bluuebunny/crossref_metadata_2025 huggingface dataset:
Clinical and Histopathologic Characteristics of Recurrent Sarcoidosis in Posttransplant Lungs
Authors: Lu Liang , Wein Alexander N. , Villanueva Ana , Jones Christopher , Anderson Adam , Ritter Jon , Lin Chieh-Yu
Published: June 2023

Lung transplantation is the definitive therapy for end-stage pulmonary sarcoidosis. While recurrent sarcoidosis in allografts has been described in several case reports, the incidence and clinicopathologic characteristics remain unclear. In this study, we characterize the clinical and histopathologic features of recurrent sarcoidosis diagnosed in posttransplant lung surveillance transbronchial biopsies (TBBx). We identified 35 patients who underwent lung transplant for pulmonary sarcoidosis during the study period. Among them, 18 patients (51%) experienced recurrent sarcoidosis posttransplant. These included 7 females and 11 males with mean age at recurrence of 51.6 years. The average time interval from transplant to recurrence was 252 days (22 to 984 d). All TBBx contained >4 pieces of alveolated lung tissue with no evidence of International Society for Heart and Lung Transplantation (ISHLT) grade A2, A3, or A4 acute cellular rejection; chronic rejection; or antibody-mediated rejection. There were 33 surveillance TBBx that contained granulomatous inflammation with a mean of 3.6 well-formed granulomas per TBBx (range: 1 to >20). Multinucleated giant cells were identified in 11 TBBx (33.3%), with 1 case containing asteroid bodies. While most of the granulomas were “naked granulomas,” 5 cases (15.2%) showed prominent lymphoid cuffing. Two cases showed evidence of fibrosis. One of the granulomas had focal necrosis; however, no infectious organisms were identified by special stains and clinical correlation suggested this case represented recurrent sarcoidosis. Biopsies of recurrent sarcoidosis usually show multiple well-formed granulomas with giant cells in more than half of the cases, while lymphoid cuffing, fibrosis, asteroid bodies, and necrotizing granulomas are uncommon findings. Pathologists should be aware of these features, as recurrence of sarcoidosis following lung transplant occurs in more than half of patients.
Quantitative methods used to evaluate balance, postural control, and the fear of falling in lower limb prosthesis users: A systematic review
Authors: Johansson Robin , Jensen Louise , Barnett Cleveland T. , Rusaw David F.
Published: June 2023

Problems with balance, postural control, and fear of falling are highly prevalent in lower limb prosthesis users, with much research conducted to understand these issues. The variety of tools used to assess these concepts presents a challenge when interpreting research outcomes. This systematic review aimed to provide a synthesis of quantifiable methods used in the evaluation of balance, postural control, and fear of falling in lower limb prosthesis users with an amputation level at or proximal to the ankle joint. A systematic search was conducted in CINAHL, Medline, AMED, Cochrane, AgeLine, Scopus, Web of Science, Proquest, PsycINFO, PsycArticles, and PubPsych databases followed by additional manual searching via reference lists in the reviewed articles databases. Included articles used quantitative measure of balance or postural control as one of the dependent variables, lower limb prosthesis users as a sample group, and were published in a peer-reviewed journal in English. Relevant assessment questions were created by the investigators to rate the assessment methods used in the individual studies. Descriptive and summary statistics are used to synthesize the results. The search yielded (n = 187) articles assessing balance or postural control (n = 5487 persons in total) and (n = 66) articles assessing fear of falling or balance confidence (n = 7325 persons in total). The most used test to measure balance was the Berg Balance Scale and the most used test to measure fear of falling was the Activities-specific Balance Confidence scale. A large number of studies did not present if the chosen methods were valid and reliable for the lower limb prosthesis users. Among study limitations, small sample size was common.
Evaluation of the Lingual Splitting Patterns and the Lateral Bone Cut Ends Following Mandibular Bilateral Sagittal Split Osteotomy Using Cone Beam Computed Tomography (CBCT)
Authors: Khaleel Ameen A. , Bede Salwan Y.
Published: June 2023

The bilateral sagittal split osteotomy (BSSO) is the most popular orthognathic procedure performed by maxillofacial surgeons to treat skeletal class II and class III and to correct mandibular asymmetries. The study aimed to evaluate the lingual splitting patterns and lateral bone cut end (LBCE) in bilateral sagittal split osteotomy (BSSO) and their relation with the ramal thickness and the presence of impacted third molars using cone beam computed tomography (CBCT). This prospective observational study included patients with mandibular prognathism who were treated with BSSO with or without Le Fort I osteotomy. Cone beam computed tomography was used to measure the ramal thickness preoperatively and to evaluate the LBCE, and the lingual splitting patterns postoperatively. Twenty-one patients (42 sides) were included in this study. The most commonly observed lingual splitting pattern was type III (47.6%), while the most common LBCE was type B (59.5%). The bad split was encountered 8 times on 42 sides (16.7%). A nonsignificant relationship between the ramal thickness and bad splitting was observed (P=0.901). Impacted third molars were present in 16 of the 42 sides (38.1%) and had no significant effect on the occurrence of bad splitting (P=0.063). Type III lingual splitting pattern and type B LBCE were the most commonly observed patterns. No direct association was observed concerning the presence of impacted mandibular third molars and the thickness of the ramus with the occurrence of bad splitting.
Preoperative Nutritional Laboratory Values, Demographics, and Wound Healing Following Facial Trauma Surgery: Which Variables Predict Postoperative Complications?
Authors: Fahmy Mina D. , Clegg Devin J. , Deek Andrew J. , Scott Christopher A. , Bloom Graysen , Heidel Robert E. , Hechler Benjamin L.
Published: June 2023

In individuals who have sustained maxillofacial trauma, inadequate nutrition is often a sequela and may lead to complications. The purpose of this study was to investigate the association between preoperative laboratory values and postoperative complications in patients with maxillofacial trauma requiring surgical intervention.

A retrospective cohort study of patients with maxillofacial trauma requiring surgical repair from 2014 to 2020 was performed at a single academic Level I Trauma Center. The primary predictor variables were preoperative laboratory values including serum albumin, white blood cell count, absolute neutrophil count, and lymphocyte count. Complications related to surgical reconstruction of facial injuries represented the primary outcome variable.

The patient cohort included 152 patients, of whom 50 (32.9%) were female. When controlling for all other variables, female gender (odds ratio=2.08, 95% confidence interval, 1.02–4.21; P=0.04) and number of procedures performed (P=0.02) were the only statistically significant predictors of postoperative complications. There were no significant differences between the complication groups for age (P=0.89), injury severity score (P=0.59), hospital length of stay (P=0.30), serum albumin (P=0.86), hemoglobin (P=0.06), white blood cell count (P=0.20), absolute neutrophil count (P=0.95), lymphocyte count (P=0.23), or absolute neutrophil/lymphocyte count ratio (P=0.09).

In this study, it was found that only gender and the number of procedures performed significantly predicted postoperative complications, while preoperative nutritional laboratory values did not. Further study with a larger cohort of patients is likely required.
Persistence of Poverty and its Impact on Surgical Care and Postoperative Outcomes
Authors: Lima Henrique A , Moazzam Zorays , Woldesenbet Selamawit , Alaimo Laura , Endo Yutaka , Munir Muhammad Musaab , Shaikh Chanza F , Resende Vivian , Pawlik Timothy M.
Published: June 2023

Objective:

We sought to characterize the association between prolonged county-level poverty with postoperative outcomes.

Summary Background Data:

The impact of long-standing poverty on surgical outcomes remains ill-defined.

Methods:

Patients who underwent lung resection, colectomy, coronary artery bypass graft (CABG), or lower extremity joint replacement (LEJR) were identified from Medicare Standard Analytical Files Database (2015-2017) and merged with data from the American Community Survey and United States Department of Agriculture. Patients were categorized according to duration of high poverty status from 1980-2015 (i.e., never high poverty [NHP], persistent poverty [PP]). Logistic regression was used to characterize the association between duration of poverty and postoperative outcomes. Principal component and generalized structural equation modeling were used to assess the effect of mediators in achievement of textbook outcomes (TO).

Results:

Overall, 335,595 patients underwent lung resection (10.1%), colectomy (29.4%), CABG (36.4%) or LEJR (24.2%). While 80.3% of patients lived in NHP, 4.4% resided in PP counties. Compared with NHP, patients residing in PP were at increased risk of serious postoperative complications (OR=1.10, 95%CI 1.05-1.15), 30-day readmission (OR=1.09, 95%CI 1.01-1.16), 30-day mortality (OR=1.08, 95%CI 1.00-1.17) and higher expenditures (mean difference, $1,010.0, 95%CI 643.7-1376.4)(all P<0.05). Notably, PP was associated with lower odds of achieving TO (OR=0.93, 95%CI 0.90-0.97, P<0.001); 65% of this effect was mediated by other social determinant factors. Minority patients were less likely to achieve TO (OR=0.81, 95%CI 0.79-0.84, P<0.001), and the disparity persisted across all poverty categories.

Conclusions:

County-level poverty duration was associated with adverse postoperative outcomes and higher expenditures. These effects were mediated by various socioeconomic factors and were most pronounced among minority patients.
The futility of closed chest compressions after trauma: A multi-institutional study
Authors: Fierro Nicole M. , Dhillon Navpreet K. , Park Greigory , Stupinski John , Drevets Peter , Zheng Dennis J. , Tillou Areti , Ugarte Chaiss , Schellenberg Morgan , Tay-Lasso Erika , Nahmias Jeffry , Parker Paige , Ley Eric J.
Published: June 2023

BACKGROUND

The desire to deliver appropriate care after trauma creates challenges when deciding to proceed if care appears futile. This study aimed to analyze survival rates for trauma patients who undergo closed chest compressions by decade of life.

METHODS

A multicenter retrospective review of trauma patients with an Injury Severity Score ≥16 who underwent closed chest compressions from 2015 to 2020 at four large, urban, academic Level I trauma centers was conducted. Those with intraoperative arrest were excluded. The primary endpoint was survival to discharge.

RESULTS

Of the 247 patients meeting inclusion criteria, 18% were 70 years or older, 78% were male, and 24% presented due to a penetrating mechanism of injury. Compressions occurred in the prehospital setting (56%), emergency department (21%), intensive care unit (19%), and on the floor (3%). On average, patients arrested on hospital day 2, and survived 1 day after arrest if return of spontaneous circulation was achieved. Overall mortality was 92%. Average hospital length of stay was lower in patients 70 years or older (3 days vs. 6 days, p < 0.01). Survival was highest in patients 60 years to 69 years (24%), and although patients 70 years or older presented with lower Injury Severity Scores (28 vs. 32, p = 0.04), no patient 70 years or older survived to hospital discharge (0% v 9%, p = 0.03).

CONCLUSION

Closed chest compressions are associated with a high mortality rate after moderate to severe trauma with 100% mortality in patients older than 70 years. This information may assist with the decision to withhold chest compression, especially in older adults.

LEVEL OF EVIDENCE

Prognostic and Epidemiological; Level IV.
Vibrio intestinalis sp. nov., isolated from intestine of seahorse
Authors: Yu Libo , Wei Shiping , Zhou Zhidong , Shao Zongze
Published: June 2023

A novel Gram-stain-negative, catalase- and oxidase-positive, facultatively anaerobic, and rod-shaped motile bacterial strain, designated as YLB-11T, was isolated from seahorse intestine. The 16S rRNA gene sequencing analysis showed that YLB-11T was most closely related

Vibrio mytili

LMG 19157T (98.9 % nucleotide sequence identity). Phylogenetic analysis placed strain YLB-11T within the genus

Vibrio

. The major cellular fatty acids were summed feature 3 (C16: 1
ω6c/C16 : 1
ω7c, 36.4 %), C16 : 0 (19.1 %) and summed feature 8 (C18:1
ω6c/C18:1
ω7c, 12.3 %). The DNA G+C content of YLB-11T was 44.7 mol %. The in silico DNA–DNA hybridization and average nucleotide identity values for whole-genome sequence comparisons between YLB-11T and related species were clearly below the thresholds used for the delineation of a novel species. Therefore, YLB-11T is considered to represent novel species of the genus

Vibrio

, for which the name Vibrio intestinalis sp. nov. is proposed. The type strain is YLB-11T (=MCCC 1A17441T=KCTC 72604T).
Defining the single base importance of human mRNAs and lncRNAs
Authors: Fan Rui , Ji Xiangwen , Li Jianwei , Cui Qinghua , Cui Chunmei
Published: June 2023

As the fundamental unit of a gene and its transcripts, nucleotides have enormous impacts on molecular function and evolution, and thus on phenotypes and diseases. Given that different nucleotides on one gene often exhibit diverse levels of effects, it is quite crucial to comprehensively and quantitatively measure the importance of each base on a gene transcript, however, tools are still not available. Here we proposed Base Importance Calculator (BIC), an algorithm to calculate the importance score of single bases based on sequence information of human mRNAs and long noncoding RNAs (lncRNAs). We then confirmed its power by applying BIC to three different tasks. Firstly, we revealed that BIC can effectively evaluate the pathogenicity of both genes and single bases by analyzing the BIC scores and the pathogenicity of single nucleotide variations (SNVs). Moreover, the BIC score in the Cancer Genome Atlas (TCGA) somatic mutations is able to predict the prognosis of some cancers. Finally, we show that BIC can also precisely predict the transmissibility of SARS-CoV-2. The above results indicate that BIC is a useful tool for evaluating the single base important of human mRNAs and lncRNAs.

Key Points

BIC could measure the single base importance of human mRNAs and lncRNAs.

BIC could be applied to many aspects including measuring the pathogenicity of SNVs and enhancing the ability of predicting cancer survival.

BIC could predict the transmissibility of SARS-CoV-2
Glycochenodeoxycholic acid and ceramide suppress the antiviral effect of 25-hydroxycholesterol against human norovirus infection in human intestinal enteroids
Authors: Mboko Wadzanai P. , Chhabra Preeti , Montmayeur Anna , Xu Ruijie , Costantini Verónica , Vinjé Jan
Published: June 2023

The human intestinal enteroid (HIE) cell culture system with the support of glycine-conjugated bile acid glycochenodeoxycholic acid (GCDCA) and ceramide (C2) facilitate successful replication of several norovirus strains. Here we investigate how the presence of GCDCA/C2 impacts gene expression of norovirus-infected HIE and the impact of 25 hydroxycholesterol (25-HC), a key regulator of cholesterol homeostasis and bile acid production on norovirus replication. In absence of GCDCA/C2, 0.01 and 0.1 μM 25-HC suppressed virus (GII.4 Sydney[P16]) replication by 1.3 log and 1.1 log respectively (p<0.05). In the presence of GCDCA/C2, 5 μM 25-HC was required to achieve a 1 log decrease (p<0.05) in viral titers demonstrating that 25-HC restricts norovirus replication in HIE. RNA sequence analysis showed that during human norovirus infection, 25-HC downregulated expression of genes (CYP3A4, APOB, APOA1, and ABCG1) involved in cholesterol metabolism and transport as well as interferon stimulated genes such as ISG15 and IFIT1. GCDCA/C2 counteracts the suppressive effect of 25-HC expression of some genes related to these pathways including APOA4 and CYP27A1 however, other cholesterol genes such as APOA1 were further suppressed in the presence of GCDCA/C2.

Importance

Norovirus is the leading cause of epidemic and endemic acute gastroenteritis worldwide and currently, there are no effective therapeutic strategies against this highly contagious pathogen. Our study provides insights into the effect of bile during norovirus infection, highlight the role of the cholesterol/oxysterol pathways during human norovirus replication, and demonstrate the potential utility of oxysterols in developing norovirus therapeutics.
Partially hydrolyzed guar gum attenuates the symptoms of SARS-CoV-2 infection through gut microbiota modulation in an animal model
Authors: Yang Jiayue , Song Isaiah , Saito Misa , Hartanto Tenagy , Ichinohe Takeshi , Fukuda Shinji
Published: June 2023

The coronavirus disease 2019 (COVID-19) pandemic has caused worldwide health issues. Although several vaccines have been developed, it is still difficult to prevent and reduce the inflammation caused by the infection. Studies have shown that there are correlations between the gut environment and severity of symptoms caused by SARS-CoV-2 infection. Several gut metabolites produced by the gut microbiota such as SCFAs and the secondary bile acid UDCA are reported to improve the survival rate of the host after viral infection in an animal model through modulation of the host immune system. Therefore, in this study, we attempted to use the prebiotic dietary fiber PHGG to modulate the gut microbiome and intestinal metabolites for improvement of host survival rate after SARS-CoV-2 infection in a Syrian hamster model. We were able to show that PHGG significantly improved the host survival rate and body weight reduction. Analysis of the gut microbiome, serum, and intestinal metabolites revealed that PHGG significantly increased the concentrations of several intestinal SCFAs, fecal secondary bile acids, and serum secondary bile acids. Furthermore, several microbial species and metabolites identified in this study are consistent with reports in humans. Taken together, our data suggest that PHGG is a candidate prebiotic food for reducing the morbidity of COVID-19.
IKKα kinase coordinates BRD4 and JAK/STAT signaling to subvert DNA damage-based anticancer therapy
Authors: Pecharromán Irene , Solé Laura , Álvarez-Villanueva Daniel , Lobo-Jarne Teresa , Alonso-Marañón Josune , Bertran Joan , Guillén Yolanda , Montoto Ángela , Martínez-Iniesta María , García-Hernández Violeta , Giménez Gemma , Salazar Ramon , Santos Cristina , Garrido Marta , Borràs Eva , Sabidó Eduard , Bonfill-Teixido Ester , Iurlaro Raffaella , Seoane Joan , Villanueva Alberto , Iglesias Mar , Bigas Anna , Espinosa Lluís
Published: June 2023

Activation of the IKK kinase complex has recurrently been linked to colorectal cancer (CRC) initiation and progression. However, identification of downstream effectors other than NF-κB has remained elusive.

Analysis of IKK-dependent substrates after UV-treatment revealed that BRD4 phosphorylation by IKKα is required for chromatin-binding dynamics upon damage. Moreover, IKKα induces the NF-κB-dependent transcription of LIF leading to STAT3 activation, association of BRD4 to STAT3 and recruitment to specific target genes. IKKα abrogation results in defective BRD4 and STAT3 function leading to irreparable DNA damage and apoptotic cell death upon different stimuli. Simultaneous inhibition of BRAF-dependent IKKα activity or BRD4 and the JAK/STAT pathway enhanced the therapeutic potential of 5-FU plus irinotecan in CRC cells, and is curative in a chemotherapy-resistant CRC xenograft model. Coordinated expression of LIF and IKKα is a poor prognosis marker for CRC patients.

Our data uncover a functional link between IKKα, BRD4 and JAK/STAT signaling with clinical relevance.
A window to the brain: ultrasound imaging of human neural activity through a permanent acoustic window
Authors: Rabut Claire , Norman Sumner L. , Griggs Whitney S. , Russin Jonathan J. , Jann Kay , Christopoulos Vasileios , Liu Charles , Andersen Richard A. , Shapiro Mikhail G.
Published: June 2023

Recording human brain activity is crucial for understanding normal and aberrant brain function. However, available recording methods are either highly invasive or have relatively low sensitivity. Functional ultrasound imaging (fUSI) is an emerging technique that offers sensitive, large-scale, high-resolution neural imaging. However, fUSI cannot be performed through adult human skull. Here, we use a polymeric skull replacement material to create an acoustic window allowing ultrasound to monitor brain activity in fully intact adult humans. We design the window through experiments in phantoms and rodents, then implement it in a participant undergoing reconstructive skull surgery. Subsequently, we demonstrate fully non-invasive mapping and decoding of cortical responses to finger movement, marking the first instance of high-resolution (200 μm) and large-scale (50 mmx38 mm) brain imaging through a permanent acoustic window.
Fusion crystallization reveals the behavior of both the 1TEL crystallization chaperone and the TNK1 UBA domain
Authors: Nawarathnage Supeshala , Tseng Yi Jie , Soleimani Sara , Smith Tobin , Pedroza Romo Maria J , Abiodun Wisdom Oshireku , Egbert Christina M. , Madhusanka Deshan , Bunn Derick , Woods Bridger , Tsubaki Evan , Stewart Cameron , Brown Seth , Doukov Tzanko , Andersen Joshua L. , Moody James D.
Published: June 2023

Human thirty-eight-negative kinase-1 (TNK1) is implicated in cancer progression. The TNK1-UBA domain binds polyubiquitin and plays a regulatory role in TNK1 activity and stability. Sequence analysis suggests an unusual architecture for the TNK1 UBA domain, but an experimentally-validated molecular structure is undetermined. To gain insight into TNK1 regulation, we fused the UBA domain to the 1TEL crystallization chaperone and obtained crystals diffracting as far as 1.53 Å. A 1TEL search model enabled solution of the X-ray phases. GG and GSGG linkers allowed the UBA to reproducibly find a productive binding mode against its host 1TEL polymer and to crystallize at protein concentrations as low as 0.1 mg/mL. Our studies support a mechanism of TELSAM fusion crystallization and show that TELSAM fusion crystals require fewer crystal contacts than traditional protein crystals. Modeling and experimental validation suggest the UBA domain may be selective for both the length and linkages of polyubiquitin chains.
Dengue virus preferentially uses human and mosquito non-optimal codons
Authors: Castellano Luciana A , McNamara Ryan J , Pallares Horacio M , Gamarnik Andrea V , Alvarez Diego E , Bazzini Ariel A
Published: June 2023

Codon optimality refers to the effect codon composition has on messenger RNA (mRNA) stability and translation level and implies that synonymous codons are not silent from a regulatory point of view. Here, we investigated the adaptation of virus genomes to the host optimality code using mosquito-borne dengue virus (DENV) as a model. We defined which codons are associated with unstable and stable (non-optimal and optimal codons, respectively) mRNAs in mosquito cells and showed that DENV preferentially uses non-optimal codons and avoids codons that are defined as optimal in either human or mosquito cells. Human genes enriched in the codons preferentially and frequently used by DENV are up-regulated during infection, and so is the tRNA decoding the non-optimal and DENV preferentially used codon for arginine. We found that synonymous mutations towards DENV’s preferred non-optimal codons (e.g., AGA) increase fitness of DENV during serial passaging in human or mosquito cells. Finally, our analyses revealed that hundreds of viruses preferentially use non-optimal codons, with those infecting a single host displaying an even stronger bias, suggesting that synonymous codon choice is a key aspect of host-pathogen interaction.
Aerobic denitrification as N2O source in microbial communities
Authors: Roothans Nina , Gabriëls Minke , Pabst Martin , van Loosdrecht Mark C. M. , Laureni Michele
Published: June 2023

Nitrous oxide (N2O) is a potent greenhouse gas of primarily microbial origin. Aerobic and anoxic emissions are commonly ascribed to nitrification and denitrification, respectively. Beyond this established dichotomy, we quantitatively prove that heterotrophic denitrification can significantly contribute to aerobic nitrogen turnover and N2O emissions in complex microbiomes exposed to frequent oxic/anoxic transitions. Planktonic, nitrification-inhibited denitrifying enrichments respired over a third of the influent organic substrate with nitrate at high oxygen concentrations. N2O accounted for up to one quarter of the aerobically respired nitrate. The constitutive detection of all denitrification enzymes in both anoxic and oxic periods highlight the selective advantage offered by metabolic preparedness in dynamic environments. We posit that aerobic denitrification and associated N2O formation is currently underestimated in dynamic microbial ecosystems.
Hexokinase regulates Mondo-mediated longevity via the PPP and organellar dynamics
Authors: Laboy Raymond , Ndoci Marjana , Vonolfen Maximilian , Ballhysa Eugen , Syed Shamsh Tabrez , Droth Tim , Schilling Klara , Löhrke Anna , Atanassov Ilian , Antebi Adam
Published: June 2023

The transcriptional complex Mondo/Max-like, MML-1/MXL-2, acts as a convergent transcriptional regulatory output of multiple longevity pathways inCaenorhabditis elegans. These transcription factors coordinate nutrient sensing with carbohydrate and lipid metabolism across the evolutionary spectrum. While most studies have focused on the downstream outputs, little is known about the upstream inputs that regulate these transcription factors in a live organism. Here, we found that knockdown of various glucose metabolic enzymes decreases MML-1 localization in the nucleus and identified two hexokinase isozymes,hxk-1andhxk-2,as the most vigorous regulators of MML-1 function. Upon hexokinase knockdown, MML-1 redistributes to mitochondria and lipid droplets (LD) and concomitantly, transcriptional targets are downregulated and germline longevity is abolished. Further, we found thathxk-1regulates MML-1 through mitochondrial β-oxidation, whilehxk-2regulates MML-1 by modulating the pentose phosphate pathway (PPP) and its coordinated association with lipid droplets. Similarly, inhibition of the PPP rescues mammalian MondoA nuclear translocation and transcriptional function upon starvation. These studies reveal how metabolic signals and organellar communication regulate a key convergent metabolic transcription factor to promote longevity.
AutoRNC: an automated modeling program for building atomic models of ribosome-nascent chain complexes
Authors: McDonnell Robert T. , Elcock Adrian H.
Published: June 2023

The interpretation of experimental studies of co-translational protein folding often benefits from the use of computational methods that seek to model the nascent chain and its interactions with the ribosome. Ribosome-nascent chain (RNC) constructs studied experimentally can vary significantly in size and the extent to which they contain secondary and tertiary structure, and building realistic 3D models of them therefore often requires expert knowledge. To circumvent this issue, we describe here AutoRNC, an automated modeling program capable of constructing large numbers of plausible atomic models of RNCs within minutes. AutoRNC takes input from the user specifying any regions of the nascent chain that contain secondary or tertiary structure and attempts to build conformations compatible with those specifications – and with the constraints imposed by the ribosome – by sampling and progressively piecing together dipeptide conformations extracted from the RCSB. We first show that conformations of completely unfolded proteins built by AutoRNC in the absence of the ribosome have radii of gyration that match well with the corresponding experimental data. We then show that AutoRNC can build plausible conformations for a wide range of RNC constructs for which experimental data have already been reported. Since AutoRNC requires only modest computational resources, we anticipate that it will prove to be a useful hypothesis generator for experimental studies, for example, in providing indications of whether designed constructs are likely to be capable of folding, as well as providing useful starting points for downstream atomic or coarse-grained simulations of the conformational dynamics of RNCs.
Hyperglycosylation of prosaposin in tumor DCs promotes immune escape in cancer
Authors: Sharma Pankaj , Zhang Xiaolong , Ly Kevin , Kim Ji Hyung , Wan Qi , Kim Jessica , Lou Mumeng , Kain Lisa , Teyton Luc , Winau Florian
Published: June 2023

Tumors develop strategies to evade immunity by suppressing antigen presentation. Here, we show that prosaposin drives CD8 T cell-mediated tumor immunity and that its hyperglycosylation in tumor DCs leads to cancer immune escape. We found that lysosomal prosaposin and its single saposin cognates mediated disintegration of tumor cell-derived apoptotic bodies to facilitate presentation of membrane-associated antigen and T cell activation. In the tumor microenvironment, TGF-β induced hyperglycosylation of prosaposin and its subsequent secretion, which ultimately caused depletion of lysosomal saposins. In melanoma patients, we found similar prosaposin hyperglycosylation in tumor-associated DCs, and reconstitution with prosaposin rescued activation of tumor-infiltrating T cells. Targeting tumor DCs with recombinant prosaposin triggered cancer protection and enhanced immune checkpoint therapy. Our studies demonstrate a critical function of prosaposin in tumor immunity and escape and introduce a novel principle of prosaposin-based cancer immunotherapy.

One Sentence Summary

Prosaposin facilitates antigen cross-presentation and tumor immunity and its hyperglycosylation leads to immune evasion.
Functional Sexual Dimorphism in Human Nociceptors
Authors: Stratton Harrison , Dolatyari Mahdi , Dumaire Nicolas , Moutal Aubin , Ghetti Andre , Cotta Tamara , Mitchell Stefanie , Yue Xu , Navratilova Edita , Porreca Frank
Published: June 2023

The recent demonstration of differences in transcript expression in human post-mortem sensory neurons suggests the possibility of sexually dimorphic pain mechanisms. To date, however, the concept of “male” and “female” nociceptors has not been demonstrated at a functional level. We now report sensitization of female, but not male, human nociceptors by prolactin revealing a female-selective mechanism that can be exploited to improve the treatment of pain in women.
Predicting T cell activation based on intracellular calcium fluctuations
Authors: This Sébastien , Costantino Santiago , Melichar Heather J.
Published: June 2023

Adoptive T cell therapies rely on the transduction of T cells with a predetermined antigen receptor which redirects their specificity towards tumor-specific antigens. Despite the development of multiple platforms for tumor-specific T cell receptor (TCR) discovery, this process remains time consuming and skewed toward high-affinity TCRs. Specifically, the methods for identifying therapeutically-relevant TCR sequences, predominantly achieved through the enrichment of antigen-specific T cells, represents a major bottleneck for the broader application of TCR-engineered cell therapies. Fluctuation of intracellular calcium levels in T cells is a well described, proximal readout of TCR signaling. Hence, it is an attractive candidate marker for identifying antigen-specific T cells that does not requirein vitroantigen-specific T cell expansion. However, calcium fluctuations downstream of TCR engagement with antigen are highly variable; we propose that appropriately-trained machine learning algorithms may allow for T cell classification from complex datasets such as those related to polyclonal T cell signaling events. Using deep learning tools, we demonstrate efficient and accurate prediction of antigen-specificity based on intracellular Ca2+fluctuations ofin vitro-stimulated CD8+T cells. Using a simple co-culture assay to activate monoclonal TCR transgenic T cells of known specificity, we trained a convolutional neural network to predict T cell reactivity, and we test the algorithm against T cells bearing a distinct TCR transgene as well as a polyclonal T cell response. This approach provides the foundation for a new pipeline to fast-track antigen specific TCR sequence identification for use in adoptive T cell therapy.

Significance Statement

While T cells engineered to express a cancer-specific T cell receptor (TCR) are emerging as a viable approach for personalized therapies, the platforms for identifying clinically-relevant TCR sequences are often limited in the breadth of antigen receptors they identify or are cumbersome to implement on a personalized basis. Here, we show that imaging of intracellular calcium fluctuations downstream of TCR engagement with antigen can be used, in combination with artificial intelligence approaches, to accurately and efficiently predict T cell specificity. The development of cancer-specific T cell isolation methods based on early calcium fluctuations may avoid the biases of current methodologies for the isolation of patient-specific TCR sequences in the context of adoptive T cell therapy.
Myosin 10 uses its MyTH4 and FERM domains differentially to support two aspects of spindle pole biology required for mitotic spindle bipolarity
Authors: Yim Yang-In , Pedrosa Antonio , Wu Xufeng , Chinthalapudi Krishna , Cheney Richard E. , Hammer John A.
Published: June 2023

Myosin 10 (Myo10) has the ability to link actin filaments to integrin-based adhesions and to microtubules by virtue of its integrin-binding FERM domain and microtubule-binding MyTH4 domain, respectively. Here we used Myo10 knockout cells to define Myo10’s contribution to the maintenance of spindle bipolarity, and complementation to quantitate the relative contributions of its MyTH4 and FERM domains. Myo10 knockout HeLa cells and mouse embryo fibroblasts (MEFs) both exhibit a pronounced increase in the frequency of multipolar spindles. Staining of unsynchronized metaphase cells showed that the primary driver of spindle multipolarity in knockout MEFs and knockout HeLa cells lacking supernumerary centrosomes is pericentriolar material (PCM) fragmentation, which creates y-tubulin-positive acentriolar foci that serve as additional spindle poles. For HeLa cells possessing supernumerary centrosomes, Myo10 depletion further accentuates spindle multipolarity by impairing the clustering of the extra spindle poles. Complementation experiments show that Myo10 must interact with both integrins and microtubules to promote PCM/pole integrity. Conversely, Myo10’s ability to promote the clustering of supernumerary centrosomes only requires that it interact with integrins. Importantly, images of Halo-Myo10 knock-in cells show that the myosin localizes exclusively within adhesive retraction fibers during mitosis. Based on these and other results, we conclude that Myo10 promotes PCM/pole integrity at a distance, and that it facilitates supernumerary centrosome clustering by promoting retraction fiber-based cell adhesion, which likely provides an anchor for the microtubule-based forces driving pole focusing.
Lego-like Mixing and Matching of Engineered Bacteria Configure Full Subtractor and Adder Through an Artificial Neural Network Type Architecture
Authors: Bonnerjee Deepro , Chakraborty Saswata , Bagh Sangram
Published: June 2023

One of the long-term goals of synthetic bioengineering is to create configurable and programmable biological systems by just mixing and matching "LEGO"-like bio-modules. Here, we introduce a configurable and modular multi-cellular system where, from a small library of nine discrete engineered bacterial cells, a full subtractor and a full adder can be built on demand by just mixing and matching seven appropriate cell types in a culture. Here, each set of engineered bacteria was modelled as an ‘artificial neuro-synapse’ that, in a co-culture, formed a single layer artificial neural network (ANN) type architecture that worked as a biochemical full subtractor or full adder. The system is configurable with interchangeable cellular modules, whereby through simply interchanging two cell types in the subtractor culture, a full adder can be built and vice versa. This Lego-like mix and match system is mathematically predictive, and provide a flexible and scalable means to build complex cellular functions. This work may have significance in biocomputer technology development, multi-cellular synthetic biology, and cellular hardware for ANN.
Structure of a heteropolymeric type 4 pilus from a monoderm bacterium
Authors: Anger Robin , Pieulle Laetitia , Shahin Meriam , Valette Odile , Le Guenno Hugo , Kosta Artemis , Pelicic Vladimir , Fronzes Rémi
Published: June 2023

Type 4 pili (T4P) are important virulence factors, which belong to a superfamily of nanomachines ubiquitous in prokaryotes, called type 4 filaments (T4F). T4F are defined as helical polymers of type 4 pilins. Recent advances in cryo-electron microscopy (cryo-EM) led to structures of several T4F. This revealed that the long N-terminal α-helix, the trademark of pilins, packs in the centre of the filaments to form a hydrophobic core, which in bacteria is accompanied by the melting (unfolding) of a portion of α1. Since all available bacterial T4F structures are from diderm species, we tested whether this architecture is conserved in phylogenetically distant species by determining the structure of the T4P of the monodermStreptococcus sanguinis. Our 3.7 A resolution cryo-EM structure of this heteropolymeric T4P, and the resulting full atomic model including all minor pilins, highlight universal features of bacterial T4F and have widespread implications in understanding their biology.
Neuromechanical Justification of Lower-Limb Functional Tests for a Return to Running: A Muscle Coordination Analysis
Authors: Saito Hiroki , Yamano Ayu , Suzuki Nanae , Matsushita Kazuya , Yokoyama Hikaru , Sasaki Atsushi , Takahashi Tatsuya , Nakazawa Kimitaka
Published: June 2023

Introduction

This study aimed to explore the shared muscle synergies between running and functional tests that are commonly used when considering the return to running (RTR) after sports-related injuries. We hypothesized that shared muscle synergies would differ among tasks, providing insights into prioritizing functional tests in the context of RTR.

Methods

Ten healthy male participants were recruited to perform running and 9 functional tasks and their 16 lower limb and trunk muscle activities were recorded using electromyography (EMG). Non-negative matrix factorization (NMF) was applied to the collected EMG data to explore shared muscle synergies between running and the functional tasks. We compared the percentages of shared synergies and temporal patterns between running and each functional test.

Results

Although all functional tests exhibited shared muscle synergies with running, the walk (75% [40%-100%]), single leg hops with 30% of maximum distance (SLH30) (60% [20%-100%]), and stepup (63% [0%-100%]) tasks displayed significantly higher percentages of shared synergies compared to other tests. However, significant differences in temporal patternss were observed between running and all functional tasks, indicating varying activation profiles of shared muscle synergies.

Conclusion

Although all functional tests shared muscle synergies with running, variations in the degree of shared synergies and temporal patterns imply that walking, SLH30, and step-up tests may be the most beneficial in predicting running behavior post-ACL injuries. However, functional tests cannot fully replicate running dynamics, suggesting the need for a careful interpretation when assessing readiness for RTR.
Water distribution in human hair microstructure elucidated by spin contrast variation small-angle neutron scattering
Authors: Noda Yohei , Koizumi Satoshi , Maeda Tomoki , Inada Takumi , Ishihara Aya
Published: June 2023

Dynamic nuclear polarization (DNP) is effective for controlling the neutron scattering length of protons and can be utilized for contrast variation in small-angle neutron scattering (SANS). Using the TEMPOL solution soaking method as electron spin doping, the DNP–SANS technique was applied to human hair fiber for the first time. For dry and D2O-swollen hair samples, a drastic change in the SANS profile was observed at high polarization conditions (|P
H
P
N| ∼ 60%, where P
H and P
N are the proton and neutron spin polarization, respectively). The SANS profile as a function of the magnitude of the scattering vector, q, was composed of a low-q upturn, a middle-q oscillation and a high-q flat region. The low-q upturn was assumed to be a combination of two power-law functions, q
−4 due to a large structure interface (Porod's law) and q
−2 due to random coil. The middle-q oscillation was well reproduced by numerical calculation based on the structure model of intermediate filaments (IFs) as proposed by Er Rafik et al. [Biophys. J. (2004), 86, 3893–3904]: one pair of keratin coiled-coils is located at the center and surrounded by seven pairs of keratin coiled-coils located in a circle (called the `7 + 1' model), and a collection of IFs is arranged in a quasi-hexagonal manner. For the observed SANS profiles for different P
H
P
N, the IF term contribution maintained a constant q-dependent profile, despite significant changes in intensity. This indicates that the macrofibril is composed of two domains (keratin coiled-coils and matrix). In addition, D2O swelling enhanced the IF term intensity and shifted the polarization-dependent local minimum to higher P
H
P
N. This behavior was reproduced by contrast factor calculation based on the two-domain model. Scattering length densities of keratin coiled-coil and surrounding matrix domains were calculated by use of the known amino acid composition, considering the hydrogen–deuterium exchange reaction during soaking with D2O solution of TEMPOL. As a result, it was found that for keratin coiled-coil domains, about 40% of the peptide backbone amide NH protons were replaced with deuterons. This means that 68% of the α-helix domain is rigid, but the rest is flexible to allow dynamic dissociation of the hydrogen bond. Furthermore, the local mass density of each domain was precisely evaluated. The obtained data are expected to be a guide for further detailed investigation of keratin and keratin-associated protein distribution. This approach is expected to be applied to a wide variety of bio-derived materials, which are water absorbing in general.
Exploring the impact of incoherent Compton scattering on X-ray pair distribution function analysis of disordered materials
Authors: Jeong Il-Kyoung
Published: June 2023

X-ray atomic pair distribution function (XPDF) measurements using a two-dimensional area detector have been of great value in studying atomic structures of materials with varying degrees of disorder. However, an area detector does not have energy resolution. Thus, incoherent inelastic Compton scattering and fluorescence are not discriminated, contaminating coherent elastic scattering. This paper investigates the effects of random noise from incoherent scattering on XPDF analysis. To conduct the study, the elastic scattering, Compton scattering and fluorescence of In0.33Ga0.67As alloy were separately measured using an intrinsic Ge solid-state detector with energy resolution. It is found that the addition of Compton scattering with a noise-to-signal ratio of about 0.8% results in the smearing of diffuse scattering in the high-Q region. Moreover, adding extra noise from fluorescence increases the smearing, overwhelming the diffuse scattering. Additionally, simulated data of elastic and Compton scattering on ferroelectric Ba(Ti0.8Zr0.2)O3 were used to investigate the evolution of noise fluctuation and its effects on the XPDF as a function of total intensity.
In situ biaxial loading and multi-scale deformation measurements of nanostructured materials at the CoSAXS beamline at MAX IV Laboratory
Authors: Mota-Santiago Pablo , Engqvist Jonas , Hall Stephen , Appio Roberto , Maghe Maxime , Sathikumar Gautham , Ristinmaa Matti , Plivelic Tomás S.
Published: June 2023

Characterization of the mechanical response of polymers and composite materials relies heavily on the macroscopic stress–strain response in uniaxial tensile configurations. To provide representative information, the deformation process must be homogeneous within the gauge length, which is a condition that is rarely achieved due to stress concentration or inhomogeneities within the specimen. In this work, the development of a biaxial mechanical testing device at the CoSAXS beamline at MAX IV Laboratory is presented. The design facilitates simultaneous measurement of small- and wide-angle X-ray scattering (SAXS/WAXS), allowing assessment of the microstructural configuration before, after and during the continuous deformation process at multiple length scales. The construction also supports multiple deformation conditions, while guaranteeing stability even at high loads. Furthermore, the mechanical experiments can be complemented with spatially resolved mesoscopic surface deformation measurements using 3D-surface digital image correlation (DIC). Polycarbonate (PC) was used to demonstrate the varied material response to multi-axial deformation, as PC is isotropic with a high glass transition temperature (∼150°) and high strength. As a result, a clear correlation between full-field methods and the microstructural information determined from WAXS measurements is demonstrated. When a uniaxial load is applied, homogeneous strain regions could be observed extending perpendicular to the applied load. When a secondary axial load was added (biaxial mode), it was observed that high strain domains were created near the centre of the sample and at the boundaries after yield. With increased strain, the deformation in the main deformation direction also increases. Mechanical reliability was demonstrated by carrying out static loading of polyacrylonitrile-based carbon fibre (CF) bundles. As a result, the nonlinear stiffening behaviour typically observed in CFs was seen, while no evidence of the creation of new voids during loading was observed. The results support the reliability and broad applicability of the developed technique.