bluuebunny/crossref_metadata_2025 huggingface dataset:
Biological washout effect in in-beam PET: animal studies
Authors: Toramatsu C , Mohammadi A , Wakizaka H , Seki C , Nishikido F , Sato S , Kanno I , Takahashi M , Karasawa K , Hirano Y , Yamaya T
Published: October 2020

Positron emission tomography (PET) is a practical tool for range verification of hadron therapy. As well, the quantitative washout of the positron emitters has a potential usefulness as a diagnostic index, but the modelling for this has not been established. In this study, we measured washout rates of rabbit brain and performed kinetic analysis to explore the washout mechanism. Six rabbit brains were irradiated by 11C and 15O ion beams, and dynamic PET scan was performed using our original depth of interest (DOI)-PET prototype. The washout rate was obtained based on the two-compartment model, where efflux from tissue to blood (k2), influx (k3) and efflux (k4) from the first to second compartments in tissue were evaluated. The observed k2, k3 and k4 of 11C were 0.086, 0.137 and 0.007 min−1, and those of 15O were 0.502, 0.360 and 0.007 min−1, respectively. It was suggested permeability of a molecule containing 11C atoms might be regulated by a transporter. The k2 of 15O was comparable with 15O-water. This study provides basic data for modelling of the washout effect.
Safety Evaluation of a Long-Lived Tumour-Specific Gadolinium (Gd)-Based Imaging Agent in Proton Therapy
Authors: Velten Christian , Tomé Wolfgang A.
Published: October 2020

We assessed the dosimetric safety of a potential diapeutic Gadolinium-based contrast agent for diagnostic MR imaging and MR-guided radiotherapy by calculating depth-dependent reactions rates in a spread-out Bragg peak (SOBP) in water. Energy-dependent cross-sections for inelastic proton reactions on Gadolinium were folded with proton energy spectra at depth. Particle transport, dose, and phase space scoring was performed using Geant4-based TOPAS Monte Carlo software. The isotopic Terbium yield at depth was calculated to be between 103 to 105 atoms/mmolnatGd per Gray SOBP dose in a 2.4 cm3 volume. At currently achievable Gadolinium concentrations of 0.2 μmol/cm3 this yields approximately 26 atoms/(cm3 GySOBP), corresponding to less than 1 Bq activity. Additional dose from evaporation neutrons and subsequent capture gammas is on the order of 1 μSv/GySOBP. Thus, use of this long-lived contrast agent is dosimetrically safe at current concentrations and induced radioactivity is negligible.
Assessing Heterogeneity of Treatment Effects in Observational Studies
Authors: Robertson Sarah E , Leith Andrew , Schmid Christopher H , Dahabreh Issa J
Published: October 2020

Here we describe methods for assessing heterogeneity of treatment effects over prespecified subgroups in observational studies, using outcome-model–based (g-formula), inverse probability weighting, doubly robust, and matching estimators of subgroup-specific potential outcome means, conditional average treatment effects, and measures of heterogeneity of treatment effects. We compare the finite-sample performance of different estimators in simulation studies where we vary the total sample size, the relative frequency of each subgroup, the magnitude of treatment effect in each subgroup, and the distribution of baseline covariates, for both continuous and binary outcomes. We find that the estimators’ bias and variance vary substantially in finite samples, even when there is no unobserved confounding and no model misspecification. As an illustration, we apply the methods to data from the Coronary Artery Surgery Study (August 1975–December 1996) to compare the effect of surgery plus medical therapy with that of medical therapy alone for chronic coronary artery disease in subgroups defined by previous myocardial infarction or left ventricular ejection fraction.
Does Alcohol Hangover Affect Emotion Regulation Capacity? Evidence From a Naturalistic Cross-Over Study Design
Authors: Gunn Craig , Fairchild Graeme , Verster Joris C , Adams Sally
Published: October 2020

Aims

The aim of this study was to investigate the effects of alcohol hangover on emotion regulation.

Methods

Forty-five non-smoking, healthy participants aged between 18 and 30 years completed a lab-based emotion regulation task assessing cognitive reappraisal and an emotion regulation questionnaire (State-Difficulties in Emotion Regulation Scale [S-DERS]) when hungover (morning following a night of heavy drinking) and under a no-hangover condition in a naturalistic, within-subjects design study.

Results

Participants reported poorer emotion regulation overall (P < 0.001, d = 0.75), and for the subscales ‘Non-Acceptance’, ‘Modulation’ and ‘Clarity’ (Ps ≤ 0.001, ds ≥ 0.62), but not ‘Awareness’ on the S-DERS, in the hangover versus the no-hangover condition. Hangover did not impair emotion regulation ability as assessed using the lab-based task (Ps ≥ 0.21, ds ≤ 0.40), but there was a general negative shift in valence ratings (i.e. all images were rated more negatively) in the hangover relative to the no-hangover condition (P < 0.001, d = 1.16).

Conclusion

These results suggest that emotion regulation in everyday life and emotional reactivity may be adversely affected by alcohol hangover, but some emotion regulation strategies (e.g. deliberate cognitive reappraisal) may be unaffected.
Transforming pediatric neuropsychology through video-based teleneuropsychology: an innovative private practice model pre-COVID-19
Authors: Salinas Christine M , Bordes Edgar Veronica , Berrios Siervo Gretchen , Bender Heidi A
Published: October 2020

Objective

In pediatric neuropsychology multiple barriers such as long wait times until an appointment, insurance coverage, and limited providers who are bilingual/bicultural or who sub-specialize in pediatric neuropsychology, often slow families from receiving diagnoses and interventions in a timely and affordable manner. This paper focuses on increasing accessibility through the development of a video-based, pediatric teleneuropsychology (TeleNP) practice model that was developed in a private practice 2 years before the COVID-19 pandemic.

Method

‘Design thinking’ methodology to problem-solving was utilized to innovate the traditional neuropsychology practice model in under-served areas who may have limited financial and healthcare resources. The practice model approach to include a virtual diagnostic clinic with increased patient and provider efficiency was created to enhance accessibility for patients and sustainability for providers.

Results

Video-based TeleNP screenings were conducted for 67 children with developmental (i.e., attention deficit hyperactivity disorder, autism spectrum disorder) and language disorders, as well as concussion and psychiatric diagnoses. Additional comorbidities were identified in 65.6% of children. Follow-up data approximately 2 months later revealed 98.5% of children were receiving new interventions as a result of the video-based TeleNP assessment.

Conclusion

Video-based TeleNP benefits the consumer as it can reduce wait times, decrease family financial burden (i.e., travel and parent time off work), expedite referrals for interventions, and provide geographically under-served populations access to providers who are linguistically and culturally responsive. For providers, this model revealed improvements with direct implications for cost-saving, thereby facilitating long-term economic sustainability within a private practice healthcare marketplace.
DReSS: a method to quantitatively describe the influence of structural perturbations on state spaces of genetic regulatory networks
Authors: Yin Ziqiao , Guo Binghui , Ma Shuangge , Sun Yifan , Mi Zhilong , Zheng Zhiming
Published: October 2020

Structures of genetic regulatory networks are not fixed. These structural perturbations can cause changes to the reachability of systems’ state spaces. As system structures are related to genotypes and state spaces are related to phenotypes, it is important to study the relationship between structures and state spaces. However, there is still no method can quantitively describe the reachability differences of two state spaces caused by structural perturbations. Therefore, Difference in Reachability between State Spaces (DReSS) is proposed. DReSS index family can quantitively describe differences of reachability, attractor sets between two state spaces and can help find the key structure in a system, which may influence system’s state space significantly. First, basic properties of DReSS including non-negativity, symmetry and subadditivity are proved. Then, typical examples are shown to explain the meaning of DReSS and the differences between DReSS and traditional graph distance. Finally, differences of DReSS distribution between real biological regulatory networks and random networks are compared. Results show most structural perturbations in biological networks tend to affect reachability inside and between attractor basins rather than to affect attractor set itself when compared with random networks, which illustrates that most genotype differences tend to influence the proportion of different phenotypes and only a few ones can create new phenotypes. DReSS can provide researchers with a new insight to study the relation between genotypes and phenotypes.
DeepSELEX: inferring DNA-binding preferences from HT-SELEX data using multi-class CNNs
Authors: Asif Maor , Orenstein Yaron
Published: October 2020

Motivation

Transcription factor (TF) DNA-binding is a central mechanism in gene regulation. Biologists would like to know where and when these factors bind DNA. Hence, they require accurate DNA-binding models to enable binding prediction to any DNA sequence. Recent technological advancements measure the binding of a single TF to thousands of DNA sequences. One of the prevailing techniques, high-throughput SELEX, measures protein–DNA binding by high-throughput sequencing over several cycles of enrichment. Unfortunately, current computational methods to infer the binding preferences from high-throughput SELEX data do not exploit the richness of these data, and are under-using the most advanced computational technique, deep neural networks.

Results

To better characterize the binding preferences of TFs from these experimental data, we developed DeepSELEX, a new algorithm to infer intrinsic DNA-binding preferences using deep neural networks. DeepSELEX takes advantage of the richness of high-throughput sequencing data and learns the DNA-binding preferences by observing the changes in DNA sequences through the experimental cycles. DeepSELEX outperforms extant methods for the task of DNA-binding inference from high-throughput SELEX data in binding prediction in vitro and is on par with the state of the art in in vivo binding prediction. Analysis of model parameters reveals it learns biologically relevant features that shed light on TFs’ binding mechanism.

Availability and implementation

DeepSELEX is available through github.com/OrensteinLab/DeepSELEX/.

Supplementary information

Supplementary data are available at Bioinformatics online.
HiTea: a computational pipeline to identify non-reference transposable element insertions in Hi-C data
Authors: Jain Dhawal , Chu Chong , Alver Burak Han , Lee Soohyun , Lee Eunjung Alice , Park Peter J
Published: October 2020

Hi-C is a common technique for assessing 3D chromatin conformation. Recent studies have shown that long-range interaction information in Hi-C data can be used to generate chromosome-length genome assemblies and identify large-scale structural variations. Here, we demonstrate the use of Hi-C data in detecting mobile transposable element (TE) insertions genome-wide. Our pipeline Hi-C-based TE analyzer (HiTea) capitalizes on clipped Hi-C reads and is aided by a high proportion of discordant read pairs in Hi-C data to detect insertions of three major families of active human TEs. Despite the uneven genome coverage in Hi-C data, HiTea is competitive with the existing callers based on whole-genome sequencing (WGS) data and can supplement the WGS-based characterization of the TE-insertion landscape. We employ the pipeline to identify TE-insertions from human cell-line Hi-C samples.

Availability and implementation

HiTea is available at https://github.com/parklab/HiTea and as a Docker image.

Supplementary information

Supplementary data are available at Bioinformatics online.
Selectin-targeting glycosaminoglycan-peptide conjugate limits neutrophil-mediated cardiac reperfusion injury
Authors: Dehghani Tima , Thai Phung N , Sodhi Harkanwalpreet , Ren Lu , Sirish Padmini , Nader Carol E , Timofeyev Valeriy , Overton James L , Li Xiaocen , Lam Kit S , Chiamvimonvat Nipavan , Panitch Alyssa
Published: October 2020

Aims

One of the hallmarks of myocardial infarction (MI) is excessive inflammation. During an inflammatory insult, damaged endothelial cells shed their glycocalyx, a carbohydrate-rich layer on the cell surface which provides a regulatory interface to immune cell adhesion. Selectin-mediated neutrophilia occurs as a result of endothelial injury and inflammation. We recently designed a novel selectin-targeting glycocalyx mimetic (termed DS-IkL) capable of binding inflamed endothelial cells. This study examines the capacity of DS-IkL to limit neutrophil binding and platelet activation on inflamed endothelial cells, as well as the cardioprotective effects of DS-IkL after acute myocardial infarction.

Methods and results

In vitro, DS-IkL diminished neutrophil interactions with both recombinant selectin and inflamed endothelial cells, and limited platelet activation on inflamed endothelial cells. Our data demonstrated that DS-IkL localized to regions of vascular inflammation in vivo after 45 min of left anterior descending coronary artery ligation-induced MI. Further, findings from this study show DS-IkL treatment had short- and long-term cardioprotective effects after ischaemia/reperfusion of the left anterior descending coronary artery. Mice treated with DS-IkL immediately after ischaemia/reperfusion and 24 h later exhibited reduced neutrophil extravasation, macrophage accumulation, fibroblast and endothelial cell proliferation, and fibrosis compared to saline controls.

Conclusions

Our findings suggest that DS-IkL has great therapeutic potential after MI by limiting reperfusion injury induced by the immune response.
Selection of nitrite-degrading and biogenic amine-degrading strains and its involved genes
Authors: Li Yuxin , Yu Zhihui , Zhu Yingchun , Cao Zhixiang
Published: October 2020

Objectives

Accumulation of nitrite and biogenic amines (BAs) in fermented meat products is a matter of public health concern. The study aimed to screen nitrite-degrading and BA-degrading strains from sour porridges and sausages and bacon products in China.

Materials and Methods

After screening out 12 strains, the degradation of nitrite, the degradation of BAs, the activities of nitrite-reducing enzymes, and the detection of genes involved in the BAs were assessed by spectrophotometry method with hydrochloric acid naphthalene ethylenediamine, high-performance liquid chromatography, GENMED kit, and polymerase chain reaction, respectively.

Results

Pediococcus pentosaceus labelled M SZ1 2 and M GC 2, Lactobacillus plantarum labelled M SZ2 2, and Staphylococcus xylosus labelled Y CC 3 were selected. The activity of nitrite-reducing enzyme in M SZ2 2 was 2.663 units/mg. The degradation rate of total BAs of M SZ2 2 was 93.24%. The degradation rates of nitrite and BAs of M SZ1 2 were 86.49% and 37.87%, respectively. The activity of nitrite-reducing enzyme in M SZ1 2 was up to 1.962 units/mg. M GC 2 showed higher degradation rates of nitrite (89.19%) and Y CC 3 showed higher degradation rates of BAs (36.16%). The genes encoding the multicopper oxidases (suf I/D2EK17) were detected in the four strains, which also did not contain BAs (histidine decarboxylase (hdc), tyrosine decarboxylase (tdc), ornithine decarboxylase (odc), lysine decarboxylase (ldc)) formation encoding genes.

Conclusion

These four strains (M SZ1 2, M GC 2, M SZ2 2, and Y CC 3) are promising candidates to use as starter cultures for nitrite and BAs in fermented sausages.
The genetics-BIDS extension: Easing the search for genetic data associated with human brain imaging
Authors: Moreau Clara A , Jean-Louis Martineau , Blair Ross , Markiewicz Christopher J , Turner Jessica A , Calhoun Vince D , Nichols Thomas E , Pernet Cyril R
Published: October 2020

Metadata are what makes databases searchable. Without them, researchers would have difficulty finding data with features they are interested in. Brain imaging genetics is at the intersection of two disciplines, each with dedicated dictionaries and ontologies facilitating data search and analysis. Here, we present the genetics Brain Imaging Data Structure extension, consisting of metadata files for human brain imaging data to which they are linked, and describe succinctly the genomic and transcriptomic data associated with them, which may be in different databases. This extension will facilitate identifying micro-scale molecular features that are linked to macro-scale imaging repositories, facilitating data aggregation across studies.
NanoGalaxy: Nanopore long-read sequencing data analysis in Galaxy
Authors: de Koning Willem , Miladi Milad , Hiltemann Saskia , Heikema Astrid , Hays John P , Flemming Stephan , van den Beek Marius , Mustafa Dana A , Backofen Rolf , Grüning Björn , Stubbs Andrew P
Published: October 2020

Background

Long-read sequencing can be applied to generate very long contigs and even completely assembled genomes at relatively low cost and with minimal sample preparation. As a result, long-read sequencing platforms are becoming more popular. In this respect, the Oxford Nanopore Technologies–based long-read sequencing “nanopore" platform is becoming a widely used tool with a broad range of applications and end-users. However, the need to explore and manipulate the complex data generated by long-read sequencing platforms necessitates accompanying specialized bioinformatics platforms and tools to process the long-read data correctly. Importantly, such tools should additionally help democratize bioinformatics analysis by enabling easy access and ease-of-use solutions for researchers.

Results

The Galaxy platform provides a user-friendly interface to computational command line–based tools, handles the software dependencies, and provides refined workflows. The users do not have to possess programming experience or extended computer skills. The interface enables researchers to perform powerful bioinformatics analysis, including the assembly and analysis of short- or long-read sequence data. The newly developed “NanoGalaxy" is a Galaxy-based toolkit for analysing long-read sequencing data, which is suitable for diverse applications, including de novo genome assembly from genomic, metagenomic, and plasmid sequence reads.

Conclusions

A range of best-practice tools and workflows for long-read sequence genome assembly has been integrated into a NanoGalaxy platform to facilitate easy access and use of bioinformatics tools for researchers. NanoGalaxy is freely available at the European Galaxy server https://nanopore.usegalaxy.eu with supporting self-learning training material available at https://training.galaxyproject.org.
Political Comedy as a Gateway to News Use, Internal Efficacy, and Participation: A Longitudinal Mediation Analysis
Authors: Long Jacob A , Jeong Min Seon , Lavis Simon M
Published: October 2020

Despite a great deal of research, much about the effects of political comedy programming on its viewers remains uncertain. One promising line of work has focused on increased internal political efficacy—the sense that one is competent to engage with politics—as an outcome of exposure to political comedy programs. This may explain results showing that viewers are more likely to participate in politics. We extend this approach by considering the role of political comedy’s “gateway” effect in encouraging political media consumption, which can promote additional increases in efficacy and participation. This study provides a theoretical synthesis of prior research and a rigorous empirical test using a representative panel survey of adults in the United States, providing evidence of a relationship between political comedy and participation with both news use and internal efficacy serving as mediators. Furthermore, we find that only political satire, not late-night talk shows, appear to produce these effects.
Comparative evaluation of webinar, powerpoint presentation and lecture as oral health educational interventions among school children: a randomized controlled trial
Authors: Deokar Rahul , Dodamani Arun , Vishwakarma Prashanth , Jadhav Harish , Khairnar Mahesh , Marathe Pratiksha , Bhandari Rahul , Khobragade Vrushali
Published: October 2020

The study compared the effectiveness of three teaching methods on the oral health status of high school children. The study population of 791 school children selected from three different schools was randomly allocated to one of three intervention groups: (i) Webinar group (Online presentation)—260 subjects, (ii) Face to Face lecture using PowerPoint presentation (F2F PP group)—261 subjects and (iii) Control group (Only lecture)—270 subjects. Subjects from the Webinar group and F2F PP group received oral health education at an interval of 15 days starting from baseline. Subjects from the control group received oral health education only at baseline. Oral Hygiene Index (OHI) and Gingival Index (GI) were measured at baseline, at 1 month, 2 months’ and 3 months’ interval. OHI and GI showed a significant reduction (P = 0.001) in the Webinar group and F2F PP group; However, in the control group, OHI and GI reduced from baseline till second month and showed an increase at 3 months’ interval. F2F PP group showed a maximum reduction in OHI and GI followed by the Webinar group. It can be concluded that F2F PowerPoint-based oral health education was most effective followed by the webinar method.
Evaluation of mediastinoscopy in mediastinal lymph node staging for non-small-cell lung cancer
Authors: Diebels Ian , Hendriks Jeroen M H , Van Meerbeeck Jan P , Lauwers Patrick , Janssens Annelies , Yogeswaran Suresh K , Van Schil Paul E Y
Published: October 2020

OBJECTIVES

The purpose of this study was to assess the quality of video-assisted cervical mediastinoscopy (VACM) in the staging of non-small-cell lung cancer (NSCLC) at the Antwerp University Hospital with a focus on test effectiveness indicators, morbidity and unforeseen pN2 results.

METHODS

All consecutive VACM workups of cases of NSCLC performed between January 2010 and December 2015 were included to assess overall test quality and effectiveness. Quality assurance was performed in accordance with the recommendations of the European Society of Gastrointestinal Endoscopy and European Society of Thoracic Surgeons (ESTS) where appropriate.

RESULTS

A total of 168 video-assisted cervical mediastinoscopies were included. A total of 91.7% of the procedures were performed in accordance with the ESTS guideline. An unforeseen pN2 staging was identified in 10 anatomical lung resections (8.6%). Statistical analysis showed no significant association between VACM performed in accordance with the ESTS guideline and the presence of pN2 positive lymph nodes [χ2 (1) = 0.61; P = 0.57] and no association between VACM performed in accordance with the ESTS guideline and overall futile thoracotomy [χ2 (1) = 0.76; P = 0.50]. Calculations revealed a sensitivity of 81.8 [95% confidence interval (CI) 69.1–90.9], specificity of 100%, positive predictive value of 100%, negative predictive value of 91.9% (95% CI 86.6–95.2) and diagnostic accuracy of 94.1% (95% CI 89.33–97.11).

CONCLUSIONS

Overall, 91.7% of the VACM were performed in accordance with the ESTS guideline. This process resulted in a sensitivity of 81.8%, a negative predictive value of 91.9% and an unforeseen pN2 rate of 8.6%.
Faster Johnson–Lindenstrauss transforms via Kronecker products
Authors: Jin Ruhui , Kolda Tamara G , Ward Rachel
Published: October 2020

The Kronecker product is an important matrix operation with a wide range of applications in signal processing, graph theory, quantum computing and deep learning. In this work, we introduce a generalization of the fast Johnson–Lindenstrauss projection for embedding vectors with Kronecker product structure, the Kronecker fast Johnson–Lindenstrauss transform (KFJLT). The KFJLT reduces the embedding cost by an exponential factor of the standard fast Johnson–Lindenstrauss transform’s cost when applied to vectors with Kronecker structure, by avoiding explicitly forming the full Kronecker products. We prove that this computational gain comes with only a small price in embedding power: consider a finite set of $p$ points in a tensor product of $d$ constituent Euclidean spaces $\bigotimes _{k=d}^{1}{\mathbb{R}}^{n_k}$, and let $N = \prod _{k=1}^{d}n_k$. With high probability, a random KFJLT matrix of dimension $m \times N$ embeds the set of points up to multiplicative distortion $(1\pm \varepsilon )$ provided $m \gtrsim \varepsilon ^{-2} \, \log ^{2d - 1} (p) \, \log N$. We conclude by describing a direct application of the KFJLT to the efficient solution of large-scale Kronecker-structured least squares problems for fitting the CP tensor decomposition.
Administering an appeasing substance to optimize performance and health responses in feedlot receiving cattle
Authors: Colombo Eduardo A , Cooke Reinaldo F , Brandão Alice P , Wiegand Jacob B , Schubach Kelsey M , Duff Glenn C , Gouvêa Vinícius N , Cappellozza Bruno I
Published: October 2020

This experiment evaluated the impacts of administering a bovine appeasing substance (BAS) at feedlot entry to receiving cattle. Angus-influenced steers (n = 342) from 16 sources were purchased from an auction yard on day –1, and transported (12 hr; 4 trucks) to the feedlot. Upon arrival on day 0, shrunk body weight (BW; 240 ± 1 kg) was recorded and steers were ranked by load, shrunk BW, and source and assigned to receive BAS (IRSEA Group, Quartier Salignan, France; n = 171) or placebo (diethylene glycol monoethyl ether; CON; n = 171). The BAS is a mixture of fatty acids that replicate the composition of the bovine appeasing pheromone. Treatments (5 mL) were topically applied to each individual steer on their nuchal skin area. Steers were allocated to 1 of 24 drylot pens (12 pens/treatment) and received a free-choice diet until day 46. Steers were assessed daily for bovine respiratory disease (BRD) signs, and feed intake was recorded from each pen daily. Steer unshrunk BW was recorded on days 7, 17, 31, 45, and 46. Shrunk BW on day 0 was added an 8% shrink to represent initial BW, and final BW was calculated by averaging BW from days 45 and 46. Blood samples were collected from 5 steers/pen on days 0, 7, 11, 31, and 45. Pen was considered the experimental unit. Steer BW gain was greater (P = 0.04) in BAS vs. CON (1.01 vs. 0.86 kg/d, SEM = 0.05). Feed intake did not differ (P = 0.95) between treatments, resulting in greater (P = 0.05) feed efficiency in BAS vs. CON (171 vs. 142 g/kg, SEM = 10). Plasma cortisol concentration was greater (P = 0.05) and plasma glucose concentration was less in CON vs. BAS on day 7 (treatment × day; P = 0.07 and <0.01, respectively). Mean plasma β-hydroxybutyrate concentration was greater (P < 0.01) in BAS vs. CON (3.23 and 2.75 mg/mL; SEM = 0.12). Incidence of BRD was greater (P ≤ 0.05) in BAS vs. CON from days 6 to 10 and days 19 to 23 (treatment × day; P < 0.01), although overall BRD incidence did not differ (P = 0.20) between treatments (82.4% vs. 76.6%, respectively; SEM = 3.2). A greater proportion (P = 0.04) of BAS steers diagnosed with BRD required one antimicrobial treatment to regain health compared with CON (59.3% vs. 47.6%, SEM = 4.2). Hence, BAS administration to steers upon feedlot arrival improved BW gain during a 45-d receiving period by enhancing feed efficiency. Moreover, results suggest that BAS improved steer performance by facilitating early detection of BRD signs, lessening the disease recurrence upon first antimicrobial treatment.
Clinical Course of Cancer Patients With COVID-19: A Retrospective Cohort Study
Authors: Alpert Naomi , Rapp Joseph L , Marcellino Bridget , Lieberman-Cribbin Wil , Flores Raja , Taioli Emanuela
Published: October 2020

Background

Complications in cancer patients with coronavirus disease 2019 (COVID-19) have not been examined. This analysis aimed to compare characteristics of COVID-19 patients with and without cancer and assess whether cancer is associated with COVID-19 morbidity or mortality.

Methods

COVID-19–positive patients with an inpatient or emergency encounter at the Mount Sinai Health System between March 1, 2020, and May 27, 2020, were included and compared across cancer status on demographics and clinical characteristics. Multivariable logistic regressions were used to model the associations of cancer with sepsis, venous thromboembolism, acute kidney injury, intensive care unit admission, and all-cause mortality.

Results

There were 5556 COVID-19–positive patients included, 421 (7.6%) with cancer (325 solid, 96 nonsolid). Those with cancer were statistically significantly older, more likely to be non-Hispanic Black and to be admitted to the hospital during their encounter, and had more comorbidities than noncancer COVID-19 patients. Cancer patients were statistically significantly more likely to develop sepsis (adjusted odds ratio [ORadj] = 1.31, 95% confidence interval [CI] = 1.06 to 1.61) and venous thromboembolism (ORadj = 1.77, 95% CI = 1.01 to 3.09); there was no statistically significant difference in acute kidney injury (ORadj = 1.10, 95% CI = 0.87 to 1.39), intensive care unit admissions (ORadj = 1.04, 95% CI = 0.80 to 1.34), or mortality (ORadj = 1.02, 95% CI = 0.81 to 1.29).

Conclusions

COVID-19 patients with cancer may have a higher risk for adverse outcomes. Although there was no statistically significant difference in mortality, COVID-19 patients with cancer have statistically significantly higher risk of thromboembolism and sepsis. Further research is warranted into the potential effects of cancer treatments on inflammatory and immune responses to COVID-19 and on the efficacy of anticoagulant therapy in these patients.
Small bowel obstruction due to retroperitoneal hernia following renal transplant: a case report
Authors: Nawabi Atta , Kahle Adam C , King Clay D , Nawabi Perwaiz
Published: October 2020

Para duodenal hernias, the most common type of retroperitoneal hernias, are thought to occur naturally from abnormal gut rotation because of fusion folds within the peritoneum. Retroperitoneal hernias are a rare postoperative complication and have not been described after renal transplantation via a retroperitoneal approach. This case report presents a 48-year-old male with intestinal obstruction after renal transplant due to herniation into the retroperitoneum via an incidentally created peritoneal defect. We suggest computed tomography with oral contrast be used in the early postoperative phase to assess for obstruction in patients with prolonged ileus of unclear etiology who have undergone retroperitoneal dissection. Small peritoneal defects should be closed during dissection. Larger, or multiple peritoneal defects should be extended to make a single, large defect to decrease the possibility of bowel herniating and becoming incarcerated.
Ten Zen Koans Translated from Japanese, Mandarin, Wu, Vietnamese, Thai, Fujian, Korean, Tibetan, Hakka, Javenese, Mizo, Nepal Bhasa, Khasi, Buryat, Malay, Paiwan, Burmese, Ryukyuan, and Okinawan by Jackson Bliss
Authors: Bliss Jackson
Published: October 2020

In this satirical short story about Zen poetry scholarship that explores the limited and often impossible process of linguistic and spiritual translation, the primary text does not exist at all, making this piece both a spiritual embodiment of Zen according to the writing of many of its most dedicated practitioners and devoted scholars, but also a textual and spatial oxymoron since footnotes are obviously ancillary information used to elaborate and contextualize arguments made on the primary text, which, in this case, does not exist; this poses a basic question: can there be footnotes without a primary text? The footnotes, in their own way, mock any attempt to transliterate a spiritual state of being or a school of thought such as Zen Buddhism since language is constrained by itself from adequately describing the very process that the text actively prevents the reader from doing at all.
A scalable random forest regressor for combining neutron-star equation of state measurements: a case study with GW170817 and GW190425
Authors: Hernandez Vivanco Francisco , Smith Rory , Thrane Eric , Lasky Paul D
Published: October 2020

Gravitational-wave observations of binary neutron star coalescences constrain the neutron-star equation of state by enabling measurement of the tidal deformation of each neutron star. This deformation is well approximated by the tidal deformability parameter Λ, which was constrained using the first binary neutron star gravitational-wave observation, GW170817. Now, with the measurement of the second binary neutron star, GW190425, we can combine different gravitational-wave measurements to obtain tighter constraints on the neutron-star equation of state. In this paper, we combine data from GW170817 and GW190425 to place constraints on the neutron-star equation of state. To facilitate this calculation, we derive interpolated marginalized likelihoods for each event using a machine learning algorithm. These likelihoods, which we make publicly available, allow for results from multiple gravitational-wave signals to be easily combined. Using these new data products, we find that the radius of a fiducial 1.4 M⊙ neutron star is constrained to $11.6^{+1.6}_{-0.9}$ km at 90 per cent confidence and the pressure at twice the nuclear saturation density is constrained to $3.1^{+3.1}_{-1.3}\times 10^{34}$ dyne cm−2 at 90 per cent confidence. Combining GW170817 and GW190425 produces constraints indistinguishable from GW170817 alone and is consistent with findings from other works.
Monism, Spinoza’s Way
Authors: Garrett Don
Published: October 2020

Monism, characterized by Jonathan Schaffer as the thesis that the cosmos is the one and only basic actual concrete object, has been the subject of a great deal of recent interest. Spinoza is often taken, rightly, to be an important forebear. This article seeks to explain the distinctive content and basis of Spinoza’s monistic metaphysics and to compare it to contemporary Monism. It then argues that although Spinoza’s monistic metaphysics is not strictly a version of Monism as defined, it has a number of theoretical advantages that make central aspects of it worthy of serious consideration.
The World Just Is the Way It Is
Authors: Builes David
Published: October 2020

What is the relationship between objects and properties? According to a standard view, there are primitive individuals (or ‘particulars’, or ‘substrata’) that ‘instantiate’ or ‘have’ various properties. According to a rival view, objects are mere ‘bundles’ of properties. While there are a number of reasons to be skeptical of primitive individuals, there are also a number of challenges that the bundle theorist faces. The goal of this paper is to formulate a view about the relationship between objects and properties that avoids many of the problems inherent in both of these views. The view I will end up defending implies a particularly radical version of Monism, and it collapses the object-property distinction altogether.
deepBase v3.0: expression atlas and interactive analysis of ncRNAs from thousands of deep-sequencing data
Authors: Xie Fangzhou , Liu Shurong , Wang Junhao , Xuan Jiajia , Zhang Xiaoqin , Qu Lianghu , Zheng Lingling , Yang Jianhua
Published: October 2020

Eukaryotic genomes encode thousands of small and large non-coding RNAs (ncRNAs). However, the expression, functions and evolution of these ncRNAs are still largely unknown. In this study, we have updated deepBase to version 3.0 (deepBase v3.0, http://rna.sysu.edu.cn/deepbase3/index.html), an increasingly popular and openly licensed resource that facilitates integrative and interactive display and analysis of the expression, evolution, and functions of various ncRNAs by deeply mining thousands of high-throughput sequencing data from tissue, tumor and exosome samples. We updated deepBase v3.0 to provide the most comprehensive expression atlas of small RNAs and lncRNAs by integrating ∼67 620 data from 80 normal tissues and ∼50 cancer tissues. The extracellular patterns of various ncRNAs were profiled to explore their applications for discovery of noninvasive biomarkers. Moreover, we constructed survival maps of tRNA-derived RNA Fragments (tRFs), miRNAs, snoRNAs and lncRNAs by analyzing >45 000 cancer sample data and corresponding clinical information. We also developed interactive webs to analyze the differential expression and biological functions of various ncRNAs in ∼50 types of cancers. This update is expected to provide a variety of new modules and graphic visualizations to facilitate analyses and explorations of the functions and mechanisms of various types of ncRNAs.
Clinical Cutaneous Features of Patients Infected With SARS-CoV-2 Hospitalized for Pneumonia: A Cross-sectional Study
Authors: Mascitti Hélène , Bonsang Benjamin , Dinh Aurélien , Assan Florence , Perronne Véronique , Leblanc Thibault , Duran Clara , Bouchand Frédérique , Matt Morgan , Le Gal Aurélie , N’guyen Van Thanh Julia , Lanore Aymeric , Jacob Louis , Kiavue Nicolas , Siméon Soline , Bessis Simon , de Truchis Pierre , Landowski Stéphanie , Davido Benjamin , Moreau Frédérique , Rameix-Welti Marie-Anne , Gault Elyanne , Gaillard Jean-Louis , Roux Anne-Laure , Sivadon-Tardy Valérie , Salomon Elsa , El Sayed Faten , Carlier Robert , Emile Jean-François , Perronne Christian , Bourgault-Villada Isabelle
Published: October 2020

Background

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of a current pandemic worldwide. This virus can reach all organs and disturbs the immune system, leading to a cytokine storm in severe forms. We aimed to report cutaneous features among coronavirus disease 2019 (COVID-19) hospitalized patients.

Methods

We performed a cross-sectional study on 1 given day among all patients hospitalized in acute care for COVID-19 and included all patients with cutaneous features. Follow-up 48 hours later was obtained.

Results

Among 59 adult patients hospitalized on the day of the study in an infectious diseases ward for SARS-CoV-2 infection who were confirmed by molecular assay and/or radiological findings (computed tomography scan), 40 were included. Several cutaneous manifestations were found: macular exanthema (80%), face edema (32%), livedo (13%), urticarial rash (8%), purpura (5%), oral lichenoid lesions (33%), and conjunctivitis (18%). Cutaneous biopsy was performed in 17 patients. Histological findings showed mast cell hyperplasia (100%), superficial perivascular infiltrate of lymphocytes (94%), and superficial edema (47%) consistent with capillary leak.

Conclusions

Various dermatological signs can be encountered during COVID-19. A macular rash was the most frequent. All cutaneous features could be related to a vascular leak process.
Randomized Trial Evaluating the Neurotoxicity of Dolutegravir/Abacavir/Lamivudine and Its Reversibility After Switching to Elvitegravir/Cobicistat/Emtricitabine/Tenofovir Alafenamide: GESIDA 9016
Authors: Perez Valero Ignacio , Cabello Alfonso , Ryan Pablo , De La Fuente-Moral Sara , Santos Ignacio , Vivancos Maria Jesus , Gonzalez Alicia , Gorgolas Miguel , Cuevas Guillermo , Diaz De Santiago Alberto , Cano Joanna , Rua Guadalupe , Yllescas Maria , González García Juan Julian
Published: October 2020

Background

Despite evidence shown of dolutegravir (DTG)-related neurotoxicity, which may be more common when combined with abacavir (ABC), its reversibility has not been explored in a clinical trial.

Methods

We conducted a randomized, multicenter, open-label, pilot trial to evaluate the reversibility of patient-reported neuropsychiatric symptoms, developed or worsened on DTG/ABC/lamivudine (DTG/ABC/3TC), in virologically suppressed patients switched to cobicistat-boosted-elvitegravir/emtricitabine/tenofovir-alafenamide (EVG/COBI/FTC/TAF). Participants were randomized to immediate switch (baseline) or to defer switch (week 4), and then all completed 24 weeks of follow up on EVG/COBI/FTC/TAF. At each visit, participants completed Pittsburgh Sleep Quality Index (PSQI) and Hospital Anxiety and Depression (HAD) scales and were interviewed about 11 neuropsychiatric symptoms potentially related with DTG through a questionnaire. At baseline and at the end of follow up, they also performed neurocognitive testing. Our primary objective was to compare changes in neuropsychiatric symptoms and PSQI and HAD scales between arms at week 4. Secondary objectives were to evaluate changes in neuropsychiatric symptoms and PSQI and HAD scales at weeks 4, 12, and 24 after switching to EVG/COBI/FTC/TAF and in neurocognitive performance and magnetic resonance imaging biomarkers at end of follow up.

Results

Thirty-eight participants were included. Study arms were similar at baseline. At week 4, neuropsychiatric symptoms and PSQI and HAD scores remained unchanged in participants receiving DTG/ABC/3TC and improved significantly in participants receiving EVG/COBI/FTC/TAF. These significant improvements were also observed at weeks 4, 12, and 24 after all participants switched to EVG/COBI/FTC/TAF. In addition, global neurocognitive performance improved (NPZ-7) after switching to EVG/COBI/FTC/TAF.

Conclusions

Neuropsychiatric symptoms in patients on DTG/ABC/3TC could resolve or improve after switching to EVG/COBI/FTC/TAF.
Toxoplasmosis among cancer patients undergoing chemotherapy: a population study based on the serological, molecular and epidemiological aspects
Authors: Hosseini Seyed Abdollah , Sharif Mehdi , Sarvi Shahabeddin , Janbabai Ghasem , Keihanian Shahrbanoo , Abediankenari Saeid , Gholami Sara , Amouei Afsaneh , Javidnia Javad , Saberi Reza , Shekarriz Ramin , Daryani Ahmad
Published: October 2020

Background

Toxoplasmosis is highly prevalent in northern Iran and immunocompromised individuals are more susceptible to this infection. The present study aimed to determine the seroprevalence, parasitism and genetic diversity of Toxoplasma gondii among patients with cancer undergoing chemotherapy in northern Iran.

Methods

A total of 350 serum samples obtained from cancer patients were collected from laboratory centers in northern Iran. Immunodiagnosis and DNA detection were accomplished by ELISA and PCR. Thereafter, multiplex-nested PCR-restriction fragment length polymorphism was used for the genotyping of T. gondii.

Results

In general, out of 350 patients, 264 (75.4%) and 9 (2.57%) cases were positive for anti-T. gondii IgG and IgM, respectively. Moreover, 19 (5.43%) samples contained T. gondii DNA. From 19 positive samples, 10 high-quality samples with sharp and non-smear bands were selected to determine the genotypes of T. gondii. Accordingly, the samples were classified as genotype #1 (type II clonal; n=4, 40%), genotype #2 (type III clonal; n=3, 30%), genotype #10 (type I clonal; n=2, 20%) and genotype #27 (type I variant; n=1, 10%).

Conclusions

As evidenced by the results, due to the high prevalence of T. gondii, cancer patients in northern Iran are at serious risk of severe toxoplasmosis and its complications. Therefore, oncologists need to regard this critical health problem as a matter requiring urgent attention.
Some morphologically distinguishable hypotrich ciliates share identical 18S rRNA gene sequences – taxonomic insights from a case study onOxytrichaspecies (Protista, Ciliophora)
Authors: Fan Xinpeng , Yao Shunli , Luo Xiaotian , Dong Tianyao , Xu Yuan , Chen Lingyun , Bourland William , Zhao Yan , Huang Jie
Published: October 2020

Modern taxonomic studies of ciliated protozoa require both morphological and molecular data. One dilemma is how to distinguish morphologically similar species with few nucleotide differences in the widely used marker, the 18S rRNA gene. In the present study, two Oxytricha species were morphologically documented using light and electron microscopy. The mitochondrial cytochrome c oxidase subunit I (COI) gene and a fragment of the rRNA gene covering the 18S-ITS1-5.8S-ITS2-28S rRNA gene regions were sequenced. Phylogenetic analyses of all available Oxytricha granulifera-related populations were performed to reveal the internal relationships of this group. We described a new species, Oxytricha atypica sp. nov., distinguished from its congeners by having seven postoral ventral cirri resulting from the additional fragmentation of anlage V during ontogenesis. Although their 18S rRNA genes differ by only one nucleotide, divergence of the COI gene is as high as 11.8% between O. atypica and the closely related species, O. granulifera. All but one of the COI nucleotide substitutions were synonymous. We documented the highly conserved nature of the 18S rRNA gene in the morphospecies of Oxytricha. Based on these findings, we speculate that O. granulifera contains cryptic species or morphospecies needing further characterization, and new insights for the taxonomy of hypotrich ciliates are also discussed.
The first known riodinid ‘cuckoo’ butterfly reveals deep-time convergence and parallelism in ant social parasites
Authors: Kaminski Lucas A , Volkmann Luis , Callaghan Curtis J , DeVries Philip J , Vila Roger
Published: October 2020

Mutualistic interactions between butterflies and ants can evolve into complex social parasitism. ‘Cuckoo’ caterpillars, known only in the Lycaenidae, use multimodal mimetic traits to achieve social integration into ant societies. Here, we present the first known ‘cuckoo’ butterfly in the family Riodinidae. Aricoris arenarum remained in taxonomic limbo for > 80 years, relegated to nomen dubium and misidentified as Aricoris gauchoana. We located lost type material, designated lectotypes and documented the morphology and natural history of the immature stages. The multifaceted life cycle of A. arenarum can be summarized in three phases: (1) females lay eggs close to honeydew-producing hemipterans tended by specific Camponotus ants; (2) free-living caterpillars feed on liquids (honeydew and ant regurgitations); and (3) from the third instar onward, the caterpillars are fed and tended by ants as ‘cuckoos’ inside the ant nest. This life cycle is remarkably similar to that of the Asian lycaenid Niphanda fusca, despite divergence 90 Mya. Comparable eco-evolutionary pathways resulted in a suite of ecomorphological homoplasies through the ontogeny. This study shows that convergent interactions can be more important than phylogenetic proximity in shaping functional traits of social parasites.
Progressive and accurate assembly of multi-domain protein structures from cryo-EM density maps
Authors: Zhou Xiaogen , Li Yang , Zhang Chengxin , Zheng Wei , Zhang Guijun , Zhang Yang
Published: October 2020

Progress in cryo-electron microscopy (cryo-EM) has provided the potential for large-size protein structure determination. However, the solution rate for multi-domain proteins remains low due to the difficulty in modeling inter-domain orientations. We developed DEMO-EM, an automatic method to assemble multi-domain structures from cryo-EM maps through a progressive structural refinement procedure combining rigid-body domain fitting and flexible assembly simulations with deep neural network inter-domain distance profiles. The method was tested on a large-scale benchmark set of proteins containing up to twelve continuous and discontinuous domains with medium-to-low-resolution density maps, where DEMO-EM produced models with correct inter-domain orientations (TM-score >0.5) for 98% of cases and significantly outperformed the state-of-the-art methods. DEMO-EM was applied to SARS-Cov-2 coronavirus genome and generated models with average TM-score/RMSD of 0.97/1.4Å to the deposited structures. These results demonstrated an efficient pipeline that enables automated and reliable large-scale multi-domain protein structure modeling with atomic-level accuracy from cryo-EM maps.