bluuebunny/crossref_metadata_2025 huggingface dataset:
The impact of learning Unified Medical Language System knowledge embeddings in relation extraction from biomedical texts
Authors: Weinzierl Maxwell A , Maldonado Ramon , Harabagiu Sanda M
Published: August 2020

Objective

We explored how knowledge embeddings (KEs) learned from the Unified Medical Language System (UMLS) Metathesaurus impact the quality of relation extraction on 2 diverse sets of biomedical texts.

Materials and Methods

Two forms of KEs were learned for concepts and relation types from the UMLS Metathesaurus, namely lexicalized knowledge embeddings (LKEs) and unlexicalized KEs. A knowledge embedding encoder (KEE) enabled learning either LKEs or unlexicalized KEs as well as neural models capable of producing LKEs for mentions of biomedical concepts in texts and relation types that are not encoded in the UMLS Metathesaurus. This allowed us to design the relation extraction with knowledge embeddings (REKE) system, which incorporates either LKEs or unlexicalized KEs produced for relation types of interest and their arguments.

Results

The incorporation of either LKEs or unlexicalized KE in REKE advances the state of the art in relation extraction on 2 relation extraction datasets: the 2010 i2b2/VA dataset and the 2013 Drug-Drug Interaction Extraction Challenge corpus. Moreover, the impact of LKEs is superior, achieving F1 scores of 78.2 and 82.0, respectively.

Discussion

REKE not only highlights the importance of incorporating knowledge encoded in the UMLS Metathesaurus in a novel way, through 2 possible forms of KEs, but it also showcases the subtleties of incorporating KEs in relation extraction systems.

Conclusions

Incorporating LKEs informed by the UMLS Metathesaurus in a relation extraction system operating on biomedical texts shows significant promise. We present the REKE system, which establishes new state-of-the-art results for relation extraction on 2 datasets when using LKEs.
Advanced Glycation End Product Formation in Human Cerebral Cortex Increases With Alzheimer-Type Neuropathologic Changes but Is Not Independently Associated With Dementia in a Population-Derived Aging Brain Cohort
Authors: Chambers Annabelle , Bury Joanna J , Minett Thais , Richardson Connor D , Brayne Carol , Ince Paul G , Shaw Pamela J , Garwood Claire J , Heath Paul R , Simpson Julie E , Matthews Fiona E , Wharton Stephen B
Published: August 2020

Diabetes mellitus is a risk factor for dementia, and nonenzymatic glycosylation of macromolecules results in formation of advanced glycation end-products (AGEs). We determined the variation in AGE formation in brains from the Cognitive Function and Ageing Study population-representative neuropathology cohort. AGEs were measured on temporal neocortex by enzyme-linked immunosorbent assay (ELISA) and cell-type specific expression on neurons, astrocytes and endothelium was detected by immunohistochemistry and assessed semiquantitatively. Fifteen percent of the cohort had self-reported diabetes, which was not significantly associated with dementia status at death or neuropathology measures. AGEs were expressed on neurons, astrocytes and endothelium and overall expression showed a positively skewed distribution in the population. AGE measures were not significantly associated with dementia. AGE measured by ELISA increased with Consortium to Establish a Registry for Alzheimer’s Disease (CERAD) neurofibrillary tangle score (p = 0.03) and Thal Aβ phase (p = 0.04), while AGE expression on neurons (and astrocytes), detected immunohistochemically, increased with increasing Braak tangle stage (p < 0.001), CERAD tangle score (p = 0.002), and neuritic plaques (p = 0.01). Measures of AGE did not show significant associations with cerebral amyloid angiopathy, microinfarcts or neuroinflammation. In conclusion, AGE expression increases with Alzheimer’s neuropathology, particular later stages but is not independently associated with dementia. AGE formation is likely to be important for impaired brain cell function in aging and Alzheimer’s.
Commissioning of total body irradiation using plastic bead bags
Authors: Akino Yuichi , Maruoka Shintaro , Yano Katsuyuki , Abe Hiroshi , Isohashi Fumiaki , Seo Yuji , Tamari Keisuke , Hirata Takero , Kawakami Manabu , Nakae Yoshiki , Tanaka Yoshihiro , Ogawa Kazuhiko
Published: August 2020

The goal of total body irradiation (TBI) is to deliver a dose to the whole body with uniformity within ±10%. The purpose of this study was to establish the technique of TBI using plastic bead bags. A lifting TBI bed, Model ORP-TBI-MN, was used. The space between the patient’s body and the acrylic walls of the bed was filled with polyacetal bead bags. Patients were irradiated by a 10 MV photon beam with a source to mid-plane distance of 400 cm. The monitor unit (MU) was calculated by dose-per-MU, tissue-phantom-ratio and a spoiler factor measured in solid water using an ionization chamber. The phantom-scatter correction factor, off-center ratio and the effective density of the beads were also measured. Diode detectors were used for in vivo dosimetry (IVD). The effective density of the beads was 0.90 ± 0.09. The point doses calculated in an I’mRT phantom with and without heterogeneity material showed good agreement, with measurements within 3%. An end-to-end test was performed using a RANDO phantom. The mean ± SD (range) of the differences between the calculated and IVD-measured mid-plane doses was 1.1 ± 4.8% (−5.9 to 5.0%). The differences between the IVD-measured doses and the doses calculated with Acuros XB of the Eclipse treatment planning system (TPS) were within 5%. For two patients treated with this method, the differences between the calculated and IVD-measured doses were within ±6% when excluding the chest region. We have established the technique of TBI using plastic bead bags. The TPS may be useful to roughly estimate patient dose.
Ethephon-induced changes in antioxidants and phenolic compounds in anthocyanin-producing black carrot hairy root cultures
Authors: Barba-Espín Gregorio , Chen Shih-Ti , Agnolet Sara , Hegelund Josefine Nymark , Stanstrup Jan , Christensen Jan H , Müller Renate , Lütken Henrik
Published: August 2020

Hairy root (HR) cultures are quickly evolving as a fundamental research tool and as a bio-based production system for secondary metabolites. In this study, an efficient protocol for establishment and elicitation of anthocyanin-producing HR cultures from black carrot was established. Taproot and hypocotyl explants of four carrot cultivars were transformed using wild-type Rhizobium rhizogenes. HR growth performance on plates was monitored to identify three fast-growing HR lines, two originating from root explants (lines NB-R and 43-R) and one from a hypocotyl explant (line 43-H). The HR biomass accumulated 25- to 30-fold in liquid media over a 4 week period. Nine anthocyanins and 24 hydroxycinnamic acid derivatives were identified and monitored using UPLC-PDA-TOF during HR growth. Adding ethephon, an ethylene-releasing compound, to the HR culture substantially increased the anthocyanin content by up to 82% in line 43-R and hydroxycinnamic acid concentrations by >20% in line NB-R. Moreover, the activities of superoxide dismutase and glutathione S-transferase increased in the HRs in response to ethephon, which could be related to the functionality and compartmentalization of anthocyanins. These findings present black carrot HR cultures as a platform for the in vitro production of anthocyanins and antioxidants, and provide new insight into the regulation of secondary metabolism in black carrot.
Persistent Challenges in the Hepatitis C Virus Care Continuum for Patients in a Central Texas Public Health System
Authors: Reader Shane W , Kim Hyun-seok , El-Serag Hashem B , Thrift Aaron P
Published: August 2020

Background

Direct-acting antiviral treatment regimens cure >95% of chronic hepatitis C virus (HCV) infections, but recent studies indicate that <25% of patients in the United States receive treatment. Patients need to overcome barriers on the steps of the care continuum in order to be prescribed treatment. We aimed to examine the steps of the HCV care continuum up to prescription of HCV therapy among patients receiving care within a large safety net health care system in Houston, Texas.

Methods

We used electronic medical records to identify patients with positive screening tests for HCV antibodies between July 1, 2017, and June 30, 2018, and abstracted data on their advancement through the care continuum for HCV. We used logistic regression to identify factors associated with patient navigation through the continuum.

Results

Of the 2450 patients screening positive for HCV antibodies, 2016 (82.3%) received quantitative RNA testing, of whom 1081 (53.6%) exhibited chronic infection. Providers referred 915 (84.6%) to specialty care for evaluation, 540 of these patients (50.0%) received their specialist evaluation, and 299 (27.7%) received a prescription for treatment. Patients with history of substance use were less likely to be prescribed treatment (adjusted odds ratio, 0.66; 95% CI, 0.49–0.88).

Conclusions

We found substantial attrition at each stage of the HCV care continuum. In particular, history of substance abuse was a predictor of nonprescription. Challenges in the care continuum motivate increased provider education as well as the adoption of recent innovations in patient care.
Investigating the Perceived Impact of Psychosis on Suicidal Thoughts and Behaviors
Authors: Harris Kamelia , Gooding Patricia , Peters Sarah , Haddock Gillian
Published: August 2020

There is evidence showing a link between experiencing psychosis and suicidal thoughts and behaviors. However, individual accounts of the impact of psychosis on suicidal experiences have not been examined in detail. This study aimed to investigate the perceived impact of psychosis on suicidal thoughts and behaviors from the perspectives of individuals with these experiences. Semi-structured interviews with 20 people with non-affective psychosis and lifetime experiences of suicidal thoughts and/or behaviors were conducted. Data were analyzed using inductive Thematic Analysis. Based on participants’ experiences of psychosis and suicidal thoughts and behaviors, 3 themes were identified, including (1) Psychosis experiences are immensely distressing, (2) Changes in behaviors and appraisals of self, and (3) Suicidality as a means of escaping distress. A practical heuristic was proposed, describing a vicious cycle between psychological distress and changes in behaviors and self-appraisals, whereby suicidality was perceived as the only way to escape immense psychological pain. Hallucinations and delusions were central to the development of suicidal experiences. However, certain types of delusions, such as grandiose delusions, were sometimes found to reduce the intensity of suicidal experiences and associated psychological distress. It is necessary to examine the impact of psychosis on individuals, in order to assess the possibility of suicide-related experiences, as certain aspects of psychosis can have an amplifying effect, whereas others can have a weakening effect on those experiences. Minimizing the immense psychological pain experienced by some people with psychosis and the inter-related suicidal thoughts and behaviors is of paramount importance for clinical practice.
Fungicide Resistance Profiles of Botrytis cinerea Isolates From Michigan Vineyards and Development of a TaqMan Assay for Detection of Fenhexamid Resistance
Authors: Alzohairy S. A. , Gillett J. , Saito S. , Naegele R. N. , Xiao C. L. , Miles T. D.
Published: August 2020

Botrytis cinerea on grapes causes bunch rot at both pre- and postharvest stages, in which losses can reach up to 100%. Chemical control primarily relies on the prophylactic use of site-specific fungicides. Repeated applications of these products raise the risk of fungicide resistance development in B. cinerea populations, which can result in disease control failures. To determine the extent of resistance, B. cinerea isolates were collected from grape clusters in the northwest and southwest grape growing regions of Michigan in 2014 and 2018 (n = 115 and 125, respectively). These isolates were phenotyped using discriminatory doses of eight fungicides to determine the levels of resistance. Fungicide resistance increased from 2014 to 2018, mostly affecting the active ingredients fenhexamid, fluopyram, and iprodione. B. cinerea isolates resistant to multiple fungicides were detected in 2014 and 2018, with a higher frequency of resistance in 2018. TaqMan real-time PCR has been developed to detect B. cinerea fungicide resistance to fenhexamid and to differentiate the erg27 F412S/I/V alleles. The TaqMan assay was tested for sensitivity, specificity, and reproducibility on purified DNA and infected grape tissue samples. Our data provide essential information to growers about the efficacy for B. cinerea control using the available botryticides. Furthermore, the developed fenhexamid markers will be transferred to diagnostic clinics to assist growers in the management of bunch rot before resistance-related control failures occur.
Learning in Faculty Development: The Role of Social Networks
Authors: Buckley Heather , Nimmon Laura
Published: August 2020

Purpose

Faculty development is increasingly acknowledged as an important aspect of health professions education. Its conceptualization has evolved from an individual skills training activity to contemporary notions that draw on an organizational model. This organizational model recognizes relationships and networks as important mediators of knowledge mobilization. Although such conceptual advancements are critical, we lack empirical evidence and robust insights into how social networks function to shape learning in faculty development. The purpose of this study was to understand how informal professional social networks influence faculty development learning in the health professions.

Method

This study used a qualitative social network approach to explore how teaching faculty’s relationships influenced their learning about teaching. The study was conducted in 2018 in an undergraduate course at a Canadian medical school. Eleven faculty participants were recruited, and 3 methods of data collection were employed: semistructured interviews, participant-drawn sociograms, and demographic questionnaires.

Results

The social networks of faculty participants influenced their learning about teaching in the following 4 dimensions: enabling and mobilizing knowledge acquisition, shaping identity formation, expressing vulnerability, and scaffolding learning.

Conclusions

Faculty developers should consider faculty’s degree of social embeddedness in their professional social networks, as our study suggests this may influence their learning about teaching. The findings align with recent calls to conceptually reorient faculty development in the health professions as a dynamic social enterprise.
Predicting Performance on Clerkship Examinations and USMLE Step 1: What Is the Value of Open-Ended Question Examination?
Authors: Boscardin Christy K. , Earnest Gillian , Hauer Karen E.
Published: August 2020

Purpose

Despite advances in learning sciences that highlight the efficacy of elaborative interrogation, in which students explain and elaborate on concepts in their own words, assessment techniques in medical education have commonly employed multiple-choice questions (MCQs). Educators’ reluctance to consider alternatives such as open-ended questions (OEQs) stems from practical advantages of MCQs and the lack of empirical data on the predictability of OEQs for performance on other high-stakes assessments. In this study, the authors compared the predictive value of preclerkship assessments using OEQs for the outcomes of clerkship examinations and United States Medical Licensing Examination (USMLE) Step 1.

Method

The authors compared outcomes of 2 assessment formats using multiyear performance data (2015 and 2016 cohorts) on preclerkship MCQ versus OEQ examinations for predicting students’ subsequent performance on 6 clerkship examinations and USMLE Step 1. The authors conducted a regression analysis to compare the predictability of MCQs and OEQs by using clerkship exam scores and Step 1 scores as dependent variables and performance on MCQs and OEQs as predictors in the models.

Results

Regression models with OEQs were consistently higher for predicting clerkship exam (NBME shelf-exam) scores, except for one clerkship, compared with models using MCQs. For Step 1, R-square using MCQs was higher with 59% of the variance explained compared with 46% with OEQs, but the OEQ cohort scored significantly higher on Step 1.

Conclusions

OEQ examinations predict performance on subsequent high-stakes MCQ examinations. Given the predictive value and closer alignment with scientific principles of effective learning, OEQ examinations are an examination format worthy of consideration in preclerkship medical education programs.
The Influence of Relationship-Centered Coaching on Physician Perceptions of Peer Review in the Context of Mandated Regulatory Practices
Authors: Arabsky Sherylyn , Castro Nadya , Murray Michael , Bisca Ioana , Eva Kevin W.
Published: August 2020

Purpose

Medical regulatory authorities are legally mandated to protect patients by monitoring the practice of medicine. While principally a matter of public safety, many pursue this mission by establishing quality improvement initiatives that prioritize professional development for all rather than identification of substandard performers. Engaging practitioners in directed learning opportunities, however, is rife with challenge given inherent social complexities. This study was run to explore whether relationship-centered coaching could improve physicians’ perceptions of the value of engaging with College-mandated peer review.

Method

A quasi-experimental analysis was performed on physician ratings of the effectiveness of peer assessor interactions and assessment processes during 3 time periods: (1) an historical control (March 2016–December 2016; n = 296); (2) a period after assessors were trained to deliver feedback using relationship-centered coaching (December 2016–March 2017; n = 96); and (3) after physicians were given more capacity to choose patient records for peer review and engage in discussion about multisource feedback results (March 2017–December 2018; n = 448).

Results

Psychometric analyses supported the aggregation of survey items into assessor interaction and assessment process subscores. Training assessors to engage in relationship-centered coaching was related with higher assessor interaction scores (4.64 vs 4.47; P < .05; d = 0.37). Assessment process scores did not increase until after additional program enhancements were made in period 3 (4.33 vs 4.17, P < .05, d = 0.29).

Conclusions

Despite peer interactions being inherently stressful for physicians when they occur in the context of regulatory authority visits, efforts to establish a quality improvement culture that prioritizes learning can improve physicians’ perceptions of peer review.
Fat Grafting as a Novel Treatment for Xerostomia
Authors: Bamba Ravinder , Shadfar Scott , Van Natta Bruce W.
Published: August 2020

Purpose:

Within the context of xerostomia, there is evidence that adipose-derived stem cells (ASCs) can differentiate into salivary gland cells in the appropriate environment. The purpose of this study was to preliminarily investigate whether fat grafting as practiced in the United States would be an effective treatment for xerostomia.

Methods:

Patients were selected for the study if they were seeking treatment for xerostomia after radiation treatment to the head and neck for cancer treatment. Fat grafting was performed in bilateral parotid and submandibular glands. Visual Analog Scale (VAS) of xerostomia was used both preoperatively and postoperatively to assess the effect upon xerostomia symptoms.

Results:

Nine patients were included in this study. All patients had complaints of long-standing xerostomia. The average preoperative VAS score was 9.1. All patients tolerated all rounds of fat grafting with no complications. The average postoperative VAS score was 6.0. Compared to preoperative scores, all patients had improvement in VAS scores. The decrease in average VAS score postoperatively (9.1 versus 6.0) was statistically significant (P = 0.007).

Conclusions:

Our study showed that there was improvement in xerostomia symptoms with autologous fat transfer alone. This is a novel finding for fat grafting demonstrating regenerative potential. There has been extensive basic research that has shown that adipose-derived mesenchymal stem cells can have a protective and restorative role after salivary gland radiation damage. Our case series is the first report of fat grafting having a similar reported outcome.

Level of Evidence: 4
Upper Airway Changes Following Different Orthognathic Surgeries, Evaluated by Cone Beam Computed Tomography: A Systematic Review and Meta-analysis
Authors: Shokri Abbas , Ramezani Kousar , Afshar Arghavan , Poorolajal Jalal , Ramezani Navid
Published: August 2020

Purpose:

This study sought to assess the upper airway changes following different orthognathic surgeries using cone-beam computed tomography.

Methods:

An electronic search of the literature was conducted in major electronic databases including Medline (PubMed), Web of Science, Scopus, and Open Grey for articles published up to January 20, 2018. Human studies that evaluated the changes in the volume and minimum cross-sectional area of the upper airway or its subdivisions in patients who had undergone orthognathic surgery by use of cone-beam computed tomography were included. Manual search of the bibliographies of the included articles was also conducted. The included studies underwent risk of bias assessment.

Results:

A total of 1330 articles were retrieved. After excluding the duplicates and irrelevant articles, 41 studies fulfilled the eligibility criteria for this systematic review; out of which, 30 entered the meta-analysis. The majority of studies had a medium risk of bias. Mandibular setback, and maxillary advancement + mandibular setback decreased the volume of the upper airway (−6042.87 mm3 and −1498.78 mm3, respectively) and all its subdivisions in long-term (>3 months), except for the nasopharynx, the volume of which increased following maxillary advancement + mandibular setback. Mandibular advancement and maxillomandibular advancement both increased the upper airway volume in long-term (7559.38 mm3 and 7967.06 mm3, respectively); however, only the changes after the former procedure were significant. The minimum cross-sectional area increased after maxillomandibular advancement (161.43 mm2), and decreased following maxillary advancement + mandibular setback (−23.79 mm2) in long-term.

Conclusion:

There is moderate evidence to suggest that mandibular advancement is the only orthognathic movement that provides a statistically significant change in long-term upper airway volume.
A novel hemA mutation is responsible for a small-colony-variant phenotype in Escherichia coli
Authors: Hubbard Alasdair T. M. , Bulgasim Issra , Roberts Adam P.
Published: August 2020

We identified a small colony variant (SCV) of an amoxicillin/clavulanic acid-resistant derivative of a clinical isolate of

Escherichia coli

from Malawi, which was selected for in vitro in a subinhibitory concentration of gentamicin. The SCV was auxotrophic for hemin and had impaired biofilm formation compared to the ancestral isolates. A single novel nucleotide polymorphism (SNP) in hemA, which encodes a glutamyl-tRNA reductase that catalyses the initial step of porphyrin biosynthesis leading to the production of haem, was responsible for the SCV phenotype. We showed the SNP in hemA resulted in a significant fitness cost to the isolate, which persisted even in the presence of hemin. However, the phenotype quickly reverted during sequential sub-culturing in liquid growth media. As hemA is not found in mammalian cells, and disruption of the gene results in a significant fitness cost, it represents a potential target for novel drug development specifically for the treatment of catheter-associated urinary tract infections caused by

E. coli

.
SARS-CoV-2 surveillance in decedents in a large, urban medical examiner’s office
Authors: Brouwer Andrew F. , Myers Jeffrey L. , Martin Emily T. , Konopka Kristine E. , Lauring Adam S. , Eisenberg Marisa C. , Lephart Paul R. , Nguyen Teresa , Jaworski Andrea , Schmidt Carl J.
Published: August 2020

Background

SARS-CoV-2 has become a global pandemic. Given the challenges in implementing widespread SARS-CoV-2 testing, there is increasing interest in alternative surveillance strategies.

Methods

We tested nasopharyngeal swabs from 821 decedents in the Wayne County Medical Examiner’s office for SARS-CoV-2. All decedents were assessed by a COVID-19 checklist, and decedents flagged by the checklist (237) were preferentially tested. A random sample of decedents not flagged by the checklist were also tested (584). We statistically analyzed the characteristics of decedents (age, sex, race, and manner of death), differentiating between those flagged by the checklist and not and between those SARS-CoV-2 positive and not.

Results

Decedents were more likely to be male (70% vs 48%) and Black (55% vs 36%) than the catchment population. Seven-day average percent positivity among flagged decedents closely matched the trajectory of percent positivity in the catchment population, particularly during the peak of the outbreak (March and April). After a lull in May to mid-June, new positive tests in late June coincided with increased case detection in the catchment. We found large racial disparities in test results: despite no statistical difference in the racial distribution between those flagged and not, SARS-CoV-2 positive decedents were substantially more likely to be Black (89% vs 51%). SARS-CoV-2 positive decedents were also more likely to be older and to have died of natural causes, including of COVID-19 disease.

Conclusions

Disease surveillance through medical examiners and coroners could supplement other forms of surveillance and may serve as a possible early outbreak warning sign.
Association of mental disorders with SARS-CoV-2 infection and severe health outcomes: a nationwide cohort study
Authors: Jeon Ha-Lim , Kwon Jun Soo , Park So-Hee , Shin Ju-Young
Published: August 2020

Background

No epidemiological data exists for the association between mental disorders and the risk of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and coronavirus disease 2019 (COVID-19) severity.

Aims

To evaluate the association between mental disorders and the risk of SARS-CoV-2 infection and severe outcomes following COVID-19.

Methods

We performed a cohort study using the Korean COVID-19 patient database based on the national health insurance data. Each patient with a mental or behavioral disorder (diagnosed during six months prior to the first SARS-CoV-2 test) was matched by age, sex, and Charlson comorbidity index with up to four patients without mental disorders. SARS-CoV-2 positivity risk and risk of death or severe events (intensive care unit admission, use of mechanical ventilation, and acute respiratory distress syndrome) post-infection were calculated using conditional logistic regression analysis.

Results

Among 230,565 patients tested for SARS-CoV-2, 33,653 (14.6%) had mental disorders, 928/33,653 (2.76%) tested positive, and 56/928 (6.03%) died. In multivariate analysis with the matched cohort, there was no association between mental disorders and SARS-CoV-2 positivity risk (odds ratio [OR], 1.02; 95% confidence interval [CI], 0.92-1.12); however, a higher risk was associated with schizophrenia-related disorders (OR, 1.36; 95% CI, 1.02-1.81). Among confirmed cases, mortality risk significantly increased in patients with mental disorders (OR, 1.84, 95% CI, 1.07-3.15).

Conclusion

Mental disorders are likely contributing factors of mortality following COVID-19. Although the infection risk did not increase in overall mental disorders, patients with schizophrenia-related disorders were more vulnerable to the infection.
Thermodynamics of DNA Hybridization from Atomistic Simulations
Authors: Zerze Gül H. , Stillinger Frank H. , Debenedetti Pablo G.
Published: August 2020

Studying the DNA hybridization equilibrium via brute force molecular dynamics (MD) or commonly used advanced sampling approches is notoriously difficult at atomistic lengthscale. However, besides providing a more realistic modeling of this microscopic phenomenon, atomistic resolution is a necessity for some fundamental research questions, such as the ones related to DNA’s chirality. Here, we describe an order parameter-based advanced sampling technique to calculate the free energy surface of hybridization and estimate melting temperature of DNA oligomers at atomistic resolution, using a native topology-based order parameter. We show that the melting temperatures estimated from our atomistic simulations follow an order consistent with the predictions from melting experiments and those from the nearest neighbor model, for a range of DNA sequences of different GC content. Moreover, free energy surfaces and melting temperatures are calculated to be identical for D- and L-enantiomers of Drew-Dickerson dodecamer.

Abstract Figure

Graphical TOC Entry
Antisense oligonucleotides against monoacylglycerol acyltransferase 1 (Mogat1) improve glucose metabolism independently ofMogat1
Authors: Lutkewitte Andrew J. , Singer Jason M. , Shew Trevor M. , Martino Michael R. , Hall Angela M. , Finck Brian N.
Published: August 2020

Objective

Monoacylglycerol acyltransferase (MGAT) enzymes catalyze the synthesis of diacylglycerol from monoacylglycerol. Previous work has suggested the importance of MGAT activity in the development of obesity-related hepatic insulin resistance. Indeed, antisense oligonucleotide (ASO)-mediated knockdown of the gene encoding MGAT1,Mogat1, reduced hepatic MGAT activity and improved glucose tolerance and insulin resistance in high fat diet (HFD) fed mice. However, recent work has suggested that some ASOs may have off-target effects on body weight and metabolic parameters via activation of the interferon alpha/beta receptor 1 (IFNAR-1) pathway.

Methods

Mice with whole-bodyMogat1knockout or a floxed allele forMogat1to allow for liver-specificMogat1-knockout (by either a liver-specific transgenic or adeno-associated virus-driven Cre recombinase) were generated. These mice were placed on a high fat diet and glucose metabolism and insulin sensitivity was assessed after 16 weeks on diet. In some experiments, mice were treated with control orMogat1or control ASOs in the presence or absence of IFNAR-1 neutralizing antibody.

Results

Genetic deletion of hepaticMogat1, either acutely or chronically, did not improve hepatic steatosis, glucose tolerance, or insulin sensitivity in HFD-fed mice. Furthermore, constitutiveMogat1knockout in all tissues actually exacerbated HFD-induced weight gain, insulin resistance, and glucose intolerance on a HFD. Despite markedly reducedMogat1expression, liver MGAT activity was unaffected in all knockout mouse models.Mogat1overexpression hepatocytes increased liver MGAT activity and TAG content in low-fat fed mice, but did not cause insulin resistance. Interestingly,Mogat1ASO treatment improved glucose tolerance in both wild-type andMogat1null mice, suggesting an off target effect. Inhibition of IFNAR-1 did not block the effect ofMogat1ASO on glucose homeostasis.

Conclusion

These results indicate that genetic loss ofMogat1does not affect hepatic MGAT activity or metabolic homeostasis on HFD and show thatMogat1ASOs improve glucose metabolism through effects independent of targetingMogat1or activation of IFNAR-1 signaling.

Abstract Figure

Highlights

Mogat1 liver-specific KO or KD does not improve metabolism in HFD fed mice.

Whole-body Mogat1-deletion impairs insulin tolerance in HFD fed mice.

Mogat1 ASOs improves whole body metabolism independently of gene knockdown.

Blockade of the INFR response does not prevent off-target effects of Mogat1 ASOs.
Investigating the effects of molecular crowding on the kinetics of protein aggregation
Authors: Schreck John S. , Bridstrup John , Yuan Jian-Min
Published: August 2020

The thermodynamics and kinetics of protein folding and protein aggregationin vivoare of great importance in numerous scientific areas including fundamental biophysics research, nanotechnology, and medicine. However, these processes remain poorly understood in bothin vivoandin vitrosystems. Here we extend an established model for protein aggregation that is based on the kinetic equations for the moments of the polymer size distribution by introducing macromolecular crowding particles into the model using scaled-particle and transition-state theories. The model predicts that the presence of crowders can either speed up, cause no change to, or slow down the progress of the aggregation compared to crowder-free solutions, in striking agreement with experimental results from nine different amyloid-forming proteins that utilized dextran as the crowder. These different dynamic effects of macromolecular crowding can be understood in terms of the change of excluded volume associated with each reaction step.
MeCP2 deficiency exacerbates the neuroinflammatory setting and autoreactive response during an autoimmune challenge: implications for Rett Syndrome
Authors: Zalosnik MI , Fabio MC , Bertoldi ML , Castañares CL , Degano AL
Published: August 2020

Background

Rett syndrome is a severe and progressive neurological disorder linked to mutations in the MeCP2 gene located on the X chromosome. So far it has not been established how the presence of a mutant form of MeCP2 can maintain essential regulation of immune responses to support the normal homeostasis of individuals. Since MeCP2 is mostly expressed as a “partially functional” protein in humans with RTT, the aim of our work was to evaluate whether a mutation in MeCP2 interferes with the induction of neuroinflammatory responses in real time.

Methods

We used MeCP2308/ymouse model (MUT) and exposed it to an autoimmune challenge, experimental autoimmune encephalomyelitis (EAE). WT and MUT mice were immunized with CFA-MOG or CFA alone (control) and clinical scores were evaluated daily. Animals were sacrificed at either 12 days post-induction (dpi, acute stage) or 30 dpi (chronic stage) and spleen and spinal cord were collected from individual mice for further studies. Cellular infiltration and microgliosis was evaluated by IHC. Cytokine production was assessed in spinal cord and in cultured splenocytes after MOG activation ex-vivo by cytometry and real time RT-PCR.

Results

Our results showed that MeCP2 deficiency increased the susceptibility to develop EAE, along with a defective induction of anti-inflammatory responses and an exacerbated MOG-specific reactivity with high IFNγ expression in peripheral immune sites. During the chronic stage, an increase in gene expression of pro-inflammatory cytokines (IFNγ, TNFα and IL-1β) and downregulation of genes relevant for immune regulation (IL-10, FoxP3 and CX3CR1) was found in MUT-EAE spinal cords.

Conclusions

This is the first study performed in a MeCP2 mutant mouse model that explores the pathophysiology and neuroinflammation in the context of an autoimmune challenge. We could establish that an MeCP2 mutation act intrinsically affecting neuroimmune interactions by promoting an inflammatory environment and a deficient immune regulatory setting. These results are relevant for understanding the consequences of MeCP2 mutations on immune homeostasis in MeCP2-related disorders, as well as setting the bases for further therapeutic interventions that consider the immune status in patients.
Rodent mnemonic similarity task performance requires the prefrontal cortex
Authors: Johnson Sarah A. , Zequeira Sabrina , Turner Sean M. , Maurer Andrew P. , Bizon Jennifer L. , Burke Sara N.
Published: August 2020

Mnemonic similarity task performance, in which a known target stimulus must be distinguished from similar lures, is supported by the hippocampus and perirhinal cortex and is known to decline in advanced age. Interestingly, disrupting hippocampal activity leads to mnemonic discrimination impairments when lures are novel, but not when they are familiar. This observation suggests other brain structures can support discrimination abilities as stimuli are learned. The prefrontal cortex (PFC) is critical for retrieval of remote events and executive functions, such as working memory, and is also particularly vulnerable to dysfunction in aging. Importantly, the medial PFC is reciprocally connected to the perirhinal cortex and neuron firing in this region coordinates communication between lateral entorhinal and perirhinal cortices to presumably modulate hippocampal activity. This anatomical organization and function of the medial PFC suggests that it contributes to mnemonic discrimination; however, this notion has not been empirically tested. In the current study, young adult male and female F344 x Brown Norway F1 hybrid rats were trained on a rodent object-based mnemonic similarity task, and surgically implanted with guide cannulae targeting prelimbic and infralimbic regions of the medial PFC. Prior to mnemonic discrimination tests, rats received PFC infusions of the GABAAagonist muscimol. Analyses of expression of the neuronal activity-dependent immediate-early geneArcin medial PFC and adjacent cortical regions confirmed muscimol infusions led to neuronal inactivation in the infralimbic and prelimbic cortices. Moreover, muscimol infusions in PFC impaired mnemonic discrimination performance relative to the vehicle control across all testing blocks when lures shared 50-90% feature overlap with the target. Thus, in contrast to prior results from rats given hippocampal muscimol infusions, PFC inactivation impaired target-lure discrimination regardless of the novelty or familiarity of the lures. These findings indicate the PFC plays a critical role in mnemonic similarity task performance, but the time course of PFC involvement is dissociable from that of the hippocampus.
IL-4 receptor targeting as an effective immunotherapy against triple-negative breast cancer
Authors: Parveen Sadiya , Siddharth Sumit , Cheung Laurene S , Kumar Alok , Murphy John R , Sharma Dipali , Bishai William R
Published: August 2020

In many solid tumors including triple-negative breast cancer (TNBC), IL-4 receptor (IL-4R) upregulation has been shown to promote cancer cell proliferation, apoptotic resistance, metastatic potential and a Th2 response in the tumor microenvironment (TME). Immunosuppressive cells in the TME including myeloid-derived suppressor cells (MDSCs) and tumor-associated macrophages (TAMs) also express the IL4-R. We hypothesized that selective depletion of IL4-R bearing cells in TNBC may have dual cytotoxic and immunotherapeutic benefit. To selectively target IL-4R+cells, we genetically constructed, expressed and purified DABIL-4, a fusion protein toxin consisting of the catalytic and translocation domains of diphtheria toxin fused to murine IL-4. We found that DABIL-4 has potent and specific cytotoxic activity against TNBC cellsin vitro. In murine TNBC models, DABIL-4 significantly reduced tumor growth, splenomegaly and lung metastases, and this was associated with reductions in MDSC, TAM and regulatory T-cells (Tregs) populations with a concomitant increase in the proportion of IFNγ+CD8 T-cells. The anti-tumor activity of DABIL-4 was absent in IL-4R KO mice directly implicating IL-4R directed killing as the mechanism of anti-tumor activity. Moreover, NanoString analysis of DABIL-4 treated TNBC tumors revealed marked decline in mRNA transcripts that promote tumorigenesis and metastasis. Our findings demonstrate that DABIL-4 is a potent targeted antitumor agent which depletes both IL-4R bearing tumor cells as well as immunosuppressive cell populations in the TME.

STATEMENT OF SIGNIFICANCE

In solid tumors like breast cancer, Interleukin-4 receptor (IL-4R) expression in the tumor microenvironment aids tumor growth and metastasis. IL-4R expression upon host immune cells further dampens antitumor immunity. In this study, we have genetically constructed a fusion protein toxin, DABIL-4, composed of the catalytic and translocation domains of diphtheria toxin and murine IL-4. DABIL-4 showed specific cytotoxicity against triple-negative breast cancer (TNBC) cells in vitro. DABIL-4 also markedly inhibited TNBC tumor growth and metastasis in vivo. The primary activity of DABIL-4 was found to be depletion of IL-4R+ immune cells in combination with direct elimination of tumor cells. In conclusion, DABIL-4 targeting of both tumor and immunosuppressive host cells is a versatile and effective treatment strategy for TNBC.
Diversity of sea star-associated densoviruses and transcribed endogenized viral elements of densovirus origin
Authors: Jackson Elliot W. , Wilhelm Roland C. , Johnson Mitchell R. , Lutz Holly L. , Danforth Isabelle , Gaydos Joseph K. , Hart Michael W. , Hewson Ian
Published: August 2020

A viral etiology of Sea Star Wasting Syndrome (SSWS) has been largely explored using metagenomics leading to the conclusion that a densovirus is the predominant DNA virus associated with this syndrome, and, thus, the most promising viral candidate pathogen. Single-stranded DNA viruses are however highly diverse and pervasive among eukaryotic organisms which we hypothesize may confound the association between densoviruses and SSWS in sea stars. To test this hypothesis and assess the association of densoviruses to SSWS, we compiled past metagenomic data with new metagenomic-derived viral genomes from sea stars collected from Antarctica, California, Washington, and Alaska. We used 179 publicly available sea star transcriptomes to complement our approaches for densovirus discovery. Lastly, we focus the study to SSaDV, the first sea star densovirus discovered, by documenting its biogeography and putative tissue tropism. Transcriptomes contained mostly endogenized densovirus elements similar to the NS1 gene, while >30 complete and near-complete densoviral genomes were recovered from viral metagenomes. SSaDV was associated with nearly all tested species from southern California to Alaska, and in contrast to previous work, we show SSaDV is one genotype among a high diversity of densoviruses present in sea stars across the west coast of the United States and globally that are commonly associated with grossly normal (i.e. healthy or asymptomatic) animals. The diversity and ubiquity of these viruses in wild sea stars confounds the original hypothesis that one densovirus was the etiologic agent of SSWD.

Importance

The primary interest in sea star densoviruses, specifically SSaDV, has been their association with Sea Star Wasting Syndrome (SSWS), a disease that has decimated sea star populations across the west coast of the United States since 2013. The association of SSaDV to SSWS was originally drawn from metagenomic analyses concluding that it was (1) the only densovirus present in the metagenomic data and (2) the most likely viral candidate based on representation in symptomatic sea stars. We reassessed the original metagenomic data with additional genomic datasets and found that SSaDV was one of ten densoviruses present in the original dataset and was no more represented in symptomatic sea stars than in asymptomatic sea stars. Instead, SSaDV appears to be a widespread, generalist virus that exists among a large diversity of densoviruses present in sea star populations.
The emergence of phase separation as an organizing principle in bacteria
Authors: Azaldegui C.A. , Vecchiarelli A.G. , Biteen J.S.
Published: August 2020

Recent investigations in bacteria suggest that membraneless organelles play a crucial role in the subcellular organization of bacterial cells. However, the biochemical functions and assembly mechanisms of these compartments have not yet been completely characterized. This Review assesses the current methodologies used in the study of membraneless organelles in bacteria, highlights the limitations in determining the phase of complexes in cells that are typically an order of magnitude smaller than a eukaryotic cell, and identifies gaps in our current knowledge about the functional role of membraneless organelles in bacteria. Liquid-liquid phase separation (LLPS) is one proposed mechanism for membraneless organelle assembly. Overall, we outline the framework to evaluate LLPSin vivoin bacteria, we describe the bacterial systems with proposed LLPS activity, and we comment on the general role LLPS plays in bacteria and how it may regulate cellular function. Lastly, we provide an outlook for super-resolution microscopy and single-molecule tracking as tools to assess condensates in bacteria.

Statement of Significance

Though membraneless organelles appear to play a crucial role in the subcellular organization and regulation of bacterial cells, the biochemical functions and assembly mechanisms of these compartments have not yet been completely characterized. Furthermore, liquid-liquid phase separation (LLPS) is one proposed mechanism for membraneless organelle assembly, but it is difficult to determine subcellular phases in tiny bacterial cells. Thus, we outline the framework to evaluate LLPSin vivoin bacteria and we describe the bacterial systems with proposed LLPS activity in the context of these criteria.
The role of anionic amino acids in hydrolysis of poly-β-(1,6)-N-acetylglucosamine exopolysaccharides by the biofilm dispersing glycosidase Dispersin B
Authors: Breslawec Alexandra P. , Wang Shaochi , Li Crystal , Poulin Myles B.
Published: August 2020

The exopolysaccharide poly-β-(1→6)-N-acetylglucosamine (PNAG) is a major structural determinant of bacterial biofilms responsible for persistent and nosocomial infections. The enzymatic dispersal of biofilms by PNAG-hydrolyzing glycosidase enzymes, such as Dispersin B (DspB), is a possible approach to treat biofilm dependent bacterial infections. The cationic charge resulting from partial de-N-acetylation of native PNAG is critical for PNAG-dependent biofilm formation. We recently demonstrated that DspB has increased catalytic activity with de-N-acetylated PNAG oligosaccharides; however, there is still little known about the molecular interaction required for DspB to bind native de-N-acetylated PNAG polysaccharides. Here, we analyze the role of anionic amino acids surrounding the catalytic pocket of DspB in PNAG substrate recognition and hydrolysis using a combination of site directed mutagenesis, activity measurements using synthetic PNAG oligosaccharide analogs, andin vitrobiofilm dispersal assays. The results of these studies support a model in which bound PNAG is weakly associated with a shallow anionic groove on the DspB protein surface with recognition driven by interactions with the –1 GlcNAc residue in the catalytic pocket. An increased rate of hydrolysis for cationic PNAG was driven, in part, by interaction with D147 on the anionic surface. Moreover, we identified that a DspB mutant with improved hydrolysis of fully acetylated PNAG oligosaccharides correlates with improvedin vitrodispersal of PNAG dependent Staphylococcus epidermidis biofilms. These results provide insight into the mechanism of substrate recognition by DspB and suggest a method to improve DspB biofilm dispersal activity by mutation of the amino acids within the anionic binding surface.