bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation and validation of reference genes for RT-qPCR gene expression in Naegleria gruberi
Authors: Martín-Pérez Tania , Köhsler Martina , Walochnik Julia 
Published: June 2023

Abstract
Naegleria fowleri is the etiologic agent of Primary Amoebic Meningoencephalitis (PAM). PAM occurs world-wide and it is considered a rare disease, but its fatality rate is high (96%) due to the delay in initiation of treatment due to misdiagnosis and lack of a specific treatment. The analysis of gene expression by quantitative real-time PCR (qRT-PCR) could be a highly efficient means to understand the pathogenicity and also to find drug targets. Accurate RT-qPCR analysis requires correct normalization of gene expression data using reference genes (RG), whose expression should be constant under different experimental conditions. In this study, six genes, representing the most frequently used housekeeping genes, were selected for evaluation as reference genes in N. gruberi. The expression and stability of these genes was evaluated employing four algorithms (GeNorm, NormFinder, BestKeeper and RefFinder). Moreover, in order to validate normalization with the two most promising reference genes, a target gene was used (HSP90), and its expression was studied.
Periodic Oscillations of Doppler Frequency Excited by the Traveling Ionospheric Disturbances Associated with the Tonga Eruption in 2022
Authors: Nakata Hiroyuki , Hosokawa Keisuke , Saito Susumu , Otsuka Yuichi , Tomizawa Ichiro 
Published: June 2023

Abstract
The explosive eruption of the Hunga Tonga-Hunga Ha’apai volcano on 15 January 2022 generated atmospheric waves traveling around the Earth, which caused ionospheric disturbances on various spatio-temporal scales. A HF Doppler (HFD) sounding system in Japan detected characteristic ionospheric disturbances showing periodic oscillations in the Doppler frequency with a period of ~ 4 minutes. In this study, such periodic oscillations were examined by comparing HFD data with those of GNSS (Global Navigation Satellite System) Total Electron Content (TEC) observation. The observed periodic oscillations in the Doppler Frequency were characterized by a S-letter shaped variation, implying the passage of the Traveling Ionospheric Disturbances (TIDs) through the reflection points of the HFD sounding system. It was also found that the periodic oscillations occurred prior to the arrival of the tropospheric Lamb wave excited by the Tonga eruption. From the GNSS TEC data, the TIDs causing the periodic oscillations were excited by the tropospheric Lamb waves at the conjugate point in the southern hemisphere, namely, the electric field perturbations due to the Lamb waves in the southern hemisphere mapped onto the sensing area of the HFD system in the northern hemisphere along the magnetic field lines. The periodic oscillations were observed only in the path between Chofu transmitter and Sarobetsu receiver, whose the radio propagation path is almost aligned in the north-south direction. This suggests that the TID has a structure elongating in the meridional direction. The variation in the Doppler frequency was reproduced by using a simple model of the TID propagation and the resultant motion of the reflection point. As a result, the vertical motion of the reflection point associated with the periodic oscillations was estimated to be about 1 km. It is known that ~ 4 minute period variations are sometime observed in association with earthquakes, which is due to resonances of acoustic mode waves propagating between the ground and the lower ionosphere. Therefore, a similar resonance structure in the southern hemisphere, that was caused by the passage of the tropospheric Lamb wave excited by the Tonga eruption, is the plausible source of the TIDs detected in the northern hemisphere.
Hearing for nursing home residents: Study protocol for development and testing of improved care and hearing aid provision in nursing care homes in Germany (zusammenHÖREN)
Authors: Buchholz Annika , Fleischmann Nina , Wittland Michael , Branding Melina , Brähler Jannik , Holte Anja Pähler von der , Krech Lisa , Bock Merle , Ricke Meike , Seidel Martin , Welkoborsky Hans-Jürgen , Lesinski-Schiedat Anke , Sgraja Sophia , Heitz Katharina 
Published: June 2023

Abstract
Background: Adequate hearing is an important component of quality of life due to its role in social interaction and community participation. Current evidence suggests that nursing home residents’ quality of life is significantly impacted by impaired sensory functions including hearing. The aim of the study is to improve hearing health of nursing home residents by creating effective structures of cooperation and clearly defined processes.
Methods: We perform an analyzation of residents’ hearing status and all care processes around hearing aids. Each resident will be physically examined by an ear, nose and throat specialist. Subjective and objective hearing tests will be carried out. The residents will also participate in a questionnaire-based survey. Interviews and focus group discussions with residents, relatives, nursing home staff and hearing experts will add qualitative data.
Discussion: The aim of this project is to identify and define personal and structural factors that impede optimal hearing care, concentrating on three focus groups: residents, caregivers (relatives, nursing home staff) and health care providers (audiologists, doctors). Within the project several approaches to solve smaller issues in the given setting / structure of the German health care system will be developed and tested. However, creating long-lasting, large-scale improvements of the hearing status in nursing homes will still require a lot of political effort.
Trial registration: Deutsches Register Klinischer Studien (DRKS00026809) "Untersuchung der Hörfähigkeit und dementieller Entwicklung von Personen in ausgewählten stationären Pflegeeinrichtungen in Niedersachsen/ Investigation on Hearing and Dementia in selected Nursing Homes in and around Hannover/Lower Saxony."
Contributing factor for the pirfenidone dose reduction in patients with idiopathic interstitial pneumonia in real-world settings—A dose-specific analysis
Authors: Takeshita Yuri , Sugimoto Naoya , Kobayashi Konomi , Toyota Hikaru , Ito Ayaka , Ujino Mariko , Ishizuka Mana , Hattori Saya , Uehara Yuuki , Suzuki Yuki , Koizumi Yuta , Nagase Hiroyuki 
Published: June 2023

Abstract
Background
Pirfenidone slows the progression of interstitial lung disease; however, in real-world settings, many patients discontinue or reduce its dosage owing to its adverse events. The contributing factors of low maintenance doses of pirfenidone have not been fully analyzed in a dose-specific manner. The aim of the current study is to identify the contributing factor of low-dose pirfenidone at < 1,200 or ≤ 1,200 mg/day in a dose-specific manner in real-world settings and to investigate the survival of patients stratified by the dose of pirfenidone as an exploratory analysis.
Methods
We retrospectively reviewed the clinical information and data from medical records of 85 patients with idiopathic interstitial pneumonia treated with different doses of pirfenidone at the University Hospital from April 2009 to August 2019. The contributing factors of the treatment dose were analyzed by performing a multivariate logistic regression analysis.
Results
The mean administered dose of pirfenidone was 1,242 mg/day, and the doses were 1,800, 1,200, and < 1,200 mg/day in 25.9%, 54.1%, and 20% of patients, respectively. The treatment doses in the ≤ 1,200 and < 1,200 mg/day groups were 1047.6 ± 255.8 and 635.3 ± 78.6 mg/day, respectively. Patients’ age was significantly related to the treatment dose of ≤ 1,200 mg/day, with most patients receiving 1,200 mg/day. Contrarily, pulmonary dysfunction and hypoalbuminemia were related to a dose of < 1,200 mg/day. Survival was significantly shorter in the < 1,200 mg/day group than in the 1,800 mg/day group. The pirfenidone dosage of < 1,200 mg/day and low forced vital capacity were independently associated with a poor prognosis.
Conclusions
Pulmonary dysfunction and hypoalbuminemia were identified as contributing factors of the maintenance of low-dose pirfenidone at < 1,200 mg/day. Early intervention is important before the progression to severe disease accompanied by decreased pulmonary function or malnutrition.
Fixed-Time Event-Triggered Obstacle Avoidance Control for Heterogeneous Multi-Agent Systems with Input Delay
Authors: Wang Linling , Xu Xiaoyan 
Published: June 2023

Abstract
An in-depth study on the fixed-time event-triggered obstacle avoidance consensus control in heterogeneous USV-AUV systems with input delay and uncertain disturbances are conducted in this paper. The desired heterogeneous USV-AUV formation can be achieved by fixed-time consensus control, within a fixed predetermined time, regardless of the initial states. Besides, an event-triggered communication strategy among the agents is introduced in the system, significantly reducing communication energy consumption. By employing the proposed control strategy, the Zeno behavior also can be avoided. Additionally, an obstacle avoidance control algorithm for the heterogeneous USV-AUV system based on improved artificial potential fields (IAPF) is designed, which helps in avoiding both static and dynamic obstacles. Compared to existing research, this algorithm reduces control input jitter, resulting in smoother obstacle avoidance paths. Through extensive simulation experiments and comparisons with other methods, effectiveness and superiority of the proposed algorithm is validated.
Application of warm saline injection combined with tube delivery in the prevention of PICC tube delivery difficulties and mechanical phlebitis caused by vasospasm
Authors: wang hui , jia hongyu , jiang guichun , qu huan , xu ning , li yongmin , yu lejing 
Published: June 2023

Abstract
Purpose The objective of this study was to investigate the effectiveness of warm saline injection during PICC catheterization in preventing vasospasm and reducing mechanical phlebitis caused by vasospasm in tumor patients.
Methods The study included 262 inpatients in the colorectal surgery department of our hospital who required PICC placement between January and December 2022. They were randomly divided into two groups, with the experimental group (n=132) receiving warm saline injection during catheterization and the control group (n=130) receiving conventional catheterization. The incidence of vasospasm, catheterization time, and mechanical phlebitis during PICC catheterization were compared between the two groups.
Results The incidence of vasospasm in the experimental group was 1.52%, with 3.3% of patients taking more than 5 minutes to complete catheter delivery, and an incidence of mechanical phlebitis was 0.8%. In the control group, the incidence of vasospasm was 12.31%, with 15.3% of patients taking more than 5 minutes to complete catheter delivery, and an incidence of mechanical phlebitis of 9.2%. The difference between the two groups was statistically significant (P<0.05).
Conclusion Warm saline injection during PICC catheterization can effectively prevent vasospasm during PICC catheterization, shorten catheterization time, and reduce the incidence of mechanical phlebitis in tumor patients. This method is simple and feasible and can be considered for clinical application.
The role of hepatitis B core-related antigen in predicting the occurrence and recurrence of hepatocellular carcinoma in patients with chronic hepatitis B: a systemic review and meta-analysis
Authors: Cao Qi-Hang , Liu Hui , Yan Lun-Jie , Ding Zi-Niu , Yang Long-Shan , Mao Xin-Chen , Pan Guo-Qiang , Tian Bao-Wen , Han Chen-Long , Dong Zhao-Ru , Wang Dong-Xu , Yan Yu-Chuan , Li Tao 
Published: June 2023

Abstract

Background
The purpose of the current study was to investigate the predictive value of hepatitis B core-related antigen (HBcrAg) on the occurrence and recurrence of hepatocellular carcinoma (HCC) in patients with chronic hepatitis B (CHB).
Methods
Based on PubMed, Embase, Scopus, and Web of Science, we conducted a systematic review and meta-analysis of original clinical literature. The primary outcomes were the occurrence and recurrence of HCC assessed by the hazard ratio (HR) or odds ratio (OR) with 95% confidence interval (CI).
Results
A total of 18 publications with 9039 CHB patients were included in the preliminary analysis. The pooled results suggest that HBcrAg positivity (adjusted HR = 3.10, 95%CI: 2.07–4.64, P < 0.001, I2 = 62.4%, P = 0.021; OR = 5.65, 95%CI: 3.44–5.82, P < 0.001, I2 = 0.00%, P = 0.42) was an independent risk factor for the occurrence of HCC. Further subgroup analysis revealed that 4.0 logU/ml may be the optimal cut-off value for HBcrAg to predict the occurrence of HCC. Our meta-analysis also suggests that HBcrAg is a predictor of HCC recurrence during antiviral therapy (adjusted HR = 1.71, 95%CI: 1.26–2.32; I2 = 78.6%, P = 0.031) and is closely related to recurrence-free survival (RFS) after curative treatment of HCC (P = 0.001).
Conclusion
For patients with CHB, serum HBcrAg level is closely associated with the occurrence of HCC, regardless of whether nucleoside/nucleotide analogues (NAs) are administered, may also serve as a novel prognostic biomarker of recurrence in HCC. Confirmation of these findings requires more research.
Dynamic rainfall thresholds for landslide early warning in Progo Catchment, Java, Indonesia
Authors: Satyaningsih Ratna , Jetten Victor , Ettema Janneke , Sopaheluwakan Ardhasena , Lombardo Luigi , Nuryanto Danang Eko 
Published: June 2023

Abstract
This study set out to derive empirical rainfall thresholds for landslides in the Progo Catchment, Indonesia, using high-resolution satellite-based precipitation products (SPPs) and rain gauge data. The SPPs are the gauge-adjusted version of the Global Satellite Mapping of Precipitation (GSMaP-GNRT) and the bias-corrected version of the Climate Prediction Center morphing method (CMORPH-CRT). First, we evaluate the detection capacity and accuracy of each SPP. Then we determine rainfall events responsible for landslides by using a dynamic window that allows us to adapt rainfall events by extending or shortening their duration depending on the rainfall signal persistence. Based on 213 landslides that occurred in the Progo Catchment from 2012 to 2021, we derive multiple rainfall thresholds corresponding to various exceedance probability levels. Results indicate that both GSMaP-GNRT and CMORPH-CRT products fail to capture high-intensity rainfall in the Progo Catchment and overestimate light rainfall compared to rain gauge observations. Nevertheless, when accumulated to define the rainfall threshold, the overall performance of GSMaP-GNRT and gauge-based data in Progo Catchment is comparable. Gauge-based data performed slightly better than GSMaP-GNRT, while CMORPH-CRT performed the worst for all exceedance probabilities. By maximising true skill scores, the suitable exceedance probability for early warning purposes in Progo Catchment can be decided, e.g., 10% (15%) if using gauge-based data (GSMaP-GNRT). These findings can be viewed as an attempt to improve the landslide early warning system in Indonesia. Further study is required, using a numerical weather model that reliably forecasts weather systems producing the rainfall events triggering landslides.
The influence of laser pulse shape and cleanliness on two-photon microscopy
Authors: Chong Shau Poh , Török Peter 
Published: June 2023

Abstract
Nonlinear microscopy, including two-photon microscopy, requires pulsed lasers as light source. Typically, when choosing the appropriate pulsed laser for two-photon microscopy, the pulse repetition rate, pulse width, total power output, and output beam diameter are among the critical parameters which are often emphasised. Here, we demonstrate that the pulse shape, often overlooked, can have significant impact on the two-photon microscopy excitation efficiency and the effective signal brightness. We provide metrics to ease practical selection of pulsed laser sources for two-photon microscopy.
Variational quantum metrology for multiparameter estimation under dephasing noise
Authors: Le Trung Kien , Nguyen Hung Q. , Ho Le Bin 
Published: June 2023

Abstract
We present a hybrid quantum-classical variational scheme to enhance precision in quantum metrology. In the scheme, both the initial state and the measurement basis in the quantum part are parameterized and optimized via the classical part. It enables the maximization of information gained about the measured quantity. We discuss specific applications to 3D magnetic field sensing under several dephasing noise modes. Indeed, we demonstrate its ability to simultaneously estimate all parameters and surpass the standard quantum limit, making it a powerful tool for metrological applications.
ncDBCN: A Method for Family Prediction of Noncoding RNAs Based on Raw Sequence Data
Authors: Wang Jiahao , Zhu Xiaodong , Chen Kai , Hao Lei , Liu Yuanning 
Published: June 2023

Abstract

Background: Noncoding RNAs (ncRNAs) play a significant role in various biological processes. Despite the availability of a large quantity of ncRNA data through high-throughput technologies, only a few ncRNAs have been functionally validated. Existing evidence suggests that ncRNAs belonging to the same family often share similar functions, highlighting the crucial importance of predicting ncRNA families to understand their functionality. However, traditional biological methods for ncRNA family prediction are inadequate to meet the demands of high-throughput analysis and are cost-prohibitive. Although computational methods based on the secondary structure can predict ncRNA families, their processes are complex, and the accuracy of tools used for predicting secondary structure is limited. In comparison, prediction methods based on ncRNA sequences are not only operationally straightforward but also exhibit relatively higher accuracy. Nevertheless, current sequence-based prediction methods for ncRNA still have some limitations, and their accuracy needs further improvement.
Results: To address the aforementioned issues, this paper proposes an ncRNA sequence-based family prediction method called "ncDBCN". The ncDBCN method consists of four components: a word2vec encoding method combined with 3k-mer, dynamic bidirectional gated recurrent unit (dynamic Bi-GRU), attention mechanism, and ConvNeXt. Compared with existing computational methods, ncDBCN achieves significant improvements in five key performance metrics: accuracy, sensitivity, precision, F score, and MCC.
Conclusions: The proposed ncDBCN method not only reduces the cost of ncRNA family prediction but also significantly improves prediction accuracy, providing valuable assistance for the study of ncRNA functionality.
Post Recovery Impact of the Second and Third Sars-Cov-2 Infection Waves on Healthcare Resource Utilization in Lombardy, Italy
Authors: Harari Sergio , Mannucci Pier Mannuccio , Nobili Alessandro , Galbussera Alessia Antonella , Fortino Ida , Leoni Olivia , Remuzzi Giuseppe , D’Avanzo Barbara , Tettamanti Mauro 
Published: June 2023

Abstract
Background. The administrative claims database of the Italian region Lombardy, the first in Europe to be hit by the SARS-CoV-2 pandemic, was employed to evaluate the impact on healthcare resource utilization following recovery from the second (mainly alpha-related variant) and third (delta-related) infection waves.
Setting and design. 317.164 individuals recovered from the infection and became negative after the second wave, 271.180 after the third. Of them, 1571 (0.5%) and 1575 (0.6%) died in the first 6 post-negativization months. In the remaining cases (315.593 after the second wave and 269.605 after the third),hospitalizations, attendances to emergency rooms and outpatient visits were compared with those recorded in the same pre-pandemic time periods in 2019. Dispensation of drugs as well as of imaging, functional and biochemical diagnostic tests were also compared as additional proxies of the healthcare impact of the second and third SARS-CoV-2 infection waves.
Main results. Following both waves, hospitalizations, attendances at emergency rooms and outpatient visits were similar in number and rates to the pre-pandemic periods. However, there was an increased dispensation of drugs and diagnostic tests, particularly those addressing the cardiorespiratory and blood systems.
Conclusions. In a large region such as Lombardy taken as a relevant model because early and severely hit by the SARS-CoV-2 pandemic, the post- COVID burden on healthcare facilities was mildly relevant in cases who recovered from the second and third infection waves regarding such pivotal events as deaths, hospitalizations and need for emergency room and outpatient visits, but was high regarding the dispensation of a few drug classes and types of diagnostic tests.
Maternal Obesity Effect on Offspring Pancreatic Endocrine Cells: Investigation of the Cell Transdifferentiation
Authors: Feyat Mehmet Sedat , Yanik Tulin 
Published: June 2023

Abstract
Type 2 Diabetes (T2D) is a disease characterized by impaired functioning of pancreatic beta cells. In the later stages of the disease, beta cell dysfunction is defined as a decrease in functional cell count. Our hypothesis was that obesity-induced hyperglycemia of the mother could lead to dedifferentiation and/or transdifferentiation in their offspring's pancreatic beta cells. In our study, the mother Wistar rats whose obesity was brought on by the human-liked processed food which is called cafeteria diet (CAF), and their offspring were breastfed throughout the lactation phase and then given standard rat chow. Pancreatic tissues of both mother and offspring were obtained to elucidate the transformation profile with gene expression analysis, RT-qPCR. It was revealed that functional beta cell marker gene expressions decreased while progenitor marker gene expressions increased in the CAF group. We also discovered that dedifferentiation was partially presented at the protein level in the pancreas tissues of the CAF mother and offspring groups after analyzing glucagon and insulin protein expressions. Our findings suggest that processed food-induced maternal obesity and consequently T2D may have an impact on the dedifferentiation of pancreatic beta cells in offspring and may be a predisposing effect for diabetes.
The interplay between Diabetes Mellitus and Soft Tissue infections in general surgical patients
Authors: Cheng Stephanie , Poh Benjamin , Tay Vivyan Wei Yen , Mathur Sachin 
Published: June 2023

Abstract
Background
Diabetes mellitus (DM) is a worldwide pandemic affecting 500 million people. It is known to be associated with increased susceptibility to soft tissue infections (STI). Despite being a major public health burden, the literature relating the effects of DM and the presentation, severity and healing of STIs in general surgical patients remain limited.
Method
We conducted a retrospective review of all patients admitted with STI in a tertiary teaching hospital over a 12-month period. Patient demographics and surgical outcomes were collected and analysed.
Results
During the study period, 1059 patients were admitted for STIs, of which 936 (88%) required surgical intervention. Diabetic patients presented with higher body-mass index (BMI) (28 vs 26), larger abscess size (24 vs 14 cm2) and had a longer length of stay (LOS)(4.4 days vs 2.9 days). They also underwent a higher proportion of wide debridement as well as application of negative pressure wound therapy (NPWT) (42% vs 35%). More diabetic patients underwent subsequent re-operation within the same sitting (8 vs 4). There were no differences in re-admission rates within 30 days nor subsequent abscess formation in those followed for 6 months.
Conclusion
The incidence of STIs among DM patients represent a significant disease burden, surgeons should consider intensive patient counselling and partnering with primary care providers in order to help reduce the incidence of future STI admissions based upon lifestyle modification and glucose control