bluuebunny/crossref_metadata_2025_split huggingface dataset:
A transcriptome software comparison for the analyses of treatments expected to give subtle gene expression responses
Authors: Thawng Cung Nawl , Smith Geoffrey Battle 
Published: June 2022

Abstract
Background
In this comparative study we evaluate the performance of four software tools: DNAstar-D (DESeq2), DNAstar-E (edgeR), CLC Genomics and Partek Flow for identification of differentially expressed genes (DEGs) using a transcriptome of E. coli. The RNA-seq data are from the effect of below-background radiation 5.5 nGy total dose (0.2nGy/hr) on E. coli grown shielded from natural radiation 655 m below ground in a pre-World War II steel vault. The gene expression response to three supplemented sources of radiation designed to mimic natural background, 1952 – 5720 nGy in total dose (71–208 nGy/hr), are compared to this “radiation-deprived” treatment. In addition, RNA-seq data of Caenorhabditis elegans nematode from similar radiation treatments was analyzed by three of the software packages.

Results
In E. coli, the four software programs identified one of the supplementary sources of radiation (KCl) to evoke about 5 times more transcribed genes than the minus-radiation treatment (69–114 differentially expressed genes, DEGs), and so the rest of the analyses used this KCl vs “Minus” comparison. After imposing a 30-read minimum cutoff, one of the DNAStar options shared two of the three steps (mapping, normalization, and statistic) with Partek Flow (they both used median of ratios to normalize and the DESeq2 statistical package), and these two programs identified the highest number of DEGs in common with each other (53). In contrast, when the programs used different approaches in each of the three steps, between 31 and 40 DEGs were found in common. Regarding the extent of expression differences, three of the four programs gave high fold-change results (15–178 fold), but one (DNAstar’s DESeq2) resulted in more conservative fold-changes (1.5–3.5). In a parallel study comparing three qPCR commercial validation software programs, these programs also gave variable results as to which genes were significantly regulated. Similarly, the C. elegans analysis showed exaggerated fold-changes in CLC and DNAstar’s edgeR while DNAstar-D was more conservative.

Conclusions
Regarding the extent of expression (fold-change), and considering the subtlety of the very low level radiation treatments, in E. coli three of the four programs gave what we consider exaggerated fold-change results (15 – 178 fold), but one (DNAstar’s DESeq2) gave more realistic fold-changes (1.5–3.5). When RT-qPCR validation comparisons to transcriptome results were carried out, they supported the more conservative DNAstar-D’s expression results. When another model organism’s (nematode) response to these radiation differences was similarly analyzed, DNAstar-D also resulted in the most conservative expression patterns. Therefore, we would propose DESeq2 (“DNAstar-D”) as an appropriate software tool for differential gene expression studies for treatments expected to give subtle transcriptome responses.
The association between cardiac drug therapy and anxiety among cardiac patients: results from the national DenHeart survey
Authors: Rotvig Camilla , Christensen Anne Vinggaard , Juel Knud , Svendsen Jesper Hastrup , Jørgensen Martin Balslev , Rasmussen Trine Bernholdt , Borregaard Britt , Thrysoee Lars , Thorup Charlotte Brun , Mols Rikke Elmose , Berg Selina Kikkenborg 
Published: June 2022

Abstract
Background
Neuropsychiatric side effects of cardiac drugs such as nervousness, mood swings and agitation may be misinterpreted as symptoms of anxiety. Anxiety in cardiac patients is highly prevalent and associated with poor outcomes, thus an accurate identification is essential. The objectives were to: (I) describe the possible neuropsychiatric side effects of common cardiac drug therapies, (II) describe the use of cardiac drug therapy in cardiac patients with self-reported symptoms of anxiety compared to those with no symptoms of anxiety, and (III) investigate the association between the use of cardiac drug therapy and self-reported symptoms of anxiety.

Methods
DenHeart is a large national cross-sectional survey combined with national register data. Symptoms of anxiety were measured by the Hospital Anxiety and Depression Scale (HADS-A) on patients with ischemic heart disease, arrhythmia, heart failure and heart valve disease. Side effects were obtained from ‘product summaries’, and data on redeemed prescriptions obtained from the Danish National Prescription Registry. Multivariate logistic regression analyses explored the association between cardiac drug therapies and symptoms of anxiety (HADS-A ≥ 8).

Results
Among 8998 respondents 2891 (32%) reported symptoms of anxiety (HADS-A ≥ 8). Neuropsychiatric side effects were reported from digoxin, antiarrhythmics, beta-blockers, ACE-inhibitors and angiotensin receptor antagonists. Statistically significant higher odds of reporting HADS ≥ 8 was found in users of diuretics, lipid-lowering agents, nitrates, antiarrhythmics and beta-blockers compared to patients with no prescription.

Conclusion
Some cardiac drugs were associated with self-reported symptoms of anxiety among patients with cardiac disease. Of these drugs neuropsychiatric side effects were only reported for antiarrhythmics and beta-blockers. Increased awareness about the possible adverse effects from these drugs are important.
Development and evaluation of a nomogram for adverse outcomes of preeclampsia in Chinese pregnant women
Authors: Zheng Jiangyuan , Zhang Li , Zhou Yang , Xu Lin , Zhang Zuyue , Luo Yaling 
Published: June 2022

Abstract
Objective
Preeclampsia, the main cause of maternal and perinatal deaths, is associated with several maternal complications and adverse perinatal outcomes. Some prediction models are uesd to evaluate adverse pregnancy outcomes. However, some of the current prediction models are mainly carried out in developed countries, and many problems are still exist. We, thus, developed and validated a nomogram to predict the risk of adverse pregnancy outcomes of preeclampsia in Chinese pregnant women.

Methods
The clinical data of 720 pregnant women with preeclampsia in seven medical institutions in Chongqing from January 1, 2010, to December 31, 2020, were analyzed retrospectively. The patients were divided into two groups: 180 cases (25%) with adverse outcomes and 540 cases (75%) without adverse outcomes. The indicators were identified via univariate analysis. Logistic regression analysis was used to establish the prediction model, which was displayed by a nomogram. The performance of the nomogram was evaluated in terms of the area under the receiver operating characteristic (ROC) curve, calibration, and clinical utility.

Results
Univariate analysis showed that 24 indicators were significantly different (P < 0.05). Logistic regression analysis showed that gestational age, 24 h urine protein qualitative, and TT were significantly different (P < 0.05). The area under the ROC curve was 0.781 (95% CI 0.737–0.825) in training set and 0.777 (95% CI 0.689–0.865) in test set. The calibration curve of the nomogram showed good agreement between prediction and observation. The analysis of the clinical decision curve showed that the nomogram is of practical significance.

Conclusion
Our study identified gestational age, 24 h urine protein qualitative, and TT as risk factors for adverse outcomes of preeclampsia in pregnant women, and constructed a nomogram that can easily predict and evaluate the risk of adverse pregnancy outcomes in women with preeclampsia.
A network meta-analysis for efficacies and toxicities of different concurrent chemoradiotherapy regimens in the treatment of locally advanced non-small cell lung cancer
Authors: Zheng Qiangqiang , Min Shihui , Zhou Yunfeng 
Published: June 2022

Abstract
Background
Concurrent chemoradiotherapy (CCRT) has become the cornerstone of treatment for patients with locally advanced non-small cell lung cancer (LA-NSCLC). The aim of this study was to compare the efficacies and toxicities of different CCRT regimens in the treatment of LA-NSCLC by adopting a network meta-analysis (NMA).

Methods
An exhaustive search of PubMed, EMBASE, Web of Science, and the Cochrane Central Register of Controlled Trials (CENTRAL) was conducted to identify relevant studies from inception to October 1, 2020. Direct and indirect evidence was combined to calculate the odds radios (ORs) and 95% confidence intervals (CIs), as well as to plot the surface under the cumulative ranking (SUCRA) curves. Cluster analyses were adopted to compare the efficacies and toxicities of different CCRT regimens according to the similarity of 2 variables. Publication bias was detected by comparison-adjusted funnel plots.

Results
Twenty-two studies were enrolled in this NMA, including 18 regimens: CCRT (cisplatin + etoposide), CCRT (carboplatin + paclitaxel), CCRT (pemetrexed + carboplatin), CCRT (pemetrexed + cisplatin), CCRT (docetaxel + cisplatin), CCRT (S-1 + cisplatin), CCRT (mitomycin + vindesine + cisplatin), CCRT (cisplatin + vinorelbine), CCRT (cisplatin), CCRT (etoposide + cisplatin + amifostine), RT, CCRT (5-FU), CCRT (paclitaxel + cisplatin), CCRT (irinotecan + carboplatin), CCRT (nedaplatin), CCRT (carboplatin + etoposide), CCRT (paclitaxel), and CCRT (carboplatin). The results indicated that the regimens with CCRT (cisplatin + etoposide), CCRT (carboplatin + paclitaxel), CCRT (pemetrexed + cisplatin), CCRT (S-1 + cisplatin), and CCRT (cisplatin + vinorelbine) had relatively better efficacies compared with other regimens. As for toxicities of different CCRT regimens, the CCRT (carboplatin + paclitaxel), CCRT (pemetrexed + cisplatin), and CCRT (docetaxel + cisplatin) were relatively lower.

Conclusions
Our study demonstrated that CCRT (pemetrexed + cisplatin) and CCRT (carboplatin + paclitaxel) might be the best options for the treatment of LA-NSCLC, and CCRT (pemetrexed + cisplatin) had the highest 3-year overall survival (OS) rate.
Contribution and clinical relevance of germline variation to the cancer transcriptome
Authors: Pereira Bernard , Labrot Emma , Durand Eric , Korn Joshua M. , Kauffmann Audrey , Campbell Catarina D. 
Published: June 2022

Abstract
Background
Somatic alterations in the cancer genome, some of which are associated with changes in gene expression, have been characterized in multiple studies across diverse cancer types. However, less is known about germline variants that influence tumor biology by shaping the cancer transcriptome.

Methods
We performed expression quantitative trait loci (eQTL) analyses using multi-dimensional data from The Cancer Genome Atlas to explore the role of germline variation in mediating the cancer transcriptome. After accounting for associations between somatic alterations and gene expression, we determined the contribution of inherited variants to the cancer transcriptome relative to that of somatic variants. Finally, we performed an interaction analysis using estimates of tumor cellularity to identify cell type-restricted eQTLs.

Results
The proportion of genes with at least one eQTL varied between cancer types, ranging between 0.8% in melanoma to 28.5% in thyroid cancer and was correlated more strongly with intratumor heterogeneity than with somatic alteration rates. Although contributions to variance in gene expression was low for most genes, some eQTLs accounted for more than 30% of expression of proximal genes. We identified cell type-restricted eQTLs in genes known to be cancer drivers including LPP and EZH2 that were associated with disease-specific mortality in TCGA but not associated with disease risk in published GWAS. Together, our results highlight the need to consider germline variation in interpreting cancer biology beyond risk prediction.
Long-term surgical outcomes of Ahmed valve implantation in refractory glaucoma according to the type of glaucoma
Authors: Kang Yong Koo , Shin Jae Pil , Kim Dai Woo 
Published: June 2022

Abstract
Background
We evaluated the long-term efficacy and surgical outcomes of Ahmed glaucoma valve (AGV) implantation in patients with refractory glaucoma by glaucoma type.

Methods
In total, 135 eyes of 135 patients diagnosed with refractory glaucoma and underwent AGV implantation between 2002 and 2018 were reviewed retrospectively. The best-corrected visual acuity (BCVA), intraocular pressure (IOP), and number of antiglaucoma medications were investigated at baseline and follow-up. The cumulative probability of qualified success according to the glaucoma type was evaluated at 12, 24, 36, and 60 months postoperatively.

Results
The mean IOP of all patients was 35.7 ± 11.7 mmHg, which was significantly reduced 12.7 ± 7.0 mmHg at 1 week, 16.2 ± 7.5 mmHg at 2 weeks, 17.6 ± 6.8 mmHg at 1 month, 17.5 ± 6.4 mmHg at 3 months, 16.1 ± 6.0 mmHg at 6 months, 16.7 ± 8.0 mmHg at 12 months, 16.4 ± 6.6 mmHg at 24 months, 15.6 ± 5.0 mmHg at 36 months, and 15.6 ± 5.6 mmHg at 60 months after surgery (p < 0.001, respectively). The mean number of antiglaucoma medications was 3.7 ± 1.3, which significantly decreased to 0.4 ± 0.9 at 1 week, 0.3 ± 0.8 at 2 weeks, 0.7 ± 0.9 at 1 month, 1.1 ± 1.1 at 3 months, 1.4 ± 1.0 at 6 months, 1.5 ± 1.1 at 12 months, 1.6 ± 1.2 at 24 months, 1.7 ± 1.2 at 36 months, and 1.8 ± 1.3 at 60 months after surgery (p < 0.001, respectively). The mean BCVA significantly improved from postoperative 2 weeks. Although 71 (52.6%) eyes had postoperative complications, the cumulative probability of surgical success was 72.6% at 12 months, 66.7% at 24 months, and 63.7% at 36 and 60 months. According to the glaucoma type, the success rate of AGV implantation was more than 50% even after 60 months follow-up, except subgroup of neovascular glaucoma (NVG) due to retinal vein occlusion (RVO).

Conclusions
AGV implantation in patients with refractory glaucoma was, after long-term follow-up, successful overall. Therefore, AGV implantation can be an effective surgical option to reduce the IOP and number of antiglaucoma medications and to improve visual acuity for various glaucoma types.
Tools for assessing lung fluid in neonates with respiratory distress
Authors: Yoon So Jin , Han Jung Ho , Cho Kee Hyun , Park Joonsik , Lee Soon Min , Park Min Soo 
Published: June 2022

Abstract
Background
Transient tachypnea of the newborn (TTN), as a common cause of neonatal respiratory distress, needs to be distinguished from respiratory distress syndrome (RDS). Various modalities such as lung ultrasonography, cytokine analysis, and electrical cardiometry for the evaluation of lung fluid can be helpful for the exact diagnosis, however, clinical diagnosis has been applied mainly. This study aimed to evaluate the usefulness of the various tools for the diagnosis of TTN and RDS in neonates.

Methods
This study evaluated 22 late-preterm and term infants admitted to the neonatal intensive care unit of Gangnam Severance Hospital because of respiratory distress. Total 9 neonates were diagnosed with TTN and 13 had RDS. In addition to chest radiography, the LUS score was calculated by a neonatologist using the portable ultrasound device. Cytokines in the bronchoalveolar lavage fluid supernatant were measured. Thoracic fluid content was measured using an electrical cardiometry device.

Results
We enrolled 22 patients with median gestational age, 37.1 weeks, and birth weight 3100 g. There is no difference in patient characteristics between RDS and TTN group. Lung ultrasound score was significantly higher in RDS than TTN (11 vs 6, p = 0.001). Score 0 is shown in all infants with TTN. Score 1 is shown as significantly more in RDS than TTN. Between the TTN and RDS groups, there were significant differences in the changes of thoracic fluid content (2 vs − 1.5, p < 0.001), IL-1β levels (2.5 vs 11.3, p = 0.02), and TNF-α levels (20.1 vs 11.2, p = 0.04).

Conclusion
We found lung ultrasound and electrical cardiometry to be reliable diagnostic tools for assessing infants with respiratory distress among late-preterm and term infants. Further studies with a large number of patients are needed to confirm their clinical usefulness.
Biomechanical evaluation of percutaneous cement discoplasty by finite element analysis
Authors: Jia Hongwei , Xu Bin , Qi Xiangbei 
Published: June 2022

Abstract
Background
Percutaneous cement discoplasty (PCD) is a minimally invasive treatment for degenerative lumbar spine disease, but the relationship between decompression effect on the nerve root and different doses of bone cement is uncertain.

Purpose
To investigate the indirect decompression effect of cement with different doses on nerve roots and the biomechanical changes on the spine during PCD using finite element analysis (FEA).

Methods
FEA was adapted to analyze the mechanical changes in the lumbar vertebrae before and after the application of PCD.CT scan images of adult males were utilized to establish a finite element model of the lumbar vertebral body using mimics and Pro/E software. The images were divided into four models: the normal model (normal, model N), the disc degeneration model (high, model H), the intervertebral disc injected with 3 mL of bone cement (model H1), and the intervertebral disc injected with 5 mL of bone cement (model H2). All models were analyzed using the ABAQUS6.14.2 software. The normal physiological movements were simulated, and the mechanical changes in the lumbar vertebrae were observed prior to and after the cement filling application.

Results
The stress of the nerve root in model H was the largest. The nerve root stress in the model H2 was the smallest during flexion, extension, left bending, right bending, left rotation, and right rotation at 90%, 44%, 25%, 56%, 56%, and 51% of the normal benchmark, respectively. After the injection of bone cement, the nerve root stress is reduced. The greater the amount of cement, the lesser the nerve root stress. The motion was reduced in models H, H1, and H2, and there were differences between models H1 and H2. Cartilage endplate stress was less in model H2 than in model H1.

Conclusions
The nerve root stress increased after degeneration and decreased after intervertebral height recovery through cement injection, resulting in a significant indirect decompression effect.The stress of the nerve root decreased with the increase in the amount of cement injection.
Bone mineral density and muscle mass in adults with developmental skeletal discrepancies
Authors: Sharifi Reza , Kordi Sheida , Noravesh Farhad , Aghababaei Yasaman , Ramezani Majid , Maghbooli Zhila 
Published: June 2022

Abstract
Background
It was aimed to investigate the musculoskeletal status in individuals diagnosed with skeletal discrepancies.

Methods
This case–control study was performed on 35 patients with developmental skeletal discrepancies listed for orthognathic surgery as a case group and 33 patients who were nominated for wisdom tooth removal as a control group. All participants were aged 18–40 years and the research was carried out in the period between May 2018 and May 2019. Dual X-ray absorptiometry (DEXA) was used to assess bone mass density at three bone sites: total hip, femoral neck, and the spinal lumbar vertebrae (L1-L4). The appendicular muscle mass index (ASMI) was measured based on the four limbs from the DEXA scan.

Results
Our data showed that 45.7% (16) of the case group were osteopenic or osteoporotic while in the control group only 21.2% (7) were osteopenic in at least one region (total hip, femoral neck, or lumbar) (p-value = 0.03).
Regarding muscle mass, there was significantly lower SMI in subjects with skeletal discrepancies (case group) compared with the control group (median (IQR) 5.9 (2.5) vs. 6.8 (2.9) (kg/m2), respectively, p = 0.04).

Conclusions
There is an essential need for more studies to understand the exact interrelationship between musculoskeletal status and skeletal jaw discrepancies.
Modified rubber band ligation for treatment of grade II/III hemorrhoids: clinical efficacy and safety evaluation—a retrospective study
Authors: Yu Jiazi , Zhong Jie , Peng Tao , Jin Liangbin , Shen Leibin , Yang Mian 
Published: June 2022

Abstract
Background
Massive, delayed bleeding (DB) is the most common major complication of Rubber Band Ligation (RBL) for internal hemorrhoids caused by premature band slippage. In this study we modified conventional RBL to prevent early rubber band slippage and evaluated its clinical efficacy and safety.

Methods
Study participants were consecutive patients with grade II or III internal hemorrhoids treated with RBL at Ningbo Medical Center of Lihuili Hospital from January 2019 to December 2020. Postoperative minor complications such as pain, swelling, anal edema, prolapse recurrence and major complications like DB were retrospectively reviewed.

Results
A total of 274 patients were enrolled, including 149 patients treated with modified RBL and 125 treated with conventional RBL. There was no statistically significant difference between the two groups at baseline. Five cases of postoperative DB have been observed in the conventional RBL group, compared to none in the modified ones, with a significant difference (P < 0.05). Within three months after surgery, 8 cases in the modified RBL group experienced a recurrence rate of 5.4%, whereas 17 patients in the conventional RBL group experienced a recurrence rate of 13.6%. The difference was statistically significant (P < 0.05). The VAS score, edema, and incidence of sensation of prolapse between the two groups were not significantly different at 3 and 7 days after surgery (P < 0.05). There were also no significant differences in HDSS and SHS scores between the two groups after surgery (P > 0.05).

Conclusion
Modified RBL may be associated with a lower rate of complications, especially with lower DB rate in comparison with standard RBL. Further studies in larger samples and different design are necessary to confirm these results.