bluuebunny/crossref_metadata_2025 huggingface dataset:
Augmentation Rhinoplasty in Cleft Lip Nasal Deformity Using Alloplastic Material and Autologous Cartilage
Authors: Hoang Tuan-Anh , Lee Kevin C. , Dung Vu , Chuang Sung-Kiang
Published: August 2022

Secondary cleft rhinoplasty typically requires large amounts of cartilage grafts for augmentation. The purpose of this study was to present our short-term experience with alloplastic implants in cleft rhinoplasty. This was a retrospective cohort study of cleft lip and palate patients treated with secondary rhinoplasty at Hanoi Medical University Hospital and Ruby Hospital between 2017 and 2020. All rhinoplasty procedures consisted of lower lateral cartilage repositioning, a dorsal augmentation with silicone implant, columellar strut implant or graft, and onlay tip grafts. Cartilage was obtained from the septum and concha, and no cartilage was harvested from the rib. The study outcomes included the Rhinoplasty Outcome Evaluation (ROE) survey, a modified Mortier scoring scale, 8 intranasal measures of symmetry, and 4 nasofacial measures of tip projection and nasal length. Changes in patient satisfaction and nasal esthetics were compared before and after surgery. A total of 38 patients were included in the final study sample, of whom 65.79% had unilateral clefts. The overall complication rate was 7.89%, and there were 2 cases of infection and 1 case of dorsal implant displacement. Following rhinoplasty, ROE satisfaction scores significantly increased (+39.36, P<0.01) and Mortier severity scores decreased (−3.06, P<0.01). Nostril symmetry nearly normalized in width, height, and inclination. Mean columellar deviation decreased from 8.82 to 2.08 degrees, and nasal projection increased as assessed on multiple analyses. Patients with bilateral clefts had similar improvements in ROE and Mortier scores. In our experience, synthetic implants simplified the correction of cleft nasal deformity and eliminated the need for costal cartilage. We found that our protocol produced acceptable and stable short-term clinical results without increasing the complication rate above what has been reported with autologous grafts.
The Perceptions and Experiences of Undergraduate Healthcare Students With Debriefing Methods
Authors: Arabi Asma N. , Kennedy Catherine A.
Published: August 2022

Summary Statement

We performed a systematized review examining the existing literature on undergraduate healthcare students' perceptions and experiences with debriefing methods in simulation-based education. Twenty empirical research articles published in English between 2008 and 2020 were identified during a systematic search of 4 electronic databases. Data derived from these articles underwent critical appraisal and thematic analysis.

Students valued the opportunity in debriefing for reflection, raising self-awareness of skills and learning. They preferred structured debriefing for promoting analytic skills and transfer of learning, favored video-assisted debriefing for fast recall and improving communication skills, and benefited most from instructor-led rather than peer-led debriefing. However, students appreciated group debriefing for aiding the construction of new understandings. There was no consensus on the preferred timing of debriefing, and students highlighted their concern about the disclosure of errors across different debriefing methods. Recommendations for educators to improve debriefing experiences and for future research are considered.
The Diagnostic Efficacy of an App-based Diagnostic Health Care Application in the Emergency Room: eRadaR-Trial. A prospective, Double-blinded, Observational Study
Authors: Faqar-Uz-Zaman Sara F. , Anantharajah Luxia , Baumartz Philipp , Sobotta Paula , Filmann Natalie , Zmuc Dora , von Wagner Michael , Detemble Charlotte , Sliwinski Svenja , Marschall Ursula , Bechstein Wolf O. , Schnitzbauer Andreas A.
Published: August 2022

Objective:

To evaluate the diagnostic accuracy of the app-based diagnostic tool Ada and the impact on patient outcome in the emergency room (ER).

Background:

Artificial intelligence-based diagnostic tools can improve targeted processes in health care delivery by integrating patient information with a medical knowledge base and a machine learning system, providing clinicians with differential diagnoses and recommendations.

Methods:

Patients presenting to the ER with abdominal pain self-assessed their symptoms using the Ada-App under supervision and were subsequently assessed by the ER physician. Diagnostic accuracy was evaluated by comparing the App-diagnoses with the final discharge diagnoses. Timing of diagnosis and time to treatment were correlated with complications, overall survival, and length of hospital stay.

Results:

In this prospective, double-blinded study, 450 patients were enrolled and followed up until day 90. Ada suggested the final discharge diagnosis in 52.0% (95% CI [0.47, 0.57]) of patients compared with the classic doctor-patient interaction, which was significantly superior with 80.9% (95% CI [0.77, 0.84], P<0.001). However, when diagnostic accuracy of both were assessed together, Ada significantly increased the accuracy rate (87.3%, P<0.001), when compared with the ER physician alone. Patients with an early time point of diagnosis and rapid treatment allocation exhibited significantly reduced complications (P<0.001) and length of hospital stay (P<0.001).

Conclusion:

Currently, the classic patient-physician interaction is superior to an AI-based diagnostic tool applied by patients. However, AI tools have the potential to additionally benefit the diagnostic efficacy of clinicians and improve quality of care.
Palliative care delivery changes during COVID-19 and enduring implications in oncology nursing: a rapid review
Authors: Levoy Kristin , Foxwell Anessa , Rosa William E.
Published: August 2022

Purpose of review

A rapid review was conducted to synthesize evidence of palliative care delivery changes during the COVID-19 pandemic. Changes were synthesized according to the eight domains of high-quality palliative care and enduring implications for oncology nurses beyond the pandemic discussed.

Recent findings

The most significant changes occurred in the structure and processes of palliative care (Domain 1), where increased utilization of telehealth was critical in circumventing barriers imposed by COVID-19 mitigation. The suboptimal availability of community-based psychosocial supports for patients and caregivers and inadequate health system-based psychosocial supports for healthcare providers were highlighted (Domains 3–5). The pandemic also ushered in an increased emphasis on the need for advance care planning (ACP), where integrating its delivery earlier in the outpatient setting and shifting policy to promote subsequent virtual documentation (Domain 8) were essential to ensure care preferences were clarified and accessible before health crises occurred.

Continuing to embrace and sustain systems-level changes with respect to telehealth, psychosocial supports, and ACP are critical to bridging gaps in palliative care delivery underscored by the pandemic. Oncology nurses are well positioned to fill these gaps in care beyond the pandemic by providing evidence-based, palliative care throughout the cancer continuum.
Graph Theory Analysis of Semantic Fluency in Russian–English Bilinguals
Authors: Sinha Vidushi , Lissemore Frances , Lerner Alan J.
Published: August 2022

Background:

Semantic category fluency is a widely used task involving language, memory, and executive function. Previous studies of bilingual semantic fluency have shown only small differences between languages. Graph theory analyzes complex relationships in networks, including node and edge number, clustering coefficient, average path length, average number of direct neighbors, and scale-free and small-world properties.

Objective:

To shed light on whether the underlying neural processes involved in semantic category fluency testing yield substantially different networks in different languages.

Method:

We compared languages and methods using both network analysis and conventional analysis of word production. We administered the animal naming task to 51 Russian–English bilinguals in each language. We constructed network graphs using three methods: (a) simple association of unique co-occurring neighbors, (b) corrected associations between consecutive words occurring beyond chance, and (c) a network community approach using planar maximally filtered graphs. We compared the resultant network analytics as well as their scale-free and small-world properties.

Results:

Participants produced more words in Russian than in English. Small-worldness metrics were variable between Russian and English but were consistent across the three graph theory analytical methods.

Conclusion:

The networks had similar graph theory properties in both languages. The optimal methodology for creating networks from semantic category fluency remains to be determined.
Keratinophyton chongqingense sp. nov. and Keratinophyton sichuanense sp. nov., from soil in China
Authors: Li Xin , Zhang Zhi-Yuan , Chen Wan-Hao , Liang Jian-Dong , Liang Zong-Qi , Han Yan-Feng
Published: August 2022

Keratinophyton is a genus of well-known keratinophilic fungi found in various terrestrial habitats. During a survey of keratinolytic fungi in China, a total of 12 isolates of Keratinophyton species, representing eight taxa, were obtained from the soil. Two of these isolates were described as new species based on their morphological characteristics and molecular analyses of the internal transcribed spacer region and the rRNA gene of the nuclear large subunit. Descriptions and illustrations of these two novel species, which are named Keratinophyton chongqingense sp. nov. and Keratinophyton sichuanense sp. nov., are provided herein.
Arsenophonus apicola sp. nov., isolated from the honeybee Apis mellifera
Authors: Nadal-Jimenez Pol , Siozios Stefanos , Frost Crystal L. , Court Rebecca , Chrostek Ewa , Drew Georgia C. , Evans Jay D. , Hawthorne David J. , Burritt James B. , Hurst Gregory D. D.
Published: August 2022

The genus

Arsenophonus

has been traditionally considered to comprise heritable bacterial symbionts of arthropods. Recent work has reported a microbe related to the type species

Arsenophonus nasoniae

as infecting the honey bee, Apis mellifera. The association was unusual for members of the genus in that the microbe–host interaction arose through environmental and social exposure rather than vertical transmission. In this study, we describe the in vitro culture of ArsBeeUST, a strain of this microbe isolated from A. mellifera in the USA. The 16S rRNA sequence of the isolated strain indicates it falls within the genus

Arsenophonus

. Biolog analysis indicates the bacterium has a restricted range of nutrients that support growth. In vivo experiments demonstrate the strain proliferates rapidly on injection into A. mellifera hosts. We further report the closed genome sequence for the strain. The genome is 3.3 Mb and the G+C content is 37.6 mol%, which is smaller than

A. nasoniae

but larger than the genomes reported for non-culturable

Arsenophonus

symbionts. The genome is complex, with six extrachromosomal elements and 11 predicted intact phage elements, but notably less complex than

A. nasoniae

. Strain ArsBeeUST is clearly distinct from the type species

A. nasoniae

on the basis of genome sequence, with 92 % average nucleotide identity. Based on our results, we propose Arsenophonus apicola sp. nov., with the type strain ArsBeeUST (CECT 30499T=DSM113403T=LMG 32504T).
Identification of micro-organism from positive blood cultures: comparison of three different short culturing methods to the Rapid Sepsityper workflow
Authors: Pranada Arthur B. , Cordovana Miriam , Meyer Markus , Hubert Hilke , Abdalla Mohammad , Ambretti Simone , Steinmann Joerg
Published: August 2022

Sepsis is one of the leading causes of death worldwide. The rapid identification (ID) of the causative micro-organisms is crucial for the patients’ clinical outcome. MALDI-TOF MS has been widely investigated to speed up the time-to-report for ID from positive blood cultures, and many different procedures and protocols were developed, all of them attributable either to the direct separation of microbial cells from the blood cells, or to a short subculture approach. In this study, the Rapid Sepsityper workflow (MBT Sepsityper IVD Kit, Bruker Daltonics GmbH and Co. KG, Bremen, Germany) was compared to three different short subculturing methods, established into the routine practice of three different clinical microbiology laboratories. A total of N=503 routine samples were included in this study and tested in parallel with the two approaches. Results of the rapid procedures were finally compared to routine proceedings with Gram-staining and overnight subculture. Among monomicrobial samples, the Rapid Sepsityper workflow enabled overall the correct identification of 388/443 (87.6 %) micro-organisms, while the short subculturing methods of 267/435 (61.8 %). Except for the performance with

Streptococcus pneumoniae

, in each one of the three sites the Rapid Sepsityper workflow proved to be superior to the short subculture method, regardless of the protocol applied, and it delivered a result from 1 to 5 h earlier.
Genome scan of landrace populations of the self-fertilizing crop species rice, collected across time, revealed climate changes’ selective footprints in the genes network regulating flowering time
Authors: Ahmadi Nour , Barry Mamadou Billo , Frouin Julien , de Navascués Miguel , Toure Mamadou Aminata
Published: August 2022

Analysis of the genetic bases of adaptation to climate changes are often conducted on natural populations. We report here on a study based on diachronic sampling (1980 & 2010) of the self-fertilising crop species, Oryza sativa (Asian rice) and Oryza glaberrima (African rice), in the tropical forest and the Sudanian savannah of West Africa. First, using historical meteorological data we confirmed changes in temperatures (+1°C on average) and rainfall regime (less predictable and reduced amount) in the target area. Second, phenotyping the populations for phenology, we observed significantly earlier heading time (up to 10 days) in the 2010 samples. Third, we implemented two genome-scan methods, one of which specially developed for selfing species, and detected 31 independent selection footprints. These loci showed significant enrichment in genes involved in reproductive processes and bore known heading time QTLs and genes, including OsGI, Hd1 and OsphyB. This rapid adaptive evolution, originated from subtle changes in the standing variation in genetic network regulating heading time, did not translate into predominance of multilocus genotypes, as it is often the case in selfing plants, and into notable selective sweeps. We argue that this high adaptive potential results from the multiline genetic structure of the rice landraces, and the rather large and imbricated genetic diversity of the rice meta-population at the farm, the village and the region levels, that hosted the adaptive variants in multiple genetic backgrounds well before the advent of the environmental selective pressure. The complex selection footprints observed in this empirical study calls for further model development on genetic bases of plant adaptation to environmental changes.
Genetically encoded photocatalytic protein labeling enables spatially-resolved profiling of intracellular proteome
Authors: Zheng Fu , Yu Chenxin , Zhou Xinyue , Zou Peng
Published: August 2022

Mapping the subcellular organization of proteins is crucial for understanding their biological functions. Herein, we report a reactive oxygen species induced protein labeling and identification (RinID) method for profiling subcellular proteome in the context of living cells. Our method capitalizes on a genetically encoded photocatalyst, miniSOG, to locally generate singlet oxygen that reacts with proximal proteins. Labeled proteins are conjugated in situ with an exogenously supplied nucleophilic probe, which serves as a functional handle for subsequent affinity enrichment and mass spectrometry-based protein identification. From a panel of nucleophilic compounds, we identify biotin-conjugated aniline and propargyl amine as highly reactive probes. As a demonstration of the spatial specificity and depth of coverage in mammalian cells, we apply RinID in the mitochondrial matrix, capturing 394 mitochondrial proteins with 97% specificity. We further demonstrate the broad applicability of RinID in various subcellular compartments, including the nucleus and the endoplasmic reticulum.
Addictions may be driven by competition-induced microbiome dysbiosis
Authors: Lewin-Epstein Ohad , Jaques Yanabah , Feldman Marcus W , Kaufer Daniela , Hadany Lilach
Published: August 2022

Recent studies revealed mechanisms by which the microbiome affects its host’s brain, behavior and wellbeing, and that dysbiosis – persistent microbiome-imbalance – is associated with the onset and progress of various chronic diseases, including addictive behaviors. Yet, understanding of the ecological and evolutionary processes that shape the host-microbiome ecosystem and affect the host state, is still limited. Here we propose that competition dynamics within the microbiome, associated with host-microbiome mutual regulation, may promote dysbiosis and aggravate addictive behaviors. We constructed a mathematical framework, modeling the dynamics of the host-microbiome ecosystem in response to alterations. We find that when this ecosystem is exposed to substantial perturbations, the microbiome may shift towards a composition that reinforces the new host state. Such positive feedback loop augments post-perturbation imbalances, hindering attempts to return to the initial equilibrium, thus promoting relapse episodes and prolonged addictions. We also find that the initial microbiome composition is a key factor: a diverse microbiome enhances the ecosystem’s resilience, whereas lower microbiome diversity is more prone to reach dysbiosis, exacerbating addictions. This framework provides novel evolutionary and ecological perspectives on host-microbiome interactions and their implications for host behavior and health, while offering verifiable predictions with potential relevance to clinical treatments.
Interactions between culturable bacteria are predicted by individual species’ growth
Authors: Nestor Einat , Toledano Gal , Friedman Jonathan
Published: August 2022

Predicting interspecies interactions is a key challenge in microbial ecology, as such interactions shape the composition and functioning of microbial communities. However, predicting microbial interactions is challenging since they can vary considerably depending on species’ metabolic capabilities and environmental conditions. Here, we employ machine learning models to predict pairwise interactions between culturable bacteria based on their phylogeny, monoculture growth capabilities, and interactions with other species. We trained our models on one of the largest available pairwise interactions dataset containing over 7500 interactions between 20 species from 2 taxonomic groups that were cocultured in 40 different carbon environments. Our models accurately predicted both the sign (accuracy of 88%) and the strength of effects (R2of 0.87) species had on each other’s growth. Encouragingly, predictions with comparable accuracy could be made even when not relying on information about interactions with other species, which are often hard to measure. However, species’ monoculture growth was essential to the model, as predictions based solely on species’ phylogeny and inferred metabolic capabilities were significantly less accurate. These results bring us a step closer to a predictive understanding of microbial communities, which is essential for engineering beneficial microbial consortia.
Elevated urine BMP phospholipids in LRRK2 and VPS35 mutation carriers with and without Parkinson’s disease
Authors: Gomes Sara , Garrido Alicia , Tonelli Francesca , Obiang Donina , Tolosa Eduardo , Marti Maria Jose , Ruiz-Martinez Javier , Aragon Ana Vinagre , Hernandez-Eguiazu Haizea , Croitoru Ioana , Marshall Vicky L , Koenig Theresa , Hotzy Christoph , Hsieh Frank , Sakalosh Marianna , Tengstrand Elizabeth , Padmanabhan Shalini , Merchant Kalpana , Bruecke Christof , Pirker Walter , Zimprich Alexander , Sammler Esther
Published: August 2022

Elevated urine bis(monoacylglycerol)phosphate (BMP) levels have been found in gain-of-kinase function LRRK2 G2019S mutation carriers. Here, we have expanded urine BMP analysis to other Parkinson’s disease (PD) associated mutations and found them to be consistently elevated in carriers of LRRK2 G2019S and R1441G/C as well as VPS35 D620N mutations. Urine BMP levels are promising biomarkers for patient stratification and potentially target engagement in clinical trials of emerging targeted PD therapies.
Ex vivo drug testing in an ultra-rare sarcoma reveals therapeutic vulnerability and resistance
Authors: Yi Chan Sharon Pei , Luo Baiwen , Chen Benjamin Jieming , Villanueva Andre , Xiu Sam Xin , Farah Benjamin Livingstone , Shannon Nicholas , Ong Chin-Ann Johnny , Chia Claramae Shulyn , Yong Ming-Hui , Kumar Krishan , Ooi London Lucien , Yong Tay Timothy Kwang , Woo Xing Yi , Toh Tan Boon , Chow Edward Kai-Hua , Yang Valerie Shiwen
Published: August 2022

Solitary fibrous tumors (SFTs) are rare soft tissue sarcomas for which therapeutic options are limited and ineffective. We successfully demonstrated how functional personalized treatment was implemented in the clinic for an ultra-rare sarcoma with otherwise limited options, through a combined strategy of patient-derived model development and computational drug analytics. Molecular profiling of tumours and patient-derived models uncovered potential biomarkers to predict responses to specific drugs.

We generated patient-derived SFT cells (PDSC) and used a computational combinatorial drug screening analytics platform, Quadratic Phenotypic Optimization Platform (QPOP), to determine therapeutic vulnerability and resistance in an ultra-rare locally recurrent brain SFT and its distant liver metastasis. QPOP derived and ranked the efficacy of 531,441 drug combinations, revealing BETi-pazopanib synergy in the liver lesion that outperforms standard-of-care combination doxorubicin-ifosfamide, which was antagonistic. In tumour and PDSC from the pazopanib-resistant brain lesion, transcriptomic analyses identified the UGT1A family as potential biomarkers of pazopanib resistance. Eribulin sensitivity was predicted to be shared across both lesions. Our patient was therefore treated with eribulin and successfully gained clinically meaningful disease control.
Store-operated Ca2+ entry regulatory factor (SARAF) alters murine metabolic state age-dependent via hypothalamic pathways
Authors: Gataulin Diana , Kuperman Yael , Tsoory Michael , Biton Inbal E. , Karbat Izhar , Meshcheriakova Anna , Reuveny Eitan
Published: August 2022

Store-operated Ca2+ entry (SOCE) is a vital process aimed at refilling cellular internal Ca2+ stores, and a primary cellular-signaling driver of transcription factors entry to the nucleus. SARAF (SOCE associated regulatory factor)/TMEM66 is an endoplasmic reticulum (ER) resident transmembrane protein that promotes SOCE inactivation and prevents Ca2+ overfilling of the cell. Here we demonstrate that mice deficient in SARAF develop age-dependent sarcopenic obesity with decreased energy expenditure, lean mass and locomotion without affecting food consumption. Moreover, SARAF ablation reduces hippocampal proliferation, modulates the activity of the hypothalamus-pituitary-adrenal (HPA) axis, and mediates changes in anxiety-related behaviors. Interestingly, selective SARAF ablation in the paraventricular nucleus (PVN) of the hypothalamus protects from old age-induced obesity and preserves locomotion, lean mass and energy expenditure, suggesting an opposing, site-specific role for SARAF. Lastly, SARAF ablation in hepatocytes leads to elevated SOCE, elevated vasopressin-induced Ca2+ oscillations, and an increased mitochondrial spare respiratory capacity, thus providing insights into the cellular mechanisms that may affect the global phenotypes. These effects may be mediated via the liver X receptor (LXR) and IL-1 signaling metabolic regulators explicitly altered in SARAF ablated cells. In short, our work supports both central and peripheral roles of SARAF in regulating metabolic, behavioral, and cellular responses.

Highlights

Loss/absence of SARAF facilitates age-dependent obesity with decreased metabolic rate, lean mass, and locomotion, without affecting food consumption.

Loss of SARAF leads to lipid droplet hypertrophy, BAT whitening and age-dependent hepatic steatosis.

Mice lacking SARAF expression in the PVN have an increased metabolic rate, decreased BAT whitening, and are protected from sarcopenic obesity.

SARAF ablation in hepatocytes increases SOCE, elevates Ca2+ oscillation in response to vasopressin, and increases the mitochondria’s spare respiratory capacity.

Loss of SARAF leads to decreased hippocampal proliferation, sensitized HPA-axis and changes in anxiety-related behavior.
Rules for hardening influenza A virus liquid condensates
Authors: Etibor Temitope Akhigbe , Vale-Costa Sílvia , Sridharan Sindhuja , Brás Daniela , Becher Isabelle , Mello Victor Hugo , Ferreira Filipe , Alenquer Marta , Savitski Mikhail M , Amorim Maria João
Published: August 2022

Multiple viral infections form biomolecular condensates in the host cell to compartmentalize viral reactions. Accumulating evidence indicates that these viral condensates may be hardened, a strategy with potential for exploitation as novel antiviral therapy, given that viral reactions rely on specific material properties for function. However, there is no molecular understanding on how to specifically and efficiently modify the material properties of viral condensates, a pre-requisite for overcoming off-target effects by rational drug design.In vitro, the material properties of biological condensates are modified by different thermodynamic parameters, including free energy, concentration, and type/strength of interactions. Here, we used influenza A virus liquid cytosolic condensates, A.K.A viral inclusions, to provide a proof of concept that modulating the type/strength of transient interactions among the interactome in IAV inclusions is more efficient at hardening these structures than varying the temperature or concentration, both inin vitroand inin vivomodels. This stabilization can be achieved by a known pharmacological sticker that can specifically change the material properties of viral inclusions without affecting host proteome abundance nor solubility. Our work supports the development of antivirals targeting the material properties of biomolecular condensates in viral infections. It also provides a framework for the selection of compounds with this activity for general application and thus provides an advance in disease therapy.
An end-to-end pipeline based on open source deep learning tools for reliable analysis of complex 3D images of Medaka ovaries
Authors: Lesage Manon , Bugeon Jérôme , Thomas Manon , Pécot Thierry , Thermes Violette
Published: August 2022

Computational analysis of bio-images by deep learning (DL) algorithms has made exceptional progress in recent years and has become much more accessible to non-specialists with the development of ready-to-use tools. The study of oogenesis mechanisms and female reproductive success in fish has also recently benefited from the development of efficient three-dimensional (3D) imaging protocols on entire ovaries. Such large datasets have a great potential for the generation of new quantitative data on oogenesis but are, however, complex to analyze due to imperfect fluorescent signals and the lack of efficient image analysis workflows. Here, we applied two open-source DL tools, Noise2Void and Cellpose, to analyze the oocyte content of medaka ovaries at larvae and adult stages. These tools were integrated into end-to-end analysis pipelines that include image pre-processing, cell segmentation, and image post-processing to filter and combine labels. Our pipelines thus provide effective solutions to accurately segment complex 3D images of entire ovaries with either irregular fluorescent staining or low autofluorescence signal. In the future, these pipelines will be applicable to extensive cellular phenotyping in fish for developmental or toxicology studies.

Summary statement

An accessible image analysis method for biologists, which includes easy-to-use deep learning algorithms, designed for accurate quantitative measurement of ovarian content from complex 3D fluorescent images.
Double-dose mRNA vaccination to SARS-CoV-2 progressively increases recognition of variants-of-concern by Spike RBD-specific memory B cells
Authors: Hartley Gemma E. , Edwards Emily S.J. , Varese Nirupama , Boo Irene , Aui Pei M. , Bornheimer Scott J. , Hogarth P. Mark , Drummer Heidi E. , O’Hehir Robyn E. , van Zelm Menno C.
Published: August 2022

Background

SARS-CoV-2 vaccination with BNT162b2 (Pfizer BioNTech) has been shown to be 95% effective.1 Double-dose vaccination generates high levels of spike-specific antibodies, memory B cells (Bmem) and T cells. However, variants of concern (VoC) with mutations in the spike Receptor Binding Domain (RBD) can evade antibody responses. Booster vaccinations improve antibody recognition of VoC, but it is unclear if this is due to higher total antibodies or their capacity to bind VoC. We here addressed the capacity of surface Ig on single Wuhan-specific Bmem after first and second dose BNT162b2 vaccination to recognize variant RBD.

Methods

Samples were collected from 30 healthy COVID-19 naive individuals pre-BNT162b2 vaccination, 3 weeks post-dose 1 and 4-weeks post-dose 2. Plasma antibodies and Bmem were evaluated using recombinant RBD proteins of the Wuhan, Gamma and Delta strains.

Results

All individuals generated a robust antibody response to BNT162b2 vaccination with all participants producing neutralizing antibodies following dose 2. IgM+ and IgG+ RBD-specific Bmem were generated after one vaccine dose, and those expressing IgG1 increased in absolute number after dose 2. The majority of RBD-specific Bmem bound the Gamma and/or Delta variants, and this proportion significantly increased after the second dose.

Conclusion

The second dose of BNT162b2 increases the number of circulating Ig-class switched RBD-specific Bmem. Importantly, the second dose of vaccination is required for a high frequency of RBD-specific Bmem to recognize Gamma and Delta variants. This suggests that dose 2 not only increases the number of RBD-specific Bmem but also the affinity of the Bmem to overcome the point mutations in VoC.
"I don't know what to do or where to go". experiences of accessing healthcare support from the perspectives of people living with Long Covid and healthcare professionals: A qualitative study in Bradford, UK.
Authors: Baz Sarah Akhtar , Fang Chao , Carpentieri JD , Sheard Laura
Published: August 2022

Abstract

Background: In July 2022 it was estimated 2 million people in the UK have self-reported Long Covid (LC).1 Many people have reported not receiving adequate healthcare support. There is a lack of research which provides an in-depth exploration of the barriers faced by people with LC in accessing healthcare support. It is important to understand these barriers to provide better support, care and advice for those experiencing LC.
Objective: To understand the barriers faced in accessing primary, secondary and specialist healthcare support for people with LC.
Design and participation: 40 interviews were conducted with people with LC alongside 12 interviews with healthcare professionals (HCPs) providing LC support in Bradford, as part of a UK wide qualitative longitudinal study.
Results: People living with LC had a large degree of difficulty in accessing healthcare services for LC support. We categorised the healthcare access experiences of participants into five main types: 1) being unable to access primary care 2) accessing primary care but receiving (perceived) inadequate support 3) extreme persistence 4) alternatives to mainstream healthcare 5) positive experiences. There was a severe lack of access to specialist LC services. Ethnic minority participants faced a further barrier of mistrust and fear of services deterring them from accessing support. HCPs discussed systemic barriers to delivering services. Experiences were embedded in macro structural issues further exacerbated by the pandemic.
Conclusion: To better support people with LC the barriers faced in accessing healthcare support must be addressed. Of significance, improvements to GP access are required; especially as GPs are the first line of support for people living with LC.
Patient and public involvement: A PPI group is engaged at regular intervals in the project.
The effect of intimate partner violence on women's risk of HIV acquisition and engagement in the HIV treatment and care cascade: an individual-participant data meta-analysis of nationally representative surveys in sub-Saharan Africa
Authors: Kuchukhidze Salome , Panagiotoglou Dimitra , Boily Marie-Claude , Diabaté Souleymane , Eaton Jeffrey W , Mbofana Francisco , Sardinha LynnMarie , Schrubbe Leah , Söckl Heidi , Wanyenze Rhoda K , Maheu-Giroux Mathieu
Published: August 2022

Background:
Achieving the 95-95-95 targets for HIV diagnosis, treatment, and viral load suppression (VLS) to end the HIV/AIDS epidemic hinges on eliminating structural inequalities, including intimate partner violence (IPV). Sub-Saharan Africa (SSA) has among the world's highest prevalence of IPV and HIV. We aim to examine the impact of IPV on recent HIV infection and women's engagement in the HIV care cascade.

Methods:
We pooled individual-level data from nationally representative surveys with information on physical and/or sexual IPV and HIV in SSA (2000-2020). We used Poisson regressions with robust standard errors to estimate adjusted prevalence ratios (aPR) of past year experience of IPV on recent HIV infection (measured using recency assays), past-year HIV testing, antiretroviral therapy (ART) uptake, and VLS among ever-partnered (currently/formerly married or cohabitating) women. Models were adjusted for women's age, age at sexual debut, residence type, marital status, education, and the survey's identifier (proxy of country and year).

Findings:
Fifty-seven surveys were available from thirty countries, encompassing 280,259 (N) individuals. One-fifth of women reported physical and/or sexual IPV in the past year. Six surveys had information on recent HIV infection and seven had data on ART uptake and VLS. Women experiencing past year IPV were 3.22 times (95%CI: 1.51-6.85, N=19,179) more likely to have a recent HIV infection, adjusting for potential confounders. Past year IPV was not associated with HIV testing (aPR=0.99, 95%CI: 0.98-1.01, N=274,506) or ART uptake (aPR=0.96, 95%CI:0.90-1.03, N=5,629). Women living with HIV (WLHIV) experiencing IPV in the past year were 9% less likely to achieve VLS (aPR=0.91, 95%CI: 0.85-0.98, N=5,627).

Interpretation:
Past year IPV was associated with recent HIV acquisition and lower VLS among WLHIV. Preventing IPV is inherently imperative but eliminating IPV could also be crucial to ending HIV/AIDS.
Host-pathogen sympatry and differential transmissibility ofMycobacterium tuberculosis complex
Authors: Gröschel Matthias I , Pérez-Llanos Francy J. , Diel Roland , Vargas Roger , Escuyer Vincent , Musser Kimberlee , Trieu Lisa , Meissner Jeanne Sullivan , Knorr Jillian , Klinkenberg Don , Kouw Peter , Homolka Susanne , Samek Wojciech , Mathema Barun , van Soolingen Dick , Niemann Stefan , Ahuja Shama , Farhat Maha R
Published: August 2022

The obligate human pathogenMycobacteriumtuberculosis complex (Mtbc) separates genetically into nine lineages several of which demonstrate sympatry with their human host i.e. have distinct and restricted patterns of geographical distribution globally.1–3Geographically restrictedMtbclineages have been hypothesized to be adapted to infect and/or transmit among sympatric human hosts,i.e. to be niche specialists, but this is yet to be confirmed while controlling for exposure, social networks and risk of disease after exposure.1,4Here we show that strains of geographically restricted (Mtbclineages L1,L2restricted, L3,L4restricted, L5,L6 are intrinsically less transmissible than widespreadMtbclineages (L2widespread, L4widespread) across Western European and North American cosmopolitan populations. Comparing transmissibility between sympatric and allopatric contact-pathogen pairs, we find the first controlled evidence for a biological impact of sympatry betweenMtbcstrains and their human hosts; allopatric host-pathogen exposures has a 38% decrease in the odds of infection among contacts compared with sympatric exposures. We measure 10- fold lower phagocytosis and growth rates of L6 geographically restricted strains compared to L4widespreadinin vitroallopatric macrophage infections. Long-term co-existence ofMtbcstrains and humans has resulted in differential transmissibility between allopatric and sympatric hosts for strains of geographically restricted lineages. Understanding the specific genetic and immunological underpinnings of sympatry in TB may inform rational vaccine design and TB control.
Viral Kinetics of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Omicron Infection in mRNA-Vaccinated Individuals Treated and Not Treated with Nirmatrelvir-Ritonavir
Authors: Dai Eric Y. , Lee Kannon A. , Nathanson Audrey B. , Leonelli Ariana T. , Petros Brittany A. , Brock-Fisher Taylor , Dobbins Sabrina T. , MacInnis Bronwyn L. , Capone Amelia , Littlehale Nancy , Boucau Julie , Marino Caitlin , Barczak Amy K. , Sabeti Pardis C. , Springer Michael , Stephenson Kathryn E.
Published: August 2022

We measured viral kinetics of SARS-CoV-2 Omicron infection in 36 mRNA-vaccinated individuals, 11 of whom were treated with nirmatrelvir-ritonavir (NMV-r). We found that NMV-r was associated with greater incidence of viral rebound compared to no treatment. For those that did not rebound, NMV-r significantly reduced time to PCR conversion.
Mec1-Independent Activation of the Rad53 Checkpoint Kinase Revealed by Quantitative Analysis of Protein Localization Dynamics
Authors: Ho Brandon , Sanford Ethan J. , Torres Nikko P. , Smolka Marcus B. , Brown Grant W.
Published: August 2022

The replication checkpoint is essential for accurate DNA replication and repair, and maintenance of genomic integrity when a cell is challenged with genotoxic stress. Several studies have defined the complement of proteins that change subcellular location in the budding yeast Saccharomyces cerevisiae following chemically-induced DNA replication stress using methyl methanesulfonate (MMS) or hydroxyurea (HU). How these protein movements are regulated remains largely unexplored. We find that the essential checkpoint kinases Mec1 and Rad53 are responsible for regulating the subcellular localization of 159 proteins during MMS-induced replication stress. Unexpectedly, Rad53 regulation of the localization of 52 proteins is independent of its known kinase activator, Mec1, and in some scenarios independent of Tel1, or mediator components, Rad9 and Mrc1. We demonstrate that Rad53 is phosphorylated and active following MMS exposure in cells lacking Mec1 and Tel1. This non-canonical mode of Rad53 activation depends partly on the retrograde signaling transcription factor Rtg3, which also facilitates proper DNA replication dynamics. We conclude that there are biologically important modes of Rad53 protein kinase activation that respond to replication stress and operate in parallel to Mec1 and Tel1.
Genome wide CRISPR screen for Pasteurella multocida toxin (PMT) binding proteins reveals LDL Receptor Related Protein1 (LRP1) as crucial cellular receptor
Authors: Schöllkopf Julian , Müller Thomas , Hippchen Lena , Müller Teresa , Großmann Sonja , Reuten Raphael , Backofen Rolf , Klugbauer Norbert , Orth Joachim , Schmidt Gudula
Published: August 2022

PMT is a protein toxin produced by Pasteurella multocida serotypes A and D. As causative agent of atrophic rhinitis in swine, it leads to rapid degradation of the nasal turbinate bone. The toxin acts as a deamidase to modify a crucial glutamine in heterotrimeric G proteins, which results in constitutive activation of the G proteins and permanent stimulation of numerous downstream signaling pathways.

Using a lentiviral based genome wide CRISPR knockout screen in combination with a lethal toxin chimera, consisting of full length inactive PMT and the catalytic domain of diphtheria toxin, we identified the LRP1 gene encoding the Low-Density Lipoprotein Receptor-related protein 1 as a critical host factor for PMT function. Loss of LRP1 reduced PMT binding and abolished the cellular response and deamidation of heterotrimeric G proteins, confirming LRP1 to be crucial for PMT uptake. Expression of LRP1 or cluster 4 of LRP1, respectively, restored intoxication of the knockout cells. In summary our data demonstrate secretory cells as entry site of PMT into airway epithelia and present LRP1 as crucial host entry factor for PMT intoxication by acting as its primary cell surface receptor.
Cellular Uptake of His-Rich Peptide Coacervates Occurs by a Macropinocytosis-Like Mechanism
Authors: Shebanova Anastasia , Perrin Quentin , Gudlur Sushanth , Sun Yue , Lim Zhi Wei , Sun Ruoxuan , Lim Sierin , Ludwig Alexander , Miserez Ali
Published: August 2022

Coacervates are dense microdroplets formed by liquid-liquid phase separation (LLPS) of macromolecules that have gained increasing attention as drug delivery vehicles. Recently, we have reported a new intracellular delivery system based on self-coacervating histidine (His)-rich beak peptides (HBpep and HBpep-SP) inspired by beak proteins of the Humboldt squid. These peptide microdroplets combine excellent encapsulation efficiency of therapeutics with high transfection rate and low cytotoxicity. However, the mechanism by which they cross the cell membrane remains elusive. Previous inhibitor studies provided incomplete clues into the detail uptake pathway, although they suggested a cholesterol-dependent and, possibly, an energy-independent non-classical mechanism of internalization. In this study, we improved our understanding of coacervates/cell membrane interactions using model membranes, namely Giant Unilamellar Vesicles (GUVs) and Giant Plasma Membrane Vesicles (GPMVs). We also employ a combination of electron microscopy techniques to gain detailed structural insights into the cell uptake of HBpep and HBpep-SP coacervates. We demonstrate that modulating lipid charge and cholesterol level influence coacervate attachment to GUVs. However, they are not able to cross the GUV’s lumen in an energy-independent manner. We then show that the coacervates enter HeLa and HepG2 cells via a mechanism sharing morphological features of macropinocytosis and phagocytosis, in particular involving cytoskeleton rearrangement and capture by filipodia. Our study provides key insights into the interaction of HPpep and HBpep-SP coacervates with model membranes as well as their cellular uptake pathway.
A specific anti-IFITM2 antibody bars the way to SARS-CoV-2 entry into host cells
Authors: Basile Anna , Zannella Carla , De Marco Margot , Franci Gianluigi , Galdiero Massimiliano , Sanna Giuseppina , Manzin Aldo , Chetta Massimiliano , Turco Maria Caterina , Rosati Alessandra , Marzullo Liberato
Published: August 2022

The early steps of viral infection involve protein complexes and structural lipid rearrangements, which mark the characteristic strategies of each virus in entering permissive host cells. Human IFITM proteins have been described as inhibitors of a broad range of viruses. Despite their homology and functional redundancy, recently it has been surprisingly shown that SARS-CoV-2 is able to specifically hijack the IFITM2 protein. Here has been reported the characterization of a newly generated specific anti-IFITM2 mAb able to impair SARS-CoV-2 Spike protein internalization and, consequently, to reduce the SARS-CoV-2 cytopathic effects and syncytia formation. Importantly, as evidence of the more general involvement of IFITM2 in virus entry, the anti-IFITM2 mAb was able to efficiently reduce HSVs- and RSV-dependent cytopathic effects. Hence, IFITM proteins could be promising targets that can foster the development of biological antiviral molecules, or suggest additional therapeutic strategies for the treatment of viral infections.

GRAPHICAL ABSTRACT
Tuning the resorption-formation balance in anin vitro3D osteoblast-osteoclast co-culture model of bone
Authors: Remmers Stefan J.A. , van der Heijden Freek C. , de Wildt Bregje W. M. , Ito Keita , Hofmann Sandra
Published: August 2022

The aim of the present study was to further improve anin vitro3D osteoblast (OB) – osteoclast (OC) co-culture model of bone by tuning it towards states of formation, resorption, and equilibrium for their future applications in fundamental research, drug development and personalized medicine. This was achieved by varying culture medium composition and monocyte seeding density, the two external parameters that affect cell behavior the most. Monocytes were seeded at two seeding densities onto 3D silk-fibroin constructs pre-mineralized by MSC-derived OBs and were co-cultured in one of three different media (OC stimulating, Neutral and OB stimulating medium) for three weeks. Histology showed mineralized matrix after co-culture and OC markers in the OC medium group. Scanning Electron Microscopy showed large OC-like cells in the OC medium group. Micro-computed tomography showed increased formation in the OB medium group, equilibrium in the Neutral medium group and resorption in the OC medium group. Culture supernatant samples showed high early TRAP release in the OC medium group, a later and lower release in the Neutral medium group, and almost no release in the OB medium group. Increased monocyte seeding density showed a less-than-proportional increase in TRAP release and resorption in OC medium, while it proportionally increased TRAP release in Neutral medium without affecting net resorption. The 3D OB-OC co-culture model was effectively used to show an excess of mineral deposition using OB medium, resorption using OC medium, or an equilibrium using Neutral medium. All three media applied to the model may have their own distinct applications in fundamental research, drug development, and personalized medicine.
Precision engineering of biological function with large-scale measurements and machine learning
Authors: Tack Drew S. , Tonner Peter D. , Pressman Abe , Olson Nathanael D. , Levy Sasha F. , Romantseva Eugenia F. , Alperovich Nina , Vasilyeva Olga , Ross David
Published: August 2022

As synthetic biology expands and accelerates into real-world applications, methods for quantitatively and precisely engineering biological function become increasingly relevant. This is particularly true for applications that require programmed sensing to dynamically regulate gene expression in response to stimuli. However, few methods have been described that can engineer biological sensing with any level of quantitative precision. Here, we present two complementary methods for precision engineering of genetic sensors:in silicoselection and machine-learning-enabled forward engineering. Both methods use a large-scale genotype-phenotype dataset to identify DNA sequences that encode sensors with quantitatively specified dose response. First, we show thatin silicoselection can be used to engineer sensors with a wide range of dose-response curves. To demonstratein silicoselection for precise, multi-objective engineering, we simultaneously tune a genetic sensor’s sensitivity (EC50) and saturating output to meet quantitative specifications. In addition, we engineer sensors with inverted dose-response and specifiedEC50. Second, we demonstrate a machine-learning-enabled approach to predictively engineer genetic sensors with mutation combinations that are not present in the large-scale dataset. We show that the interpretable machine learning results can be combined with a biophysical model to engineer sensors with improved inverted dose-response curves.