bluuebunny/crossref_metadata_2025 huggingface dataset:
The Indirect Purchaser Rule and Private Enforcement of Antitrust Law: A Reassessment
Authors: Smith Spencer
Published: December 2020

Despite broad statutory language authorizing “any person” injured by an antitrust law violation to sue for damages, the Supreme Court of the United States has construed that language to bar antitrust damages claims by indirect purchasers, such as consumers two or more steps removed from antitrust violators. The Court and some scholars have justified the indirect purchaser rule on the ground that assigning direct purchasers exclusive rights to recover antitrust damages increases the likelihood of suit. But this article presents new evidence that the rule reduced private antitrust litigation by twenty percent. It argues that the rule should be abandoned, consistent with the statutory text.
Profiles After Acute Traumatic Injury: The Non-battle Injury Impact on Readiness at a Single Military Treatment Facility
Authors: Aranda Marcos , Poloni Dana , Coffin Elisabeth , Hendren Bryan
Published: December 2020

Introduction

Physical profiling is critical to the individual medical readiness of all military service members. This classification system provides detailed information about an individual’s functional abilities. Profile information is used in determining whether a service member is medically deployable or non-deployable. Limited research has been conducted on the impact of acute traumatic injuries on duty status and profiles in the non-deployed setting. The purpose of this study was to characterize injured service members presenting to a CONUS MTF emergency department whose acute traumatic injury resulted in a profile.

Materials and Methods

A retrospective review of patients who presented to the Dwight D. Eisenhower Army Medical Center emergency department with traumatic injuries from January 1, 2019, to December 31, 2019, was performed. Patients were identified by searching electronic encounter records for trauma-specific ICD-10 codes. Returned patient records were then reviewed for active duty status, branch, age, gender, rank, mechanism, protective equipment, substance use, procedures, and disposition. Profiles of soldiers were reviewed for indication and duration. Patients with profiles were compared to those without profiles. Correlation with age was determined by t-test, correlation with profile length was determined by ANOVA, and correlation with the remaining categorical variables was determined with chi-squared analysis.

Results

Eight hundred and thirty-two service members were reviewed. One hundred and eight (13%) soldiers had a profile. Patients were 23.2% female with no difference between the two groups. Patients were an average of 28.7 years old. The most common mechanisms were physical training (PT) (33.1%) and falls (12.9%). Physical training and motor vehicle collisions were more common in the profile group. Combatives and crush injuries of the hand were less common in the profile group. Major procedures were more common in the profile group, and minor procedures were less common. Admissions, quarters, immediate referrals, and release without limitations were more common in the profile group. The mean duration of profiles was 48.9 days, and 7.4% were permanent.

Conclusions

Non-battle injuries in the garrison setting are a significant threat to readiness. This analysis of acute traumatic injuries suggests that mechanism of injury was similar to previous reports with PT and falls being most common. Interventions should be targeted at PT and motor vehicle collisions as these were more common in the profile group. This series is also similar to previous reports that extremity injuries are the most common cause of profiles. However, TBIs were more common in our analysis. Further research that encompasses all garrison MTF acute traumatic injuries is needed to define the true impact on readiness and guide development of injury prevention strategies.
Fifty years of University-industry collaboration: a global bibliometrics overview
Authors: Bastos Elisa Cordeiro , Sengik Aline Rossales , Tello-Gamarra Jorge
Published: December 2020

This article presents a bibliometric overview of publications on university-industry collaboration (UIC) from the last fifty years (1969–2018). Among the results that were obtained, three main ones come to light. First, this article presents a complete panorama of UIC research from the past fifty years. Secondly, we were able to note that the UIC research trajectory can be divided into four generations which are represented by different phases: the discovery phase (1969–1979), the development phase (1980–1999), the expansion phase (2000–2010) and the consolidation phase (2011–2018). Furthermore, the connections and evolution pertaining to these four generations were identified. The third result was the identification of eight research trends within the UIC context: ‘UIC topics’ (especially: motivation, channels, barriers and results), ‘engineering education’, ‘societies and institutions’, ‘knowledge transfer’, ‘innovation’, ‘entrepreneurial university’, ‘sustainability’ and ‘developing countries’.
Save the Economy, Liberty, and Yourself: Christian Nationalism and Americans’ Views on Government COVID-19 Restrictions
Authors: Perry Samuel L , Whitehead Andrew L , Grubbs Joshua B
Published: December 2020

During the COVID-19 pandemic, state and local governments implemented lockdown restrictions that were tremendously polarizing. Those on the cultural and political left supported restrictions hoping to protect the vulnerable, while those on the cultural and political right challenged restrictions citing threats to the economy and liberty. We theorize that libertarian and authoritarian impulses within Christian nationalism undergirded much of the resistance to government restrictions. Analyzing national panel data collected before and during the pandemic, we find Christian nationalism is either the first or second strongest predictor that Americans prioritize the economy and liberty and deprioritize the vulnerable when asked about government restrictions. Religiosity works in the opposite direction, however. Findings underscore the centrality of Christian nationalism as an ideological driver of far-right discourse shaping COVID-19 responses.
The Long-term Impact of Whiplash Injuries on Patient Symptoms and the Associated Degenerative Changes Detected Using MRI
Authors: Watanabe Kota , Daimon Kenshi , Fujiwara Hirokazu , Nishiwaki Yuji , Okada Eijiro , Nojiri Kenya , Watanabe Masahiko , Katoh Hiroyuki , Shimizu Kentaro , Ishihama Hiroko , Fujita Nobuyuki , Ichihara Daisuke , Tsuji Takashi , Nakamura Masaya , Matsumoto Morio
Published: December 2020

Study Design.

A longitudinal, 20-year comparative study of patients with whiplash-associated disorders (WAD).

Objective.

The aim of this study was to clarify the long-term impact of WAD on patient symptoms and on magnetic resonance imaging (MRI) findings of the cervical spine, in comparison with asymptomatic volunteers.

Summary of Background Data.

The long-term impact of WAD has not been fully elucidated.

Methods.

Between 1993 and 1996, we conducted a cross-sectional comparative study of 508 acute WAD patients and 497 asymptomatic volunteers, all of whom underwent MRI on cervical spine and physical examinations. For this 20-year follow-up comparative study, 75 WAD patients and 181 control subjects aged <60 years were recruited from the original cohort. The MRI findings, including discs’ signal intensities, posterior disc protrusions, anterior dural compressions, spinal cord disc space narrowing, and foraminal stenoses, were evaluated using two to four numerical grades. The results of the WAD patients and control subjects were compared.

Results.

In this follow-up, the prevalence of shoulder stiffness (72.0% vs. 45.9%), headache (24.0% vs. 12.2%), and arm pain (13.3% vs. 3.9%) were significantly greater in WAD patients than in control subjects. The multiregression analysis revealed that a history of WAD was associated with shoulder stiffness (odds ratio [OR]: 3.36), headache (OR: 2.39), and arm pain (OR: 3.82). Although MRI findings in WAD patients were more degenerated than in control subjects in the initial study, all MRI findings were similar at the 20-year follow-up. There were no significant correlations between clinical cervical symptoms and progression in each MR finding in either group.

Conclusion.

After 20 years, whiplash injuries significantly impacted the residual symptoms of shoulder stiffness, headache, and arm pain when compared with initially asymptomatic volunteers. The progression of degenerative changes in the cervical intervertebral discs after 20 years revealed no association with existing whiplash injuries, neither did the residual cervical-related symptoms.

Level of Evidence: 3
Intradural Neuroanatomy in the Cervical Spinal Canal
Authors: Kong Chao , Liu Li , Liu Yadong , Yuan Xin , Guan Yun , Gao Yan , Chen Xueming
Published: December 2020

Mini

This study defined different anatomic zones within the cervical spinal canal and provides detailed anatomical quantitative data for an accurate diagnosis of cervical spondylosis and a safe and effective anterior decompression surgery.

Study Design.

A dissection-based study of 10 embalmed human cadavers.

Objective.

To provide an anatomic basis to examine the underlying mechanisms of cervical spondylosis.

Summary of Background Data.

Detailed anatomical quantitative data of cervical spine is limited in current literature.

Methods.

Ten cervical spines from C2 to T1 were obtained. We defined three zones from midline to lateral part (zone I, II, and III) and two zones from cranial to caudal (zone P and zone IP) on the coronal plane within the cervical spinal canal. Quantitative anatomy of the zones at different cervical segments were measured including: (1) horizontal widths of zone I, II, and III; (2) length of the cervical spinal cord segment at the ventral rootlets (LV); (3) the pedicle height (PH, zone P) and the inter-pedicle height (IPH, zone IP); (4) the distance between the superior margin of pedicle and the exit of the uppermost ventral nerve rootlet (PN).

Results.

The value of zone II at C4 was significantly less than that at other levels. The value of zone III increases from C4 to C8, and the values at C7 and C8 were significantly higher than those at C4, C5, and C6. PHs and IPHs were not significantly different between different levels. The values of LV at C4 and C8 were smaller than those of C5, C6, and C7. The value of PN showed an increasing trend. At C4, the uppermost ventral rootlet was at about the same height as C3 pedicle, while C8 uppermost ventral rootlet was at the same level as the inferior part of C6 pedicle. Ventral intradural intersegmental connections were found in three intersegments out of 20 intersegments.

Conclusion.

The current definition of anatomic zones may be useful for an accurate diagnosis of cervical spondylosis and a safe and effective anterior decompression surgery.

Level of Evidence: N/A
Gene Therapy for Primary Immunodeficiency
Authors: Houghton Benjamin C. , Booth Claire
Published: December 2020

Over the past 3 decades, there has been significant progress in refining gene therapy technologies and procedures. Transduction of hematopoietic stem cells ex vivo using lentiviral vectors can now create a highly effective therapeutic product, capable of reconstituting many different immune system dysfunctions when reinfused into patients. Here, we review the key developments in the gene therapy landscape for primary immune deficiency, from an experimental therapy where clinical efficacy was marred by adverse events, to a commercialized product with enhanced safety and efficacy. We also discuss progress being made in preclinical studies for challenging disease targets and emerging gene editing technologies that are showing promising results, particularly for conditions where gene regulation is important for efficacy.
PERIPHERAL OPTICAL COHERENCE TOMOGRAPHY FINDINGS IN A CHOROIDEREMIA CARRIER
Authors: Corvi Federico , Corradetti Giulia , Wong Alice , Eng Jeffrey G. , Sadda SriniVas
Published: December 2020

Purpose:

To describe the peripheral optical coherence tomography findings in a female choroideremia carrier.

Methods:

A 56-year-old woman was referred for visual disturbance complaining of some occasional photopsias and increasing difficulty with her vision at night in both eyes. Best-corrected visual acuity was 20/20 in the right eye and 20/150 in the left eye. Fundus examination revealed mildly tilted disks and peripapillary atrophy with subtle retinal pigment epithelial changes in the periphery.

Results:

Macular optical coherence tomography in the right eye appeared unremarkable, but the in the left eye, there was diffuse ellipsoid zone band disruption. Green-light fundus autofluorescence revealed mottled areas of decreased autofluorescence in the mid and far periphery creating an irregular mosaic pattern. Peripheral optical coherence tomography scans revealed more diffuse ellipsoid zone alterations than were apparent on the fundus autofluorescence imaging. Genetic testing revealed a heterozygous pathogenic variant in the CHM gene (c.715C>T, p.Arg239). An additional heterozygous mutation was noted in the CNGB1 gene (c.290+2T>C, splice donor).

Conclusion:

Choroideremia carriers may manifest widespread photoreceptor alterations, which may be more extensive than apparent on fundus autofluorescence imaging.
REACTIVE AMYLOID A PROTEIN AMYLOIDOSIS IN THE SETTING OF INFECTIVE ENDOCARDITIS MANIFESTING AS BILATERAL ORBITOPATHY AND CHOROIDOPATHY
Authors: Carrera William , Rosco Michael G. , Safo Myra , Peng Michelle Yun , Ng Caleb , Agarwal Anita
Published: December 2020

Purpose:

To describe a case of amyloid A protein amyloidosis that produced an orbital inflammatory response with a novel presentation.

Methods:

Case report.

Results:

A 24-year-old Caucasian women with a history of intravenous heroin use was hospitalized for tricuspid valve endocarditis and methicillin-resistant Staphylococcus aureus bacteremia, as well as acute renal failure. She received hemodialysis and intravenous daptomycin and had negative blood cultures for 3 weeks, when she developed sudden bilateral orbital swelling and blurred vision. Visual acuity was 20/200 in the right eye and 20/400 in the left eye. Examination revealed proptosis, conjunctival chemosis and desiccation, optic disk swelling, creamy choroidal infiltrates, and inferiorly located exudative retinal detachments in both eyes. Multimodal imaging demonstrated thickening of the sclera, choroid, and choriocapillaris as well as outer retinal disruption, subretinal fluid, and deposits of hyperfluorescent debris within the choriocapillaris, outer retina, and vitreous. Oral prednisone at 60 mg per day resolved the choroidal infiltrates and exudative detachments. Persistent nephrotic syndrome called for a renal biopsy, which demonstrated amyloid A protein amyloidosis.

Conclusion:

Orbital and choroidal Amyloid A protein amyloidosis can induce a local inflammatory response manifesting as orbital swelling, papillitis, posterior scleritis, choroiditis, and exudative retinal detachment, which responds to steroid therapy. The underlying pathology is likely a reactive inflammatory, vasoocclusive process involving the choriocapillaris and orbital vasculature to the presence of amyloid fibrils.
Phenotyping peripheral neuropathic pain in male and female adolescents: pain descriptors, somatosensory profiles, conditioned pain modulation, and child–parent reported disability
Authors: Verriotis Madeleine , Peters Judy , Sorger Clarissa , Walker Suellen M.
Published: December 2020

Neuropathic pain (NeuP) can be difficult to diagnose and manage in children. Data regarding prevalence and sex-dependent differences are limited, and more detailed phenotyping is needed. This observational cohort study recruited adolescents (10-17 years) with NeuP or complex regional pain syndrome (CRPS). After pain history and NeuP questionnaires, quantitative sensory testing was performed. Individual z-score plots were calculated with body-region control measures and matched to mechanism-related sensory profiles (sensory loss, thermal hyperalgesia, and mechanical hyperalgesia). Conditioned pain modulation was assessed with pressure pain threshold and a contralateral cold conditioning stimulus, and meaningful conditioned pain modulation defined as twice the standard error of measurement. Patients and parents completed validated questionnaires for child quality of life (QoL), pain catastrophizing, and self-reported anxiety/depression. Males (n = 23) and females (n = 43) with NeuP (n = 52) or CRPS (n = 14) reported moderate–severe pain with neuropathic sensory descriptors. Mixed patterns of sensory gain/loss at pain sites were not sex-dependent. Thermal hyperalgesia was common in both NeuP and CRPS, whereas sensory loss occurred only with NeuP and in a smaller proportion than adult cohorts. Conditioned pain modulation was inhibitory in 54%, facilitatory in 14%, and nonresponders had variable cold conditioning sensitivity. Males and females reported marked impairment of QoL, increased emotional distress, and pain catastrophising. Child–parent QoL scores correlated, but catastrophizing scores were discordant when parents or adolescents reported higher anxiety/depression. NeuP in adolescents is associated with significant pain, physical impairment, and psychosocial impairment. Quantifying alterations in somatosensory profiles, descending modulation, child and parent psychological function will inform individualized therapy and stratification for future clinical trials.
Imaging-based navigation technologies in head and neck surgery
Authors: Eu Donovan , Daly Michael J. , Irish Jonathan C.
Published: December 2020

Purpose of review

Image guided navigation has had significant impact in head and neck surgery, and has been most prolific in endonasal surgeries. Although conventional image guidance involves static computed tomography (CT) images attained in the preoperative setting, the continual evolution of surgical navigation technologies is fast expanding to incorporate both real-time data and bioinformation that allows for improved precision in surgical guidance. With the rapid advances in technologies, this article allows for a timely review of the current and developing techniques in surgical navigation for head and neck surgery.

Recent findings

Current advances for cross-sectional-based image-guided surgery include fusion of CT with other imaging modalities (e.g., magnetic resonance imaging and positron emission tomography) as well as the uptake in intraoperative real-time ‘on the table’ imaging (e.g., cone-beam CT). These advances, together with the integration of virtual/augmented reality, enable potential enhancements in surgical navigation. In addition to the advances in radiological imaging, the development of optical modalities such as fluorescence and spectroscopy techniques further allows the assimilation of biological data to improve navigation particularly for head and neck surgery.

The steady development of radiological and optical imaging techniques shows great promise in changing the paradigm of head and neck surgery.
Targeting the Ras pathway in pediatric hematologic malignancies
Authors: Pikman Yana , Stieglitz Elliot
Published: December 2020

Purpose of review

Ras pathway mutations are one of the most common type of alterations in pediatric hematologic malignancies and are frequently associated with adverse outcomes. Despite ongoing efforts to use targeted treatments, there remain no Food and Drug Administration (FDA)-approved medications specifically for children with Ras pathway-mutated leukemia. This review will summarize the role of Ras pathway mutations in pediatric leukemia, discuss the current state of Ras pathway inhibitors and highlight the most promising agents currently being evaluated in clinical trials.

Recent findings

Efficacy using RAF and MEK inhibitors has been demonstrated across multiple solid and brain tumors, and these are now considered standard-of-care for certain tumor types in adults and children. Clinical trials are now testing these medications for the first time in pediatric hematologic disorders, such as acute lymphoblastic leukemia, juvenile myelomonocytic leukemia, and histiocytic disorders. Novel inhibitors of the Ras pathway, including direct RAS inhibitors, are also being tested in clinical trials across a spectrum of pediatric and adult malignancies.

Activation of the Ras pathway is a common finding in pediatric hematologic neoplasms. Implementation of precision medicine with a goal of improving outcomes for these patients will require testing of Ras pathway inhibitors in combination with other drugs in the context of current and future clinical trials.
New approaches to risk stratification for Wilms tumor
Authors: Nelson Marie V. , van den Heuvel-Eibrink Marry M. , Graf Norbert , Dome Jeffrey S.
Published: December 2020

Purpose of review

The treatment of Wilms tumor is one of the great achievements in the field of oncology. One of the key success factors has been improved risk stratification, enabling augmentation or reduction of therapy depending on a patient's risk of relapse. This article highlights the evolution of clinical and biological prognostic markers that have been applied in the treatment of Wilms tumor.

Recent findings

Historically, tumor stage and histology were the sole determinants of Wilms tumor treatment. Recent clinical trials conducted by the Children's Oncology Group (COG) and the International Society of Pediatric Oncology (SIOP) Renal Tumor Study Group have expanded the menu of prognostic factors to include histologic and volumetric response to therapy and tumor-specific loss of heterozygosity (LOH) at chromosomes 1p and 16q. Augmentation of therapy has been able to overcome the adverse risk factors. An emerging prognostic marker is chromosome 1q gain, will be incorporated into future clinical trials.

The application of new clinical and biological prognostic factors has created unprecedented ability to tailor therapy for Wilms tumor, accompanied with improved outcomes. Current and future trials will continue to enhance precision medicine for Wilms tumor.
Immunotherapy in Bacillus Calmette–Guerin (BCG) unresponsive nonmuscle invasive bladder cancer
Authors: Hugar Lee A. , Gilbert Scott M. , Sexton Wade J. , Kamat Ashish M. , Li Roger
Published: December 2020

Purpose of review

A number of promising therapies for Bacillus Calmette–Guerin (BCG) unresponsive nonmuscle invasive bladder cancer (NMIBC) are in the pipeline. In this review, we discuss the history of immunotherapy for the treatment of NMIBC and future developments, focusing on novel intravesical treatments.

Recent findings

The term BCG unresponsive NMIBC encompasses patients with both BCG refractory and BCG relapsing disease. This definition was adopted to standardize inclusion criteria for patients enrolling in clinical trials in this setting. A host of intravesical immuno-oncologic therapies that include gene therapies, oncolytic viruses, cell surface molecule delivered immunotoxins, and cytokine driven agonism of cellular immunity, are in various phases of the drug development pipeline. In addition, pembrolizumab, an immune-checkpoint inhibitor, has recently been approved as a treatment option for BCG unresponsive NMIBC.

Patients with BCG unresponsive disease face many difficulties. Although radical cystectomy is the most effective treatment option for these patients, it is associated with significant morbidity, difficult recovery challenges, and refusal by many patients. Cancer immunotherapies may provide bladder sparing options for some patients who develop BCG unresponsive disease.
A Qualitative Study of Adult Hospitalized Patients With Difficult Venous Access Experiencing Short Peripheral Catheter Insertion in a Hospital Setting
Authors: Plohal Ann
Published: December 2020

Hospitalized patients require venous access for procedures, treatments, or therapies. The short peripheral catheter (SPC) is one option for patients who need intravenous (IV) access for treatment. Patients with difficult vasculature sometimes require multiple attempts to obtain SPC access. The aim of this study was to gain an understanding of adult patients' experiences with SPC insertion, specifically those with difficult venous access. Ten participants were purposely sampled over a 2-month period for semistructured interviews from the medical, surgical, and telemetry units at an inner city, 750-bed trauma hospital in the southwestern United States. Four key themes developed from the interview data: skills and techniques of the clinicians, distress and the SPC insertion experience, physical and emotional pain, and patient/clinician communication. These themes provided ways that clinicians might improve the patient experience, including: ensuring experienced and confident inserters are available to insert SPCs, utilizing distraction and pain methods to decrease pain perception, communicating with patients regarding site selection and expectations during SPC insertion, and identifying patients with difficult vascular access to limit attempts per patient to preserve vascular sites.
Paired SARS-CoV-2 Spike Protein Mutations Observed During Ongoing SARS-CoV-2 Viral Transfer from Humans to Minks and Back to Humans
Authors: Burkholz Scott , Pokhrel Suman , Kraemer Benjamin R. , Mochly-Rosen Daria , Carback Richard T. , Hodge Tom , Harris Paul , Ciotlos Serban , Wang Lu , Herst CV , Rubsamen Reid
Published: December 2020

A mutation analysis of SARS-CoV-2 genomes collected around the world sorted by sequence, date, geographic location, and species has revealed a large number of variants from the initial reference sequence in Wuhan. This analysis also reveals that humans infected with SARS-CoV-2 have infected mink populations in the Netherlands, Denmark, United States, and Canada. In these animals, a small set of mutations in the spike protein receptor binding domain (RBD), often occurring in specific combinations, has transferred back into humans. The viral genomic mutations in minks observed in the Netherlands and Denmark show the potential for new mutations on the SARS-CoV-2 spike protein RBD to be introduced into humans by zoonotic transfer. Our data suggests that close attention to viral transfer from humans to farm animals and pets will be required to prevent build-up of a viral reservoir for potential future zoonotic transfer.
Analysis and Forecasting of Global RT-PCR Primers for SARS-CoV-2
Authors: Nayar Gowri , Seabolt Edward E. , Kunitomi Mark , Agarwal Akshay , Beck Kristen L. , Mukherjee Vandana , Kaufman James H.
Published: December 2020

Rapid tests for active SARS-CoV-2 infections rely on reverse transcription polymerase chain reaction (RT-PCR). RT-PCR uses reverse transcription of RNA into complementary DNA (cDNA) and amplification of specific DNA (primer and probe) targets using polymerase chain reaction (PCR). The technology makes rapid and specific identification of the virus possible based on sequence homology of nucleic acid sequence and is much faster than tissue culture or animal cell models. However the technique can lose sensitivity over time as the virus evolves and the target sequences diverge from the selective primer sequences. Different primer sequences have been adopted in different geographic regions. As we rely on these existing RT-PCR primers to track and manage the spread of the Coronavirus, it is imperative to understand how SARS-CoV-2 mutations, over time and geographically, diverge from existing primers used today. In this study, we analyze the performance of the SARS-CoV-2 primers in use today by measuring the number of mismatches between primer sequence and genome targets over time and spatially. We find that there is a growing number of mismatches, an increase by 2% per month, as well as a high specificity of virus based on geographic location.
Open-top axially swept light sheet microscopy
Authors: Kim Bumju , Na Myeongsu , Park Soohyun , Kim Kitae , Park Jeong-Hoon , Chung Euiheon , Chang Sunghoe , Kim Ki Hean
Published: December 2020

Open-top light sheet microscopy (OT-LSM) is a specialized microscopy for the high throughput cellular imaging of large tissues including optically cleared tissues by having all the optical setup below the sample stage. Current OT-LSM systems had relatively low axial resolutions by using weakly focused light sheets to cover the imaging field of view (FOV). In this report, open-top axially swept LSM (OTAS-LSM) was developed for high-throughput cellular imaging with the improved axial resolution. OTAS-LSM swept the tightly focused excitation light sheet across the imaging FOV by using an electro tunable lens (ETL) and collected emission light at the focus of light sheet with a camera in the rolling shutter mode. OTAS-LSM was developed by using air objective lenses and a water prism for simplicity and it had on-axis optical aberration associated with the mismatch of refractive indices between air and immersion medium. The effects of optical aberration were analyzed by both simulation and experiment. The image resolutions were 1.5-1.6μm, and approximately 140% of the aberration-free theoretical values. The newly developed OTAS-LSM was applied to the imaging of optically cleared mouse brain and small intestine and it could visualize neuronal networks in the single cell level. OTAS-LSM might be useful for the high-throughput cellular examination of optically cleared large tissues.
Activation of TIR signaling is required for pattern-triggered immunity
Authors: Tian Hainan , Chen Siyu , Wu Zhongshou , Ao Kevin , Yaghmaiean Hoda , Sun Tongjun , Huang Weijie , Xu Fang , Zhang Yanjun , Wang Shucai , Li Xin , Zhang Yuelin
Published: December 2020

Plant immune responses are mainly activated by two types of receptors. Plasma membrane-localized pattern recognition receptors (PRRs) recognize conserved features of microbes, and intracellular nucleotide-binding leucine rich repeat receptors (NLRs) recognize effector proteins from pathogens. NLRs possessing N-terminal Toll/interleukin-1 receptor (TIR) domains (TNLs) activate two parallel signaling pathways via the EDS1/PAD4/ADR1s and the EDS1/SAG101/NRG1s modules. The relationship between PRR-mediated pattern-triggered immunity (PTI) and TIR signaling is unclear. Here we report that activation of TIR signaling plays a key role in PTI. Blocking TIR signaling by knocking out components of the EDS1/PAD4/ADR1s and EDS1/SAG101/NRG1s modules results in attenuated PTI responses such as reduced salicylic acid (SA) levels and expression of defense genes, and compromised resistance against pathogens. Consistently, PTI is attenuated in transgenic plants that have reduced accumulation of NLRs. Upon treatment with PTI elicitors such as flg22 and nlp20, a large number of genes encoding TNLs or TIR domain-containing proteins are rapidly induced, likely responsible for activating TIR signaling during PTI. In support, overexpression of some of these genes results in activation of defense responses. Overall, our study reveals that TIR signaling activation is an important mechanism for boosting plant defense during PTI.
Losartan promotes cell survival following SARS-CoV-2 infectionin vitro
Authors: Nejat Reza , Sadr Ahmad Shahir , Freitas Brendan T. , Crabtree Jackelyn , Pegan Scott D. , Tripp Ralph A. , Najafi David J.
Published: December 2020

Introduction

Coronavirus disease 2019 (COVID-19) can be associated with mortality and high morbidity worldwide. There is an extensive effort to control infection and disease caused by SARS-CoV-2. This study addressed the hypothesis that angiotensin II type I receptor blocker, Losartan, may restrict pathogenesis caused by SARS-CoV-2 by decreasing viral-induced cytopathological changes by blocking angiotensin II type 1 receptor (AT1R), thus reducing the affinity of the virus for ACE2, and inhibiting papain-like protease of the virus.

Method

Losartan inhibitory effect on deubiquitination and deISGylation properties of papain-like protease was investigated using a fluorescence method and gel shift analysis determining its inhibitory effects.

The inhibitory effect of Losartan on SARS-CoV-2 cell replication was investigated both when losartan was added to the cell culture 1 hour before (pre-infection group) and 1 hour after (post-infection group) SARS-CoV-2 infection of Vero E6 cells.

Results

Losartan treatment of Vero E6 cells prior to and after SARS-CoV-2 infection reduced SARS-CoV-2 replication by 80% and 70% respectively. Losartan was not a strong deubiquitinase and deISGylase inhibitor of PLpro.

Conclusion

Losartan added pre- and post-infection to the Vero E6 cell culture significantly prevents cell destruction and replication by SARS-CoV2. Losartan has low side-effects, is readily available, and can be produced at high levels globally, all features of a promising drug in treatment of COVID-19 if validated by clinical trials.
Ribosome collision sensor Hel2 recognizes mistargeting secretory ribosome-nascent chain complexes
Authors: Matsuo Yoshitaka , Inada Toshifumi
Published: December 2020

Ribosome collision due to translational stalling is recognized as a problematic event in translation by E3 ubiquitin ligase Hel2, leading to non-canonical subunit dissociation followed by targeting of the faulty nascent peptides for degradation. Although Hel2-mediated quality control greatly contributes to maintaining cellular protein homeostasis, its physiological role in dealing with endogenous substrates remains unclear. This study utilized genome-wide analysis, based on selective ribosome profiling, to survey the endogenous substrates for Hel2. This survey revealed that Hel2 preferentially binds to the pre-engaged secretory ribosome-nascent-chain complexes (RNCs), which translate upstream of targeting signals. Notably, Hel2 recruitment into secretory RNCs was elevated under signal recognition particle (SRP)-deficient conditions. Moreover, the mitochondrial defects caused by insufficient SRP were enhanced byhel2deletion, along with the mistargeting of secretory proteins into mitochondria. Collectively, these findings provide novel insights into risk management in the secretory pathway that maintains cellular protein homeostasis.
Effect of Stapling on the Thermodynamics of mdm2-p53 Binding
Authors: Maity Atanu , Choudhury Asha Rani , Chakrabarti Rajarshi
Published: December 2020

Protein-protein interaction (PPI) is one of the key regulatory features to drive biomolecular processes and hence is targeted for designing therapeutics against diseases. Small peptides are a new and emerging class of therapeutics owing to their high specificity and low toxicity. For achieving efficient targeting of the PPI, amino acid side chains are often stapled together resulting in the rigidification of these peptides. Exploring the scope of these peptides demands a comprehensive understanding of their working principle. In this work, two stapled p53 peptides have been considered to delineate their binding mechanism with mdm2 using computational approaches. Addition of stapling protects the secondary structure of the peptides even in the case of thermal and chemical denaturation. Although the introduction of a stapling agent increases the hydrophobicity of the peptide, the enthalpic stabilization decreases. This is overcome by the lowering of the entropic penalty and the overall binding affinity improves. The mechanistic insights into the benefit of peptide stapling can be adopted for further improvement of peptide therapeutics.
The N-terminal Tail ofC. elegansCENP-A Interacts with KNL-2 and is Essential for Centromeric Chromatin Assembly
Authors: de Groot Christian , Houston Jack , Davis Bethany , Gerson-Gurwitz Adina , Monen Joost , Oegema Karen , Shiau Andrew K. , Desai Arshad
Published: December 2020

Centromeres are epigenetically defined by the presence of the centromere-specific histone H3 variant CENP-A. A specialized loading machinery, including the histone chaperone HJURP/Scm3, participates in CENP-A nucleosome assembly. However, Scm3/HJURP is missing from multiple lineages, including nematodes, which rely on a CENP-A-dependent centromere. Here, we show that the extended N-terminal tail ofC. elegansCENP-A contains a predicted structured region that is essential for centromeric chromatin assembly. Removal of this region of the CENP-A N-Tail prevents loading, resulting in failure of kinetochore assembly and defective chromosome condensation. By contrast, the N-Tail mutant CENP-A localizes normally in the presence of endogenous CENP-A. The portion of the N-Tail containing the predicted structured region binds to KNL-2, a conserved SANTA and Myb domain-containing protein (referred to as M18BP1 in vertebrates), that is specifically involved in CENP-A chromatin assembly. This direct interaction is conserved in the related nematodeC. briggsae,despite divergence of the N-Tail and KNL-2 primary sequences. Thus, the extended N-Tail of CENP-A is essential for CENP-A chromatin assembly inC. elegansand partially substitutes for the function of Scm3/HJURP, in that it mediates an interaction of the specialized histone fold of CENP-A with KNL-2. These results highlight an evolutionary variation on centromeric chromatin assembly in the absence of a dedicated CENP-A-specific chaperone/targeting factor of the Scm3/HJURP family.
Haplotype and Population Structure Inference using Neural Networks in Whole-Genome Sequencing Data
Authors: Meisner Jonas , Albrechtsen Anders
Published: December 2020

Accurate inference of population structure is important in many studies of population genetics. Here we present,HaploNet, a method for performing dimensionality reduction and clustering of genetic data. The method is based on local clustering of phased haplotypes using neural networks from whole-genome sequencing or dense genotype data. By utilizing Gaussian mixtures in a variational autoencoder framework, we are able to learn a low-dimensional latent space in which we cluster haplotypes along the genome in a highly scalable manner. We demonstrate that we can use haplotype clusters in the latent space to infer global population structure utilizing haplotype information by exploiting the generative properties of our framework. Based on fitted neural networks and its latent haplotype clusters, we can perform principal component analysis and estimate ancestry proportions based on a maximum likelihood framework. Using sequencing data from simulations and closely related human populations, we demonstrate that our approach is better at distinguishing closely related populations than standard admixture and principal component analysis software. We further show thatHaploNetis fast and highly scalable by applying it to genotype array data of the UK Biobank.
PARprolink: a photoaffinity probe for identifying poly(ADP-ribose)-binding proteins
Authors: Dasovich Morgan , Beckett Morgan Q. , Bailey Scott , Ong Shao-En , Greenberg Marc M. , Leung Anthony K. L.
Published: December 2020

Post-translational modification of proteins with poly(ADP-ribose) (PAR) is an important component of the DNA damage response. Four PAR synthesis inhibitors have recently been approved for the treatment of breast, ovarian, and prostate cancers. Despite its clinical significance, a molecular understanding of PAR function, including its binding partners, remains incomplete. In this work, we synthesize a PAR photoaffinity probe that captures and isolates endogenous PAR binders. Our method identified dozens of known PAR-binding proteins and hundreds of novel binders involved in DNA repair, RNA processing, and metabolism. PAR binding by eight candidates was confirmed using pull-down and/or electrophoretic mobility shift assays. Using PAR probes of defined lengths, we detected proteins that preferentially bind to 40-mer over 8-mer PAR, indicating that polymer length may regulate the outcome and timing of PAR signaling pathways. This investigation produces the first census of PAR-binding proteins, provides a proteome-wide view of length-selective PAR binding, and associates PAR binding with RNA metabolism and the formation of biomolecular condensates.
The replication of the human respiratory syncytial virus in a T cell line has multiple ineffective steps
Authors: de Souza Cardoso Ricardo , Coelho Ana Carolina Lunardello , de Jesus Bruna Laís Santos , Vitti Brenda Cristina , de Paula Souza Juliano , Viana Rosa Maria Mendes , Pontelli Marjorie C. , Murakami Tomoyuki , Ventura Armando Moraes , Ono Akira , Arruda Eurico
Published: December 2020

Human respiratory syncytial virus is the most frequent cause of severe respiratory disease in children. The main targets of HRSV infection are epithelial cells of the respiratory tract and the great majority of the studies regarding HRSV infection are done in respiratory cells. Recently, the interest on respiratory virus infection of lymphoid cells has been growing, but details of the interaction of HRSV with lymphoid cells remain unknown. Therefore, this study was done to assess the relationship of HRSV with A3.01 cells, a CD4+T cell line. We found by flow cytometry and fluorescent focus assay that A3.01 cells are susceptible but virtually not permissive to HRSV infection. De-quenching experiments revealed that the fusion process of HRSV in A3.01 cells is reduced in comparison to HEp-2 cells, an epithelial cell lineage. Quantification of viral RNA by qPCR determined that the replication of HRSV in A3.01 cells was modest. Western blot and quantitative flow cytometry analyses demonstrated that the production of HRSV proteins in A3.01 was significantly lower than in HEp-2 cells. Additionally, we found by fluorescence in situ hybridization that the inclusion body-associated granules (IBAG’s) are almost absent in HRSV inclusion bodies in A3.01 cells. We also assessed the intracellular trafficking of HRSV proteins and found that HRSV proteins co-localized partially with the secretory pathway in A3.01 cells, but these HRSV proteins and viral filaments are present only scarcely at the plasma membrane. HRSV infection of A3.01 CD4+T cells is virtually unproductive as compared to HEp-2 cells, with virion production hampered by low fusion, hypofunctional inclusion bodies, altered trafficking of viral proteins to the plasma membrane.
The Diversity and Evolution of Microbial Dissimilatory Phosphite Oxidation
Authors: Ewens Sophia D. , Gomberg Alexa F. S. , Barnum Tyler P. , Borton Mikayla A. , Carlson Hans K. , Wrighton Kelly C. , Coates John D.
Published: December 2020

Phosphite is the most energetically favorable chemotrophic electron donor known, with a half-cell potential (E°’) of −650 mV for the PO43-/PO33-couple. Since the discovery of microbial dissimilatory phosphite oxidation (DPO) in 2000, the environmental distribution, evolution, and diversity of DPO microorganisms (DPOM) has remained enigmatic and only two species have been identified. Here metagenomic sequencing of phosphite enriched microbial communities enabled the reconstruction and metabolic characterization of 21 novel DPOM. These DPOM spanned six classes of bacteria, including theNegativicutes, Desulfotomaculia, Synergistia, Syntrophia, DesulfobacteriaandDesulfomonilia_A. Comparing the DPO genes from the genomes of enriched organisms to over 17,000 publicly available metagenomes revealed the global existence of this metabolism in diverse anoxic environments, including wastewaters, sediments, and subsurface aquifers. Despite their newfound environmental and taxonomic diversity, metagenomic analyses suggested that the typical DPOM is a chemolithoautotroph that occupies low-oxygen environments and specializes in phosphite oxidation coupled to CO2reduction. Phylogenetic analyses indicated that the DPO genes form a highly conserved cluster that likely has ancient origins predating the split of monoderm and diderm bacteria. By coupling microbial cultivation strategies with metagenomics, these studies highlighted the unsampled metabolic versatility latent in microbial communities. We have uncovered the unexpected prevalence, diversity, biochemical specialization, and ancient origins of a unique metabolism central to the redox cycling of phosphorus, a primary nutrient on earth.

Significance Statement

Geochemical models of the phosphorus (P) cycle uniquely ignore microbial redox transformations. Yet phosphite is a reduced P source that has been detected in several environments at concentrations that suggest a contemporary P redox cycle. Microbial dissimilatory phosphite oxidation (DPO) converts soluble phosphite into phosphate, and a false notion of rarity has limited our understanding of its diversity and environmental distribution. Here we demonstrate that DPO is an ancient energy metabolism hosted by taxonomically diverse, autotrophic bacteria that exist globally throughout anoxic environments. DPO microorganisms are therefore likely to have provided bioavailable phosphate and fixed carbon to anoxic ecosystems throughout Earth’s history and continue to do so in contemporary environments.
Mitochondrial introgression by ancient admixture between two distant lacustrine fishes in Sulawesi Island
Authors: Horoiwa Mizuki , Mandagi Ixchel F. , Sutra Nobu , Montenegro Javier , Tantu Fadly Y. , Masengi Kawilarang W. A. , Nagano Atsushi J. , Kusumi Junko , Yasuda Nina , Yamahira Kazunori
Published: December 2020

Sulawesi, an island located in a biogeographical transition zone between Indomalaya and Australasia, is famous for its high levels of endemism. Ricefishes (family Adrianichthyidae) are an example of taxa that have uniquely diversified on this island. It was demonstrated that habitat fragmentation due to the Pliocene juxtaposition among tectonic subdivisions of this island was the primary factor that promoted their divergence; however, it is also equally probable that habitat fusions and resultant admixtures between phylogenetically distant species may have frequently occurred. Previous studies revealed that some individuals ofOryzias sarasinorumendemic to a tectonic lake in central Sulawesi have mitochondrial haplotypes that are similar to the haplotypes ofO. eversi, which is a phylogenetically related but geologically distant (ca. 190 km apart) adrianichthyid endemic to a small lake. In this study, we tested if this reflects ancient admixture ofO. eversiandO. sarasinorum. Population genomic analyses of genome-wide single-nucleotide polymorphisms revealed thatO. eversiandO. sarasinorumare substantially reproductively isolated from each other. Comparison of demographic models revealed that the models assuming ancient admixture fromO. eversitoO. sarasinorumwas more supported than the models assuming no admixture; this supported the idea that theO. eversi-likemitochondrial haplotype inO. sarasinorumwas introgressed fromO. eversi. This study is the first to demonstrate ancient admixture of lacustrine organisms in Sulawesi beyond 100 km. The complex geological history of this island enabled such island-wide admixture of lacustrine organisms, which usually experience limited migration.