Identification of human exTreg cells as CD16+CD56+ cytotoxic CD4+ T cells.

In atherosclerosis, some regulatory T (Treg) cells become exTreg cells. We crossed inducible Treg and exTreg cell lineage-tracker mice (FoxP3eGFP-Cre-ERT2ROSA26CAG-fl-stop-fl-tdTomato) to atherosclerosis-prone Apoe-/- mice, sorted Treg cells and exTreg cells and determined their transcriptomes by bulk RNA sequencing (RNA-seq). Genes that were differentially expressed between mouse Treg cells and exTreg cells and filtered for their presence in a human single-cell RNA-sequencing (scRNA-seq) panel identified exTreg cell signature genes as CST7, NKG7, GZMA, PRF1, TBX21 and CCL4. Projecting these genes onto the human scRNA-seq with CITE-seq data identified human exTreg cells as CD3+CD4+CD16+CD56+, which was validated by flow cytometry. Bulk RNA-seq of sorted human exTreg cells identified them as inflammatory and cytotoxic CD4+T cells that were significantly distinct from both natural killer and Treg cells. DNA sequencing for T cell receptor-ß showed clonal expansion of Treg cell CDR3 sequences in exTreg cells. Cytotoxicity was functionally demonstrated in cell killing and CD107a degranulation assays, which identifies human exTreg cells as cytotoxic CD4+T cells.

First observations of core-transiting seismic phases on Mars.

We present the first observations of seismic waves propagating through the core of Mars. These observations, made using seismic data collected by the InSight geophysical mission, have allowed us to construct the first seismically constrained models for the elastic properties of Mars' core. We observe core-transiting seismic phase SKS from two farside seismic events detected on Mars and measure the travel times of SKS relative to mantle traversing body waves. SKS travels through the core as a compressional wave, providing information about bulk modulus and density. We perform probabilistic inversions using the core-sensitive relative travel times together with gross geophysical data and travel times from other, more proximal, seismic events to seek the equation of state parameters that best describe the liquid iron-alloy core. Our inversions provide constraints on the velocities in Mars' core and are used to develop the first seismically based estimates of its composition. We show that models informed by our SKS data favor a somewhat smaller (median core radius = 1,780 to 1,810 km) and denser (core density = 6.2 to 6.3 g/cm3) core compared to previous estimates, with a P-wave velocity of 4.9 to 5.0 km/s at the core-mantle boundary, with the composition and structure of the mantle as a dominant source of uncertainty. We infer from our models that Mars' core contains a median of 20 to 22 wt% light alloying elements when we consider sulfur, oxygen, carbon, and hydrogen. These data can be used to inform models of planetary accretion, composition, and evolution.

Hydrocortisone to Improve Survival without Bronchopulmonary Dysplasia.

BACKGROUND: Bronchopulmonary dysplasia is a prevalent complication after extremely preterm birth. Inflammation with mechanical ventilation may contribute to its development. Whether hydrocortisone treatment after the second postnatal week can improve survival without bronchopulmonary dysplasia and without adverse neurodevelopmental effects is unknown. METHODS: We conducted a trial involving infants who had a gestational age of less than 30 weeks and who had been intubated for at least 7 days at 14 to 28 days. Infants were randomly assigned to receive either hydrocortisone (4 mg per kilogram of body weight per day tapered over a period of 10 days) or placebo. Mandatory extubation thresholds were specified. The primary efficacy outcome was survival without moderate or severe bronchopulmonary dysplasia at 36 weeks of postmenstrual age, and the primary safety outcome was survival without moderate or severe neurodevelopmental impairment at 22 to 26 months of corrected age. RESULTS: We enrolled 800 infants (mean [±SD] birth weight, 715±167 g; mean gestational age, 24.9±1.5 weeks). Survival without moderate or severe bronchopulmonary dysplasia at 36 weeks occurred in 66 of 398 infants (16.6%) in the hydrocortisone group and in 53 of 402 (13.2%) in the placebo group (adjusted rate ratio, 1.27; 95% confidence interval [CI], 0.93 to 1.74). Two-year outcomes were known for 91.0% of the infants. Survival without moderate or severe neurodevelopmental impairment occurred in 132 of 358 infants (36.9%) in the hydrocortisone group and in 134 of 359 (37.3%) in the placebo group (adjusted rate ratio, 0.98; 95% CI, 0.81 to 1.18). Hypertension that was treated with medication occurred more frequently with hydrocortisone than with placebo (4.3% vs. 1.0%). Other adverse events were similar in the two groups. CONCLUSIONS: In this trial involving preterm infants, hydrocortisone treatment starting on postnatal day 14 to 28 did not result in substantially higher survival without moderate or severe bronchopulmonary dysplasia than placebo. Survival without moderate or severe neurodevelopmental impairment did not differ substantially between the two groups. (Funded by the National Institutes of Health; ClinicalTrials.gov number, NCT01353313.).

An intra-tumoral niche maintains and differentiates stem-like CD8 T cells.

Tumour-infiltrating lymphocytes are associated with a survival benefit in several tumour types and with the response to immunotherapy1-8. However, the reason some tumours have high CD8 T cell infiltration while others do not remains unclear. Here we investigate the requirements for maintaining a CD8 T cell response against human cancer. We find that CD8 T cells within tumours consist of distinct populations of terminally differentiated and stem-like cells. On proliferation, stem-like CD8 T cells give rise to more terminally differentiated, effector-molecule-expressing daughter cells. For many T cells to infiltrate the tumour, it is critical that this effector differentiation process occur. In addition, we show that these stem-like T cells reside in dense antigen-presenting-cell niches within the tumour, and that tumours that fail to form these structures are not extensively infiltrated by T cells. Patients with progressive disease lack these immune niches, suggesting that niche breakdown may be a key mechanism of immune escape.

Detection of Mpox Virus Using Microbial Cell-Free DNA: The Potential of Pathogen-Agnostic Sequencing for Rapid Identification of Emerging Pathogens.

BACKGROUND: The 2022 global outbreak of Monkeypox virus (MPXV) highlighted challenges with polymerase chain reaction detection as divergent strains emerged and atypical presentations limited the applicability of swab sampling. Recommended testing in the United States requires a swab of lesions, which arise late in infection and may be unrecognized. We present MPXV detections using plasma microbial cell-free DNA (mcfDNA) sequencing. METHODS: Fifteen plasma samples from 12 case-patients were characterized through mcfDNA sequencing. Assay performance was confirmed through in silico inclusivity and exclusivity assessments. MPXV isolates were genotyped using mcfDNA, and phylodynamic information was imputed using publicly available sequences. RESULTS: MPXV mcfDNA was detected in 12 case-patients. Mpox was not suspected in 5, with 1 having documented resolution of mpox >6 months previously. Six had moderate to severe mpox, supported by high MPXV mcfDNA concentrations; 4 died. In 7 case-patients, mcfDNA sequencing detected coinfections. Genotyping by mcfDNA sequencing identified 22 MPXV mutations at 10 genomic loci in 9 case-patients. Consistent with variation observed in the 2022 outbreak, 21 of 22 variants were G > A/C > T. Phylogenetic analyses imputed isolates to sublineages arising at different time points and from different geographic locations. CONCLUSIONS: We demonstrate the potential of plasma mcfDNA sequencing to detect, quantify, and, for acute infections with high sequencing coverage, subtype MPXV using a single noninvasive test. Sequencing plasma mcfDNA may augment existing mpox testing in vulnerable patient populations or in patients with atypical symptoms or unrecognized mpox. Strain type information may supplement disease surveillance and facilitate tracking emerging pathogens.

Safety and Immunogenicity of an Anti-Zika Virus DNA Vaccine.

BACKGROUND: Although Zika virus (ZIKV) infection is typically self-limiting, other associated complications such as congenital birth defects and the Guillain-Barré syndrome are well described. There are no approved vaccines against ZIKV infection. METHODS: In this phase 1, open-label clinical trial, we evaluated the safety and immunogenicity of a synthetic, consensus DNA vaccine (GLS-5700) encoding the ZIKV premembrane and envelope proteins in two groups of 20 participants each. The participants received either 1 mg or 2 mg of vaccine intradermally, with each injection followed by electroporation (the use of a pulsed electric field to introduce the DNA sequence into cells) at baseline, 4 weeks, and 12 weeks. RESULTS: The median age of the participants was 38 years, and 60% were women; 78% were White and 22% Black; in addition, 30% were Hispanic. At the interim analysis at 14 weeks (i.e., after the third dose of vaccine), no serious adverse events were reported. Local reactions at the vaccination site (e.g., injection-site pain, redness, swelling, and itching) occurred in approximately 50% of the participants. After the third dose of vaccine, binding antibodies (as measured on enzyme-linked immunosorbent assay) were detected in all the participants, with geometric mean titers of 1642 and 2871 in recipients of 1 mg and 2 mg of vaccine, respectively. Neutralizing antibodies developed in 62% of the samples on Vero-cell assay. On neuronal-cell assay, there was 90% inhibition of ZIKV infection in 70% of the serum samples and 50% inhibition in 95% of the samples. The intraperitoneal injection of postvaccination serum protected 103 of 112 IFNAR knockout mice (bred with deletion of genes encoding interferon-α and interferon-ß receptors) (92%) that were challenged with a lethal dose of ZIKV-PR209 strain; none of the mice receiving baseline serum survived the challenge. Survival was independent of the neutralization titer. CONCLUSIONS: In this phase 1, open-label clinical trial, a DNA vaccine elicited anti-ZIKV immune responses. Further studies are needed to better evaluate the safety and efficacy of the vaccine. (Funded by GeneOne Life Science and others; ZIKA-001 ClinicalTrials.gov number, NCT02809443.).

Evaluation of Automated Processing of Electronically Reported Serological Tests for Syphilis Using Current and Historical Syphilis Results Compared With Traditional Reactor Grid Processing in Florida.

BACKGROUND: Syphilis in Florida increased 49% from 2016 to 2020. Moreover, many serological tests for syphilis (STS) do not indicate current infection. Traditionally, syphilis surveillance systems used reactor grids, a method for prioritizing STS for investigation based on age, nontreponemal titer, and/or sex. In 2022, Florida's sexually transmitted disease surveillance system implemented an automated method for processing electronically reported STS (eSTS), expanding upon the reactor grid, using an individual's current STS (treponemal and nontreponemal), treatment history, and historical STS results aiming for more efficiently processing eSTS. We compared the new method of processing eSTS results against the reactor grid and determined potential value in time/cost savings of this change. METHODS: All eSTSs (n = 4144) from January 2, 2023 to January 8, 2023, were compared by how the logic-based method processed test results versus how the reactor grid processed test results. Each method was compared using measurements of accuracy (e.g., sensitivity/specificity). Time and cost savings in eSTS processing were estimated. RESULTS: Using the surveillance case definition as reference, the accuracy of the logic-based method for processing eSTS was nearly double (82.3% vs. 43.6%), had greater specificity (79.0% vs. 33.0%), and increased positive predictive value (47.5% vs. 22.0%) when compared with the reactor grid method. Sensitivity (99.5% vs. 98.6%) and negative predictive value (99.9% vs. 99.2%) remained similar. The logic-based method is estimated to save 7783 hours annually (~$185,000). CONCLUSIONS: Processing eSTS based on current and historical STS results is significantly more accurate than using a reactor grid. Moreover, these improvements save time and resources that can be better allocated to other program prevention activities.

Comprehensive Assessment of Herbicide Toxicity on Navicula sp. Algae: Effects on Growth, Chlorophyll Content, Antioxidant System, and Lipid Metabolism.

This study investigated the effects of herbicide exposure on Navicula sp. (MASCC-0035) algae, focusing on growth density, chlorophyll content, antioxidant system, and lipid metabolism. Navicula cultures were exposed to different concentrations of atrazine (ATZ), glyphosate (Gly), and acetochlor (ACT) for 96 h. Results showed a significant decrease in cell numbers, with higher herbicide concentrations having the most noticeable impacts. For instance, Gly-G2 had reduced cell populations by 21.00% at 96 h. Chlorophyll content varied, with Gly having a greater impact on chlorophyll a compared to ATZ and ACT. Herbicide exposure also affected the antioxidant system, altering levels of soluble sugar, soluble protein, and reactive oxygen species (ROS). Higher herbicide rates increased soluble sugar content (e.g., ATZ, Gly, and ACT-G2 had increased by 14.03%, 19.88%, and 19.83%, respectively, at 72 h) but decreased soluble protein content, notably in Gly-G2 by 11.40%, indicating cellular stress. Lipid metabolism analysis revealed complex responses, with changes in free proline, fatty acids, and lipase content, each herbicide exerting distinct effects. These findings highlight the multifaceted impacts of herbicide exposure on Navicula algae, emphasizing the need for further research to understand ecological implications and develop mitigation strategies for aquatic ecosystems.

Structural basis for the specificity of PPM1H phosphatase for Rab GTPases.

LRRK2 serine/threonine kinase is associated with inherited Parkinson's disease. LRRK2 phosphorylates a subset of Rab GTPases within their switch 2 motif to control their interactions with effectors. Recent work has shown that the metal-dependent protein phosphatase PPM1H counteracts LRRK2 by dephosphorylating Rabs. PPM1H is highly selective for LRRK2 phosphorylated Rabs, and closely related PPM1J exhibits no activity towards substrates such as Rab8a phosphorylated at Thr72 (pThr72). Here, we have identified the molecular determinant of PPM1H specificity for Rabs. The crystal structure of PPM1H reveals a structurally conserved phosphatase fold that strikingly has evolved a 110-residue flap domain adjacent to the active site. The flap domain distantly resembles tudor domains that interact with histones in the context of epigenetics. Cellular assays, crosslinking and 3-D modelling suggest that the flap domain encodes the docking motif for phosphorylated Rabs. Consistent with this hypothesis, a PPM1J chimaera with the PPM1H flap domain dephosphorylates pThr72 of Rab8a both in vitro and in cellular assays. Therefore, PPM1H has acquired a Rab-specific interaction domain within a conserved phosphatase fold.

Best practice approach for redo-surgeries after sleeve gastrectomy, an expert's modified Delphi consensus.

BACKGROUND: Sleeve gastrectomy (SG) is the most common metabolic and bariatric surgical (MBS) procedure worldwide. Despite the desired effect of SG on weight loss and remission of obesity-associated medical problems, there are some concerns regarding the need to do revisional/conversional surgeries after SG. This study aims to make an algorithmic clinical approach based on an expert-modified Delphi consensus regarding redo-surgeries after SG, to give bariatric and metabolic surgeons a guideline that might help for the best clinical decision. METHODS: Forty-six recognized bariatric and metabolic surgeons from 25 different countries participated in this Delphi consensus study in two rounds to develop a consensus on redo-surgeries after SG. An agreement/disagreement ≥ 70.0% on statements was considered to indicate a consensus. RESULTS: Consensus was reached for 62 of 72 statements and experts did not achieve consensus on 10 statements after two rounds of online voting. Most of the experts believed that multi-disciplinary team evaluation should be done in all redo-procedures after SG and there should be at least 12 months of medical and supportive management before performing redo-surgeries after SG for insufficient weight loss, weight regain, and gastroesophageal reflux disease (GERD). Also, experts agreed that in case of symptomatic GERD in the presence of adequate weight loss, medical treatment for at least 1 to 2 years is an acceptable option and agreed that Roux-en Y gastric bypass is an appropriate option in this situation. There was disagreement consensus on efficacy of omentopexy in rotation and efficacy of fundoplication in the presence of a dilated fundus and GERD. CONCLUSION: Redo-surgeries after SG is still an important issue among bariatric and metabolic surgeons. The proper time and procedure selection for redo-surgery need careful considerations. Although multi-disciplinary team evaluation plays a key role to evaluate best options in these situations, an algorithmic clinical approach based on the expert's consensus as a guideline can help for the best clinical decision-making.

Effect of reduced versus usual lipid emulsion dosing on bilirubin neurotoxicity and neurodevelopmental impairment in extremely preterm infants: study protocol for a randomized controlled trial.

BACKGROUND: Bilirubin neurotoxicity (BN) occurs in premature infants at lower total serum bilirubin levels than term infants and causes neurodevelopmental impairment. Usual dose lipid infusions in preterm infants may increase free fatty acids sufficiently to cause bilirubin displacement from albumin, increasing passage of unbound bilirubin (UB) into the brain leading to BN and neurodevelopmental impairment not reliably identifiable in infancy. These risks may be influenced by whether cycled or continuous phototherapy is used to control bilirubin levels. OBJECTIVE: To assess differences in wave V latency measured by brainstem auditory evoked responses (BAER) at 34-36 weeks gestational age in infants born ≤ 750 g or < 27 weeks' gestational age randomized to receive usual or reduced dose lipid emulsion (half of the usual dose) irrespective of whether cycled or continuous phototherapy is administered. METHODS: Pilot factorial randomized controlled trial (RCT) of lipid dosing (usual and reduced) with treatment groups balanced between cycled or continuous phototherapy assignment. Eligible infants are born at ≤ 750 g or < 27 weeks' gestational age enrolled in the NICHD Neonatal Research Network RCT of cycled or continuous phototherapy. Infants will randomize 1:1 to reduced or usual dose lipid assignment during the first 2 weeks after birth and stratified by phototherapy assignment. Free fatty acids and UB will be measured daily using a novel probe. BAER testing will be performed at 34-36 weeks postmenstrual age or prior to discharge. Blinded neurodevelopmental assessments will be performed at 22-26 months. Intention-to-treat analyses will be performed with generalized linear mixed models with lipid dose and phototherapy assignments as random effects covariates, and assessment for interactions. Bayesian analyses will be performed as a secondary analysis. DISCUSSION: Pragmatic trials are needed to evaluate whether lipid emulsion dosing modifies the effect of phototherapy on BN. This factorial design presents a unique opportunity to evaluate both therapies and their interaction. This study aims to address basic controversial questions about the relationships between lipid administration, free fatty acids, UB, and BN. Findings suggesting a reduced lipid dose can diminish the risk of BN would support the need for a large multicenter RCT of reduced versus usual lipid dosing. TRIAL REGISTRATION: Clinical Trials.gov, NCT04584983, Registered 14 October 2020, https://clinicaltrials.gov/ct2/show/NCT04584983 Protocol version: Version 3.2 (10/5/2022).

Exploring the Therapeutic Properties of Alga-Based Silver Nanoparticles: Anticancer, Antibacterial, and Free Radical Scavenging Capabilities.

The current study was designed to evaluate the antioxidant, anticancer and antimicrobial activities of silver nanoparticles (AgNPs) biosynthesized by Spirulina platensis extract. The biosynthesized silver nanoparticles were characterized using Fourier transform infrared (FT-IR) analysis, scanning electron microscopy (SEM), transmission electron microscopy (TEM) and X-ray diffraction (XRD) analysis. The antioxidant activity of the biosynthesized AgNPs were determined via DPPH radical scavenging assay while its anticancer activity was determined using the MTT assay. The antimicrobial activity of the biosynthesized AgNPs were analyzed by disc diffusion method. Spirulina platensis acts as a reducing and capping agent. The efficacy of silver nanoparticles (AgNPs) in inhibiting the growth of Gram-negative bacteria, specifically Acetobacter, Klebsiella, Proteus vulgaris, and Pseudomonas aeruginosa, was assessed by the utilisation of the diffusion method. The study aimed to evaluate the efficacy of biosynthesized silver nanoparticles (AgNPs) against many strains of Pseudomonas aeruginosa bacteria. The findings of the study revealed that when administered in doses of 50 µl, 75 µl, and 100 µl, the largest observed zone of inhibition corresponded to measurements of 10.5 mm, 14 mm, and 16 mm, respectively. A zone of inhibition with dimensions of 8 mm, 10.5 mm, and 12 mm was detected during testing against Acetobacter at concentrations of 50 µl, 75 µl, and 100 µl, respectively. The findings also indicate that there is a positive correlation between the concentration of AgNP and the DPPH scavenging ability of silver nanoparticles. The percentage of inhibition observed at concentrations of 500 µg/ml, 400 µg/ml, 300 µg/ml, 200 µg/ml, and 100 µg/ml were recorded as 80±1.98, 61±1.98, 52±1.5, 42±1.99, and 36±1.97, respectively. In addition, it was observed that the silver nanoparticles exhibited the greatest antioxidant activity at a concentration of 500 g/ml, with a measured value of 80.89±1.99. The IC-50 values, representing the inhibitory concentration required to achieve 50 % inhibition, were found to be 8.16, 19.15, 30.14, 41.13, and 63.11 at inhibition levels of 36±1.97, 42±1.99, 52±1.5, 61±1.98, and 80±1.98, respectively.

Designing and Developing a Vision-Based System to Investigate the Emotional Effects of News on Short Sleep at Noon: An Experimental Case Study.

Background: Sleep is a critical factor in maintaining good health, and its impact on various diseases has been recognized by scientists. Understanding sleep patterns and quality is crucial for investigating sleep-related disorders and their potential links to health conditions. The development of non-intrusive and contactless methods for analyzing sleep data is essential for accurate diagnosis and treatment. Methods: A novel system called the sleep visual analyzer (VSleep) was designed to analyze sleep movements and generate reports based on changes in body position angles. The system utilized camera data without requiring any physical contact with the body. A Python graphical user interface (GUI) section was developed to analyze body movements during sleep and present the data in an Excel format. To evaluate the effectiveness of the VSleep system, a case study was conducted. The participants' movements during daytime naps were recorded. The study also examined the impact of different types of news (positive, neutral, and negative) on sleep patterns. Results: The system successfully detected and recorded various angles formed by participants' bodies, providing detailed information about their sleep patterns. The results revealed distinct effects based on the news category, highlighting the potential impact of external factors on sleep quality and behaviors. Conclusions: The sleep visual analyzer (VSleep) demonstrated its efficacy in analyzing sleep-related data without the need for accessories. The VSleep system holds great potential for diagnosing and investigating sleep-related disorders. The proposed system is affordable, easy to use, portable, and a mobile application can be developed to perform the experiment and prepare the results.

A Seinhorst Model Determined the Host-Parasite Relationships of Meloidogyne Javanica Infecting Fenugreek Cv. UM202.

Root-knot nematodes (RKNs) have been shown to be challenging and persistent pests of economic crops worldwide. Among RKNs, Meloidogyne javanica is particularly important, as it rapidly spreads and has a diverse host range. Measuring its damaging threshold level will help us to develop management strategies for adequate plant protection against nematodes. In our study, we observed the relationship between a linear series of 12 initial population densities (Pi) of M. javanica, i.e., 0, 0.125, 0.25, 0.5, 1, 2, 4, 8, 16, 32, 64, and 128 second-staged juveniles (J2s) g-1 soil, and fenugreek cv. UM202 growth parameters were investigated using a Seinhorst model. A Seinhorst model was fitted to shoot length and dry weight data for fenugreek plants. A positive correlation was found between J2s inoculum levels and percent reductions in growth parameters. The 1.3 J2s of M. javanica g-1 soil were found to damage threshold levels with respect to shoot length and shoot dry weight of fenugreek plants. The minimum relative values (m) for shoot length and shoot dry weight were 0.15 and 0.17, respectively, at Pi =128 J2s g-1 soil. The maximum nematode reproduction rate (Pf /Pi) was 31.6 at an initial population density (Pi) of 2 J2s g-1 soil.

Effects of Half-Somersault and Brandt-Daroff exercise on dizziness, fear of fall and quality of life in patients with posterior canal benign paroxysmal positional vertigo: A randomised control trial.

The aim of this study was to compare the effects of Half-Somersault and Brandt-Daroff exercises on dizziness, fear of fall, and quality of life in patients with posterior canal benign paroxysmal positional vertigo (PC-BPPV). This study was conducted from July 2020 to November 2020. A total of 20 patients were enrolled in the study, through sealed envelope method, and assigned to two groups, A and B (10 in each). Vestibular activity and participation measure and Fall Efficacy Scale (FES) were used. The mean age of the patients was 36.70±11.58 years. There was a significant (p=0.05) difference between the Vestibular activities and participation measure (VAP) score at post intervention and Fall Efficacy Scale (FES) (p<0.05) between the groups. Within group analysis showed significant results (p=0.01). This study concluded that both manoeuvers are significantly effective in the treatment of PC-BPPV, but patients treated with Brandt-Daroff exercises reported more improvement in terms of quality of life and residual dizziness compared to the Half Somersault group. Clinical Trials.gov identifier (NCT number): NCT04469309.

Characterization of HLA-A*33:03 epitopes via immunoprecipitation and LC-MS/MS.

Human leukocyte antigen (HLA) class I has more than 18,000 alleles, each of which binds to a set of unique peptides from the cellular degradome. Deciphering the interaction between antigenic peptides and HLA proteins is crucial for understanding immune responses in autoimmune diseases and cancer. In this study, we aimed to characterize the peptidome that binds to HLA-A*33:03, which is one of the most prevalent HLA-A alleles in the Northeast Asian population, but poorly studied. For this purpose, we analyzed the HLA-A*33:03 monoallelic B cell line using immunoprecipitation of HLA-A and peptide complexes, followed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). In this study, we identified 5731 unique peptides that were associated with HLA A*33:03, and experimentally validated the affinity of 40 peptides for HLA-A*33:03 and their stability in HLA A*33:03-peptides complexes. To our knowledge, this study represents the largest dataset of peptides associated with HLA-A*33:03. Also, this is the first study in which HLA A*33:03-associated peptides were experimentally validated.

Phosphorylation of Rab GTPases in the regulation of membrane trafficking.

Rab GTPases are master regulators of membrane trafficking in eukaryotic cells. Phosphorylation of Rab GTPases was characterized in the 1990s and there have been intermittent reports of its relevance to Rab functions. Phosphorylation as a regulatory mechanism has gained prominence through the identification of Rabs as physiological substrates of leucine-rich repeat kinase 2 (LRRK2). LRRK2 is a Ser/Thr kinase that is associated with inherited and sporadic forms of Parkinson disease. In recent years, numerous kinases and their associated signaling pathways have been identified that lead to phosphorylation of Rabs. These emerging studies suggest that serine/threonine and tyrosine phosphorylation of Rabs may be a widespread and under-appreciated mechanism for controlling their membrane trafficking functions. Here we survey current knowledge of Rab phosphorylation and discuss models for how this post-translational mechanism exerts control of membrane trafficking.

Sarcopenia and systemic inflammation are associated with decreased survival after cytoreductive nephrectomy for metastatic renal cell carcinoma.

BACKGROUND: This study was aimed at assessing the associations of sarcopenia, muscle density, adiposity, and inflammation with overall survival (OS) after cytoreductive nephrectomy (CN) for metastatic renal cell carcinoma. METHODS: In all, 158 patients undergoing CN from 2001 to 2014 had digitized preoperative imaging for tissue segmentation via Slice-O-Matic software (version 5.0) at the mid-L3 level. The skeletal muscle index was calculated with the skeletal muscle area (cm2 ) normalized for height (m2 ), and the skeletal muscle density (SMD) was calculated with average Hounsfield units. Adiposity was measured with the cross-sectional area (cm2 ) of visceral, subcutaneous, and intramuscular adiposity compartments and was similarly normalized for height. The average fat density was obtained in Hounsfield units. OS was estimated with the Kaplan-Meier method. Associations between body composition, inflammation metrics, and relevant clinicopathology and OS were assessed with univariable and multivariate Cox analyses. RESULTS: Seventy-six of the 158 patients (48%) were sarcopenic. Sarcopenia was associated with elevated neutrophil to lymphocyte ratios (NLRs; P = .02), increased age (P = .001), lower body mass indices (P = .009), greater modified Motzer scores (P = .019), and lower SMD (P = .006). The median OS was 15.0 and 29.4 months for sarcopenic and nonsarcopenic patients, respectively (P = .04). Elevated inflammation (NLR or C-reactive protein), in addition to sarcopenia, was independently associated with OS, with an elevated NLR ≥ 3.5 and sarcopenia associated with the poorest OS at 10.2 months. No associations were observed between measurements of muscle density or adiposity and OS. CONCLUSIONS: Sarcopenia and measures of high systemic inflammation are additively associated with inferior OS after CN and may be of use in preoperative risk stratification. LAY SUMMARY: Body composition and sarcopenia (a deficiency in skeletal musculature) have been shown to affect outcomes in cancer. We found that sarcopenic patients had poor survival in comparison with nonsarcopenic patients in the setting of metastatic renal cell carcinoma (mRCC). Patients with both elevated inflammation and sarcopenia had the poorest survival. Sarcopenia is an objective measure of nutrition that can assist in therapeutic counseling and decision-making for individualized treatment in mRCC.

Lack of association between cognitive impairment and systemic inflammation in asymptomatic carotid stenosis.

BACKGROUND: Asymptomatic carotid atherosclerotic stenosis (ACAS) is associated with cognitive impairment. Systemic inflammation occurs in patients with systemic atherosclerosis and is also associated with cognitive impairment. The goal of this study was to determine if cognitive impairment in patients with ACAS is the result of systemic inflammation. METHODS: A cross-sectional analysis of 104 patients (63 patients with ACAS, 41 controls) with cognitive function and inflammatory biomarker assessments was performed. Venous blood was assayed for proinflammatory biomarkers (IL-1ß, IL-6, IL-6R, IL-8, IL-17, tumor necrosis factor-α, matrix metalloproteinase [MMP]-1, MMP-2, MMP-7, MMP-9, vascular cell adhesion molecule, and high-sensitivity C-reactive protein). The patients also underwent comprehensive cognitive testing to compute five domain-specific cognitive scores per patient. We first assessed the associations between carotid stenosis and cognitive function, and between carotid stenosis and systemic inflammation in separate regression models. We then determined whether cognitive impairments persisted in patients with carotid stenosis after accounting for inflammation by adjusting for inflammatory biomarker levels in a combined model. RESULTS: Patients with ACAS and control patients differed in age, race, coronary artery disease prevalence, and education. Stenosis patients had worse cognitive scores in two domains: learning and memory (P = .05) and motor and processing speed (P = .002). Despite adjusting for inflammatory biomarker levels, patients with ACAS still demonstrated deficits in the domains of learning and memory and motor and processing speed. CONCLUSIONS: Although systemic atherosclerosis-induced inflammation is a well-recognized cause for cognitive impairment, our data suggest that it is not the primary underlying mechanism behind cognitive impairments seen in ACAS. Cognitive impairments in learning and memory and motor and processing speed seen in patients with ACAS persist after adjusting for systemic inflammation. Thus, alternative mechanisms should be explored to account for the observed functional impairments.

Computed tomography angiographic biomarkers help identify vulnerable carotid artery plaque.

OBJECTIVE: The current risk assessment for patients with carotid atherosclerosis relies primarily on measuring the degree of stenosis. More reliable risk stratification could improve patient selection for targeted treatment. We have developed and validated a model to predict for major adverse neurologic events (MANE; stroke, transient ischemic attack, amaurosis fugax) that incorporates a combination of plaque morphology, patient demographics, and patient clinical information. METHODS: We enrolled 221 patients with asymptomatic carotid stenosis of any severity who had undergone computed tomography angiography at baseline and ≥6 months later. The images were analyzed for carotid plaque morphology (plaque geometry and tissue composition). The data were partitioned into training and validation cohorts. Of the 221 patients, 190 had complete records available and were included in the present analysis. The training cohort was used to develop the best model for predicting MANE, incorporating the patient and plaque features. First, single-variable correlation and unsupervised clustering were performed. Next, several multivariable models were implemented for the response variable of MANE. The best model was selected by optimizing the area under the receiver operating characteristic curve (AUC) and Cohen's kappa statistic. The model was validated using the sequestered data to demonstrate generalizability. RESULTS: A total of 62 patients had experienced a MANE during follow-up. Unsupervised clustering of the patient and plaque features identified single-variable predictors of MANE. Multivariable predictive modeling showed that a combination of the plaque features at baseline (matrix, intraplaque hemorrhage [IPH], wall thickness, plaque burden) with the clinical features (age, body mass index, lipid levels) best predicted for MANE (AUC, 0.79), In contrast, the percent diameter stenosis performed the worst (AUC, 0.55). The strongest single variable for discriminating between patients with and without MANE was IPH, and the most predictive model was produced when IPH was considered with wall remodeling. The selected model also performed well for the validation dataset (AUC, 0.64) and maintained superiority compared with percent diameter stenosis (AUC, 0.49). CONCLUSIONS: A composite of plaque geometry, plaque tissue composition, patient demographics, and clinical information predicted for MANE better than did the traditionally used degree of stenosis alone for those with carotid atherosclerosis. Implementing this predictive model in the clinical setting could help identify patients at high risk of MANE.