bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deep Local Analysis evaluates protein docking conformations with locally oriented cubes
Authors: Mohseni Behbahani Yasser , Crouzet Simon , Laine Elodie , Carbone Alessandra 
Published: August 2022

AbstractMotivationWith the recent advances in protein 3D structure prediction, protein interactions are becoming more central than ever before. Here, we address the problem of determining how proteins interact with one another. More specifically, we investigate the possibility of discriminating near-native protein complex conformations from incorrect ones by exploiting local environments around interfacial residues.ResultsDeep Local Analysis (DLA)-Ranker is a deep learning framework applying 3D convolutions to a set of locally oriented cubes representing the protein interface. It explicitly considers the local geometry of the interfacial residues along with their neighboring atoms and the regions of the interface with different solvent accessibility. We assessed its performance on three docking benchmarks made of half a million acceptable and incorrect conformations. We show that DLA-Ranker successfully identifies near-native conformations from ensembles generated by molecular docking. It surpasses or competes with other deep learning-based scoring functions. We also showcase its usefulness to discover alternative interfaces.Availability and implementationhttp://gitlab.lcqb.upmc.fr/dla-ranker/DLA-Ranker.gitSupplementary informationSupplementary data are available at Bioinformatics online.
Circulating Tumor DNA as a Biomarker for Monitoring Patients with Solid Cancers: Comparison with Standard Protein Biomarkers
Authors: Duffy Michael J , Crown John 
Published: August 2022

Abstract

Background
Protein-based biomarkers are widely used in monitoring patients with diagnosed cancer. These biomarkers however, lack specificity for cancer and have poor sensitivity in detecting early recurrences and monitoring therapy effectiveness. Emerging data suggest that the use of circulating tumor DNA (ctDNA) has several advantages over standard biomarkers.

Content
Following curative-intent surgery for cancer, the presence of ctDNA is highly predictive of early disease recurrence, while in metastatic cancer an early decline in ctDNA following the initiation of treatment is predictive of good outcome. Compared with protein biomarkers, ctDNA provides greater cancer specificity and sensitivity for detecting early recurrent/metastatic disease. Thus, in patients with surgically resected colorectal cancer, multiple studies have shown that ctDNA is superior to carcinoembryonic antigen (CEA) in detecting residual disease and early recurrence. Similarly, in breast cancer, ctDNA was shown to be more accurate than carbohydrate antigen 15-3 (CA 15-3) in detecting early recurrences. Other advantages of ctDNA over protein biomarkers in monitoring cancer patients include a shorter half-life in plasma and an ability to predict likely response to specific therapies and identify mechanisms of therapy resistance. However, in contrast to proteins, ctDNA biomarkers are more expensive to measure, less widely available, and have longer turnaround times for reporting. Furthermore, ctDNA assays are less well standardized.

Summary
Because of their advantages, it is likely that ctDNA measurements will enter clinical use in the future, where they will complement existing biomarkers and imaging in managing patients with cancer. Hopefully, these combined approaches will lead to a better outcome for patients.
Outcomes of aortic valve repair: early results from the German Aortic Valve Registry
Authors: Girdauskas Evaldas , Petersen Johannes , Balaban Ümniye , Herrmann Eva , Bauer Timm , Beckmann Andreas , Bekeredjian Raffi , Ensminger Stephan , Frerker Christian , Möllmann Helge , Walther Thomas , Bleiziffer Sabine 
Published: August 2022

Abstract

OBJECTIVES
Aortic valve (AV) repair is an evolving surgical strategy in the treatment of young patients with aortic regurgitation (AR) and/or aortic root aneurysm. We aimed to determine the clinical outcome following AV repair/AV-sparing root surgery using real-world data from the German Aortic Valve Registry.

METHODS
A total of 2327 patients with AR (mean age 55.2 ± 15.0 years, 76% men), who underwent AV repair/AV-sparing root surgery between 2011 and 2015 (i.e. 5% of 42 868 AV surgery patients enrolled in the German Aortic Valve Registry during the same period) were included. Study cohort was subdivided according to the technique of AV repair: isolated AV repair without root surgery (group I) (n = 914), AV-sparing root surgery (i.e. reimplantation or remodelling) without cusp repair (group II) (n = 1077) and AV-sparing root surgery (i.e. reimplantation or remodelling) with simultaneous cusp repair (group III) (n = 336). Primary end point was 1-year survival after AV repair/AV-sparing root surgery. Secondary end points were freedom from cardiac adverse events and freedom from AV reinterventions at 1-year follow-up.

RESULTS
Thirty-day mortality was 19 (0.8%) in the whole study cohort without significant differences in the 3 subgroups [4 (0.4%) patients in group I vs 14 (1.3%) patients in group II vs 1 (0.3%) patient in group III (P = 0.054)]. Postoperatively, 1445 (74%) patients had no residual AR, 474 (24%) patients had mild AR and 40 (2%) patients had moderate/severe AR at the time of hospital discharge. One-year survival (95% confidence interval) was 97.7% (97.1–98.3) in the whole study cohort and without significant difference among the 3 subgroups. One-year cardiac adverse event-free survival (95% confidence interval) was 85.7% (84.2–87.1) and was similar in all 3 study groups in propensity score-weighted analysis. A total of 38 (1.6%) patients required AV reintervention during a 1-year follow-up, without significant difference among subgroups (P = 0.11).

CONCLUSIONS
AV repair/AV-sparing root surgery is performed in 5% of patients requiring AV surgery in Germany. Our data demonstrate very satisfactory periprocedural and 1-year survival and cardiac event-free survival after AV repair surgery. Implementation of specific surgical techniques during the index procedure seems to result in comparable outcomes.
The efficiency of health resource allocation and its influencing factors: evidence from the super efficiency slack based model-Tobit model
Authors: Gong Jing , Shi Leiyu , Wang Xiaohan , Sun Gang 
Published: August 2022

Abstract

Background
This study aims to analyze the health resource allocation efficiency in Sichuan Province from 2010 to 2018 and provide other countries with China's experience.

Methods
We used the super efficiency slack based model (SBM) model and Malmquist index to analyze the super efficiency and inter-period efficiency of health resource allocation in 19 cities in Sichuan Province from 2010 to 2018 and propose the input-output optimization scheme of health resource allocation in 2018. Finally, the Tobit model was used to estimate the influencing factors of health resource allocation efficiency.

Results
The total allocation of health resources in Sichuan Province was increasing in addition to the total number of visits from 2010 to 2018. The super efficiency SBM results identified that the sample's average score was between 0.651 and 3.244, with an average of 1.041, of which 15 cities had not reached data envelopment analysis effectiveness. According to the Malmquist index, the average total factor productivity index of Sichuan Province was 0.930, which showed an imbalance in resource input, and its fluctuation was mainly related to the technological progress index and scale efficiency. The efficiency score was affected by the average annual income of residents, population density and education level.

Conclusions
The amount of health resource allocation in Sichuan Province had shown an overall upward trend since 2010. However, resource allocation efficiency was not high, and there were problems such as significant regional differences, insufficient technological innovation capabilities and unscientific allocation of resource scale. To optimize the resource allocation structure, we suggest that the relevant departments pay attention to the impact of natural disasters, the average annual income of residents, population density and education level on efficiency to allocate health resources scientifically.
Iconological Dualism Re-Thought: A New Variation on Two Old Theories
Authors: Wecker Frédéric 
Published: August 2022

Abstract
This article aims at defending the old theory of iconological dualism that opposes ‘handmade’ pictures to photographic pictures. I defend a new version of that theory, according to which photographs always enable viewers to have singular thoughts on the things photographed, while handmade pictures by themselves never enable viewers to have singular thoughts but only enable them to have what I call ‘thoughts by depiction’. To this end, I defend the old theory according to which singular thoughts require a special relation—called ‘acquaintance’—between the thinker and the object thought about. I put this traditional view forward thanks to a new version of the classic spy argument for the acquaintance constraint on singular thoughts.
Why we should rethink the third-person effect: disentangling bias and earned confidence using behavioral data
Authors: Lyons Benjamin A 
Published: August 2022

Abstract
Although positioned as a cognitive bias, third-person effect research has relied on self-reported difference scores that fail to capture bias appropriately. I use pre-registered and exploratory analyses of three nationally representative surveys (N = 10,004) to examine perceptions of susceptibility to false news and behavioral measures of actual susceptibility. Americans consistently exhibit third-person perception. However, some of this perceptual gap may be “earned.” I show that 62–68% of those exhibiting TPP are in fact less susceptible than average. Accordingly, I construct a performance-derived measure of true overconfidence. I find domain-involvement correlates of TPP tend not to hold for actual overconfidence. I also find significant differences in potential behavioral outcomes suggesting the traditional measure may often reflect genuine differences in self and others’ susceptibility to media, rather than a self-serving bias of presumed invulnerability. These results have important implications for our understanding and measurement of perceptual biases in communication research.
Bilateral correction of asphyxiating thoracic dystrophy
Authors: Wang Wenlin , Long Weiguang , Liu Yang , Cai Bin 
Published: August 2022

Abstract
Several operations for asphyxiating thoracic dystrophy (ATD) have been used previously, but they all have disadvantages. We report a 25-year-old male ATD patient who had significant depressions on both sides of thorax. We designed a special operation for him, which had not only eliminated the depression, but also increased the volume of the thorax. The results show that this operation is a reasonable choice for this kinds of patient.
Rare case of papillary fibroelastoma resection with concomitant cox-maze IV procedure
Authors: Hooda Zamaan , Ramaprasad Ganesh , Cerda Luis , Zuberi Jamshed , Connolly Mark 
Published: August 2022

Abstract
Primary cardiac tumors represent 0.1% of all cardiac tumors, making them a rare pathologic phenomenon. The second most common cardiac tumors are papillary fibroelastomas, which also represent the most common valvular tumors. This report examines a rare case of a patient that underwent resection of papillary fibroelastoma with simultaneous Cox-Maze IV procedure for treatment of atrial fibrillation. This 67-year-old male patient was initially scheduled for transcatheter ablation for treatment of rate-controlled atrial fibrillation. During a pre-procedural trans-thoracic echocardiogram, it was discovered that the patient had a moderately sized pedunculated mass on the aortic valve, suspicious of papillary fibroelastoma. Despite the patient having no history of embolic events or aortic insufficiency from the papillary fibroelastoma, the transcatheter ablation procedure was canceled. He was referred to cardiothoracic surgery for further evaluation, and it was determined that this patient was a candidate for papillary fibroelastoma resection along with Cox-Maze IV procedure for atrial fibrillation.
The development of natural gas in Asia—the results of the forecast scenarios of the POLES model
Authors: Le Minh Thong 
Published: August 2022

Abstract
Many studies have shown the important role of natural gas in worldwide energy transition to gradually reduce the impacts on climate change. Asia is considered the centre of future gas demand growth. With a view to demonstrating the role of natural gas in the energy transition in Asia, this article will analyse the results from the scenarios forecasting the development of natural gas based on the Prospective Outlook on Long-term Energy Systems energy forecasting model.
The effect of magnetic field on the inner Galactic rotation curve
Authors: Chan Man Ho , Del Popolo Antonino 
Published: August 2022

ABSTRACT
In the past few decades, some studies pointed out that magnetic field might affect the rotation curves in galaxies. However, the impact is relatively small compared with the effects of dark matter and the baryonic components. In this letter, we revisit the impact of magnetic field on the rotation curve of our Galaxy. We show that the inner Galactic rotation curve could be affected significantly by the magnetic field. The addition of the inner bulge component, which has been proposed previously to account for the inner rotation curve data, is not necessary. The magnetic field contribution can fully account for the excess of the inner rotation velocity between 5 to 50 pc from the Galactic Centre. Our analysis can also constrain the azimuthal component of the central regular magnetic field strength to $B_0 \sim 50-60\, \mu$G, which is consistent with the observed range.
Concordance Between Genomic Alterations Detected by Tumor and Germline Sequencing: Results from a Tertiary Care Academic Center Molecular Tumor Board
Authors: Green Michelle F , Watson Catherine H , Tait Sarah , He Jie , Pavlick Dean C , Frampton Garrett , Riedel Jinny , Plichta Jennifer K , Armstrong Andrew J , Previs Rebecca A , Kauff Noah , Strickler John H , Datto Michael B , Berchuck Andrew , Menendez Carolyn S 
Published: August 2022

AbstractObjectiveThe majority of tumor sequencing currently performed on cancer patients does not include a matched normal control, and in cases where germline testing is performed, it is usually run independently of tumor testing. The rates of concordance between variants identified via germline and tumor testing in this context are poorly understood. We compared tumor and germline sequencing results in patients with breast, ovarian, pancreatic, and prostate cancer who were found to harbor alterations in genes associated with homologous recombination deficiency (HRD) and increased hereditary cancer risk. We then evaluated the potential for a computational somatic-germline-zygosity (SGZ) modeling algorithm to predict germline status based on tumor-only comprehensive genomic profiling (CGP) results.MethodsA retrospective chart review was performed using an academic cancer center’s databases of somatic and germline sequencing tests, and concordance between tumor and germline results was assessed. SGZ modeling from tumor-only CGP was compared to germline results to assess this method’s accuracy in determining germline mutation status.ResultsA total of 115 patients with 146 total alterations were identified. Concordance rates between somatic and germline alterations ranged from 0% to 85.7% depending on the gene and variant classification. After correcting for differences in variant classification and filtering practices, SGZ modeling was found to have 97.2% sensitivity and 90.3% specificity for the prediction of somatic versus germline origin.ConclusionsMutations in HRD genes identified by tumor-only sequencing are frequently germline. Providers should be aware that technical differences related to assay design, variant filtering, and variant classification can contribute to discordance between tumor-only and germline sequencing test results. In addition, SGZ modeling had high predictive power to distinguish between mutations of somatic and germline origin without the need for a matched normal control, and could potentially be considered to inform clinical decision-making.
Meconium-Stained Amniotic Fluid: Impact on Prognosis of Neonatal Bacterial Meningitis
Authors: Li Ya-Ting , Li Cai-Xia , Huang Chu-Jun , Wen Qian-Yu , Deng Shu-Min , Zhu Ling-Ping , Liu Zi-Feng , Chen Zhuang-Gui 
Published: August 2022

AbstractObjectivesClinical data with respect to the impact of meconium on the prognosis of neonatal bacterial meningitis are scarce. Therefore, in this study, we aimed to determine whether meconium-stained amniotic fluid (MSAF) represents a risk factor for poor prognosis of neonatal bacterial meningitis in a confirmed case population.MethodsThis was a retrospective cohort study of 256 neonates diagnosed with bacterial meningitis hospitalized at one of three hospitals in Shantou, China, between October 2013 and September 2018. Clinical manifestation, laboratory test results and treatment were compared between the two groups, with outcomes dichotomized into ‘good’ or ‘poor’ prognosis. Multivariate analysis and follow-up logistic regression analysis were used to identify predictive factors of a poor outcome.ResultsOf the 256 neonates with BM, 95 (37.1%) had a good prognosis at discharge and 161 (62.9%) had a poor prognosis. In the poor prognosis group, 131/161 (79.4%) neonates had a permanent neurological sequelae and 19 (11.8%) had ≥2 sequelae. Of note, 11 neonates died. The rate of poor prognosis of BM was significantly higher among neonates with than without MSAF (26.1% vs. 12.6%, respectively; p &lt; 0.05). A logistic multivariate analysis to evaluate the prognostic effect of MSAF to BM showed that neonatal with MSAF is more likely to have a worse prognosis of BM [unadjusted odds ratio (OR), 2.44, 95% confidence interval (CI), 1.24–5.10; adjusted OR, 2.31; 95% CI, 1.09–5.17].ConclusionMSAF is significantly associated with poor prognosis of neonatal bacterial meningitis. Therefore, in case of MSAF, more attention should be paid to neonatal bacterial meningitis.
XIIIThe Victorian Period
Authors: Garza Ana Alicia , Burke Lois , Snailham Fiona , Blackburn-Daniels Sally , Hind Heather , Baker William 
Published: August 2022

AbstractThis chapter has six sections: 1. General and Prose, including Dickens; 2. The Novel; 3. Poetry; 4. Periodicals, Publishing History; 5. Miscellaneous; 6. Drama. Section 1 is by Ana Alicia Garza; section 2 is by Lois Burke and Fiona Snailham; section 3 is by Sally Blackburn-Daniels; section 4 is by Heather Hind; sections 5 and 6 are by William Baker.
PREVALENCE, CHARACTERISTICS, AND OUTCOMES OF RHEGMATOGENOUS RETINAL DETACHMENT IN EYES WITH TRABECULECTOMY OR GLAUCOMA DRAINAGE DEVICES
Authors: Starr Matthew R. , Huang Denis , Wong Jae-Chiang , Patel Luv G. , Ammar Michael , Hsu Jason , Sivalingam Arunan , Mehta Sonia , Ho Allen C. , Kuriyan Ajay E. , Khan M. Ali , Cohen Michael N. , Xu David , Lee Daniel , Moster Marlene R. , Yonekawa Yoshihiro 
Published: August 2022

Purpose:
To describe the prevalence, management, and outcomes of rhegmatogenous retinal detachment (RRD) after incisional glaucoma filtering surgery.

Methods:
All patients with a history of trabeculectomy or glaucoma drainage device surgery who were subsequently diagnosed with an RRD from January 1, 2016, to January 1, 2021, at the Wills Eye Hospital were identified.

Results:
Forty-six eyes met the inclusion criteria. The mean age was 60.7 ± 19.6 years, and 15 patients (32.6%) were female. Of all eyes, 34 (73.9%) were diagnosed with primary open-angle glaucoma. The mean time from most recent incisional glaucoma surgery to RRD diagnosis was 1,133 ± 1,644 days. There were 19 eyes (41.3%) with preoperative proliferative vitreoretinopathy (9 eyes [19.6%] with Grade C proliferative vitreoretinopathy) and 35 eyes (76.1%) had macula-off RRD at the time of presentation. At RRD presentation, 4 eyes (8.7%) had concomitant endophthalmitis, 5 (10.9%) had concurrent choroidal detachment, and 2 (4.7%) had concurrent vitreous hemorrhage. Primary vitrectomy was performed in most (91.3%) cases. Silicone oil tamponade was often required (71.1%). The single surgery success rate was 65.2% (30 of 46). The mean preoperative logarithm of the minimum angle of resolution visual acuity was 1.72 ± 0.78 (Snellen acuity 20/1,050), and the mean final postoperative logarithm of the minimum angle of resolution was 1.59 ± 0.89 (20/778, P = 0.2853). Of glaucoma surgeries performed, the 5-year prevalence of RRD was 0.71% (26 of 3,664, 95% Poisson confidence interval 0.48%–1.04%).

Conclusion:
The 5-year prevalence of RRDs after trabeculectomy or glaucoma drainage device was 0.71%. Most patients presented with macula-involving detachments, often with proliferative vitreoretinopathy. Anatomical and visual outcomes were poor.
LONG-TERM EFFECTS OF ANTI-VEGF MONOTHERAPY FOR RETINOPATHY OF PREMATURITY ON THE RETINAL AND REFRACTIVE DEVELOPMENT OF EYE
Authors: Sukgen Emine Alyamaç , Atalay Hatice Tuba , Özdek Şengül 
Published: August 2022

Purpose:
To evaluate vascular maturation of retina, axial, refractive, and foveal development after anti-VEGF treatment including bevacizumab, ranibizumab, and aflibercept in infants with treatment requiring retinopathy of prematurity (ROP) in long term.

Methods:
This retrospective chart review study included children with a history of any anti-VEGF monotherapy for ROP in Zone 1 or posterior Zone 2 who have reached at least 24 months of corrected age. The records of ophthalmologic examination including strabismus evaluation, visual acuity measurement, refractive and axial measurements, optical coherence tomography, and fundus fluorescein angiography examinations with RetCam III were reviewed.

Results:
A total of 36 eyes of 18 children met the inclusion criteria. The mean gestational age at birth was 27.8

2.13 (23–30) weeks, and ocular assessments were performed between 33 and 61.5 (mean: 42.58

8.6) months of corrected age. Treatment was with bevacizumab in 10 eyes, with ranibizumab in 14 eyes, and with aflibercept in 12 eyes. The mean spherical equivalent was −0.25

1.82; axial length was 20.81

0.62 mm. There was no significant difference among three anti-VEGF groups regarding the abnormal vascular retinal development (P = 0.183) or leakage (P = 0.842) on fluorescein angiography.

Conclusion:
All the anti-VEGF agents provided similar adequate axial and refractive development as well as similar abnormal vascular development in the peripheral retina. The long-term impact of this abnormally vascularized peripheral retina is a curiosity issue. From this point of view, it is an important need to determine the follow-up period and method after the anti-VEGF treatment for ROP.
Neurofibromatosis Type 2
Authors: Filizoglu Nuh , Ozguven Salih 
Published: August 2022

Abstract
Neurofibromatosis type 2 (NF2) is an autosomal-dominant tumor predisposing syndrome that results from mutations in the NF2 tumor suppressor gene on chromosome 22. The development of bilateral vestibular schwannomas is the characteristic feature of the disease. However, other nervous system tumors, including meningiomas, ependymomas, and schwannomas, can be seen frequently. Herein, we present 68Ga-DOTATATE PET/CT findings of 2 siblings with NF2.