Prediction of tumor-reactive T cell receptors from scRNA-seq data for personalized T cell therapy.

The identification of patient-derived, tumor-reactive T cell receptors (TCRs) as a basis for personalized transgenic T cell therapies remains a time- and cost-intensive endeavor. Current approaches to identify tumor-reactive TCRs analyze tumor mutations to predict T cell activating (neo)antigens and use these to either enrich tumor infiltrating lymphocyte (TIL) cultures or validate individual TCRs for transgenic autologous therapies. Here we combined high-throughput TCR cloning and reactivity validation to train predicTCR, a machine learning classifier that identifies individual tumor-reactive TILs in an antigen-agnostic manner based on single-TIL RNA sequencing. PredicTCR identifies tumor-reactive TCRs in TILs from diverse cancers better than previous gene set enrichment-based approaches, increasing specificity and sensitivity (geometric mean) from 0.38 to 0.74. By predicting tumor-reactive TCRs in a matter of days, TCR clonotypes can be prioritized to accelerate the manufacture of personalized T cell therapies.

[Decision conflicts with relatives in the intensive care unit]. / Entscheidungskonflikte mit Angehörigen auf der Intensivstation.

BACKGROUND: If medicine is coming close to its limits conflicts sometimes occur. Most conflicts in the intensive care unit (ICU) involve the medical team and patients' relatives. In particular decisions about withholding and withdrawing life-sustaining therapy lead to conflicts. Decisions about limiting life-sustaining treatment are burdened by conflicts and put an enormous strain particularly on relatives. AIM: Illustration of currently available studies and existing recommendations on how to manage potentially conflict-laden decision-finding discussions on the ICU are presented. MATERIAL AND METHODS: This article is based on a selective literature research in the PubMed database. RESULTS: Studies have been carried out to evaluate posttraumatic stress disorders in relatives who were involved in life-limiting treatment decisions. Conflicts on the ICU put an emotional strain on relatives. Evidence-based recommendations are available regarding physicians' attitudes during discussions about therapy decisions, communication style and other contextual factors. Study results show that the emotional stress level relatives have to endure can be reduced if conversations between patients' families and the clinical personnel were conducted according to these recommendations. The involvement of a clinical ethics committee can prevent conflicts and has been shown to have no impact on the mortality rate but does decrease the time life-sustaining measures were unsuccessfully pursued. CONCLUSION: To prevent conflicts between the medical personnel and patients' relatives on the ICU, a timely, congruent and empathic conversation style in an appropriate, quiet environment is essential. Consultation with clinical ethics committees is recommended to de-escalate disputes.

Homologues of neisserial heme oxygenase in gram-negative bacteria: degradation of heme by the product of the pigA gene of Pseudomonas aeruginosa.

The oxidative cleavage of heme to release iron is a mechanism by which some bacterial pathogens can utilize heme as an iron source. The pigA gene of Pseudomonas aeruginosa is shown to encode a heme oxygenase protein, which was identified in the genome sequence by its significant homology (37%) with HemO of Neisseria meningitidis. When the gene encoding the neisserial heme oxygenase, hemO, was replaced with pigA, we demonstrated that pigA could functionally replace hemO and allow for heme utilization by neisseriae. Furthermore, when pigA was disrupted by cassette mutagenesis in P. aeruginosa, heme utilization was defective in iron-poor media supplemented with heme. This defect could be restored both by the addition of exogenous FeSO4, indicating that the mutant did not have a defect in iron metabolism, and by in trans complementation with pigA from a plasmid with an inducible promoter. The PigA protein was purified by ion-exchange chromotography. The UV-visible spectrum of PigA reconstituted with heme showed characteristics previously reported for other bacterial and mammalian heme oxygenases. The heme-PigA complex could be converted to ferric biliverdin in the presence of ascorbate, demonstrating the need for an exogenous reductant. Acidification and high-performance liquid chromatography analysis of the ascorbate reduction products identified a major product of biliverdin IX-beta. This differs from the previously characterized heme oxygenases in which biliverdin IX-alpha is the typical product. We conclude that PigA is a heme oxygenase and may represent a class of these enzymes with novel regiospecificity.

Type II protein secretion by Pseudomonas aeruginosa: genetic suppression of a conditional mutation in the pilin-like component XcpT by the cytoplasmic component XcpR.

Pseudomonas aeruginosa exports a number of hydrolytic enzymes and toxins using the type II or general secretion pathway, found in a variety of Gram-negative bacteria and requiring the functions of at least 12 gene products (XcpP-Z and PilD/XcpA in P. aeruginosa). A number of these gene products are homologues of components of the type IV pilus biogenesis system, including four proteins, XcpT-W, which are highly similar to the pilin subunit in their size, localization and post-translational modifications. These proteins, in addition to the pilin subunit, are cleaved and methylated by the PilD/XcpA prepilin peptidase, but their interactions with other components of the export apparatus are unclear. Using a medium developed for the selection of export-proficient P. aeruginosa strains, we have isolated temperature-sensitive mutations in the xcpT gene and extragenic suppressors for one of the mutants. These suppressors fall into two classes, one that maps outside of the xcpP-Z gene cluster and may define additional cellular functions that are required for export, and a second that maps to the xcpR gene product and indicates a potential protein-protein interaction connecting two different cellular compartments and required for the assembly or function of the export apparatus.

Prohibiting smoking in restaurants: effects on restaurant sales.

PURPOSE: The purpose of this study was to assess the impact of prohibiting smoking in restaurants on total restaurant sales in Flagstaff, Arizona. DESIGN: Flagstaff restaurant and retail sales data were collected for periods approximately 3.5 years prior to enactment of a no-smoking-in-restaurants ordinance and 1.5 years after enactment of the ordinance. Data were compared with six comparison areas utilizing four methods of analyses. SETTING: The city of Flagstaff, Arizona, was the community in this study that prohibited smoking in restaurants. SUBJECTS: Flagstaff restaurant and retail sales were compared to sales in two similar Arizona cities, three counties, and the entire state of Arizona. INTERVENTION: A city ordinance that prohibited smoking in all Flagstaff, Arizona, restaurants. MEASURES: Taxable restaurant sales were collected from Flagstaff and all comparison areas. Retail sales data were also collected to determine if changes occurred in the ratio of restaurant to retail sales. RESULTS: All analyses resulted in the same conclusions: prohibiting smoking in restaurants did not affect restaurant sales. CONCLUSIONS: Study findings indicate that prohibiting smoking in Flagstaff, Arizona, restaurants has had no effect on restaurant sales.

A breast feeding education and promotion program: effects on knowledge, attitudes, and support for breast feeding.

This study was undertaken to determine the effects of a partner-support, incentive-based educational program on breast feeding knowledge, attitudes and support and to examine the relationship between feeding intentions and feeding behavior among low-income women. Women who expressed a willingness to participate in the intervention were randomly assigned to "intervention" and "usual breast feeding" (control) groups. Sixty-eight primipara women with expected due dates between May and December, 1992, volunteered to participate in the study. Of these, 34 were randomly assigned to each of the two groups. Approximately 81 percent of the women completed the study, leaving n = 29 in the control group and n = 26 in the intervention group. The intervention consisted of special incentives (prizes) for women and their partners to participate in several breast feeding education and promotion activities. Intervention group women and their partners experienced positive changes in breast feeding knowledge and attitudes. Furthermore, the intervention seemed to have influenced more women in the treatment group to breast feed despite their prenatal feeding intentions. In addition, the partners of intervention group women were perceived to be more supportive of breast feeding than control group partners. These findings suggest that incentives, such as donated prizes, can be used to attract lower socioeconomic group women and their partners to breast feeding promotion interventions. Participation in such interventions can produce positive changes in breast feeding knowledge, attitudes, and support, and can have a dramatic effect in promoting breast feeding.

Influences on breast-feeding by lower-income women: an incentive-based, partner-supported educational program.

OBJECTIVE: To determine the effects of a partner-supported, incentive-based educational program on rates and duration of breast-feeding among low-income women. DESIGN: Women who expressed a willingness to participate in the breast-feeding educational program were randomly assigned to one of two groups: an intervention group and a control group who received usual breast-feeding education. SETTING: Clinics of the Special Supplemental Food Program for Women, Infants, and Children in Flagstaff, Ariz. SUBJECTS: Sixty-eight primiparous pregnant women with expected due dates between May 1992 and December 1992 were willing to participate in the study. Of these, 34 were randomly assigned to the intervention group and 34 to the control group. Approximately 81% of the women completed the study: 29 in the control group and 26 in the intervention group. INTERVENTION: The intervention consisted of special incentives (prizes) for women and their partners to participate in a breast-feeding class for expectant couples and an educational series on childbirth. Women were also encouraged to use a breast-feeding support program in which peers serve as role models. MAIN OUTCOME MEASURES: The primary outcome measure was infant feeding method. Data were collected from mothers in both groups at the time of discharge from the hospital and at 2 weeks, 6 weeks, and 3 months postpartum. STATISTICAL ANALYSES PERFORMED: Binomial proportional analyses of the feeding data were performed. RESULTS: Women in the intervention group reported a higher percentage of breast-feeding at all measurement times. APPLICATIONS: These findings suggest that incentives, such as donated prizes, can be used to attract primiparous women from lower socioeconomic groups, along with their partners, to participate in educational interventions designed to promote breast-feeding. Participation by couples in breast-feeding promotion activities can dramatically increase the rate and duration of breast-feeding.