bluuebunny/crossref_metadata_2025 huggingface dataset:
Curcuma longa L. Effects on Akt/mTOR Pathway and NF-κB Expression During Skin Wound Healing: An Immunohistochemical Study
Authors: Danilevicz Chris K. , Wagner Vivian P. , Ferreira Nilson , Bock Hugo , Salles Pilar Emily F. , Webber Liana P. , Schmidt Tuany R. , Alonso Ellen C.P. , de Mendonça Elismauro F. , Valadares Marize C. , Marreto Ricardo N. , Martins Manoela D.
Published: July 2021

Skin ulcers, wounds, or burns represent a burden for health care worldwide. Our aim was to explore the effects of mucoadhesive formulation with Curcuma longa L. extract mucoadhesive formulation containing curcumin (MFC) on skin healing in Wistar rats. Fifty-four rats were randomly allocated into 3 groups: control, vehicle, and MFC. A full-thickness circular wound was induced on the back of each animal. Two daily applications of the products were performed according to the experimental group. On days 3, 10, and 21, 6 animals in each group were euthanized. Clinical analysis was based on wound area. Histologic analysis was performed in hematoxylin and eosin-stained sections, with re-epithelization and inflammation being assessed by means of semiquantitative scores. To analyze the Akt/mTOR pathway, immunohistochemistry for phospho Akt (pAkt) and phospho ribosomal protein S6 were investigated. In addition, nuclear factor kappa-light-chain-enhancer of activated B cells immunolabeling was performed. Clinical analysis revealed wounds with a smaller area on days 3 and 10 in curcumin-treated animals. Histologically, MFC had a significant impact on inflammatory events on days 3 and 10 and promoted faster re-epithelization, which was evidenced on day 10. MFC-treated wounds exhibited pAkt upregulation on day 10 and both pAkt and phospho ribosomal protein S6 downregulation on day 21. Nuclear factor kappa-light-chain-enhancer of activated B cells expression varied through the evaluation periods; however, no significant difference was observed between groups. Collectively, our results indicate that MFC is efficient in accelerating cutaneous wound repair through modulation of the inflammatory process and stimulus of re-epithelization by an Akt/mTOR-dependent mechanism.
Readmission to an Acute Care Hospital During Inpatient Rehabilitation After Stroke
Authors: Herrmann Amanda A. , Chrenka Ella A. , Niemioja Gretchen M. , Othman Sally I. , Podoll Katherine R. , Oie Annika K. , Hussein Haitham M.
Published: July 2021

Objective

The aim of the study was to identify causes for readmission to acute care of patients admitted to inpatient rehabilitation facility after stroke.

Design

The institutional Uniform Data System for Medical Rehabilitation database was used to identify stroke patients who experienced readmission to acute care and an equal number of age-/sex-matched group of patients who successfully completed their inpatient rehabilitation facility stay during 2005–2018. Retrospective chart review was used to extract clinical data. The two study groups were compared using univariate and multivariate analyses.

Results

The rate of readmission to acute care was 4.7% (n = 89; age = 65 ± 14 yrs; 37% female; 65% White; 73% ischemic stroke). The most common indications for transfer were neurological (31%) and cardiovascular (28%). Compared with control group, the readmission to acute care group had statistically higher rates of comorbid conditions, lower median (interquartile range) Functional Independence Measure score on inpatient rehabilitation facility admission (55 [37–65] vs. 64 [51–78], P < 0.001), and a higher rate of sedative/hypnotic prescription (82% vs. 23%, P < 0.001).

Conclusions

Readmission to acute care is not common in our cohort. Patients who experienced readmission to acute care had higher medical complexity and were prescribed more sedative/hypnotic medications than the control group. Practitioners should be vigilant in patients who meet these criteria.
Week 96 extension results of a Phase 3 study evaluating long-acting cabotegravir with rilpivirine for HIV-1 treatment
Authors: Swindells Susan , Lutz Thomas , Van Zyl Lelanie , Porteiro Norma , Stoll Matthias , Mitha Essack , Shon Alyssa , Benn Paul , Huang Jenny O. , Harrington Conn M. , Hove Kai , Ford Susan L. , Talarico Christine L. , Chounta Vasiliki , Crauwels Herta , Van Solingen-Ristea Rodica , Vanveggel Simon , Margolis David A. , Smith Kimberly Y. , Vandermeulen Kati , Spreen William R.
Published: July 2021

Background:

ATLAS (NCT02951052), a phase 3, multicenter, open-label study, demonstrated that switching to injectable cabotegravir (CAB) with rilpivirine (RPV) long-acting dosed every 4 weeks was noninferior at week (W) 48 to continuing three-drug daily oral current antiretroviral therapy (CAR). Results from the W 96 analysis are presented.

Methods and design:

Participants completing W 52 of ATLAS were given the option to withdraw, transition to ATLAS-2M (NCT03299049), or enter an Extension Phase to continue long-acting therapy (Long-acting arm) or switch from CAR to long-acting therapy (Switch arm). Endpoints assessed at W 96 included proportion of participants with plasma HIV-1 RNA less than 50 copies/ml, incidence of confirmed virologic failure (CVF; two consecutive HIV-1 RNA ≥200 copies/ml), safety and tolerability, pharmacokinetics, and patient-reported outcomes.

Results:

Most participants completing the Maintenance Phase transitioned to ATLAS-2M (88%, n = 502/572). Overall, 52 participants were included in the W 96 analysis of ATLAS; of these, 100% (n = 23/23) and 97% (n = 28/29) in the Long-acting and Switch arms had plasma HIV-1 RNA less than 50 copies/ml at W 96, respectively. One participant had plasma HIV-1 RNA 50 copies/ml or higher in the Switch arm (173 copies/ml). No participants met the CVF criterion during the Extension Phase. No new safety signals were identified. All Switch arm participants surveyed preferred long-acting therapy to their previous daily oral regimen (100%, n = 27/27).

Conclusion:

In this subgroup of ATLAS, 98% (n = 51/52) of participants at the Extension Phase W 96 analysis maintained virologic suppression with long-acting therapy. Safety, efficacy, and participant preference results support the therapeutic potential of long-acting CAB+RPV treatment for virologically suppressed people living with HIV-1.
The future of Clostridioides difficile diagnostics
Authors: Mizusawa Masako , Carroll Karen C.
Published: July 2021

Purpose of review

Although the epidemiology of Clostridioides difficile has changed, this organism continues to cause significant morbidity and mortality. This review addresses current and future approaches to the diagnosis of C. difficile disease.

Recent findings

Over the last several years, large prospective studies have confirmed that there is no single optimal test for the diagnosis of C. difficile disease. The pendulum has swung from a focus on rapid molecular diagnosis during the years of the ribotype 027 epidemic, to a call for use of algorithmic approaches that include a test for toxin detection. In addition, diagnostic stewardship has been shown to improve test utilization, especially with molecular methods. Advances in testing include development of ultrasensitive toxin tests and an expansion of biomarkers that may be more C. difficile specific. Microbiome research may be leveraged to inform novel diagnostic approaches based on measurements of volatile and nonvolatile organic compounds in stool.

As rates of C. difficile infection decline, emphasis is now on improving test utilization and a quest for improved diagnostic approaches. These approaches may involve implementation of technologies that improve toxin testing, predict patients likely to have disease and/or a severe outcome, and harnessing research on changes in the microbiome to advance metabolomics.
Reasons for Hospitalization and In-Hospital Mortality in Adults With Dermatomyositis and Polymyositis
Authors: Pavon Mavi Rivera , Sanchez Juan Eduardo , Pescatore Jay , Edigin Ehizogie , Richardson Carrie , Manadan Augustine
Published: July 2021

Objective

Dermatomyositis (DM) and polymyositis (PM) are systemic autoimmune diseases that have been associated with high in-hospital mortality (IHM). The aim of this study was to use the National Inpatient Sample (NIS), a large US population database, to determine the reasons for hospitalization and IHM in patients with DM and PM.

Methods

We conducted a medical records review of adult DM/PM hospitalizations in 2016 and 2017 in acute care hospitals across the United States using the NIS. The reasons for IHM and reasons for hospitalization were divided into 19 broad categories based on their principal International Classification of Diseases, Tenth Revision, Clinical Modification (ICD-10) diagnosis.

Results

A total of 27,140 hospitalizations carried either a principal or secondary ICD-10 code for DM or PM. The main reasons for hospitalization were rheumatologic (22%, n = 6085), cardiovascular (15%, n = 3945), infectious (13%, n = 3515), respiratory (12%, n = 3170), and gastrointestinal, (8%, n = 2150). A total of 3.5% of all patients experienced IHM. Infectious (34%, n = 325), respiratory (23%, n = 215), and cardiovascular (15%, n = 140) diagnoses were the most common reasons for IHM. Sepsis ICD-10 A41.9 was the most frequent specific principal diagnosis for both hospitalizations and IHM.

Conclusions

Our analysis demonstrated that in the NIS the most common reasons for hospitalization in patients with DM/PM were rheumatologic diagnoses. However, IHM in these patients was most frequently from infectious diagnoses, highlighting the need for increased attention to infectious complications in these patients.
Impact of Field Strength in Clinical Cardiac Magnetic Resonance Imaging
Authors: Holtackers Robert J. , Wildberger Joachim E. , Wintersperger Bernd J. , Chiribiri Amedeo
Published: July 2021

Cardiac magnetic resonance imaging (MRI) is widely applied for the noninvasive assessment of cardiac structure and function, and for tissue characterization. For more than 2 decades, 1.5 T has been considered the field strength of choice for cardiac MRI. Although the number of 3-T systems significantly increased in the past 10 years and numerous new developments were made, challenges seem to remain that hamper a widespread clinical use of 3-T MR systems for cardiac applications. As the number of clinical cardiac applications is increasing, with each having their own benefits at both field strengths, no “holy grail” field strength exists for cardiac MRI that one should ideally use. This review describes the physical differences between 1.5 and 3 T, as well as the effect of these differences on major (routine) cardiac MRI applications, including functional imaging, edema imaging, late gadolinium enhancement, first-pass stress perfusion, myocardial mapping, and phase contrast flow imaging. For each application, the advantages and limitations at both 1.5 and 3 T are discussed. Solutions and alternatives are provided to overcome potential limitations. Finally, we briefly elaborate on the potential use of alternative field strengths (ie, below 1.5 T and above 3 T) for cardiac MRI and conclude with field strength recommendations for the future of cardiac MRI.
An Evaluation of Racial Diversity in Craniofacial Surgery Literature
Authors: Sobol Danielle L. , Cho Daniel Y. , Massie Jonathan P. , Burns Jacob R. , Crowe Christopher S. , Kneib Cameron J. , Lane Megan , Shakir Afaaf , Morrison Shane D. , Ettinger Russell E.
Published: July 2021

Implicit bias can lead to discrimination of certain populations within healthcare. Representation in medical literature is no exception and it is hypothesized that images with lighter skin tone are more prevalent than darker skin tones in craniofacial literature. Clinical photographs and figure graphics from 5 journals were examined for pre-defined years. Annals of Plastic Surgery, Aesthetic Surgery Journal, Journal of Craniofacial Surgery, Journal of Plastic, Reconstructive and Aesthetic Surgery, and Plastic and Reconstructive Surgery journals were reviewed. All craniofacial-focused articles containing at least one color image depicting human skin were included. 10,477 images and 627 graphics were evaluated using the Fitzpatrick scale as a guide. Most journals trended toward broader inclusion of nonwhite photographs and graphics over time. In 2016, 47% of articles published in Journal of Craniofacial Surgery included nonwhite images compared to Annals of Plastic Surgery (16%), Aesthetic Surgery Journal (40%), Journal of Plastic, Reconstructive and Aesthetic Surgery (25%), and Plastic and Reconstructive Surgery (7%). Comparison of domestic and international publications demonstrated that author's country of origin impacted the percentage of nonwhite clinical photographs for most journals. Comparisons of publications by country demonstrated increased diversity in Asia and the Middle East for clinical photographs but not graphics. The frequency of nonwhite figure graphics was staggeringly low, identified in only 18 articles across all journals and years. Craniofacial literature more commonly reflects white skin tones. The trend over time suggests increasing inclusion of racial diversity in clinical photographs; however, figure graphics remain less racially diverse. Time, country of origin, and publishing journal appear to play a role.
NLRP3 Inflammasome Mediates Neurodegeneration in Rats with Chronic Neuropathic Pain
Authors: Ren Changhe , Chen Milian , Mu Guo , Peng Suangchun , Liu Xiangbo , Ou Cehua
Published: July 2021

Patients with chronic neuropathic pain (NP) have a significantly increased risk of central nervous degeneration. Trigeminal neuralgia (TN) is a typical NP, and this manifestation is more obvious. In addition to severe pain, patients with TN are often accompanied by cognitive dysfunction and have a higher risk of central nervous system degeneration, but the mechanism is not clear. The NOD-like receptor 3 (NLRP3) inflammasome assembles inside of microglia on activation, which plays an important role in neurodegeneration such as Alzheimer disease. MCC950 is a specific blocker of NLRP3 inflammasome, which can improve the performance of degenerative diseases. Although NLRP3 inflammasome assembles inside of microglia on activation has been shown to be essential for the development and progression of amyloid pathology, its whether it mediates the neurodegeneration caused by NP is currently unclear. By constructing a rat model of chronic TN, we found that as the course of the disease progresses, TN rats have obvious cognitive and memory deficit. In addition, Tau hyperphosphorylation and Aβ expression increase in the cortex and hippocampus of the brain. At the same time, we found that NLRP3 expression increased significantly in model rats. Interestingly, NLRP3 specific blocker MCC950 can alleviate the neurodegeneration of trigeminal neuralgia rats to a certain extent. It is suggested that our NLRP3 inflammasome plays an important role in the neurodegeneration of trigeminal neuralgia rats. And it is related to the activation of central nervous system inflammation.
Value Analysis of Methods of Inguinal Hernia Repair
Authors: Glasgow Robert E. , Mulvihill Sean J. , Pettit Jacob C. , Young Jeffrey , Smith Brigitte K. , Vargo Daniel J. , Ray David M. , Finlayson Samuel R. G.
Published: July 2021

Objective:

Value is defined as health outcomes important to patients relative to cost of achieving those outcomes: Value = Quality/Cost. For inguinal hernia repair, Level 1 evidence shows no differences in long-term functional status or recurrence rates when comparing surgical approaches. Differences in value reside within differences in cost. The aim of this study is to compare the value of different surgical approaches to inguinal hernia repair: Open (Open-IH), Laparoscopic (Lap-IH), and Robotic (R-TAPP).

Methods:

Variable and fixed hospital costs were compared among consecutive Open-IH, Lap-IH, and R-TAPP repairs (100 each) performed in a university hospital. Variable costs (VC) including direct materials, labor, and variable overhead ($/min operating room [OR] time) were evaluated using Value Driven Outcomes, an internal activity-based costing methodology. Variable and fixed costs were allocated using full absorption costing to evaluate the impact of surgical approach on value. As cost data is proprietary, differences in cost were normalized to Open-IH cost.

Results:

Compared to Open-IH, VC for Lap-IH were 1.02X higher (including a 0.81X reduction in cost for operating room [OR] time). For R-TAPP, VC were 2.11X higher (including 1.36X increased costs for OR time). With allocation of fixed cost, a Lap-IH was 1.03X more costly, whereas R-TAPP was 3.18X more costly than Open-IH. Using equivalent recurrence as the quality metric in the value equation, Lap-IH decreases value by 3% and R-TAPP by 69% compared to Open-IH.

Conclusions:

Use of higher cost technology to repair inguinal hernias reduces value. Incremental health benefits must be realized to justify increased costs. We expect payors and patients will incorporate value into payment decisions.
Five Hundred Patients With Gut Malrotation
Authors: Abu-Elmagd Kareem , Mazariegos George , Armanyous Sherif , Parekh Neha , ElSherif Ayat , Khanna Ajai , Kosmach-Park Beverly , D’Amico Giuseppe , Fujiki Masato , Osman Mohammed , Scalish Marissa , Pruchnicki Amanda , Newhouse Elizabeth , Abdelshafy Ahmed A. , Remer Erick , Costa Guilherme , Walsh R. Matthew
Published: July 2021

Objectives:

Define clinical spectrum and long-term outcomes of gut malrotation. With new insights, an innovative procedure was introduced and predictive models were established.

Methods:

Over 30-years, 500 patients were managed at 2 institutions. Of these, 274 (55%) were children at time of diagnosis. At referral, 204 (41%) patients suffered midgut-loss and the remaining 296 (59%) had intact gut with a wide range of digestive symptoms. With midgut-loss, 189 (93%) patients underwent surgery with gut transplantation in 174 (92%) including 16 of 31 (16%) who had autologous gut reconstruction. Ladd's procedure was documented in 192 (38%) patients with recurrent or de novo volvulus in 41 (21%). For 80 patients with disabling gastrointestinal symptoms, gut malrotation correction (GMC) surgery “Kareem's procedure” was offered with completion of the 270° embryonic counterclockwise-rotation, reversal of vascular-inversion, and fixation of mesenteric-attachments. Concomitant colonic dysmotility was observed in 25 (31%) patients.

Results:

The cumulative risk of midgut-loss increased with volvulus, prematurity, gastroschisis, and intestinal atresia whereas reduced with Ladd's and increasing age. Transplant cumulative survival was 63% at 10-years and 54% at 20-years with best outcome among infants and liver-containing allografts. Autologous gut reconstruction achieved 78% and GMC had 100% 10-year survival. Ladd's was associated with 21% recurrent/de novo volvulus and worsening (P > 0.05) of the preoperative National Institute of Health patient-reported outcomes measurement information system gastrointestinal symptom scales. GMC significantly (P ≤ 0.001) improved all of the symptomatology domains with no technical complications or development of volvulus. GMC improved quality of life with restored nutritional autonomy (P < 0.0001) and daily activities (P < 0.0001).

Conclusions:

Gut malrotation is a clinicopathologic syndrome affecting all ages. The introduced herein definitive correction procedure is safe, effective, and easy to perform. Accordingly, the current standard of care practice should be redefined in this orphan population.
Centromedian Nucleus and Epilepsy
Authors: Velasco Francisco , Saucedo-Alvarado Pablo Eduardo , Reichrath Azari , Valdés-Quiroz Haydeé , Aguado-Carrillo Gustavo , Velasco Ana Luisa
Published: July 2021

Centromedian thalamic nucleus is an intralaminar nucleus with vast connectivity to cerebral cortex and basal ganglia. It receives afferents from the brain stem through the central tegmental tract and is part of the diffuse thalamic projection system. Because the reticulothalamic system has been related to initiation and propagation of epileptic activity (centroencephalic theory of epilepsy), deep brain stimulation has been proposed to interfere with seizure genesis or propagation. Centromedian thalamic nucleus is a large nucleus laying nearby the anatomical references for stereotaxis and therefore a convenient surgical target to approach. Electrodes are implanted in the anterior ventral lateral part of the nucleus (parvocellular area), guided by intraoperative recruiting responses elicited by unilateral 6 to 8 Hz electrical stimulation delivered through the deep brain stimulation electrode. Therapeutic stimulation is delivered with the following parameters: 60 Hz, 450 μs, 3.0 V. Seizure control runs between 69% and 83% in different reports, decreasing mainly generalized seizures from the start, with significant improvement in neuropsychological performance. Significant decrease in seizure occurs from hours to days after the onset of deep brain stimulation. Some reports refer that seizure improvement may occur by the simple insertion of the deep brain stimulation electrodes, and therefore, it was used to treat refractory epileptic status.
Glacieibacterium frigidum gen. nov., sp. nov., a novel member of the family Sphingosinicellaceae isolated from a glacier
Authors: Liu Qing , Yang Lei-Lei , Liu Hong-Can , Zhang Guo-Qing , Xin Yu-Hua
Published: July 2021

A novel Gram-stain-negative, rod-shaped, yellow bacterium, designated as LB1R16T, was isolated from the Laigu glacier on the Tibetan Plateau, PR China. Strain LB1R16T was catalase-positive, oxidase-negative and grew at 0–28 °C, pH 6.0–8.0 and in the absence of NaCl. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain LB1R16T belongs to the family

Sphingosinicellaceae

but formed an independent lineage. The highest level of 16S rRNA gene sequence similarities were found to

Polymorphobacter arshaanensis

DJ1R-1T (95.24 %),

Sphingoaurantiacus capsulatus

YLT33T (94.78 %) and

Sandarakinorhabdus limnophila

DSM 17366T (94.67 %). The genomic DNA G+C content was 68.8 mol%. The main cellular fatty acids were summed feature 8 (C18 : 1
 ω7c/C18 : 1
 ω6c), summed feature 3 (C16 : 1
 ω7c/C16 : 1
 ω6c), C16 : 0 and C12 : 0-OH. The respiratory quinone was ubiquinone-10. The polar lipids were phosphatidylethanolamine, phosphatidylglycerol, one sphingoglycolipid, one unidentified aminolipid, one unidentified phospholipid and two unidentified polar lipids, which were different from the type strains of

Polymorphobacter arshaanensis

,

Sphingoaurantiacus capsulatus

and

Sandarakinorhabdus limnophila

. Based on a polyphasic approach, a novel species of a new genus, Glacieibacterium frigidum gen. nov., sp. nov., within the family

Sphingosinicellaceae

is proposed. The type strain is LB1R16T (=CGMCC 1.11941T=NBRC 113873T).
uPTI: uniaxial permittivity tensor imaging of intrinsic density and anisotropy
Authors: Yeh Li-Hao , Ivanov Ivan E. , Byrum Janie R. , Chhun Bryant B. , Guo Syuan-Ming , Foltz Cameron , Hashemi Ezzat , Pérez-Bermejo Juan A. , Wang Huijun , Yu Yanhao , Kazansky Peter G. , Conklin Bruce R. , Han May H. , Mehta Shalin B.
Published: July 2021

Biological architecture is intrinsically tensorial. The permittivity tensor (PT) of biological material reports the density, angular anisotropy, symmetry, and 3D orientation of biomolecules. High-resolution measurement of PT can enable quantitative and label-free analysis of organelle, cell, and tissue architecture, but remains challenging. We report uniaxial permittivity tensor imaging (uPTI), a label-free computational imaging method for volumetric measurement of PT with diffraction-limited resolution. uPTI encodes the components of PT into intensity modulations using oblique illumination and polarization-resolved imaging. The high-dimensional data is decoded with a vectorial image formation model and a multi-channel convex optimization, assuming that the molecular distribution in each voxel has uniaxial symmetry. We describe a modular implementation of uPTI that can be multiplexed with complementary imaging modalities. We report volumes of uPT in mouse brain tissue, SARS-CoV-2 infected cardiomyocytes, RSV infected A549 cells, H&E stained tissue sections, isotropic beads, and anisotropic glass targets. uPTI enabled volumetric imaging of the 3D orientation and symmetry of organelles, cells, and tissue components with higher spatio-angular resolution than current vectorial tomography, ptychography, and light-field microscopy methods. We provide anopen sourceimplementation of the image formation model and reconstruction algorithms.
Transcriptomic divergence predicts morphological and ecological variation underlying an adaptive radiation
Authors: Bernal Moisés A. , Yule Daniel L. , Stott Wendylee , Evrard Lori , Dowling Thomas E. , Krabbenhoft Trevor J.
Published: July 2021

Groups of sympatric taxa with low inter-specific genetic differentiation, but considerable ecological differences, offer great opportunities to study the dynamics of divergence and speciation. This is the case of ciscoes (Coregonusspp.) in the Laurentian Great Lakes, which are characterized by a complex evolutionary history and are commonly described as having undergone an adaptive radiation. In this study, morphometrics, stable isotopes and transcriptome sequencing were used to study the relationships within theCoregonus artedicomplex in western Lake Superior. We observed general concordance for morphological, ecological and genomic variation, but the latter was more taxonomically informative as it showed less overlap among species in multivariate space. Low levels of genetic differentiation were observed between individuals morphologically identified asC. hoyiandC. zenithicus, and we hypothesize this could be associated with recent hybridization between the two species. Transcriptome-based single nucleotide polymorphisms exhibited significant divergence for genes associated with vision, development, metabolism and immunity, among species that occupy different habitats. This study highlights the importance of using an integrative approach when studying groups of taxa with a complex evolutionary history, as individual-level analyses of multiple independent datasets can provide a clearer picture of the patterns and processes associated with the origins of biodiversity.
A novel benzoxaborole works by targeting FabI inEscherichia coli
Authors: Mandal Soma , Parish Tanya
Published: July 2021

To combat the looming crisis of antimicrobial-resistant infections, there is an urgent need for novel antimicrobial discovery and drug target identification. The benzoxaborole series were previously identified as inhibitors of mycobacterial growth. Here, we demonstrate that a benzoxaborole is also active against the Gram negative bacterium,Escherichia coliin vitro. We isolated resistant mutants ofE. coliand subjected them to whole genome sequencing. We found mutations in the enoyl acyl carrier protein FabI. Mutations mapped around the active center site located close to the co-factor binding site. This site partially overlaps with the binding pocket of triclosan, a known FabI inhibitor. Similar to triclosan, the interaction of the benzoxaborole with FabI was dependent on the co-factor NAD+. Identification of the target of this compound inE. coliprovides scope for further development and optimization of this series for Gram negative pathogens.
Pervasiveciseffects of variation in copy number of large tandem repeats on local epigenetics and gene expression
Authors: Garg Paras , Martin-Trujillo Alejandro , Rodriguez Oscar L. , Gies Scott J. , Jadhav Bharati , Sharp Andrew J.
Published: July 2021

Variable Number Tandem Repeats (VNTRs) are composed of large tandemly repeated motifs, many of which are highly polymorphic in copy number. However, due to their large size and repetitive nature, they remain poorly studied. To investigate the regulatory potential of VNTRs, we used read-depth data from Illumina whole genome sequencing to perform association analysis between copy number of ~70,000 VNTRs (motif size ≥10bp) with both gene expression (404 samples in 48 tissues) and DNA methylation (235 samples in peripheral blood), identifying thousands of VNTRs that are associated with local gene expression (eVNTRs) and DNA methylation levels (mVNTRs). Using large-scale replication analysis in an independent cohort we validated 73-80% of signals observed in the two discovery cohorts, providing robust evidence to support that these represent genuine associations. Further, conditional analysis indicated that many eVNTRs and mVNTRs act as QTLs independently of other local variation. We also observed strong enrichments of eVNTRs and mVNTRs for regulatory features such as enhancers and promoters. Using the Human Genome Diversity Panel, we defined sets of VNTRs that show highly divergent copy numbers among human populations, show that these are enriched for regulatory effects on gene expression and epigenetics, and preferentially associate with genes that have been linked with human phenotypes through GWAS. Our study provides strong evidence supporting functional variation at thousands of VNTRs, and defines candidate sets of VNTRs, copy number variation of which potentially plays a role in numerous human phenotypes.
MRBLE-pep measurements reveal accurate binding affinities for B56, a PP2A regulatory subunit
Authors: Hein Jamin B. , Cyert Martha S. , Fordyce Polly M.
Published: July 2021

Signal transduction pathways rely on dynamic interactions between protein globular domains and short linear motifs (SLiMs). The weak affinities of these interactions are essential to allow fast rewiring of signaling pathways and downstream responses, but pose technical challenges for interaction detection and measurement. We recently developed a technique (MRBLE-pep) that leverages spectrally encoded hydrogel beads to measure binding affinities between a single protein and 48 different peptide sequences in a single small volume. In prior work, we applied it to map the binding specificity landscape between calcineurin and the PxIxIT SLiM (Nguyen et al. 2019). Here, using peptide sequences known to bind the PP2A regulatory subunit B56, we systematically compare affinities measured by MRBLE-pep or isothermal calorimetry (ITC) and confirm that MRBLE-pep accurately quantifies relative affinity over a wide dynamic range while using a fraction of the material required for traditional methods such as ITC.
Phospho-RNA sequencing with CircAID-p-seq
Authors: Piano Alessia Del , Barbieri Ruggero , Schmid Michael , Brocchieri Luciano , Tornaletti Silvia , Firrito Claudia , Minati Luca , Bernabo Paola , Signoria Ilaria , Lauria Fabio , Gillingwater Thomas H. , Viero Gabriella , Clamer Massimiliano
Published: July 2021

Accurate positional information concerning ribosomes and RNA binding proteins with respect to their transcripts is important to understand the global regulatory network underlying protein and RNA fate in living cells. Most footprinting approaches generate RNA fragments bearing a phosphate or cyclic phosphate groups at their 3′ end. Unfortunately, all current protocols for library preparation rely only on the presence of a 3′ hydroxyl group. Here, we developed circAID-p-seq, a PCR-free library preparation for 3′ phospho-RNA sequencing. We applied circAID-p-seq to ribosome profiling, which produces fragments protected by ribosomes after endonuclease digestion. CircAID-p-seq, combined with the dedicated computational pipeline circAidMe, facilitates accurate, fast, highly efficient and low-cost sequencing of phospho-RNA fragments from eukaryotic cells and tissues. While assessing circAID-p-seq to portray ribosomes engaged with transcripts, we provide a versatile tool to unravel any 3′-phospho RNA molecules.
DNR orders in SARS-CoV-2 patients: a retrospective validation study in a Swiss COVID-19 Center
Authors: Lo Presti Giorgia , Biggiogero Maira , Glotta Andrea , Biondi Carola , Horvath Zsofia , Leo Rosambra , Bona Giovanni , Franzetti-Pellanda Alessandra , Saporito Andrea , Ceruti Samuele , Capdevila Xavier
Published: July 2021

Background

The worldwide pandemic situation forced many hospitals to adapt COVID-19 management strategies. In this scenario, theSwiss Academy of Medical Sciences(SAMW/ASSM) organized national guidelines based on expert opinion to identify Do-Not-Resuscitate (DNR) patients, to reduce futile ICU admission and resource misuse. However, the practical impact of this standardized national protocol has not been yet evaluated. In our specialized COVID-19 Center, we investigated characteristics and mortality of DNR patients identified according to national standardized protocol, comparing them to non-DNR patients.

Methods

This was a pilot retrospective validation study, evaluating consecutive hospital admitted COVID-19 patients. Primary outcome was 30-days survival ofDNR patientsin comparison to thecontrol group. Secondary outcomes reported quality of treatment of deceased patients, especially of agitation/sedation and dyspnea, using respectively the Richmond Agitation-Sedation Scale – Palliative care (RASS-PAL) for sedation and agitation (+4/-5) and the modified Borg Scale for dyspnea (1-10).

Results

From March 16 to April 1, 2020, 213 consecutive patients were triaged; at 30-days follow-up, 9 patients (22.5%) died in theDNR group, 4 (2.2%) in thecontrol group. The higher mortality rate in theDNR groupwas further confirmed by Log-Rank Mantel-Cox (23.104, p < 0.0001). In theDNR-groupdeceased patients, end-of-life support was performed with oxygen (100%), opioids (100%) and sedatives (89%); the mean RASS-PAL improved from 2.2 to -1.8 (p < 0.0001) and the Borg scale improved from 5.7 to 4.7 (p = 0.581).

Conclusion

A national standardized protocol identified patients at higher risk of short-term death. Although the legal status of DNRs varies from country to country, the implementation of national standardized protocol could be the way to guarantee a better treatment of COVID-19 patients in a pandemic situation with limited resources.
Modeling COVID-19 vaccine efficacy and coverage towards herd-immunity in the Basque Country, Spain
Authors: Stollenwerk Nico , Mar Javier , Van-Dierdonck Joseba Bidaurrazaga , Ibarrondo Oliver , Estadilla Carlo , Aguiar Maíra
Published: July 2021

Vaccines have measurable efficacies, obtained first from vaccine trials. However, vaccine efficacy is not a static measure upon licensing, and the long term population studies are very important to evaluate vaccine performance and impact. COVID-19 vaccines were developed in record time and although the extent of sterilizing immunity is still under evaluation, the currently licensed vaccines are extremely effective against severe disease, with vaccine efficacy significantly higher after the full immunization schedule. We investigate the impact of vaccines which have different efficacies after first dose and after the second dose administration schedule, eventually considering different efficacies against severe disease as opposed to overall infection. As a proof of concept, we model the vaccine performance of hospitalization reduction at the momentary scenario of the Basque Country, Spain, with population in a mixed vaccination setting, giving insights into the population coverage needed to achieve herd immunity in the current vaccination context.
Longitudinal monitoring of DNA viral loads in transplant patients using quantitative metagenomic next-generation sequencing
Authors: Carbo Ellen C. , Russcher Anne , Kraakman Margriet E.M. , de Brouwer Caroline S. , Sidorov Igor A. , Feltkamp Mariet C.W. , Kroes Aloys C.M. , Claas Eric C.J. , de Vries Jutte J.C.
Published: July 2021

Introduction

Immunocompromised patients are prone to reactivations of multiple latent DNA viruses. Viral load monitoring by single-target quantitative PCRs (qPCR) is the current cornerstone for virus quantification. In this study, a metagenomic next-generation sequencing (mNGS) approach was used for identification and load monitoring of transplantation-related DNA viruses.

Methods

Longitudinal plasma samples from six patients that were qPCR-positive for cytomegalovirus (CMV), Epstein-Barr virus (EBV), BK polyoma virus (BKV, adenovirus (ADV), parvovirus B19 (B19V), and torque teno-virus (TTV) were sequenced using the quantitative metagenomic Galileo Viral Panel Solution (Arc Bio, LLC) reagents and bioinformatics pipeline combination. Qualitative and quantitative performance was analysed with focus on viral load ranges relevant for clinical decision-making.

Results

All pathogens identified by qPCR were also identified by mNGS. In addition, BKV, CMV, and HHV6B were detected by mNGS which were not ordered initially but could be confirmed by qPCR. Viral loads determined by mNGS correlated with the qPCR results, with inter-method differences in viral load per virus ranging from 0.19 log10 IU/ml for EBV to 0.90 log10 copies/ml for ADV. TTV, analysed by mNGS in a semi-quantitative way, showed a mean difference of 3.0 log10 copies/ml. Trends over time in viral load determined by mNGS and qPCR were comparable, and clinical thresholds for initiation of treatment were equally indicated by mNGS.

Conclusion

The Galileo Viral Panel for quantitative mNGS performed comparable to qPCR with regard to detection and viral load determination, within clinically relevant ranges of patient management algorithms.
Changes in seam number and location induce holes within microtubules assembled from porcine brain tubulin and in Xenopus egg cytoplasmic extracts
Authors: Guyomar Charlotte , Bousquet Clément , Ku Siou , Heumann John , Guilloux Gabriel , Gaillard Natacha , Heichette Claire , Duchesne Laurence , Steinmetz Michel O. , Gibeaux Romain , Chrétien Denis
Published: July 2021

Microtubules are tubes of about 25 nm in diameter that are critically involved in a variety of cellular functions including motility, compartmentalization, and division. They are considered as pseudo-helical polymers whose constituent αβ-tubulin heterodimers share lateral homotypic interactions, except at one unique region called the seam. Here, we used a segmented sub-tomogram averaging strategy to reassess this paradigm and analyze the organization of the αβ-tubulin heterodimers in microtubules assembled from purified porcine brain tubulin in the presence of GTP and GMPCPP, and in Xenopus egg cytoplasmic extracts. We find that in all conditions, microtubules incorporate variable protofilament and/or tubulin subunit helical-start numbers, as well as variable numbers of seams. Strikingly, the seam number and location vary along individual microtubules, generating holes of one to a few subunits in size within their lattices. Together, our results reveal that the formation of mixed and discontinuous microtubule lattices is an intrinsic property of tubulin that requires the formation of unique lateral interactions without longitudinal ones. They further suggest that microtubule assembly is tightly regulated in a cytoplasmic environment.
Structure of bacterial communities in Japanese-style bathrooms: Comparative sequencing of bacteria in shower water and showerhead biofilms using a portable nanopore sequencer
Authors: Fujiyoshi So , Nishiuchi Yukiko , Maruyama Fumito
Published: July 2021

Showers are one of the main exposure routes to diverse microbes for end users in built environments. Bacteria in water are responsible for biofilm formation on surfaces, and the inside of a showerhead is a specific niche. Here, for the purpose of microbial characterization, source estimation and possibility of infection, the bacterial compositions of both shower water and showerhead biofilms in the same bathroom were determined and compared using a portable nanopore sequencer. The results suggest that specific bacteria in source water would primarily adhere to the surface of the showerhead where they subsequently form biofilms, and the community compositions within biofilms largely vary depending on environmental factors. The relative abundance of several pathogenic bacterial genera in both water and biofilm samples was low. We suggest that it is important to manage risk of infection in each household, and rapid on-site analysis of microbial communities will allow the realization.
The myotendinous junction marker collagen XXII enables zebrafish postural control learning and optimal swimming performance through its force transmission activity
Authors: Malbouyres Marilyne , Guiraud Alexandre , Lefrançois Christel , Salamito Mélanie , Nauroy Pauline , Bernard Laure , Sohm Frédéric , Allard Bruno , Ruggiero Florence
Published: July 2021

Although the myotendinous junction (MTJ) is essential for skeletal muscle integrity, its contribution to skeletal muscle function remains largely unknown. Here, we show that CRISPR-Cas9-mediated gene ablation of the MTJ marker col22a1 in zebrafish identifies two distinctive phenotypic classes: class 1 individuals reach adulthood with no overt muscle phenotype while class 2 display severe movement impairment and eventually dye before metamorphosis. Yet mutants that are unequally affected are all found to display defective force transmission attributed to a loss of ultrastructural integrity of the MTJ and myosepta, though with distinct degrees of severity. The behavior-related consequences of the resulting muscle weakness similarly reveal variable phenotypic expressivity. Movement impairment at the critical stage of swimming postural learning eventually causes class 2 larval death by compromising food intake while intensive exercise is required to uncover a decline in muscle performance in class 1 adults. By confronting MTJ gene expression compensation and structural, functional and behavioral insights of MTJ dysfunction, our work unravels variable expressivity of col22a1 mutant phenotype. This study also underscores COL22A1 as a candidate gene for myopathies associated with dysfunctional force transmission and anticipates a phenotypically heterogeneous disease.
Joint Gene Network Construction by Single-Cell RNA Sequencing Data
Authors: Dong Meichen , He Yiping , Jiang Yuchao , Zou Fei
Published: July 2021

Summary

In contrast to differential gene expression analysis at single gene level, gene regulatory networks (GRN) analysis depicts complex transcriptomic interactions among genes for better understandings of underlying genetic architectures of human diseases and traits. Recently, single-cell RNA sequencing (scRNA-seq) data has started to be used for constructing GRNs at a much finer resolution than bulk RNA-seq data and microarray data. However, scRNA-seq data are inherently sparse which hinders direct application of the popular Gaussian graphical models (GGMs). Furthermore, most existing approaches for constructing GRNs with scRNA-seq data only consider gene networks under one condition. To better understand GRNs under different but related conditions with single-cell resolution, we propose to construct Joint Gene Networks with scRNA-seq data (JGNsc) using the GGMs framework. To facilitate the use of GGMs, JGNsc first proposes a hybrid imputation procedure that combines a Bayesian zero-inflated Poisson (ZIP) model with an iterative low-rank matrix completion step to efficiently impute zero-inflated counts resulted from technical artifacts. JGNsc then transforms the imputed data via a nonparanormal transformation, based on which joint GGMs are constructed. We demonstrate JGNsc and assess its performance using synthetic data. The application of JGNsc on two cancer clinical studies of medulloblastoma and glioblastoma identifies novel findings in addition to confirming well-known biological results.
Nucleotide Biosynthesis Links Glutathione Metabolism to Ferroptosis Sensitivity
Authors: Tarangelo Amy , Kim Joon Tae , Long Jonathan Z. , Dixon Scott J.
Published: July 2021

Nucleotide synthesis is a metabolically demanding process essential for cell division. Several anti-cancer drugs that inhibit nucleotide metabolism induce apoptosis. How inhibition of nucleotide metabolism impacts non-apoptotic cell death is less clear. Here, we report that inhibition of nucleotide metabolism by the p53 pathway is sufficient to suppress the non-apoptotic cell death process of ferroptosis. Mechanistically, stabilization of wild-type p53 and induction of the p53 target gene CDKN1A (p21) leads to decreased expression of the ribonucleotide reductase (RNR) subunits RRM1 and RRM2. RNR is the rate-limiting enzyme of de novo nucleotide synthesis that reduces ribonucleotides to deoxyribonucleotides in a glutathione-dependent manner. Direct inhibition of RNR conserves glutathione which can then be used to limit the accumulation of toxic lipid peroxides, preventing the onset of ferroptosis. These results support a mechanism linking p53-dependent regulation of nucleotide metabolism to non-apoptotic cell death.
Circular-Linear Copulae for Animal Movement Data
Authors: Hodel Florian H. , Fieberg John R.
Published: July 2021

Animal movement is often modeled in discrete time, formulated in terms of steps taken between successive locations at regular time intervals. Steps are characterized by the distance between successive locations (step-lengths) and changes in direction (turn angles). Animals commonly exhibit a mix of directed movements with large step lengths and turn angles near 0 when traveling between habitat patches and more wandering movements with small step lengths and uniform turn angles when foraging. Thus, step-lengths and turn angles will typically be cross-correlated.

Most models of animal movement assume that step-lengths and turn angles are independent, likely due to a lack of available alternatives. Here, we show how the method of copulae can be used to fit multivariate distributions that allow for correlated step lengths and turn angles.

We describe several newly developed copulae appropriate for modeling animal movement data and fit these distributions to data collected on fishers (Pekania pennanti). The copulae are able to capture the inherent correlation in the data and provide a better fit than a model that assumes independence. Further, we demonstrate via simulation that this correlation can impact movement patterns (e.g. rates of dispersion overtime).

We see many opportunities to extend this framework (e.g. to consider autocorrelation in step attributes) and to integrate it into existing frameworks for modeling animal movement and habitat selection. For example, copula could be used to more accurately sample available locations when conducting habitat-selection analyses.
An efficient polymer cocktail-based transportation method for cartilage tissue, yielding chondrocytes with enhanced hyaline cartilage expression during in vitro culturing
Authors: Katoh Shojiro , Yoshioka Hiroshi , Suzuki Shoji , Nakajima Hiroyuki , Iwasaki Masaru , Senthilkumar Rajappa , Preethy Senthilkumar , Abraham Samuel JK
Published: July 2021

Chondrocytes are used in cell-based therapies such as autologous chondrocyte implantation (ACI) and matrix-associated cartilage implantation (MACI). To transport the cartilage tissue to the laboratory for in vitro culturing, phosphate-buffered saline (PBS), Euro-Collins solution (ECS) and Dulbecco Modified Eagle Medium (DMEM) are commonly employed at 4-8 deg C. In this study, eight samples of human cartilage biopsy tissues from elderly patients with severe osteoarthritis undergoing arthroscopy, which would otherwise have been discarded, were used. The cartilage tissue samples were compared to assess the cell yield between two transportation groups: i) a thermo-reversible gelation polymer (TGP) based method without cool preservation (~25 deg C) and ii) ECS transport at 4 deg C. These samples were subjected to in vitro culture in a two-dimensional (2D) monolayer for two weeks and subsequently in a three-dimensional (3D) TGP scaffold for six weeks. The cell count obtained from the tissues transported in TGP was higher (0.2 million cells) than those transported in ECS (0.08 million cells) both after initial processing and after in vitro culturing for 2 weeks in 2D (18 million cells compared with 10 million cells). In addition, mRNA quantification demonstrated significantly higher expression of Col2a1 and SOX-9 in 3D-TGP cultured cells and lower expression of COL1a1 in RT-PCR, characteristic of the hyaline cartilage phenotype, than in 2D culture. This study confirms that the TGP cocktail is suitable for both the transport of human cartilage tissue and for in vitro culturing to yield better-quality cells for use in regenerative therapies.