bluuebunny/crossref_metadata_2025 huggingface dataset:
PD-L1 Expression in Metaplastic Breast Carcinoma Using the PD-L1 SP142 Assay and Concordance Among PD-L1 Immunohistochemical Assays
Authors: Grabenstetter Anne , Jungbluth Achim A. , Frosina Denise , Hoda Raza , Dos Anjos Carlos H. , Patil Sujata , Sevilimedu Varadan , Weigelt Britta , Reis-Filho Jorge S. , Zhang Hong , Traina Tiffany , Robson Mark E. , Brogi Edi , Wen Hannah Y.
Published: June 2021

Immunotherapy for the treatment of programmed death-ligand 1 (PD-L1) positive locally advanced or metastatic triple negative breast cancer may benefit patients with metaplastic breast cancer (MpBC). Previous study of PD-L1 in MpBC scored tumor cells (TCs), different from Food and Drug Administration-approved scoring methods. We sought to define PD-L1 expression in MpBCs and to evaluate concordance of 3 PD-L1 assays. Primary, treatment naive MpBC treated at our Center from 1998 to 2019 were identified. PD-L1 expression was assessed using SP142, E1L3n, and 73-10. We evaluated PD-L1 expression on tumor infiltrating immune cells (IC) and also in TCs. For each assay, we scored PD-L1 expression using ≥1% IC expression according to the IMpassion130 trial criteria and using combined positive score (CPS) ≥10 according to the KEYNOTE-355 trial cutoff. A total of 42 MpBCs were identified. Most MpBC had PD-L1 positivity in ≥1% IC with all 3 assays (95%, 95%, 86%) in contrast to a maximum 71% with a CPS ≥10. PD-L1 IC expression was comparable between the SP142 and 73-10 assays and was lowest with E1L3n. PD-L1 TC expression was lowest using SP142. The overall concordance for IC scoring was 88% while 62% had concordant CPS. For each assay, the results of the 2 scoring algorithms were not interchangeable. The SP142 assay showed distinct expression patterns between IC (granular, dot-like) and TC (membranous) while 73-10 and E1L3n showed membranous and/or cytoplasmic expression in both IC and TC. Most MpBC in our cohort were positive for PD-L1 indicating eligibility for anti-PD-L1/programmed death-1 immunotherapy.
Rates of new HIV diagnoses among Indigenous peoples in Canada, Australia, New Zealand, and the United States: 2009–2017
Authors: Koehn Katrina , Cassidy-Matthews Chenoa , Pearce Margo , Aspin Clive , Pruden Harlan , Ward James , Mullen Marama , Hogg Robert S. , Nicholson Valerie
Published: June 2021

Objective:

To compare rates and trends of HIV diagnoses among Indigenous peoples in Canada (First Nations, Métis, Inuit, and other non-specified), Australia (Aboriginal and Torres Strait Islanders), the USA (American Indian, Alaska Native, Native Hawaiian, and Other Pacific Islanders), and New Zealand (Māori).

Design:

We employed publicly available surveillance data from 2009 to 2017 to estimate the rate per 100 000 of HIV diagnoses. Estimated annual percentage change (EAPC) in diagnosis rates was calculated using Poisson regression.

Setting:

The four countries have passive population-based HIV surveillance programs.

Participants:

Population estimates from respective census programs were used as rate denominators.

Main outcome measures:

Estimated annual HIV diagnosis rate per 100 000 and EAPC were calculated for total Indigenous peoples, women, and men.

Results:

As of 2017, rates of HIV were highest in Canada (16.22, 95% confidence interval (CI): 14.30--18.33) and lowest in New Zealand (1.36, 95% CI: 0.65--2.50). Australia had a rate of 3.81 (95% CI: 2.59--5.40) and the USA 3.22 (95% CI: 2.85--3.63). HIV diagnosis rates among the total Indigenous population decreased in Canada (−7.92 EAPC, 95% CI: −9.34 to −6.49) and in the USA (−4.25 EAPC, 95% CI: −5.75 to −2.73) but increased in Australia (5.10 EAPC, 95% CI: 0.39--10.08). No significant trends over time were observed in New Zealand (2.23 EAPC, 95% CI: −4.48 to 9.47).

Conclusion:

Despite limitations to conducting cross-national comparisons, there are substantial differences in HIV diagnosis rates in these four countries that may be reflective of divergent national policies and systems that affect the health status of Indigenous peoples.
The Joint United Nations Programme on HIV/AIDS 95–95–95 targets: worldwide clinical and cost benefits of generic manufacture
Authors: Heath Katherine , Levi Jacob , Hill Andrew
Published: June 2021

Background:

The Joint United Nations Programme on HIV/AIDS aims for HIV testing, treatment and viral suppression rates to be 95%--95%--95% by 2025. Patented drug prices remain a barrier to HIV treatment. Generic alternatives are being produced and exported from countries without patent barriers at a fraction of the cost.

Methods:

We collated export records of active pharmaceutical ingredient for HIV drugs to estimate the minimum costs of production. Using epidemiological data describing national HIV epidemics, we calculated the cost to treat 164 countries at 95%--95%-95%. Using weighted log-linear regression models, we estimated the mother-to-child transmissions (MTCTs), HIV-related deaths and new HIV infections preventable every year by increased treatment.

Findings:

We estimated that TDF/3TC/DTG could be produced for $59 per person per year. At this price, the 164 countries in our analysis could be treated at 95%--95%--95% for $2 billion a year, preventing 66 308 MTCTs, 241 811 HIV-related deaths and 631 398 new HIV infections every year. In comparison, global expenditure on HIV pharmaceuticals in 2019 was $28 billion.

Interpretation:

At $2 billion/year, the 164 countries in our analysis could be treated for the price of 4 weeks of current global sales. Global access to generic alternatives could reduce expenditure and improve clinical outcomes.
TNF-α inhibition in the setting of undiagnosed HIV infection: a call for enhanced screening guidelines
Authors: Claytor Jennifer D. , Viramontes Omar , Conner Stephanie , Wen Kwun W. , Beck Kendall , Chin-Hong Peter V. , Henrich Timothy J. , Peluso Michael J.
Published: June 2021

Background:

Despite the risks of immunosuppression, recommendations regarding screening for HIV infection prior to initiation of biologic therapies targeting common rheumatologic disorders, including inflammatory bowel disease (IBD) and inflammatory arthritides, are limited. Few cases of patients started on biologics while living with undiagnosed HIV infection have been reported.

Methods:

We report three cases of patients initiated on biologics in the absence of recent or concurrent HIV screening who developed refractory disease or unanticipated complications and were later found to have undiagnosed chronic HIV infection.

Results:

In Case 1, a 53-year-old MSM with negative HIV testing 2 years prior presented with presumed rheumatoid arthritis. He did not respond to methotrexate, so adalimumab was started. HIV testing to evaluate persistent symptoms was positive 9 months later; CD4+ T-cell count was 800 cells/μl. Antiretroviral therapy (ART) resulted in resolution of symptoms, which were attributed to HIV-associated arthropathy. In Case 2, a 55-year-old woman with injection drug use in remission and no prior HIV testing presented with hidradenitis suppurativa. She started infliximab and methotrexate therapy with good response. After she developed weight loss and lymphopenia, an HIV test was positive; CD4+ T-cell count was 334 cells/μl. Biologic hidradenitis suppurativa therapy was discontinued, with subsequent poor hidradenitis suppurativa control. In Case 3, a 32-year-old MSM with no prior HIV testing presented with presumed IBD; infliximab and steroids were started. Symptoms progressed despite IBD-directed therapy, and he was diagnosed with extensive Kaposi sarcoma with visceral and cutaneous involvement, likely exacerbated by immunosuppression. HIV testing was positive; CD4+ T-cell count was 250 cells/μl. Kaposi sarcoma initially worsened due to ART-associated immune reconstitution inflammatory syndrome. He is now improving with systemic chemotherapy and ART. HIV-associated Kaposi sarcoma is presumed to be the underlying diagnosis.

Conclusion:

All three patients had elevated risk for HIV infection, and two had final diagnoses attributed to chronic HIV infection, not warranting therapeutic immunosuppression. Screening for HIV infection prior to initiation of biologic therapy should be incorporated into clinical practice guidelines.
18F-THK5351 PET Can Identify Core Lesions in Different Amyotrophic Lateral Sclerosis Phenotypes
Authors: Higashihara Mana , Ishibashi Kenji , Tokumaru Aya M. , Iwata Atsushi , Ishii Kenji
Published: June 2021

Two patients with different amyotrophic lateral sclerosis (ALS) phenotypes underwent 18F-THK5351 PET to visualize lesions undergoing astrogliosis by measuring monoamine oxidase B activity. Patient 1 was a 57-year-old man with flail leg syndrome. Elevated uptake was observed inside the motor cortex, corresponding to the leg area in a cortical homunculus. Patient 2 was a 64-year-old man with ALS-frontotemporal dementia semantic variant. Elevated uptake was observed around the left anterior temporal lobe. Both core lesions were consistent with their respective neurological features. Hence, 18F-THK5351 PET is a useful technique to assess ALS pathophysiology by visualizing the core lesions.
Prognostic Impact of 18F-FDG PET/CT in Patients With Aggressive B-Cell Lymphoma Treated With Anti-CD19 Chimeric Antigen Receptor T Cells
Authors: Sesques Pierre , Tordo Jérémie , Ferrant Emmanuelle , Safar Violaine , Wallet Florent , Dhomps Anthony , Brisou Gabriel , Bouafia Fadhela , Karlin Lionel , Ghergus Dana , Golfier Camille , Lequeu Helène , Lazareth Anne , Vercasson Marlène , Hospital-Gustem Carole , Schwiertz Vérane , Choquet Marion , Sujobert Pierre , Novelli Silvana , Mialou Valérie , Hequet Olivier , Carras Sylvain , Fouillet Ludovic , Lebras Laure , Guillermin Yann , Leyronnas Cécile , Cavalieri Doriane , Janier Marc , Ghesquières Hervé , Salles Gilles , Bachy Emmanuel
Published: June 2021

Purpose of the Report

We aimed to evaluate the role of 18F-FDG PET/CT in predicting patient outcome following chimeric antigen receptor T (CAR T) cells infusion in aggressive B-cell lymphoma.

Methods

18F-FDG PET/CT data before leukapheresis, before CAR T-cell infusion and 1 month (M1) after CAR T-cell infusion, from 72 patients were retrospectively analyzed. SUVmax, total lesion glycolysis (TLG), metabolic tumor volume (MTV), and parameters describing tumor kinetics were calculated for each 18F-FDG PET/CT performed. The aim was to evaluate the prognostic value of 18F-FDG PET/CT metabolic parameters for predicting progression-free survival (PFS) and overall survival (OS) following CAR T-cell therapy.

Results

Regarding PFS, ∆MTVpre-CAR and ∆TLGpre-CAR were found to be more discriminating compared with metabolic parameters at preinfusion. Median PFS in patients with a ∆MTVpre-CAR of less than 300% was 6.8 months (95% confidence interval [CI], 2.8 months to not reached) compared with 2.8 months (95% CI, 0.9–3.0 months) for those with a value of 300% or greater (P = 0.004). Likewise, median PFS in patients with ∆TLGpre-CAR of less than 420% was 6.8 months (95% CI, 2.8 months to not reached) compared with 2.7 months (95% CI, 1.3–3.0 months) for those with a value of 420% or greater (P = 0.0148). Regarding OS, metabolic parameters at M1 were strongly associated with subsequent outcome. SUVmax at M1 with a cutoff value of 14 was the most predictive parameter in multivariate analysis, outweighing other clinicobiological variables (P < 0.0001).

Conclusions

Disease metabolic volume kinetics before infusion of CAR T cells seems to be superior to initial tumor bulk itself for predicting PFS. For OS, SUVmax at M1 might adequately segregate patients with different prognosis.
COVID-19 Vaccination–Associated Lymphadenopathy on FDG PET/CT
Authors: Shin Muheon , Hyun Chae Young , Choi Yoon Ho , Choi Joon Young , Lee Kyung-Han , Cho Young Seok
Published: June 2021

Purpose

This study investigated 18F-FDG PET/CT features of adenovirus-vectored vaccination against COVID-19 in healthy subjects.

Patients and Methods

Thirty-one health care workers had been vaccinated Vaxzevria and underwent FDG PET/CT as an optional test for a cancer screening program. Size and FDG uptake of the hypermetabolic lymph nodes were measured. Uptake value of spleen was also measured with liver for comparison.

Results

All examinees who underwent FDG PET/CT within 14 days’ interval showed hypermetabolic lymphadenopathies ipsilateral to vaccine injection. All examinees with hypermetabolic lymphadenopathy had simultaneous muscular uptakes until 23 days’ interval. Among 12 examinees who underwent FDG PET/CT more than 15 days after vaccination, only 3 male examinees did not show hypermetabolism in the axillary lymph nodes. There was no female examinee with negative hypermetabolic lymphadenopathy until 29 days after vaccination.

Conclusions

Hypermetabolic reactive lymphadenopathy in the ipsilateral axillary area with or without supraclavicular area is most likely to occur in a healthy person with recent adenovirus-vectored COVID-19 vaccination on FDG PET/CT.
COVID-19–Related Lung Parenchymal Uptake on 18F-PSMA-1007 PET/CT
Authors: Nawwar Ayah A. , Searle Julie , Green Jes S. , Lyburn Iain D.
Published: June 2021

A 70-year-old man with newly diagnosed prostate cancer underwent 18F-PSMA-1007 PET/CT for staging. PSMA-avid primary prostatic malignancy was identified. Incidental intense patchy peripheral lung uptake was also noted. The patient tested positive for COVID-19 infection.
Integrated synteny- and similarity-based inference on the polyploidization–fractionation cycle
Authors: Zhang Yue , Yu Zhe , Zheng Chunfang , Sankoff David
Published: June 2021

Whole-genome doubling, tripling or replicating to a greater degree, due to fixation of polyploidization events, is attested in almost all lineages of the flowering plants, recurring in the ancestry of some plants two, three or more times in retracing their history to the earliest angiosperm. This major mechanism in plant genome evolution, which generally appears as instantaneous on the evolutionary time scale, sets in operation a compensatory process called fractionation, the loss of duplicate genes, initially rapid, but continuing at a diminishing rate over millions and tens of millions of years. We study this process by statistically comparing the distribution of duplicate gene pairs as a function of their time of creation through polyploidization, as measured by sequence similarity. The stochastic model that accounts for this distribution, though exceedingly simple, still has too many parameters to be estimated based only on the similarity distribution, while the computational procedures for compiling the distribution from annotated genomic data is heavily biased against earlier polyploidization events—syntenic ‘crumble’. Other parameters, such as the size of the initial gene complement and the ploidy of the various events giving rise to duplicate gene pairs, are even more inaccessible to estimation. Here, we show how the frequency of
unpaired
genes, identified via their embedding in stretches of duplicate pairs, together with previously established constraints among some parameters, adds enormously to the range of successive polyploidization events that can be analysed. This also allows us to estimate the initial gene complement and to correct for the bias due to crumble. We explore the applicability of our methodology to four flowering plant genomes covering a range of different polyploidization histories.
Testing the genomic stability of the Brazilian yellow fever vaccine strain using next-generation sequencing data
Authors: Serrão de Andrade Amanda Araújo , Soares André E. R. , Paula de Almeida Luiz Gonzaga , Ciapina Luciane Prioli , Pestana Cristiane Pinheiro , Aquino Carolina Lessa , Medeiros Marco Alberto , Ribeiro de Vasconcelos Ana Tereza
Published: June 2021

The live attenuated yellow fever (YF) vaccine was developed in the 1930s. Currently, the 17D and 17DD attenuated substrains are used for vaccine production. The 17D strain is used for vaccine production by several countries, while the 17DD strain is used exclusively in Brazil. The cell passages carried out through the seed-lot system of vaccine production influence the presence of quasispecies causing changes in the stability and immunogenicity of attenuated genotypes by increasing attenuation or virulence. Using next-generation sequencing, we carried out genomic characterization and genetic diversity analysis between vaccine lots of the Brazilian YF vaccine, produced by BioManguinhos–Fiocruz, and used during 11 years of vaccination in Brazil. We present 20 assembled and annotated genomes from the Brazilian 17DD vaccine strain, eight single nucleotide polymorphisms and the quasispecies spectrum reconstruction for the 17DD vaccine, through a pipeline here introduced. The V2IDA pipeline provided a relationship between low genetic diversity, maintained through the seed lot system, and the confirmation of genetic stability of lots of the Brazilian vaccine against YF. Our study sets precedents for use of V2IDA in genetic diversity analysis and
in silico
stability investigation of attenuated viral vaccines, facilitating genetic surveillance during the vaccine production process.
Predicted pH-dependent stability of SARS-CoV-2 spike protein trimer from interfacial acidic groups
Authors: Lobo Vanessa R. , Warwicker Jim
Published: June 2021

Transition between receptor binding domain (RBD) up and down forms of the SARS-CoV-2 spike protein trimer is coupled to receptor binding and is one route by which variants can alter viral properties. It is becoming apparent that key roles in the transition are played by pH and a more compact closed form, termed locked. Calculations of pH-dependence are made for a large set of spike trimers, including locked form trimer structures that have recently become available. Several acidic sidechains become sufficiently buried in the locked form to give a predicted pH-dependence in the mild acidic range, with stabilisation of the locked form as pH reduces from 7.5 to 5, consistent with emerging characterisation by cryo-electron microscopy. The calculated pH effects in pre-fusion spike trimers are modulated mainly by aspartic acid residues, rather than the more familiar histidine role at mild acidic pH. These acidic sidechains are generally surface located and weakly interacting when not in a locked conformation. In this model, their replacement (perhaps with asparagine) would remove the pH-dependent destabilisation of locked spike trimer conformations, and increase their recovery at neutral pH. This would provide an alternative or supplement to the insertion of disulphide linkages for stabilising spike protein trimers, with potential relevance for vaccine design.
Towards Development of Guidelines for Virtual Administration of Standardized Language and Literacy Assessments: Considerations for Clinicians and Researchers
Authors: Wood Emily , Bhalloo Insiya , McCaig Brittany , Feraru Cristina , Molnar Monika
Published: June 2021

Objectives

Previous virtual care literature within the field of speech-language pathology has focused primarily on validating the virtual use of intervention programs. There are fewer articles addressing the validity of conducting standardized paediatric oral language and literacy assessments virtually. Additionally, there is a lack of practical recommendations available on how best to conduct these assessment measures virtually. Given the rapid rise in virtual care as a result of the COVID-19 pandemic, clinicians and researchers require guidance on best practices for virtual administration of these tools imminently.

Methods

We identified six key themes for recommendations based on two sources (1) our lab meeting discussions and (2) the outcomes of a narrative review of the extant literature. We then conducted semi-structured interviews with a group of 12 clinicians, students and researchers who had administered standardized language and literacy assessments with a variety of monolingual and multilingual school-aged children, with and without speech and language difficulties, in clinical and research settings to generate recommendations within these themes. Subsequently, in line with the Guidelines International Network, these recommendations were rated by group members, and reviewed by external stakeholders. A quasi-delphi consensus procedure was used to reach agreement on ratings for recommendations.

Results

We have developed recommendations for the use of standardized language and literacy assessments in virtual care, across six key themes: candidacy for virtual assessment, communication and collaboration with caregivers, technology and equipment, virtual administration, ethics, consent and confidentiality, and considerations for bilingual populations.

Conclusions

This paper is one of the first to share practical recommendations for virtual assessment in the domain of paediatric oral language and literacy assessment. We hope these recommendations will facilitate future clinical research and that as the body of research grows, that this paper will act as a basis for the development of formal Clinical Practice Guidelines.
Genome and epigenome wide studies of plasma protein biomarkers for Alzheimer’s disease implicate TBCA and TREM2 in disease risk
Authors: Hillary Robert F. , Gadd Danni A. , McCartney Daniel L. , Shi Liu , Campbell Archie , Walker Rosie M. , Ritchie Craig W. , Deary Ian J. , Evans Kathryn L. , Nevado-Holgado Alejo J. , Hayward Caroline , Porteous David J. , McIntosh Andrew M. , Lovestone Simon , Robinson Matthew R. , Marioni Riccardo E.
Published: June 2021

The levels of many blood proteins are associated with Alzheimer’s disease or its pathological hallmarks. Elucidating the molecular factors that control circulating levels of these proteins may help to identify proteins causally associated with the disease. Here, genome-wide and epigenome-wide studies (nindividuals≤1,064) were performed on plasma levels of 281 Alzheimer’s disease-associated proteins, identified by a systematic review of the literature. We quantified the contributions of genetic and epigenetic variation towards inter-individual variability in plasma protein levels. Sixty-one independent genetic and 32 epigenetic loci were associated with expression levels of 49 proteins; eight and 24 of these respective findings are previously unreported. Novel findings included an association between plasma TREM2 levels and a polymorphism and CpG site within theMS4A4Alocus. Through Mendelian randomisation analyses, causal associations were observed between higher plasma TBCA and TREM2 levels and lower Alzheimer’s disease risk. Our data inform the regulation of biomarker levels and their relationships with Alzheimer’s disease.
Prescribed footwear and orthoses are not prophylactic in preventing lower extremity injuries in military tactical athletes. A systematic review with meta-analysis
Authors: Paradise Scott L. , Beer Joshua R. , Cruz Chris A. , Fechner Ken M. , MacGregor Andrew J. , Fraser John J.
Published: June 2021

Introduction

Military members are exposed to high cumulative physical loads that frequently lead to injury. Prescribed footwear and orthoses have been used to prevent injury. The purpose of this systematic review with meta-analysis was to assess if prescribed prophylactic footwear or foot orthoses reduced lower extremity injury risk in military tactical athletes.

Methods

MEDLINE, Embase, Web of Science, CINAHL, SportDiscus, and DTIC databases were searched for randomized controlled trials published at any time that compared foot orthoses or prescribed footwear (to include shock-absorbing insoles and socks) to a placebo intervention or a no-treatment control. Methodological quality was assessed and numbers of injuries, population at risk, and the duration of the study epoch were extracted and relative risk (RR) calculated. An omnibus meta-analysis was performed assessing all prescribed footwear and orthoses intervention studies, with subgroup analyses conducted on studies with similar interventions [i.e., basketball athletic shoes; athletic shoes (prescribed by foot type); foot orthoses; shock-absorbing insoles; socks; tropical combat boots].

Results

Of 1,673 studies identified, 22 studies were included. Three of eight studies that employed orthoses demonstrated significantly reduced overuse injuries compared to no treatment controls (RR range: 0.34-0.68); one study showed neoprene insoles significantly decreased overuse injuries (RR: 0.75). There were no other significant effects in the individual studies, and no protective effects observed in the omnibus meta-analysis or in the component sub analyses.

Conclusions

Prescribed footwear and orthoses do not appear to have a prophylactic effect on lower quarter MSKI in military members and cannot be recommended at this time.
Intensified stimulation targeting lateral and medial prefrontal cortices for the treatment of social anxiety disorder: A randomized, double-blind, parallel-group, dose-comparison study
Authors: Jafari Eisa , Alizadehgoradel Jaber , Koluri Fereshteh Pourmohseni , Nikoozadehkordmirza Ezzatollah , Refahi Meysam , Taherifard Mina , Nejati Vahid , Hallajian Amir-Homayun , Ghanavati Elham , Vicario Carmelo M. , Nitsche Michael A. , Salehinejad Mohammad Ali
Published: June 2021

Background

Social Anxiety Disorder (SAD) is the most common anxiety disorder while remains largely untreated. Disturbed amygdala-frontal network functions are central to the pathophysiology of SAD, marked by hypoactivity of the lateral prefrontal cortex (PFC), and hypersensitivity of the medial PFC and amygdala. The objective of this study was to determine whether modulation of dorsolateral and medial PFC activity with a novel intensified stimulation protocol reduces SAD core symptoms, improves treatment-related variables, and reduces attention bias to threatening stimuli.

Methods

In this randomized, sham-controlled, double-blind trial, we assessed the efficacy of an intensified stimulation protocol (20 min, twice-daily sessions with 20 min intervals, 5 consecutive days) in two intensities (1 vs 2 mA) compared to sham stimulations. 45 patients with SAD were randomized in three tDCS arms. SAD symptoms, treatment-related variables (worries, depressive state, emotion regulation, quality of life), and attention bias to threatening stimuli (dot-probe paradigm) were assessed before and right after the intervention. SAD symptoms were also assessed at 2-month follow-up.

Results

Both 1 mA and 2mA protocols significantly reduced fear/avoidance symptoms, worries and improved, emotion regulation and quality of life after the intervention compared to the sham group. Improving effect of the 2 mA protocol on avoidance symptoms, worries and depressive state was significantly larger than the 1 mA group. Only the 2 mA protocol reduced attention bias to threat-related stimuli, the avoidance symptom at follow-up, and depressive states, as compared to the sham group.

Conclusions

Modulation of lateral-medial PFC activity with intensified stimulation can improve cognitive control, motivation and emotion networks in SAD and thereby results in therapeutic effects. These effects can be larger with 2 mA vs 1 mA intensities, though a linear relationship between intensity and efficacy should not be concluded.
A year of Covid-19 GWAS results from the GRASP portal reveals potential SARS-CoV-2 modifiers
Authors: Thibord Florian , Chan Melissa V. , Chen Ming-Huei , Johnson Andrew D.
Published: June 2021

Host genetic variants influence the susceptibility and severity of several infectious diseases, and the discovery of novel genetic associations with Covid-19 phenotypes could help developing new therapeutic strategies to reduce its burden.

Between May 2020 and June 2021, we used Covid-19 data released periodically by UK Biobank and performed 65 Genome-Wide Association Studies (GWAS) in up to 18 releases of Covid-19 susceptibility (N=18,481 cases in June 2021), hospitalization (N=3,260), severe outcomes (N=1,244) and death (N=1,104), stratified by sex and ancestry.

In coherence with previous studies, we observed 2 independent signals at the chr3p21.31 locus (rs73062389-A, OR=1.21, P=4.26×10−15 and rs71325088-C, OR=1.62, P=2.25×10−9) modulating susceptibility and severity, respectively, and a signal influencing susceptibility at the ABO locus (rs9411378-A, OR=1.10, P=3.30×10−12), suggesting an increased risk of infection in non-O blood groups carriers. Additional signals at the APOE (associated with severity and death) LRMDA (susceptibility in non-European) and chr2q32.3 (susceptibility in women) loci were also identified but did not replicate in independent datasets. We then devised an original approach to extract variants exhibiting an increase in significance over time. When applied to the susceptibility, hospitalization and severity analyses, this approach revealed the known DPP9, RPL24 and MAPT loci, amongst thousands of other signals. Finally, this significance trajectory analysis was applied to the larger Covid-19hgi meta-analyses, where additional loci of interest, related to the immune system, were identified.

These results, freely available on the GRASP portal, provide new insights on the genetic mechanisms involved in Covid-19 phenotypes.
Multiscale dynamics underlying neocortical slow oscillations
Authors: Mattia Maurizio , Perez-Zabalza Maria , Tort-Colet Núria , Dasilva Miguel , Muñoz Alberto , Sanchez-Vives Maria V.
Published: June 2021

Slow oscillations in the sleeping and anesthetized brain invariantly emerge as an alternation between Up (high firing) and Down (almost quiescent) states. In cortex, they occur simultaneously in cell assemblies in different layers and propagate as traveling waves, a concerted activity at multiple scales whose interplay and role is still under debate. Slow oscillations have been reported to start in deep layers, more specifically in layer 5. Here, we studied the laminar organization of slow oscillations in the anesthetized rat cortex and we found that the activity leading to Up states actually initiates in layer 6, then spreads towards upper layers. Layer 5 cell assemblies have a threshold-like activation that can persist after layer 6 inactivation, giving rise to hysteresis loops like in “flip-flop” computational units. We found that such hysteresis is finely tuned by the columnar circuitry depending on the recent history of the local ongoing activity. Furthermore, thalamic inactivation reduced infragranular excitability without affecting the columnar activation pattern. We propose a role for layer 6 acting as a hub unraveling a hierarchy of cortical loops.
All-optical mechanobiology interrogation of YAP in human cancer and normal cells using a novel multi-functional system
Authors: Luo Qin , Huang Miao , Liang Chenyu , Zhang Justin , Lin Gaoming , Yu Sydney , Tanaka Mai , Lepler Sharon , Guan Juan , Siemann Dietmar , Tang Xin
Published: June 2021

Long-term multi-functional imaging and analysis of live cells require streamlined functional coordination of various hardware and software platforms. However, manual control of various equipment produced by different manufacturers is labor-intensive and time-consuming, potentially decreasing the accuracy, reproducibility, and quality of acquired data. Therefore, an all-in-one and user-programmable system that enables automatic, multi-functional, and long-term image acquisition and is compatible with most fluorescent microscopy platforms can desirably benefit the scientific community. In this paper, we introduce the full operating protocols of utilizing a novel integrated software system that consists of (1) a home-built software program, titled “Automatic Multi-functional Integration Program (AMFIP)”, which enables automatic multi-channel imaging acquisition, and (2) a suite of quantitative imaging analysis and cell traction computation packages. We applied this integrated system to reveal the previously unknown relationship between the spatial-temporal distribution of mechano-sensitive Yes-associated protein (YAP) and the cell mechanics, including cell spreading and traction, in human normal cells (B2B) and lung cancer cells (PC9). Leveraging our system’s capability of multi-channel control and readout, we found: (1) B2B normal cells and PC9 cancer cells show distinct YAP expression, traction, and cell dynamics relationship during cell spreading and migration processes; and (2) PC9 cancer cells apply noticeable peri-nuclear forces on substrates. In summary, this paper presents a detailed stepwise protocol on how to utilize an integrated user-programmable system that enables automatic multi-functional imaging and analysis to elucidate YAP mechanosensitivity. These tools open the possibility for detailed explorations of multifaceted signaling dynamics in the context of cell physiology and pathology.

This paper presents a detailed stepwise protocol on how to utilize an integrated user-programmable system that enables all-optical electro-mechanobiology interrogation to elucidate YAP mechanosensitivity.
Inferring global-scale temporal latent topics from news reports to predict public health interventions for COVID-19
Authors: Wen Zhi , Powell Guido , Chafi Imane , Buckeridge David , Li Yue
Published: June 2021

The COVID-19 pandemic has highlighted the importance of non-pharmacological interventions (NPI) for controlling epidemics of emerging infectious diseases. Despite their importance, NPI have been monitored mainly through the manual efforts of volunteers. This approach hinders measurement of the NPI effectiveness and development of evidence to guide their use to control the global pandemic. We present EpiTopics, a machine learning approach to support automation of the NPI prediction and monitoring at both the document-level and country-level by mining the vast amount of unlabelled news reports on COVID-19. EpiTopics uses a 3-stage, transfer-learning algorithm to classify documents according to NPI categories, relying on topic modelling to support result interpretation. We identified 25 interpretable topics under 4 distinct and coherent COVID-related themes. Importantly, the use of these topics resulted in significant improvements over alternative automated methods in predicting the NPIs in labelled documents and in predicting country-level NPIs for 42 countries.
Functional redundancy of WDR31 with GTPase-activating proteins ELMOD and RP2 in regulating IFT trains via BBSome
Authors: Cevik Sebiha , Peng Xiaoyu , Beyer Tina , Pir Mustafa S. , Yenisert Ferhan , Woerz Franziska , Hoffmann Felix , Altunkaynak Betul , Pir Betul , Boldt Karsten , Karaman Asli , Cakiroglu Miray , Sadik Oner S. , Cao Ying , Ueffing Marius , Kaplan Oktay I.
Published: June 2021

The correct intraflagellar transport (IFT) assembly at the ciliary base and the IFT turnaround at the ciliary tip are key for the IFT to perform its function, but we still have poor understanding about how these processes are regulated. Here, we identify WDR31 as a new ciliary protein, and analysis from zebrafish andCaenorhabditis elegansreveals the role ofWDR31in regulating the cilia morphology. We find that loss of WDR-31 together with RP-2 and ELMD-1 (the sole ortholog ELMOD1-3) results in ciliary accumulations of IFT Complex B components and KIF17 kinesin, with fewer IFT/BBSome particles traveling along cilia in both anterograde and retrograde directions, suggesting that the IFT/BBSome entry into cilia and exit from cilia are impacted. Furthermore, anterograde IFT in the middle segment travel at increased speed inwdr-31;rpi-2;elmd-1. Remarkably, a non-ciliary protein leaks into cilia ofwdr-31;rpi-2;elmd-1possible due to IFT defects. This work reveals WDR31-RP-2-ELMD-1 as IFT and BBSome trafficking regulators.
NDR1 and the Arabidopsis Plasma Membrane ATPase AHA5 are Required for Processes that Converge on Drought Tolerance and Immunity
Authors: Lu Yi-Ju , Chen Huan , Corrion Alex , Buyuk Ilker , Li Pai , Samaradivakara Saroopa , Wai Ching Man , Sakamoto Hikaru , Santos Patrícia , VanBuren Robert , Kim Yongsig , Day Brad
Published: June 2021

NON-RACE-SPECIFIC DISEASE RISISTANCE1 (NDR1) is a key component of plant immune signaling, required for defense against the bacterial pathogen Pseudomonas syringae. Plant stress responses have overlapping molecular, physiological, and cell biology signatures, and given the central role of NDR1 during biotic stress perception and signaling, we hypothesized that NDR1 also functions in abiotic stress responses, including in a role that mediates signaling at the plasma membrane (PM) - cell wall (CW) continuum. Here, we demonstrate that NDR1 is required for the induction of drought stress responses in plants, a role that couples stress signaling in an abscisic acid-dependent manner. We show that NDR1 physically associates with the PM-localized H+-ATPases AHA1, AHA2, and AHA5 and is required for proper regulation of H+-ATPase activity and stomatal guard cell dynamics, providing a mechanistic function of NDR1 during drought responses. In the current study, we demonstrate that NDR1 functions in signaling processes associated with both biotic and abiotic stress response pathways, a function we hypothesize represents NDR1’s role in the maintenance of cellular homeostasis during stress. We propose a role for NDR1 as a core transducer of signaling between cell membrane processes and intercellular stress response activation.
Identification of ACE2 modifiers by CRISPR screening
Authors: Sherman Emily J. , Mirabelli Carmen , Tang Vi T. , Khan Taslima G. , Kennedy Andrew A. , Graham Sarah E. , Willer Cristen J. , Tai Andrew W. , Sexton Jonathan Z. , Wobus Christiane E. , Emmer Brian T.
Published: June 2021

SARS-CoV-2 infection is initiated by binding of the viral spike protein to its receptor, ACE2, on the surface of host cells. ACE2 expression is heterogeneous both in vivo and in immortalized cell lines, but the molecular pathways that govern ACE2 expression remain unclear. We now report high-throughput CRISPR screens for functional modifiers of ACE2 surface abundance. We identified 35 genes whose disruption was associated with a change in the surface abundance of ACE2 in HuH7 cells. Enriched among these ACE2 regulators were established transcription factors, epigenetic regulators, and functional networks. We further characterized individual cell lines with disruption of SMAD4, EP300, PIAS1, or BAMBI and found these genes to regulate ACE2 at the mRNA level and to influence cellular susceptibility to SARS-CoV-2 infection. Collectively, our findings clarify the host factors involved in SARS-CoV-2 entry and suggest potential targets for therapeutic development.
Point-estimating observer models for latent cause detection
Authors: Lee Jennifer Laura , Ma Wei Ji
Published: June 2021

The spatial distribution of visual items allows us to infer the presence of latent causes in the world. For instance, a spatial cluster of ants allows us to infer the presence of a common food source. However, optimal inference requires the integration of a computationally intractable number of world states in real world situations. For example, optimal inference about whether a common cause exists based on N spatially distributed visual items requires marginalizing over both the location of the latent cause and 2N possible affiliation patterns (where each item may be affiliated or non-affiliated with the latent cause). How might the brain approximate this inference? We show that subject behaviour deviates qualitatively from Bayes-optimal, in particular showing an unexpected positive effect of N (the number of visual items) on the false-alarm rate. We propose several “point-estimating” observer models that fit subject behaviour better than the Bayesian model. They each avoid a costly computational marginalization over at least one of the variables of the generative model by “committing” to a point estimate of at least one of the two generative model variables. These findings suggest that the brain may implement partially committal variants of Bayesian models when detecting latent causes based on complex real world data.
Brain-wide analysis of the supraspinal connectome reveals anatomical correlates to functional recovery after spinal injury
Authors: Wang Zimei , Romanski Adam , Mehra Vatsal , Wang Yunfang , Campbell Benjamin C. , Petsko Gregory A. , Tsoulfas Pantelis , Blackmore Murray
Published: June 2021

The supraspinal connectome is essential for normal behavior and homeostasis and consists of numerous sensory, motor, and autonomic projections from brain to spinal cord. Study of supraspinal control and its restoration after damage has focused mostly on a handful of major populations that carry motor commands, with only limited consideration of dozens more that provide autonomic or crucial motor modulation. We now provide an experimental platform and associated web-based resource to rapidly profile the entire supraspinal mesoconnectome in adult mice. Optimized viral labeling, 3D imaging, and registration to a mouse digital neuroanatomical atlas assigned tens of thousands of supraspinal neurons to more than 60 identified regions. We demonstrate the approach’s ability to clarify essential points of topographic mapping between spinal levels, to measure population-specific sensitivity to spinal injury, and to resolve previously unexplained variability in functional recovery. This work will spur progress by broadening understanding and enabling analyses of essential but understudied supraspinal populations.
A CRISPR toolbox for generating intersectional genetic mice for functional, molecular, and anatomical circuit mapping
Authors: Lusk Savannah J. , McKinney Andrew , Hunt Patrick J. , Fahey Paul G. , Patel Jay , Chang Andersen , Sun Jenny J. , Martinez Vena K. , Zhu Ping Jun , Egbert Jeremy R. , Allen Genevera , Jiang Xiaolong , Arenkiel Benjamin R. , Tolias Andreas S. , Costa-Mattioli Mauro , Ray Russell S.
Published: June 2021

Background

A full understanding of circuits and cellular mechanisms governing health and disease requires the dissection and multi-faceted study of discrete cell subtypes in developing and adult animal models. Recombinase-driven expression of transgenic response alleles represents a significant and powerful approach to delineate cell populations for functional, molecular, and anatomical study. In addition to single recombinase systems, the expression of two recombinases in distinct, but partially overlapping, populations allow for more defined target expression. Although the application of this method is becoming increasingly popular, the expense and difficulty associated with production of customized intersectional mouse lines have limited widespread application to more common allele manipulations that are often commercially produced at great expense.

Results

We present a simplified CRISPR toolkit for rapid, inexpensive, and facile intersectional allele production. Briefly, we produced 7 intersectional mouse lines using a dual recombinase system, one mouse line with a single recombinase system, and three embryonic stem (ES) cell lines that are designed to study how functional, molecular, and anatomical features relate to each other in building circuits that underlie physiology and behavior. As a proof-of-principle, we applied three of these lines to different neuronal populations for anatomical mapping and functional in vivo investigation of respiratory control. We also generated a mouse line with a single recombinase-responsive allele that controls the expression of the calcium sensor Twitch-2B. This mouse line was applied globally to study the effects of follicle stimulating hormone (FSH) and luteinizing hormone (LH) on calcium release in the ovarian follicle.

Conclusions

Lines presented here are representative examples of outcomes possible with the successful application of our genetic toolkit for the facile development of diverse, modifiable animal models. This toolkit will allow labs to create single or dual recombinase effector lines easily for any cell population or subpopulation of interest when paired with the appropriate Cre and FLP recombinase mouse lines or viral vectors. We have made our tools and derivative intersectional mouse and ES cell lines openly available for non-commercial use through publicly curated repositories for plasmid DNA, ES cells, and transgenic mouse lines.
Identifying proximal RNA interactions from cDNA-encoded crosslinks with ShapeJumper
Authors: Christy Thomas W. , Giannetti Catherine A. , Laederach Alain , Weeks Kevin M.
Published: June 2021

SHAPE-JuMP is a concise strategy for identifying close-in-space interactions in RNA molecules. Nucleotides in close three-dimensional proximity are crosslinked with a bi-reactive reagent that covalently links the 2’-hydroxyl groups of the ribose moieties. The identities of crosslinked nucleotides are determined using an engineered reverse transcriptase that jumps across crosslinked sites, resulting in a deletion in the cDNA that is detected using massively parallel sequencing. Here we introduce ShapeJumper, a bioinformatics pipeline to process SHAPE-JuMP sequencing data and to accurately identify through-space interactions. ShapeJumper identifies proximal interactions with near-nucleotide resolution using an alignment strategy that is optimized to tolerate the unique non-templated reverse-transcription profile of the engineered crosslink-traversing reverse-transcriptase. JuMP-inspired strategies are now poised to replace adapter-ligation for detecting RNA-RNA interactions in most crosslinking experiments.
Selective sweeps influence diversity over large regions of the mouse genome
Authors: Booker Tom R. , Jackson Benjamin C. , Craig Rory J. , Charlesworth Brian , Keightley Peter D.
Published: June 2021

To what extent do substitutions in protein-coding versus gene-regulatory regions contribute to fitness change over time? Answering this question requires estimates of the extent of selection acting on beneficial mutations in the two classes of sites. New mutations that have advantageous or deleterious fitness effects can induce selective sweeps and background selection, respectively, causing variation in the level of neutral genetic diversity along the genome. In this study, we analyse the profiles of genetic variability around protein-coding and regulatory elements in the genomes of wild mice to estimate the parameters of positive selection. We find patterns of diversity consistent with the effects of selection at linked sites, which are similar across mouse taxa, despite differences in effective population size and demographic history. By fitting a model that combines the effects of selective sweeps and background selection, we estimate the strength of positive selection and the frequency of advantageous mutations. We find that strong positive selection is required to explain variation in genetic diversity across the murid genome. In particular, we estimate that beneficial mutations in protein-coding regions have stronger effects on fitness than do mutations in gene-regulatory regions, but that mutations in gene-regulatory regions are more common. Overall though, our parameter estimates suggest that the cumulative fitness changes brought about by beneficial mutations in protein-coding may be greater than those in gene-regulatory elements.