bluuebunny/crossref_metadata_2025 huggingface dataset:
Intravenous levothyroxine stewardship program at a tertiary academic medical center
Authors: Marino Kaylee K , Crowley Kaitlin E , Tran Lena K , Sylvia Daniel , Dell’Orfano Heather , DeGrado Jeremy R , Szumita Paul M
Published: April 2021

Purpose

Based on the pharmacokinetic profile of levothyroxine, a 3-day hold guideline for adult patients ordered for intravenous (IV) levothyroxine was implemented at a tertiary academic medical center. The purpose of this study was to evaluate the impact of the implementation of an IV levothyroxine hold guideline.

Methods

This single-center, retrospective analysis identified patients ordered for IV levothyroxine during a 13-week period before and after implementation of the guideline. The primary outcome was guideline adherence, defined as full implementation of the 3-day hold. Secondary outcomes included the number of IV levothyroxine administrations avoided in the post-guideline group, extrapolated yearly cost avoidance (EYCA) after guideline implementation, reasons for guideline non-adherence, and number of safety reports involving IV levothyroxine.

Results

A total of 166 and 134 patients met inclusion criteria for the pre- and post-guideline groups, respectively. Guideline adherence was observed in 94 (70.1%) patients, resulting in 276 vials saved in the 13-week post-guideline period, which translated to an EYCA of $139,877. Forty orders (29.9%) were non-adherent to the guideline, with the most common reason stated as nil per os (NPO). No difference in safety outcomes was seen between the pre- and post-guideline groups, as evidenced by 1 safety report in each group.

Conclusion

We observed a high rate of adherence to an IV levothyroxine hold guideline. This was associated with a substantial cost savings over the study period with no increase in reported safety events. To our knowledge, this is the first published report of an inpatient IV levothyroxine 3-day hold guideline.
Revisiting the risk of undesired appeal in investment treaty arbitration: is deference to the tribunal’s award still less likely in the ICSID context?
Authors: Marcopoulos Alexander J
Published: April 2021

Although they are generally not subject to appeal the way court decisions typically are, investor-State arbitration awards can be reviewed—and potentially set aside—in a number of ways and on various bases. In this respect, investor-State arbitration under the auspices of ICSID is notable in that it provides a self-contained system for the review of arbitral awards by ICSID-appointed ad hoc committees. In the period 2000–2010, this feature of the ICSID system attracted criticism as ad hoc committees appeared to be overreaching in their review of arbitral awards, exercising less deference to the tribunal’s decisions than what would be expected given the narrow bases for setting aside an award under the ICSID Convention. This article revisits the issue 10 years later, exploring whether ICSID practice has evolved in these areas and whether there remains a greater risk of unexpected de novo review by ICSID ad hoc committees. Looking at recent ICSID annulment decisions as well as the case law of arbitration-friendly jurisdictions, the article concludes that although the ICSID ad hoc committees have recently shown more restraint, they continue to interfere more with the tribunal’s reasoning and decisions than many courts exercising the same function.
DeepImmuno: deep learning-empowered prediction and generation of immunogenic peptides for T-cell immunity
Authors: Li Guangyuan , Iyer Balaji , Prasath V B Surya , Ni Yizhao , Salomonis Nathan
Published: April 2021

Cytolytic T-cells play an essential role in the adaptive immune system by seeking out, binding and killing cells that present foreign antigens on their surface. An improved understanding of T-cell immunity will greatly aid in the development of new cancer immunotherapies and vaccines for life-threatening pathogens. Central to the design of such targeted therapies are computational methods to predict non-native peptides to elicit a T-cell response, however, we currently lack accurate immunogenicity inference methods. Another challenge is the ability to accurately simulate immunogenic peptides for specific human leukocyte antigen alleles, for both synthetic biological applications, and to augment real training datasets. Here, we propose a beta-binomial distribution approach to derive peptide immunogenic potential from sequence alone. We conducted systematic benchmarking of five traditional machine learning (ElasticNet, K-nearest neighbors, support vector machine, Random Forest and AdaBoost) and three deep learning models (convolutional neural network (CNN), Residual Net and graph neural network) using three independent prior validated immunogenic peptide collections (dengue virus, cancer neoantigen and SARS-CoV-2). We chose the CNN as the best prediction model, based on its adaptivity for small and large datasets and performance relative to existing methods. In addition to outperforming two highly used immunogenicity prediction algorithms, DeepImmuno-CNN correctly predicts which residues are most important for T-cell antigen recognition and predicts novel impacts of SARS-CoV-2 variants. Our independent generative adversarial network (GAN) approach, DeepImmuno-GAN, was further able to accurately simulate immunogenic peptides with physicochemical properties and immunogenicity predictions similar to that of real antigens. We provide DeepImmuno-CNN as source code and an easy-to-use web interface.
A case report of cobalt cardiomyopathy leading to electric storm and cardiogenic shock: the importance of the orthopaedic background in patients with heart failure of unknown aetiology
Authors: Castrillo Bustamante Cristina , Canteli Álvarez Ángela , Burgos Palacios Virginia , Sarralde Aguayo Jose Aurelio , Serrano Lozano David , Arana Achaga Xabier , Nuñez Rodríguez Álvaro , Cobo Belaustegui Manuel
Published: April 2021

Background 

The first series of cobalt cardiomyopathy was described in the 60s in relation to the abuse of a cobalt containing beer. Since then, millions of metal hip arthroplasties have been performed and a small number of cobalt cardiomyopathies related to metal prosthesis have been reported.

Case summary 

We report a case of a 48-year-old man who developed a severe non-dilated restrictive cardiomyopathy in the setting of a systemic metallosis following several hip arthroplasties. The diagnosis was suspected by exclusion of other more common causes for restrictive cardiomyopathies and confirmed by the levels of cobalt and chromium in the serum and the endomyocardial biopsy performance that showed metal deposits in myocardial tissue. Despite the removal of the metal prosthesis and a significant decrease in serum metal levels, he suffered cardiogenic shock (CS) and electric storm that required emergency mechanical circulatory support as a bridge to heart transplant.

Discussion 

Cobalt cardiomyopathy is a rare condition that has been observed in patients who develop cobalt toxicity after metal hip arthroplasty. The condition may improve after diagnosis and removal of the prosthesis or get worse and progress to end-stage heart failure or CS. The concern about the metal toxicity associated with metal hip prosthesis has increased in the last few years. Orthopaedic surgeons and cardiologists should be aware of this severe complication that is probably under diagnosed.
Vascular reconstruction of segmental intestinal grafts using autologous internal iliac vessels
Authors: Wu Guosheng , Wu Yinglun , Wang Mian , Zhang Wentong , Liu Chaoxu , Liang Tingbo
Published: April 2021

Background

The aim of this study was to assess whether the autologous internal iliac artery and vein could be used as an interpositional graft for vascular reconstruction in segmental intestinal allografts and autografts.

Methods

Thirty-four intestinal transplants (19 living-related allografts and 15 autografts) were conducted in our programs between January 2011 and January 2019. Patient characteristics, type of vascular reconstruction, and post-operative complications were reviewed.

Results

There were 20 males and 14 females with a median age of 35 years. Of 34 grafts, 22 (64.7%) (11 allografts and 11 autografts) were revascularized using the autologous internal iliac artery and vein for reconstruction. Vascular reconstruction on the back table took 21 ± 6 min to complete. Both total operative time and cold ischemia time tended to be longer in the vascular-reconstruction group than in the direct-anastomosis group (530 ± 226 vs 440 ± 116 and 159 ± 49 vs 125 ± 66 min, respectively), but these differences were not significant. The incidence of vascular thrombosis tended to be higher in the direct-anastomosis group than in the vascular-reconstruction group (16.7% vs 0%, P = 0.118). At a median follow-up of 36.9 months, no stenosis or pseudoaneurysms developed. In 19 allografts, acute rejection occurred in 4 (21.1%) and chronic rejection occurred in 1 (5.2%).

Conclusions

Our results indicate that the use of an autologous internal iliac interposition graft greatly facilitates intestinal graft implantation and minimizes the risk of vascular complications.
The use of two-sample methods for Mendelian randomization analyses on single large datasets
Authors: Minelli Cosetta , Del Greco M. Fabiola , van der Plaat Diana A , Bowden Jack , Sheehan Nuala A , Thompson John
Published: April 2021

Background

With genome-wide association data for many exposures and outcomes now available from large biobanks, one-sample Mendelian randomization (MR) is increasingly used to investigate causal relationships. Many robust MR methods are available to address pleiotropy, but these assume independence between the gene-exposure and gene-outcome association estimates. Unlike in two-sample MR, in one-sample MR the two estimates are obtained from the same individuals, and the assumption of independence does not hold in the presence of confounding.

Methods

With simulations mimicking a typical study in UK Biobank, we assessed the performance, in terms of bias and precision of the MR estimate, of the fixed-effect and (multiplicative) random-effects meta-analysis method, weighted median estimator, weighted mode estimator and MR-Egger regression, used in both one-sample and two-sample data. We considered scenarios differing by the: presence/absence of a true causal effect; amount of confounding; and presence and type of pleiotropy (none, balanced or directional).

Results

Even in the presence of substantial correlation due to confounding, all two-sample methods used in one-sample MR performed similarly to when used in two-sample MR, except for MR-Egger which resulted in bias reflecting direction and magnitude of the confounding. Such bias was much reduced in the presence of very high variability in instrument strength across variants (IGX2 of 97%).

Conclusions

Two-sample MR methods can be safely used for one-sample MR performed within large biobanks, expect for MR-Egger. MR-Egger is not recommended for one-sample MR unless the correlation between the gene-exposure and gene-outcome estimates due to confounding can be kept low, or the variability in instrument strength is very high.
Animal Models of COVID-19 II. Comparative Immunology
Authors: Veenhuis Rebecca T , Zeiss Caroline J
Published: April 2021

Developing strong animal models is essential for furthering our understanding of how the immune system functions in response to Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection. The alarming speed at which SARS-CoV-2 has spread, and the high mortality rate of severe Coronavirus Disease 2019 (COVID-19), has required both basic science and clinical research to move at an unprecedented pace. Models previously developed to study the immune response against SARS-CoV have been rapidly deployed to now study SARS-CoV-2. To date, both small and large animal models are remarkably consistent when infected with SARS-CoV-2; however, certain models have proven more useful when answering specific immunological questions than others. Small animal models, such as Syrian hamsters, ferrets, and mice carrying the hACE2 transgene, appear to reliably recapitulate the initial cytokine surge seen in COVID-19 as well as show significant innate and adaptive cell infiltration in to the lung early in infection. Additionally, these models develop strong antibody responses to the virus, are protected from reinfection, and genetically modified versions exist that can be used to ask specific immunological questions. Large animal models such as rhesus and cynomologus macaques and African green monkeys are critical to understanding how the immune system responds to SARS-CoV-2 infection because they are considered to be the most similar to humans. These models are considered the gold standard for assessing vaccine efficacy and protection, and recapitulate the initial cytokine surge, immune cell infiltration into the lung, certain aspects of thrombosis, and the antibody and T-cell response to the virus. In this review, we discuss both small and large animal model studies previously used in SARS-CoV-2 research that may be useful in elucidating the immunological contributions to hallmark syndromes observed with COVID-19.
Resistance to Fipronil in the Common Bed Bug (Hemiptera: Cimicidae)
Authors: González-Morales María A , DeVries Zachary , Sierras Angela , Santangelo Richard G , Kakumanu Madhavi L , Schal Coby
Published: April 2021

Cimex lectularius L. populations have been documented worldwide to be resistant to pyrethroids and neonicotinoids, insecticides that have been widely used to control bed bugs. There is an urgent need to discover new active ingredients with different modes of action to control bed bug populations. Fipronil, a phenylpyrazole that targets the GABA receptor, has been shown to be highly effective on bed bugs. However, because fipronil shares the same target site with dieldrin, we investigated the potential of fipronil resistance in bed bugs. Resistance ratios in eight North American populations and one European population ranged from 1.4- to >985-fold, with highly resistant populations on both continents. We evaluated metabolic resistance mechanisms mediated by cytochrome P450s, esterases, carboxylesterases, and glutathione S-transferases using synergists and a combination of synergists. All four detoxification enzyme classes play significant but variable roles in bed bug resistance to fipronil. Suppression of P450s and esterases with synergists eliminated resistance to fipronil in highly resistant bed bugs. Target-site insensitivity was evaluated by sequencing a fragment of the Rdl gene to detect the A302S mutation, known to confer resistance to dieldrin and fipronil in other species. All nine populations were homozygous for the wild-type genotype (susceptible phenotype). Highly resistant populations were also highly resistant to deltamethrin, suggesting that metabolic enzymes that are responsible for pyrethroid detoxification might also metabolize fipronil. It is imperative to understand the origins of fipronil resistance in the development or adoption of new active ingredients and implementation of integrated pest management programs.
SARS-CoV-2 reinfections among hospital staff in the greater Paris area
Authors: Davido Benjamin , De Truchis Pierre , Lawrence Christine , Annane Djillali , Domart-Rancon Martine , Gault Elyanne , Saleh-Mghir Azzam , Delarocque-Astagneau Elisabeth , Gautier Sylvain
Published: April 2021

After 1 year, among 236 hospital staff members (HSMs) tested positive for SARS-CoV-2, we observed five cases of suspected reinfection in our teaching hospital in France. No probable reinfection was retained considering PCR Cycle Threshold and clinical context. Focus should concern COVID-free HSMs still not vaccinated rather than the ones previously infected.
The nature of the Eastern Extent in the outer halo of M31
Authors: Preston Janet , Collins Michelle , Rich R Michael , Ibata Rodrigo , Martin Nicolas F , Fardal Mark
Published: April 2021

We present the first comprehensive spectroscopic study of the Andromeda galaxy’s Eastern Extent. This ∼4° long filamentary structure, located 70–90 kpc from the centre of M31, lies perpendicular to Andromeda’s minor axis and the Giant Stellar Stream and overlaps Stream C. In this work, we explore the properties of the Eastern Extent to look for possible connections between it, the Giant Stellar Stream and Stream C. We present the kinematics and photometry for ∼50 red giant branch stars in seven fields along the Eastern Extent. We measure the systemic velocities for these fields and find them to be −368  km s−1 ≲ $\textit {v}$ ≲ −331  km s−1, with a slight velocity gradient of −0.51 ± 0.21  km s−1 kpc−1 towards the Giant Stellar Stream. We derive the photometric metallicities for stars in the Eastern Extent, finding them to be metal-poor with values of −1.0 ≲ [Fe/H]phot ≲ −0.7 with an 〈[Fe/H]phot〉 ∼ −0.9. We find consistent properties for the Eastern Extent, Stream B and one of the substructures in Stream C, Stream Cr, plausibly linking these features. Stream Cp and its associated globular cluster, EC4, have distinctly different properties indicative of a separate structure. When we compare the properties of the Eastern Extent to those of the Giant Stellar Stream, we find them to be consistent, albeit slightly more metal-poor, such that the Eastern Extent could plausibly comprise stars stripped from the progenitor of the Giant Stellar Stream.
Chemogenetics: Beyond Lesions and Electrodes
Authors: Poth Kelly M , Texakalidis Pavlos , Boulis Nicholas M
Published: April 2021

The field of chemogenetics has rapidly expanded over the last decade, and engineered receptors are currently utilized in the lab to better understand molecular interactions in the nervous system. We propose that chemogenetic receptors can be used for far more than investigational purposes. The potential benefit of adding chemogenetic neuromodulation to the current neurosurgical toolkit is substantial. There are several conditions currently treated surgically, electrically, and pharmacologically in clinic, and this review highlights how chemogenetic neuromodulation could improve patient outcomes over current neurosurgical techniques. We aim to emphasize the need to take these techniques from bench to bedside.
Strategies for Disseminating and Implementing COVID-19 Vaccines in Rural Areas
Authors: Prusaczyk Beth
Published: April 2021

The United States has well-documented rural–urban health disparities, and it is imperative that these are not exacerbated by an inefficient rollout of coronavirus disease 2019 (COVID-19) vaccines to rural areas. In addition to the preexisting barriers to delivering and receiving health care in rural areas, such as high patient:provider ratios and long geographic distances between patients and providers, rural residents are significantly more likely to say they have no intention of receiving a COVID-19 vaccine, compared with urban residents. To overcome these barriers and ensure that rural residents receive the vaccine, officials and communities should look to previous research on how to communicate vaccine information and implement successful vaccination programs in rural areas for guidance and concrete strategies to use in their local efforts.

Graphical Abstract
Lymphopenia Is Associated With Poor Outcomes of Patients With Community-Acquired Pneumonia and Sepsis
Authors: Cilloniz Catia , Peroni Héctor José , Gabarrús Albert , García-Vidal Carolina , Pericàs Juan M , Bermejo-Martin Jesús , Torres Antoni
Published: April 2021

Background

Lymphopenia is a marker of poor prognosis in patients with community-acquired pneumonia (CAP), yet its impact on outcomes in patients with CAP and sepsis remains unknown. We aim to investigate the impact of lymphopenia on outcomes, risk of intensive care unit (ICU) admission, and mortality in CAP patients with sepsis.

Methods

This was a retrospective, observational study of prospectively collected data from an 800-bed tertiary teaching hospital (2005–2019).

Results

Of the 2203 patients with CAP and sepsis, 1347 (61%) did not have lymphopenia, while 856 (39%) did. When compared with the nonlymphopenic group, patients with sepsis and lymphopenia more frequently required ICU admission (P = .001), had a longer hospital length of stay (P ˂ .001), and presented with a higher rate of in-hospital (P ˂ .001) and 30-day mortality (P = .001). Multivariable analysis showed that C-reactive protein ≥15 mg/dL, lymphopenia, pleural effusion, and acute respiratory distress syndrome within 24 hours of admission were risk factors for ICU admission; age ≥80 years was independently associated with decreased ICU admission. In addition, age ≥80 years, chronic renal disease, chronic neurologic disease, being a nursing home resident, lymphopenia, and pleural effusion were independently associated with increased 30-day mortality, whereas pneumococcal vaccination, diabetes mellitus, and fever were independently associated with reduced 30-day mortality.

Conclusions

Lymphopenia was independently associated with risk of ICU admission and higher in-hospital and 30-day mortality in patients with CAP and sepsis. Early identification of lymphopenia could help identify septic patients with CAP who require or will shortly require critical care.
What Factors Shape the Substantive Representation of Lesbians, Gays and Bisexuals in Parliament? Testing the Impact of Minority Membership, Political Values and Awareness
Authors: Bönisch Lea Ewe
Published: April 2021

The importance of minority parliamentarians for substantive representation is widely acknowledged, but little research exists on further explanations. By studying the substantive representation of the interests of lesbians, gays, and bisexuals (LGBs), this study analyses why parliamentarians stand in for interests of minorities with an invisible characteristic. A quantitative content analysis of more than 950,000 British and Irish parliamentary questions provides the basis for the analysis (2002–2017). The study considers parliamentarians’ characteristics as explanatory factors. The results indicate that parliamentary presence is vital for LGBs. However, the most active parliamentarians are non-minority members: political values and awareness are also at play. Moreover, there are differences between the two parliaments.
Perspectives on Police Specialization in Art Theft Investigations
Authors: Runhovde Siv Rebekka
Published: April 2021

The concept of specialization is accepted in many fields of policing, yet most national law enforcement authorities do not regard art and cultural heritage crime as one deserving of specialist attention. Drawing on interviews with Norwegian and international stakeholders, the analysis identifies what separates art theft investigations from other investigations and when specialist knowledge becomes necessary. Findings reveal compelling arguments for specialization and establishing dedicated art crime units. Respondents voiced clear concerns regarding the level of prioritization and knowledge of art theft in the police; yet, the analysis cannot conclude that art theft investigations in Norway have necessarily suffered from an absence of specialization. To justify the establishment of a dedicated unit, first there is a need to develop consistent crime recording practices, create a national database for stolen or missing art and conduct comprehensive and systematic research to determine what characterizes the crimes and the current criminal justice response.
Translating evidence-based behavioral weight loss into a multi-level, community intervention within a community-based participatory research framework: the Wellness Engagement (WE) Project
Authors: LaRose Jessica Gokee , Lanoye Autumn , Ferrell Dwala , Lu Juan , Mosavel Maghboeba
Published: April 2021

Black Americans and individuals from economically disadvantaged backgrounds are at disproportionate risk for obesity, yet are underrepresented in behavioral weight loss (BWL) trials and experience less benefit from traditional programs. The Wellness Engagement (WE) Project sought to translate evidence-based BWL within a CBPR framework to promote change across multiple domains of influence in an under-resourced, predominantly Black community. The purpose of this paper is to describe the efforts we undertook to translate data from our extensive formative phase into programming well suited to meet the needs of the Petersburg community. In addition, we present data from our pilot work on feasibility and acceptability. Formative data were collected using a variety of methods including a community-wide survey, asset mapping, house chats, focus groups, and key informant interviews. In collaboration with key stakeholders and community members, evidence-based approaches to weight loss were adapted to meet the needs of the community with respect to both content and delivery modality. Materials were adapted to focus on small, realistic changes appropriate for the specific context. Behavioral groups, experiential nutrition and exercise sessions, and walking groups leveraged existing assets and were open to all community members. Feasibility and acceptability ratings were promising. Furthermore, the WE Project appeared to contribute to a culture of wellness. CBPR might be a viable approach for engaging under-resourced Black communities in behavioral weight management; larger scale implementation and evaluation efforts are needed.
Naturalistic assessment of patterns and predictors of acute headache medication use among women with comorbid migraine and overweight or obesity
Authors: Smith Kathryn E , Thomas J Graham , Steffen Kristine J , Lipton Richard B , Farris Samantha G , Pavlovic Jelena M , Bond Dale S
Published: April 2021

Lay Summary

Obesity may contribute to more severe migraine symptoms and negatively impact migraine treatment outcomes. The present study aimed to understand patterns of acute medication use among 170 women with migraine and obesity who were seeking behavioral migraine treatment. Data were collected in participants’ natural environment using experience sampling methodology, during which participants reported daily migraine symptoms for 4 weeks. Approximately, 30% of attacks were not treated with any medications, and one in five attacks (i.e., 20%) was treated with migraine-specific medication. Participants were more likely to use medication during longer and more severe attacks that started earlier in the day. Participants were also more likely to use migraine-specific medication when attacks were precipitated by an aura and associated with work-related pain interference. Questionnaire-assessed factors were not related to medication use, although older age and higher educational attainment related to more frequent use. In general, these results also suggest that naturalistically assessed factors are more salient correlates of medication use compared to questionnaires. Additional investigation of barriers to medication use is needed among younger individuals and those of lower socioeconomic status.
‘Never so at home’: Charles Elton and the Woods of Wytham
Authors: Montgomery Georgina M.
Published: April 2021

Focusing on the history of an ecological site northwest of Oxford, UK, this essay explores the people, research and values behind the development of Wytham Woods as a scientific environment. A small patch of woodland, Wytham has long been identified by ecologists as a site of great scientific value. In addition to traditional sources of scientific value, such as species diversity, this article examines the role of emotional connection and aesthetics in how scientific sites are formed and maintained over long periods of time. As such, this history of Wytham Woods sheds light on the multiple factors that nurture the relationships formed when researchers dedicate decades to long-term studies conducted in specific scientific environments.
Investigating the mechanisms of indocyanine green (ICG) cellular uptake in sarcoma
Authors: Chan Corey D , Brookes Marcus J , Tanwani Riya , Hope Chloe , Pringle Toni A , Knight James C , Rankin Kenneth S
Published: April 2021

Introduction

Indocyanine green (ICG) is a near infrared (NIR) dye which has been used clinically for over 50 years and has recently been utilised for fluorescence guided surgery in a number of cancer types, including sarcoma. ICG is taken up and retained by sarcoma tumours to a greater extent than normal tissue, demonstrating its potential to aid in visualisation of tumour margins. However, the mechanisms surrounding preferential ICG uptake in tumours are poorly understood.

Methods

In vitroICG cellular uptake studies were performed across a panel of four sarcoma cell lines and one breast cancer cell line, exhibiting varying proliferation rates and phenotypes. The effects of ICG concentration, incubation time, inhibition of clathrin mediated endocytosis and cell line proliferation rate on the cellular uptake of ICG were investigated using fluorescence microscopy and flow cytometry. The spatial orientation of ICG was also assessed in a patient specimen.

Results

The level of ICG cellular uptake was dependent on ICG concentration and incubation time. Cell line proliferation rate correlated significantly to ICG uptake within 30 minutes (Rs= 1, p<0.001), whilst retention of ICG after 24hrs did not (Rs= 0.3, p=0.624). From our data, the primary mechanism of ICG uptake in sarcoma cells is via clathrin mediated endocytosis. Following the resection of a grade 3 leiomyosarcoma, ICG signal was detectable macroscopically and on 3μm sections, whilst being negative on the muscle control.

Conclusions

The use of ICG for tumour detection in sarcoma surgery may demonstrate higher utility in high grade tumours compared to low grade tumours, due to the observation of higher ICG uptake in more proliferative cell lines. It is likely that the enhanced permeability and retention (EPR) effect plays a significant role in the retention of ICG within tumours. Future work on the detection of ICG at the cellular level within human tissue sections is required, with the aid of purpose built NIR microscopes.
An intein-split transactivator for intersectional neural imaging and optogenetic manipulation
Authors: Chen Hao-Shan , Zhang Xiao-Long , Yang Rong-Rong , Wang Guang-Ling , Zhu Xin-Yue , Xu Yuan-Fang , Wang Dan-Yang , Zhang Na , Qiu Shou , Zhan Li-Jie , Shen Zhi-Ming , Xu Xiao-Hong , Long Gang , Xu Chun
Published: April 2021

The complexity of brain circuitry is manifested by numerous cell types based on genetic marker, location and neural connectivity. Cell-type specific recording and manipulation is essential to disentangle causal neural mechanisms in physiology and behavior; however, many current approaches are largely limited by number of intersectional features, incompatibility of common effectors and insufficient gene expression. To tackle these limitations, we devise an intein-based intersectional synthesis of transactivator (IBIST) to selectively control gene expression of common effectors in specific cell types defined by a combination of multiple features. We validate the specificity and sufficiency of IBIST to control common effectors including fluorophores, optogenetic opsins and Ca2+indicators in various intersectional conditionsin vivo. Using IBIST-based Ca2+imaging, we show that the IBIST can intersect up to five features, and that hippocampal cells tune differently to distinct emotional valences depending on the pattern of projection targets. Collectively, the IBIST multiplexes the capability to intersect cell-type features and is compatible with common effectors to effectively control gene expression, monitor and manipulate neural activities.
Identification of biomarkers and pathways of mouse embryonic fibroblasts with the dysfunction of mitochondrial DNA
Authors: Gu Hanming
Published: April 2021

Mitochondrial diseases are clinically heterogeneous which involve multiple systems such as organs that are highly dependent on metabolism. Dysfunction of mtDNA is the main cause of mitochondrial diseases that trigger inflammation and immune responses. Here, we aim to identify the biological function and pathways of MEFs with the dysfunction of mtDNA through deletion of YME1L. The gene expression profiles of GSE161735 dataset were originally created by the Illumina NovaSeq 6000 (Mus musculus) for gene biogenesis and function panel. The biological and functional pathways were analyzed by the Kyoto Encyclopedia of Genes and Genomes pathway (KEGG), Gene Ontology (GO), and Reactom visual map. KEGG and GO results showed the metabolism and immune responses were mostly affected by the loss of mtDNA. Moreover, we discovered several interacting genes including POLR2F, HIST1H2BJ, PPP1CC, HOXB4, ARG1, APITD1, BUB1B, POLR2K, HOXC4, and HOXB3 were involved in the regulation of metabolic or cancer diseases. Further, we predicted several regulators that had the ability to affect mitochondria during the dysfunction of mtDNA by L1000fwd analysis. Thus, this study provides further insights into the mechanism of mtDNA in metabolic diseases.
Constrained evolutionary paths to macrolide resistance in aNeisseriacommensal converge on ribosomal genes through sequence duplication
Authors: Raisman Jordan C. , Fiore Michael A. , Tomin Lucille , Adjei Joseph K.O. , Aswad Virginia , Chu Jonathan , Domondon Christina J. , Donahue Ben A. , Masciotti Claudia A. , McGrath Connor G. , Melita Jo , Podbielski Paul A. , Schreiner Madelyn R. , Trumpore Lauren J. , Wengert Peter C. , Wrightstone Emalee A. , Hudson André O. , Wadsworth Crista B.
Published: April 2021

Neisseriacommensals are an indisputable source of resistance for their pathogenic relatives; however, the evolutionary paths commensal species take to reduced susceptibility in this genus have been relatively underexplored. Here, we leveragein vitroselection as a powerful screen to identify the genetic adaptations that produce azithromycin resistance (≤ 2 μg/mL) in theNeisseriacommensal,N. elongata. Across multiple lineages (n=7/16), we find mutations encoding resistance converge on the gene encoding the 50S ribosomal L34 protein (rpmH) and the intergenic region proximal to the 30S ribosomal S3 protein (rpsC)through duplication events. Importantly, one of the laboratory evolved mutations inrpmHis identical, and two nearly identical, to those recently reported to confer high-level resistance to azithromycin inN. gonorrhoeae. Transformations into the ancestralN. elongatalineage confirmed the causality of bothrpmHandrpsCmutations. Though most lineages inheriting duplications sufferedin vitrofitness costs, one variant showed no growth defect, suggesting the possibility that it may be sustained in natural populations. Finally, we assessed the potential of horizontal transfer of derived resistance mutations into multiple strains ofN. gonorrhoeae. Though we were unable to transformN. gonorrhoeaein this case, studies like this will be critical for predicting commensal alleles that are at risk of rapid dissemination into pathogen populations.

Importance

Commensal bacterial populations have been increasingly recognized for their importance as sources of resistance for pathogens, however the collection of antimicrobial resistance (AMR) mechanisms within these communities are often understudied. The risk of reduced antibiotic susceptibility as a result of horizontal gene transfer (HGT) is amplified in highly recombinogenic genera, such as theNeisseria. Indeed, there have been multiple documented cases of macrolide and beta-lactam resistance acquisition in the pathogenN. gonorrhoeaefrom close commensal relatives. This work uncovers multiple novel azithromycin resistance-conferring mutations in aNeisseriacommensal through experimental evolution, investigates their fitness impacts, and explores the possibility of transfer toN. gonorrhoeae. Ultimately these types of studies will illuminate those resistance mutations that may rapidly be acquired across species boundaries.
Ripple Band Phase Precession of Place Cell Firing during Replay
Authors: Bush Daniel , Olafsdottir Freyja , Barry Caswell , Burgess Neil
Published: April 2021

Phase coding offers several theoretical advantages for information transmission compared to an equivalent rate code. Phase coding is shown by place cells in the rodent hippocampal formation, which fire at progressively earlier phases of the movement related 6-12Hz theta rhythm as their spatial receptive fields are traversed. Importantly, however, phase coding is independent of carrier frequency, and so we asked whether it might also be exhibited by place cells during 150-250Hz ripple band activity, when they are thought to replay information to neocortex. We demonstrate that place cells which fire multiple spikes during candidate replay events do so at progressively earlier ripple phases, and that spikes fired across all replay events exhibit a negative relationship between decoded location within the firing field and ripple phase. These results provide insights into the mechanisms underlying phase coding and place cell replay, as well as the neural code propagated to downstream neurons.
Klebsiella pneumoniaeBolA contributes to cell morphology, siderophore production, stresses challenge, cell adhesion and virulence
Authors: Yan Xiangjin , Zhang Feiyang , Ding Manlin , Xiang Li , Bai Jiawei , Li Qin , Zhou Yingshun
Published: April 2021

Klebsiella pneumoniaeinfection is one of the important reasons for the increased of morbidity and mortality. The main virulence factors ofK. pneumoniaeinclude capsule polysaccharide, lipopolysaccharide, fimbriae, outer membrane proteins and siderophores. BolA homologues form a broadly conserved family of proteins in prokaryotes and eukaryotes. InEscherichia coli, bolAexpression is quickly induced in response to different stresses or stationary phase that rapidly adapt to changing environments. In this report, we confirmed thatbolAmutant strain exhibited increased sensitivity to bile and oxidative stresses. In addition, gene deletion showed thatbolAhas an important role for the adherence ofK. pneumoniaeto host cell and establishment in mice, including liver, spleen, kidney and lung tissues, and induce the formation of liver abscess in mice. Our results also demonstrated thatK. pneumoniae bolAincreases the production of siderophore and virulence in Galleria mellonella larvae. Collectively, our results demonstrated thatK. pneumoniaeBolA is a new virulence factor which contributes to survival in different stresses and overcome host defense. These findings are helpful for the research of new treatment strategies forK. pneumoniaeinfection.

IMPORTANCE

Klebsiella pneumoniaeis an important conditional pathogen causing nosocomial infections and community-acquired infections. It can resistant to multiple antibiotics, causing refractory infections and public health threat. Therefore, new treatments are required to fight the pathogen, and a better understanding of its virulence factors are needed to develop new drugs. Here, we unraveled the role of BolA in survival under different stresses and overcome host defense. Our results suggested thatbolAactively contributes to cell morphology, stresses challenge, cell adhesion and siderophore production that are tightly related to bacterial virulence. Therefore,bolAmutant strain reduces the virulence ofK. pneumoniaein G. mellonella larvae and its colonization ability in mice. These results reportedbolAis a key virulence factor inK. pneumoniae, and they are helpful for research of new therapies to treat this increasingly problematic pathogen.
Extensive OMICS resource for Sf21 and Tni cell lines
Authors: Galik Bence , Landry Jonathan J.M. , Kirkpatrick Joanna M. , Fritz Markus Hsi-Yang , Baying Bianka , Blake Jonathon , Haase Bettina , Collier Paul G. , Hercog Rajna , Pavlinic Dinko , Stolt-Bergner Peggy , Besir Hüseyin , Remans Kim , Gyenesei Attila , Benes Vladimir
Published: April 2021

Insect-derived cell lines, fromSpodoptera frugiperda(Sf21) and fromTrichoplusia ni(Tni), are the two most widely used cell lines for recombinant protein expression in combination with the Baculoviral Expression Vector System (BEVS). Genomic sequences and annotations are still incomplete for Sf21 and absent for Tni. In this study, we present an approach using different sequencing data types, including short-read sequencing, long synthetic and Oxford Nanopore reads, to build genomes. The Sf21 and Tni assemblies contain 4,020 scaffolds of 463 Mb in size with N50 of 364 Kb and 2,954 scaffolds of 332 Mb in size with N50 of 326 Kb, respectively. Furthermore, we built a new gene prediction workflow, which integrates transcriptome and proteome information using pre-existing tools. Using this approach, we predicted 21,506 Sf21 and 14,159 Tni genes, generated and integrated proteomic datasets to validate predicted genes and could identify 5577 and 4919 proteins in the Sf21 and Tni cell lines respectively. This integrative approach could be theoretically applied to any uncharacterized genome and result in valuable new resources. With this information available, Sf21 and Tni cells will become even better tools for protein expression and could be used in a wider range of applications, from promoter identification to genome engineering and editing.
Emergent Spatiotemporal Population Dynamics with Cell-Length Control of Synthetic Microbial Consortia
Authors: Winkle James J. , Karamched Bhargav R. , Bennett Matthew R. , Ott William , Josić Krešimir
Published: April 2021

Abstract

Increased complexity of engineered microbial biocircuits highlights the need for distributed cell functionality due to concomitant increases of metabolic and regulatory burdens imposed on single-strain topologies. Distributed systems, however, introduce additional challenges since consortium composition and spatiotemporal dynamics of constituent strains must be robustly controlled to achieve desired circuit behaviors. Here, we address these challenges with a modeling-based investigation of emergent spatiotemporal population dynamics that result from cell-length control of monolayer, two-strain bacterial consortia. We demonstrate that with dynamic control of a strain’s division length, nematic cell alignment in close-packed monolayers can be destabilized. We found this destabilization conferred an emergent, competitive advantage on smaller-length strains—but by mechanisms that differed depending on the spatial patterns of the population. We used complementary modeling approaches to elucidate underlying mechanisms: an agent-based model to simulate detailed mechanical and signaling interactions between the competing strains and a reductive, stochastic lattice model to represent cell-cell interactions with a single rotational parameter. Our modeling suggests that spatial strain-fraction oscillations can be generated when cell-length control is coupled to quorum-sensing signaling in negative feedback topologies. Our research employs novel methods of population control and points the way to programming strain fraction dynamics in consortial synthetic biology.

Engineered microbial collectives are more versatile and robust than single strain populations. However, the function of such collectives is sensitive to their spatiotemporal organization. Here, we demonstrate control of the spatiotemporal composition of synthetic microbial consortia by dynamically modulating the average cell length of constituent strains. Such modulation confers an emergent “mechanical fitness” advantage upon the shorter length strain. We used both a biophysically realistic agent-based model to test the impact of cell shape on spatiotemporal dynamics and a conceptually simpler stochastic lattice model to explain the essential mechanisms driving the dynamics.
Engineering and crystal structure of a monomeric FLT3 ligand variant
Authors: Pannecoucke Erwin , Raes Laurens , Savvides Savvas N.
Published: April 2021

The overarching paradigm for the activation of class III and V receptor tyrosine kinases (RTKs) prescribes cytokine-mediated dimerization of the receptor ectodomains and homotypic receptor–receptor interactions. However, structural studies have shown that the hematopoietic receptor FLT3, a class III RTK, does not appear to engage in such receptor–receptor contacts, despite its efficient dimerization by dimeric FLT3 ligand (FL). As part of efforts to better understand the intricacies of FLT3 activation, we sought to engineer a monomeric FL. It was found that a Leu27Asp substitution at the dimer interface of the cytokine led to a stable monomeric cytokine (FLL27D) without abrogation of receptor binding. The crystal structure of FLL27D at 1.65 Å resolution revealed that the introduced point mutation led to shielding of the hydrophobic footprint of the dimerization interface in wild-type FL without affecting the conformation of the FLT3 binding site. Thus, FLL27D can serve as a monomeric FL variant to further interrogate the assembly mechanism of extracellular complexes of FLT3 in physiology and disease.
Numerical investigations on the hydrogen jet pressure variations in a strut based scramjet combustor
Authors: Suppandipillai Jeyakumar , Kandasamy Jayaraman , Sivakumar R. , Karaca Mehmet , K. Karthik
Published: April 2021

Purpose

This paper aims to study the influences of hydrogen jet pressure on flow features of a strut-based injector in a scramjet combustor under-reacting cases are numerically investigated in this study.

Design/methodology/approach

The numerical analysis is carried out using Reynolds Averaged Navier Stokes (RANS) equations with the Shear Stress Transport k-ω turbulence model in contention to comprehend the flow physics during scramjet combustion. The three major parameters such as the shock wave pattern, wall pressures and static temperature across the combustor are validated with the reported experiments. The results comply with the range, indicating the adopted simulation method can be extended for other investigations as well. The supersonic flow characteristics are determined based on the flow properties, combustion efficiency and total pressure loss.

Findings

The results revealed that the augmentation of hydrogen jet pressure via variation in flame features increases the static pressure in the vicinity of the strut and destabilize the normal shock wave position. Indeed, the pressure of the mainstream flow drives the shock wave toward the upstream direction. The study perceived that once the hydrogen jet pressure is reached 4 bar, the incoming flow attains a subsonic state due to the movement of normal shock wave ahead of the strut. It is noticed that the increase in hydrogen jet pressure in the supersonic flow field improves the jet penetration rate in the lateral direction of the flow and also increases the total pressure loss as compared with the baseline injection pressure condition.

Practical implications

The outcome of this research provides the influence of fuel injection pressure variations in the supersonic combustion phenomenon of hypersonic vehicles.

Originality/value

This paper substantiates the effect of increasing hydrogen jet pressure in the reacting supersonic airstream on the performance of a scramjet combustor.