bluuebunny/crossref_metadata_2025 huggingface dataset:
Opioid and Sedative-Hypnotic Prescriptions Among Post-9/11 Veteran VA Users Nationwide With Traumatic Brain Injury, 2012-2020
Authors: Holmer Haley K. , Gilbert Tess A. , Ashraf Alexandria J. , O'Neil Maya E. , Carlson Kathleen F.
Published: September 2021

Objective:

Many post-9/11 Veterans have received Department of Veterans Affairs (VA) healthcare for traumatic brain injury (TBI). Pain conditions are prevalent among these patients and are often managed with opioid analgesics. Opioids may impose unique risks to Veterans with a history of TBI, especially when combined with other psychotropic medications. We examined receipt of opioid and sedative-hypnotic prescriptions among post-9/11 Veterans with TBI who received VA care nationally between 2012 and 2020.

Setting:

Nationwide VA outpatient care.

Participants:

Veterans with, versus without, clinician-confirmed TBI based on the VA's Comprehensive TBI Evaluation (CTBIE) were followed up for subsequent years in which they received VA care.

Design:

A historical cohort study.

Main Measures:

Proportions of Veterans who received opioid, benzodiazepine, and nonbenzodiazepine sedative-hypnotic prescriptions were compared by CTBIE outcome (TBI yes/no) and by year; overlaps between medication classes, long-term opioid therapy, and high-dose opioid therapy were also examined. Among those with confirmed TBI, logistic regression was used to examine associations between veteran characteristics and likelihood of these potentially high-risk opioid use outcomes.

Results:

Among 69 752 Veterans with clinician-confirmed TBI, 26.9% subsequently received opioids. The prevalence receiving opioids each year increased from 2012 (16.7%) to 2014 (17.7%), and then decreased each of the following years through 2020 (5.8%). Among Veterans with TBI who received opioids, large proportions also received benzodiazepine (30.1%) and nonbenzodiazepine (36.0%) sedative-hypnotic prescriptions; these proportions also decreased in recent years. In both bivariable and multivariable regression models, Veterans' demographic, TBI, and clinical characteristics were associated with likelihood of potentially high-risk opioid use.

Conclusions:

VA opioid prescribing to Veterans with TBI has decreased in recent years but remains an important source of risk, particularly when considering coprescriptions of sedative-hypnotic medication. Understanding patterns of psychotropic prescription use among Veterans with TBI can highlight important healthcare and rehabilitation needs in this large patient cohort.
Admission for Isolated Low-Grade Solid Organ Injury May Not Be Necessary in Pediatric Patients
Authors: Butt Erin , Kotagal Meera , Shebesta Kaaren , Bailey Allison , Moody Suzanne , Falcone Richard
Published: September 2021

Background:

Recent publications indicate that blunt solid organ injuries can be safely managed with reduced length of stay using pathways focused on hemodynamics. We hypothesized that pediatric patients with isolated blunt Grade I or II solid organ injuries may be safely discharged after brief observation with appropriate outpatient follow-up.

Objective:

The purpose of this study is to evaluate the need for admission of pediatric trauma patients with isolated low-grade solid organ injury resulting from blunt trauma.

Methods:

We performed a retrospective cohort study of trauma registry data from 2011 to 2018 to identify isolated blunt Grade I or II solid organ injuries among children younger than 19 years. “Complication or intervention” was defined as transfusions, transfer to the intensive care unit, repeat imaging, decrease in Hgb greater than 2 g/dl, fluid bolus after initial resuscitation, operation or interventional radiology procedure, or readmission within 1 week.

Results:

A total of 51 patients were admitted to the trauma service with isolated Grade I or II blunt solid organ injuries during the 8-year study period. The average age was 11 years. Among isolated Grade I or II injuries, seven (14%) had “complication or intervention” including greater than 2 g/dl drop in Hgb in four patients (8%), follow-up ultrasonography for pain in one patient (2%), readmission for pain in one patient (2%), or a fluid bolus in two patients (4%). None required transfusion or surgery. The most common mechanism of injury was sports related (45%), and the average length of stay was 1 day.

Conclusion:

Among a cohort of 51 patients with isolated blunt Grade I or II solid organ injuries, none required a significant intervention justifying need for admission. All “complication or intervention” patients observed were of limited clinical significance. We recommend that hemodynamically stable patients with isolated low-grade solid organ injuries may be discharged from the emergency department after a brief observation along with appropriate instructions and pain management.
The Pediatric Trauma Society Annual Meeting: An Analysis of Scholarly Output From the First 5 Years
Authors: Knaus Maria E. , Berg Gina M. , Vogel Adam M. , Prince Jose M. , Burd Randall S. , Gosain Ankush
Published: September 2021

Background:

The Pediatric Trauma Society (PTS) is a multidisciplinary organization, with scientific presentations at its annual meeting addressing trauma care from prehospital through rehabilitation.

Objective:

The purpose of this study was to identify and describe the scholarly areas of focus of presentations at the annual meeting over the society's first 5 years and evaluate research dissemination.

Methods:

Data were collected on abstracts presented between 2014 and 2018, including titles, authors, and abstract classification. PubMed and Google Scholar searches identified abstracts that resulted in publications. Journal impact factors were identified.

Results:

Over 5 years, 491 of 635 (77.3%) abstracts were accepted. The number of submitted and accepted abstracts increased, but the acceptance rate was stable (range = 72.1%–81.2%, p = NS [nonsignificant]). The most frequently accepted categories included “Epidemiology,” “Abdominal or Thoracic Trauma,” and “Neurosurgery or Traumatic Brain Injury (TBI),” whereas “Trauma Nursing” and “Quality Improvement” were less common. Among the 2014–2016 abstracts, 55.4% of podium and 24.3% of poster presentations were published. Abstracts categorized as “Epidemiology,” “Education & Injury Prevention,” and “Neurosurgery or TBI” were commonly presented but uncommonly published. The median journal impact factor of publications was 2.1 and 2.0 for podium and poster presentations, respectively (ranging from 0.11 to 10.25).

Conclusion:

Most of the scholarly effort presented at the PTS remains unpublished. Published work is mainly in low-impact factor journals. Mentorship in the publication process and encouragement of multidisciplinary collaboration within the society are needed to address limitations in the number and potential impact of the scientific content of the annual meeting. This type of analysis is relevant not only to the PTS but also to any professional society seeking to improve its impact.
Cytomegalovirus-Associated Mild Encephalopathy/Encephalitis With Reversible Splenial Lesion
Authors: Fu Mao-Lin , Han Ning , Wang Wei
Published: September 2021

Introduction:

Mild encephalopathy with a reversible splenial lesion (MERS) is a clinical-radiologic syndrome presenting with a reversible lesion in the splenium of the corpus callosum. MERS is associated with many potential etiologies, including cytomegalovirus (CMV) infection in children. We report an adult patient with CMV-associated MERS.

Case Report:

A previously healthy 25-year-old man was admitted with a 4-day history of fever, headache, and vomiting. Brain magnetic resonance imaging demonstrated an isolated lesion of the splenium of the corpus callosum with hyperintensity on T2 and diffusion-weighted sequences and reduced values on apparent diffusion coefficient maps. High throughput gene detection for pathogens in cerebrospinal fluid revealed infection with CMV. The splenial lesion resolved 4 weeks after onset.

Conclusion:

This is the first report an adult patient with CMV-associated MERS. Recognition of this clinical-radiologic syndrome can guide diagnosis and management.
Pain sensitivity does not differ between obese and healthy weight individuals
Authors: Emerson Nichole M. , Nahman-Averbuch Hadas , Peugh James L. , Coghill Robert C.
Published: September 2021

Introduction:

There is emerging evidence suggesting a relationship between obesity and chronic pain.

Objectives:

The aim of this study was to determine whether pain-free obese individuals display altered pain responses to acute noxious stimuli, thus raising the possibility of greater pain sensitivity and potential susceptibility for chronic pain development.

Methods:

Psychophysical and anthropometric data were collected from 38 individuals with an obese body mass index (BMI) classification (BMI ≥ 30) and 41 age/sex-matched individuals of a healthy BMI (BMI < 24.9). Because BMI may be an inaccurate index of obesity, additional anthropometric parameters of central adiposity and percent body fat were examined. Pain responses to suprathreshold noxious heat and cold stimuli were examined. Subjects provided pain intensity and unpleasantness ratings to noxious heat (49°C) applied at varying durations and locations (ventral forearm/lower leg). Cold pain ratings, thresholds, and tolerances were obtained after immersion of the hand in a cold-water bath (0–2°C). Between-group differences in pain responses, as well as relationships between pain responses and obesity parameters, were examined. Importantly, confounds that may influence pain such as anxiety, depression, impulsivity, sleepiness, and quality of life were assessed.

Results:

No between-group differences in pain sensitivity to noxious heat and cold stimuli were found. No relationships were found between central adiposity or body fat (percentage or distribution) and pain responses to noxious heat or cold stimuli.

Conclusions:

Obesity has minimal influence on pain sensitivity. Accordingly, it is unlikely that obesity alone increases susceptibility for chronic pain development through amplification of nociceptive processes.
Brain gamma-aminobutyric acid, but not glutamine and glutamate levels are lower in older adults with chronic musculoskeletal pain: considerations by sex and brain location
Authors: Cruz-Almeida Yenisel , Forbes Megan , Cohen Ronald C. , Woods Adam J. , Fillingim Roger B. , Riley Joseph L. , Porges Eric S.
Published: September 2021

Introduction and Objectives:

GABAergic and glutamatergic neurotransmitter systems are central to the pathophysiology of chronic pain and are equally affected by aging processes. We measured levels of frontal gamma-aminobutyric acid (GABA) and the combined resonance of glutamate and glutamine (Glx) in vivo using proton magnetic resonance spectroscopy (1H-MRS) to elucidate age-specific and pain-specific associations with clinical and experimental pain in older adults.

Methods:

Younger (18–24, n = 24) and older (60–94, n = 41) individuals part of a larger study (Neuromodulatory Examination of Pain and Mobility Across the Lifespan [NEPAL]) underwent questionnaires, quantitative sensory testing, and 1H-MRS Mescher-Garwood point-resolved spectroscopy to measure GABA and Glx levels in prefrontal and sensorimotor brain regions.

Results:

Older participants had significantly lower sensorimotor, but not prefrontal, GABA and Glx levels, compared with younger controls (P's < 0.05). Younger controls had significantly higher prefrontal and sensorimotor GABA, but not Glx, levels compared with older controls and older adults with chronic pain (P's < 0.05). Older males with chronic pain had significantly lower prefrontal GABA compared with older and younger male controls (P's < 0.05). Prefrontal GABA, but not Glx, was significantly associated with self-reported and experimental pain measures (P's < 0.05). Our results are the first to focus exclusively on age and pain differences in GABA and Glx including younger and older controls to elucidate aging and pain contributions to brain GABAergic and glutamatergic processes.

Conclusion:

Evaluation of both the neuroinhibitory and neuroexcitatory mechanisms provide promising potential for improving both our understanding of the mechanisms of chronic pain in aging and opportunities for effective, individualized treatments.
Dyella telluris sp. nov. and Dyella acidiphila sp. nov., isolated from forest soil of Dinghushan Biosphere Reserve, China
Authors: Huang Tao , Fu Jia-cheng , Dong Shuo-han , Zhang Qiu-mei , Wu Ting-ting , Qiu Li-hong
Published: September 2021

Cells of bacterial strains G9T and 7MK23T, isolated from forest soil samples collected from the Dinghushan Biosphere Reserve, Guangdong Province, PR China, were Gram-stain-negative, aerobic and rod-shaped. Strain G9T was motile with single polar flagellum and grew at 12–37 °C (optimum, 28 °C), pH 4.5–8.0 (optimum, pH 6.0–7.5) and in the presence of 0–3.5 % NaCl (optimum, 1.5%, w/v); while strain 7MK23T was non-motile and grew at 12–42 °C (optimum, 28–33 °C), pH 2.5–8.5 (optimum, pH 4.5–6.5) and NaCl levels of 0–1.0 % (optimum, 0–0.5 %, w/v). Phylogenetic analysis based on 16S rRNA gene sequences revealed that both isolates fell within the cluster of the genus

Dyella

. The closely related species (with a 16S rRNA gene sequence similarity >98.65%) of strain G9T were

Dyella terrae

JS14-6T (99.0 %),

D

.

kyungheensis

THG-B117T (98.8 %) and

D

.

amyloliquefaciens

DHC06T (98.7 %) while that of strain 7MK23T were

D

.

mobilis

DHON07T (99.2 %) and

D

.

flava

DHOC52T (99.1 %), but the average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between strains G9T, 7MK23T and the closely related

Dyella

species listed above were in the ranges of 77.5–83.8 % and 22.0–27.0 %, much lower than the species demarcation lines of 95.5 and 70 %, respectively. Phylogenomic analyses using UBCG and Phylophlan also supported that these two strains represent two novel species of

Dyella

. The major fatty acids of strain G9T were iso-C15 : 0, iso-C17 : 1
 ω9c and iso-C17 : 0 while that of strain 7MK23T were iso-C15 : 0 and anteiso-C15 : 0. Ubiquinone-8 was the only respiratory quinone detected in both strains. The polar lipids of strain G9T consisted of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, and several unknown phospholipids, aminophospholipids, aminolipids and lipid while strain 7MK23T contained phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine and several unknown phospholipids and aminophospholipids. The DNA G+C contents of strains G9T and 7MK23T were 64.7 and 63.4 mol%, respectively. On the basis of 16S rRNA gene sequence phylogenetic and phylogenomic analyses as well as phenotypic data obtained, we propose that strains G9T and 7MK23T represent two novel species of the genus

Dyella

, for which the names Dyella telluris sp. nov. (type strain G9T=KACC 21725T=GDMCC 1.2132T) and Dyella acidiphila sp. nov. (type strain 7MK23T=KCTC 62739T=GDMCC 1.1446T) are proposed.
Effectiveness of COVID-19 Vaccines Against SARS-CoV-2 Infection During a Delta Variant Epidemic Surge in Multnomah County, Oregon, July 2021
Authors: Barlow Russell S. , Jian Kevin , Larson Lindsey
Published: September 2021

Background

Coronavirus disease 2019 (COVID-19) vaccines have been shown to be highly effective in preventing SARS-CoV-2 infection within controlled trials and real-world vaccine effectiveness (VE) studies. Recent reports have estimated reduced VE with the emergence and dissemination of the B.1.617.2 variant (“Delta variant”). We assess VE in Multnomah County, Oregon during a delta variant related epidemic expansion.

Methods

A test-negative design (TND) matched case-control analysis was performed to estimate the effectiveness of vaccination against SARS-CoV-2 infection during July 2021. Cases included a random sample of individuals that tested positive for SARS-CoV-2 and were reported by electronic laboratory report, were >15 years of age, and had no prior known SARS-CoV-2 infections. Controls were age and postal code matched individuals that tested negative for SARS-CoV-2 during July 2021. Immunization status was assessed using the Oregon ALERT Immunization Information system.

Results

500 case-control pairs were matched (n=1000). 40.4% of cases were up-to-date on COVID-19 immunizations compared to 64.6% of controls. Effectiveness of any completed COVID-19 immunization was 73% (95% Confidence Interval [CI] 49-86%), 74% (95% CI 65-85%) for mRNA immunizations (BNT162b2, mRNA-1273), and 72% (95% CI 47-85%) for individuals partially immunized with mRNA immunizations.

Conclusions

Our findings estimate high, yet reduced, VE during Delta variant dissemination. These results highlight the importance of COVID-19 immunizations for reducing SARS-CoV-2 infection while juxtaposing the need for additional non-pharmaceutical interventions. Importantly, the reduced VE identified here may predict future reductions in vaccine performance in the context of ongoing viral genetic drift.
Sars-Cov-2 antibody titer 3 months post-vaccination is affected by age, gender, smoking and vitamin D
Authors: Parthymou Anastasia , Habeos Evagelia E , Habeos George I , Deligakis Apostolos , Livieratos Ektoras , Marangos Markos , Chartoumpekis Dionysios V
Published: September 2021

Context

Vaccination against Sars-Cov-2 is in full swing during COVID-19 pandemic. One of the efficient methods to evaluate response to vaccination is the assessment of humoral immunity by measuring Sars-Cov-2 antibody titer. Identification of factors that affect the humoral response is important so as to ameliorate the responses to vaccination or identify vulnerable groups that may need vaccination boosters.

Objective

We investigated the effect of anthropometric parameters (age, BMI), smoking, diabetes, statin use hypertension and levels of 25(OH)D and DHEAS to the Sars-Cov-2 antibody titer.

Methods

In this longitudinal observational cohort study 712 subjects were tested for Sars-Cov-2 antibodies 3 months after the second dose of BNT162b2 vaccine. Multiple linear regression analysis was performed to identify which factors are associated with the antibody titer.

Results

We identified age to be negatively associated with antibody titer (p=0.0073) and male sex (p=0.0008). However, interaction of age and gender was significant (p<0.0001) highlighting the finding that only after the age of 40 years men had lower antibody levels than women. DHEAS, an aging marker, was not associated with the antibody titer. Smoking was also associated with low antibody titer (p=0.0008) while overweight or obese subjects did not have different antibody response compared to normal weight individuals. Although diabetic and hypertensive subjects trended towards lower antibody titer, this association was not statistically significant. Replete vitamin D levels were associated with higher antibody titers (p=0.00422).

Conclusions

Age, male sex and smoking negatively affects antibody titer while 25(OH)D is associated with increased Sars-Cov-2 antibody titers.
The locus coeruleus shows a spatial pattern of structural disintegration in Parkinson’s disease
Authors: Madelung Christopher F. , Meder David , Fuglsang Søren A. , Marques Marta M. , Boer Vincent O. , Madsen Kristoffer H. , Petersen Esben T. , Hejl Anne-Mette , Løkkegaard Annemette , Siebner Hartwig R.
Published: September 2021

Background

Parkinson’s disease (PD) leads to a loss of neuromelanin positive, noradrenergic neurons in the locus coeruleus (LC) which has been implicated in non-motor dysfunction. “Neuromelanin sensitive” magnetic resonance imaging (MRI) has emerged as a promising tool for mapping the structural integrity of LC in vivo.

Objectives

To identify spatial patterns of structural LC disintegration in PD and regions in the LC where structural disintegration is associated with specific non-motor dysfunctions.

Methods

42 patients with PD and 24 age-matched healthy volunteers underwent ultra-high field MRI of the LC using a “neuromelanin sensitive” magnetization transfer weighted (MTw) sequence. The contrast-to-noise ratio of the MTw signal (CNRMTw) served as an estimate of structural integrity, slice- and voxel-wise analyses of CNRMTw were performed to map the spatial pattern of structural disintegration, complemented by Principal Component Analysis (PCA). We also tested for correlations between CNRMTw and the severity of non-motor symptoms.

Results

Mean CNRMTw of LC was reduced in patients relative to controls. The attenuation of CNRMTw was not uniformly expressed in LC, but confined to the middle and caudal LC. CNRMTw attenuation in caudal LC scaled with the orthostatic drop in systolic blood pressure and apathy ratings. PCA identified a bilaterally expressed component that was more weakly expressed in patients. This component was characterized by a gradual change in CNRMTw along the rostro-caudal and dorso-ventral axes of the nucleus. The individual expression score of this component reflected the overall severity of non-motor symptoms.

Conclusion

PD related structural disintegration of LC mainly affects its caudal part and may determine the individual expression of specific non-motor symptoms such as orthostatic dysregulation or apathy.
Immune response elicited from heterologous SARS-CoV-2 vaccination: Sinovac (CoronaVac) followed by AstraZeneca (Vaxzevria)
Authors: Yorsaeng Ritthideach , Vichaiwattana Preeyaporn , Klinfueng Sirapa , Wongsrisang Lakkhana , Sudhinaraset Natthinee , Vongpunsawad Sompong , Poovorawan Yong
Published: September 2021

Limited COVID-19 vaccines in many countries have delayed mass-immunization. Although individuals fully vaccinated with Vaxzevria (AstraZeneca) have higher antibody levels than those with CoronaVac (Sinovac), heterologous prime-boost with CoronaVac-Vaxzevria yielded comparable antibody levels to two-dose Vaxzevria. Combination use of different available vaccines may be warranted in Thailand, which faces limited vaccine choice and supply.
Severe COVID-19 is associated with sustained biochemical disturbances and prolonged symptomatology; A retrospective single-centre cohort study
Authors: Simjanoska Marija , Mitrev Zan , Villa Gianluca , Griffin Daniel O. , Rosalia Rodney A.
Published: September 2021

This manuscript has been withdrawn following a formal investigation by the Zan Mitrev Clinic Scientific Committee.
Local SARS-CoV-2 Peptide-Specific Immune Responses in Lungs of Convalescent and Uninfected Human Subjects
Authors: Goliwas Kayla F. , Wood Anthony M. , Simmons Christopher S. , Khan Rabisa , Khan Saad A. , Wang Yong , Berry Joel L. , Athar Mohammad , Mobley James A. , Kim Young-il , Thannickal Victor J. , Harrod Kevin S. , Donahue James M. , Deshane Jessy S.
Published: September 2021

Multi-specific and long-lasting T cell immunity have been recognized as indicators for long term protection against pathogens including the novel coronavirus SARS-CoV-2, the causative agent of the COVID-19 pandemic. Functional significance of peripheral memory T cells in individuals recovering from COVID-19 (COVID-19+) are beginning to be appreciated; but little is known about lung resident memory T cells (lung TRM) in SARS-CoV-2 infection. Here, we utilize a perfused three dimensional (3D) human lung tissue model and identify pre-existing local T cell immunity against SARS-CoV-2 proteins in lung tissues. We report ex vivo maintenance of functional multi-specific IFN-γ secreting lung TRM in COVID-19+ and their induction in lung tissues of vaccinated COVID-19+. Importantly, we identify SARS-CoV-2 peptide-responding B cells and IgA+ plasma cells in lung tissues of COVID-19+ in ex vivo 3D-tissue models. Our study highlights the importance of balanced and local anti-viral immune response in the lung with persistent induction of TRM and IgA+ plasma cells for future protection against SARS-CoV-2 infection. Further, our data suggest that inclusion of multiple viral antigens in vaccine approaches may broaden the functional profile of memory T cells to combat the severity of coronavirus infection.
Patch-Clamp Proteomics of Single Neuronal Somas in Tissue Using Electrophysiology and Subcellular Capillary Electrophoresis Mass Spectrometry
Authors: Choi Sam B. , Polter Abigail M. , Nemes Peter
Published: September 2021

Understanding of the relationship between cellular function and molecular composition holds a key to next-generational therapeutics but requires measurement of all types of molecules in cells. Developments in sequencing enabled semi-routine measurement of single-cell genomes and transcriptomes, but analytical tools are scarce for detecting diverse proteins in tissue-embedded cells. To bridge this gap for neuroscience research, we report the integration of patch-clamp electrophysiology with subcellular shot-gun proteomics by high-resolution mass spectrometry (HRMS). Recording of electrical activity permitted identification of dopaminergic neurons in the substantia nigra pars compacta. Ca. 20–50% of the neuronal soma content, containing an estimated 100 pg of total protein, was aspirated into the patch pipette filled with ammonium bicarbonate. About ~1 pg of somal protein, or ~0.25% of the total cellular proteome, was analyzed on a custom-built capillary electrophoresis (CE) high-resolution mass spectrometer (HRMS). A series of experiments were conducted to systematically enhance detection sensitivity through refinements in sample processing and detection, allowing us to quantify ~275 different proteins from somal aspirate-equivalent protein digests. From single neurons, patch-clamp proteomics of the soma quantified 91, 80, and 95 different proteins from 3 different dopaminergic neurons, or 157 proteins in total. Quantification revealed detectable proteomic differences between the somal protein samples. Analysis of canonical knowledge predicted rich interaction networks between the proteins. The integration of patch-clamp electrophysiology with subcellular CE-HRMS proteomics expands the analytical toolbox of neuroscience.
PatchMAN docking: Modeling peptide-protein interactions in the context of the receptor surface
Authors: Khramushin Alisa , Tsaban Tomer , Varga Julia , Avraham Orly , Schueler-Furman Ora
Published: September 2021

Peptide docking can be perceived as a subproblem of protein-protein docking. However, due to the short length and flexible nature of peptides, many do not adopt one defined conformation prior to binding. Therefore, to tackle a peptide docking problem, not only the relative orientation between the two partners, but also the bound conformation of the peptide needs to be modeled. Traditional peptide-centered approaches use information about the peptide sequence to generate a representative conformer ensemble, which can then be rigid body docked to the receptor. Alternatively, one may look at this problem from the viewpoint of the receptor, namely that the protein surface defines the peptide bound conformation.We present PatchMAN (Patch-Motif AligNments), a novel peptide docking approach which uses structural motifs to map the receptor surface with backbone scaffolds extracted from protein structures. On a non-redundant set of protein-peptide complexes, starting from free receptor structures, PatchMAN successfully models and identifies near-native peptide-protein complexes in 62% / 81% within 2.5Å / 5Å RMSD, with corresponding sampling in 81% / 100% of the cases, outperforming other approaches. PatchMAN leverages the observation that structural units of peptides with their binding pocket can be found not only within interfaces, but also within monomers. We show that the conformation of the bound peptide is sampled based on the structural context of the receptor only, without taking into account any sequence information. Beyond peptide docking, this approach opens exciting new avenues to study principles of peptide-protein association, and to the design of new peptide binders.
Time to stop; agent-based modelling of chemoaffinity with competition
Authors: James Sebastian S. , Wilson Stuart P.
Published: September 2021

In the classic Chemoaffinity theory, the retinotectal axon projection is thought to use pairs of orthogonal signalling gradients in the retina to specify the eventual location of synapses made on the surface of the tectum/superior colliculus. Similar orthogonal gradients in the tectum provide a coordinate system which allows the axons to match their prespecified destination with the correct location. Although the Ephrins have been shown to guide axons toward their destination, there has yet to emerge a complete account of the local interactions which halt the axonal growth cones in the correct locations to recreate the topography of the retinal cells. The model of Simpson and Goodhill (2011) provides an account of the basic topographic arrangement of cells on the tectum, as well as reproducing well known surgical and genetic manipulation experiments. However, it suffers from the absence of a local chemotactic guidance mechanism. Instead, each agent in their model is given instantaneous knowledge of the vector that would move it toward its pre specified destination. In addition to the globally supervised chemoaffinity term, Simpson and Goodhill (2011) introduced a competitive interaction for space between growth cone agents and a receptor-ligand axon-axon interaction in order to account for the full set of experimental manipulations. Here, we propose the replacement of the chemoaffinity term with a gradient following model consisting of axonal growth cone agents which carry receptor molecule expression determined by their soma’s location of origin on the retina. Growth cones move on the simulated tectum guided by two pairs of opposing, orthogonal signalling molecules representing the Ephrin ligands. We show that with only the chemoaffinity term and a receptor-ligand based axon-axon interaction term (meaning that all growth cone interactions are by receptor-ligand signalling), a full range of experimental manipulations to the retinotectal system can be reproduced. Furthermore, we show that the observation that competition is not and essential requirement for axons to find their way (Gosse et al., 2008) is also accounted for by the model, due to the opposing influences of signalling gradient pairs. Finally, we demonstrate that, assuming exponentially varying receptor expression in the retina, ligand expression should either be exponential if the receptor-ligand signal induces repulsion (i.e. gradient descent) or logarithmic if the signal induces attraction (gradient ascent). Thus, we find that a model analogous to the one we presented in James et al. (2020) that accounts for murine barrel patterning is also a candidate mechanism for the arrangement of the more continuous retinotectal system.
Top-down identification of keystone species in the microbiome
Authors: Amit Guy , Bashan Amir
Published: September 2021

Keystone species in ecological communities are native species that play an especially important role in the stability of their ecosystem and can also be potentially used as its main drivers. However, we still lack an effective framework for identifying these species from the available metagenomic data without the notoriously difficult step of reconstructing the detailed network of inter-specific interactions. Here we propose a top-down identification framework, which detects keystones by their total influence on the rest of the species. Our method does not assume pairwise interactions or any specific underlying dynamics and is appropriate to both perturbation experiments and metagenomic cross-sectional surveys. When applied to real metagenomic data of the human gastrointestinal microbiome, we detect a set of candidate keystones and find that they are often part of a keystone module – multiple candidate keystones species with correlated occurrence. The keystones analysis of single-time-point cross-sectional data is also later verified by evaluation of two-time-points longitudinal sampling. Our framework represents a necessary advancement towards the reliable identification of these key players of complex, real-world microbial communities.
Transcriptome analysis reveals high tumor heterogeneity with respect to re-activation of stemness and proliferation programs
Authors: Baranovsky Artem , Ivanov Timofei , Granovskaya Marina , Papatsenko Dmitri , Pervouchine Dmitri
Published: September 2021

Significant alterations in signaling pathways and transcriptional regulatory programs together represent major hallmarks of many cancers. These, among all, include the reactivation of stemness, which is registered by the expression of pathways that are active in the embryonic stem cells (ESCs). Here, we assembled gene sets that reflect the stemness and proliferation signatures and used them to analyze a large panel of RNA-seq data from The Cancer Genome Atlas (TCGA) Consortium in order to specifically assess the expression of stemness-related and proliferation-related genes across a collection of different tumor types. We introduced a metric that captures the collective similarity of the expression profile of a tumor to that of ESCs, which showed that stemness and proliferation signatures vary greatly between different tumor types. We also observed a high degree of intertumoral heterogeneity in the expression of stemness- and proliferation-related genes, which was associated with increased hazard ratios in a fraction of tumors and mirrored by high intratumoral heterogeneity across cancer cells in single cell RNA-seq datasets. Taken together, these results indicate that the expression of stemness signatures is highly heterogeneous and cannot be used as a universal determinant of cancer. This calls into question the universal validity of diagnostic tests that are based on stem cell markers.

Author summary

Cancer is a deadly human disease which is characterized by uncontrolled proliferation of abnormal cells. Stemness, or the expression of stem cell markers, has been identified as a key feature for cancer progression and in many cases correlates with patient survival. In this work, we reanalyzed a large cohort of cancers from TCGA (The Cancer Genome Atlas) collection and single-cell cancer data, and found that the degree of stemness reactivation varies greatly between different tumor types, between different tumors of the same type, and also different cells within a tumor. The observed stemness heterogeneity implies that the expression of stemness markers cannot be used as a universal determinant of cancer and calls into question the validity of stemness-based tests that are frequently used for cancer diagnostics.
Implications of sample treatment on characterization of the riverine environmental metabolome
Authors: Nelson Amelia R. , Toyoda Jason , Chu Rosalie K. , Tolic Nikola , Garayburu-Caruso Vanessa A. , Saup Casey M. , Renteria Lupita , Wells Jacqueline R. , Stegen James C. , Wilkins Michael J. , Danczak Robert E.
Published: September 2021

High-resolution mass spectrometry techniques are widely used in the environmental sciences to characterize natural organic matter and, when utilizing these instruments, researchers must make multiple decisions regarding sample pre-treatment and the instrument ionization mode. To identify how these choices alter organic matter characterization and resulting conclusions, we analyzed a collection of 17 riverine samples from East River, CO (USA) under four PPL-based Solid Phase Extraction (SPE) treatment and electrospray ionization polarity (e.g., positive and negative) combinations: SPE (+), SPE (-), non-SPE (-), and non-SPE (+). The greatest number of formula assignments were achieved with SPE-treated samples due to the removal of compounds that could interfere with ionization. Furthermore, the SPE (-) treatment captured the most formulas across the widest chemical compound diversity. In addition to a reduced number of assigned formulas, the non-SPE datasets resulted in altered thermodynamic interpretations that could cascade into incomplete assumptions about the availability of organic matter pools for microbial heterotrophic respiration. Thus, we infer that the SPE (-) treatment is the best single method for characterizing environmental organic matter pools unless the focus is on lipid-like compounds, in which case we recommend a combination of SPE (-) and SPE (+) to adequately characterize these molecules.

Synopsis

We provide data-driven sample treatment and ionization mode recommendations to researchers who aim to use high-resolution mass spectrometry to characterize environmental organic matter.

Abstract Art
Alterations in gut microbiome composition and function in irritable bowel syndrome and increased probiotic abundance with daily supplementation
Authors: Phan Joann , Nair Divya , Jain Suneer , Montagne Thibaut , Flores Demi Valeria , Nguyen Andre , Dietsche Summer , Gombar Saurabh , Cotter Philip
Published: September 2021

Background

Irritable bowel syndrome (IBS) is characterized by abdominal discomfort and irregular bowel movements and stool consistency. Because there are different symptoms associated with IBS, it is difficult to diagnose the role of the microbiome in IBS.

Objective

Here, we present a study that includes metagenomic sequencing of stool samples from subjects with the predominant subtypes of IBS and a healthy cohort. We collected longitudinal samples from individuals with IBS who took daily made-to-order precision probiotic and prebiotic supplementation throughout the study.

Materials and Methods

This study includes a population of 489 individuals with IBS and 122 healthy controls. All stool samples were subjected to shotgun metagenomic sequencing. Precision probiotics and prebiotics were formulated for all subjects with longitudinal timepoints.

Results

There was significant variation explained in the microbiome between the healthy and IBS cohorts. Individuals with IBS had a lower gut microbiome diversity and reduced anti-inflammatory microbes compared to the healthy controls. Eubacterium rectale and Faecalibacterium prausnitzii were associated with healthy microbiomes while Shigella species were associated with IBS. Pathway analysis indicated a functional imbalance of short chain fatty acids, vitamins, and a microbial component of Gram-negative bacteria in IBS compared to healthy controls. In the longitudinal dataset, there was a significant difference in microbiome composition between timepoints 1 and 3. There was also a significant increase in the overall microbiome score and relative abundances of probiotic species used to target the symptoms associated with IBS.

Conclusions

We identified microbes and pathways that differentiate healthy and IBS microbiomes. In response to precision probiotic supplementation, we identified a significant improvement in the overall microbiome score in individuals with IBS. These results suggest an important role for probiotics in managing IBS symptoms and modulation of the microbiome as a potential management strategy.

Importance

An estimated 35 million people in the United States and 11.5% of the population globally are affected by IBS. Immunity, genetics, environment, diet, small intestinal bacterial overgrowth (SIBO), and the gut microbiome are all factors that contribute to the onset or triggers of IBS. With strong supporting evidence that the gut microbiome may influence symptoms associated with IBS, elucidating the important microbes that contribute to the symptoms and severity is important to make decisions for targeted treatment. As probiotics have become more common in treating IBS symptoms, identifying effective probiotics may help inform future studies and treatment.
Rescuing Low Frequency Variants within Intra-Host Viral Populations directly from Oxford Nanopore sequencing data
Authors: Liu Yunxi , Kearney Joshua , Mahmoud Medhat , Kille Bryce , Sedlazeck Fritz J , Treangen Todd J
Published: September 2021

Infectious disease monitoring on Oxford Nanopore Technologies (ONT) platforms offers rapid turnaround times and low cost, exemplified by well over a half of million ONT SARS-COV-2 datasets. Tracking low frequency intra-host variants has provided important insights with respect to elucidating within host viral population dynamics and transmission. However, given the higher error rate of ONT, accurate identification of intra-host variants with low allele frequencies remains an open challenge with no viable solutions available. In response to this need, we present Variabel, a novel approach and first method designed for rescuing low frequency intra-host variants from ONT data alone. We evaluated Variabel on both within patient and across patient paired Illumina and ONT datasets; our results show that Variabel can accurately identify low frequency variants below 0.5 allele frequency, outperforming existing state-of-the-art ONT variant callers for this task. Variabel is open-source and available for download at: www.gitlab.com/treangenlab/variabel.
CRISPRs are associated with bacterial expansion in the human gut during the first year of life
Authors: Wu Jiqiu , Barraclough Timothy G.
Published: September 2021

The dynamics of the gut microbiome in infancy have a profound impact on health in adulthood, but the ecological mechanism underlying the dynamics between bacteria and bacteriophages remains poorly understood. CRISPR is a bacterial adaptive immune system to resist bacteriophages; however, the role they play in the dynamics in infants’ gut microbiota is unknown. In this work, using large-scale metagenomic sequencing data from 82 Sweden infants’ gut microbiomes, 1882 candidate CRISPRs were identified and their dynamics were analyzed. The results showed CRISPRs were distributed in dominant bacteria and could target distinct bacteriophages at different time points with largely alternated spacers. In the putative identical CRISPRs, we found the CRISPRs could acquire new spacers and loss old spacers during the first year. In addition, it is the first time to report that gender was a major factor to determine the bacterial richness and the number of CRISPRs and host range of bacteriophages was narrow in silico. Therefore, we concluded that CRISPRs were associated with bacterial expansion. This work improves the understanding of the ecological mechanism behind dynamics in the early life of the human gut and substantially expands the repertoire of predicted CRISPRs providing a resource to study the function of bacterial unknown genes and to enhance the performance of these beneficial bacteria by CRISPR gene-editing technology.
A cell atlas of the fly kidney
Authors: Xu Jun , Liu Yifang , Li Hongjie , Tarashansky Alexander J. , Kalicki Colin H. , Hung Ruei-Jiun , Hu Yanhui , Comjean Aram , Kolluru Sai Saroja , Wang Bo , Quake Stephen R , Luo Liqun , McMahon Andrew P. , Dow Julian A.T. , Perrimon Norbert
Published: September 2021

Like humans, insects rely on precise regulation of their internal environments to survive. The insect renal system consists of Malpighian tubules and nephrocytes that share similarities to the mammalian kidney. Studies of the Drosophila Malpighian tubules and nephrocytes have provided many insights into our understanding of the excretion of waste products, stem cell regeneration, protein reabsorption, and as human kidney disease models. Here, we analyzed single-nucleus RNA sequencing (snRNA-seq) data sets to characterize the cell types of the adult fly kidney. We identified 11 distinct clusters representing renal stem cells (RSCs), stellate cells (SCs), regionally specific principal cells (PCs), garland nephrocyte cells (GCs) and pericardial nephrocytes (PNs). Analyses of these clusters revealed many new interesting features. For example, we found a new, previously unrecognized cell cluster: lower segment PCs that express Esyt2. In addition, we find that the SC marker genes RhoGEF64c, Frq2, Prip and CG10939 regulate their unusual cell shape. Further, we identified transcription factors specific to each cluster and built a network of signaling pathways that are potentially involved in mediating cell-cell communication between Malpighian tubule cell types. Finally, cross-species analysis allowed us to match the fly kidney cell types to mouse kidney cell types and planarian protonephridia - knowledge that will help the generation of kidney disease models. To visualize this dataset, we provide a web-based resource for gene expression in single cells (https://www.flyrnai.org/scRNA/kidney/). Altogether, our study provides a comprehensive resource for addressing gene function in the fly kidney and future disease studies.
Acropetal and basipetal cardenolide transport in Erysimum cheiranthoides (wormseed wallflower)
Authors: Alani Martin L. , Younkin Gordon C. , Mirzaei Mahdieh , Kumar Pavan , Jander Georg
Published: September 2021

Plant specialized metabolites are often subject to within-plant transport and have tissue-specific distribution patterns. Among plants in the Brassicaceae, the genus Erysimum is unique in producing not only glucosinolates but also cardenolides as defense against insect herbivory. Ten cardenolides were detected with varying abundance in different tissues of Erysimum cheiranthoides (wormseed wallflower). As is predicted by the optimal defense theory, cardenolides were most abundant in young leaves and reproductive tissues. The lowest concentrations were observed in senescing leaves and roots. Crosses between wildtype E. cheiranthoides and a mutant line with an altered cardenolide profile showed that the seed cardenolide phenotype is determined entirely by the maternal genotype. Prior to the development of the first true leaves, seedling cotyledons also had the maternal cardenolide profile. Hypocotyl grafting experiments showed that the root cardenolide profile is determined entirely by the aboveground plant genotype. In further grafting experiments, there was no evidence of cardenolide transport into the leaves, but a mixed cardenolide profile was observed in the stems and inflorescences of plants that had been grafted at vegetative and flowering growth stages, respectively. Together, these results indicate that E. cheiranthoides leaves are a site of cardenolide biosynthesis and therefore also the plant tissue that is most likely to be expressing the relevant biosynthetic genes.
The influence of 4-thiouridine labeling on pre-mRNA splicing outcomes
Authors: Altieri Jessie , Hertel Klemens J.
Published: September 2021

Metabolic labeling is a widely used tool to investigate different aspects of pre-mRNA splicing and RNA turnover. The labeling technology takes advantage of native cellular machineries where a nucleotide analog is readily taken up and incorporated into nascent RNA. One such analog is 4-thiouridine (4sU). Previous studies demonstrated that the uptake of 4sU at elevated concentrations (>50µM) and extended exposure led to inhibition of rRNA synthesis and processing, presumably induced by changes in RNA secondary structure. Thus, it is possible that 4sU incorporation may also interfere with splicing efficiency. To test this hypothesis, we carried out splicing analyses of pre-mRNA substrates with varying levels of 4sU incorporation (0-100%). We demonstrate that increased incorporation of 4sU into pre-mRNAs decreased splicing efficiency. The overall impact of 4sU labeling on pre-mRNA splicing efficiency negatively correlates with the strength of splice site signals such as the 3’ and the 5’ splice sites. Introns with weaker splice sites are more affected by the presence of 4sU. We also show that transcription by T7 polymerase and pre-mRNA degradation kinetics were impacted at the highest levels of 4sU incorporation. Increased incorporation of 4sU caused elevated levels of abortive transcripts, and fully labeled pre-mRNA is more stable than its uridine-only counterpart. Cell culture experiments show that a small number of alternative splicing events were modestly, but statistically significantly influenced by metabolic labeling with 4sU at concentrations considered to be tolerable (40 µM). We conclude that at high 4sU incorporation rates small, but noticeable changes in pre-mRNA splicing can be detected when splice sites deviate from consensus. Given these potential 4sU artifacts, we suggest that appropriate controls for metabolic labeling experiments need to be included in future labeling experiments.