , Li Lu , Chen Xiaoli , Sun Yingpu 
Published: May 2023

Abstract
Background
Recurrent pregnancy loss (RPL) and recurrent implantation failure (RIF) during in vitro fertilization (IVF) treatment are still tough problems without effective treatments; thus, they are important research topics. There is controversy on whether low molecular weight heparin (LMWH) improves pregnancy outcomes in women with unexplained RPL and RIF. Moreover, currently, there is a paucity of reports on the role of LMWH in the entire population undergoing frozen-thawed embryo transfer (FET) cycles. This study aimed to estimate the effects of LMWH on pregnancy outcomes in women undergoing FET cycles.

Methods
There were 1881 female patients included in the study. Of the 1881 patients, 107 underwent preimplantation genetic diagnosis cycles, which were analyzed individually. The patients were divided into two groups: the LMWH group received injections of 4100 IU/d LMWH from the day of transfer until 14 ± 2 days posttransplant, the control group was the comparison group (without LMWH use). The baseline characteristics and reproductive outcomes of the patients were reviewed.

Results
Of the 1774 women with normal FET cycles, no significant differences were found in the number of embryos implanted (1.31 ± 0.02 vs. 1.28 ± 0.02), embryo implantation rate, biochemical pregnancy rate, clinical pregnancy rate, live birth rate, late abortion rate, and ectopic pregnancy rate between the two groups. The LMWH group had a higher early abortion (17.8% [76/427] vs. 12.5% [55/439], p = 0.030). In the sub-group analysis, among the patients who underwent more than four transfers, the LMWH group had a lower late abortion rate (1.7% [1/60] vs. 13.2% [7/53], p = 0.043). Similarly, of the 107 women who underwent preimplantation genetic diagnosis cycles, the reproductive outcomes were comparable between the two groups.

Conclusion
In the general population and PGD patients, LMWH did not improve pregnancy outcomes. Therefore, the routine use of LMWH is not recommended for early treatment.
Efficacy of resuscitative endovascular balloon occlusion of the aorta for hemorrhage control in patients with abnormally invasive placenta: a historical cohort study
Authors: Ye Yuanhua , Li Jing , Liu Shiguo , Zhao Yang , Wang Yanhua , Chu Yijing , Peng Wei , Lu Caixia , Liu Chong , Zhou Jun 
Published: May 2023

Abstract
Background
Patients with abnormally invasive placenta (AIP) are at high risk of massive postpartum hemorrhage. Resuscitative endovascular balloon occlusion of the aorta (REBOA), as an adjunct therapeutic strategy for hemostasis, offers the obstetrician an alternative for treating patients with AIP. This study aimed to evaluate the role of REBOA in hemorrhage control in patients with AIP.

Methods
This was a historical cohort study with prospectively collected data between January 2014 to July 2021 at a single tertiary center. According to delivery management, 364 singleton pregnant AIP patients desiring uterus preservation were separated into two groups. The study group (balloon group, n = 278) underwent REBOA during cesarean section, whereas the reference group (n = 86) did not undergo REBOA. Surgical details and maternal outcomes were collected. The primary outcome was estimated blood loss and the rate of uterine preservation.

Results
A total of 278 (76.4%) participants experienced REBOA during cesarean section. The patients in the balloon group had a smaller blood loss during cesarean Sect. (1370.5 [752.0] ml vs. 3536.8 [1383.2] ml; P < .001) and had their uterus salvaged more often (264 [95.0%] vs. 23 [26.7%]; P < .001). These patients were also less likely to be admitted to the intensive care unit after delivery (168 [60.4%] vs. 67 [77.9%]; P = .003) and had a shorter operating time (96.3 [37.6] min vs. 160.6 [45.5] min; P < .001). The rate of neonatal intensive care unit admission (176 [63.3%] vs. 52 [60.4%]; P = .70) and total maternal medical costs ($4925.4 [1740.7] vs. $5083.2 [1705.1]; P = .13) did not differ between the two groups.

Conclusions
As a robust hemorrhage-control technique, REBOA can reduce intraoperative hemorrhage in patients with AIP. The next step is identifying associated risk factors and defining REBOA inclusion criteria to identify the subgroups of AIP patients who may benefit more.
Quality of maternal and newborn health care at private hospitals in Iraq: a cross-sectional study
Authors: Tappis Hannah , Lak Rebaz , Alhilfi Riyadh , Zangana Aso Hameed , Wadi Falah , Hipgrave David , Ibrahim Shaimaa 
Published: May 2023

Abstract
Background
Approximately 25% of facility births take place in private health facilities. Recent national studies of maternal and newborn health (MNH) service availability and quality have focused solely on the status of public sector facilities, leaving a striking gap in information on the quality of maternal and newborn care services.

Methods
A rapid cross-sectional assessment was conducted in November 2022 to assess the quality of MNH services at private hospitals in Iraq. Multi-stage sampling was used to select 15% of the country’s 164 private hospitals. Assessment tools included a facility assessment checklist, a structured health worker interview tool, and a structured client exit interview tool. Data collection was conducted using KoboToolbox software on Android tablets, and analysis conducted using SPSS v28.

Results
All hospitals visited provided MNH services and had skilled personnel present or on-call 24 h/day, 7 days/week. Most births (88%) documented between January and June 2022 were cesarean births. Findings indicate that nearly all hospitals have the human resources, equipment, medicines and supplies necessary for quality antenatal, intrapartum and early essential newborn care, and many are also equipped with special units and resources needed to care for small and sick babies. However, while resources are in place for basic and advanced care, there are gaps in knowledge and practice of high-impact interventions that require few or no resources to perform, including skin-to-skin thermal care and support for early initiation of breastfeeding. Person-centered maternity care scores suggest that private hospitals offer a positive experience of care for all clients, however there is room for improvement in provider–client communication.

Conclusions
This assessment highlights the need for deeper dives into factors that underly decisions about how and where to give birth, and both understanding and practice of early essential newborn care and pre-discharge examinations and counseling at private healthcare facilities in Iraq. Engaging private health facility staff in efforts to monitor and improve the quality of maternal and newborn care, with a focus on early essential newborn care and provider–client communication for all clients, will ensure that women and newborns benefit from the best care possible with available resources.
Treatment of FIGO 2018 stage IIIC cervical cancer with different local tumor factors
Authors: Ye Yanna , Li Zhiqiang , Kang Shan , Yang Yongxiu , Ling Bin , Wang Li , Yao Jilong , Li Pengfei , Wang Xueqin , Gong Shipeng , Fan Huijian , Kong Yanxiang , Cao Yuye , Lang Jinghe , Liu Ping , Chen Chunlin 
Published: May 2023

Abstract
Background
To compare the oncological outcomes of patients with FIGO 2018 stage IIIC cervical cancer (CC) involving different local tumor factors who underwent abdominal radical hysterectomy (ARH), neoadjuvant chemotherapy and radical surgery (NACT), or radical chemoradiotherapy (R-CT).

Methods
Based on tumor staging, patients with stage IIIC were divided into T1, T2a, T2b, and T3 groups. Kaplan–Meier and Cox proportional hazards regression analysis were used to compare their overall survival (OS) and disease-free survival (DFS) of 5 years.

Results
We included 4,086 patients (1,117, 1,019, 869, and 1,081 in the T1, T2a, T2b, and T3 groups, respectively). In the T1 group, NACT was correlated with a decrease in OS (hazard ratio [HR] = 1.631, 95% confidence interval [CI]: 1.150–2.315, P = 0.006) and DFS (HR = 1.665, 95% CI: 1.255–2.182, P < 0.001) than ARH. ARH and NACT were not correlated with OS (P = 0.226 and P = 0.921) or DFS (P = 0.343 and P = 0.535) than R-CT. In the T2a group, NACT was correlated with a decrease in OS (HR = 1.454, 95% CI: 1.057–2.000, P = 0.021) and DFS (HR = 1.529, 95% CI: 1.185–1.974, P = 0.001) than ARH. ARH and NACT were not correlated with OS (P = 0.736 and P = 0.267) or DFS (P = 0.714 and P = 0.087) than R-CT. In the T2b group, NACT was correlated with a decrease in DFS (HR = 1.847, 95% CI: 1.347–2.532, P < 0.001) than R-CT nevertheless was not correlated with OS (P = 0.146); ARH was not correlated with OS (P = 0.056) and DFS (P = 0.676). In the T3 group, the OS rates of ARH (n = 10), NACT (n = 18), and R-CT (n = 1053) were 67.5%, 53.1%, and 64.7% (P = 0.941), and the DFS rates were 68.6%, 45.5%, and 61.1%, respectively (P = 0.761).

Conclusion
R-CT oncological outcomes were not entirely superior to those of NACT or ARH under different local tumor factors with stage IIIC. NACT is not suitable for stage T1, T2a, and T2b. Nevertheless ARH is potentially applicable to stage T1, T2a, T2b and T3. The results of stage T3 require confirmation through further research due to disparity in case numbers in each subgroup.
Clinical characteristics, treatment and prognosis of infants with retinoblastoma: a multicenter, 10-year retrospective analysis
Authors: Zhang Yi , Wang Yizhuo , Zhi Tian , Jin Mei , Huang Dongsheng , Ma Xiaoli 
Published: May 2023

Abstract
Background
To summarize the characteristics and treatment, and analyze the prognosis of large number of infants with retinoblastoma (RB) in China through a multicenter, 10-year retrospective analysis.

Methods
The data of RB infants were collected from multiple centers. The characteristics and survival prognosis were analyzed. The overall survival (OS) rate was estimated by the Kaplan–Meier method. Multivariate Cox survival analysis was to evaluate the independent risk factors affecting the prognosis of RB infants.

Results
A total of 373 RB infants (202 boys and 171 girls) were included, the median age was 6.22 months (10 days to 11.93 months). The median follow-up time of RB infants was 18.4 (1.02–122.81 months). After excluding the lost to follow-up cases, the OS rate was 97.7% (345/353). Kaplan–Meier survival analysis indicated that 9 cases died and the median survival time was not reached. Univariate analysis of prognostic factors revealed eye affected, presenting signs, left eye stage and recurrence to be poor prognostic factors for OS rate in RB infants (all P < 0.05). Multivariate Cox regression analyses for OS showed recurrence (HR = 1.376, 95% CI: 0.878–2.156, P = 0.048) was an independent factor for prognosis of infants with RB. The median survival time of infants underwent chemotherapy + intra-arterial chemotherapy (IAC) + enucleation + vitrectomy was the longest than other treatments (n = 9, 47.64 months, OS = 100%, all P < 0.05). There was a history of RB in 17 infants' lineal relatives. Kaplan-merier survival analysis indicated 1 case died and the median survival time was not reached.

Conclusion
Recurrence is an independent factor for prognosis of RB infants, which still needs attention after treatment. Early screening, comprehensive treatments and follow-up of patients may lead to improvements of prognosis of RB infants.