bluuebunny/crossref_metadata_2025_split huggingface dataset:
CyanoOmicsDB: an integrated omics database for functional genomic analysis of cyanobacteria
Authors: Zhou Peng , Wang Li , Liu Hai , Li Chunyan , Li Zhimin , Wang Jinxiang , Tan Xiaoming 
Published: September 2021

Abstract
With their photosynthetic ability and established genetic modification systems, cyanobacteria are essential for fundamental and biotechnological research. Till now, hundreds of cyanobacterial genomes have been sequenced, and transcriptomic analysis has been frequently applied in the functional genomics of cyanobacteria. However, the massive omics data have not been extensively mined and integrated. Here, we describe CyanoOmicsDB (http://www.cyanoomics.cn/), a database aiming to provide comprehensive functional information for each cyanobacterial gene. CyanoOmicsDB consists of 8 335 261 entries of cyanobacterial genes from 928 genomes. It provides multiple gene identifiers, visualized genomic location, and DNA sequences for each gene entry. For protein-encoding genes, CyanoOmicsDB can provide predicted gene function, amino acid sequences, homologs, protein-domain super-families, and accession numbers for various public protein function databases. CyanoOmicsDB integrates both transcriptional and translational profiles of Synechocystis sp. PCC 6803 under various environmental culture coditions and genetic backgrounds. Moreover, CyanoOmicsDB includes 23 689 gene transcriptional start sites, 94 644 identified peptides, and 16 778 post-translation modification sites obtained from transcriptomes or proteomes of several model cyanobacteria. Compared with other existing cyanobacterial databases, CyanoOmicsDB comprises more datasets and more comprehensive functional information. CyanoOmicsDB will provide researchers in this field with a convenient way to retrieve functional information on cyanobacterial genes.
USP39 promotes non-homologous end-joining repair by poly(ADP-ribose)-induced liquid demixing
Authors: Kim Jae Jin , Lee Seo Yun , Hwang Yiseul , Kim Soyeon , Chung Jee Min , Park Sangwook , Yoon Junghyun , Yun Hansol , Ji Jae-Hoon , Chae Sunyoung , Cho Hyeseong , Kim Chan Gil , Dawson Ted M , Kim Hongtae , Dawson Valina L , Kang Ho Chul 
Published: September 2021

Abstract
Mutual crosstalk among poly(ADP-ribose) (PAR), activated PAR polymerase 1 (PARP1) metabolites, and DNA repair machinery has emerged as a key regulatory mechanism of the DNA damage response (DDR). However, there is no conclusive evidence of how PAR precisely controls DDR. Herein, six deubiquitinating enzymes (DUBs) associated with PAR-coupled DDR were identified, and the role of USP39, an inactive DUB involved in spliceosome assembly, was characterized. USP39 rapidly localizes to DNA lesions in a PAR-dependent manner, where it regulates non-homologous end-joining (NHEJ) via a tripartite RG motif located in the N-terminus comprising 46 amino acids (N46). Furthermore, USP39 acts as a molecular trigger for liquid demixing in a PAR-coupled N46-dependent manner, thereby directly interacting with the XRCC4/LIG4 complex during NHEJ. In parallel, the USP39-associated spliceosome complex controls homologous recombination repair in a PAR-independent manner. These findings provide mechanistic insights into how PAR chains precisely control DNA repair processes in the DDR.
Anesthesia triggers drug delivery to experimental glioma in mice by hijacking caveolar transport
Authors: Spieth Lena , Berghoff Stefan A , Stumpf Sina K , Winchenbach Jan , Michaelis Thomas , Watanabe Takashi , Gerndt Nina , Düking Tim , Hofer Sabine , Ruhwedel Torben , Shaib Ali H , Willig Katrin , Kronenberg Katharina , Karst Uwe , Frahm Jens , Rhee Jeong Seop , Minguet Susana , Möbius Wiebke , Kruse Niels , von der Brelie Christian , Michels Peter , Stadelmann Christine , Hülper Petra , Saher Gesine 
Published: September 2021

Abstract

Background
Pharmaceutical intervention in the CNS is hampered by the shielding function of the blood–brain barrier (BBB). To induce clinical anesthesia, general anesthetics such as isoflurane readily penetrate the BBB. Here, we investigated whether isoflurane can be utilized for therapeutic drug delivery.

Methods
Barrier function in primary endothelial cells was evaluated by transepithelial/transendothelial electrical resistance, and nanoscale STED and SRRF microscopy. In mice, BBB permeability was quantified by extravasation of several fluorescent tracers. Mouse models including the GL261 glioma model were evaluated by MRI, immunohistochemistry, electron microscopy, western blot, and expression analysis.

Results
Isoflurane enhances BBB permeability in a time- and concentration-dependent manner. We demonstrate that, mechanistically, isoflurane disturbs the organization of membrane lipid nanodomains and triggers caveolar transport in brain endothelial cells. BBB tightness re-establishes directly after termination of anesthesia, providing a defined window for drug delivery. In a therapeutic glioblastoma trial in mice, simultaneous exposure to isoflurane and cytotoxic agent improves efficacy of chemotherapy.

Conclusions
Combination therapy, involving isoflurane-mediated BBB permeation with drug administration has far-reaching therapeutic implications for CNS malignancies.
Shift work tolerance
Authors: Degenfellner J , Schernhammer E 
Published: September 2021

Abstract

Background
Shift work is widespread due to 24-h work in many occupations. Understanding differences in individual shift work tolerance (SWT) can help develop coping strategies for shift workers.

Aims
This in-depth qualitative review elucidates the architecture of SWT, providing an overview of the research advances in the last decade (2011–2021).

Methods
We searched Google Scholar, PubMed and Medline for different word combinations concerning SWT. Genome-wide association studies (GWAS) for the potential genetic basis of SWT were additionally searched in GWAS Central and GWAS Catalogue.

Results
Eleven new studies were published since 2011, with the proportion of longitudinal studies on SWT having more than doubled in the past decade. They consolidate prior findings (e.g. hardiness most consistently associated with SWT) and discovered additional aspects of SWT like resistance to change and job stress. The 15 large-scale GWAS identified, most of which using UK Biobank (UKB) and 23andMe data, involved mapped genes showing overlap especially within analysis of the same phenotype (e.g. PER2/3 for morningness, PAX8 for sleep duration and LINGO1 for neuroticism). Individual GWAS for additional traits such as resilience have also been published though assessments of gene overlap are not yet possible.

Conclusions
Progress regarding longitudinal studies on SWT has been made though a more consistent definition of SWT remains crucial for future research. Non-genetic studies on SWT suggest several important traits and factors; many of which have now also been explored using GWAS. Such evidence could serve as basis for individualized risk prediction and disease prevention approaches for night-shift workers.
‘Frank’s sign: dermatological marker for coronary artery disease’
Authors: Elawad Omer Ali Mohamed Ahmed , Albashir Ahmed Abdalazim Dafallah 
Published: September 2021

ABSTRACT
Frank’ sign or diagonal earlobe crease (DELC) is a diagonal earlobe crease that extends backwards from the tragus at an angle of 45 degree across the lobule to the ear edge of the auricle. It has been described as a dermatological marker for coronary artery disease. Frank’s sign is a useful clinical sign for coronary artery disease. Inspection of the earlobes should be considered as integral part of the physical examination in clinical practice for patients with suspected coronary artery disease.
Embedded Leverage
Authors: Frazzini Andrea , Pedersen Lasse Heje 
Published: September 2021

Abstract
Many financial instruments are designed with embedded leverage, such as options and leveraged exchange-traded funds (ETFs). Embedded leverage alleviates investors’ leverage constraints, and, therefore, we hypothesize that embedded leverage lowers required returns. Consistent with this hypothesis, we find empirically that options and leveraged ETFs provide significant amounts of embedded leverage; this embedded leverage increases return volatility in proportion to the embedded leverage; and higher embedded leverage is associated with lower risk-adjusted returns. The results are statistically and economically significant, and we provide extensive robustness tests and discuss the broader implications of embedded leverage for financial economics. (JEL G02, G11, G12, G13, G14, G20)
Distributions from Foreign Foundations and Trusts—The Case-law of the German Federal Fiscal Court (BFH)
Authors: Niermann Marcus , Muscheites Erik 
Published: September 2021

Abstract
The taxation of distributions from foreign foundations and trusts to beneficiaries resident in Germany is highly relevant in practice, but continues to be fraught with uncertainties. The article shows that recent case-law of the German Federal Fiscal Court (BFH) has clarified the position only partially. It is shown that economic double taxation burdens can only be avoided with careful planning which should ideally start before establishing German tax residency.
Modeling the effects of steroid implant use on the environmental and economic sustainability of Brazilian beef production
Authors: Capper Judith L , De Carvalho Thiago B , Hancock Andrew S , Sá Filho Ocilon G , Odeyemi Isaac , Bartram David J 
Published: September 2021

Abstract
Brazilian beef systems contribute 14.9% of global beef production, therefore given climate change concerns, there is a clear need to reduce environmental impacts while maintaining economic viability. This study evaluated the hypothesis that steroid implant use in Brazilian beef cattle would reduce resource use, greenhouse gas (GHG) emissions and economic costs of production, thereby improving environmental and economic sustainability. A deterministic model based on beef cattle population demographics, nutrition and performance was used to quantify resource inputs and GHG emissions per 1.0 × 106 kg of hot carcass weight (HCW) beef. System boundaries extended from cropping input manufacture to cattle arriving at the slaughterhouse. Beef systems were modeled using herd population dynamics, feed and performance data sourced from producers in four Brazilian states, with additional data from global databases. Implants were used in calves, growing and finishing cattle at low (LI), medium (MI), and high (HI) levels of performance enhancement, compared to nonimplanted (NI) controls. Feed use results were used in combination with producer-derived input costs to assess the economic impacts of implant use, including production costs and returns on investment. Improved FCE, ADG, and carcass weights conferred by implant use reduced the number of cattle and the time taken to produce 1.0 × 106 kg HCW beef. Compared to NI controls, the quantities of feed, land, water and fossil fuels required to produce 1.0 × 106 kg HCW beef was reduced in implanted cattle, with reductions proportional to the performance-enhancing effect of the implant (HI &gt; MI &gt; LI). Implant use reduced GHG emissions per 1.0 × 106 kg HCW beef by 9.4% (LI), 12.6% (MI), or 15.8% (HI). Scaling up the MI effects to represent all eligible Brazilian cattle being implanted, revealed avoided GHG emissions equivalent to the annual exhaust emissions of 62.0 × 106 cars. Economic impacts of implant use reflected the environmental results, resulting in a greater margin for the producers within each system (cow-calf through to finishing). The 6.13% increase in kg of HCW beef produced generates a cost reduction of 3.76% and an increase in the return on invested capital of 4.14% on average. Implants offer the opportunity for Brazilian beef producers to demonstrate their dedication to improving environmental and economic sustainability through improved productivity, although care must be taken to avoid negative trade-offs.
Unmarked Gene Editing in Clavibacter michiganensis Using CRISPR/Cas9 and 5-Fluorocytosine Counterselection
Authors: Chen Xing , Tan Qing , Lyu Qingyang , Yu Chengxuan , Jiang Na , Li Jianqiang , Luo Laixin 
Published: September 2021

Plant-pathogenic bacteria in the genus Clavibacter are important quarantine species that cause considerable economic loss worldwide. The development of effective gene editing techniques and additional selectable markers is essential to expedite gene functional analysis in this important Gram-positive genus. The current study details a highly efficient unmarked CRISPR/Cas9-mediated gene editing system in Clavibacter michiganensis, which couples the expression of cas9 and single-guide RNA with homology-directed repair templates and the negative selectable marker codA::upp within a single plasmid. Initial experiments indicated that CRISPR/Cas9-mediated transformation could be utilized for both site-directed mutagenesis, in which an A to G point mutation was introduced at the 128th nucleotide of the C. michiganensis rpsL gene to generate a streptomycin-resistant mutant, and complete gene knockout, in which the deletion of the C. michiganensis celA or katA genes resulted in transformants that lacked cellulase and catalase activity, respectively. In subsequent experiments, the introduction of the codA::upp cassette into the transformation vector facilitated the counterselection of unmarked transformants by incubation in the absence of the selective antibiotic, followed by plating on M9 agar containing 5-fluorocytosine at 100 μg/ml, in which an unmarked katA mutant lacking the transformation vector was recovered. Compared with conventional homologous recombination, the unmarked CRISPR/Cas9-mediated system was more useful and convenient because it allowed the template plasmid to be reused repeatedly to facilitate the editing of multiple genes, which constitutes a major advancement that could revolutionize research into C. michiganensis and other Clavibacter spp. [Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Hypoxemia in Young Children Undergoing One-lung Ventilation: A Retrospective Cohort Study
Authors: Templeton T. Wesley , Miller Scott A. , Lee Lisa K. , Kheterpal Sachin , Mathis Michael R. , Goenaga-Díaz Eduardo J. , Templeton Leah B. , Saha Amit K. ,   for the Multicenter Perioperative Outcomes Group Investigators
Published: September 2021

Background
One-lung ventilation in children remains a specialized practice with low case numbers even at tertiary centers, preventing an assessment of best practices. The authors hypothesized that certain case factors may be associated with a higher risk of intraprocedural hypoxemia in children undergoing thoracic surgery and one-lung ventilation.

Methods
The Multicenter Perioperative Outcomes database and a local quality improvement database were queried for documentation of one-lung ventilation in children 2 months to 3 yr of age inclusive between 2010 and 2020. Patients undergoing vascular or other cardiac procedures were excluded. All records were reviewed electronically for the presence of hypoxemia, oxygen saturation measured by pulse oximetry (Spo
2) less than 90% for 3 min or more continuously, and severe hypoxemia, Spo
2 less than 90% for 5 min or more continuously during one-lung ventilation. Records were also assessed for hypercarbia, end-tidal CO2 greater than 60 mmHg for 5 min or more or a Paco
2 greater than 60 on arterial blood gas. Covariates assessed for association with these outcomes included age, weight, American Society of Anesthesiologists (Schaumburg, Illinois) Physical Status 3 or greater, duration of one-lung ventilation, preoperative Spo
2 less than 98%, bronchial blocker versus endobronchial intubation, left operative side, video-assisted thoracoscopic surgery, lower tidal volume ventilation (tidal volume less than or equal to 6 ml/kg plus positive end expiratory pressure greater than or equal to 4 cm H2O for more than 80% of the duration of one-lung ventilation), and type of procedure.

Results
Three hundred six cases from 15 institutions were included for analysis. Hypoxemia and severe hypoxemia occurred in 81 of 306 (26%) patients and 56 of 306 (18%), respectively. Hypercarbia occurred in 153 of 306 (50%). Factors associated with lower risk of hypoxemia in multivariable analysis included left operative side (odds ratio, 0.45 [95% CI, 0.251 to 0.78]) and bronchial blocker use (odds ratio, 0.351 [95% CI, 0.177 to 0.67]). Additionally, use of a bronchial blocker was associated with a reduced risk of severe hypoxemia (odds ratio, 0.290 [95% CI, 0.125 to 0.62]).

Conclusions
Use of a bronchial blocker was associated with a lower risk of hypoxemia in young children undergoing one-lung ventilation.

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What This Article Tells Us That Is New
Evaluation of Appropriate Use of Preoperative Echocardiography before Major Abdominal Surgery: A Retrospective Cohort Study
Authors: Tank Allyson , Hughey Robert , Ward R. Parker , Nagele Peter , Rubin Daniel S. 
Published: September 2021

Background
Preoperative resting echocardiography is often performed before noncardiac surgery, but indications for preoperative resting echocardiography are limited. This study aimed to investigate appropriateness of preoperative resting echocardiography using the Appropriate Use Criteria for Echocardiography, which encompass indications from the guidelines on perioperative cardiovascular evaluation and management and nonperioperative indications independent of the perioperative period. The authors hypothesized that patients are frequently tested without an appropriate indication.

Methods
Records of patients in the Truven Health MarketScan Commercial and Medicare Supplemental Databases who underwent a major abdominal surgery from 2005 to 2017 were included. These databases contain de-identified records of health services for more than 250 million patients with primary or Medicare supplemental health insurance coverage through employer-based fee-for-service, point-of-service, or capitated plans. Patients were classified based on the presence of an outpatient claim for resting transthoracic echocardiography within 60 days of surgery. Appropriateness was determined via International Classification of Diseases, Ninth Revision–Clinical Modification, and International Classification of Diseases, Tenth Revision–Clinical Modification principal and secondary diagnosis codes associated with the claims, and classified as “appropriate,” “rarely appropriate,” or “unclassifiable” using the Appropriate Use Criteria for Echocardiography.

Results
Among 230,535 patients in the authors’ cohort, preoperative resting transthoracic echocardiography was performed in 6.0% (13,936) of patients. There were 12,638 (91%) studies classifiable by the Appropriate Use Criteria for Echocardiography, and 1,298 (9%) were unable to be classified. Among the classifiable studies, 8,959 (71%) were deemed “appropriate,” while 3,679 (29%) were deemed “rarely appropriate.” Surveillance of chronic ischemic heart disease and uncomplicated hypertension accounted for 43% (1,588 of 3,679) of “rarely appropriate” echocardiograms.

Conclusions
More than one in four preoperative resting echocardiograms were considered “rarely appropriate” according to the Appropriate Use Criteria for Echocardiography. A narrow set of patient characteristics accounts for a large proportion of “rarely appropriate” preoperative resting echocardiograms.

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Post-LASIK corneal epithelial irregularities October consultation #1
Authors: Moshirfar Majid , Bundogji Nour 
Published: September 2021

A 55-year-old man with a history of bilateral laser-assisted in situ keratomileusis (LASIK) and subsequent enhancement over 15 years ago presented to our facility to investigate refractive surgery options. The patient reported progressive blurring and fluctuation of vision and desired independence from contact lenses and spectacles. Uncorrected distance visual acuity (UDVA) was 20/30 −2.0 in the right eye and 20/400 in the left eye, corrected to 20/60 in the left eye. Manifest refraction was +0.75 −1.75 × 180 diopters (D) in the right eye and −3.50 −3.50 × 64 D in the left eye. Keratometry readings were 43.9/41.1 @ 25 in the right eye and 49.3/46.8 @ 2 in the left eye. On slitlamp examination, the patient showed diffuse subepithelial fibrosis and confluent circumferential elevation, respecting the LASIK flap margin and extending centrally into the visual axis (Figure 1

JOURNAL/jcrs/04.03/02158034-202110000-00025/figure1/v/2023-08-19T002620Z/r/image-tiff

). Fluorescein pooling was also observed. Anterior segment ocular coherence tomography (OCT) demonstrated subepithelial hyperreflective density in the left eye (Figure 2

JOURNAL/jcrs/04.03/02158034-202110000-00025/figure2/v/2023-08-19T002620Z/r/image-tiff

). Pentacam showed irregularity and inferior steepening up to 52.0 D (Figure 3

JOURNAL/jcrs/04.03/02158034-202110000-00025/figure3/v/2023-08-19T002620Z/r/image-tiff

).
A review of the patient's records from 4 years ago revealed UDVA of 20/30 −2 in the right eye and 20/20 in the left eye with manifest refraction of +1.00 −1.50 × 30 D in the right eye and −0.25 D in the left eye. Keratometry then showed 39.52/40.91 @ 98 in the right eye and 39.85/40.42 @ 75 in the left eye. Patient's slitlamp examination revealed minimal subepithelial irregularity without endothelial changes in both eyes. At current presentation, the patient was not deemed a candidate for further refractive surgery given a low residual stromal bed after original LASIK with enhancement. The patient was seeking help and advice for his declining vision.
What is the most likely diagnosis, and what other conditions are on your differential? What would be your next step? Would you request additional diagnostic workup? What medical and surgical interventions would you recommend?
Intraindividual pain variability and phenotypes of pain in sickle cell disease: a secondary analysis from the Pain in Sickle Cell Epidemiology Study
Authors: Bakshi Nitya , Gillespie Scott , McClish Donna , McCracken Courtney , Smith Wally R. , Krishnamurti Lakshmanan 
Published: September 2021

Abstract
Mean pain intensity alone is insufficient to describe pain phenotypes in sickle cell disease (SCD). The objective of this study was to determine impact of day-to-day intraindividual pain variability on patient outcomes in SCD. We calculated metrics of pain variability and pain intensity for 139 participants with <10% missing data in the first 28 days of the Pain in Sickle Cell Epidemiology Study. We performed Spearman rank correlations between measures of intraindividual pain variability and outcomes. We then used k-means clustering to identify phenotypes of pain in SCD. We found that pain variability was inversely correlated with health-related quality of life, except in those with daily or near-daily pain. Pain variability was positively correlated with affective coping, catastrophizing, somatic symptom burden, sickle cell stress, health care utilization, and opioid use. We found 3 subgroups or clusters of pain phenotypes in SCD. Cluster 1 included individuals with the lowest mean pain, lowest temporal instability and dependency, lowest proportion of days with pain and opioid use, and highest physical function. Cluster 2 included individuals with the highest mean pain, highest temporal dependency, highest proportion of days with pain and opioid use, and lowest physical function. Cluster 3 included individuals with high levels of mean pain, highest temporal instability, but with lower temporal dependency, proportion of days with pain and opioid use, and physical function compared with cluster 2. We conclude that intraindividual pain variability is associated with patient outcomes and psychological characteristics in SCD and is useful in delineating phenotypes of pain in SCD.