bluuebunny/crossref_metadata_2025_split huggingface dataset:
The effect of genome graph expressiveness on the discrepancy between genome graph distance and string set distance
Authors: Qiu Yutong , Kingsford Carl 
Published: April 2022

AbstractMotivationIntra-sample heterogeneity describes the phenomenon where a genomic sample contains a diverse set of genomic sequences. In practice, the true string sets in a sample are often unknown due to limitations in sequencing technology. In order to compare heterogeneous samples, genome graphs can be used to represent such sets of strings. However, a genome graph is generally able to represent a string set universe that contains multiple sets of strings in addition to the true string set. This difference between genome graphs and string sets is not well characterized. As a result, a distance metric between genome graphs may not match the distance between true string sets.ResultsWe extend a genome graph distance metric, Graph Traversal Edit Distance (GTED) proposed by Ebrahimpour Boroojeny et al., to FGTED to model the distance between heterogeneous string sets and show that GTED and FGTED always underestimate the Earth Mover’s Edit Distance (EMED) between string sets. We introduce the notion of string set universe diameter of a genome graph. Using the diameter, we are able to upper-bound the deviation of FGTED from EMED and to improve FGTED so that it reduces the average error in empirically estimating the similarity between true string sets. On simulated T-cell receptor sequences and actual Hepatitis B virus genomes, we show that the diameter-corrected FGTED reduces the average deviation of the estimated distance from the true string set distances by more than 250%.Availability and implementationData and source code for reproducing the experiments are available at: https://github.com/Kingsford-Group/gtedemedtest/.Supplementary informationSupplementary data are available at Bioinformatics online.
scSampler: fast diversity-preserving subsampling of large-scale single-cell transcriptomic data
Authors: Song Dongyuan , Xi Nan Miles , Li Jingyi Jessica , Wang Lin 
Published: April 2022

AbstractSummaryThe number of cells measured in single-cell transcriptomic data has grown fast in recent years. For such large-scale data, subsampling is a powerful and often necessary tool for exploratory data analysis. However, the easiest random subsampling is not ideal from the perspective of preserving rare cell types. Therefore, diversity-preserving subsampling is required for fast exploration of cell types in a large-scale dataset. Here, we propose scSampler, an algorithm for fast diversity-preserving subsampling of single-cell transcriptomic data.Availability and implementationscSampler is implemented in Python and is published under the MIT source license. It can be installed by “pip install scsampler” and used with the Scanpy pipline. The code is available on GitHub: https://github.com/SONGDONGYUAN1994/scsampler. An R interface is available at: https://github.com/SONGDONGYUAN1994/rscsampler.Supplementary informationSupplementary data are available at Bioinformatics online.
iSFun: an R package for integrative dimension reduction analysis
Authors: Fang Kuangnan , Ren Rui , Zhang Qingzhao , Ma Shuangge 
Published: April 2022

AbstractSummaryIn the analysis of high-dimensional omics data, dimension reduction techniques—including principal component analysis (PCA), partial least squares (PLS) and canonical correlation analysis (CCA)—have been extensively used. When there are multiple datasets generated by independent studies with compatible designs, integrative analysis has been developed and shown to outperform meta-analysis, other multidatasets analysis, and individual-data analysis. To facilitate integrative dimension reduction analysis in daily practice, we develop the R package iSFun, which can comprehensively conduct integrative sparse PCA, PLS and CCA, as well as meta-analysis and stacked analysis. The package can conduct analysis under the homogeneity and heterogeneity models and with the magnitude- and sign-based contrasted penalties. As a ‘byproduct’, this article is the first to develop integrative analysis built on the CCA technique, further expanding the scope of integrative analysis.Availability and implementationThe package is available at https://CRAN.R-project.org/package=iSFun.Supplementary informationSupplementary materials are available at Bioinformatics online.
Underground metabolism as a rich reservoir for pathway engineering
Authors: Kovács Szabolcs Cselgő , Szappanos Balázs , Tengölics Roland , Notebaart Richard A , Papp Balázs 
Published: April 2022

AbstractMotivationBioproduction of value-added compounds is frequently achieved by utilizing enzymes from other species. However, expression of such heterologous enzymes can be detrimental due to unexpected interactions within the host cell. Recently, an alternative strategy emerged, which relies on recruiting side activities of host enzymes to establish new biosynthetic pathways. Although such low-level ‘underground’ enzyme activities are prevalent, it remains poorly explored whether they may serve as an important reservoir for pathway engineering.ResultsHere, we use genome-scale modeling to estimate the theoretical potential of underground reactions for engineering novel biosynthetic pathways in Escherichia coli. We found that biochemical reactions contributed by underground enzyme activities often enhance the in silico production of compounds with industrial importance, including several cases where underground activities are indispensable for production. Most of these new capabilities can be achieved by the addition of one or two underground reactions to the native network, suggesting that only a few side activities need to be enhanced during implementation. Remarkably, we find that the contribution of underground reactions to the production of value-added compounds is comparable to that of heterologous reactions, underscoring their biotechnological potential. Taken together, our genome-wide study demonstrates that exploiting underground enzyme activities could be a promising addition to the toolbox of industrial strain development.Availability and implementationThe data and scripts underlying this article are available on GitHub at https://github.com/pappb/Kovacs-et-al-Underground-metabolism.Supplementary informationSupplementary data are available at Bioinformatics online.
Climate change negatively affects Amazonian social wasps
Authors: Dejean Alain , Corbara Bruno , Azémar Frédéric , Petitclerc Frédéric , Burban Benoit , Talaga Stanislas , Compin Arthur 
Published: April 2022

Abstract
The impact of climate change is intensifying in Amazonia through, among other causes, the higher frequency of both severe droughts and floods due to El Niño and La Niña events as well as an Atlantic influence. Over a 25-year period (1997–2021) we examined in French Guiana the impact of different climatic parameters on the most frequent social wasp, Polybia bistriata (Polistinae). As it commonly nests on Clusia grandiflora (Clusiaceae), its nests are easily found. Heavy rainfall, particularly during the 1999–2000 La Niña episode, negatively affected this social wasp species as the percentage of Clusia sheltering an active P. bistriata nest decreased from ≈ 40% during the pre-2000 period to zero in 2021. We conclude that extreme wet seasons related to climate change translated into the decline of this species and likely were detrimental to many other polistine wasps of north-eastern Amazonia.
Body size is not correlated with the evolution of male coloration in darters (Percidae: Etheostomatinae)
Authors: Ciccotto Patrick J , Mendelson Tamra C 
Published: April 2022

AbstractColoration and body size are among the many morphological traits that vary among fish lineages. Elaborate coloration and body size covary in other animal groups, but relationships between these two morphological characteristics have not been rigorously examined in fishes. We formally test for correlations between coloration and body size in darters (Percidae: Etheostomatinae), a group of North American freshwater fishes that vary in the presence of male coloration and maximum body size. Although uncorrected analyses indicate a significant correlation between colour traits and body size in darters, phylogenetically corrected logistic regression models and ANOVAs revealed no significant correlations, suggesting body size does not act as a constraint on elaborate coloration or vice versa. These results are discussed in an ecological and behavioural context.
Compression following treatment of superficial venous incompetence: systematic review
Authors: Mohamed Abduraheem H , Thadani Simran , Mohamed Sundus Hussein , Sidapra Misha , Smith George , Chetter Ian , Carradice Daniel 
Published: April 2022

Abstract

Background
International guidelines recommend postprocedural compression when treating symptomatic superficial venous incompetence (SVI). This updated review of RCTs investigated the requirement for postprocedural compression and how it can be applied optimally.

Methods
The National Institute for Health and Care Excellence’s Healthcare Databases Advanced Search engine was used to identify all English-language RCTs of compression following treatment for SVI. Outcomes of interest included postprocedural pain, venous thromboembolism, health-related quality of life (HRQoL), and anatomical occlusion.

Results
A total of 18 studies were included comprising some 2584 treated limbs. Compression was compared with no compression in four studies, nine studies compared different durations of compression, and a further five compared different types of compression. A 1–2-week period of compression was associated with a mean reduction of 11 (95 per cent c.i. 8 to 13) points in pain score on a 100-mm visual analogue scale compared with a shorter duration (P &lt; 0.001). This was associated with improved HRQoL and patient satisfaction. Longer durations of compression did not add further benefit. There was low-quality evidence suggesting that 35-mmHg compression with eccentric thigh compression achieved lower pain scores than lower interface pressures. There were no significant differences in venous thromboembolism rates or technical success in any group, including no compression.

Conclusion
Postprocedural compression of 1–2 weeks after SVI treatment is associated with reduced pain compared with a shorter duration. The optimal interface pressure and type of compression, and the impact on venous thromboembolism risk, remain to be determined.
Adverse events following robotic surgery: population-based analysis
Authors: Muaddi Hala , Stukel Therese A , de Mestral Charles , Nathens Avery , Pautler Stephen E , Shayegan Bobby , Hanna Waël C , Schlachta Christopher , Breau Rodney H , Hopkins Laura , Jackson Timothy , Karanicolas Paul J 
Published: April 2022

Abstract

Background
Robotic surgery was integrated into some healthcare systems despite there being few well designed, real-world studies on safety or benefit. This study compared the safety of robotic with laparoscopic, thoracoscopic, and open approaches in common robotic procedures.

Methods
This was a population-based, retrospective study of all adults who underwent prostatectomy, hysterectomy, pulmonary lobectomy, or partial nephrectomy in Ontario, Canada, between 2008 and 2018. The primary outcome was 90-day total adverse events using propensity score overlap weights, and secondary outcomes were minor or major morbidity/adverse events.

Results
Data on 24 741 prostatectomy, 75 473 hysterectomy, 18 252 pulmonary lobectomy, and 6608 partial nephrectomy operations were included. Relative risks for total adverse events in robotic compared with open surgery were 0.80 (95 per cent c.i. 0.74 to 0.87) for radical prostatectomy, 0.44 (0.37 to 0.52) for hysterectomy, 0.53 (0.44 to 0.65) for pulmonary lobectomy, and 0.72 (0.54 to 0.97) for partial nephrectomy. Relative risks for total adverse events in robotic surgery compared with a laparoscopic/thoracoscopic approach were 0.94 (0.77 to 1.15), 1.00 (0.82 to 1.23), 1.01 (0.84 to 1.21), and 1.23 (0.82 to 1.84) respectively.

Conclusion
The robotic approach is associated with fewer adverse events than an open approach but similar to a laparoscopic/thoracoscopic approach. The benefit of the robotic approach is related to the minimally-invasive approach rather than the platform itself.
Influence of patient sex on outcomes after pancreatic surgery: multicentre study
Authors: Damanakis Alexander I , Toader Justus , Wahler Isabell , Plum Patrick , Quaas Alexander , Ernst Angela , Popp Felix , Gebauer Florian , Bruns Christiane 
Published: April 2022

Abstract

Background
Recent findings support the hypothesis of sex-related differences in inflammatory and immunological responses to trauma. The aim of this study was to address sex-specific aspects in patients who underwent pancreatic surgery.

Methods
This retrospective study used data from the German StuDoQ registry. Patients who underwent pancreatic surgery between 2010 and 2020 were stratified according to procedure (pancreatic head resection, distal pancreatectomy (DP), total pancreatectomy (TP)). Each cohort underwent propensity score matching (PSM) with the co-variables BMI, ASA, age, coronary heart disease (CHD), diabetes, hypertension with medication, and histology to level the distribution of co-morbidities between men and women. The main outcomes were morbidity and mortality.

Results
The total cohort consisted of 10 224 patients (45.3 per cent women). Men had higher ASA grades, and more often had CHD, diabetes, and hypertension with medication. Women had fewer overall complications (57.3 versus 60.1 per cent; P = 0.005) and a lower mortality rate (3.4 versus 4.9 per cent; P &lt; 0.001). Rates of pancreatic surgery-specific complications, such as clinically relevant postoperative pancreatic fistula (POPF) (grade B/C: 14 versus 17 per cent; P &lt; 0.001), delayed gastric emptying (grade B/C: 7.8 versus 9.2 per cent; P = 0.014), and postpancreatectomy haemorrhage (grade B/C: 7.1 versus 9.0 per cent; P &lt; 0.001), were also lower in women. After PSM, 8358 patients were analysed. In the pancreatic head resection cohort (5318 patients), women had fewer complications (58.6 versus 61.4 per cent; P = 0.044), a lower in-hospital mortality rate (3.6 versus 6.1 per cent; P &lt; 0.001), and less often had clinically relevant POPF (11.6 versus 16.2 per cent; P &lt; 0.001). After DP, the clinically relevant POPF rate was lower in women (22.5 versus 27.3 per cent; P = 0.012). In the TP cohort, men more often developed intra-abdominal abscess requiring drainage (5.0 versus 2.3 per cent; P = 0.050).

Conclusion
Women had favourable outcomes after pancreatic surgery.
Green Multiplex Chromatographic Determination of Nine Penicillin Antibiotics Residues in Industrial Air Dust and Wastewater Environmental Samples
Authors: El-Kimary Eman I , Korany Mohammed A , Issa Ahmed E , Basuny Mohamed G 
Published: April 2022

Abstract
Determination of penicillin residues in different industrial effluents including wastewater and air samples is important to prevent exposure to residual amounts of penicillin and the development of antibiotic resistance. A green high performance liquid chromatography (HPLC) method coupled with diode array detection has been developed and validated for multiplex determination of nine penicillin antibiotics in the industrial air dust and wastewater environmental samples of penicillin facility in addition to the monitoring of facility surface cleaning. Separation was performed on C18 column with gradient elution of methanol and phosphate buffer (pH 4) at a flow rate of 1.5 mL min-1 and ultra violet (UV) detection at 220 nm. Low limits of detection were achieved (0.1–0.3 μg mL-1) indicating good sensitivity of the proposed. The method was applied for ensuring the efficiency of cleaning validation after worst-case selection. Recovery studies of the studied penicillins from fortified stainless steel and polycarbonate surfaces and swabs were between 91.91 and 100.22% with relative standard deviation 0.11–1.79%. The presence of any of the studied penicillins in wastewater samples from penicillin plant drainage was checked. Also, total air dust concentration (mg m–3) and % of penicillin active material residues in air dust were calculated from the area of the exposed group in suspension, tablet and vial production lines. The proposed method can be recommended for routine analysis of air and wastewater environmental samples for the detection of penicillin antibiotics at low levels as well as monitoring of facility surface cleaning with high accuracy and precision.
Precision Vaccine Adjuvants for Older Adults: A Scoping Review
Authors: Nanishi Etsuro , Angelidou Asimenia , Rotman Chloe , Dowling David J , Levy Ofer , Ozonoff Al 
Published: April 2022

Abstract
Older adults, defined as those ≥60 years of age, are a growing population vulnerable to infections including severe acute respiratory syndrome coronavirus 2. Although immunization is a key to protecting this population, immunosenescence can impair responses to vaccines. Adjuvants can increase the immunogenicity of vaccine antigens but have not been systematically compared in older adults. We conducted a scoping review to assess the comparative effectiveness of adjuvants in aged populations. Adjuvants AS01, MF59, AS03, and CpG-oligodeoxynucleotide, included in licensed vaccines, are effective in older human adults. A growing menu of investigational adjuvants, such as Matrix-M and CpG plus alum, showed promising results in early phase clinical trials and preclinical studies. Most studies assessed only 1 or 2 adjuvants and no study has directly compared &gt;3 adjuvants among older adults. Enhanced preclinical approaches enabling direct comparison of multiple adjuvants including human in vitro modeling and age-specific animal models may derisk and accelerate vaccine development for older adults.
Legal Enforcement of the National Emissions Trading Scheme and the Environmental Protection Tax in China: Heavy Hand or Light Touch?
Authors: Geroe Steven , Zhang Hao 
Published: April 2022

Abstract
This article evaluates the severity of legal enforcement measures for the 2021 National Carbon Emissions Trading Management (Trial) Measures (ETS Trial Measures) and the Environment Protection Tax (EPT) as a potential model or basis for carbon taxation. While the focus is on the content of specific regulatory provisions, evidence of enforcement action forms part of their evaluation. The ETS Trial Measures are compared to the enforcement provisions in Chinese regional emission-trading scheme (ETS) pilots, the 2019 and 2020 opinion solicitation drafts (OSDs), and the March 2021 OSD for a proposed State Council regulation, drawing on the scholarly literature and interviews in the specialist Chinese government and professional and research institutions. The current ETS enforcement measures are weaker and less comprehensive than those in some pilots and in all of the OSDs. Adopting measures recommended by interviewees as effective in the pilots could augment their stringency. The EPT has a stronger basis for enforcement through existing taxation and environmental laws. While its enforcement has been backed by an increasingly centralized environmental governance system, design elements that allow regional flexibility in implementation and inconsistent enforcement have reduced its effectiveness. These outcomes may be influenced by trade-offs between central government objectives and subnational economic and industrial priorities and resistance by powerful commercial interests. These limiting factors can be addressed by effective regulatory implementation, successful trading, and combining stringent penalties with measures that have a lighter touch, such as capacity building, leading to deepening acceptance by all stakeholders.
Guiding Covid policy: cost-benefit analysis and beyond
Authors: Aldred Jonathan 
Published: April 2022

Abstract
Cost-benefit analysis (CBA) is inappropriate as an aid to Covid policy-making because the plural, incommensurable values at stake are not all amenable to monetary measurement. CBA for Covid policy is also undermined by pervasive uncertainty and ignorance, and has some troubling distributional implications. However, non-consequentialist alternatives to CBA tend towards implausibly absolutist prohibitions on risk imposition. Arguments for setting aside consequentialism for special circumstances (the precautionary principle, or a medical rule of rescue) are also problematic when applied to Covid policy. A broad consequentialist approach to policy guidance is defended, one which does not demand commensuration on a common monetary scale. Despite the absence of commensuration, policy guidance is still possible.
From WEDA to EDTA to ERA: 60 years of supporting European nephrology and counting
Authors: Wanner Christoph 
Published: April 2022

ABSTRACTNephrology has evolved from treating kidney failure, first with dialysis and then with kidney transplantation, to identifying and treating early stages of kidney disease and eventually to prevent kidney disease from occurring. Similarly, the name of the European scientific society caring for people with kidney disease has evolved from the West European Dialysis Society Association to the European Dialysis and Transplant Association to the European Renal Association. These name changes reflect a deeper change in the mission of the society to the current mission of leading European nephrology by promoting kidney health for all, improving kidney care for patients, and strengthen the kidney community and the vision of a Europe where kidney health is prioritized, kidney health is accessible and the kidney community is thriving. We now review the major changes in the society over the years and present its current structure and focus as we face the largest projected increase to date in the global burden of kidney diseases.
The hidden diabetic kidney disease in a university hospital-based population: a real-world data analysis
Authors: Marques María , López-Sánchez Paula , Tornero Fernando , Gargantilla Pedro , Maroto Alba , Ortiz Alberto , Portolés José 
Published: April 2022

ABSTRACT

Background
Correct identification of diabetic kidney disease (DKD) in type 2 diabetes mellitus (T2DM) patients is crucial to implement therapeutic interventions that may prevent disease progression.

Methods
We compared the real prevalence of DKD in T2DM patients according to actual serum and urine laboratory data with the presence of the diagnostic terms DKD and/or CKD on the electronic medical records (EMRs) using a natural language processing tool (SAVANA Manager). All patients ˃18 years of age and diagnosed with T2DM were selected. DKD was defined as an estimated glomerular filtration rate (eGFR) &lt;60 mL/min/1.73 m2 or a urinary albumin:creatinine ratio (UACR) &gt;30 mg/g or a urinary protein:creatinine ratio (UPCR) &gt;0.3 g/g after excluding acute kidney injury.

Results
A total of 15 304 T2DM patients identified on EMRs were eligible to enter the study. A total of 4526 (29.6%) T2DM patients had DKD according to lab criteria. However, the terms CKD or DKD were only present in 33.1% and 7.5%, representing a hidden prevalence of CKD and DKD of 66.9% and 92.5%, respectively. Less severe kidney disease (lower UACR or UPCR, higher eGFR values), female sex and lack of insulin prescription were associated with the absence of DKD or CKD terms in the EMRs (P &lt; .001)

Conclusions
The prevalence of DKD among T2DM patients defined by lab data is significantly higher than that reported on hospital EMRs. This could imply underdiagnosis of DKD, especially in patients with the least severe disease who may benefit the most from optimized therapy.