bluuebunny/crossref_metadata_2025 huggingface dataset:
Correlations from structure and phylogeny combine constructively in the inference of protein partners from sequences
Authors: Gerardos Andonis , Dietler Nicola , Bitbol Anne-Florence
Published: May 2022

Inferring protein-protein interactions from sequences is an important task in computational biology. Recent methods based on Direct Coupling Analysis (DCA) or Mutual Information (MI) allow to find interaction partners among paralogs of two protein families. Does successful inference mainly rely on correlations from structural contacts or from phylogeny, or both? Do these two types of signal combine constructively or hinder each other? To address these questions, we generate and analyze synthetic data produced using a minimal model that allows us to control the amounts of structural constraints and phylogeny. We show that correlations from these two sources combine constructively to increase the performance of partner inference by DCA or MI. Furthermore, signal from phylogeny can rescue partner inference when signal from contacts becomes less informative, including in the realistic case where inter-protein contacts are restricted to a small subset of sites. We also demonstrate that DCA-inferred couplings between non-contact pairs of sites improve partner inference in the presence of strong phylogeny, while deteriorating it otherwise. Moreover, restricting to non-contact pairs of sites preserves inference performance in the presence of strong phylogeny. In a natural data set, as well as in realistic synthetic data based on it, we find that non-contact pairs of sites contribute positively to partner inference performance, and that restricting to them preserves performance, evidencing an important role of phylogeny.
Feasibility of continuous distal body temperature for passive, early pregnancy detection
Authors: Grant Azure , Smarr Benjamin
Published: May 2022

Most American women become aware of pregnancy ~3–7 weeks after conceptive sex, and all must seek testing to confirm their pregnant status. The delay between conceptive sex and pregnancy awareness is often a time in which contraindicated behaviors take place. However, there is long standing evidence that passive, early pregnancy detection may be possible using body temperature. To address this possibility, we analyzed 30 individuals’ continuous distal body temperature (DBT) in the 180 days surrounding self-reported conceptive sex in comparison to self-reported pregnancy confirmation. Features of DBT nightly maxima changed rapidly following conceptive sex, reaching uniquely elevated values after a median of 5.5 ± 3.5 days, whereas individuals reported a positive pregnancy test result at a median of 14.5 ± 4.2 days. Together, we were able to generate a retrospective, hypothetical alert a median of 9 ± 3.9 days prior to the date at which individuals received a positive pregnancy test. Continuous temperature-derived features can provide early, passive indication of pregnancy onset. We propose these features for testing and refinement in clinical settings, and for exploration in large, diverse cohorts. The development of pregnancy detection using DBT may reduce the delay from conception to awareness and increase the agency of pregnant individuals.
Structure and kinase activity of bacterial cell cycle regulator CcrZ
Authors: Wozniak Katherine J. , Burby Peter E. , Nandakumar Jayakrishnan , Simmons Lyle A.
Published: May 2022

CcrZ is a recently discovered cell cycle regulator that connects DNA replication initiation with cell division in pneumococci and may have a similar function in related bacteria. CcrZ is also annotated as a putative kinase, suggesting that CcrZ homologs could represent a novel family of bacterial kinase-dependent cell cycle regulators. Here, we investigate the CcrZ homolog inBacillus subtilisand show that cells lackingccrZare sensitive to a broad range of DNA damage. We demonstrate that increased expression ofccrZresults in over-initiation of DNA replication. In addition, increased expression of CcrZ activates the DNA damage response. Using sensitivity to DNA damage as a proxy, we show that the negative regulator for replication initiation (yabA) andccrZfunction in the same pathway. We show that CcrZ interacts with replication initiation proteins DnaA and DnaB, further suggesting that CcrZ is important for replication timing. To understand how CcrZ functions, we solved the crystal structure bound to AMP-PNP to 2.6 Å resolution. The CcrZ structure most closely resembles choline kinases, consisting of a bilobal structure with a cleft between the two lobes for binding ATP and substrate. Inspection of the structure reveals a major restructuring of the substrate-binding site of CcrZ relative to the choline-binding pocket of choline kinases, consistent with our inability to detect activity with choline for this protein. Instead, CcrZ shows activity on D-ribose and 2-deoxy-D-ribose, indicating adaptation of the choline kinase fold in CcrZ to phosphorylate a novel substrate. We show that integrity of the kinase active site is required for ATPase activityin vitroand for functionin vivo. This work provides structural, biochemical, and functional insight into a newly identified, and conserved group of bacterial kinases that regulate DNA replication initiation.
Translation model for CW chord to angle Alpha derived from a Monte-Carlo simulation based on raytracing
Authors: Langenbucher Achim , Szentmáry Nóra , Cayless Alan , Weisensee Johannes , Wendelstein Jascha , Hoffmann Peter
Published: May 2022

Background

The Chang-Waring chord is provided by many ophthalmic instruments, but proper interpretation of this chord for use in centring refractive procedures at the cornea is not fully understood. The purpose of this study is to develop a strategy for translating the Chang-Waring chord (position of pupil centre relative to the Purkinje reflex PI) into angle Alpha using raytracing techniques.

Methods

The retrospective analysis was based on a large dataset of 8959 measurements of 8959 eyes from 1 clinical centre, using the Casia2 anterior segment tomographer. An optical model based on: corneal front and back surface radius Ra and Rp, asphericities Qa and Qp, corneal thickness CCT, anterior chamber depth ACD, and pupil centre position (X-Y position: PupX and PupY), was defined for each measurement. Using raytracing rays with an incident angle IX and IY the CW chord (CWX and CWY) was calculated. Using these data, a multivariable linear model was built up in terms of a Monte-Carlo simulation for a simple translation of incident ray angle to CW chord.

Results

Raytracing allows for calculation of the CW chord CWX/CWY from biometric measures and the incident ray angle IX/IY. In our dataset mean values of CWX = 0.32±0.30 mm and CWY = -0.10±0.26 mm were derived for a mean incident ray angle (angle Alpha) of IX = -5.02±1.77° and IY = 0.01±1.47°. The raytracing results could be modelled with a linear multivariable model, and the effect sizes for the prediction model for CWX are identified as Ra, Qa, Rp, CCT, ACD, PupX, PupY, IX, and for CWY they are Ra, Rp, PupY, and IY.

Conclusion

Today the CW chord can be directly measured with any biometer, topographer or tomographer. If biometric measures of Ra, Qa, Rp, CCT, ACD, PupX, PupY are available in addition to the CW chord components CWX and CWY, a prediction of angle Alpha is possible using a simple matrix operation.
Institutional dynamics and learning networks
Authors: Poon Philip , Flack Jessica C. , Krakauer David C.
Published: May 2022

Institutions have been described as ‘the humanly devised constraints that structure political, economic, and social interactions.’ This broad definition of institutions spans social norms, laws, companies, and even scientific theories. We describe a non-equilibrium, multi-scale learning framework supporting institutional quasi-stationarity, periodicity, and switching. Individuals collectively construct ledgers constituting institutions. Agents read only a part of the ledger–positive and negative opinions of an institution—its “public position” whose value biases one agent’s preferences over those of rivals. These positions encode collective perception and action relating to laws, the power of parties in political office, and advocacy for scientific theories. We consider a diversity of complex temporal phenomena in the history of social and research culture (e.g. scientific revolutions) and provide a new explanation for ubiquitous cultural resistance to change and novelty–a systemic endowment effect through hysteresis.
A custom ddPCR method for the detection of copy number variations in the nebulin triplicate region
Authors: Sagath Lydia , Lehtokari Vilma-Lotta , Wallgren-Pettersson Carina , Pelin Katarina , Kiiski Kirsi
Published: May 2022

The human genome contains repetitive regions, such as segmental duplications, known to be prone to copy number variation. Segmental duplications are highly identical and homologous sequences, posing a specific challenge for most mutation detection methods. The giant nebulin gene is expressed in skeletal muscle. It harbors a large segmental duplication region composed of eight exons repeated three times, the so-called triplicate region. Mutations in nebulin are known to cause nemaline myopathy and other congenital myopathies. Using our custom targeted Comparative Genomic Hybridization arrays, we have previously shown that copy number variations in the nebulin triplicate region are pathogenic when the copy number of the segmental duplication block deviates two or more copies from the normal number, which is three per allele. To complement our Comparative Genomic Hybridization arrays, we have established a custom Droplet Digital PCR method for the detection of copy number variations within the nebulin triplicate region. The custom Droplet Digital PCR assays allow sensitive, rapid, high-throughput, and cost-effective detection of copy number variations within this region and is ready for implementation a screening method for disease-causing copy number variations of the nebulin triplicate region. We suggest that Droplet Digital PCR may also be used in the study and diagnostics of other segmental duplication regions of the genome.
Validation study of a wellbeing scale (SPANE) in the Arab Gulf region: A multicountry study
Authors: Yaaqeib Saad , Lambert Louise , Hadjisolomou Stavros , Al-Fazari Manal , Selim Heyla , Haque Amber
Published: May 2022

The Scale of Positive and Negative Experience (SPANE) is an emerging wellbeing scale to measure the frequency of positive and negative emotions. This study explores the psychometric properties of SPANE on a sample from the Arab Gulf region. The Arab Gulf region shares cultural elements with the broader Muslim and Arab world, but maintains distinct features that warrants validation studies for psychological instruments. There were 1393 participants from Saudi Arabia, Oman, Kuwait and other Arab Gulf countries. The factorial structure of SPANE was examined using a principal axis factor analysis, followed up with a confirmatory factor analysis. The convergent validity was examined by correlating SPANE with the Satisfaction with Life Scale (SWLS). The findings confirmed a two-factor structure of SPANE, and demonstrated adequate psychometric properties and convergent validity. In conclusion, this study indicates that SPANE shows sufficient validity for use as a measure of wellbeing in the Arab Gulf region.
Prevalence and determinants of oral and cervicogenital HPV infection: Baseline analysis of the Michigan HPV and Oropharyngeal Cancer (MHOC) cohort study
Authors: Brouwer Andrew F. , Campredon Lora P. , Walline Heather M. , Marinelli Brittany M. , Goudsmit Christine M. , Thomas Trey B. , Delinger Rachel L. , Lau Yan Kwan , Andrus Emily C. , Yost Monica L. , McCloskey Jodi K. , Sullivan Taylor S. , Mortensen Alex S. , Huang Suiyuan , Murphy Keith , Cheng Bonnie , Stanek Kayla , Nair Thankam , Carey Thomas E. , Meza Rafael , Eisenberg Marisa C.
Published: May 2022

We determined baseline oral and cervicogenital human papillomavirus (HPV) prevalence and determinants of infection in the Michigan HPV and Oropharyngeal Cancer (MHOC) study. We enrolled 394 college-age and older participants of both sexes in Ann Arbor, Michigan and the surrounding area. All participants provided an oral sample at baseline, and 130 females provided a cervicogenital sample. Samples were tested for 18 HPV genotypes using polymerase chain reaction (PCR) MassArray. Participants filled out sociodemographic and behavioral questionnaires. Prevalence ratios for HPV oral or cervicogenital prevalence by predictor variables were estimated in univariable log-binomial models. Analysis was conducted 2018–20. In the full cohort, baseline oral HPV prevalence was 10.0% for any detected genotype (among the 338 valid oral tests at baseline) and 6.5% for high-risk types, and cervicogenital prevalence was 20.0% and 10.8%, respectively (among the 130 first valid cervicogenital tests). Oral HPV prevalence did not vary by sex, with 10.5% of women and 9.0% of men having an infection. We found a high prevalence of oral and cervicogenital HPV infection in college-age participants reporting no lifetime sexual partners. Reporting a single recent partner was associated with a lower oral HPV prevalence (PR 0.39, 95% CI: 0.16, 0.96) than reporting no recent (but at least one ever) partner. No similar protective effect was seen for cervicogenital HPV. Both oral and cervicogenital prevalence increased with the number of recent partners for most sexual behaviors. We observed an ecological fallacy masking the direction of impact of vaccination on HPV prevalence in the full cohort compared to the college-aged and the age 23+ populations considered separately. Substance use was not significantly associated with oral or cervicogenital HPV infection. Many studies report substantially higher oral HPV infection prevalence in men than in women. That difference may not be uniform across populations in the US.
Suillin: A mixed-type acetylcholinesterase inhibitor from Suillus luteus which is used by Saraguros indigenous, southern Ecuador
Authors: Andrade José Miguel , Pachar Pamela , Trujillo Luisa , Cartuche Luis
Published: May 2022

Suillus luteus(L.) Roussel is an edible mushroom commonly known as slippery jack or “Kallampa” by indigenous people from Loja province. It is used in traditional medicine to manage gastrointestinal disorders and headaches. In addition, edible mushrooms have been used for neurodegenerative diseases; however, there is no report about the anticholinesterase effect produced by this species. The aim of this work was to isolate the main secondary metabolite ofSuillus luteusand characterize its inhibitory potential against acetylcholinesterase. Fruiting bodies were extracted with ethanol (EtOH) and ethyl acetate (EtOAc). From the EtOAc, suillin, is reported as the major compound. The cholinesterase inhibitory potential of extracts and the major isolated compound was assessed by Ellman´s method and progression curves were recorded at 405 nm for 60 min. Donepezil hydroclhoride was used as a positive control. The samples were dissolved in methanol at 10 mg/mL and two more 10× dilutions were included to obtain final concentrations of 1, 0.1 and 0.01 mg/mL at the mix of reaction. IC50,Km, Vmax, andKiwere calculated for suillin. Suillin (200 mg) along with linoleic acid, ergosterol peroxide and ergosterol were isolated. The EtOH and EtOAc extracts exerted a moderate inhibitory effect (IC50> 200 μg/mL. In adittion, suillin exerted a non-competitive mixed mechanism. against AChE with an IC50value of 31.50 μM and Ki of 17.25 μM. To the best of our knowledge, this is the first report of the anticholinesterase effect ofSuillus luteusand suillin. The kinetic parameters and the moderate potency of the compound determined in this study, encourage us to propose suillin as a promising chemopreventing agent for the treatment of neurodegenerative diseases such as Alzheimer.
Health disparities and COVID-19: A retrospective study examining individual and community factors causing disproportionate COVID-19 outcomes in Cook County, Illinois
Authors: Unruh Larissa H. , Dharmapuri Sadhana , Xia Yinglin , Soyemi Kenneth
Published: May 2022

Early data from the COVID-19 pandemic suggests that the disease has had a disproportionate impact on communities of color with higher infection and mortality rates within those communities. This study used demographic data from the 2018 US census estimates, mortality data from the Cook County Medical Examiner’s office, and testing results from the Illinois Department of Public Health to perform bivariate and multivariate regression analyses to explore the role race plays in COVID-19 outcomes at the individual and community levels. We used the ZCTA Social Deprivation Index (SDI), a measure of ZCTA area level deprivation based on seven demographic characteristics to quantify the socio-economic variation in health outcomes and levels of disadvantage across ZCTAs. Principal findings showed that: 1) while Black individuals make up 22% of Cook County’s population, they account for 28% of the county’s COVID-19 related deaths; 2) the average age of death from COVID-19 is seven years younger for Non-White compared with White decedents; 3) residents of Minority ZCTA areas were 1.02 times as likely to test positive for COVID-19, (Incidence Rate Ratio (IRR) 1.02, [95% CI 0.95, 1.10]); 1.77 times as likely to die (IRR 1.77, [95% CI 1.17, 2.66]); and were 1.15 times as likely to be tested (IRR 1.15, [95% CI 0.99, 1.33]). There are notable differences in COVID-19 related outcomes between racial and ethnic groups at individual and community levels. This study illustrates the health disparities and underlying systemic inequalities experienced by communities of color.
Prognostic significance of severe coronary microvascular dysfunction post-PCI in patients with STEMI: A systematic review and meta-analysis
Authors: Canu Marjorie , Khouri Charles , Marliere Stéphanie , Vautrin Estelle , Piliero Nicolas , Ormezzano Olivier , Bertrand Bernard , Bouvaist Hélène , Riou Laurent , Djaileb Loic , Charlon Clémence , Vanzetto Gerald , Roustit Matthieu , Barone-Rochette Gilles
Published: May 2022

Coronary microvascular dysfunction (CMVD) is common and associated with poorer outcomes in patients with ST Segment Elevation Myocardial Infarction (STEMI). The index of microcirculatory resistance (IMR) and the index of hyperemic microvascular resistance (HMR) are both invasive indexes of microvascular resistance proposed for the diagnosis of severe CMVD after primary percutaneous coronary intervention (pPCI). However, these indexes are not routinely assessed in STEMI patients. Our main objective was to clarify the association between IMR or HMR and long-term major adverse cardiovascular events (MACE), through a systematic review and meta-analysis of observational studies. We searched Medline, PubMed, and Google Scholar for studies published in English until December 2020. The primary outcome was a composite of cardiovascular death, non-cardiovascular death, non-fatal myocardial infarction, non-fatal stroke, and rehospitalization for heart failure occurring after at least 6 months following CMVD assessment. We identified 6 studies, reporting outcomes in 1094 patients (mean age 59.7 ± 11.4 years; 18.2% of patients were women) followed-up from 6 months to 7 years. Severe CMVD, defined as IMR > 40 mmHg or HMR > 3mmHg/cm/sec was associated with MACE with a pooled HR of 3.42 [2.45; 4.79]. Severe CMVD is associated with an increased risk of long-term adverse cardiovascular events in patients with STEMI. Our results suggest that IMR and HMR are useful for the early identification of severe CMVD in patients with STEMI after PCI, and represent powerful prognostic assessments as well as new therapeutic targets for clinical intervention.
A national study of moral distress among U.S. internal medicine physicians during the COVID-19 pandemic
Authors: Sonis Jeffrey , Pathman Donald E. , Read Susan , Gaynes Bradley N.
Published: May 2022

Background

There have been no studies to date of moral distress during the COVID-19 pandemic in national samples of U.S. health workers. The purpose of this study was to determine, in a national sample of internal medicine physicians (internists) in the U.S.: 1) the intensity of moral distress; 2) the predictors of moral distress; 3) the outcomes of moral distress.

Methods

We conducted a national survey with an online panel of internists, representative of the membership of the American College of Physicians, the largest specialty organization of physicians in the United States, between September 21 and October 8, 2020. Moral distress was measured with the Moral Distress Thermometer, a one-item scale with a range of 0 (“none”) to 10 (“worst possible”). Outcomes were measured with short screening scales.

Results

The response rate was 37.8% (N = 810). Moral distress intensity was low (mean score = 2.4, 95% CI, 2.2–2.6); however, 13.3% (95% CI, 12.1% - 14.5%) had a moral distress score greater than or equal to 6 (“distressing”). In multiple linear regression models, perceived risk of death if infected with COVID-19 was the strongest predictor of higher moral distress (β (standardized regression coefficient) = 0.26, p < .001), and higher perceived organizational support (respondent belief that their health organization valued them) was most strongly associated with lower moral distress (β = -0.22, p < .001). Controlling for other factors, high levels of moral distress, but not low levels, were strongly associated (adjusted odds ratios 3.0 to 11.5) with screening positive for anxiety, depression, posttraumatic stress disorder, burnout, and intention to leave patient care.

Conclusions

The intensity of moral distress among U.S. internists was low overall. However, the 13% with high levels of moral distress had very high odds of adverse mental health outcomes. Organizational support may lower moral distress and thereby prevent adverse mental health outcomes.
Altered corticospinal excitability of scapular muscles in individuals with shoulder impingement syndrome
Authors: Chung Ya-Chu , Chen Chao-Ying , Chang Chia-Ming , Lin Yin-Liang , Liao Kwong-Kum , Lin Hsiu-Chen , Chen Wen-Yin , Yang Yea-Ru , Shih Yi-Fen
Published: May 2022

The purpose of this study is to assess and compare corticospinal excitability in the upper and lower trapezius and serratus anterior muscles in participants with and without shoulder impingement syndrome (SIS). Fourteen participants with SIS, and 14 without SIS were recruited through convenient sampling in this study. Transcranial magnetic stimulation assessment of the scapular muscles was performed while the participants were holding their arm at 90 degrees scaption. The motor-evoked potential (MEP), active motor threshold (AMT), latency of MEP, cortical silent period (CSP), activated area and center of gravity (COG) of cortical mapping were compared between groups using the Mann-Whitney U tests. The SIS group demonstrated following significances, higher AMTs of the lower trapezius (SIS: 0.60 ± 0.06; Comparison: 0.54 ± 0.07,p= 0.028) and the serratus anterior (SIS: 0.59 ± 0.04; Comparison: 0.54 ± 0.06,p= 0.022), longer CSP of the lower trapezius (SIS: 62.23 ± 22.87 ms; Comparison: 45.22 ± 14.64 ms,p= 0.019), and posteriorly shifted COG in the upper trapezius (SIS: 1.88 ± 1.06; Comparison: 2.76 ± 1.55,p= 0.048) and the serratus anterior (SIS: 2.13 ± 1.02; Comparison: 3.12 ± 1.88,p= 0.043), than the control group. In conclusion, participants with SIS demonstrated different organization of the corticospinal system, including decreased excitability, increased inhibition, and shift in motor representation of the scapular muscles.
Ehrlichia SLiM ligand mimetic activates Hedgehog signaling to engage a BCL-2 anti-apoptotic cellular program
Authors: Byerly Caitlan D. , Mitra Shubhajit , Patterson LaNisha L. , Pittner Nicholas A. , Velayutham Thangam S. , Paessler Slobodan , Veljkovic Veljko , McBride Jere W.
Published: May 2022

Ehrlichia chaffeensis(E.chaffeensis) has evolved eukaryotic ligand mimicry to repurpose multiple cellular signaling pathways for immune evasion. In this investigation, we demonstrate that TRP120 has a novel repetitiveshortlinearmotif (SLiM) that activates the evolutionarily conserved Hedgehog (Hh) signaling pathway to inhibit apoptosis.In silicoanalysis revealed that TRP120 has sequence and functional similarity with Hh ligands and a candidate Hh ligand SLiM was identified. siRNA knockdown of Hh signaling and transcriptional components significantly reduced infection. Co-immunoprecipitation and surface plasmon resonance demonstrated that rTRP120-TR interacted directly with Hh receptor Patched-2 (PTCH2).E.chaffeensisinfection resulted in early upregulation of Hh transcription factor GLI-1 and regulation of Hh target genes. Moreover, soluble recombinant TRP120 (rTRP120) activated Hh and induced gene expression consistent with the eukaryotic Hh ligand. The TRP120-Hh-SLiM (NPEVLIKD) induced nuclear translocation of GLI-1 in THP-1 cells and primary human monocytes and induced a rapid and expansive activation of Hh pathway target genes. Furthermore, Hh activation was blocked by an α-TRP120-Hh-SLiM antibody. TRP120-Hh-SLiM significantly increased levels of Hh target, anti-apoptotic protein B-cell lymphoma 2 (BCL-2), and siRNA knockdown of BCL-2 dramatically inhibited infection. Blocking Hh signaling with the inhibitor Vismodegib, induced a pro-apoptotic cellular program defined by decreased mitochondria membrane potential, significant reductions in BCL-2, activation of caspase 3 and 9, and increased apoptotic cells. This study reveals a novelE.chaffeensisSLiM ligand mimetic that activates Hh signaling to maintainE.chaffeensisinfection by engaging a BCL-2 anti-apoptotic cellular program.
Metaeffector interactions modulate the type III effector-triggered immunity load of Pseudomonas syringae
Authors: Martel Alexandre , Laflamme Bradley , Breit-McNally Clare , Wang Pauline , Lonjon Fabien , Desveaux Darrell , Guttman David S.
Published: May 2022

The bacterial plant pathogen Pseudomonas syringae requires type III secreted effectors (T3SEs) for pathogenesis. However, a major facet of plant immunity entails the recognition of a subset of P. syringae’s T3SEs by intracellular host receptors in a process called Effector-Triggered Immunity (ETI). Prior work has shown that ETI-eliciting T3SEs are pervasive in the P. syringae species complex raising the question of how P. syringae mitigates its ETI load to become a successful pathogen. While pathogens can evade ETI by T3SE mutation, recombination, or loss, there is increasing evidence that effector-effector (a.k.a., metaeffector) interactions can suppress ETI. To study the ETI-suppression potential of P. syringae T3SE repertoires, we compared the ETI-elicitation profiles of two genetically divergent strains: P. syringae pv. tomato DC3000 (PtoDC3000) and P. syringae pv. maculicola ES4326 (PmaES4326), which are both virulent on Arabidopsis thaliana but harbour largely distinct effector repertoires. Of the 529 T3SE alleles screened on A. thaliana Col-0 from the P. syringae T3SE compendium (PsyTEC), 69 alleles from 21 T3SE families elicited ETI in at least one of the two strain backgrounds, while 50 elicited ETI in both backgrounds, resulting in 19 differential ETI responses including two novel ETI-eliciting families: AvrPto1 and HopT1. Although most of these differences were quantitative, three ETI responses were completely absent in one of the pathogenic backgrounds. We performed ETI suppression screens to test if metaeffector interactions contributed to these ETI differences, and found that HopQ1a suppressed AvrPto1m-mediated ETI, while HopG1c and HopF1g suppressed HopT1b-mediated ETI. Overall, these results show that P. syringae strains leverage metaeffector interactions and ETI suppression to overcome the ETI load associated with their native T3SE repertoires.
Yersinia pseudotuberculosis doxycycline tolerance strategies include modulating expression of genes involved in cell permeability and tRNA modifications
Authors: Alvarez-Manzo Hector S. , Davidson Robert K. , Van Cauwelaert de Wyels Jasper , Cotten Katherine L. , Nguyen Benjamin H. , Xiao Melody , Zhu Zeyu , Anthony Jon , van Opijnen Tim , Davis Kimberly Michele
Published: May 2022

Antibiotic tolerance is typically associated with a phenotypic change within a bacterial population, resulting in a transient decrease in antibiotic susceptibility that can contribute to treatment failure and recurrent infections. Although tolerant cells may emerge prior to treatment, the stress of prolonged antibiotic exposure can also promote tolerance. Here, we sought to determine how Yersinia pseudotuberculosis responds to doxycycline exposure, to then verify if these gene expression changes could promote doxycycline tolerance in culture and in our mouse model of infection. Only four genes were differentially regulated in response to a physiologically-relevant dose of doxycycline: osmB and ompF were upregulated, tusB and cnfy were downregulated; differential expression also occurred during doxycycline treatment in the mouse. ompF, tusB and cnfy were also differentially regulated in response to chloramphenicol, indicating these could be general responses to ribosomal inhibition. cnfy has previously been associated with persistence and was not a major focus here. We found deletion of the OmpF porin resulted in increased antibiotic accumulation, suggesting expression may promote diffusion of doxycycline out of the cell, while OsmB lipoprotein had a minor impact on antibiotic permeability. Overexpression of tusB significantly impaired bacterial survival in culture and in the mouse, suggesting that tRNA modification by tusB, and the resulting impacts on translational machinery, promotes survival during treatment with an antibiotic classically viewed as bacteriostatic. We believe this may be the first observation of bactericidal activity of doxycycline under physiological conditions, which was revealed by reversing tusB downregulation.
Storytelling nights: Performing (post)memory of Cape Verdean migration to Rotterdam
Authors: Krakowska Rodrigues Kamila
Published: May 2022

The Cape Verdean community in Rotterdam (the third biggest Cape Verdean diaspora in the world) have left a clear imprint on Rotterdam’s culture especially in terms of music production. Recently, this cultural and historical legacy has been gaining more recognition. In the field of performing arts, which constitute a relevant aspect of the urban nightlife (when not impacted by the current COVID-19 restrictions), the stories of migration circulating among the community have inspired Dutch-Cape Verdean artists to create thought-provoking plays on diasporic identity negotiations and belonging. In this regard, two theatre storytelling pieces by second-generation Dutch-Cape Verdean female artists, Lena Évora’s Muziek en Verhalen uit Mijn Geboorteland (‘Music and stories from my homeland’) (2018) and Sonya Dias’s Het Verhaal van Mijn Moeder (‘The story of my mother’) (2017), engage with the notions of ‘home’ and ‘story’ in a particularly thought-provoking way, especially in what concerns night aesthetics. By close reading these two plays within the framework of Diaspora and Critical Archival Studies, this article aims to address how arts play a role in creating imaginary records of Cape Verdean migration history and contribute towards a more inclusive recognition of Rotterdam’s multicultural social texture and its nightlife.
Meme layers in the times of pandemic
Authors: Sederholm Helena , Haapalainen Riikka , Pusa Tiina
Published: May 2022

During the first wave of the COVID-19 pandemic in spring 2020, art teachers put remote teaching in Finnish comprehensive schools into operation in varying ways. One popular implementation was classical art memes, an assignment that art teachers shared through professional networks in social media. This phenomenon brought out the question: what kind of meanings did art history-related memes construct during the pandemic in Finland? The authors collected and analysed empirical data that consisted of a questionnaire for art teachers (N = 14), students’ meme works (N = 45) sent to the authors by the teachers, and assignments that were given. The research approach was critical inquiry. The main components of the theoretical framework were meme theories and crisis pedagogy, with which the authors confronted the national curriculum. Although Finland has not been among the most afflicted countries by the pandemic, the sudden flip to remote teaching created anxiety and a sense of crisis among teachers, who tried to find a balance between their own workload, students’ confusion with the new learning situation and the demands of the curriculum. The analysis concentrated on four themes: the COVID-19 crisis in meme manifestations, teaching art history, art education through making and art education as copying and repeating. The authors concluded that it is crucial to highlight the conceptualizing and contextualizing of art beside actual art-making. From this emerges an essential challenge for in-service training: critical knowledge production and discourse practices.
TikTok and museum education: A visual content analysis
Authors: Huebner Emma June
Published: May 2022

Although TikTok has been downloaded 2.6 billion times and is widely used around the world, cultural organizations have been slow to join the trend. The few museums that use the app have had contrasting approaches to their content creation. This study employs a case study methodology to examine the use of TikTok by the Uffizi Gallery (Florence) and the Rijksmuseum (Amsterdam) through a visual content analysis of their posts. Considering theories of learning and teaching in the museum, as well as of connectivism, the central guiding questions are: how are museums using TikTok? In what ways do these short-form videos connect visitors with their collections? What are the implications for museum education? The findings from this study reveal that museums use either expository and didactic teaching practices on TikTok or performative TikTok practices, which include collaboration with youth. The study has implications for museum educators who wish to use TikTok as an educational tool.
Terror melodrama, race and the nation: Ulaa Salim’s Sons of Denmark
Authors: Doxtater Amanda
Published: May 2022

Ulaa film,Sons of Denmark, employs terror melodrama, an iteration of the melodramatic mode related to 9/11 that represents the nation as innocent and violated. This allows the film to raise questions about masculinity, systemic racism and white innocence in the decades-long rise of far-right political parties in Denmark.
Aristotle (384-322 BC): the beginnings of Embryology
Authors: Zagris Nikolas
Published: May 2022

Aristotle made important contributions to many fields-biology, physics, metaphysics, logic, ethics, rhetoric, psychology, aesthetics, poetry- that are now cultivated by specialized experts, but he never lost sight of the aim of unifying knowledge, of understanding the world as an organized whole. Aristotle was the first to combine wet, field biology with daring cosmological thinking. He is the father of natural history and the first embryologist known to history. Aristotle’s classic treatises History of Animals/Περί ζῴων ἱστορίαι, and On the Generation of Animals/ Περί ζῴων γενέσεως “enjoyed for more than fifteen hundred years an authority altogether without parallel”. Over the last four decades, the introduction of molecular techniques has gradually overturned the entire structure of the biological sciences. Biology, initially a science of inventory and classification in the hands of the 19
th-century comparative naturalists, has become a science of codes and regulatory circuits. Aristotle was the first to codify laws of pure logic, and so he founded what is today known as ‘proof theory’ in mathematics. Aristotle was an inveterate collector and a classifier, the master scientist of his time. His main concern was to classify “the ultimate furniture of the world”, under basic headings and categories, a powerful human strategy to organize knowledge for comprehension and action. This was part of Aristotle’s attempt to create a theory of reality, one strongly opposed to Plato’s otherworldly doctrine of the ideal ‘forms’. To many generations of thinkers in the great era of Scholastic philosophy, Aristotle was known simply as “The Philosopher”.
Limited dose-dependent effects of vedolizumab on various leukocyte subsets
Authors: Becker Emily , Schweda Anna , Ullrich Karen A.-M. , Voskens Caroline , Atreya Raja , Müller Tanja M. , Atreya Imke , Neurath Markus F. , Zundler Sebastian
Published: May 2022

Background:

The anti-α4β7 integrin antibody vedolizumab (VDZ) is successfully used for the treatment of inflammatory bowel diseases (IBD). However, only a subgroup of patients respond to therapy. Vedolizumab is administered at a fixed dose, leading to a wide range of serum concentrations in patients. Previous work from our group showed a dose-dependent preferential binding of vedolizumab to effector compared to regulatory CD4+ T cells. Therefore, we aimed to determine the dose-dependent binding profile of vedolizumab to other leukocyte subsets.

Methods:

We characterised α4β7 integrin expression on CD8+ T cells, CD19+ B cells, CD14+ monocytes, natural killer (NK) cells and eosinophils from IBD patients and healthy controls. We studied the binding of vedolizumab to these cells at different concentrations and investigated the functional consequences for dynamic adhesion and transmigration in vitro.

Results:

The expression of α4β7 differed between the analysed leukocyte subsets and was significantly higher on eosinophils from patients compared to controls. Almost all α4β7-expressing cells from these subsets were bound by vedolizumab at a concentration of 10 µg/ml. Dynamic cell adhesion was significantly impaired in all subsets, but there were no dose-dependent differences in the inhibition of adhesion.

Discussion:

Our data suggest that α4β7-expressing CD8+ T cells, CD19+ B cells, CD14+ monocytes, NK cells and eosinophils are a target of vedolizumab. However, there do not seem to be concentration-dependent differences regarding the effects on these cells in the clinically relevant range. Thus, the reported exposure efficacy characteristic of vedolizumab can probably mainly be attributed to CD4+ T cell subsets.
Language learning anxiety in a group of psychology students at Universidad del Norte
Authors: Robles Heydi
Published: May 2022

This article shows the results of a research on anxiety caused by language learning. It focuses on language learning anxiety related to speaking skill. This study intended to find out the external factors that produce anxiety in the development of the oral competence in a group of psychology students. In order to attain the objectives of this study, the instruments used were diaries, questionnaires, recordings (personal opinions, short oral presentations) and interviews. With regard to external factors that produce anxiety in relation to activities, results show that all kind of oral activities produce a high degree of anxiety in students, especially non prepared oral tasks. They also show a lack of participation in class with a strong rejection to oral learning tasks. Among the possible causes of this reticence, it is the fact that they do not want to be mocked in class. Also, Speaking skill was not encouraged in the first levels in the prior approach. It is vital to mention that students are aware of their lack of some aspects of the language, such as, vocabulary, grammar and fluency.
Ciência e Literatura: análise de um poema de gedeão para o ensino de Física à luz da interdisciplinaridade e da teoria bakhtiniana
Authors: Faur de Castro Catarino Giselle , De Almeida Barbosa Lima Maria da Conceição
Published: May 2022

Apresentamos neste artigo uma proposta didática para o ensino de Física, tendo como foco a união entre Ciência e Arte, mais especificamente Física e Literatura. Para isso, trabalhamos o Poema para Galileo de António Gedeão em uma disciplina da licenciatura em Física de uma Universidade pública do Rio de Janeiro e realizamos a Análise de Discurso, baseada na perspectiva dialógica bakhtiniana, dos dados coletados via registro escrito dos licenciandos. Baseamo-nos nos conceitos de autor, herói, ouvinte, cronotopo e gênero de discurso de Mikhail Bakthin para analisar as atividades didáticas que envolveram o poema. Como considerações, apontamos que a apresentação da Física de maneira interdisciplinar com a Literatura, ou com a Arte de maneira geral, possibilita a compreensão da Física como parte da cultura e revela possíveis abordagens com foco na Interdisciplinaridade e na História da Ciência, promovendo a humanização da Ciência e incentivo à reflexão crítica e contínua sobre sua natureza.
Analytical solution of the first problem of the manipulators' dynamics
Authors:   South Ural State University, Telegin Aleksandr I.
Published: May 2022

The aim is to solve the problem of deriving an explicit analytical form and the cumbersome of the equa-tions of dynamics of body systems. The research methods refer to the mechanics of body systems and systems analysis. The research results allow to write out formulas for calculating forces and moments of forces in the joints of the systems of bodies with one open branch. It is demonstrated in examples of writing out analytical types of equations of dynamics of industrial robot arms with three and six degrees of freedom in space. Three kinds of equations of dynamics were obtained for such manipula-tors. The first equations are written out in scalar-coordinate form with explicit quasi-accelerations and ve-locities, whose role is played by the projections of absolute angular accelerations and velocities of bodies on their connected axes. The second ones are written in vector-matrix form and are obtained from the former in the process of replacing quasi-accelerations by relative linear and angular accelerations of bodies with the allocation of a symmetric matrix of inertial coefficients. The third kind of equations of dynamics is ob-tained from the second one in the process of replacing quasi-velocities by relative linear and angular veloci-ties of bodies. In the third form, the centrifugal, Coriolis, and gyroscopic inertial forces are clearly ex-pressed. Gyroscopic inertial forces allow us to simplify the formula for calculating the power consumption of drives, as well as to simplify the Timofeev formula for calculating the driving forces and moments of forces that provide control of the program motion of manipulator bodies with a given quality. A technique for reusing formulas for manipulators with matching kinematic diagrams of their subsystems is demonstra-ted in the examples . Geometric, kinematic, static and inertial parameters of bodies are explicitly expressed in the equations of dynamics The multipliers for accelerations and products of velocities in the equations of dynamics are optimal in the sense of the minimum of arithmetic operations (additions and multiplica-tions) required for their calculations. Conclusion. All analytical types of equations of dynamics are veri-fied. They occupy several lines of text and further simplification is practically impossible.
Model and Algorithm for Predicting Technological Tool Sticking by Wellbore Depth Based on the Four-Module Neural Network
Authors:   South Ural State University, Qodirov Shahboz Sh. , Shestakov Aleksandr L. ,   South Ural State University
Published: May 2022

Sticking the technological tools is considered one of the most capital-intensive types of accidents in oil and gas well drilling, which have a significant impact on the cost of the well. The prediction of stuck tools at the design stage and in the process of drilling allows to minimize the risks of its occurrence, and also allows to choose the optimal method of prevention for specific geological and technical conditions. The work is devoted to the model and algorithm of predicting technological tool sticking by the wellbore depth based on a 4-module neural network. In the work presented classification of a group of methods for predicting sticking and the main disadvantages of existing methods. In the paper is presented the method of transformation the input data elements, on the example of textual and categorical data types. Due to this, it is possible to include into the list of input data elements such geological parameters as rock types, which are one of the most important factors influencing the process of sticking tools, and previously not perceived by models. In order to form a list of significant input data elements, the calculation of correlation coefficients between input data elements and target variables is presented.The type and architecture, as well as the hyperparameters of the modular neural network are chosen experimentally. Based on the trained and tested 4-module prediction model, we propose an algorithm for conducting a sticking tool prediction procedure at the design and drilling stage of the well. A specific feature of the proposed method is that the prediction model uses a wide diapason of universal factors as input data elements, such as geological, technological and rheological parameters of drilling mud as well as technical and technological parameters of drilling influencing the process of all types of stuck tools. Model in perspective has the ability to retrain and adapt to new data, which often happens when drilling wells in new fields.
Frontal-occipital network alterations while viewing 2D & 3D movies: a source-level EEG and graph theory approach
Authors: Yu Minchang , Xiao Shasha , Tian Feng , Li Yingjie
Published: May 2022

Many researchers have measured the differences in electroencephalography (EEG) while viewing 2D and 3D movies to uncover the neuromechanism underlying distinct viewing experiences. Using whole-brain network analyses of scalp EEG, our previous study reported that beta and gamma bands presented higher global efficiencies while viewing 3D movies. However, scalp EEG is influenced by volume conduction, not allowing inference from a neuroanatomy perspective; thus, source reconstruction techniques are recommended. This paper is the first to measure the differences in the frontal-occipital networks in EEG source space during 2D and 3D movie viewing. EEG recordings from 40 subjects were performed during 2D and 3D movie viewing. We constructed frontal-occipital networks of alpha, beta, and gamma bands in EEG source space and analyzed network efficiencies. We found that the beta band exhibited higher global efficiency in 3D movie viewing than in 2D movie viewing; however, the alpha global efficiency was not statistically significant. In addition, a support vector machine (SVM) classifier, taking functional connectivities as classification features, was built to identify whether the frontal-occipital networks contain patterns that could distinguish 2D and 3D movie viewing. Using the 6 most important functional connectivity features of the beta band, we obtained the best accuracy of 0.933. Our findings shed light on uncovering the neuromechanism underlying distinct experiences while viewing 2D and 3D movies.