bluuebunny/crossref_metadata_2025_split huggingface dataset:
AFSE: towards improving model generalization of deep graph learning of ligand bioactivities targeting GPCR proteins
Authors: Yin Yueming , Hu Haifeng , Yang Zhen , Jiang Feihu , Huang Yihe , Wu Jiansheng 
Published: February 2022

Abstract
Ligand molecules naturally constitute a graph structure. Recently, many excellent deep graph learning (DGL) methods have been proposed and used to model ligand bioactivities, which is critical for the virtual screening of drug hits from compound databases in interest. However, pharmacists can find that these well-trained DGL models usually are hard to achieve satisfying performance in real scenarios for virtual screening of drug candidates. The main challenges involve that the datasets for training models were small-sized and biased, and the inner active cliff cases would worsen model performance. These challenges would cause predictors to overfit the training data and have poor generalization in real virtual screening scenarios. Thus, we proposed a novel algorithm named adversarial feature subspace enhancement (AFSE). AFSE dynamically generates abundant representations in new feature subspace via bi-directional adversarial learning, and then minimizes the maximum loss of molecular divergence and bioactivity to ensure local smoothness of model outputs and significantly enhance the generalization of DGL models in predicting ligand bioactivities. Benchmark tests were implemented on seven state-of-the-art open-source DGL models with the potential of modeling ligand bioactivities, and precisely evaluated by multiple criteria. The results indicate that, on almost all 33 GPCRs datasets and seven DGL models, AFSE greatly improved their enhancement factor (top-10%, 20% and 30%), which is the most important evaluation in virtual screening of hits from compound databases, while ensuring the superior performance on RMSE and $r^2$. The web server of AFSE is freely available at http://noveldelta.com/AFSE for academic purposes.
Repeat liver resection for recurrent intrahepatic cholangiocarcinoma: meta-analysis
Authors: Ramouz Ali , Ali-Hasan-Al-Saegh Sadeq , Shafiei Saeed , Fakour Sanam , Khajeh Elias , Majlesara Ali , Adeliansedehi Ali , Probst Pascal , Springfeld Christoph , Chang De-Hua , Rupp Christian , Carvalho Carlos , Golriz Mohammad , Hoffmann Katrin , Mehrabi Arianeb 
Published: February 2022

Abstract

Background
Intrahepatic cholangiocarcinoma (ICC) is a relatively rare malignancy. The aim of this meta-analysis was to evaluate outcomes of repeat liver resection and non-surgical approaches for treatment of recurrent ICC.

Methods
PubMed, Embase, and Web of Science databases were searched from their inception until March 2021 for studies of patients with recurrent ICC. Studies not published in English were excluded. Two meta-analyses were performed: a single-arm meta-analysis of studies reporting pooled short- and long-term outcomes after repeat liver resection for recurrent ICC (meta-analysis A), and a meta-analysis of studies comparing 1-, 3-, and 5-year overall survival (OS) rates after repeat liver resection and non-surgical approaches for recurrent ICC (meta-analysis B).

Results
Of 543 articles retrieved in the search, 28 were eligible for inclusion. Twenty-four studies (390 patients) were included in meta-analysis A and nine studies (591 patients) in meta-analysis B. After repeat liver resection, 1-, 3-, and 5-year OS rates were 87 (95 per cent c.i. 81 to 91), 58 (48 to 68), and 39 (29 to 50) per cent respectively. The 1-, 3-, and 5-year OS rates were higher after repeat liver resection than without surgery: odds ratio 2.70 (95 per cent c.i. 1.28 to 5.68), 2.89 (1.15 to 7.27), and 5.91 (1.59, 21.90) respectively.

Conclusion
Repeat liver resection is a suitable strategy for recurrent ICC in selected patients. It improves short- and long-term outcomes compared with non-surgical treatments.
Insular-associated causal network of structural covariance evaluating progressive gray matter changes in major depressive disorder
Authors: Lu Fengmei , Cui Qian , Chen Yuyan , He Zongling , Sheng Wei , Tang Qin , Yang Yang , Luo Wei , Yu Yue , Chen Jiajia , Li Di , Deng Jiaxin , Zeng Yuhong , Chen Huafu 
Published: February 2022

Abstract

Background
Morphometric studies demonstrated wide-ranging distribution of brain structural abnormalities in major depressive disorder (MDD).

Objective
This study explored the progressive gray matter volume (GMV) changes pattern of structural network in 108 MDD patients throughout the illness duration by using voxel-based morphometric analysis.

Methods
The causal structural covariance network method was applied to map the causal effects of GMV alterations between the original source of structural changes and other brain regions as the illness duration prolonged in MDD. This was carried out by utilizing the Granger causality analysis to T1-weighted data ranked based on the disease progression information.

Results
With greater illness duration, the GMV reduction was originated from the right insula and progressed to the frontal lobe, and then expanded to the occipital lobe, temporal lobe, dorsal striatum (putamen and caudate) and the cerebellum. Importantly, results revealed that the right insula was the prominent node projecting positive causal influences (i.e., GMV decrease) to frontal lobe, temporal lobe, postcentral gyrus, putamen, and precuneus. While opposite causal effects were detected from the right insula to the angular, parahippocampus, supramarginal gyrus and cerebellum.

Conclusions
This work may provide further information and vital evidence showing that MDD is associated with progressive brain structural alterations.
Planning for resilient central-city shopping districts in the post-Covid era: an explanatory case study of the Hoddle Grid in Melbourne
Authors: Rao Fujie , Han Sun Sheng , Pan Ran 
Published: February 2022

AbstractThis research explores how central-city shopping districts could be transformed to support a post-Covid lifestyle, where people re-embrace community, local streets and walking while relying more on online shopping. By reviewing metropolitan/city development plans since the 1980s and mapping changes of retail provisions, urban environment and pedestrian movements in Melbourne’s Hoddle Grid in the twenty-first century, this paper shows that planning policies focusing on people-centred experiences in the central-city shopping district helped to improve retail resilience. This paper thus adds insights to understanding the relentless retail landscape changes and has implications for central-city retail planning in the post-Covid era.
A case report of COVID-19-associated acute hand ischaemia in a young professional volleyball player
Authors: Achim Alexandru , Kákonyi Kornél , Jambrik Zoltán , Ruzsa Zoltán 
Published: February 2022

AbstractBackgroundSeveral coronavirus disease-19 (COVID-19)-associated complications are being increasingly reported, including arterial and venous thrombo-embolic events that may lead to amputation of the affected limbs. So far, acute upper limb ischaemia (ULI) has been reported only in critically ill patients.Case summaryHerein, we aimed to present a case of a 29-year-old, otherwise healthy male volleyball player, with acute ischaemic signs in the upper extremity who was diagnosed with COVID-19 1 month before the ischaemic event. It has been shown that volleyball players experience repetitive stress that involves their hands and, in particular, their fingers. Repetitive trauma can lead to local vascular abnormalities, such as reduced capillarization and lower resting blood flow that can lead to pain and cold digits, but never acute ULI.DiscussionTo our knowledge, this is the first case of such a hypercoagulable synergistic mechanism that leads to a high thrombus burden. Intra-arterial local thrombolysis and percutaneous transluminal angioplasty failed to succeed, and percutaneous large-bore embolectomy with the Indigo Aspiration System (Penumbra Inc., CA, USA) was deemed necessary.
Long-term outcomes with the On-X bileaflet mitral valve: clinical events up to 17 years in 661 patients
Authors: Reyes Guillermo , Muñoz Daniel , Monguio Emilio , Berastegui Elisabet , Camara Maria Luisa , de Antonio Nieves , Julia Ignasi , Aguirre Maria Fernanda , Fernandez Claudio , Badia Sara , Muñoz-Guijosa Christian 
Published: February 2022

Abstract

OBJECTIVES
This study reports long-term clinical outcomes—up to 17 years—among patients undergoing mitral valve replacement with the On-X bileaflet mechanical valve. Prior data regarding long-term outcomes with the On-X mitral valve have been limited.

METHODS
This retrospective observational study included all patients who underwent mitral valve replacement with the On-X (Standard or Conform-X) valve at 2 major Spanish cardiac surgery centres between 2001 and 2018. The primary study end point was freedom from death. The secondary study end points included surgical mortality and freedom from any valve-related events. Data were obtained from an institutional database, medical records review, direct telephone interviews or the Spanish population registry. Statistical and Kaplan–Meier analyses were performed.

RESULTS
A total of 661 patients (mean age 63.1 ± 10.9 years, 63% female) were followed for a mean of 5.6 years (range, 0–17.4 years). Survival at 5, 10 and 15 years was 85%, 71% and 63%, respectively. Surgical mortality was 7.3% (48/661). The linearized rate of global mortality was 1.3% patient-year. Freedom from reoperation was 97%, 95% and 92% at 5, 10 and 15 years, respectively; freedom from anticoagulation-related events was 94%, 89% and 89%, respectively. Multivariable analysis showed that mortality increased with total length of stay, age, smoking history, severe pulmonary hypertension and a permanent pacemaker. Patients who received the On-X 25 -mm valve had decreased long-term survival relative to patients who received other On-X valve sizes, possibly due to underlying risk factors.

CONCLUSIONS
Patients in this study showed good long-term survival and freedom from valve-related events.
Impact of different valve-in-valve positions on the hydrodynamic performance of the newest-generation self-expanding transcatheter heart valve
Authors: Sadat Najla , Bruhn Denise , Scharfschwerdt Michael , Schaller Tim , Aboud Anas , Saisho Hiroyuki , Eitel Ingo , Ensminger Stephan , Fujita Buntaro 
Published: February 2022

Abstract

OBJECTIVES
Transcatheter aortic valve-in-valve (ViV) procedures are increasingly performed for the treatment of degenerated surgical aortic valves with a high risk for a redo operation. For an optimal functional result, precise positioning of the transcatheter heart valve (THV) inside the SHV is crucial. The aim of this study was to systematically investigate the impact of implantation depth on the functional result after a ViV procedure in a standardized in vitro setting.

METHODS
A THV 23 mm (Evolut PRO) and 3 SHV 21 mm (Perimount Magna Ease, Trifecta and Hancock II) were used for hydrodynamic testing with a constant heartbeat 64/min and a range of 55–105 ml of stroke volume in 5 different positions of the THV. The following parameters were analysed: mean pressure gradient (MPG), effective orifice area (EOA), geometric orifice area, minimal internal diameter and pin-wheeling index.

RESULTS
MPG and EOA differed significantly regarding the position of the THV in the same SHV. The highest EOA and the lowest MPG were recorded for Evolut PRO with significance for both parameters in Hancock II at 4 vs 5 mm (P &lt; 0.001), in Magna Ease at 2 mm (vs 3 mm and vs 6 mm, P &lt; 0.001) and in Trifecta at 4 mm (vs 5 and 6 mm, P &lt; 0.001). Leaflet coadaptation, minimal internal diameter and maximal geometric orifice area of the same TAV differ regarding the position of the TAV.

CONCLUSIONS
The optimal position for hydrodynamic performance of the THV as ViV differs among specific SHV models. The findings may be useful for planning a ViV procedure using the Evolut PRO THV.
The Polish Government-in-Exile: The United Nations War Crimes Commission and the Holocaust
Authors: Fleming Michael 
Published: February 2022

Abstract
The author discusses the engagement of the Polish Government-in-Exile with the issue of German war crimes and its involvement with the United Nations War Crimes Commission during the Second World War. Information sent by the Polish Underground State allowed the Polish War Crimes Office to compile its charge file submissions for the UNWCC in a strategic and organized manner. According to the author, the War Crimes Office attempted to ensure that German crimes against Jews received due attention in its charge file submissions.
A genome-wide analysis of 340 318 participants identifies four novel loci associated with the age of first spectacle wear
Authors: Patasova Karina , Khawaja Anthony P , Wojciechowski Robert , Mahroo Omar A , Falchi Mario , Rahi Jugnoo S , Hammond Chris J , Hysi Pirro G ,   the UK Biobank Eye & Vision Consortium, Shah R L , Guggenheim J A 
Published: February 2022

Abstract
Refractive errors, particularly myopia, are the most common eye conditions, often leading to serious visual impairment. The age of onset is correlated with the severity of refractive error in adulthood observed in epidemiological and genetic studies and can be used as a proxy in refractive error genetic studies. To further elucidate genetic factors that influence refractive error, we analysed self-reported age of refractive error correction data from the UK Biobank European and perform genome-wide time-to-event analyses on the age of first spectacle wear (AFSW). Genome-wide proportional hazards ratio analyses were conducted in 340 318 European subjects. We subsequently assessed the similarities and differences in the genetic architectures of refractive error correction from different causes. All-cause AFSW was genetically strongly correlated (rg = −0.68) with spherical equivalent (the measured strength of spectacle lens required to correct the refractive error) and was used as a proxy for refractive error. Time-to-event analyses found genome-wide significant associations at 44 independent genomic loci, many of which (GJD2, LAMA2, etc.) were previously associated with refractive error. We also identified six novel regions associated with AFSW, the most significant of which was on chromosome 17q (P = 3.06 × 10−09 for rs55882072), replicating in an independent dataset. We found that genes associated with AFSW were significantly enriched for expression in central nervous system tissues and were involved in neurogenesis. This work demonstrates the merits of time-to-event study design in the genetic investigation of refractive error and contributes additional knowledge on its genetic risk factors in the general population.
Root-commando operation for a ruptured left ventricular outflow tract
Authors: Takaki Hidenobu , Hashizume Kenichi , Ikebata Koki , Ohno Masatoshi 
Published: February 2022

Abstract
Prosthetic valve endocarditis, especially when complicated by an aortic root abscess and a left ventricular outflow tract rupture, is a life-threatening condition. We present a case of infective prosthetic aortic valve endocarditis with a ruptured left ventricular outflow tract successfully treated with a root-commando operation using a secure anastomosis for reconstruction of the damaged aortic annulus.
Novel thoracoscopic segmentectomy combining preoperative three-dimensional image simulation and intravenous administration of indocyanine green
Authors: Matsuura Natsumi , Igai Hitoshi , Ohsawa Fumi , Numajiri Kazuki , Kamiyoshihara Mitsuhiro 
Published: February 2022

Abstract

OBJECTIVES
The aim of this study is to assess prospectively the validity and feasibility of segmentectomy using preoperative simulation and intravenous indocyanine green (ICG) with near-infrared (NIR) light thoracoscope to ensure a sufficient surgical margin.

METHODS
This study was a prospective, single-centre, phase II, feasibility study. From February to July 2021, 20 patients were enrolled in this study. All patients underwent preoperative three-dimensional computed tomography angiography and bronchography using simulation software. The dominant pulmonary artery of the targeted segment was selected to determine the dissection line and measure the surgical margin to the tumour. Intraoperatively, after the planned dissection of the pulmonary artery, ICG (0.3 mg/kg) was administered intravenously and observed with NIR, and dissection was performed along the line determined by preoperative simulation. Postoperatively, the pathological margin was compared with the simulation margin.

RESULTS
All surgeries were performed via an uniport (3.5–4.0-cm skin incision). The regions of segmentectomy were S2, S3, S6, S9 + 10 and S10 of the right side and S1 + 2 + 3, S3, S3 + 4 + 5, S6 and S8 of the left side. The difference between the simulation margin and the pathological margin was not significant (simulation 30.5 ± 10.1 vs pathological 31.0 ± 11.0 mm, P = 0.801). The simulation margin was well correlated with the pathological margin (R2 = 0.677). The proportion of cases successfully achieving the pathological margin of error of plus or minus 10 mm of the simulation margin was 90% (18 of 20 cases).

CONCLUSIONS
The combination of preoperative three-dimensional computed tomography simulation and ICG–NIR was effective for securing a sufficient margin in segmentectomy.
A systematic review of the outcomes reported in the treatment of uncomplicated urinary tract infection clinical trials
Authors: Duane Sinead , Beecher Claire , Vellinga Akke , Murphy Andrew W. , Cormican Martin , Smyth Andrew , Healy Patricia , Moore Michael , Little Paul , Devane Declan 
Published: February 2022

Abstract

Background
Uncomplicated urinary tract infections (UTIs) are amongst the most frequent infections presenting in the outpatient setting. A growing number of clinical trials are assessing the most effective treatment interventions for uncomplicated UTI. Due to the heterogeneity of the outcomes reported in these trials, however, comparing these outcomes is challenging.

Objectives
Identify the core outcomes that have been reported in trials and systematic reviews of interventions treating uncomplicated UTI in adults.

Methods
We conducted a systematic search for core outcomes used to evaluate treatments of UTIs. We searched the Cochrane Database of Systematic Reviews, PubMed and Embase. One researcher independently screened each article for inclusion, and the Core Outcome Set for treatment of Urinary Tract Infections (COSUTI) team acted as second reviewers. All included articles were screened by two reviewers. All outcomes were extracted verbatim, and similar outcomes were grouped into domains and subdomains.

Results
In total, 334 outcomes were reported across 41 papers, the average number of outcomes reported being 8. Outcomes were categorized across 18 domains, the majority of which were related to clinical cure outcomes. Many outcomes varied in the timepoints within which the outcome was measured and reported.

Conclusions
Comparing the outcomes of trials investigating uncomplicated UTI treatment remains challenging due to the difference in outcomes currently reported. Consistency of reporting of outcomes would be improved by developing a minimum number of consistent outcomes that should be reported in all trials.
Hybrid molecule between platanic acid and LCL-161 as a yes-associated protein degrader
Authors: Nakano Naoko , Fukuda Kazuo , Tashiro Etsu , Ishikawa Haruka , Nagano Waka , Kawamoto Rie , Mori Alice , Watanabe Misao , Yamazaki Ryu , Nakane Takahisa , Naito Mikihiko , Okamoto Iwao , Itoh Susumu 
Published: February 2022

Abstract
Dysregulated yes-associated protein (YAP) is involved in several malignant cancers. However, discovering a druggable YAP inhibitor(s) is difficult because YAP itself does not have any enzymatic activity. In such cases, targeted protein degradation strategies based on hybrid molecules that bind to the target protein and an E3 ubiquitin ligase are useful for suppressing proteins that exhibit aberrant activation and/or excessive expression. Upon screening YAP-interacting small compounds, we identified HK13, a platanic acid, as a novel compound that interacts with YAP. Next, we synthesized hybrid compounds of platanic acid and LCL-161, which reportedly shows a high affinity for cIAP, one of E3 ubiquitin ligases. Among these compounds, HK24 possessed the ability to inhibit the growth of YAP overexpressing NCI-H290 cells. This inhibitory activity may be mediated by YAP degradation, although HK24 exhibited weak YAP degradation. Furthermore, we confirmed involvement of proteasome pathway in HK24-dependent YAP degradation by culturing NCI-H290 cells in the presence of a proteasome inhibitor. Therefore, it is possible that platanic acid is a potential candidate for molecular medicine targeting YAP.
Reverse β-oxidation pathways for efficient chemical production
Authors: Tarasava Katia , Lee Seung Hwan , Chen Jing , Köpke Michael , Jewett Michael C , Gonzalez Ramon 
Published: February 2022

Abstract
Microbial production of fuels, chemicals, and materials has the potential to reduce greenhouse gas emissions and contribute to a sustainable bioeconomy. While synthetic biology allows readjusting of native metabolic pathways for the synthesis of desired products, often these native pathways do not support maximum efficiency and are affected by complex regulatory mechanisms. A synthetic or engineered pathway that allows modular synthesis of versatile bioproducts with minimal enzyme requirement and regulation while achieving high carbon and energy efficiency could be an alternative solution to address these issues. The reverse β-oxidation (rBOX) pathways enable iterative non-decarboxylative elongation of carbon molecules of varying chain lengths and functional groups with only four core enzymes and no ATP requirement. Here, we describe recent developments in rBOX pathway engineering to produce alcohols and carboxylic acids with diverse functional groups, along with other commercially important molecules such as polyketides. We discuss the application of rBOX beyond the pathway itself by its interfacing with various carbon-utilization pathways and deployment in different organisms, which allows feedstock diversification from sugars to glycerol, carbon dioxide, methane, and other substrates.