bluuebunny/crossref_metadata_2025 huggingface dataset:
Induction Immunosuppression Does Not Worsen Tumor Recurrence After Liver Transplantation for Hepatocellular Carcinoma
Authors: Durkin Claire , Schaubel Douglas E. , Xu Yuwen , Mahmud Nadim , Kaplan David E. , Abt Peter L. , Bittermann Therese
Published: January 2023

Background.

Prior studies are inconsistent regarding the impact of antibody induction therapy on outcomes after liver transplantation (LT) for hepatocellular carcinoma (HCC).

Methods.

Adults transplanted with HCC exception priority were identified from February 27, 2002, to March 31, 2019, using the United Network for Organ Sharing database. Time-to-event analyses evaluated the association of antibody induction therapy (none, nondepleting induction [NDI], depleting induction [DI]) with overall post-LT patient survival and HCC recurrence. Separate multivariable models adjusted for tumor characteristics on either last exception or on explant. The interaction of induction and maintenance regimen at LT discharge was investigated.

Results.

Among 22 535 LTs for HCC, 17 688 (78.48%) received no antibody induction, 2984 (13.24%) NDI, and 1863 (8.27%) DI. Minimal differences in patient and tumor characteristics were noted between induction groups, and there was significant center variability in practices. NDI was associated with improved survival, particularly when combined with a calcineurin inhibitor (CNI) and antimetabolite (hazard ratio [HR] 0.73 versus no induction plus 3-drug therapy in the last exception model [P < 0.001]; HR 0.64 in the explant model [P = 0.011]). The combination of DI with CNI alone was also protective (HR 0.43; P = 0.003). Neither NDI nor DI was associated with tumor recurrence (all P > 0.1). However, increased HCC recurrence was observed with no induction plus CNI monotherapy (HR 1.47, P = 0.019; versus no induction plus 3-drug therapy).

Conclusions.

In conclusion, induction immunosuppression was not associated with worse post-LT outcomes in patients transplanted with HCC exception priority. An improvement in survival was possibly observed with NDI.
Seasonal habitat preference and foraging behaviour of post-moult Weddell seals in the western Ross Sea
Authors: Goetz Kimberly T. , Dinniman Michael S. , Hückstädt Luis A. , Robinson Patrick W. , Shero Michelle R. , Burns Jennifer M. , Hofmann Eileen E. , Stammerjohn Sharon E. , Hazen Elliott L. , Ainley David G. , Costa Daniel P.
Published: January 2023

Weddell seals (Leptonychotes weddellii) are important predators in the Southern Ocean and are among the best-studied pinnipeds on Earth, yet much still needs to be learned about their year-round movements and foraging behaviour. Using biologgers, we tagged 62 post-moult Weddell seals in McMurdo Sound and vicinity between 2010 and 2012. Generalized additive mixed models were used to (i) explain and predict the probability of seal presence and foraging behaviour from eight environmental variables, and (ii) examine foraging behaviour in relation to dive metrics. Foraging probability was highest in winter and lowest in summer, and foraging occurred mostly in the water column or just above the bottom; across all seasons, seals preferentially exploited the shallow banks and deeper troughs of the Ross Sea, the latter providing a pathway for Circumpolar Deep Water to flow onto the shelf. In addition, the probability of Weddell seal occurrence and foraging increased with increasing bathymetric slope and where water depth was typically less than 600 m. Although the probability of occurrence was higher closer to the shelf break, foraging was higher in areas closer to shore and over banks. This study highlights the importance of overwinter foraging for recouping body mass lost during the previous summer.
Environmental control of social goals: using Pavlovian-to-instrumental transfer to test cue-based pro-self and pro-social outcome responses
Authors: Qin Kaiyang , Marien Hans , Custers Ruud , Aarts Henk
Published: January 2023

A large amount of literature demonstrates that social behaviour can be triggered by environmental cues. A long-standing debate involves the question of whether such stimuli trigger behaviour directly (i.e. habits) or whether these effects mediate goals. As studies on automatic goal pursuit typically use real-world cues that are already associated with the behaviour and potentially the goal, it is impossible to make strong claims about the nature of the effects. In the present paper, we use a paradigm inspired by the Pavlovian-to-instrumental transfer (PIT) literature to examine how the environment can trigger goal-directed behaviour. Building on the essence of pro-self and pro-social motives in humans, two experiments explored the PIT effect when the outcomes were framed in terms of self- versus other-interest. Participants performed actions to earn money for themselves or a charity. Each outcome was linked to a different cue. The results showed that a cue predictive of self-interest outcomes facilitated responses instrumental in gaining the outcome, while such specific PIT effect for other-interest outcomes only emerged when participants were free to donate the money. We briefly discuss these findings reflecting on whether the PIT effect in our paradigm is indeed sensitive to the value of social goals.
The credibility crisis and democratic governance: how to reform university governance to be compatible with the nature of science
Authors: Dienes Zoltan
Published: January 2023

To address the credibility crisis facing many disciplines, change is needed at the institutional level. Science will only function optimally if the culture by which it is governed becomes aligned with the way of thinking required in science itself. The paper suggests a series of graduated reforms to university governance, to radically reform the operation of universities. The reforms are based on existing established open democratic practices. The aim is for universities to become consistent with the flourishing of science and research more generally.
Removal of As(V) from aqueous solution using modified Fe
3
O
4
nanoparticles
Authors: Zhao Yuling , Shi Hao , Du Ze , Zhou Jinlong , Yang Fangyuan
Published: January 2023

The removal of arsenic contamination from the aqueous environment is of great importance in the conservation of the Earth's water resources, and surfactants are a promising material used to modify magnetic nanoparticles to improve adsorption properties. Therefore, it is important to develop efficient and selective adsorbents for arsenic. Surface modification of Fe
3
O
4
was carried out using anionic, cationic and zwitterionic surfactants to obtain composite Fe
3
O
4
@SDS, Fe
3
O
4
@CTAB, Fe
3
O
4
@SNC 16 and Fe
3
O
4
@NPC 16 (collectively referred to as Fe
3
O
4
@surfactants). The synthesized composite Fe
3
O
4
@surfactants magnetic nanoparticles were characterized by XRD, TEM and FTIR. The As(V) removal characteristics of the composite magnetic nanoparticles from the aqueous solution were evaluated by adsorption batch experiments which indicated the possibility of effective application of the surfactant-modified Fe
3
O
4
magnetic nanoparticles for the removal of As(V) from aqueous solution. The adsorption equilibrium of the composites was reached in 30 min and the kinetic data followed the pseudo-second-order model. Langmuir equation could represent the adsorption isotherm data very well. Moreover, under the identical conditions, Fe
3
O
4
@CTAB showed maximum capacity of adsorption for As(V) (55.671 mg g
−1
), with its removal efficiency being much higher than that of the other composites. In addition, the Fe
3
O
4
@surfactants composite magnetic nanoparticles retained 93.5% of its initial arsenic removal efficiency even after re-using it five times. The mechanism of arsenic adsorption by Fe
3
O
4
@surfactants composite magnetic nanoparticles was proved to be complexation via electrostatic attraction, which was mainly innersphere in nature.
The relationship between psycho-environmental characteristics and wellbeing in non-spending players of certain mobile games
Authors: Petrovskaya Elena , Zendle David
Published: January 2023

Revenue generation in modern digital games is often dependent on in-game continuous player spending. This brings concerns that games may be including features which drive player spending in potentially harmful ways. Moreover, it is unknown what types of individuals may be vulnerable to these design-driven harms. We used player-donated, objective data of playtime and in-game spending from a sample of 295 players of games previously identified as ‘designed to drive spending’. We combined this with psycho-environmental characteristics and wellbeing measures administered to the players. Quantile regression analyses did not show an interaction between player characteristics and playtime/spend as predictors of wellbeing outcomes; nor did we find a difference in wellbeing between players of these games and games with alternative monetization models. This is discussed in light of a low proportion of spenders in the sample, which may affect results pertaining to the moderating role of spend. However, it suggests that while design features in games aiming to drive player spend may be unethical and problematic, they may not necessarily cause harm to the normative player.
Refractory Giardiasis in a Child with Steroid Resistant Nephrotic Syndrome
Authors: Kalita Jitu Mani , Sharma Kirtika , Mohammad Naila , Tak Vibhor , Mittal Aliza , Nag Vijaya Lakshmi
Published: January 2023

Giardiasis is an infection of the small intestine caused by the protozoan parasite Giardia intestinalis and one of the most common parasitic intestinal diseases in humans worldwide. It mainly manifests as a self-limited illness in case of immunocompetent patients and don’t usually require any treatment. However, immunodeficiency is a risk factor for the onset of severe Giardia infection. In this report, a case of recurrent giardiasis refractory to nitroimidazole therapy is presented. A 7-year-old male patient with steroid resistant nephrotic syndrome came to our hospital because of chronic diarrhoea. Patient was on immunosuppressive therapy for long duration. Microscopic examination of stool showed a significant number of trophozoites and cysts of Giardia intestinalis . Treatment with metronidazole for longer duration than recommended has failed to clear the parasite in the present case.
Acute polymicrobial airway infections: analysis in cystic fibrosis mice
Authors: Lindgren Natalie R. , McDaniel Melissa S. , Novak Lea , Swords W. Edward
Published: January 2023

Cystic fibrosis (CF) is a genetic disorder affecting epithelial ion transport, which among other impacts results in defective mucociliary clearance and innate defenses in the respiratory tract. Consequently, people with CF experience lifelong infections of the respiratory mucosa that are chronic and polymicrobial in nature. Young children with CF are initially colonized by opportunists like nontypeable

Haemophilus influenzae

(NTHi), which normally resides within the microbiome of the nasopharynx and upper airways and can also cause infections of the respiratory mucosa that include bronchitis and otitis media. NTHi is typically supplanted by other microbes as patients age; for example, people with CF are often chronically infected with mucoid strains of

Pseudomonas aeruginosa

, which prior work in our laboratory has shown to promote colonization and persistence by other opportunists that include

Stenotrophomonas maltophilia

. Our previous work has shown that polymicrobial infection impacts host colonization and persistence of incoming microbes via diverse mechanisms that include priming of host immunity that can promote microbial clearance, and cooperativity within polymicrobial biofilms, which can promote persistence. In infection studies with BALB/c Cftrtm1UNC mice, results showed, as previously observed for WT BALB/c mice, preceding infection with NTHi decreased colonization and persistence by

P. aeruginosa

. Likewise, polymicrobial infection of BALB/c Cftrtm1UNC and C57BL/6 Cftrtm1UncTg(FABPhCFTR)1Jaw/J mice showed correlation between

S. maltophilia

and

P. aeruginosa

, with increased bacterial colonization and lung pathology. Based on these results, we conclude that our previous observations regarding polymicrobial infections with CF opportunists in WT mice are also validated using CF mice.
Shift from a Simplified to Complex Gut Microbiota Reduces Adenoma Burden in a Preclinical Rat Model of Colon Cancer
Authors: Busi Susheel Bhanu , Davis Daniel , Moskowitz Jacob , Amos-Landgraf James
Published: January 2023

Specific bacterial taxa in the gastrointestinal tract have been strongly associated with cases of colorectal cancer (CRC) cancer in familial adenomatous polyposis and spontaneous disease cases in humans. This has been recapitulated in animal models of CRC with positive correlations with many commensals and pathogens. However, many of these studies are performed either in germ-free animals or employ an antibiotic regime, overlooking the complex interactions of the commensals within the colon. To simplify the challenges associated with the complexity of the microbiota in the GI tract we established the Pirc rat model of colon cancer on an Altered Schaedler Flora (ASF) gut microbiota (GM), maintained in a barrier room. To elucidate the role of the simplified (ASF) and conventional GMs on disease susceptibility, We conventionalized ASF Pirc littermates. We found that the conventionalized F1 rats had increased microbial diversity and decreased colonic adenoma multiplicity. Our findings show that the complexity and the interactions of the GM community and not aFirmicutestoBacteroidetesratio are an important factor affecting disease susceptibility.
Survey of National Practices for Postgraduate Year Two Critical Care and Emergency Medicine Pharmacy Residency Emergency Response Training
Authors: Philips Eli , Cycz Clare , Liu Ji T. , Eche I. Mary , Wong Adrian
Published: January 2023

Introduction

Medical emergency response within the hospital involves an interdisciplinary team, including pharmacists. Pharmacist involvement in these teams has increased over time due to published benefits of their involvement. Development of emergency response skills may start during pharmacy residency, although limited data suggest how this is best implemented.

Objectives

Limited data evaluate post-graduate year 2 (PGY2) pharmacy resident training for emergency response, as well as PGY2 program values for this in screening/ranking candidates. A survey may help PGY2 programs improve their own programs and allow post-graduate year one (PGY1) pharmacy residents to identify residency programs that are a good fit for their career goals.

Methods

A list of PGY2 critical care (CC) and emergency medicine (EM) programs were identified. The questionnaire included program demographics, characteristics of PGY2 emergency response training, and PGY2 residency program values of PGY1 emergency response exposure for screening and ranking applicants for their programs. A Fisher’s exact test was used to compare differences between CC and EM programs for these outcomes.

Results

A total of 85 complete responses were analyzed (response rate: CC = 36.4%; EM = 32.1%). Emergency response training was often with both core and longitudinal experiences (72.9%), although differed by type of programs (p<0.001). Both CC and EM programs considered PGY1 pharmacy resident exposure to emergency response in screening candidates (33.9% and 57.7%, respectively), as well as ranking candidates (22% and 38.5%, respectively). For CC programs, both Advanced Cardiovascular Life Support certification and quantity of PGY1 emergency response ranked as the most important characteristics, while EM programs ranked quantity as the most important.

Conclusion

The results of this survey indicate heterogeneity in PGY2 CC and EM emergency response training. PGY1 applicants for these programs should consider their experience with emergency response as a factor in identifying an appropriate program for their initial training.
Impact of Perioperative Dexamethasone in the Context of Neurosurgical Brain Metastasis Resection
Authors: Wasilewski David , Bukatz Jan , Peukert Ricarda , Shaked Zoe , Poeser Paul , Karbe Anna-Gila , Anna-Trelinska-Finger  , Jelgersma Claudius , Früh Anton , Raspe Matthias , Radbruch Helena , Capper David , Schlaak Max , Thuss-Patience Peter , Bischoff Philip , Horst David , Krenzke Marcel , Xu Ran , Ehret Felix , Kaul David , Misch Martin , Bullinger Lars , Frost Nikolaj , Vajkoczy Peter , Onken Julia
Published: January 2023

Background

Patients with brain metastases that undergo brain metastasis resection regularly receive perioperative dexamethasone. We sought to evaluate whether perioperative dexamethasone in brain metastases is linked to survival.

Methods

Retrospective data on perioperative dexamethasone dosage in resected brain metastasis patients at three hospital sites of the Charité from 2010-2022 were collected. Cut-off values for cumulative perioperative dexamethasone dose as a continuous predictor variable for survival were determined using maximally selected rank statistics. Patients were dichotomized based on determined cut-offs of cumulative dexamethasone (pre-operative: < 40 mg vs ≥40 mg; post-operative: < 180 mg vs ≥ 180 mg) and pre- and postoperative: < 281 mg vs ≥ 281 mg). Medical records included baseline demographic, radiological, histopathological and treatment-related characteristics. Based on cut-off values for dexamethasone downstream statistical analyses included Kaplan-Meier, Cox proportional hazards regression for overall survival with adjustment for potential confounders including age, gender, Karnofsky performance status and presence of extracranial metastasis via propensity score matching.

Results

539 patients were included. Median follow-up time was 58,97 months. After adjusting for age, gender, Karnofsky performance status and presence of extracranial metastasis patients with higher cumulative perioperative dexamethasone (≥281 mg) showed shorter survival (HR: 1.47 (1.20-1.80, p<0.001) as compared to patients with lower cumulative doses (<281 mg). This effect remained significant after correction for patients that died within 2 months after resection and for patients with KPS below 50% and, independently from this approach performing propensity score matched-based analysis of the total cohort of patients, respectively.

Conclusion

Cumulative perioperative dexamethasone is associated with decreased survival in the context of brain metastasis resection. Strict dosage, down taper or methods reducing corticosteroid dependency should be regularly evaluated in clinical practice in patients with brain metastases.
Clinical characteristics and results of patients who underwent minor salivary gland biopsy with the suspicion of Sjogren syndrome
Authors: Kutluk Oznur , Cay Hasan Fatih
Published: January 2023

OBJECTIVES

To evaluate the value and accuracy of biopsy in diagnosing Sjogren’s syndrome (SS) by evaluating the results of patients who underwent mınor salivary gland biopsy (MSGB) with the suspicion of SS.

MATERIALS and METHODS

The study was planned with retrospective assessment of 127 patients with biopsy performed for SS diagnosis. The clinical and laboratory characteristics of the patients who underwent MSGB were recorded from their files. SS diagnosis was placed using the rating system according to 2016 ACR/EULAR classification criteria or based on expert opinion.

RESULTS

113 patients met the ınclusion criteria. 72 patients diagnosed with SS. 56 were diagnosed according to the 2016 ACR/EULAR classification criteria and 16 were diagnosed according to expert opinion. There were 57 patients with positive MSGB outcome (55 SS, 2 not SS). There were 56 patients with MSGB negative outcome (17 SS, 39 not SS). The sensitivity of MSGB for SS diagnosis was 76.4%, and specificity was 95.1%.

CONCLUSION

All of our patients had antibody test results, but the number of objective tests included in the classification criteria such as salivary flow rate and Schirmer was low. Although MSGB is considered an invasive technique, it appears to be a safe technique as long as it is performed by experienced professionals. It will assist in the final decision for patients with SS suspicion and who cannot undergo other objective tests.
Putative APOBEC3 deaminase editing in MPXV as evidence for sustained human transmission since at least 2016
Authors: O’Toole Áine , Neher Richard A. , Ndodo Nnaemeka , Borges Vitor , Gannon Ben , Gomes João Paulo , Groves Natalie , King David J , Maloney Daniel , Lemey Philippe , Lewandowski Kuiama , Loman Nicholas , Myers Richard , Suchard Marc A. , Worobey Michael , Chand Meera , Ihekweazu Chikwe , Ulaeto David , Adetifa Ifedayo , Rambaut Andrew
Published: January 2023

Mpox is often described as being endemic in West and Central Africa as a zoonotic disease that transmits through contact with the reservoir rodent host, likely a species of African squirrel. In May 2022, human cases of Mpox were detected spreading internationally beyond countries with known endemic reservoirs. At time of writing, 84,700 confirmed cases have been reported in 110 countries. When the first cases from 2022 were sequenced, it was seen that they shared 42 single nucleotide differences from the closest mpox virus (MPXV) genome sampled in 2018. This number of changes within 3-4 years is unexpectedly large and points to a much greater evolutionary rate than expected for a poxvirus. Strikingly, most nucleotide changes are of a specific type – a dinucleotide change from TC->TT or its reverse complement GA->AA. This mutation type is characteristic of the action of APOBEC3 deaminases; host-enzymes with reported antiviral function. Analysis of MPXV genomes sampled from 2017 to 2022 showed further evidence of TC->TT mutation pattern enrichment, with 93% of transmitted single nucleotide mutations since 2017 consistent with APOBEC3 editing. Assuming APOBEC-editing is characteristic of MPXV infection in human hosts, we propose an APOBEC clock that – at a rate of ~6 APOBEC3 mutations per year – estimates MPXV has been circulating in humans since 2016. This evolutionary pattern of host-enzyme editing has implications for the longer-term fitness of the virus in this epidemic as such mechanisms are primarily antiviral in function, but in the context of a poxvirus also provide a source of variation that may conceivably facilitate adaptation.
Improvements to the Gulf PipefishSyngnathus scovelliGenome
Authors: Ramesh B , Small CM , Healey H , Johnson B , Barker E , Currey M , Bassham S , Myers M , Cresko WA , Jones AG
Published: January 2023

The Gulf pipefishSyngnathus scovellihas emerged as an important species in the study of sexual selection, development, and physiology, among other topics. The fish family Syngnathidae, which includes pipefishes, seahorses, and seadragons, has become an increasingly attractive target for comparative research in ecological and evolutionary genomics. These endeavors depend on having a high-quality genome assembly and annotation. However, the first version of theS. scovelligenome assembly was generated by short-read sequencing and annotated using a small set of RNA-sequence data, resulting in limited contiguity and a relatively poor annotation. Here, we present an improved genome assembly and an enhanced annotation, resulting in a new official gene set forS. scovelli. By using PacBio long-read high-fidelity (Hi-Fi) sequences and a proximity ligation (Hi-C) library, we fill small gaps and join the contigs to obtain 22 chromosome-level scaffolds. Compared to the previously published genome, the gaps in our novel genome assembly are smaller, the N75 is much larger (13.3 Mb), and this new genome is around 95% BUSCO complete. The precision of the gene models in the NCBI’s eukaryotic annotation pipeline was enhanced by using a large body of RNA-Seq reads from different tissue types, leading to the discovery of 28,162 genes, of which 8,061 were non-coding genes. This new genome assembly and the annotation are tagged as a RefSeq genome by NCBI and thus provide substantially enhanced genomic resources for future research involvingS. scovelli.
Regulation of the hypertonic stress response by the 3’ mRNA cleavage and polyadenylation complex
Authors: Urso Sarel J. , Sathaseevan Anson , Derry W. Brent , Lamitina Todd
Published: January 2023

Maintenance of osmotic homeostasis is one of the most aggressively defended homeostatic setpoints in physiology. One major mechanism of osmotic homeostasis involves the upregulation of proteins that catalyze the accumulation of solutes called organic osmolytes. To better understand how osmolyte accumulation proteins are regulated, we conducted forward genetic screen inC. elegansfor mutants with no induction of osmolyte biosynthesis gene expression (Nio mutants).nio-3mutants encoded a missense mutation incpf-2/CstF64 whilenio-7mutants encoded a missense mutation insymk-1/Symplekin. Bothcpf-2andsymk-1are nuclear components of the highly conserved 3’ mRNA cleavage and polyadenylation complex.cpf-2andsymk-1block the hypertonic induction ofgpdh-1and other osmotically induced mRNAs, suggesting they act at the transcriptional level. We generated a functional auxin-inducible degron (AID) allele forsymk-1and found that acute, post-developmental degradation in the intestine and hypodermis was sufficient to cause the Nio phenotype.symk-1andcpf-2exhibit genetic interactions that strongly suggest they function through alterations in 3’ mRNA cleavage and/or alternative polyadenylation. Consistent with this hypothesis, we find that inhibition of several other components of the mRNA cleavage complex also cause a Nio phenotype.cpf-2andsymk-1specifically affect the osmotic stress response since heat shock-induced upregulation of ahsp-16.2::GFPreporter is normal in these mutants. Our data suggest a model in which alternative polyadenylation of one or more mRNAs is essential to regulate the hypertonic stress response.
Natural methylation epialleles correlate with gene expression in maize
Authors: Zeng Yibing , Dawe R. Kelly , Gent Jonathan I.
Published: January 2023

DNA methylation (5-methylcytosine) represses transposon activity and contributes to inaccessible chromatin structure of repetitive DNA in plants. It is depleted from cis regulatory elements in and near genes but is present in some gene bodies, including exons. Methylation in exons solely in the CG context is called gene body methylation (gbM). Methylation in exons in both CG and non-CG contexts is called TE-like methylation (teM). Assigning functions to both forms of methylation in genes has proven to be challenging. Toward that end, we utilized recent genome assemblies, gene annotations, transcription data, and methylome data to quantify common patterns of gene methylation and their relations to gene expression in maize. To compare between genomes, we analyzed each data source relative to its own genome assembly rather than the easier but less accurate method of using one assembly as reference for all. We found that gbM genes exist in a continuum of CG methylation levels without a clear demarcation between unmethylated genes and gbM genes. Analysis of expression levels across diverse maize stocks and tissues revealed a weak but highly significant positive correlation between gbM and gene expression except in endosperm. gbM epialleles were associated with an approximately 3% increase in steady-state expression level relative to unmethylated epialleles. In contrast to gbM genes, which were conserved and were broadly expressed across tissues, we found that teM genes, which make up about 12% of genes, are mainly silent, are limited to specific maize stocks, and exhibit evidence of annotation errors. We used these data to flag all teM genes in the 26 NAM founder genome assemblies. While some teM genes are likely functional, these data suggest that the majority are not, and their inclusion can confound interpretation of whole-genome studies.
Conformationally responsive dyes enable protein-adaptive differential scanning fluorimetry
Authors: Wu Taiasean , Yu Joshua C. , Suresh Arundhati , Gale-Day Zachary J. , Alteen Matthew G. , Woo Amanda S. , Millbern Zoe , Johnson Oleta T. , Carroll Emma C. , Partch Carrie L. , Fourches Denis , Vinueza Nelson R. , Vocadlo David J. , Gestwicki Jason E.
Published: January 2023

Flexiblein vitromethods alter the course of biological discoveries. Differential Scanning Fluorimetry (DSF) is a particularly versatile technique which reports protein thermal unfolding via fluorogenic dye. However, applications of DSF are limited by widespread protein incompatibilities with the available DSF dyes. Here, we enable DSF applications for 66 of 70 tested proteins (94%) including 10 from the SARS-CoV2 virus using a chemically diverse dye library, Aurora, to identify compatible dye-protein pairs in high throughput. We find that this protein-adaptive DSF platform (paDSF) not only triples the previous protein compatibility, but also fundamentally extends the processes observable by DSF, including interdomain allostery in O-GlcNAc Transferase (OGT). paDSF enables routine measurement of protein stability, dynamics, and ligand binding.

One-Sentence Summary

Next generation protein-adaptive DSF (paDSF) enables rapid and general measurements of protein stability and dynamics.
Genome-wide CRISPR screens identify noncanonical translation factor eIF2A as an enhancer of SARS-CoV-2 programmed –1 ribosomal frameshifting
Authors: Wei Lian-Huan , Sun Yu , Guo Junjie U.
Published: January 2023

Many positive-strand RNA viruses, including all known coronaviruses, employ programmed –1 ribosomal frameshifting (–1 PRF) to regulate the translation of polycistronic viral RNAs. However, only a few host factors have been shown to regulate –1 PRF. Through a reporter-based genome-wide CRISPR/Cas9 knockout screen, we identified several host factors that either suppressed or enhanced –1 PRF of SARS-CoV-2. One of these factors is eukaryotic translation initiation factor 2A (eIF2A), which specifically and directly enhanced –1 PRF in vitro and in cells. Consistent with the crucial role of efficient –1 PRF in transcriptase/replicase expression, loss of eIF2A reduced SARS-CoV-2 replication in cells. Transcriptome-wide analysis of eIF2A-interacting RNAs showed that eIF2A primarily interacted with 18S ribosomal RNA near the contacts between the SARS-CoV-2 frameshift-stimulatory element (FSE) and the ribosome. Thus, our results revealed an unexpected role for eIF2A in modulating the translation of specific RNAs independent of its previously described role during initiation.
Mechanism of glycoform specificity and protection against antibody dependent enhancement by an anti-afucosylated IgG nanobody
Authors: Gupta Aaron , Kao Kevin , Yamin Rachel , Oren Deena A. , Goldgur Yehuda , Du Jonathan , Lollar Pete , Sundberg Eric J. , Ravetch Jeffrey V.
Published: January 2023

Immunoglobulin G (IgG) antibodies contain a single, complexN-glycan on each IgG heavy chain protomer embedded in the hydrophobic pocket between its Cγ2 domains. The presence of this glycan contributes to the structural organization of the Fc domain and determines its specificity for Fcγ receptors, thereby determining distinct cellular responses. On the Fc, the variable construction of this glycan structure leads to a family of highly-related, but non-equivalent glycoproteins known as glycoforms. We previously reported the development of synthetic nanobodies that distinguish IgG glycoforms without cross-reactivity to off-target glycoproteins or free glycans. Here, we present the X-ray crystal structure of one such nanobody, X0, in complex with its specific binding partner, the Fc fragment of afucosylated IgG1. Two X0 nanobodies bind a single afucosylated Fc homodimer at the upper Cγ2 domain, making both protein-protein and protein-carbohydrate contacts and overlapping the binding site for Fcγ receptors. Upon binding, the elongated CDR3 loop of X0 undergoes a conformational shift to access the buriedN-glycan and acts as a ‘glycan sensor’, forming hydrogen bonds with the afucosylated IgGN-glycan that would otherwise be sterically hindered by the presence of a core fucose residue. Based on this structure, we designed X0 fusion constructs that disrupt pathogenic afucosylated IgG1-FcγRIIIa interactions and rescue mice in a model of dengue virus infection.
Cell-type-specific inhibitory circuitry from a connectomic census of mouse visual cortex
Authors: Schneider-Mizell Casey M , Bodor Agnes L. , Brittain Derrick , Buchanan JoAnn , Bumbarger Daniel J. , Elabbady Leila , Gamlin Clare , Kapner Daniel , Kinn Sam , Mahalingam Gayathri , Seshamani Sharmishtaa , Suckow Shelby , Takeno Marc , Torres Russel , Yin Wenjing , Dorkenwald Sven , Bae J. Alexander , Castro Manuel A. , Halageri Akhilesh , Jia Zhen , Jordan Chris , Kemnitz Nico , Lee Kisuk , Li Kai , Lu Ran , Macrina Thomas , Mitchell Eric , Mondal Shanka Subhra , Mu Shang , Nehoran Barak , Popovych Sergiy , Silversmith William , Turner Nicholas L. , Wong William , Wu Jingpeng ,   The MICrONS Consortium, Reimer Jacob , Tolias Andreas S. , Seung H Sebastian , Reid R. Clay , Collman Forrest , Maçarico da Costa Nuno
Published: January 2023

Mammalian cortex features a vast diversity of neuronal cell types, each with characteristic anatomical, molecular and functional properties. Synaptic connectivity powerfully shapes how each cell type participates in the cortical circuit, but mapping connectivity rules at the resolution of distinct cell types remains difficult. Here, we used millimeter-scale volumetric electron microscopy1to investigate the connectivity of all inhibitory neurons across a densely-segmented neuronal population of 1352 cells spanning all layers of mouse visual cortex, producing a wiring diagram of inhibitory connections with more than 70,000 synapses. Taking a data-driven approach inspired by classical neuroanatomy, we classified inhibitory neurons based on the relative targeting of dendritic compartments and other inhibitory cells and developed a novel classification of excitatory neurons based on the morphological and synaptic input properties. The synaptic connectivity between inhibitory cells revealed a novel class of disinhibitory specialist targeting basket cells, in addition to familiar subclasses. Analysis of the inhibitory connectivity onto excitatory neurons found widespread specificity, with many interneurons exhibiting differential targeting of certain subpopulations spatially intermingled with other potential targets. Inhibitory targeting was organized into “motif groups,” diverse sets of cells that collectively target both perisomatic and dendritic compartments of the same excitatory targets. Collectively, our analysis identified new organizing principles for cortical inhibition and will serve as a foundation for linking modern multimodal neuronal atlases with the cortical wiring diagram.
Quantifying paddling kinematic through muscle activation and whole body coordination during maximal sprint of different duration on a kayak ergometer: a pilot study
Authors: Garnier Y.M. , Hilt P. M. , Sirandre C. , Ballay Y. , Lepers R. , Paizis C.
Published: January 2023

Paddling technique and stroke kinematics are important performance factors in flatwater sprint kayaking that require important energetic demand and high strength from the muscles of the trunk and upper limb. The various distance competed (from 200-m to 1000-m) requires the athletes to optimize their pacing strategy to maximize power output distribution throughout the race. This study aims to characterize paddling technique and stroke kinematics during two maximal sprints of different duration. Nine national-trained participants performed a 40-seconds and a 4-min sprint at maximal intensity on a kayak ergometer. The main findings demonstrated a significantly greater mean stroke power (237 ± 80 W vs 170 ± 48 W) and rate (131 ± 8 spm vs 109 ± 7 spm) during the 40-s sprint compared to the 4-min sprint. Athletes used an all-out strategy for the 40-sec exercise and a parabolic-shape strategy during the 4-min. Despite different strategies implemented and higher muscular activation during the 40-s sprint, no change in paddling technique and body coordination occurred during the sprints. The findings of the present study suggest that athletes constructed a well-defined profile that is not affected by fatigue despite a decrease in power output during the all-out strategy. Also, they regulate paddling kinematics during longer exercise with no change in paddling technique and body coordination.
Y-complex nucleoporins independently contribute to nuclear pore assembly and gene regulation in neuronal progenitors
Authors: Orniacki Clarisse , Verrico Annalisa , Pelletier Stéphane , Souquet Benoit , Coulpier Fanny , Jourdren Laurent , Benetti Serena , Doye Valérie
Published: January 2023

From their essential function in building up the nuclear pore complexes, nucleoporins have expanded roles beyond nuclear transport. Hence, their contribution to chromatin organization and gene expression has set them as critical players in development and pathologies. We previously reported that Nup133 and Seh1, two components of the Y-complex subunit of the nuclear pore scaffold, are dispensable for mouse embryonic stem cell viability but required for their survival during neuroectodermal differentiation. Here, a transcriptomic analysis revealed that Nup133 regulates a subset of genes at early stages of neuroectodermal differentiation, includingLhx1 and Nup210L, encoding a newly validated nucleoporin. These genes were also misregulated inNup133∆Midneuronal progenitors, in which NPC basket assembly is impaired, as previously observed in pluripotent cells. However, a four-fold reduction of Nup133, despite affecting basket assembly, is not sufficient to alterNup210LandLhx1regulation. Finally, these two genes are also misregulated inSeh1-deficient neural progenitors that only show a mild decrease in NPC density. Together these data reveal a shared function of Y-complex nucleoporins in gene regulation during neuroectodermal differentiation, which seem independent of nuclear pore basket assembly.
A miniature cellulosome with novel interaction modes
Authors: Allan John , Black Gary W
Published: January 2023

Cellulosomes are efficient enzymatic nanomachines which have arisen for the degradation of cellulosic biomass. They are found abundantly in soil-dwelling microbes and bacteria which thrive in the stomachs of ruminant mammals. Two protein domains, cohesins and dockerins, characterise cellulosomes. These domains interact with each other to form enormous complexes with as many as 130 individual proteins. Annotation of the genome ofCellulosilyticum lenotcellumDSM 5427 revealed one single cohesin and one single dockerin domain. This pales in comparison to most cellulosomal organisms. We have recombinantly produced the proteins which bear these domains and demonstrated cellulase activity, which is enhanced by interaction between the two proteins. Moreover we have identified additional novel interacting partners for this unique cellulosome complex. This broadens the repertoire and definitions of cellulosomes overall.
Neo-natal castration leads to subtle differences in porcine anterior cruciate ligament morphology and function in adolescence
Authors: Thompson Jacob D. , Howe Danielle , Griffith Emily H. , Fisher Matthew B.
Published: January 2023

Female adolescent athletes are at a higher risk of tearing their anterior cruciate ligament (ACL) than male counterparts. While most work related to hormones has focused on the effects of estrogen to understand the increased risk of ACL injury, there are other understudied factors, including testosterone. The purpose of this study was to determine how surgical castration in the male porcine model influences ACL size and function across skeletal growth. Thirty-six male Yorkshire crossbreed pigs were raised to 3 (juvenile), 4.5 (early adolescent), and 6 months (adolescent) of age. Animals were either castrated (barrows) within 1-2 weeks after birth or were left intact (boars). Post-euthanasia, joint and ACL size were assessed via MRI, and biomechanics were assessed via a robotic testing system. Joint size increased throughout age, yet barrows had smaller joints than boars (p<0.001 for all measures). ACL cross-sectional area (CSA), length, volume, and stiffness increased with age (p<0.0001), as did ACL anteromedial (AM) bundle percent contribution to resisting loads (p=0.012). Boar ACL, AM bundle, and PL bundle volumes were 19% (p=0.002), 25% (p=0.003), and 15% (p=0.04) larger than barrows across ages. However, CSA, stiffness, and bundle contribution were similar between boars and barrows (p>0.05). The barrows had smaller temporal increases in AM bundle percent function than boars, but these data were highly variable. Thus, early and sustained loss in testosterone leads to subtle differences in ACL morphology, but may not influence measures associated with increased injury risk, such as CSA or bundle forces in response to applied loads.
Functional connectivity between the amygdala and prefrontal cortex underlies processing of emotion ambiguity
Authors: Sun Sai , Yu Hongbo , Yu Rongjun , Wang Shuo
Published: January 2023

Processing facial expressions of emotion draws on a distributed brain network. In particular, judging ambiguous facial emotions involves coordination between multiple brain areas. Here, we applied multimodal functional connectivity analysis to achieve network-level understanding of the neural mechanisms underlying perceptual ambiguity in facial expressions. We found directional effective connectivity between the amygdala, dorsomedial prefrontal cortex (dmPFC), and ventromedial PFC, supporting both bottom-up affective processes for ambiguity representation/perception and top-down cognitive processes for ambiguity resolution/decision. Direct recordings from the human neurosurgical patients showed that the responses of amygdala and dmPFC neurons were modulated by the level of emotion ambiguity, and amygdala neurons responded earlier than dmPFC neurons, reflecting the bottom-up process for ambiguity processing. We further found parietal-frontal coherence and delta-alpha cross-frequency coupling involved in encoding emotion ambiguity. We replicated the EEG coherence result using independent experiments and further showed modulation of the coherence. EEG source connectivity revealed that the dmPFC top-down regulated the activities in other brain regions. Lastly, we showed altered behavioral responses in neuropsychiatric patients who may have dysfunctions in amygdala-PFC functional connectivity. Together, using multimodal experimental and analytical approaches, we have delineated a neural network that underlies processing of emotion ambiguity.

Significance Statement

A large number of different brain regions participate in emotion processing. However, it remains elusive how these brain regions interact and coordinate with each other and collectively encode emotions, especially when the task requires orchestration between different brain areas. In this study, we employed multimodal approaches that well complemented each other to comprehensively study the neural mechanisms of emotion ambiguity. Our results provided a systematic understanding of the amygdala-PFC network underlying emotion ambiguity with fMRI-based connectivity, EEG coordination of cortical regions, synchronization of brain rhythms, directed information flow of the source signals, and latency of single-neuron responses. Our results further shed light on neuropsychiatric patients who have abnormal amygdala-PFC connectivity.
Increased Ca2+signaling through CaV1.2 induces tendon hypertrophy with increased collagen fibrillogenesis and biomechanical properties
Authors: Li Haiyin , Korcari Antonion , Ciufo David , Mendias Christopher L. , Rodeo Scott A. , Buckley Mark R. , Loiselle Alayna E. , Pitt Geoffrey S. , Cao Chike
Published: January 2023

Tendons are tension-bearing tissues transmitting force from muscle to bone for body movement. This mechanical loading is essential for tendon development, homeostasis, and healing after injury. While Ca2+signaling has been studied extensively for its roles in mechanotransduction, regulating muscle, bone and cartilage development and homeostasis, knowledge about Ca2+signaling and the source of Ca2+signals in tendon fibroblast biology are largely unknown. Here, we investigated the function of Ca2+signaling through CaV1.2 voltage-gated Ca2+channel in tendon formation. Using a reporter mouse, we found that CaV1.2 is highly expressed in tendon during development and downregulated in adult homeostasis. To assess its function, we generatedScxCre;CaV1.2TSmice that express a gain-of-function mutant CaV1.2 channel (CaV1.2TS) in tendon. We found that tendons in the mutant mice were approximately 2/3 larger and had more tendon fibroblasts, but the cell density of the mutant mice decreased by around 22%. TEM analyses demonstrated increased collagen fibrillogenesis in the hypertrophic tendon. Biomechanical testing revealed that the hypertrophic Achilles tendons display higher peak load and stiffness, with no changes in peak stress and elastic modulus. Proteomics analysis reveals no significant difference in the abundance of major extracellular matrix (ECM) type I and III collagens, but mutant mice had about 2-fold increase in other ECM proteins such as tenascin C, tenomodulin, periostin, type XIV and type VIII collagens, around 11-fold increase in the growth factor of TGF-β family myostatin, and significant elevation of matrix remodeling proteins including Mmp14, Mmp2 and cathepsin K. Taken together, these data highlight roles for increased Ca2+signaling through CaV1.2 on regulating expression of myostatin growth factor and ECM proteins for tendon collagen fibrillogenesis during tendon formation.
Metabolically Primed Multipotent Hematopoietic Progenitors Fuel Innate Immunity
Authors: Cosgrove Jason , Lyne Anne-Marie , Rodriguez Ildefonso , Cabeli Vincent , Conrad Cecile , Tenreira-Bento Sabrina , Tubeuf Emilie , Russo Erica , Tabarin Fanny , Belloucif Yannis , Maleki-Toyserkani Shayda , Reed Sophie , Monaco Federica , Ager Ann , Lobry Camille , Bousso Philippe , Fernández-Marcos Pablo Jose , Isambert Herve , Argüello Rafael J. , Perié Leïla
Published: January 2023

Following infection, hematopoietic stem and progenitor cells (HSPCs) support immunity by increasing the rate of innate immune cell production but the metabolic cues that guide this process are unknown. To address this question, we developed MetaFate, a method to trace the metabolic expression state and developmental fate of single cellsin vivo. Using MetaFate we identified a gene expression program of metabolic enzymes and transporters that confers differences in myeloid differentiation potential in a subset of HSPCs that express CD62L. Using single-cell metabolic profiling, we confirmed that CD62Lhighmyeloid-biased HSPCs have an increased dependency on oxidative phosphorylation and glucose metabolism. Importantly, metabolism actively regulates immune-cell production, with overexpression of the glucose-6-phosphate dehydrogenase enzyme of the pentose phosphate pathway skewing MPP output from B-lymphocytes towards the myeloid lineages, and expansion of CD62LhighHSPCs occurring to support emergency myelopoiesis. Collectively, our data reveal the metabolic cues that instruct innate immune cell development, highlighting a key role for the pentose phosphate pathway. More broadly, our results show that HSPC metabolism can be manipulated to alter the cellular composition of the immune system.