bluuebunny/crossref_metadata_2025 huggingface dataset:
3D rapid printing–assisted individualized total nasal reconstruction based on a database of normal external noses
Authors: Wei Hanxiao , Zhang Aijun , Tao Changbo , Li Xueyang , Li Qiang , Shen Caiqi , Wang Pingping , Jin Peisheng
Published: August 2022

Background:

The nose is an unpaired facial structure. Applying three-dimensional (3D) rapid printing to total nose reconstruction is difficult because no paired structure is available for reference. In this study, 3D laser scanning was used to create a database of normal external noses of Han Chinese individuals in East China to assist in total nose reconstruction.

Methods:

3D laser scanning was used to create a database of normal external noses. Based on this database, patients with nasal reconstruction had their measurements scaled according to head circumference and facial proportions to simulate a new reconstructed shape for the residual nose. The personalized new shape was rapidly 3D-printed for preoperative evaluation and surgical design.

Results:

In the database of external noses, the medium nose type was the main type among Han adults in East China (64.15%), followed by the narrow nose type (26.34%). Quantitative analysis showed that blood loss and operative times were lower in the study group than in the traditional surgery group (P<0.05). A postoperative nasal appearance satisfaction questionnaire showed that the appearance satisfaction rate, daily life measures, and perioperative comfort were significantly better in the study group (P<0.05).

Conclusion:

The database of external noses can bridge 3D printing with total nasal reconstruction. The database has important clinical significance for optimizing the shape of the nose, reducing intraoperative bleed loss, shortening the operative time, and improving patient satisfaction. This study provides new insight for the application of computer-guided 3D scanning and rapid printing in organ reconstruction.
Common bile duct stones management: A network meta-analysis
Authors: Mohseni Shahin , Bass Gary Alan , Forssten Maximilian Peter , Casas Isidro Martínez , Martin Matthew , Davis Kimberly A. , Haut Elliott R. , Sugrue Michael , Kurihara Hayato , Sarani Babak , Cao Yang , Coimbra Raul
Published: August 2022

BACKGROUND

Timely management is critical for treating symptomatic common bile duct (CBD) stones; however, a single optimal management strategy has yet to be defined in the acute care setting. Consequently, this systematic review and network meta-analysis, comparing one-stage (CBD exploration or intraoperative endoscopic retrograde cholangiopancreatography [ERCP] with simultaneous cholecystectomy) and two-stage (precholecystectomy or postcholecystectomy ERCP) procedures, was undertaken with the main outcomes of interest being postprocedural complications and hospital length of stay (LOS).

METHODS

PubMed, SCOPUS, MEDLINE, Embase, and Cochrane Central Register of Controlled Trials were methodically queried for articles from 2010 to 2021. The search terms were a combination of medical subject headings terms and the subsequent terms: gallstone; common bile duct (stone); choledocholithiasis; cholecystitis; endoscopic retrograde cholangiography/ERCP; common bile duct exploration; intraoperative, preoperative, perioperative, and postoperative endoscopic retrograde cholangiography; stone extraction; and one-stage and two-stage procedure. Studies that compared two procedures or more were included, whereas studies not recording complications (bile leak, hemorrhage, pancreatitis, perforation, intra-abdominal infections, and other infections) or LOS were excluded. A network meta-analysis was conducted to compare the four different approaches for managing CBD stones.

RESULTS

A total of 16 studies (8,644 participants) addressing the LOS and 41 studies (19,756 participants) addressing postprocedural complications were included in the analysis. The one-stage approaches were associated with a decrease in LOS compared with the two-stage approaches. Common bile duct exploration demonstrated a lower overall risk of complications compared with preoperative ERCP, but there were no differences in the overall risk of complications in the remaining comparisons. However, differences in specific postprocedural complications were detected between the four different approaches managing CBD stones.

CONCLUSION

This network meta-analysis suggests that both laparoscopic CBD exploration and intraoperative ERCP have equally good outcomes and provide a preferable single-anesthesia patient pathway with a shorter overall length of hospital stay compared with the two-stage approaches.

LEVEL OF EVIDENCE

Systematic Review/Meta Analysis; Level III.
Immunogenicity After a Heterologous BNT262b2 Versus Homologous Booster in Kidney Transplant Recipients Receiving 2 Doses of CoronaVac Vaccine: A Prospective Cohort Study
Authors: Medina-Pestana José , Almeida Viana Laila , Nakamura Monica Rika , Lucena Elizabeth França , Granato Celso Francisco Hernandes , Dreige Yasmim Cardoso , Amorim Laysla Verhalen Pouzo , Chow Charles Yea Zen , Demarchi Foresto Renato , Roberto Requião-Moura Lucio , Tedesco-Silva Helio , Cristelli Marina Pontello
Published: August 2022

Background.

Comparative studies of third heterologous doses following the CoronaVac vaccine against coronavirus disease 2019 (COVID-19) in kidney transplant recipients are lacking.

Methods.

This prospective, single-center cohort study included kidney transplant recipients without previous COVID-19. Patients received a third heterologous (BNT162b2 mRNA) or homologous dose at least 4 wk after 2 doses of the CoronaVac vaccine. Immunoglobulin G antibody response and seroprevalence for neutralizing anti–severe acute respiratory syndrome coronavirus 2 antibodies immediately before and 28 d after third doses were compared between the groups.

Results.

There were 307 patients in the heterologous group and 777 in the homologous group. Patients in the heterologous group were older (54 versus 50 y; P < 0.0001), with a longer time since transplant (11 versus 6 y; P < 0.0001). Immediately before the third dose, immunoglobulin G seroprevalence (36% versus 34%; P = 0.597) and antibody titers (246 versus 268 AU/mL; P = 0.279) were similar. After booster, seroconversion was higher in the heterologous group (49% versus 32%; P < 0.0001), resulting in a higher seroprevalence (67% versus 55%; P = 0.0003); however, 42% of all patients remained seronegative. Antibody titers after booster in seropositive patients were higher in the heterologous group (7771 versus 599 AU/mL; P < 0.0001). These results persisted after adjusting for confounding variables. Lastly, a similar proportion of patients became seropositive for neutralizing antibodies (98% versus 94%; P = 0.098).

Conclusions.

In kidney transplant recipients fully vaccinated with CoronaVac, a third dose with an mRNA vaccine produced a higher seroconversion rate and antibody titers than a third homologous dose. However, both boosters achieved equivalent seroprevalence for neutralizing antibodies. The high proportion of still seronegative patients indicates the need for alternative strategies of protection.
Communicative roots of complex sociality and cognition: neuropsychological mechanisms underpinning the processing of social information
Authors: Roberts Sam G. B. , Dunbar Robin I. M. , Roberts Anna I.
Published: August 2022

Primate social bonds are described as being especially complex in their nature, and primates have unusually large brains for their body size compared to other mammals. Communication in primates has attracted considerable attention because of the important role it plays in social bonding. It has been proposed that differentiated social relationships are cognitively complex because primates need to continuously update their knowledge about different types of social bonds. Therefore, primates infer whether an opportunity for social interaction is rewarding (valuable to individual goals) based on their knowledge of the social relationships of the interactants. However, exposure to distraction and stress has detrimental effects on the dopaminergic system, suggesting that understanding social relationships as rewarding is affected in these conditions. This paper proposes that complex communication evolved to augment the capacity to form social relationships during stress through flexibly modifying intentionality in communication (audience checking, response waiting and elaboration). Intentional communication may upregulate dopamine dynamics to allow recognition that an interaction is rewarding during stress. By examining these associations between complexity of communication and stress, we provide new insights into the cognitive skills involved in forming social bonds in primates and the evolution of communication systems in both primates and humans.

This article is part of the theme issue ‘Cognition, communication and social bonds in primates’.
Socioecological complexity in primate groups and its cognitive correlates
Authors: Shultz Susanne , Dunbar Robin I. M.
Published: August 2022

Characterizing non-human primate social complexity and its cognitive bases has proved challenging. Using principal component analyses, we show that primate social, ecological and reproductive behaviours condense into two components:
socioecological complexity
(including most social and ecological variables) and
reproductive cooperation
(comprising mainly a suite of behaviours associated with pairbonded monogamy). We contextualize these results using a meta-analysis of 44 published analyses of primate brain evolution. These studies yield two main consistent results: cognition, sociality and cooperative behaviours are associated with absolute brain volume, neocortex size and neocortex ratio, whereas diet composition and life history are consistently associated with relative brain size. We use a path analysis to evaluate the causal relationships among these variables, demonstrating that social group size is predicted by the neocortex, whereas ecological traits are predicted by the volume of brain structures other than the neocortex. That a range of social and technical behaviours covary, and are correlated with social group size and brain size, suggests that primate cognition has evolved along a continuum resulting in an increasingly flexible, domain-general capacity to solve a range of socioecological challenges culminating in a capacity for, and reliance on, innovation and social information use in the great apes and humans.

This article is part of the theme issue ‘Cognition, communication and social bonds in primates’.
Coevolution of social and communicative complexity in lemurs
Authors: Fichtel Claudia , Kappeler Peter M.
Published: August 2022

The endemic lemurs of Madagascar (Lemuriformes: Primates) exhibit great social and communicative diversity. Given their independent evolutionary history, lemurs provide an excellent opportunity to identify fundamental principles in the coevolution of social and communicative traits. We conducted comparative phylogenetic analyses to examine patterns of interspecific variation among measures of social complexity and repertoire sizes in the vocal, olfactory and visual modality, while controlling for environmental factors such as habitat and number of sympatric species. We also examined potential trade-offs in signal evolution as well as coevolution between body mass or brain size and communicative complexity. Repertoire sizes in the vocal, olfactory and visual modality correlated positively with group size, but not with environmental factors. Evolutionary changes in social complexity presumably antedated corresponding changes in communicative complexity. There was no trade-off in the evolution of signals in different modalities and neither body mass nor brain size correlated with any repertoire size. Hence, communicative complexity coevolved with social complexity across different modalities, possibly to service social relationships flexibly and effectively in pair- and group-living species. Our analyses shed light on the requirements and adaptive possibilities in the coevolution of core elements of social organization and social structure in a basal primate lineage.

This article is part of the theme issue ‘Cognition, communication and social bonds in primates’.
Thermal imaging reveals social monitoring during social feeding in wild chimpanzees
Authors: Barrault Claire , Soldati Adrian , Hobaiter Catherine , Mugisha Stephen , De Moor Delphine , Zuberbühler Klaus , Dezecache Guillaume
Published: August 2022

Understanding the affective lives of animals has been a long-standing challenge in science. Recent technological progress in infrared thermal imaging has enabled researchers to monitor animals' physiological states in real-time when exposed to ecologically relevant situations, such as feeding in the company of others. During social feeding, an individual's physiological states are likely to vary with the nature of the resource and perceptions of competition. Previous findings in chimpanzees have indicated that events perceived as competitive cause decreases in nasal temperatures, whereas the opposite was observed for cooperative interactions. Here, we tested how food resources and audience structure impacted on how social feeding events were perceived by wild chimpanzees. Overall, we found that nasal temperatures were lower when meat was consumed as compared to figs, consistent with the idea that social feeding on more contested resources is perceived as more dangerous and stressful. Nasal temperatures were significant affected by interactions between food type and audience composition, in particular the number of males, their dominance status, and their social bond status relative to the subject, while no effects for the presence of females were observed. Our findings suggest that male chimpanzees closely monitor and assess their social environment during competitive situations, and that infrared imaging provides an important complement to access psychological processes beyond observable social behaviours.

This article is part of the theme issue ‘Cognition, communication and social bonds in primates’.
Language as a tool for social bonding: evidence from wild chimpanzee gestural, vocal and bimodal signals
Authors: Damjanovic Ljubica , Roberts Sam G. B. , Roberts Anna Ilona
Published: August 2022

The evolution of language has fascinated anthropologists, psychologists and biologists for centuries, seeking to infer language origins from the communication of primates, our closest living relatives. Capacity for intentional signalling is a key feature of transition to language in our hominin ancestors, facilitating complex social dynamics in complex social groups. However whether vocal, gestural and bimodal signals are differentiated according to intentional use and hence complex sociality has not been studied, making unclear the modality of language evolution. We addressed this question in wild chimpanzees. We found that larger social network size was associated with a larger network of gestural but not vocal or bimodal signals. Response waiting was more common in association with gestures than vocalizations, but elaborations were more common in vocal than gestural or bimodal signals. Overall, chimpanzees were more likely to manage weak social bonds through vocalizations, whereas strong social bonds were managed through gestures and bimodal signals. However, when social bonds were weak, gestures accompanied by response waiting were more likely to elicit approaches than vocalizations accompanied by elaboration, which elicited avoidance. This suggests that gestures were the primary modality of language evolution and that the use of more sophisticated gestural signalling led to evolution of complex social groups of hominin ancestors.

This article is part of the theme issue ‘Cognition, communication and social bonds in primates’.
Croceicoccus hydrothermalis sp. nov., isolated from shallow-sea hydrothermal system off Kueishantao Island
Authors: Chen Beihan , Ye Youting , Lin Dan , Zhang Mu , Sun Jia , Tang Kai
Published: August 2022

A Gram-stain-negative, strictly aerobic, non-motile, ovoid or short-rod shaped, orange-pigmented bacterial strain, designated as strain JLT1T, was isolated from seawater of the shallow-sea hydrothermal system, near Kueishantao Islet. Growth was observed at 5–45°C (optimum, 30 °C) and pH 5.0–11.0 (optimum, pH 7.0). The salinity range for growth was 0–12 % (optimum, 2–4 %) (w/v) NaCl. JLT1T contained ubiquinone-10 as the main respiratory quinone. Iso-C12 : 0, summed feature 3 (C16 : 1ω7c/ω6c) and summed feature 8 (C18 : 1ω6c/ω7c) were identified as the major cellular fatty acids. Polar lipids included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, three unidentified phospholipids, eight unidentified glycolipids and an unidentified lipid. The 16S rRNA gene of JLT1T shared the greatest similarity (96.31 %) with those of

Croceicoccus pelagius

Ery9T and

Croceicoccus ponticola

GM-16T. The draft genome size of JLT1T is 3.56 Mb, with 3578 potential genes and a genomic DNA G+C content of 63.24 mol %. Average nucleotide identity and digital DNA–DNA hybridization values of JLT1T compared with

C. pelagius

Ery9T,

C. ponticola

GM-16T,

Croceicoccus sediminis

S2-4-2T,

Croceicoccus mobilis

Ery22T and

Croceicoccus marinus

E4A9T were 74.5, 73.9, 74.4, 74.3 and 74.8 % and 20.6, 19.2, 20.0, 20.5 and 19.8%, respectively. On the basis of these phylogenetic, chemotaxonomic and phenotypic features, JLT1T is concluded to represent a novel species of the genus

Croceicoccus

, for which the name Croceicoccus hydrothermalis sp. nov. is proposed. The type strain is JLT1T (=CGMCC 1.15786T =JCM 31508T).
Anatomical and functional maturation of the mid-gestation human intestine
Authors: Dershowitz Lori B. , Li Li , Pasça Anca M. , Kaltschmidt Julia A.
Published: August 2022

Gastrointestinal (GI) maturation is a key determinant of survival for extremely preterm infants. The enteric nervous system (ENS) controls GI motility, and immature GI motility limits enteral feeding and causes severe health complications.1 Due to the significant challenges in obtaining and studying human fetal tissue, little is known about when the human ENS becomes mature enough to carry out vital functions. Here we define the progressive anatomical maturation of the human fetal ENS and analyze GI motility in the second trimester of in utero development. We identify substantial structural changes in the ENS including the emergence of striped neuronal cytoarchitecture and a shift in the representation of excitatory and inhibitory neurons. We further analyze and pharmacologically manipulate GI motility in freshly collected human fetal intestines, which, to our knowledge, is a first functional analysis of intact human fetal organs ex vivo. We find that the ENS influences GI motility beginning at 21 postconceptional weeks (PCW), the earliest reported evidence of neurogenic GI motility. Our study provides unprecedented insight into human fetal ENS development, foundational knowledge which facilitates comparisons with common animal models to advance translational disease investigations and testing of pharmacological agents to enhance GI motility in prematurity.
Role of the two flagellar stators in swimming motility ofPseudomonas putida
Authors: Pfeifer Veronika , Beier Sönke , Alirezaeizanjani Zahra , Beta Carsten
Published: August 2022

In the soil bacteriumPseudomonas putida, the motor torque for flagellar rotation is generated by the two stators MotAB and MotCD. Here, we construct mutant strains, in which one or both stators are knocked out and investigate their swimming motility in fluids of different viscosity and in heterogeneous structured environments (semisolid agar). Besides bright-field imaging of single cell trajectories and spreading cultures, dual color fluorescence microscopy allows us to quantify the role of the stators in formingP. putida’sthree different swimming modes, where the flagellar bundle pushes, pulls, or wraps around the cell body. The MotAB stator is essential for swimming motility in liquids, while spreading in semisolid agar is not affected. Moreover, if the MotAB stator is knocked out, wrapped mode formation under low viscosity conditions is strongly impaired and only partly restored for increased viscosity and in semisolid agar. In contrast, when the MotCD stator is missing, cells are indistinguishable from the wild-type in fluid experiments, but spread much slower in semisolid agar. Analysis of the microscopic trajectories reveals that the MotCD knockout strain forms sessile clusters thereby reducing the number of motile cells, while the swimming speed is unaffected. Together, both stators ensure a robust wild-type that swims efficiently under different environmental conditions.

IMPORTANCE

Because of its heterogeneous habitat, the soil bacteriumPseudomonas putidaneeds to swim efficiently under very different environmental conditions. In this paper, we knocked out the stators MotAB and MotCD to investigate their impact on swimming motility ofP. putida. While the MotAB stator is crucial for swimming in fluids, in semisolid agar both stators are sufficient to sustain a fast swimming phenotype and increased frequencies of the wrapped mode, which is know to be beneficial for escaping mechanical traps. However, in contrast to the MotAB knock-out, a culture of MotCD knock-out cells spreads much slower in the agar as it forms non-motile clusters that reduce the amount of motile cells.
Who is pregnant? defining real-world data-based pregnancy episodes in the National COVID Cohort Collaborative (N3C)
Authors: Jones Sara , Bradwell Katie R. , Chan Lauren E. , Olson-Chen Courtney , Tarleton Jessica , Wilkins Kenneth J. , Qin Qiuyuan , Faherty Emily Groene , Lau Yan Kwan , Xie Catherine , Kao Yu-Han , Liebman Michael N. , Mariona Federico , Challa Anup , Li Li , Ratcliffe Sarah J. , McMurry Julie A. , Haendel Melissa A. , Patel Rena C. , Hill Elaine L.
Published: August 2022

Objective

To define pregnancy episodes and estimate gestational aging within electronic health record (EHR) data from the National COVID Cohort Collaborative (N3C).

Materials and Methods

We developed a comprehensive approach, named Hierarchy and rule-based pregnancy episode Inference integrated with Pregnancy Progression Signatures (HIPPS) and applied it to EHR data in the N3C from 1 January 2018 to 7 April 2022. HIPPS combines: 1) an extension of a previously published pregnancy episode algorithm, 2) a novel algorithm to detect gestational aging-specific signatures of a progressing pregnancy for further episode support, and 3) pregnancy start date inference. Clinicians performed validation of HIPPS on a subset of episodes. We then generated three types of pregnancy cohorts based on the level of precision for gestational aging and pregnancy outcomes for comparison of COVID-19 and other characteristics.

Results

We identified 628,165 pregnant persons with 816,471 pregnancy episodes, of which 52.3% were live births, 24.4% were other outcomes (stillbirth, ectopic pregnancy, spontaneous abortions), and 23.3% had unknown outcomes. We were able to estimate start dates within one week of precision for 431,173 (52.8%) episodes. 66,019 (8.1%) episodes had incident COVID-19 during pregnancy. Across varying COVID-19 cohorts, patient characteristics were generally similar though pregnancy outcomes differed.

Discussion

HIPPS provides support for pregnancy-related variables based on EHR data for researchers to define pregnancy cohorts. Our approach performed well based on clinician validation.

Conclusion

We have developed a novel and robust approach for inferring pregnancy episodes and gestational aging that addresses data inconsistency and missingness in EHR data.
Nanoblades allow high-level genome editing in organoids
Authors: Tirolle Victor , Krug Adrien , Bokobza Emma , Bulcaen Mattijs , Ensinck Marjolein M. , Geurts Maarten H. , Hendriks Delilah , Vermeulen François , Larbret Frédéric , Gutierrez-Guerrero Alejandra , Medaer Louise , Gijsbers Rik , Mangeot Philippe E. , Clevers Hans , Carlon Marianne S. , Bost Frederic , Verhoeyen Els
Published: August 2022

Genome engineering has become more accessible thanks to the RNA programmable endonucleases such as the CRISPR/Cas9 system. However, using this editing technology in synthetic organs called ‘organoids’ is still very inefficient. This is due to the delivery methods used for the CRISPR-Cas9 machinery, which include electroporation of CRISPR/Cas9 DNA, mRNA or ribonucleoproteins (RNPs) containing the CAS9-gRNA complex. However, these procedures are toxic to some extent for the organoids. Here we describe the use of the ‘Nanoblade’ technology, which outperformed by far knock-out (KO) levels achieved to date by gene editing in murine and human tissue derived organoids. We reached up to 80% of gene KO in organoids after treatment with nanoblades. Indeed, high-level nanoblade-mediated KO for the androgen receptor (AR) encoding gene and the cystic fibrosis transmembrane conductance regulator (CFTR) gene was achieved with single gRNA or dual gRNA containing nanoblades in murine prostate and colon organoids. Likewise, nanoblades achieved high levels of gene editing in human organoids ranging between 20% and 50%.

Most importantly, in contrast to other gene editing methods, this was obtained without toxicity for the organoids. Only four weeks are required to obtain stable gene KO in organoids and nanoblades simplify and allow rapid genome editing in organoids with little to no side-effects such as possible unwanted INDELS in off-target sites.
Factors influencing the effectiveness of nature–based Interventions (NBIs) aimed at improving mental health and wellbeing: Protocol of an umbrella review
Authors: Shrestha Topaz , Chi Cheryl Voon Yi , Cassarino Marica , Foley Sarah , Di Blasi Zelda
Published: August 2022

Several systematic reviews support the use of nature–based interventions (NBIs) as a mechanism of enhancing mental health and wellbeing. However, the available evidence for the effectiveness of these interventions is fragmentary and mixed. The heterogeneity of existing evidence and significant fragmentation of knowledge within the field make it difficult to draw firm conclusions regarding the effectiveness of NBIs. The aim of this mixed method umbrella review is to synthesise evidence on the effectiveness of nature–based interventions through a summative review of existing published systematic reviews and meta-analyses. A systematic search in PsycINFO, PubMed, Greenfile, Web of Science, Embase, Scopus, Academic Search Complete (EBSCO), Environment Complete (EBSCO), Cochrane Library, CINAHL, Health Policy Reference Center and Google Scholar will be performed from inception to May 2022. The search strategy will aim to find published systematic reviews of nature–based interventions (NBIs) where improving health and wellbeing is an explicit goal. This is a mixed method review and systematic reviews with both quantitative and qualitative data synthesis will be considered. Two authors will independently perform the literature search, record screening, data extraction, and quality assessment of each included systematic review and meta-analysis. The individual qualitative and quantitative syntheses will be conducted in parallel and then combined in an overarching narrative synthesis. The quantitative evidence will be used to assess the strength and direction of effect of nature–based interventions on mental health and wellbeing outcomes. Evidence drawn from qualitative studies will be analysed and synthesised to understand the various pathways to engagement, process of involvement and experiential factors which may mediate experiences. The risk of bias of the systematic reviews will be assessed using a 16-item Assessment of Multiple Systematic Reviews 2 (AMSTAR2) checklist. This review is registered on PROSPERO (CRD42022329179).
Modulation of cannabinoid receptor signaling by endocannabinoids
Authors: Kumar Kaavya Krishna , Robertson Michael J. , Thadhani Elina , Wang Haoqing , Suomivuori Carl-Mikael , Powers Alexander S. , Ji Lipin , Nikas Spyros P. , Gerasi Maria , Vemuri Kiran , Dror Ron O. , Inoue Asuka , Makriyannis Alexandros , Skiniotis Georgios , Kobilka Brian
Published: August 2022

Endocannabinoids (eCBs) are endogenous lipid molecules that activate the cannabinoid receptor 1 (CB1), a G protein coupled receptor (GPCR) that signals primarily through the Gi/o family of G proteins to regulate neurotransmitter release. Consequently, CB1 is an important therapeutic target for several neurological disorders. How eCBs interact with CB1 is not known and the downstream signaling they activate is not well understood. In this study we show that eCBs do not activate Gi1 as much as synthetic cannabinoids. To characterize activation of CB1 by eCB, we formed an eCB analogue-bound (AMG315) CB1-Gi signaling complex for structural studies. The structure reveals differences in the orthosteric ligand binding pocket not seen in the previous CB1 structures, providing insights into the structural determinants of ligand efficacy. In combination with signaling and simulation data, this study provides mechanistic insights into CB1 activation by different classes of ligands, and sheds light on the G protein preferences between endogenous and exogenous ligands.
A Universal Language for Finding Mass Spectrometry Data Patterns
Authors: Jarmusch Alan K. , Aron Allegra T. , Petras Daniel , Phelan Vanessa V. , Bittremieux Wout , Acharya Deepa D. , Ahmed Mohammed M. A. , Bauermeister Anelize , Bertin Matthew J. , Boudreau Paul D. , Borges Ricardo M. , Bowen Benjamin P. , Brown Christopher J. , Chagas Fernanda O. , Clevenger Kenneth D. , Correia Mario S. P. , Crandall William J. , Crüsemann Max , Damiani Tito , Fiehn Oliver , Garg Neha , Gerwick William H , Gilbert Jeffrey R. , Globisch Daniel , Gomes Paulo Wender P. , Heuckeroth Steffen , James C. Andrew , Jarmusch Scott A. , Kakhkhorov Sarvar A. , Kang Kyo Bin , Kersten Roland D , Kim Hyunwoo , Kirk Riley D. , Kohlbacher Oliver , Kontou Eftychia E. , Liu Ken , Lizama-Chamu Itzel , Luu Gordon T. , Knaan Tal Luzzatto , Marty Michael T. , McAvoy Andrew C. , McCall Laura-Isobel , Mohamed Osama G. , Nahor Omri , Niedermeyer Timo H.J. , Northen Trent R. , Overdahl Kirsten E. , Pluskal Tomáš , Rainer Johannes , Reher Raphael , Rodriguez Elys , Sachsenberg Timo T. , Sanchez Laura M. , Schmid Robin , Stevens Cole , Tian Zhenyu , Tripathi Ashootosh , Tsugawa Hiroshi , Nishida Kozo , Matsuzawa Yuki , van der Hooft Justin J.J. , Vicini Andrea , Walter Axel , Weber Tilmann , Xiong Quanbo , Xu Tao , Zhao Haoqi Nina , Dorrestein Pieter C. , Wang Mingxun
Published: August 2022

Even though raw mass spectrometry data is information rich, the vast majority of the data is underutilized. The ability to interrogate these rich datasets is handicapped by the limited capability and flexibility of existing software. We introduce the Mass Spec Query Language (MassQL) that addresses these issues by enabling an expressive set of mass spectrometry patterns to be queried directly from raw data. MassQL is an open-source mass spectrometry query language for flexible and mass spectrometer manufacturer-independent mining of MS data. We envision the flexibility, scalability, and ease of use of MassQL will empower the mass spectrometry community to take fuller advantage of their mass spectrometry data and accelerate discoveries.
“Multiphoton holographic photostimulation induces potassium-dependent spike silencing in label-free mouse cortex in vivo”
Authors: Papaioannou Stylianos , Zakrisson Johan , Kuznetsova Tatiana , Medini Paolo
Published: August 2022

Multiphoton microscopy allows measurement of network activity as well as the manipulation of cell type specific or functionally identified neuronal subpopulations with optogenetic holographic stimulation. When neurons co-express an activity reporter (e.g. calcium or voltage-sensitive indicators) and an (excitatory or inhibitory) opsin, such “all optical” interrogation approaches in vivo allows to draw causal links between function of cell-type specific microcircuits and behaviour. However, the net effects of near-infrared stimulation on network activity per se remain to be adequately investigated in vivo. Here we show that multicell holographic photostimulation with near-infrared radiation with total powers to sample used in current literature halves the spike rate of the non-illuminated neurons in label-free mouse cortex in vivo. The effect is not mediated by GABA release, but depends on NIR-dependent gating of potassium channels as it is absent when neurons are intracellularly perfused with the broad potassium channel blocker cesium ions, and are possibly mediated by heating. The phenomenon may contribute to set an upper limit to holographic photostimulation efficacy, calls for the need to control the effects of holographic stimulation protocols per se in label free preparations, and might be of relevance to interpret the therapeutical effects on infrared stimulation in psychiatry and neurology.

Highlights

- Holographic multi-cell, infrared illumination halves spike rates of no-target neurons

- The effect happens with total powers to sample used in “all-optical” literature

- Infrared-driven spike killing is GABA-independent but depends on potassium channels
Object representation in a gravitational reference frame
Authors: Emonds Alexandriya M.X. , Srinath Ramanujan , Nielsen Kristina J. , Connor Charles E.
Published: August 2022

When your head tilts laterally, as in sports, reaching, and resting, your eyes counterrotate less than 20%, and thus eye images rotate, over a total range of about 180°. Yet, the world appears stable and vision remains normal. We discovered a neural strategy for rotational stability in anterior inferotemporal cortex (IT), the final stage of object vision in primates. We measured object orientation tuning of IT neurons in macaque monkeys tilted +25 and –25° laterally, producing ∼40° difference in retinal image orientation. Among IT neurons with consistent object orientation tuning, 63% remained stable with respect to gravity across tilts. Gravitational tuning depended on vestibular/somatosensory but also visual cues, consistent with previous evidence that IT processes scene cues for gravity’s orientation. In addition to stability across image rotations, an internal gravitational reference frame is important for physical understanding of a world where object position, posture, structure, shape, movement, and behavior interact critically with gravity.
Pupil dynamics-derived sleep stage classification of a head-fixed mouse using a recurrent neural network
Authors: Kobayashi Goh , Tanaka Kenji F. , Takata Norio
Published: August 2022

The standard method for sleep state classification is thresholding amplitudes of electroencephalography (EEG) and electromyography (EMG), followed by an expert’s manual correction. Although popular, the method entails some shortcomings: 1) the time-consuming manual correction by human experts is sometimes a bottleneck hindering sleep studies; 2) EEG electrodes on the skull interfere with wide-field imaging of the cortical activity of a head-fixed mouse under a microscope; 3) invasive surgery to fix the electrodes on the thin skull of a mouse risks brain tissue injury; and 4) metal electrodes for EEG and EMG are difficult to apply to some experiment apparatus such as that for functional magnetic resonance imaging. To overcome these shortcomings, we propose a pupil dynamics-based vigilance state classification for a head-fixed mouse using a long short-term memory (LSTM) model, a variant of recurrent neural networks, for multi-class labeling of NREM, REM, and WAKE states. For supervisory hypnography, EEG and EMG recording were performed for a head-fixed mouse, combined with left eye pupillometry using a USB camera and a markerless tracking toolbox, DeepLabCut. Our open-source LSTM model with feature inputs of pupil diameter, location, velocity, and eyelid opening for 10 s at a 10 Hz sampling rate achieved vigilance state estimation with a higher classification performance (macro F1 score, 0.77; accuracy, 86%) than a feed forward neural network. Findings from diverse pupillary dynamics implied subdivision of a vigilance state defined by EEG and EMG. Pupil dynamics-based hypnography can expand the scope of alternatives for sleep stage scoring of head fixed mice.
Multiple pathways for SARS-CoV-2 resistance to nirmatrelvir
Authors: Iketani Sho , Mohri Hiroshi , Culbertson Bruce , Hong Seo Jung , Duan Yinkai , Luck Maria I. , Annavajhala Medini K. , Guo Yicheng , Sheng Zizhang , Uhlemann Anne-Catrin , Goff Stephen P. , Sabo Yosef , Yang Haitao , Chavez Alejandro , Ho David D.
Published: August 2022

Nirmatrelvir, an oral antiviral targeting the 3CL protease of SARS-CoV-2, has been demonstrated to be clinically useful in reducing hospitalization or death due to COVID-191,2. However, as SARS-CoV-2 has evolved to become resistant to other therapeutic modalities3–9, there is a concern that the same could occur for nirmatrelvir. Here, we have examined this possibility by in vitro passaging of SARS-CoV-2 in increasing concentrations of nirmatrelvir using two independent approaches, including one on a large scale in 480 wells. Indeed, highly resistant viruses emerged from both, and their sequences revealed a multitude of 3CL protease mutations. In the experiment done at a larger scale with many replicates, 53 independent viral lineages were selected with mutations observed at 23 different residues of the enzyme. Yet, several common mutational pathways to nirmatrelvir resistance were preferred, with a majority of the viruses descending from T21I, P252L, or T304I as precursor mutations. Construction and analysis of 13 recombinant SARS-CoV-2 clones, each containing a unique mutation or a combination of mutations showed that the above precursor mutations only mediated low-level resistance, whereas greater resistance required accumulation of additional mutations. E166V mutation conferred the strongest resistance (~100-fold), but this mutation resulted in a loss of viral replicative fitness that was restored by compensatory changes such as L50F and T21I. Structural explanations are discussed for some of the mutations that are proximal to the drug-binding site, as well as cross-resistance or lack thereof to ensitrelvir, another clinically important 3CL protease inhibitor. Our findings indicate that SARS-CoV-2 resistance to nirmatrelvir does readily arise via multiple pathways in vitro, and the specific mutations observed herein form a strong foundation from which to study the mechanism of resistance in detail and to inform the design of next generation protease inhibitors.
A benchmark study of protein folding algorithms on nanobodies
Authors: Liang Shibo , Liang Ziquan , Wu Zecheng , Huang Feijuan , Wang Xu , Tan Zihao , He Rui , Lu Zeyi , Cai Yuanzhe , Huang Bingding , Wang Xin
Published: August 2022

Nanobodies, also known as single domain or VHH antibodies, are the artificial recombinant variable domains of heavy-chain-only antibodies. Nanobodies have many unique properties, including small size, good solubility, superior stability, rapid clearance from blood, and deep tissue penetration. Therefore, nanobodies have emerged as promising tools for diagnosing and treating diseases. In recent years, many deep-learning-based protein structure prediction methods have emerged that require only protein sequences as input to obtain highly-credible 3D protein structures. Among them, AlphaFold2, RoseTTAFold, DeepAb, NanoNet, and tFold performed excellently in protein prediction or antibody/nanobody prediction. In this study, we selected 60 nanobody samples with known experimental 3D structures in the Protein Data Bank (PDB). Next, we predicted their 3D structures using these five prediction algorithms from only their 2D amino acid sequences. Then, we individually compared the predicted and experimental structures. Finally, the results are analyzed and discussed.
Functional interplay between SWI/SNF complexes underlies BRD9 dependency in SMARCB1-mutant cancers
Authors: Mobley Robert J. , Myers Jacquelyn A. , Wills Kendall M. , Malone Hayden A. , Manzano Trishabelle I. , Partridge Janet F. , Roberts Charles W. M.
Published: August 2022

Genes encoding subunits of SWI/SNF (BAF) chromatin remodeling complexes are mutated in >20% of cancers. SWI/SNF complexes exist in three distinct families that each contribute to regulation of transcription, although the functional interactions between the families are not well understood. Rhabdoid tumors constitute an informative model system as these highly aggressive cancers are driven by inactivation of a single SWI/SNF subunit, SMARCB1, which is present in two SWI/SNF families (cBAF and PBAF) but not in the third (GBAF/ncBAF). We and others have shown that BRD9, a therapeutically targetable member of ncBAF, is essential specifically in SMARCB1-deficient cancers, suggesting key functional relationships between SMARCB1-containing complexes and BRD9/ncBAF. However, the mechanistic underpinnings of these relationships are poorly understood. Here, we demonstrate that genomic binding of BRD9 is largely dependent upon SMARCB1 such that the absence of SMARCB1 results in significantly reduced BRD9 binding. At select sites, however, we show that SMARCB1-loss results in gain of BRD9 binding and BRD9-dependent accessibility. We find that this gain is associated with expression of genes promoting cell migration. Our results define relationships between SWI/SNF complex families, elucidate mechanisms by which SMARCB1 loss drives oncogenesis, and provide mechanistic insight into the synthetic-lethal relationship between SMARCB1 and BRD9.
High-Voltage Biomolecular Sensing Using a Bacteriophage Portal Protein Covalently Immobilized Within a Solid-State Nanopore
Authors: Mojtabavi Mehrnaz , Greive Sandra J. , Antson Alfred A. , Wanunu Meni
Published: August 2022

The application of nanopores as label-free, single-molecule biosensors for electrical or optical probing of structural features in biomolecules has been widely explored. While biological nanopores (membrane proteins and bacteriophage portal proteins) and solid-state nanopores (thin films and two-dimensional materials) have been extensively employed, the third class of nanopores known as hybrid nanopores, where an artificial membrane substitutes the organic support membrane of proteins, has been only sparsely studied, due to challenges in implementation. G20c portal protein contains a natural DNA pore that is used by viruses for filling their capsid with viral genomic DNA. We have previously developed a lipid-free hybrid nanopore by “corking” the G20c portal protein into a SiNx nanopore. Herein, we demonstrate that through chemical functionalization of the synthetic nanopore, covalent linkage between the solid-state pore and the G20c portal protein considerably improves the hybrid pore stability, lifetime, and voltage resilience. Moreover, we demonstrate electric-field-driven and motor protein-mediated transport of DNA molecules through this hybrid pore. Our integrated protein/solid-state hybrid nanopore can serve as a robust and durable framework for sensing and sequencing at high voltages, potentially providing higher resolution, higher signal-to-noise ratio, and higher throughput compared to the more conventional membrane-embedded protein platforms.
Multiplexed and millimeter-scale fluorescence nanoscopy of cells and tissue sections via prism-illumination and microfluidics-enhanced DNA-PAINT
Authors: Rames Matthew J , Kenison John , Heineck Daniel , Civitci Fehmi , Szczepaniak Malwina , Zheng Ting , Shangguan Julia , Zhang Yujia , Esener Sadik , Nan Xiaolin
Published: August 2022

Fluorescence nanoscopy has become increasingly powerful for biomedical research, but it has historically afforded a small field-of-view (FOV) around 50 µm x 50 µm at once and more recently up to ~200 µm x 200 µm. Efforts to further increase the FOV in fluorescence nanoscopy have thus far relied on the use of fabricated waveguide substrates, adding cost and sample constraints on the applications. Here we report PRism-Illumination and Microfluidics-Enhanced DNA-PAINT (PRIME-PAINT) for multiplexed fluorescence nanoscopy across millimeter-scale FOVs. Built upon the well-established prism-type total internal reflection microscopy, PRIME-PAINT achieves robust single-molecule localization with up to ~520 µm x 520 µm single FOVs and 25-40 nm lateral resolutions. Through stitching, nanoscopic imaging over mm2sample areas can be completed in as little as 40 minutes per target. An on-stage microfluidics chamber facilitates probe exchange for multiplexing and enhances image quality particularly for formalin-fixed paraffin-embedded (FFPE) tissue sections. We demonstrate the utility of PRIME-PAINT by analyzing ~106caveolae structures in ~1,000 cells and imaging entire pancreatic cancer lesions from patient tissue biopsies. By imaging from nanometers to millimeters with multiplexity and broad sample compatibility, PRIME-PAINT will be useful for building multiscale, Google-Earth-like views of biological systems.
Use of Ganoderma lucidum grown on agricultural waste to remove antibiotics from water
Authors: Salandez Vanessa , Emami Shiva , Taha Ameer Y. , Saponara Valeria La
Published: August 2022

Antibiotic effluents from farming and medical applications into waterways pose serious risks for antibiotic drug resistance, promoting a need for effective strategies of removal from the environment. This experiment uses a novel mycoremediation approach to remove antibiotic contamination in synthetic wastewater. A white rot fungus, Ganoderma lucidum, was grown on biomass formed by agricultural waste from California (almond shells, fava bean stalks). Water containing or lacking Ganoderma lucidum was inoculated with twenty antibiotics from six different classes. The extent of antibiotic removal was measured at baseline and after 3 days with ultra-high pressure liquid chromatography coupled to tandem mass-spectrometry. In water containing Ganoderma lucidum mycelial biomass, we found a significant reduction compared to the baseline of the concentration in six (three quinolones and three sulfonamides) out of twenty tested antibiotics by Day 3, with normalized changes ranging from −24.4% to −82.4%. The mycelial biomass was particularly effective in reducing the presence of three quinolone antibiotics, a class of highly used antibiotics recalcitrant to processes in wastewater treatment plants. Our findings provide a novel approach to degrade certain antibiotics from water. This strategy could become a key component of removing antibiotic pollution using agricultural waste as part of the solution.
Structure of the Monkeypox profilin-like protein A42R reveals potential function differences from cellular profilins
Authors: Minasov George , Inniss Nicole L. , Shuvalova Ludmilla , Anderson Wayne F. , Satchell Karla J. F.
Published: August 2022

The infectious disease human monkeypox is spreading rapidly in 2022 causing a global health crisis. The genomics of the monkeypox virus (MPXV) have been extensively analyzed and reported, although little is known about the virus-encoded proteome. In particular, there is almost no structure information about MPXV proteins, other than computational models. Here we report a 1.52 Å x-ray structure of the MPXV protein A42R, the only MPXV-encoded protein with a known structure. This protein shows sequence similarity to profilins, which are cellular proteins known to function in regulation of actin cytoskeletal assembly. However, structural comparison of the A42R with known members of the profilin family reveals critical differences that support prior biochemical findings that this protein only weakly binds actin and does not bind poly(L-proline). In addition, the analysis suggests that this protein may have distinct interactions with phosphatidylinositol lipids. Overall, our data suggest that the role of A42R in replication of orthopoxviruses may not be easily determined by comparison to cellular profilins. Further, our findings support a need for increased efforts to determine high-resolution structures of other MPXV proteins to inform physiological studies of the poxvirus infection cycle and to reveal potential new strategies to combat human monkeypox should the infection become more common in the future.