bluuebunny/crossref_metadata_2025 huggingface dataset:
Conclusion
Authors: Gosewinkel Dieter
Published: December 2021

The book comes to four main conclusions. Contrary to an influential theory (Rogers Brubaker), it is, first, not discursive idioms about the nation that primarily determine the inclusive or exclusive character of citizenship. Rather, it was changing politico-social constellations—economic, demographic, and foreign policy interests and conjunctions—that defined the political form and practice of citizenship. Second, contrary to a dominant narrative, the frequently alleged qualitative divide of legal culture from Western to Eastern Europe is called into question. Third, the book’s historical cross-section supports a critical review of the widespread theory of convergence between regimes of citizenship in Europe. It specifies, instead, the historical conditions for expectations of Europeanization through law and thus for European citizenship. Fourth, the history of citizenship in Europe since the nineteenth century cannot be told as an exclusively European one. The politics and colonial practices of affiliation in the European powers’ overseas and continental colonial empires remained in effect well into the postcolonial policies of citizenship and migration, thus also shaping the inheritance of a current policy of citizenship in Europe.
‘The Axile Tree’
Authors: Brooks Francesca
Published: December 2021

Chapter 5 asks how Jones’s vision of an early medieval culture in which Welsh and English tradition are equally dominant resonates throughout the poem’s eight poetic sequences in the image of the cross. The chapter traces a history of Jones’s encounters with The Dream of the Rood, the Ruthwell monument, and the history of early medieval Northumbria during the 1930s, and explores how this experience of the landscape and history of Northumberland informed his reading of the Old English Dream of the Rood tradition. Jones’s visual and verbal engagement with the Ruthwell monument at the climax of The Anathemata in ‘Sherthursdaye and Venus Day’ allows for the creation of a new sign of the cross for the twentieth century, a sign which draws together the English and Welsh traditions that have informed the institution of the Catholic Church in England and Wales, as well as the poet’s own Catholicism.
Music
Authors: Brown Steven
Published: December 2021

2The defining feature of music as a cognitive function is tonality (scale structure), since rhythmic structure is a shared feature with dance and poetry. In this chapter, the author develops a 4T (tonality/timing/texture/text) model of music, which views music as a suite of coordinative features in which rhythm provides time slots for interpersonal coordination and scale structure provides pitch slots for coordination. An important topic for the study of music’s evolution is its connection with both speech and language. Music and speech share a significant number of prosodic properties. However, a unique feature of music that is not found in speech is the process by which scale types are able to convey emotional meanings. Such scale/emotion associations allow music to modulate the interpretive meaning of narrative artforms, such as film, dance, and written texts (i.e. songs).
The Innamorata Ignites
Authors: Brown Pamela Allen
Published: December 2021

The bold “woman in love” evolved from trends in commedia erudita and commedia grave that ignited when actresses reshaped the role to showcase their stellar skills. This amorous agent was a radical change from the passive virgo of regular comedies that followed classical precedent. The ambitious diva created her own vehicles full of pathos and variety, and played tragedy and tragicomedy as well as comedy. Elizabeth and her court heard glowing reports about Italian players in Paris, and soon brought Italian actors and actresses to England. Several Italian troupes played in London in the 1570s, as more information streamed in from travelers, touring actors, foreign newsletters, and popular pamphlets. When paying theaters opened, audiences clamored for amorous and amusing Italian plots. Playwrights began to feature the imported innamorata, expanding the size and importance of the role, stressing her southern passions, and emulating the diva’s glamour, a strategy that “Italianated” the boy player.
Fatigue in early rheumatoid arthritis: data from the Early Rheumatoid Arthritis Network
Authors: Ifesemen Onosi Sylvia , McWilliams Daniel Frederick , Norton Sam , Kiely Patrick D W , Young Adam , Walsh David Andrew
Published: December 2021

Objectives

Fatigue is a disabling symptom in people with RA. This study aims to describe the prevalence, risk factors and longitudinal course of fatigue in early RA.

Methods

Demographic, clinical, quality of life (QoL), comorbidities and laboratory data were from the Early RA Network (ERAN), a UK multicentre inception cohort of people with RA. Fatigue was measured using the vitality subscale of the 36-item Short Form Health Survey, where higher values represent better QoL. Baseline prevalences of fatigue classifications were age and sex standardized. Linear regression, hierarchical growth curve modelling and group-based trajectory modelling (GBTM) were utilized.

Results

At baseline (n = 1236, 67% female, mean age 57 years), the mean vitality was 41 (s.d. 11) and disease duration was 11 months (interquartile range 7–18). Age- and sex-standardized prevalence rates of fatigue and severe fatigue were 44% (95% CI 39, 50) and 19% (95% CI 15, 23), respectively. Fatigue changed little over 3 years and five measurement occasions β = −0.13 (95% CI −0.23, −0.02). GBTM identified two subgroups, which we named ‘Fatigue’ (53%) and ‘No-fatigue’ (47%). Female sex, worse pain, mental health and functional ability were associated with greater fatigue and predicted Fatigue group membership (area under the receiver operating characteristics curve = 0.81). Objective measures of inflammation—swollen joint count and ESR—were not significantly associated with fatigue.

Conclusions

Fatigue is prevalent and persistent in early RA. Diverse characteristics indicative of central mechanisms are associated with persistent fatigue. Management of fatigue might require interventions targeted at central mechanisms in addition to inflammatory disease modification. People who require such interventions might be identified at presentation with early RA.
Transfemoral Osseointegration—a self-case study and physiotherapy assessment
Authors: Gunn Rachel , Langley Charlotte (Beth)
Published: December 2021

A patient (the first author) with a preexisting right side transfemoral amputation (20 years before) had osseointegration surgery. She was assigned a physiotherapist (the second author) and began a rehabilitation program. We provide a unique insight into the first 18 months of rehabilitation after insertion of an osseointegration bone anchor from a physiotherapist and patient perspective with the intention of informing practitioners, patients, and potential patients about the experience and identifying potential areas for improvements in the rehabilitation protocol. The experience was tracked by both the patient and the physiotherapist for 18 months post-surgery. The physiotherapist followed a specific protocol with the patient in the first part of the recovery stage. The patient kept records of subjective experiences over the same period. Loading and physiotherapy were completed in line with the protocol for the first 12-week phase including successful fitting of the prosthetic limb on day 12. Physiotherapy and other interventions evolved to meet the patient's needs over the 18-month period. The patient progressed through her rehabilitation, and new data about the patient's experience were gathered. Following the protocol enabled the patient to progress through her rehabilitation. Unforeseen setbacks (abscesses and inflammation/entheseopathies) slowed this process to some extent. Findings from these data can be used to help inform and improve future rehabilitations for patients with osseointegration: patients can be advised about possible setbacks and physiotherapy, and other interventions can be developed to treat should these problems arise.
Efficacy of adaptive seating system for the management of neuromuscular scoliosis in a young adult with cerebral cavernous malformation: A case report
Authors: Tofani Marco , Blasetti Giulia , Sabbadini Maurizio , Lucibello Luca , Castelli Enrico
Published: December 2021

Cerebral cavernous malformations (CCMs) are vascular malformations causing seizures and cerebral hemorrhages. Neurological and functional profile can differ from each individual, and the management requires high complexity. The aim of the present case report was to explore the management of neuromuscular scoliosis in a young adult with CCM, comparing the use of a scoliotic brace with a customized adaptive seating system (AdSS). X-ray examinations were performed in three different situations: sitting in a flat bench without postural support, sitting in a flat bench with scoliotic brace, and sitting in an AdSS. For the analysis of the AdSS, an experimental radiolucent device was used. Differences in spine alignment and postural support were found. The best option to care was the use of the scoliotic brace. Nevertheless, the use of a customized AdSS offers a good solution for the management of neuromuscular scoliosis, with a difference of 10 degrees with respect to the scoliotic brace. Position was maintained at 3-month follow-up, with a reduction of the overhang of the spine. The use of an AdSS represents a valid attempt for the management of neuromuscular scoliosis in people with CCM. This approach can be considered when the patient suffers the scoliotic brace and/or when the brace interferes with breathing or other clinical conditions.
Test–retest reliability of the Arabic translation of the Lower Extremity Functional Status of the Orthotics and Prosthetics Users' Survey
Authors: Alhowimel Ahmed , Alodaibi Faris , Al-Nowaisri Khalid , Alotaibi Mazyad , Ghazal Haitham
Published: December 2021

Background:

The number of amputations secondary to diverse factors in Arabic countries is expected to rise in the coming years. Therefore, there is a need for high-quality service that can be monitored by the use of standardized patient-reported outcome measures of amputee patients' functional status. This study aimed to translate the Lower Extremity Functional status Orthotics and Prosthetics Users' Survey (OPUS-LEFS) to Arabic and test its reliability in a sample of Arabic-speaking people with amputation.

Methods:

Standard forward and backward translation, followed by an examination by a team of experts, and then preliminary testing were conducted on the final translation. The OPUS-LEFS was cross-culturally validated, and its test–retest reliability was examined in patients with lower extremity amputations (N = 67).

Results:

No issues were observed concerning the patients' understanding or the meaning of the items on the Arabic translation of the OPUS-LEFS. The intraclass correlation coefficient was 0.99 (95% confidence interval [CI]: 0.985 to 0.995), and the mean difference was −0.278 (95% CI: −5.83 to 5.28), indicating excellent test–retest reliability.

Conclusions:

The study's results suggest that the Arabic translation of the OPUS-LEFS is a reliable tool that can be recommended for future use as an outcome measure for patients from Arabic-speaking nations with little knowledge of the English language.
Sentimental Tweets Classification of Symptomatic COVID-19
Authors: Tharun P
Published: December 2021

The approach I described is straightforward, related to COVID-19 SARS based tweets and the symptoms, that people tweet about. Also, social media mining for health application reports was shared in many different tasks of 2021. The motto at the back of this observe is to analyses tweets of COVID-19 based symptoms. By performing BERT model and text classification with XLNET with which uses to classify text and purpose of the texts (i.e.) tweets. So that I can get a deep understanding of the texts. When developing the system, I used two models the XLNet and DistilBERT for the text sorting task, but the outcome was XLNET out-performs the given approach to the best accuracy achieved. Now I discover a whole lot vital for as it should be categorizing tweets as encompassing self-said COVID-19 indications. Whether or not a tweets associated with COVID-19 is a non-public report or an information point out to the virus. Which gives test accuracy to an F1 score of 96%.
Complete remission in a patient with widely metastatic HER2-amplified pancreatic adenocarcinoma following multimodal therapy informed by tumor sequencing and organoid profiling
Authors: King Daniel A , Smith Amber R , Pineda Gino , Nakano Michitaka , Michelini Flavia , Goedegebuure S. Peter , Thyparambil Sheeno , Liao Wei-Li , McCormick Aaron , Ju Jihang , Cioffi Michele , Zhang Xiuli , Hundal Jasreet , Griffith Malachi , Grandori Carla , Pollastro Maddy , Rosati Rachele , Margossian Astrid , Chatterjee Payel , Ainge Trevor , Flory Marta , Ocampo Paolo , Chen Lee-may , Poultsides George A , Baron Ari D , Chang Daniel T , Herman Joseph M , Gillanders William E , Park Haeseong , Hoos William A , Nichols Mike , Fisher George A , Kuo Calvin J
Published: December 2021

Here, we demonstrate a complete clinical response achieved in a patient with HER2+ metastatic pancreatic ductal adenocarcinoma to a coordinated barrage of anti-HER2, personalized vaccine and checkpoint inhibition immunotherapy, radiation, and chemotherapy. Comprehensive organoid profiling with drug sensitivity screening and drug testing suggested a vulnerability to anti-HER2 directed therapy, facilitating personalized treatment selection for our patient, which contributed to her clinical benefit. Immune response monitoring following personalized vaccine, radiation and checkpoint inhibition showed a sustained increase in neoantigen specific T cell response.
Amyloid-PET of the white matter: relationship to free water, fiber integrity, and cognition in patients with dementia and small vessel disease
Authors: Ottoy Julie , Ozzoude Miracle , Zukotynski Katherine , Kang Min Su , Adamo Sabrina , Scott Christopher , Ramirez Joel , Swardfager Walter , Lam Benjamin , Bhan Aparna , Mojiri Parisa , Kiss Alex , Strother Stephen , Bocti Christian , Borrie Michael , Chertkow Howard , Frayne Richard , Hsiung Robin , Laforce Robert , Noseworthy Michael D. , Prato Frank S. , Sahlas Demetrios J. , Smith Eric E. , Kuo Phillip H. , Chad Jordan A. , Pasternak Ofer , Sossi Vesna , Thiel Alexander , Soucy Jean-Paul , Tardif Jean-Claude , Black Sandra E. , Goubran Maged ,   the Medical Imaging Trials Network of Canada (MITNEC) and Alzheimer’s Disease Neuroimaging Initiative (ADNI)
Published: December 2021

White matter (WM) injury is frequently observed along with dementia. Positron emission tomography with amyloid-ligands (Aβ-PET) recently gained interest for detecting WM injury. Yet, little is understood about the origin of the altered Aβ-PET signal in WM regions. Here, we investigated the relative contributions of diffusion MRI-based microstructural alterations, including free water and tissue-specific properties, to Aβ-PET in WM and to cognition. We included a unique cohort of 115 participants covering the spectrum of low-to-severe white matter hyperintensity (WMH) burden and cognitively normal to dementia. We applied a bi-tensor diffusion-MRI model that differentiates between (i) the extracellular WM compartment (represented via free water), and (ii) the fiber-specific compartment (via free water-adjusted fractional anisotropy [FA]). We observed that, in regions of WMH, a decrease in Aβ-PET related most closely to higher free water and higher WMH volume. In contrast, in normal-appearing WM, an increase in Aβ-PET related more closely to higher cortical Aβ (together with lower free water-adjusted FA). In relation to cognitive impairment, we observed a closer relationship with higher free water than with either free water-adjusted FA or WM PET. Our findings support free water and Aβ-PET as markers of WM abnormalities in patients with mixed dementia, and contribute to a better understanding of processes giving rise to the WM PET signal.
Variable loss of antibody potency against SARS-CoV-2 B.1.1.529 (Omicron)
Authors: Sheward Daniel J. , Kim Changil , Ehling Roy A. , Pankow Alec , Dopico Xaquin Castro , Martin Darren , Reddy Sai , Dillner Joakim , Karlsson Hedestam Gunilla B. , Albert Jan , Murrell Ben
Published: December 2021

The recently-emerged SARS-CoV-2 B.1.1.529 variant (Omicron) is spreading rapidly in many countries, with a spike that is highly diverged from the pandemic founder, raising fears that it may evade neutralizing antibody responses. We cloned the Omicron spike from a diagnostic sample which allowed us to rapidly establish an Omicron pseudotyped virus neutralization assay, sharing initial neutralization results only 13 days after the variant was first reported to the WHO, 8 days after receiving the sample.

Here we show that Omicron is substantially resistant to neutralization by several monoclonal antibodies that form part of clinical cocktails. Further, we find neutralizing antibody responses in pooled reference sera sampled shortly after infection or vaccination are substantially less potent against Omicron, with neutralizing antibody titers reduced by up to 45 fold compared to those for the pandemic founder. Similarly, in a cohort of convalescent sera prior to vaccination, neutralization of Omicron was low to undetectable. However, in recent samples from two cohorts from Stockholm, Sweden, antibody responses capable of cross-neutralizing Omicron were prevalent. Sera from infected-then-vaccinated healthcare workers exhibited robust cross-neutralization of Omicron, with an average potency reduction of only 5-fold relative to the pandemic founder variant, and some donors showing no loss at all. A similar pattern was observed in randomly sampled recent blood donors, with an average 7-fold loss of potency. Both cohorts showed substantial between-donor heterogeneity in their ability to neutralize Omicron. Together, these data highlight the extensive but incomplete evasion of neutralizing antibody responses by the Omicron variant, and suggest that increasing the magnitude of neutralizing antibody responses by boosting with unmodified vaccines may suffice to raise titers to levels that are protective.
SARS-CoV-2 Omicron Variant: ACE2 Binding, Cryo-EM Structure of Spike Protein-ACE2 Complex and Antibody Evasion
Authors: Mannar Dhiraj , Saville James W. , Zhu Xing , Srivastava Shanti S. , Berezuk Alison M. , Tuttle Katharine S. , Marquez Citlali , Sekirov Inna , Subramaniam Sriram
Published: December 2021

The newly reported Omicron variant is poised to replace Delta as the most rapidly spread SARS-CoV-2 variant across the world. Cryo-EM structural analysis of the Omicron variant spike protein in complex with human ACE2 reveals new salt bridges and hydrogen bonds formed by mutated residues R493, S496 and R498 in the RBD with ACE2. These interactions appear to compensate for other Omicron mutations such as K417N known to reduce ACE2 binding affinity, explaining our finding of similar biochemical ACE2 binding affinities for Delta and Omicron variants. Neutralization assays show that pseudoviruses displaying the Omicron spike protein exhibit increased antibody evasion, with greater evasion observed in sera obtained from unvaccinated convalescent patients as compared to doubly vaccinated individuals (8-vs 3-fold). The retention of strong interactions at the ACE2 interface and the increase in antibody evasion are molecular factors that likely contribute to the increased transmissibility of the Omicron variant.
Rare risk variants associate with epigenetic dysregulation in migraine
Authors: Techlo Tanya Ramdal , Chalmer Mona Ameri , Møller Peter L. , Kogelman Lisette J. A. , Olofsson Isa A. ,   DBDS Genomic Consortium, Banasik Karina , Nyegaard Mette , Olesen Jes , Hansen Thomas Folkmann
Published: December 2021

Migraine has a heritability of up to 65%. Genome-wide association studies (GWAS) on migraine have identified 123 risk loci, explaining only 10.6% of migraine heritability. Thus, there is a considerable genetic component not identified with GWAS. Further, the causality of the identified risk loci remains inconclusive. Rare variants contribute to the risk of migraine but GWAS are often underpowered to detect these. Whole genome sequencing is reliable for analyzing rare variants but is not frequently used in large-scale. We assessed if rare variants in the migraine risk loci associated with migraine. We used a large cohort of whole genome sequenced migraine patients (1,040 individuals from 155 families). The findings were replicated in an independent case-control cohort (2,027 migraine patients, 1,650 controls). We found rare variants (minor allele frequency<0.1%) associated with migraine in a Polycomb Response Element in theASTN2locus. The association was independent of the GWAS lead risk variant in the locus. The findings place rare variants as risk factors for migraine. We propose a biological mechanism by which epigenetic regulation by Polycomb Response Elements plays a crucial role in migraine etiology.
Omicron mutations enhance infectivity and reduce antibody neutralization of SARS-CoV-2 virus-like particles
Authors: Syed Abdullah M. , Ciling Alison , Khalid Mir M. , Sreekumar Bharath , Chen Pei-Yi , Kumar G. Renuka , Silva Ines , Milbes Bilal , Kojima Noah , Hess Victoria , Shacreaw Maria , Lopez Lauren , Brobeck Matthew , Turner Fred , Spraggon Lee , Taha Taha Y. , Tabata Takako , Chen Irene P. , Ott Melanie , Doudna Jennifer A.
Published: December 2021

The Omicron SARS-CoV-2 virus contains extensive sequence changes relative to the earlier arising B.1, B.1.1 and Delta SARS-CoV-2 variants that have unknown effects on viral infectivity and response to existing vaccines. Using SARS-CoV-2 virus-like particles (SC2-VLPs), we examined mutations in all four structural proteins and found that Omicron showed 3-fold higher capsid assembly and cell entry relative to Delta, a property conferred by S and N protein mutations. Thirty-eight antisera samples from individuals vaccinated with Pfizer/BioNTech, Moderna, Johnson & Johnson vaccines and convalescent sera from unvaccinated COVID-19 survivors had 15-fold lower efficacy to prevent cell transduction by VLPs containing the Omicron mutations relative to the ancestral B.1 spike protein. A third dose of Pfizer vaccine elicited substantially higher neutralization titers against Omicron, resulting in detectable neutralizing antibodies in 8 out of 8 subjects compared to 1 out of 8 pre-boost. Furthermore, the monoclonal antibody therapeutics Casirivimab and Imdevimab had robust neutralization activity against B.1, B.1.1 or Delta VLPs but no detectable neutralization of Omicron VLPs. Our results suggest that Omicron is more efficient at assembly and cell entry compared to Delta, and the antibody response triggered by existing vaccines or previous infection, at least prior to boost, will have limited ability to neutralize Omicron. In addition, some currently available monoclonal antibodies will not be useful in treating Omicron-infected patients.

One-Sentence Summary

Omicron SARS-CoV-2 virus-like particles have enhanced infectivity that is only weakly neutralized by vaccination without boost or prior infection, or antibody therapeutics.
Activity of convalescent and vaccine serum against a B.1.1.529 variant SARS-CoV-2 isolate
Authors: Carreño Juan Manuel , Alshammary Hala , Tcheou Johnstone , Singh Gagandeep , Raskin Ariel , Kawabata Hisaaki , Sominsky Levy , Clark Jordan , Adelsberg Daniel C. , Bielak Dominika , Gonzalez-Reiche Ana Silvia ,   PSP/PARIS Study Group, Srivastava Komal , Sordillo Emilia Mia , Bajic Goran , van Bakel Harm , Simon Viviana , Krammer Florian
Published: December 2021

The B.1.1.529 (Omicron) variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was identified in November of 2021 in South Africa and Botswana as well as in a sample of a traveler from South Africa in Hong Kong.1,2 Since then, B.1.1.529 has been detected in many countries globally. This variant seems to be more infectious than B.1.617.2 (Delta), has already caused super spreader events3 and has outcompeted Delta within weeks in several countries and metropolitan areas. B.1.1.529 hosts an unprecedented number of mutations in its spike gene and early reports have provided evidence for extensive immune escape and reduced vaccine effectiveness.2,4-6 Here, we investigated the neutralizing and binding activity of sera from convalescent, mRNA double vaccinated, mRNA boosted as well as convalescent double vaccinated and convalescent boosted individuals against wild type, B.1.351 and B.1.1.529 SARS-CoV-2 isolates. Neutralizing activity of sera from convalescent and double vaccinated participants was undetectable to very low against B.1.1.529 while neutralizing activity of sera from individuals who had been exposed to spike three or four times was maintained, albeit at strongly reduced levels. Binding to the B.1.1.529 receptor binding domain (RBD) and N-terminal domain (NTD) was reduced in convalescent not vaccinated but was mostly retained in vaccinated individuals.
A phosphorylation code regulates the multi-functional protein RETINOBLASTOMA-RELATED1 in Arabidopsis thaliana
Authors: Zamora-Zaragoza Jorge , Klap Katinka , Sánchez-Pérez Jaheli , Vielle-Calzada Jean-Philippe , Scheres Ben
Published: December 2021

The RETINOBLASTOMA-RELATED (RBR) proteins play a central role coordinating cell division, cell differentiation and cell survival within an environmental and developmental context. These roles reflect RBR ability to engage in multiple protein-protein interactions (PPIs), which are regulated by multi-site phosphorylation. However the functional outcomes of RBR phosphorylation in multicellular organisms remain largely unexplored. Here we test the hypothesis that phosphorylation allows diversification of RBR functions in multicellular context. Using a representative collection of transgenic loss- and gain of function point mutations in RBR phosphosites, we analysed their complementation capacity in Arabidopsis thaliana root meristems. While the number of mutated residues often correlated to the phenotypic strength of RBR phosphovariants, phospho-sites contributed differentially to distinct phenotypes. For example, the pocket-domain has a greater influence on meristematic cell proliferation, whereas the C-terminal region associates to stem cell maintenance. We found combinatorial effects between the T406 phopspho-site with others in different protein domains. Moreover, a phospho-mimetic and a phospho-defective variant, both promoting cell death, indicate that RBR controls similar cell fate choices by distinct mechanisms. Thus, additivity and specificity of RBR phospho-sites fine tune RBR activity across its multiple roles. Interestingly, a mutation disrupting RBR interactions with the LXCXE motif suppresses dominant phospho-defective RBR phenotypes. By probing protein-protein interactions of RBR variants, we found that LXCXE-containing members of the DREAM complex constitute an important component of phosphorylation-regulated RBR function, but also that RBR participates in stress or environmental responses independently of its phosphorylation state. We conclude that developmental-related, but not stress- or environmental-related functions of RBR are defined and separable by a combinatorial phosphorylation code.
The impact of Piscirickettsia Salmonis infection on genome-wide DNA methylation profile in Atlantic Salmon
Authors: Mukiibi Robert , Peñaloza Carolina , Gutierrez Alejandro , Yáñez José M. , Houston Ross D. , Robledo Diego
Published: December 2021

Salmon rickettsial septicaemia (SRS), caused by the intracellular bacteria Piscirickettsia Salmonis, generates significant mortalities to farmed Atlantic salmon, particularly in Chile. Due to its economic importance, a wealth of research has focussed on the biological mechanisms underlying pathogenicity of P. salmonis, the host response, and genetic variation in host resistance. DNA methylation is a fundamental epigenetic mechanism that influences almost every biological process via the regulation of gene expression and plays a key role in the response of an organism to stimuli. In the current study, the role of head kidney and liver DNA methylation in the response to P. salmonis infection was investigated in a commercial Atlantic salmon population. A total of 66 salmon were profiled using reduced representation bisulphite sequencing (RRBS), with head kidney and liver methylomes compared between infected animals (3 and 9 days post infection) and uninfected controls. These included groups of salmon with divergent (high or low) breeding values for resistance to P. salmonis infection, to examine the influence of genetic resistance. Head kidney and liver showed organ-specific global methylation patterns, but with similar distribution of methylation across gene features. Integration of methylation with RNA-Seq data revealed that methylation levels predominantly showed a negative correlation with gene expression, although positive correlations were also observed. Methylation within the first exon showed the strongest negative correlation with gene expression. A total of 911 and 813 differentially methylated CpG sites were identified between infected and control samples in the head kidney at 3 and 9 days respectively, whereas only 30 and 44 sites were differentially methylated in the liver. Differential methylation in the head kidney was associated with immunological processes such as actin cytoskeleton regulation, phagocytosis, endocytosis and pathogen associated pattern receptor signaling. We also identified 113 and 48 differentially methylated sites between resistant and susceptible fish in the head kidney and liver respectively. Our results contribute to the growing understanding of the role of methylation in regulation of gene expression and response to infectious diseases, and in particular reveal key immunological functions regulated by methylation in Atlantic salmon in response to P. salmonis.
Arsenal of Nanobodies for Broad-Spectrum Countermeasures against Current and Future SARS-CoV-2 Variants of Concerns
Authors: Rossotti M. A. , van Faassen H. , Tran A. , Sheff J. , Sandhu J. K. , Duque D. , Hewitt M. , Wen S. , Bavananthasivam R. , Beitari S. , Matte K. , Laroche G. , Giguère P. M. , Gervais C. , Stuible M. , Guimond J. , Perret S. , Hussack G. , Langlois M.-A. , Durocher Y. , Tanha J.
Published: December 2021

Nanobodies offer several potential advantages over mAbs for the control of SARS-CoV-2. Their ability to access cryptic epitopes conserved across SARS-CoV-2 variants of concern (VoCs) and feasibility to engineer modular, multimeric designs, make these antibody fragments ideal candidates for developing broad-spectrum therapeutics against current and continually emerging SARS-CoV-2 VoCs. Here we describe a diverse collection of 37 anti-SARS-CoV-2 spike glycoprotein nanobodies extensively characterized as both monovalent and IgG Fc-fused bivalent modalities. The panel of nanobodies were shown to have high intrinsic affinity; high thermal, thermodynamic and aerosolization stability; broad subunit/domain specificity and cross-reactivity across many VoCs; wide-ranging epitopic and mechanistic diversity; high and broad in vitro neutralization potencies; and high neutralization efficacies in hamster models of SARS-CoV-2 infection, reducing viral burden by up to six orders of magnitude to below detectable levels. In vivo protection was demonstrated with anti-RBD and previously unreported anti-NTD and anti-S2 nanobodies. This collection of nanobodies provides a therapeutic toolbox from which various cocktails or multi-paratopic formats could be built to tackle current and future SARS-CoV-2 variants and SARS-related viruses. Furthermore, the high aerosol-ability of nanobodies provides the option for effective needle-free delivery through inhalation.
Screening, Isolation and Characterization of dye degrading bacteria from textile dye effluents
Authors: Sakpal Shruti B. , Tarfe Kishori S.
Published: December 2021

Textile dye industry waste is one among the foremost serious issues within the atmosphere. The dye wastes are severely harmful to surface water bodies. The dye degradation and decolorisation processes, that embody several physical and chemical strategies having inherent drawbacks, like cost accounting, economically impracticable (require additional energy and chemicals), unable to get rid of a number of the recalcitrant dyes and production of huge quantity of sludge that if not properly treated, successively will cause secondary pollution. So, biological degradation, being eco-friendly and cheap methodology, is taken into account as an efficient methodology for the removal of nephrotoxic radical dyes. Our present study was therefore aimed to isolate dyestuff decolorizing microorganism from dyeing industry effluent associate degreed to check their characteristics so as to use them as an economical bio agent for decolorizing and mineralizing nephrotoxic radical dyes.Various microorganism like Bacillus subtilis, Aeromonas hydrophila and Bacillus Cereus, fungi & actinomycetes are found to possess dye decolorizing activity. For the aim of finding out their characteristics, water sample was subjected to enrichment culture technique and then isolated on sterile nutrient agar plates containing 0.005%, 0.01%, and 1% of Congo red dye. The probable isolated organism from Congo red dye i.e. Pantoea agglomerans was found which can possess the ability to decolorize Congo red at lower concentration. The probable isolates obtained must be additional investigated relating to varied factors like dye degradation capability, media composition affecting dye degradation & mechanism of dye degrading activity.
Molecular Dynamics Simulations of HLA-CW4-B2M-KIR2DL1 Protein and Homology Modeling of a Complex Associated with Psoriasis Disease (HLA-CW6-B2M-KIR2DS1)
Authors: Almatarneh Mansour H. , Alqaisi Ahmad M. , Ibrahim Enas K. , Kayed Ghada G. , Hollett Joshua W.
Published: December 2021

Molecular dynamics (MD) simulation was used to study the interactions of two immune proteins of HLA-Cw4-β2m-KIR2DL1 complex with small peptide QYDDAVYKL (nine amino acids) in an aqueous solution. This study aims to gain a detailed information about the conformational changes and the dynamics of the complex. The right parameters and force field for performing the MD simulations that was needed to calibrate the complex structure were determined. The non-bonded interactions (Electrostatic and van der Waals contributions), H-bond formation, and salt bridges between the ligand HLA-Cw4 and the receptor KIR2DL1 were estimated using the obtained MD trajectories. The buried surface area due to binding was calculated to get insight into the causes of specificity of receptor to ligand and explains mutations experiment. The study concluded that β2-microglobulin, one part of the complex, is not directly interacting with the peptide at the groove; therefore, it could be neglected from simulation. Our results showed that β2-microglobulin does not have any significant effect on the dynamics of the 3D-structure of the complex. This project will help in understanding to optimize candidate drug design, a small peptide that disrupts the interaction, for the optimal biological effect.
Proteasome-dependent truncation of the negative heterochromatin regulator Epe1 mediates antifungal resistance
Authors: Yaseen Imtiyaz , White Sharon A. , Torres-Garcia Sito , Spanos Christos , Lafos Marcel , Gaberdiel Elisabeth , Yeboah Rebecca , Karoui Meriem El , Rappsilber Juri , Pidoux Alison L. , Allshire Robin C.
Published: December 2021

Epe1 histone demethylase restricts H3K9-methylation-dependent heterochromatin, preventing it from spreading over, and silencing, gene-containing regions in fission yeast. External stress induces an adaptive response allowing heterochromatin island formation that confers resistance on surviving wild-type lineages. Here we investigate the mechanism by which Epe1 is regulated in response to stress. Exposure to caffeine or antifungals results in Epe1 ubiquitylation and proteasome-dependent removal of the N-terminal 150 residues from Epe1, generating truncated tEpe1 which accumulates in the cytoplasm. Constitutive tEpe1 expression increases H3K9 methylation over several chromosomal regions, reducing expression of underlying genes and enhancing resistance. Reciprocally, constitutive non- cleavable Epe1 expression decreases resistance. tEpe1-mediated resistance requires a functional JmjC demethylase domain. Moreover, caffeine-induced Epe1-to-tEpe1 cleavage is dependent on an intact cell-integrity MAP kinase stress signalling pathway, mutations in which alter resistance. Thus, environmental changes provoke a mechanism that curtails the function of this key epigenetic modifier, allowing heterochromatin to reprogram gene expression, thereby bestowing resistance to some cells within a population. H3K9me-heterochromatin components are conserved in human and crop plant fungal pathogens for which a limited number of antifungals exist. Our findings reveal how transient heterochromatin-dependent antifungal resistant epimutations develop and thus inform on how they might be countered.
Protein folding stabilities are a major determinant of oxidation rates for buried methionine residues
Authors: Walker Ethan J. , Bettinger John Q. , Welle Kevin A. , Hryhorenko Jennifer R. , Molina Vargas Adrian M. , O’Connell Mitchell R. , Ghaemmaghami Sina
Published: December 2021

The oxidation of protein-bound methionines to form methionine sulfoxides has a broad range of biological ramifications, making it important to delineate factors that influence methionine oxidation rates within a protein. This is especially important for biopharmaceuticals, where oxidation can lead to deactivation and degradation. Previously, neighboring residue effects and solvent accessibility (SA) have been shown to impact the susceptibility of methionine residues to oxidation. In this study, we provide proteome-wide evidence that oxidation rates of buried methionine residues are also strongly influenced by the thermodynamic folding stability of proteins. We surveyed the E. coli proteome using several proteomic methodologies and globally measured oxidation rates of methionines in the presence and absence of tertiary structure, as well as folding stabilities of methionine containing domains. The data indicate that buried methionines have a wide range of protection factors against oxidation which correlate strongly with folding stabilities. Concordantly, we show that in comparison to E. coli, the proteome of the thermophile T. thermophilus is significantly more stable and thus more resistant to methionine oxidation. These results indicate that oxidation rates of buried methionines from the native state of proteins can be used as a metric of folding stability. To demonstrate the utility of this correlation, we used native methionine oxidation rates to survey the folding stabilities of E. coli and T. thermophilus proteomes at various temperatures and suggest a model that relates the temperature dependence of the folding stabilities of these two species to their optimal growth temperatures.
TSC22D4 interacts with Akt1 in response to metabolic and stress signals
Authors: Demir Sevgican , Wolff Gretchen , Wieder Annika , Maida Adriano , Rahm Marco , Schnölzer Martina , Hauck Stefanie , Szendrödi Julia , Herzig Stephan , Üstünel Bilgen Ekim
Published: December 2021

Transforming Growth Factor β 1 Stimulated Clone 22 D4 (TSC22D4) is an intrinsically disordered protein that regulates cellular and physiological processes such as cell proliferation, cellular senescence as well as hepatic glucose and lipid metabolism. The molecular mechanism of TSC22D4 action in these cellular and metabolic functions, however, remains largely elusive. Here, we identified TSC22D4 as a novel protein kinase B/Akt1 interacting protein, a critical mediator of insulin/PI3K signaling pathway implicated in diverse set of diseases including type 2 diabetes, obesity and cancer. TSC22D4 interacts with Akt1 not constitutively but rather in a regulatory manner. While glucose and insulin stimulation of cells or refeeding of mice impair the hepatic TSC22D4-Akt1 interaction, inhibition of mitochondria and oxidative stress, promote it; indicating that extra- and intra-cellular cues play a key role in controlling TSC22D4-Akt1 interaction. Our results also demonstrate that together with its dimerization domain, i.e. the TSC box, TSC22D4 requires its intrinsically disordered region (D2 domain) to interact with Akt1. To understand regulation of TSC22D4 function further, we employed tandem mass spectrometry and identified 15 novel phosphorylation sites on TSC22D4. Similar to TSC22D4-Akt1 interaction, TSC22D4 phosphorylation also responds to environmental signals such as starvation, mitochondrial inhibition and oxidative stress. Interestingly, 6 out of the 15 novel phosphorylation sites lie within the TSC22D4 D2 domain, which is required for TSC22D4-Akt1 interaction. Characterization of the regulation and function of these novel phosphorylation sites, in the future, will shed light on our understanding of the role of TSC22D4-Akt1 interaction in both cell biological and physiological functions. Overall, our findings postulate a model whereby TSC22D4 acts as an environmental sensor and interacts with Akt1 to regulate cell proliferation, cellular senescence as well as maintain metabolic homeostasis.
Targeting RTN4/NoGo-Receptor reduces levels of ALS protein ataxin-2
Authors: Rodriguez Caitlin M. , Bechek Sophia C. , Jones Graham L. , Nakayama Lisa , Akiyama Tetsuya , Kim Garam , Solow-Cordero David E. , Strittmatter Stephen M. , Gitler Aaron D.
Published: December 2021

Gene-based therapeutic strategies to lower ataxin-2 levels are emerging for neurodegenerative diseases amyotrophic lateral sclerosis (ALS) and spinocerebellar ataxia type 2 (SCA2). To identify additional ways of reducing ataxin-2 levels, we performed a genome-wide screen in human cells for regulators of ataxin-2 and identified RTN4R, the gene encoding the RTN4/NoGo-Receptor, as a top hit. RTN4R knockdown, or treatment with a peptide inhibitor, was sufficient to lower ataxin-2 protein levels in mouse and human neurons in vitro and Rtn4r knockout mice have reduced ataxin-2 levels in vivo. Remarkably, we observed that ataxin-2 shares a role with the RTN4/NoGo-Receptor in limiting axonal regeneration. Reduction of either protein increases axonal regrowth following axotomy. These data define the RTN4/NoGo-Receptor as a novel therapeutic target for ALS and SCA2 and implicate the targeting of ataxin-2 as a potential treatment following nerve injury.
Small molecule v-ATPase inhibitor Etidronate lowers levels of ALS protein ataxin-2
Authors: Kim Garam , Nakayama Lisa , Blum Jacob A. , Akiyama Tetsuya , Boeynaems Steven , Chakraborty Meena , Couthouis Julien , Tassoni-Tsuchida Eduardo , Rodriguez Caitlin M. , Bassik Michael C. , Gitler Aaron D.
Published: December 2021

Antisense oligonucleotide therapy targeting ATXN2—a gene in which mutations cause neurodegenerative diseases spinocerebellar ataxia type 2 and amyotrophic lateral sclerosis—has entered clinical trials in humans. Additional methods to lower ataxin-2 levels would be beneficial not only in uncovering potentially cheaper or less invasive therapies, but also in gaining greater mechanistic insight into how ataxin-2 is normally regulated. We performed a genome-wide fluorescence activated cell sorting (FACS)-based CRISPR screen in human cells and identified multiple subunits of the lysosomal vacuolar ATPase (v-ATPase) as regulators of ataxin-2 levels. We demonstrate that Etidronate—a U.S. Food and Drug Administration (FDA)-approved drug that inhibits the v-ATPase—lowers ataxin-2 protein levels in mouse and human neurons. Moreover, oral administration of the drug to mice in their water supply and food is sufficient to lower ataxin-2 levels in the brain. Thus, we uncover Etidronate as a safe and inexpensive compound for lowering ataxin-2 levels and demonstrate the utility of FACS-based screens for identifying targets to modulate levels of human disease proteins.
Machine learning denoising of high-resolution X-ray nanotomography data
Authors: Flenner Silja , Bruns Stefan , Longo Elena , Parnell Andrew J. , Stockhausen Kilian E. , Müller Martin , Greving Imke
Published: December 2021

High-resolution X-ray nanotomography is a quantitative tool for investigating specimens from a wide range of research areas. However, the quality of the reconstructed tomogram is often obscured by noise and therefore not suitable for automatic segmentation. Filtering methods are often required for a detailed quantitative analysis. However, most filters induce blurring in the reconstructed tomograms. Here, machine learning (ML) techniques offer a powerful alternative to conventional filtering methods. In this article, we verify that a self-supervised denoising ML technique can be used in a very efficient way for eliminating noise from nanotomography data. The technique presented is applied to high-resolution nanotomography data and compared to conventional filters, such as a median filter and a nonlocal means filter, optimized for tomographic data sets. The ML approach proves to be a very powerful tool that outperforms conventional filters by eliminating noise without blurring relevant structural features, thus enabling efficient quantitative analysis in different scientific fields.
Synthesis, crystal structure and thermal properties of bis(1,3-dicyclohexylthiourea-κS)bis(isothiocyanato-κN)cobalt(II)
Authors: Krebs Christoph , Jess Inke , Näther Christian
Published: December 2021

Crystals of the title compound, [Co(NCS)2(C13H24N2S)2], were obtained by the reaction of Co(NCS)2 with 1,3-dicyclohexylthiourea in ethanol. Its crystal structure consists of discrete complexes that are located on twofold rotation axes, in which the CoII cations are tetrahedrally coordinated by two terminal N-bonded thiocyanate anions and two 1,3-dicyclohexylthiourea ligands. These complexes are linked via intermolecular N—H...S and C—H...S hydrogen bonding into chains, which elongate in the b-axis direction. These chains are closely packed in a pseudo-hexagonal manner. The CN stretching vibration of the thiocyanate anions located at 2038 cm−1 is in agreement with only terminal bonded anionic ligands linked to metal cations in a tetrahedral coordination. TG–DTA measurements prove the decomposition of the compound at about 227°C. DSC measurements reveal a small endothermic signal before decomposition at about 174°C, which might correspond to melting.
Crystal structure of diethanolbis(thiocyanato)bis(urotropine)cobalt(II) and tetraethanolbis(thiocyanato)cobalt(II)–urotropine (1/2)
Authors: Krebs Christoph , Jess Inke , Ceglarska Magdalena , Näther Christian
Published: December 2021

The reaction of one equivalent Co(NCS)2 with four equivalents of urotropine (hexamethylenetetramine) in ethanol leads to the formation of two compounds, namely, bis(ethanol-κO)bis(thiocyanato-κN)bis(urotropine-κN)cobalt(II), [Co(NCS)2(C6H12N4)2(C2H6O)2] (1), and tetrakis(ethanol-κO)bis(thiocyanato-κN)cobalt(II)–urotropine (1/2), [Co(NCS)2(C2H6O)4]·2C6H12N4 (2). In 1, the Co cations are located on centers of inversion and are sixfold coordinated by two terminal N-bonded thiocyanate anions, two ethanol and two urotropine ligands whereas in 2 the cobalt cations occupy position Wyckoff position c and are sixfold coordinated by two anionic ligands and four ethanol ligands. Compound 2 contains two additional urotropine solvate molecules per formula unit, which are hydrogen bonded to the complexes. In both compounds, the building blocks are connected via intermolecular O—H...N (1 and 2) and C—H...S (1) hydrogen bonding to form three-dimensional networks.