bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptomic analysis reveals the dynamic changes of transcription factors during early development of chicken embryo
Authors: Liao Liqin , Yao Ziqi , Kong Jie , Zhang Xinheng , Li Hongxin , Chen Weiguo , Xie Qingmei 
Published: December 2022

Abstract
Background
The transition from fertilized egg to embryo in chicken requires activation of hundreds of genes that were mostly inactivated before fertilization, which is accompanied with various biological processes. Undoubtedly, transcription factors (TFs) play important roles in regulating the changes in gene expression pattern observed at early development. However, the contribution of TFs during early embryo development of chicken still remains largely unknown that need to be investigated. Therefore, an understanding of the development of vertebrates would be greatly facilitated by study of the dynamic changes in transcription factors during early chicken embryo.

Results
In the current study, we selected five early developmental stages in White Leghorn chicken, gallus gallus, for transcriptome analysis, cover 17,478 genes with about 807 million clean reads of RNA-sequencing. We have compared global gene expression patterns of consecutive stages and noted the differences. Comparative analysis of differentially expressed TFs (FDR < 0.05) profiles between neighboring developmental timepoints revealed significantly enriched biological categories associated with differentiation, development and morphogenesis. We also found that Zf-C2H2, Homeobox and bHLH were three dominant transcription factor families that appeared in early embryogenesis. More importantly, a TFs co-expression network was constructed and 16 critical TFs were identified.

Conclusion
Our findings provide a comprehensive regulatory framework of TFs in chicken early embryo, revealing new insights into alterations of chicken embryonic TF expression and broadening better understanding of TF function in chicken embryogenesis.
Patient-reported outcomes in individuals with advanced gastrointestinal stromal tumor treated with ripretinib in the fourth-line setting: analysis from the phase 3 INVICTUS trial
Authors: Schöffski Patrick , George Suzanne , Heinrich Michael C. , Zalcberg John R. , Bauer Sebastian , Gelderblom Hans , Serrano César , Jones Robin L. , Attia Steven , D’Amato Gina , Chi Ping , Reichardt Peter , Becker Claus , Shi Kelvin , Meade Julie , Ruiz-Soto Rodrigo , Blay Jean-Yves , von Mehren Margaret 
Published: December 2022

Abstract
Background
Ripretinib is a novel switch-control kinase inhibitor that inhibits KIT and PDGFRA signaling. In the INVICTUS phase 3 trial, ripretinib increased median progression-free survival and prolonged overall survival vs. placebo in ≥ fourth-line advanced GIST. Here, we report prespecified analysis of quality of life (QoL) as assessed by patient-reported outcome (PRO) measures and an exploratory analysis evaluating the impact of alopecia on QoL.

Methods
In the INVICTUS trial (NCT03353753), QoL was assessed using the European Organisation for Research and Treatment of Cancer Quality of Life Questionnaire (EORTC QLQ-C30; physical function, role function, overall health, and overall QoL) and the EuroQoL 5-Dimension 5-Level (EQ-5D-5 L; visual analogue scale). Analysis of covariance (ANCOVA) models compared changes in scores from baseline to treatment cycle 2, day 1 within and between ripretinib and placebo. Within the ripretinib arm, repeated measures models assessed the impact of alopecia on QoL.

Results
Patients receiving ripretinib maintained QoL (as assessed by the EORTC QLQ-C30 and EQ-5D-5 L PRO measures) from baseline to cycle 2, day 1 whereas QoL declined with placebo, resulting in clinically significant differences between treatments (nominal P < 0.01). The most common treatment-emergent adverse event with ripretinib was alopecia; however, QoL was similarly maintained out to treatment cycle 10, day 1 in patients receiving ripretinib who developed alopecia and those who did not.

Conclusion
PRO assessments in the INVICTUS trial suggest that patients on ripretinib maintain their QoL out to C2D1, unlike patients receiving placebo. Longitudinal QoL was maintained for patients receiving ripretinib out to cycle 10, day 1 (approximately 8 months; past the point of median progression-free survival with ripretinib [6.3 months]), even if the patients developed alopecia.

Trial registration
ClinicalTrials.gov Identifier: NCT03353753; first posted: November 27, 2017.
Impact of coronavirus disease 2019 on the number of newly diagnosed cancer patients and examinations and surgeries performed for cancer in Japan: a nationwide study
Authors: Terashima Takeshi , Konishi Hiroshi , Sato Yasunori , Igarashi Muneki , Yanagibashi Takafumi , Konno Ryo , Saya Hideyuki , Doki Yuichiro , Kakizoe Tadao 
Published: December 2022

Abstract
Background
The coronavirus disease 2019 (COVID-19) pandemic has rapidly and dramatically influenced healthcare across Japan. However, the influence of the COVID-19 pandemic on the number of newly diagnosed cancer, surgical treatment, and diagnostic examination for cancer types have not been completely investigated all over Japan. This study aimed to analyze the number of cases before and during the COVID-19 pandemic.

Methods
This retrospective study was a survey that asked to provide the number of cases diagnosed with gastric, colorectal, lung, breast, and cervical cancer between January 2019 and December 2020. The survey was sent to tertiary healthcare hospitals, including national cancer institutions, university hospitals, and general hospitals, all over Japan. Data obtained from 105 of 486 surveyed hospitals were evaluated, and the number of cases in each quarter in 2020 was compared with that in the equivalent quarter in 2019.

Results
In the second quarter (Q2), significant reductions were observed in the median number of newly diagnosed cases from 2019 to 2020: gastric cancer, 26.7% (43 vs. 32, p <  0.001); colorectal cancer, 17.9% (52 vs. 40, p <  0.001); lung cancer, 12.3% (53.5 vs. 47, p <  0.001); and breast cancer, 13.1% (43 vs. 35.5, p <  0.001). A significant reduction of 11.4% (9 vs. 8, p = 0.03) was observed in the third quarter (Q3) for cervical cancer. In Q2, the number of cases decreased by 30.9% (25 vs. 15, p <  0.001) for stage I gastric cancer, by 27.3% (12 vs. 9, p <  0.001) for stage I colorectal cancer, and by 17.6% (13 vs. 10, p <  0.001) for stage II breast cancer. The magnitude of reduction was significant for the localized stages of gastric, colorectal, and breast cancer according to diagnostic examinations in Q2 and surgical and endoscopic treatment in Q3 rather than that for lung or cervical cancer.

Conclusions
COVID-19 has prolonged collateral effects on cancer care, including examination, diagnosis, and surgery, with significant effects on gastric cancer, followed by colorectal, lung, breast, and cervical cancer in Japan.
Pneumatic tourniquet versus no tourniquet in transfemoral amputation – a study protocol for a randomized controlled trial
Authors: Brix Anna Trier Heiberg , Nymark Tine , Schmal Hagen , Lindberg-Larsen Martin 
Published: December 2022

Abstract
Background
Lower extremity amputation patients represent a frail group with extensive comorbidity. Transfemoral amputation is a high-risk procedure with 37–50% risk of mortality in the first year. Substantial blood loss during surgery increases the risk of anemic complications and death for these already weakened patients. The use of tourniquet during surgery may reduce blood loss, the need for blood transfusions, the related complications as well as the length of the surgery. However the use of tourniquet may be related to impaired wound healing and hence the use should be investigated in a randomized controlled trial.
The primary aim of this study is to investigate the total blood loss and secondary to investigate differences in complications after transfemoral amputation between patients operated with or without tourniquet.

Methods
The total blood loss is calculated using Nadlers approach. Based on data from a pilot series, the sample size was calculated to 124, allocated 1:1 in two groups of 62 participants to ensure detection of at least 200 mL difference in the total blood loss. The primary outcome is the total blood loss. Secondary outcomes are blood transfusions, duration of surgery, length of hospital stay and risk of complications within 90 days (re-admissions, re-operations and mortality). Explorative outcomes are 1 year mortality and re-operation risk. Further explorative outcomes are postoperative quality of life (questionnaire EQ-5D-5L) and evaluation of number of prosthesis users including evaluation of prosthesis-specific function measured 3, 6, and 12 months postoperatively.

Discussion
The possibility to enhance patient safety is highly relevant and this trial will provide data for evidence based recommendations of best practice in amputation surgery.

Trial registration
The trial is registered on ClinicalTrials.gov with ID: NCT05550623. Initial release: 13/09 2022.
Protective effect of silymarin on tacrolimus-induced kidney and liver toxicity
Authors: Terzi Funda , Ciftci Mustafa Kemal 
Published: December 2022

Abstract
Background
Tacrolimus (FK506) is an immunosuppressive agent and has toxic side effects such as nephrotoxicity, hepatotoxicity, and neurotoxicity. In our study, we aimed to investigate the protective effect of silymarin on renal and hepatic toxicity considered to be tacrolimus related.

Methods
In this 6-week experimental study, 46 eight-week-old healthy male rats were used. The groups comprised the Control (healthy rats, n = 6), Tac (tacrolimus 1 mg/kg, n = 8), silymarin 100 mg/kg (SLI 100 mg/kg n = 8), Tac + SLI 100 (tacrolimus 1 mg/kg + SLI 100 n = 8), SLI 200 (SLI 200 mg/kg n = 8), and Tac + SLI 200 (tacrolimus 1 mg/kg + SLI 200 mg/kg n = 8). After 6 weeks, all rats were sacrificed, and the tissue follow-up procedure was performed for kidney and liver tissues, histopathology, and in situ TUNEL analysis. Blood samples were analyzed for the total antioxidant capacity (TAC), total oxidant capacity (TOC), alanine aminotransferase (ALT), aspartate aminotransferase (AST), gamma-glutamyl transferase (GGT), albumin, total bilirubin, creatine.

Results
Histopathological findings of kidney and liver tissue of rats were determined to increase statistically in Tac group compared to SLI 1 00 and SLI 200 groups (P < 0.05). In addition, the Tac + SLI 100 and Tac + SLI 200 groups were found to be statistically similar to the Control group (P > 0.05). The in situ TUNEL method showed that the tacrolimus increased apoptosis while the silymarin decreased it. TOC levels increased statistically in Tac groups compared to silymarin-treated groups (P < 0.05). Although the TAC level was not statistically significant among the experimental groups (P > 0.05), the lowest was measured in the Tac group. The ALT, AST, GGT, total bilirubin, and creatine values were higher in the Tac group than in the silymarin groups (P < 0.05). There was no statistically significant difference between the groups with regard to the albumin level (P > 0.05).

Conclusion
In our study, we determined that tacrolimus caused damage to kidney and liver tissue. Histopathological, biochemical and apoptotic findings show that silymarin has a protective effect against nephrotoxicity and hepatotoxicity caused by tacrolimus.
Clinical features of Kawasaki disease initially mimicking retropharyngeal abscess: a retrospective analysis
Authors: Chen Yong-chao , Pan Hong-guang , Jia De-sheng , Wang Hao-cheng , Li Lan , Teng Yi-shu 
Published: December 2022

Abstract
Objective
Incomplete Kawasaki disease (IKD) initially presenting as retropharyngeal abnormality is very rare and is prone to misdiagnosis and missed diagnosis, often leading to poor prognosis. Most patients were misdiagnosed with retropharyngeal abscesses. Here, we describe and compare IKD patients initially presenting with retropharyngeal abnormalities, typical KD patients without retropharyngeal abnormalities and retropharyngeal abscess patients.

Methods
We performed a retrospective case–control study comparing IKD patients initially presenting with retropharyngeal abnormalities to both KD patients without retropharyngeal abnormalities and retropharyngeal abscess patients admitted to Shenzhen Children’s Hospital between January 2016 and December 2021.

Results
We evaluated data from 10 IKD patients initially presenting with retropharyngeal abnormalities (Group A), 20 typical KD patients (Group B) and 16 surgical drainage confirmed retropharyngeal abscess patients (Group C). Compared to Group B, we observed that Group A was older and had a more intense inflammatory response. On the day of admission, Groups A and C had similar early clinical presentations, and there were no significant differences in any major signs or symptoms. Close observation for the development of new KD signs and symptoms and unresponsiveness to empirical antibiotic therapy after 3 days is extremely important. The CRP (p = 0.011), AST (p = 0.002) and ALT (p = 0.013) levels were significantly higher and the WBC (P = 0.040) levels were significantly lower in Group A than in Group C. Neck radiological findings, such as the presence of ring enhancement (p = 0.001) and mass effects on the airway, are also useful tools for distinguishing these two diseases.

Conclusion
The careful observation of the signs and symptoms of this disease and the comprehensive analysis of the laboratory tests and neck radiological findings may help clinicians become aware of retropharyngeal abnormality as an atypical presentation of KD. Then, unnecessary treatments could be reduced, and the occurrence of serious complications can be avoided.
Distance learning during the COVID-19 pandemic for children with ADHD and/or ASD: a European multi-center study examining the role of executive function deficits and age
Authors: Thorell Lisa B. , Fuermaier Anselm B. M. , Christiansen Hanna , Steinmayr Ricarda , Baeyens Dieter , de la Peña Almudena Giménez , Groom Madeleine J. , Idrees Iman , van der Oord Saskia , van den Hoofdakker Barbara J. , Luman Marjolein , Mammarella Irene C. , Skoglund Charlotte 
Published: December 2022

Abstract
Background
One of the COVID-19 pandemic consequences that has affected families the most is school lockdowns. Some studies have shown that distance learning has been especially challenging for families with a child with neurodevelopmental disorders such as ADHD or ASD. However, previous studies have not taken the heterogeneity of these disorders into account. The aim of the present study was therefore to investigate differences between families with a child with ADHD, ASD, or both conditions, and to examine the role of underlying deficits in executive functioning (EF) in both children and parents in relation to negative and positive effects of distance learning.

Methods
Survey data assessing both negative and positive experiences of distance learning were collected from parents with a child aged 5–19 years in seven Western European countries: the UK, Germany, Spain, Sweden, the Netherlands, Italy, and Belgium. Altogether, the study included 1010 families with a child with ADHD and/or ASD and an equally large comparison group of families with a child without mental health problems. We included measures of three different types of negative effects (i.e., effects on the child, effects on the parent, and lack of support from school) and positive effects on the family.

Results
Results confirmed that families with a child with ADHD, ASD or a combination of ADHD and ASD showed higher levels of both negative and positive effects of distance learning than the comparison group. However, few differences were found between the clinical groups. Group differences were more pronounced for older compared to younger children. Regarding the role of both ADHD/ASD diagnosis and EF deficits, primarily children’s EF deficits contributed to high levels of negative effects. Parent EF deficits did not contribute significantly beyond the influence of child EF deficits. Families of children with ADHD/ASD without EF deficits experienced the highest levels of positive effects.

Conclusions
School closings during COVID-19 have a major impact on children with EF problems, including children with neurodevelopmental disorders. The present study emphasizes that schools should not focus primarily on whether a student has a neurodevelopmental disorder, but rather provide support based on the student’s individual profile of underlying neuropsychological deficits.
The effect of biomechanical foot‐based interventions on patellofemoral joint loads during gait in adults with and without patellofemoral pain or osteoarthritis: a systematic review protocol
Authors: Kayll Samual A. , Hinman Rana S. , Bennell Kim L. , Bryant Adam L. , Rowe Patrick L. , Paterson Kade L. 
Published: December 2022

AbstractBackgroundPatellofemoral pain is highly prevalent across the lifespan, and a significant proportion of people report unfavourable outcomes years after diagnosis. Previous research has implicated patellofemoral joint loading during gait in patellofemoral pain and its sequelae, patellofemoral osteoarthritis. Biomechanical foot‐based interventions (e.g., footwear, insoles, orthotics, taping or bracing) can alter patellofemoral joint loads by reducing motions at the foot that increase compression between the patella and underlying femur via coupling mechanisms, making them a promising treatment option. This systematic review will summarise the evidence about the effect of biomechanical foot‐based interventions on patellofemoral joint loads during gait in adults with and without patellofemoral pain and osteoarthritis.MethodsMEDLINE (Ovid), the Cumulative Index to Nursing and Allied Health Literature CINAHL, The Cochrane Central Register of Controlled Trials (CENTRAL), SPORTdiscus (EBSCO) and Embase (Ovid) will be searched. Our search strategy will include terms related to ‘patellofemoral joint’, ‘loads' and ‘biomechanical foot‐based interventions'. We will include studies published in the English language that assess the effect of biomechanical foot‐based interventions on patellofemoral joint loads, quantified by patellofemoral joint pressure, patellofemoral joint reaction force and/or knee flexion moment. Two reviewers will independently screen titles and abstracts, complete full‐text reviews, and extract data from included studies. Two reviewers will assess study quality using the Revised Cochrane Risk of Bias (RoB 2) tool or the Cochrane Risk Of Bias In Non‐Randomized Studies – of Interventions (ROBINS‐I) tool. We will provide a synthesis of the included studies' characteristics and results. If three or more studies are sufficiently similar in population and intervention, we will pool the data to conduct a meta‐analysis and report findings as standardised mean differences with 95% confidence intervals. If a meta‐analysis cannot be performed, we will conduct a narrative synthesis of the results and produce forest plots for individual studies.DiscussionThis protocol outlines the methods of a systematic review that will determine the effect of biomechanical foot‐based interventions on patellofemoral joint loads. Our findings will inform clinical practice by identifying biomechanical foot‐based interventions that reduce or increase patellofemoral joint loads, which may aid the treatment of adults with patellofemoral pain and osteoarthritis.Trial registrationRegistered with PROSPERO on the 4th of May 2022 (CRD42022315207).
A novel computed tomography angiography technique: guided preoperative localization and design of anterolateral thigh perforator flap
Authors: Yu Xin-xin , Yang Shi-feng , Ji Cong-shan , Qiu Shen-qiang , Qi Yao-dong , Wang Xi-ming 
Published: December 2022

Abstract
Background
Anterolateral thigh perforator (ALTP) flap is considered a versatile flap for soft tissue reconstruction. Computed tomography angiography (CTA) is used for mapping perforator in abdominal-based reconstruction; however, it is less commonly used in ALTP due to its poor imaging efficacy. In this study, we introduced a novel CTA technique for preoperative localization and design of ALTP flap and evaluated its value in directing surgical reconstruction.

Results
Thirty-five patients with soft tissue defects were consecutively enrolled. Modified CTA procedures, such as sharp convolution kernel, ADMIRE iterative reconstruction, 80 kV tube voltage, high flow contrast agent and cinematic rendering image reconstruction, were used to map ALTPs. A total of 287 perforators (including 884 sub-branches) were determined, with a mean of 5 perforators per thigh (range 2–11). The ALTPs were mainly concentrated in the “hot zone” (42%, 121/287) or the distal zone (41%, 118/287). Most perforators originated from the descending branch of the lateral circumflex femoral artery (76%, 219/287). Three perforator types, namely musculocutaneous (62%, 177/287), septocutaneous (33%, 96/287), and mixed pattern (5%, 14/287), were identified. The median pedicle length measured by two methods was 4.1 cm (range 0.7–20.3 cm) and 17.0 cm (range 4.7–33.9 cm), respectively, and the median diameter of the skin flap nourished by one perforator was 3.4 cm (IQR 2.1–5.7 cm). Twenty-eight ALTP flaps were obtained with the guidance of CTA, and 26 flaps survived after follow-up.

Conclusions
The proposed CTA mapping technique is a useful tool for preoperative localization and design of ALTP flap.
Comparison of a deep learning-accelerated T2-weighted turbo spin echo sequence and its conventional counterpart for female pelvic MRI: reduced acquisition times and improved image quality
Authors: Ren Jing , Li Yuan , Liu Fei-Shi , Liu Chong , Zhu Jin-Xia , Nickel Marcel Dominik , Wang Xiao-Ye , Liu Xin-Yu , Zhao Jia , He Yong-Lan , Jin Zheng-Yu , Xue Hua-Dan 
Published: December 2022

Abstract
Objectives
To investigate the feasibility of a deep learning-accelerated T2-weighted turbo spin echo (TSE) sequence (T2DL) applied to female pelvic MRI, using standard T2-weighted TSE (T2S) as reference.

Methods
In total, 24 volunteers and 48 consecutive patients with benign uterine diseases were enrolled. Patients in the menstrual phase were excluded. T2S and T2DL sequences in three planes were performed for each participant. Quantitative image evaluation was conducted by calculating the signal-to-noise ratio (SNR) and contrast-to-noise ratio (CNR). Image geometric distortion was evaluated by measuring the diameters in all three directions of the uterus and lesions. Qualitative image evaluation including overall image quality, artifacts, boundary sharpness of the uterine zonal layers, and lesion conspicuity were assessed by three radiologists using a 5-point Likert scale, with 5 indicating the best quality. Comparative analyses were conducted for the two sequences.

Results
T2DL resulted in a 62.7% timing reduction (1:54 min for T2DL and 5:06 min for T2S in axial, sagittal, and coronal imaging, respectively). Compared to T2S, T2DL had significantly higher SNR (p ≤ 0.001) and CNR (p ≤ 0.007), and without geometric distortion (p = 0.925–0.981). Inter-observer agreement regarding qualitative evaluation was excellent (Kendall’s W > 0.75). T2DL provided superior image quality (all p < 0.001), boundary sharpness of the uterine zonal layers (all p < 0.001), lesion conspicuity (p = 0.002, p < 0.001, and p = 0.021), and fewer artifacts (all p < 0.001) in sagittal, axial, and coronal imaging.

Conclusions
Compared with standard TSE, deep learning-accelerated T2-weighted TSE is feasible to reduce acquisition time of female pelvic MRI with significant improvement of image quality.
On some variational inequality-constrained control problems
Authors: Treanţă Savin , Antczak Tadeusz , Saeed Tareq 
Published: December 2022

AbstractIn this paper, by considering some properties associated with scalar functionals of multiple-integral type, we study the well-posedness and generalized well-posedness for a new variational inequality-constrained optimization problems By using the set of approximating solutions, we state some characterization theorems on well-posedness and generalized well-posedness. Also, in order to validate the derived results, some examples are given.