bluuebunny/crossref_metadata_2025 huggingface dataset:
Constructing small genome graphs via string compression
Authors: Qiu Yutong , Kingsford Carl
Published: April 2021

Motivation

The size of a genome graph—the space required to store the nodes, node labels and edges—affects the efficiency of operations performed on it. For example, the time complexity to align a sequence to a graph without a graph index depends on the total number of characters in the node labels and the number of edges in the graph. This raises the need for approaches to construct space-efficient genome graphs.

Results

We point out similarities in the string encoding mechanisms of genome graphs and the external pointer macro (EPM) compression model. We present a pair of linear-time algorithms that transform between genome graphs and EPM-compressed forms. The algorithms result in an upper bound on the size of the genome graph constructed in terms of an optimal EPM compression. To further reduce the size of the genome graph, we propose the source assignment problem that optimizes over the equivalent choices during compression and introduce an ILP formulation that solves that problem optimally. As a proof-of-concept, we introduce RLZ-Graph, a genome graph constructed based on the relative Lempel–Ziv algorithm. Using RLZ-Graph, across all human chromosomes, we are able to reduce the disk space to store a genome graph on average by 40.7% compared to colored compacted de Bruijn graphs constructed by Bifrost under the default settings. The RLZ-Graph scales well in terms of running time and graph sizes with an increasing number of human genome sequences compared to Bifrost and variation graphs produced by VGtoolkit.

Availability

The RLZ-Graph software is available at: https://github.com/Kingsford-Group/rlzgraph.

Supplementary information

Supplementary data are available at Bioinformatics online.
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Viral Load Kinetics in Symptomatic Children, Adolescents, and Adults
Authors: Bellon Mathilde , Baggio Stephanie , Jacquerioz Bausch Frederique , Spechbach Hervé , Salamun Julien , Genecand Camille , Tardin Aglae , Kaiser Laurent , L’Huillier Arnaud G , Eckerle Isabella
Published: April 2021

SARS-CoV-2 viral load (VL) can serve as a correlate for infectious virus presence and transmission. Viral shedding kinetics over the first week of illness for symptomatic children (n = 279), adolescents (n = 639), and adults (n = 7109) show VLs compatible with infectious virus presence, with slightly lower VL in children than adults.
Intra- and Interlaboratory Reproducibility of the Sensitivity to Endocrine Therapy Assay for Stage II/III Breast Cancer
Authors: Bossuyt Veerle , Lau Rosanna , Young Brandon , Howe John Greg , Zhao Fengmin , Leyland-Jones Brian , Du Lili , Foli Tiffany , Hatzis Christos , Symmans W Fraser
Published: April 2021

Background

The sensitivity to endocrine therapy assay (SET2,3) predicts treatment outcomes in Stage II-III breast cancer. SET2,3 measures transcription related to estrogen and progesterone receptors (SETER/PR index) and the molecular subtype (RNA4: ESR1, PGR, ERBB2, AURKA) from formalin-fixed paraffin-embedded (FFPE) tissue sections.

Methods

We designed a nested study across 3 pathology laboratories, each testing 60 breast cancers twice in controlled batches. Laboratories macrodissected and directly homogenized the unstained FFPE tumor sections, then performed the QuantiGene Plex bead-based hybridization assay. SET2,3 was calculated centrally using predefined statistical R-scripts and applying pre-defined cutpoints. Concordance correlation coefficient (CCC) was calculated from continuous measurements and Kappa statistic from categorical results. A mixed-effects model estimated contributions to bias (fixed effects) and variance (random effects) from the replicated design.

Results

Intralaboratory (CCC 0.96–0.99) and interlaboratory (CCC 0.98–0.99) SET2,3 results were concordant, with rates of agreement for high/low categorization within (Kappa 0.83–0.93) and between laboratories (Kappa 0.87–0.88). The relative contributions to overall variance of SET2,3 measurements were 96.90% from biological differences between cancers, 0.67% from interlaboratory variability, and 2.44% from residual causes including intralaboratory replicates. Similar results were obtained with SETER/PR, the baseline prognostic index calculated using pathological or clinical tumor and nodal staging information, and the 4 individual genes (ESR1, PGR, ERBB2, and AURKA).

Conclusion

Intra- and interpathology laboratory measurements of SET2,3 and its components were highly reproducible when tested from FFPE tumor sections.
MBSO Algorithm For Handling Energy-Throughput Trade-Off In Cognitive Radio Networks
Authors: Ramchandran M , Ganesh E N
Published: April 2021

Cognitive Radio network (CRN) depends on opportunistic spectrum access and spectrum sensing for improving the wireless networks’ spectrum efficiency. Since throughput maximization can result in high-energy consumption, the spectrum sensing technique should address the energy-throughput trade-off. The spectrum sensing time has to be determined by the considering the residual battery energies of each secondary user (SU). The primary user (PU) interference degrades the throughput of the entire network. Hence, the transmit power level should be determined by considering the PU interference and SU battery energy. This paper proposes the multi-objective brain storm optimization (MBSO) algorithm for handling energy-throughput trade-off in CRN. In this work, the sensing time is adaptively determined based on the residual battery energy of SUs, and the transmit power is determined based on the energy level of the PU signal and the residual battery energy of the SUs. A multi-objective optimization problem is formulated in order to maximize the throughput and minimize the packet error rate (PER) and is solved by applying the MBSO algorithm. Experimental results show that MBSO attains improved throughput, higher residual energy with lesser PER. The spectrum sensing performance is enhanced with higher probability of detection.
Management strategies for aflatoxin risk mitigation in maize, dairy feeds and milk value chains—case study Kenya
Authors: Joutsjoki Vesa V , Korhonen Hannu J
Published: April 2021

Widespread aflatoxin contamination of a great number of food and feed crops has important implications on global trade and health. Frequent occurrence of aflatoxin in maize and milk poses serious health risks to consumers because these commodities are staple foods in many African countries. This situation calls for development and implementation of rigorous aflatoxin control measures that encompass all value chains, focusing on farms where food and feed-based commodities prone to aflatoxin contamination are cultivated. Good agricultural practices (GAP) have proven to be an effective technology in mitigation and management of the aflatoxin risk under farm conditions. The prevailing global climate change is shown to increase aflatoxin risk in tropical and subtropical regions. Thus, there is an urgent need to devise and apply novel methods to complement GAP and mitigate aflatoxin contamination in the feed, maize and milk value chains. Also, creation of awareness on aflatoxin management through training of farmers and other stakeholders and enforcement of regular surveillance of aflatoxin in food and feed chains are recommended strategies. This literature review addresses the current situation of aflatoxin occurrence in maize, dairy feeds and milk produced and traded in Kenya and current technologies applied to aflatoxin management at the farm level. Finally, a case study in Kenya on successful application of GAP for mitigation of aflatoxin risk at small-scale farms will be reviewed.
Equivariant K-Theory Classes of Matrix Orbit Closures
Authors: Berget Andrew , Fink Alex
Published: April 2021

The group $G = \textrm{GL}_r(k) \times (k^\times )^n$ acts on $\textbf{A}^{r \times n}$, the space of $r$-by-$n$ matrices: $\textrm{GL}_r(k)$ acts by row operations and $(k^\times )^n$ scales columns. A matrix orbit closure is the Zariski closure of a point orbit for this action. We prove that the class of such an orbit closure in $G$-equivariant $K$-theory of $\textbf{A}^{r \times n}$ is determined by the matroid of a generic point. We present two formulas for this class. The key to the proof is to show that matrix orbit closures have rational singularities.
Remarkable bilaterally asymmetrical gonopores and gonopods in a new genus and species of brachyuran crab from the Ryukyu Islands, Japan (Decapoda: Brachyura: Xanthidae)
Authors: Naruse Tohru , Maenosono Tadafumi , Ng Peter K L
Published: April 2021

A new genus and new species of xanthid crab, Mabui calculusn. gen., n. sp., are described from Okinawa Island, Ryukyu Islands, Japan. The new taxon is unique for Brachyura by having bilaterally asymmetrical male gonopods and female gonopores, with the particular reproductive structure always distinctly more developed on one side than in the other. This remarkable condition, so far unique among brachyurans, was observed in all specimens examined (N = 53), except for an undeveloped subadult female. The right chelae of all intact males and large females are almost always larger than the left chela, and each right chela has a large and modified cutting tooth. Other than in the asymmetrical external reproductive structures, the new taxon is morphologically closest to the xanthines Megametope ogaensis Sakai, 1974 and Jacforus cavatus (Rathbun, 1907), but can easily be distinguished by the characters of the carapace, third maxilliped, ambulatory legs, and male pleon.
Threat Assessment and Management in Higher Education
Authors: Deisinger Eugene R. D. , Nolan Jeffrey J.
Published: April 2021

This chapter provides an overview of the development, implementation, and operation of threat assessment and management practices within institutions of higher education. The authors provide a brief summary of the history and development of campus threat management over the past 25 years, noting the contributions of a range of disciplines, research, and informed practice. The chapter delineates the essential elements of a comprehensive threat assessment and management process designed to help campus practitioners to identify, assess, and intervene across the range of potential threats and concerns that may arise. The authors provide an overview of legal duties and issues relevant to threat management, referencing legal principles and cases that have informed standards of practice for the field. Finally, the authors discuss opportunities for advancing the practice of threat management to sustain and enhance the health, safety, and well-being of campus communities.
The Assessment of Anonymous Threatening Communications
Authors: Simons Andre , Tunkel Ronald F.
Published: April 2021

Perhaps now more than any time in history, anonymous threatening communications (ATCs) are easily delivered, highly disruptive, and frequently used by offenders who seek to frighten, harass, and intimidate their victims. The ability to quickly and defensibly triage and evaluate ATCs has become a necessary skill for threat assessment professionals who serve on corporate security, education, or community-based teams. In this chapter, the authors (both former members of the FBI’s Behavioral Analysis Unit) provide a step-by-step operational guide for the analysis of ATCs. The methods and strategies shared by the authors can be easily adopted and used by threat assessors to confidently address this growing challenge.
Fundamentals of Threat Assessment for Beginners
Authors: O’Toole Mary Ellen
Published: April 2021

This chapter addresses the fundamentals of threat assessment for professionals new to the field. Threat assessment is a critical thinking analysis that requires a multidisciplinary and peer review approach. Some of the fundamental concepts of threat assessment discussed in this chapter include the need for a detailed evaluation of the threatener’s background, including background patterns of behavior, motivation, and abilities to carry out the threat. The use and relevance of self-reported information in a threat assessment context must be very carefully evaluated because of the possibly deceptive motivations of the person providing it. Also discussed in this chapter are adolescents as unique offenders from a threat assessment perspective; their psychological, emotional, and brain development is unique and critical for the threat assessor to understand and to discern when evaluating their potential to make threats and carry them out. Key concepts integral to threat assessment also discussed in this chapter include evidence of escalation, injustice collecting, superficial indicators of normalcy, hatred and other emotions as motivators for carrying out threatened acts of violence, and the categories of reasons for the misinterpretation of dangerous and violent behavior by individuals close to or associated with the threatener.
Insider Threat Prevention, Detection, and Mitigation
Authors: Gelles Michael G.
Published: April 2021

This chapter looks at the history of insider threat from its roots in espionage to individuals who have access to people, information, material, and facilities and who could compromise the critical assets of an organization in the government or private sector. It examines behaviors associated with an insider threat from the decades of the past when things were driven by pen and paper, to the current world in which activity is deeply rooted in technology and where business is conducted virtually and globally. In addition to understanding the threat and the dimensions of a malicious complacent or ignorant insider, focus will be directed toward thinking about mitigating that threat, through the development of a holistic and risk-based insider threat program. The use of a framework that is focused on prevention, detection, and response is presented. Key issues addressed include policy and its relationship to setting behavioral expectations, communication and training, vetting employees and third parties, and defining potential risk indicators that reflect critical behaviors indicating a potential risk. The chapter defines and outlines how behavior can be captured in data and correlated using technology (user behavioral analytics) to proactively identify changes in behavioral patterns over time. Such technology identifies escalation and triages alerts to anomalous activity in the service of interrupting forward motion of a potential threat. Finally, the chapter highlights several statistics that define the change of insider threats today, and leading practices to help develop a strategy to mitigate the insider threat and focus on a holistic and risk-based approach to this threat management issue.
Effect of plasma screening on electron impact excitation and ionization of Fe16+ in a dense environment
Authors: Zeng Jiaolong , Li Yongjun , Yuan Jianmin
Published: April 2021

Electron impact excitation and ionization with atoms and ions within a dense plasma are fundamental microscopic processes that determine the ionization balance, physical properties (such as electron conductive opacity and thermal conductivity) and plasma formation and dynamics. While collision cross-sections and rates are well studied in dilute systems, similar investigations are scarce for dense plasmas under stellar interior conditions using an appropriate plasma-screening potential. Here we investigate the plasma-screening effect on the electron impact excitation and ionization cross-sections, effective collision strengths, and rate coefficients within plasmas under stellar interior conditions in a mass density range of 1–15.748 g cm−3 and a temperature range of 200–1000 eV. These investigations were carried out using our recently developed plasma-screening model, taking Fe16+ as an example. The results show that the cross-sections of the electron impact excitation are generally decreased, whereas they are always significantly increased for the collision ionization due to the plasma screening. In a plasma at a temperature of 200 eV and density of 15.748 g cm−3, the plasma screening causes a decrease in the excitation cross-section of 36 per cent for the dipole-allowed transition $2\mathrm{ s}^22\mathrm{ p}^6~^1\mathrm{ S}_0 \rightarrow 2\mathrm{ s}^22\mathrm{ p}^53\mathrm{ d}~^1\mathrm{ P}^o_1$ and of 50 per cent for the dipole-forbidden transition $2\mathrm{ s}^22\mathrm{ p}^6~^1\mathrm{ S}_0 \rightarrow 2\mathrm{ s}^22\mathrm{ p}^53\mathrm{ d}~^3\mathrm{ D}^o_1$. However, the collision ionization cross-section of a 2p electron from the ground level of Fe16+ is increased by 500 per cent and 100 per cent under an incident electron energy of 1500 and 10 000 eV, respectively. This results in the rate coefficient increasing by a factor of 18.5 at a temperature of 200 eV and density of 15.748 g cm−3.
Simultaneous estimation of segmented telescope phasing errors and non-common path aberrations from adaptive-optics-corrected images
Authors: Lamb Masen P , Correia Carlos , Sivanandam Suresh , Swanson Robin , Zavyalova Polina
Published: April 2021

We investigate the focal plane wavefront sensing technique, known as Phase Diversity, at the scientific focal plane of a segmented mirror telescope with an adaptive optics (AO) system. We specifically consider an optical system imaging a point source in the context of (i) an artificial source within the telescope structure and (ii) from AO-corrected images of a bright star. From our simulations, we reliably disentangle segmented telescope phasing errors from non-common path aberrations (NCPA) for both a theoretical source and on-sky, AO-corrected images where we have simulated the Keck/NIRC2 system. This quantification from on-sky images is appealing, as it is sensitive to the cumulative wavefront perturbations of the entire optical train; disentanglement of phasing errors and NCPA is therefore critical, where any potential correction to the primary mirror from an estimate must contain minimal NCPA contributions. Our estimates require a 1-min sequence of short-exposure, AO-corrected images; by exploiting a slight modification to the AO-loop, we find that 75 defocused images produce reliable estimates. We demonstrate a correction from our estimates to the primary and deformable mirror results in a wavefront error reduction of up to 67 per cent and 65 per cent for phasing errors and NCPA, respectively. If the segment phasing errors on the Keck primary are of the order of ∼130 nm RMS, we show we can improve the H-band Strehl ratio by up to 10 per cent by using our algorithm. We conclude our technique works well to estimate NCPA alone from on-sky images, suggesting it is a promising method for any AO-system.
Towards wide-scale adoption of open science practices: The role of open science communities
Authors: Armeni Kristijan , Brinkman Loek , Carlsson Rickard , Eerland Anita , Fijten Rianne , Fondberg Robin , Heininga Vera E , Heunis Stephan , Koh Wei Qi , Masselink Maurits , Moran Niall , Baoill Andrew Ó , Sarafoglou Alexandra , Schettino Antonio , Schwamm Hardy , Sjoerds Zsuzsika , Teperek Marta , van den Akker Olmo R , van't Veer Anna , Zurita-Milla Raul
Published: April 2021

Despite the increasing availability of Open Science (OS) infrastructure and the rise in policies to change behaviour, OS practices are not yet the norm. While pioneering researchers are developing OS practices, the majority sticks to status quo. To transition to common practice, we must engage a critical proportion of the academic community. In this transition, OS Communities (OSCs) play a key role. OSCs are bottom-up learning groups of scholars that discuss OS within and across disciplines. They make OS knowledge more accessible and facilitate communication among scholars and policymakers. Over the past two years, eleven OSCs were founded at several Dutch university cities. In other countries, similar OSCs are starting up. In this article, we discuss the pivotal role OSCs play in the large-scale transition to OS. We emphasize that, despite the grassroot character of OSCs, support from universities is critical for OSCs to be viable, effective, and sustainable.
Maternal Antibody Response, Neutralizing Potency, and Placental Antibody Transfer After Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection
Authors: Joseph Naima T. , Dude Carolynn M. , Verkerke Hans P. , Irby Les’Shon S. , Dunlop Anne L. , Patel Ravi M. , Easley Kirk A. , Smith Alicia K. , Stowell Sean R. , Jamieson Denise J. , Velu Vijayakumar , Badell Martina L.
Published: April 2021

OBJECTIVE:

To characterize maternal immune response after severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection during pregnancy and quantify the efficiency of transplacental antibody transfer.

METHODS:

We conducted a prospective cohort study of pregnant patients who tested positive for SARS CoV-2 infection at any point in pregnancy and collected paired maternal and cord blood samples at the time of delivery. An enzyme-linked immunosorbent assay (ELISA) and neutralization assays were performed to measure maternal plasma and cord blood concentrations and neutralizing potency of immunoglobulin (Ig)G, IgA, and IgM antibodies directed against the SARS-CoV-2 spike protein. Differences in concentrations according to symptomatic compared with asymptomatic infection and time from positive polymerase chain reaction (PCR) test result to delivery were analyzed using nonparametric tests of significance. The ratio of cord to maternal anti–receptor-binding domain IgG titers was analyzed to assess transplacental transfer efficiency.

RESULTS:

Thirty-two paired samples were analyzed. Detectable anti–receptor-binding domain IgG was detected in 100% (n=32) of maternal and 91% (n=29) of cord blood samples. Functional neutralizing antibody was present in 94% (n=30) of the maternal and 25% (n=8) of cord blood samples. Symptomatic infection was associated with a significant difference in median (interquartile range) maternal anti–receptor-binding domain IgG titers compared with asymptomatic infection (log 3.2 [3.5–2.4] vs log 2.7 [2.9–1.4], P=.03). Median (interquartile range) maternal anti–receptor-binding domain IgG titers were not significantly higher in patients who delivered more than 14 days after a positive PCR test result compared with those who delivered within 14 days (log 3.3 [3.5–2.4] vs log 2.67 [2.8–1.6], P=.05). Median (range) cord/maternal antibody ratio was 0.81 (0.67–0.88).

CONCLUSIONS:

These results demonstrate robust maternal neutralizing and anti–receptor-binding domain IgG response after SARS-CoV-2 infection, yet a lower-than-expected efficiency of transplacental antibody transfer and a significant reduction in neutralization between maternal blood and cord blood. Maternal infection does confer some degree of neonatal antibody protection, but the robustness and durability of protection require further study.
The Coronavirus (COVID-19) Effect on Public Sentiments Regarding Elective Plastic Surgery in the United States
Authors: Chen Jiaxi , Ray Edward C.
Published: April 2021

Background:

The SARS-CoV-2 coronavirus (COVID-19) has challenged the US's healthcare systems to adapt and innovate on multiple fronts. As the course of the COVID-19 pandemic changes, we explore the US public sentiments on resuming previously postponed elective plastic surgery procedures.

Methods:

A prospective national survey of one thousand US adults was conducted to study public perception of elective plastic surgery procedures during the COVID-19 pandemic. Binomial logarithmic multivariable regression modeling was employed to study the response data.

Results:

Nine hundred seventy-three participants were included in study. The majority (86.6%) believed elective plastic surgery should continue during the COVID-19 pandemic. Most (79.6%) would not delay obtaining plastic surgery more than 6 months. Participants expressed concerns of contracting COVID-19 at elective surgery centers (67.5%) or at hospitals (68.5%). Participants who reside in the Midwest (odds ratio [OR] 2.3, P < 0.05) and participants between the ages of 41 and 60 years old (OR 2.8, P < 0.03) were more likely to resume elective plastic surgery. Participants who had undergone a COVID-19 test (OR 0.13, P < 0.04), contracted the COVID-19 infection (OR 0.26, P < 0.03), or were older than 60 years (OR 0.41, P < 0.02) were less likely to resume elective plastic surgery.

Conclusion:

The majority of the US adult participants (1) agree with resuming elective plastic surgery services, (2) but harbor some concerns of contracting COVID-19 during their procedures, and (3) agree with the majority of safety protocols taken to prevent the spread of COVID-19.
Patient-reported Effects of Fedratinib, an Oral, Selective Inhibitor of Janus Kinase 2, on Myelofibrosis-related Symptoms and Health-related Quality of Life in the Randomized, Placebo-controlled, Phase III JAKARTA Trial
Authors: Mesa Ruben A. , Schaap Nicolaas , Vannucchi Alessandro M. , Kiladjian Jean-Jacques , Passamonti Francesco , Zweegman Sonja , Talpaz Moshe , Verstovsek Srdan , Rose Shelonitda , Abraham Pranav , Lord-Bessen Jennifer , Tang Derek , Guo Shien , Ye Xiaomei , Harrison Claire N.
Published: April 2021

Patients with myelofibrosis (MF) experience an array of symptoms that impair health-related quality of life (HRQoL). Fedratinib, an oral, selective Janus-kinase 2 (JAK2) inhibitor, was investigated in the randomized, placebo-controlled, phase III JAKARTA study in adult patients with intermediate- or high-risk JAK-inhibitor-naïve MF. The effect of fedratinib 400 mg/d on patient-reported MF symptoms and HRQoL in JAKARTA was assessed. Participants completed the modified Myelofibrosis Symptom Assessment Form (MFSAF v2.0), which evaluates 6 key MF symptoms (night sweats, early satiety, pruritus, pain under ribs on the left side, abdominal discomfort, bone/muscle pain). The modified MFSAF v2.0 was completed during the first 6 treatment cycles and at end of cycle 6 (EOC6). Symptom response was a ≥50% improvement from baseline in total symptom score (TSS). Overall HRQoL was assessed by EQ-5D-3L health utility index (HUI) score. The MFSAF-evaluable population comprised 91/96 patients randomized to fedratinib 400 mg and 85/96 patients randomized to placebo. Mean baseline TSS was 17.6 and 14.7 for fedratinib and placebo, respectively, and mean EQ-5D-3L HUI was 0.70 and 0.72. Fedratinib elicited statistically significant and clinically meaningful improvements in TSS from baseline versus placebo at all postbaseline visits. Symptom response rates at EOC6 were 40.4% with fedratinib and 8.6% with placebo (OR 7.0 [95% CI, 2.9-16.9]; P < 0.001), and a significantly higher proportion of fedratinib-treated patients achieved clinically meaningful improvement from baseline on the EQ-5D-3L HUI at EOC6 (23.2% versus 6.5%; P = 0.002). Fedratinib provided clinically meaningful improvements in MF symptoms and overall HRQoL versus placebo in patients with JAK-inhibitor-naïve MF.
A State of the Science on HIV Prevention Over 40 Years Among Black and Hispanic/Latinx Communities
Authors: Ramos S. Raquel , Nelson LaRon E. , Jones Sandra Gracia , Ni Zhao , Turpin Rodman E. , Portillo Carmen J.
Published: April 2021

We present a state of the science on HIV behavioral prevention interventions in Black and Hispanic/Latinx communities. The purpose of this article is threefold: (a) highlight the early documented underlying social and political barriers that constrained interventions to prevent new HIV infections; (b) address the structural inequities in HIV prevention and treatment; and (c) describe the need for increasing HIV multilevel prevention interventions that support greater HIV testing and pre-exposure prophylaxis uptake. To address HIV prevention, multilevel interventions that address individual, structural, and social level components have demonstrated more sustainable outcomes. Implications for research and clinical practice include (a) updating antiquated curricula in nursing, medicine, and public health that perpetuate racial, structural-level inequities and (b) increasing the pipeline for Black and Hispanic/Latinx persons to pursue research or clinical-focused doctorate degrees.
Spontaneous Retropharyngeal Emphysema
Authors: Long Christina M.
Published: April 2021

Spontaneous retropharyngeal emphysema (SRE) is a rare condition, occurring in the absence of trauma. Symptoms usually include acute-onset odynophagia and dyspnea. This is an interesting case of a young, healthy woman who presented to an emergency department with benign upper respiratory symptoms but took a drastic turn while in the waiting room after being triaged. The features and implications of SRE are discussed in this case, including emergent thoracic surgery consultation and additional testing.
Probiotics alleviate depressive behavior in chronic unpredictable mild stress rat models by remodeling intestinal flora
Authors: Li Qiufeng , Li Li , Niu Xueqin , Tang Chunling , Wang Huaizhi , Gao Jing , Hu Jian
Published: April 2021

Objective

To explore the effects of probiotics on depressive behavior in a chronic unpredictable mild stress (CUMS) rat model by remodeling intestinal flora.

Methods

Twenty-four male SD rats aged 6–8 weeks were randomly divided into four groups: control group, depression group (CUMS), depression+paroxetine group (Paro) and depression+probiotics group (Pro). Sucrose preference, open field and forced swimming tests were used to assess depression-like behavior in rats. ELISA was used to detect the levels of adrenocorticotropic hormone (ACTH), and corticosterone, norepinephrine and 5-hydroxytryptamine in rat serum. Real-time PCR was used to determine the changes of Lactobacillus, Bifidobacterium, Enterococcus faecalis and Escherichia coli in rat cecum.

Results

Compared with the control group, CUMS led to significant decreases of body weight, total traveled distance, duration in central area, immobility time, norepinephrine and 5-hydroxytryptamine contents in hippocampal tissues, as well as Lactobacillus and Bifidobacterium in the cecum. It also resulted in marked increases of the contents of E. faecalis and E. coli in the cecum, ACTH and corticosterone contents in the serum of rats. Paroxetine and probiotic treatment each diminished or prevented these changes.

Conclusion

By remodeling intestinal flora, probiotics can reduce the CUMS-induced depressive behavior of rats, increase the levels of norepinephrine and 5-hydroxytryptamine, and inhibit the expression of ACTH and corticosterone. Significantly, the effect of both paroxetine and probiotic on microorganisms is similar.
Effective in vitro inactivation of SARS-CoV-2 by commercially available mouthwashes
Authors: Davies Katherine , Buczkowski Hubert , Welch Stephen R. , Green Nicole , Mawer Damian , Woodford Neil , Roberts Allen D. G. , Nixon Peter J. , Seymour David W. , Killip Marian J.
Published: April 2021

Infectious SARS-CoV-2 can be recovered from the oral cavities and saliva of COVID-19 patients with potential implications for disease transmission. Reducing viral load in patient saliva using antiviral mouthwashes may therefore have a role as a control measure in limiting virus spread, particularly in dental settings. Here, the efficacy of SARS-CoV-2 inactivation by seven commercially available mouthwashes with a range of active ingredients were evaluated in vitro. We demonstrate ≥4.1 to ≥5.5 log10 reduction in SARS-CoV-2 titre following a 1 min treatment with commercially available mouthwashes containing 0.01–0.02 % stabilised hypochlorous acid or 0.58 % povidone iodine, and non-specialist mouthwashes with both alcohol-based and alcohol-free formulations designed for home use. In contrast, products containing 1.5 % hydrogen peroxide or 0.2 % chlorhexidine gluconate were ineffective against SARS-CoV-2 in these tests. This study contributes to the growing body of evidence surrounding virucidal efficacy of mouthwashes/oral rinses against SARS-CoV-2, and has important applications in reducing risk associated with aerosol generating procedures in dentistry and potentially for infection control more widely.
The herbal combination of Sugarcane, Black Myrobalan, and mastic as a supplementary treatment for COVID-19: a randomized clinical trial
Authors: Shiri Alireza Hashemi , Raiatdoost Esmaeil , Afkhami Hamid , Ravanshad Ruhollah , Hosseini Seyed Ehsan , Kalani Navid , Raoufi Rahim
Published: April 2021

Background

Given the COVID-19 pandemic’s, researchers are beseeched for effective treatments. Herbal medicine is also queried for potential supplementary treatments for COVID-19. We aimed to evaluate the effects of Sugarcane, Black Myrobalan, and Mastic herbal medications for COVID-19 patients.

Methods

This was a double-blinded randomized clinical trial study conducted over three months from May to July 2020 in patients admitted with a diagnosis of COVID-19 in Peymaniyeh Hospital in Jahrom, Iran. The intervention group received the treatment protocol approved by the Ministry of Health of Iran during the period of hospitalization and the herbal supplement obtained from the combination of black myrobalan and mastic and sugarcane, twice a day (3g of herbal supplements). All patients were compared in terms of demographic variables, vital signs, clinical and laboratory variables.

Results

72 patients with COVID-19, divided into intervention (n=37) and control (n=35) groups. intervention and control groups had not any significant difference in terms of baseline characteristics. The time-to-event analysis revealed a significant difference in 4 symptoms of cough, fever, dyspnea, and myalgia (P<0.05). The Control group had a significantly lower decrease in C-reactive protein during 7 days (P<0.05). Patients in the herbal supplement group were hospitalized for 4.12 days and in the control group were hospitalized for 8.37 days (P=0.001). ICU admission and death only happened in 3 (8.6%) patients of the control group.

Conclusion

While advanced studies with more sample size are needed; the proposed combination seems to be effective in the symptom treatment and reducing the length of hospitalization.
A Novel Family of RNA-Binding Proteins Regulate Polysaccharide Metabolism inBacteroides thetaiotaomicron
Authors: Adams Amanda N.D. , Azam Muhammad S. , Costliow Zachary A. , Ma Xiangqian , Degnan Patrick H. , Vanderpool Carin K.
Published: April 2021

Human gut microbiome composition is constantly changing, and diet is a major driver of these changes. Gut microbial species that persist in mammalian hosts for long periods of time must possess mechanisms for sensing and adapting to nutrient shifts to avoid being outcompeted. Global regulatory mechanisms mediated by RNA-binding proteins (RBPs) that govern responses to nutrient shifts have been characterized in Proteobacteria and Firmicutes but remain undiscovered in the Bacteroidetes. Here we report the identification of RBPs that are broadly distributed across the Bacteroidetes, with many genomes encoding multiple copies. Genes encoding these RBPs are highly expressed in manyBacteroidesspecies. A purified RBP, RbpB, fromBacteroides thetaiotaomicronbinds to single-stranded RNAin vitrowith an affinity similar to other characterized regulatory RBPs.B. thetaiotaomicronmutants lacking RBPs show dramatic shifts in expression of polysaccharide utilization and capsular polysaccharide loci, suggesting that these RBPs may act as global regulators of polysaccharide metabolism. AB. thetaiotaomicronΔrbpBmutant shows a growth defect on dietary sugars belonging to the raffinose family of oligosaccharides (RFOs). The ΔrbpBmutant had reduced expression ofBT1871, encoding a predicted RFO-degrading melibiase, compared to the wild-type strain. Mutation ofBT1871confirmed that the enzyme it encodes is essential for growth on melibiose and promotes growth on the RFOs raffinose and stachyose. Our data reveal that RbpB is required for optimal expression ofBT1871and other polysaccharide-related genes, suggesting that we have identified an important new family of global regulatory proteins in the Bacteroidetes.

Importance

The human colon houses hundreds of bacterial species, including many belonging to the genusBacteroides,that aid in breaking down our food to keep us healthy.Bacteroideshave many genes responsible for breaking down different dietary carbohydrates and complex regulatory mechanisms ensure that specific genes are only expressed when the right carbohydrates are available. In this study, we discovered thatBacteroidesuse a family of RNA-binding proteins as global regulators to coordinate expression of carbohydrate utilization genes. The ability to turn different carbohydrate utilization genes on and off in response to changing nutrient conditions is critical forBacteroidesto live successfully in the gut, and thus the new regulators we have identified may be important for life in the host.
Nucleic acid delivery of immune-focused SARS-CoV-2 nanoparticles drive rapid and potent immunogenicity capable of single-dose protection
Authors: Konrath Kylie M. , Liaw Kevin , Wu Yuanhan , Zhu Xizhou , Walker Susanne N. , Xu Ziyang , Schultheis Katherine , Chokkalingam Neethu , Du Jianqiu , Tursi Nicholas J. , Moore Alan , Purwar Mansi , Reuschel Emma L. , Frase Drew , Sullivan Matthew , Maricic Igor , Andrade Viviane M. , Iffland Christel , Broderick Kate E. , Humeau Laurent M. P. F. , Smith Trevor R.F. , Pallesen Jesper , Weiner David B. , Kulp Daniel W.
Published: April 2021

Antibodies from SARS-CoV-2 vaccines may target epitopes which reduce durability or increase the potential for escape from vaccine-induced immunity. Using a novel synthetic vaccinology pipeline, we developed rationally immune focused SARS-CoV-2 Spike-based vaccines. N-linked glycans can be employed to alter antibody responses to infection and vaccines. Utilizing computational modeling and comprehensive in vitro screening, we incorporated glycans into the Spike Receptor-Binding Domain (RBD) and assessed antigenic profiles. We developed glycan coated RBD immunogens and engineered seven multivalent configurations. Advanced DNA delivery of engineered nanoparticle vaccines rapidly elicited potent neutralizing antibodies in guinea pigs, hamsters and multiple mouse models, including human ACE2 and human B cell repertoire transgenics. RBD nanoparticles encoding wild-type and the P.1 SARS-CoV-2 variant induced high levels of cross-neutralizing antibodies. Single, low dose immunization protected against a lethal SARS-CoV-2 challenge. Single-dose coronavirus vaccines via DNA-launched nanoparticles provide a platform for rapid clinical translation of novel, potent coronavirus vaccines.
Mechanistic Insights on ATP’s role as Hydrotrope
Authors: Sarkar Susmita , Mondal Jagannath
Published: April 2021

Hydrotropes are small amphiphilic molecules which help in solubilizing hydrophobic entities in aqueous medium. Recent experimental investigation has provided convincing evidences that, adenosine triphosphate (ATP), besides being anenergy currency of cell, also can act ashydrotropeto inhibit the formation of protein condensates. In this work, we have designed computer simulations of prototypical macromolecules in aqueous ATP solution to dissect the molecular mechanism underlying ATP’s newly discovered role as a hydrotrope. The simulation demonstrates that ATP can unfold a single-chain of hydrophobic macromolecule as well as can disrupt the aggregation process of a hydrophobic assembly. Moreover, the introduction of charges in the macromolecule is found to reinforce ATP’s disaggregation effects in a synergistic fashion, a behaviour reminiscent of recent experimental observation of pronounced hydrotropic action of ATP in intrinsically disordered proteins. A molecular analysis indicates that this new-found ability of ATP are ingrained in its propensity of preferential binding to the polymer surface, which gets fortified in presence of charges. The investigation also renders evidence that the key to the ATP’s superior hydrotropic role over chemical hydrotrope (Sodium xylene sulfonate, NaXS) may lie in its inherent self-aggregation propensity. Overall, via employing a bottom-up approach the current investigation provides fresh mechanistic insights into the dual solubilizing and denaturing abilities of ATP.
Distortion Discovery: A Framework to Model, Spot and Explain Tumor Heterogeneity and Mitigate its Negative Impact on Cancer Risk Assessment
Authors: Elmansy Dalia
Published: April 2021

In a complex system of inter-genome interactions, false negatives remain an overwhelming problem when using omics data for disease risk prediction. This is especially clear when dealing with complex diseases like cancer in which the infiltration of stromal and immune cells into the tumor tissue can affect the degree of its tumor purity and hence its cancer signal. Previous work was done to estimate the degree of cancer purity in a tissue. In this work, we introduce a data and biomarker selection independent, information theoretic, approach to tackle this problem. We model distortion as a source of false negatives and introduce a mechanism to detect and remove its impact on the accuracy of disease risk prediction.
The YΦ Motif Defines the Structure-Activity Relationships of Human 20S Proteasome Activators
Authors: Opoku-Nsiah Kwadwo A. , de la Pena Andres H. , Williams Sarah K. , Chopra Nikita , Sali Andrej , Lander Gabriel C. , Gestwicki Jason E.
Published: April 2021

The 20S proteasome (20S) facilitates turnover of most eukaryotic proteins. Substrate entry into the 20S first requires opening of gating loops through binding of HbYX motifs that are present at the C-termini of certain proteasome activators (PAs). The HbYX motif has been predominantly characterized in the archaeal 20S, whereas little is known about the sequence preferences of the human 20S (h20S). Here, we synthesized and screened ∼120 HbYX-like peptides, revealing unexpected differences from the archaeal system and defining theh20S recognition sequence as the Y-F/Y (YΦ) motif. To gain further insight, we created a functional chimera of the optimized sequence, NLSYYT, fused to the model activator, PA26E102A.A cryo-EM structure of PA26E102A-h20S identified key interactions, including non-canonical contacts and gate-opening mechanisms. Finally, we demonstrated that the YΦ sequence preferences are tuned by valency, allowing multivalent PAs to sample greater sequence space. These results expand the model for termini-mediated gating and provide a template for the design ofh20S activators.
Micrarchaeota are covered by a proteinaceous S-Layer
Authors: Gfrerer Sabrina , Winkler Dennis , Ducassou Julia Novion , Couté Yohann , Rachel Reinhard , Gescher Johannes
Published: April 2021

In previous publications, it was hypothesized that Micrarchaeota cells are covered by two individual membrane systems. This study proofs that at least the recently cultivated “CandidatusMicrarchaeum harzensis A_DKE” possesses an S-layer covering its cytoplasmic membrane. The potential S-layer protein was found to be among the proteins with the highest abundance in A_DKE andin silicocharacterization of its primary structure indicated homologies to other known S-layer proteins. Homologs of this protein were found in other Micrarchaeota genomes, which raises the question, whether the ability to form an S-layer is a common trait within this phylum. The S-layer protein seems to be glycosylated and the Micrarchaeum expresses genes for N-glycosylation under cultivation conditions, despite not being able to synthesize carbohydrates. Electron micrographs of freeze-etched samples of a previously described co-culture, containing Micrarchaeum A_DKE and a Thermoplasmatales member as its host organism, verified the hypothesis of an S-layer on the surface of A_DKE. Both organisms are clearly distinguishable by cell size, shape and surface structure.
SenU-PTM: a novel phrase-based topic model for short-text topic discovery by exploiting word embeddings
Authors: Lu Heng-Yang , Zhang Yi , Du Yuntao
Published: April 2021

Purpose

Topic model has been widely applied to discover important information from a vast amount of unstructured data. Traditional long-text topic models such as Latent Dirichlet Allocation may suffer from the sparsity problem when dealing with short texts, which mostly come from the Web. These models also exist the readability problem when displaying the discovered topics. The purpose of this paper is to propose a novel model called the Sense Unit based Phrase Topic Model (SenU-PTM) for both the sparsity and readability problems.

Design/methodology/approach

SenU-PTM is a novel phrase-based short-text topic model under a two-phase framework. The first phase introduces a phrase-generation algorithm by exploiting word embeddings, which aims to generate phrases with the original corpus. The second phase introduces a new concept of sense unit, which consists of a set of semantically similar tokens for modeling topics with token vectors generated in the first phase. Finally, SenU-PTM infers topics based on the above two phases.

Findings

Experimental results on two real-world and publicly available datasets show the effectiveness of SenU-PTM from the perspectives of topical quality and document characterization. It reveals that modeling topics on sense units can solve the sparsity of short texts and improve the readability of topics at the same time.

Originality/value

The originality of SenU-PTM lies in the new procedure of modeling topics on the proposed sense units with word embeddings for short-text topic discovery.
Customer involvement in the new process innovation: antecedents, mediation and performance
Authors: Chang Yuan-Chieh , Chiu Wen-Hong , Wang Jian-Hang , Teng Min-Jun
Published: April 2021

Purpose

The paper proposes customer involvement can be considered an organization-level construct of knowledge creation in the new process development. Specifically, the paper evaluates three distinct organizational practices as knowledge antecedents – competitor orientation, social network and internal coordination – that can facilitate the adoption of customer involvement in the process innovation development.

Design/methodology/approach

The paper empirically tests this theory for 2,000 firms that are stratification sampled from a population of 33,844 Taiwanese firms, and a data set of 170 valid questionnaires is collected. The questionnaire was mainly modified from a Kim and Kim (2010) measure which was designed based on the 3rd edition of the Oslo Manual OECD/Eurostat 2005. The concept of customer involvement in new service development proposed by Alam (2002) was also applied to the questionnaire.

Findings

(1) The antecedents of customer involvement, which include competitor orientation, external social networks and internal coordination, function as a determinant to nourish customer involvement. (2) Customer involvement significantly positively mediates the relationship between knowledge antecedents and new process performance. (3) Customer involvement is a crucial knowledge creation for improving the new process innovation performance in manufacturing firms.

Originality/value

Two basic tenets of theory building serve as the foundation of the model in this paper. First, research on customer involvement is augmented by showing that customer involvement can emerge as a shared perception among organizational members that is distinct from individual-level involvement. Moreover, customer involvement in process innovation can help firms manage their knowledge and further enhance firm performance. Second, the knowledge management model provides a key lens through which researchers can take a process-oriented view that focuses on customer involvement as a unique capability that firms can develop in process innovation.