Teaching epistemic integrity to promote reliable scientific communication

In an age of mass communication, citizens need to learn how to detect and transmit reliable scientific information. This need is exacerbated by the transmission of news through social media, where any individual has the potential to reach thousands of other users. In this article, we argue that fighting the uncontrolled transmission of unreliable information requires improved training in broad epistemic integrity. This subcategory of research integrity is relevant to students in all disciplines, and is often overlooked in integrity courses, in contrast to topics such as fraud, plagiarism, collaboration and respect for study subjects. Teaching epistemic integrity involves training epistemic skills (such as metacognitive competences, capacity to use helpful heuristics, basic statistical and methodological principles) and values (such as love of truth, intellectual humility, epistemic responsibility). We argue that this topic should be addressed in secondary school, and later constitute a fundamental component of any university curriculum.

The quizzical failure of a nudge on academic integrity education: a randomized controlled trial

BACKGROUND

Studies on academic integrity reveal high rates of plagiarism and cheating among students. We have developed an online teaching tool, Integrity Games ( https://integgame.eu/ ), that uses serious games to teach academic integrity. In this paper, we test the impact of a soft intervention - a short quiz - that was added to the Integrity Games website to increase users' interest in learning about integrity. Based on general principles of behavioral science, our quiz highlighted the intricacy of integrity issues, generated social comparisons, and produced personalized advice. We expected that these interventions would create a need for knowledge and encourage participants to spend more time on the website.

METHODS

In a randomized controlled trial involving N = 405 students from Switzerland and France, half of the users had to take a short quiz before playing the serious games, while the other half could directly play the games. We measured how much time they spent playing the games, and, in a post-experimental survey, we measured their desire to learn about integrity issues and their understanding of integrity issues.

RESULTS

Contrary to our expectations, the quiz had a negative impact on time spent playing the serious games. Moreover, the quiz did not increase participants' desire to learn about integrity issues or their overall understanding of the topic.

CONCLUSIONS

Our quiz did not have any measurable impact on curiosity or understanding of integrity issues, and may have had a negative impact on time spent on the Integrity games website. Our results highlight the difficulty of implementing behavioral insights in a real-world setting.

TRIAL REGISTRATION

The study was preregistered at https://osf.io/73xty .

Nudging accurate scientific communication

The recent replicability crisis in social and biomedical sciences has highlighted the need for improvement in the honest transmission of scientific content. We present the results of two studies investigating whether nudges and soft social incentives enhance participants' readiness to transmit high-quality scientific news. In two online randomized experiments (Total N = 2425), participants had to imagine that they were science journalists who had to select scientific studies to report in their next article. They had to choose between studies reporting opposite results (for instance, confirming versus not confirming the effect of a treatment) and varying in traditional signs of research credibility (large versus small sample sizes, randomized versus non-randomized designs). In order to steer participants' choices towards or against the trustworthy transmission of science, we used several soft framing nudges and social incentives. Overall, we find that, although participants show a strong preference for studies using high-sample sizes and randomized design, they are biased towards positive results, and express a preference for results in line with previous intuitions (evincing confirmation bias). Our soft framing nudges and social incentives did not help to counteract these biases. On the contrary, the social incentives against honest transmission of scientific content mildly exacerbated the expression of these biases.

Replicability, Robustness, and Reproducibility in Psychological Science

Replication-an important, uncommon, and misunderstood practice-is gaining appreciation in psychology. Achieving replicability is important for making research progress. If findings are not replicable, then prediction and theory development are stifled. If findings are replicable, then interrogation of their meaning and validity can advance knowledge. Assessing replicability can be productive for generating and testing hypotheses by actively confronting current understandings to identify weaknesses and spur innovation. For psychology, the 2010s might be characterized as a decade of active confrontation. Systematic and multi-site replication projects assessed current understandings and observed surprising failures to replicate many published findings. Replication efforts highlighted sociocultural challenges such as disincentives to conduct replications and a tendency to frame replication as a personal attack rather than a healthy scientific practice, and they raised awareness that replication contributes to self-correction. Nevertheless, innovation in doing and understanding replication and its cousins, reproducibility and robustness, has positioned psychology to improve research practices and accelerate progress. Expected final online publication date for the Annual Review of Psychology, Volume 73 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Folk Moral Objectivism: The Case of Harmful Actions

It is controversial whether ordinary people regard beliefs about the wrongness of harmful actions as objectively correct. Our deflationary hypothesis, consistent with much of the evidence, is that people are objectivists about harmful actions that are perceived to involve injustice: when two parties disagree about whether such an action is wrong, people think that only one party is correct (the party believing that the action is wrong). However, Sarkissian and colleagues claimed that this evidence is misleading, showing that when the two disagreeing parties are from radically different cultures or species, people tend to think that both parties are correct (a non-objectivist position). We argue that Sarkissian et al.'s studies have some methodological limitations. In particular, participants may have assumed that the exotic or alien party misunderstood the harmful action, and this assumption, rather than a genuinely non-objectivist stance, may have contributed to the increase in non-objectivist responses. Study 1 replicated Sarkissian et al.'s results with additional follow-up measures probing participants' assumptions about how the exotic or alien party understood the harmful action, which supported our suspicion that their results are inconclusive and therefore do not constitute reliable evidence against the deflationary hypothesis. Studies 2 and 3 modified Sarkissian et al.'s design to provide a clear-cut and reliable test of the deflationary hypothesis. In Study 2, we addressed potential issues with their design, including those concerning participants' assumptions about how the exotic or alien party understood the harmful action. In Study 3, we manipulated the alien party's capacity to understand the harmful action. With these changes to the design, high rates of objectivism emerged, consistent with the deflationary hypothesis. Studies 4a and 4b targeted the deflationary hypothesis more precisely by manipulating perceptions of injustice to see the effect on objectivist responding and by probing the more specific notion of objectivism entailed by our hypothesis. The results fully supported the deflationary hypothesis.

The Effect of War Commemorations on Support for Diplomacy: A Five-Nation Study

We remember the past in order not to repeat it, but does remembrance of war in fact shape support for military or diplomatic approaches to international conflict? In seven samples from five countries (collected online, total N = 2,493), we examined support for military and diplomatic approaches to conflict during war commemorations (e.g., Veterans Day). During war commemorations in the United States, support for diplomacy increased, whereas support for military approaches did not change. We found similar results in the United Kingdom and Australia on Remembrance Day, but not in Germany, or France, nor in Australia on Anzac Day. Furthermore, support for diplomacy was predicted by concern about loss of ingroup military lives during war, independently of concern about harm to outgroup civilians. These studies expand our understanding of how collective memories of war may be leveraged to promote diplomatic approaches to contemporary geopolitical conflict.

Fluctuations of a membrane nanotube covered with an actin sleeve

Many biological functions rely on the reshaping of cell membranes, in particular into nanotubes, which are covered in vivo by dynamic actin networks. Nanotubes are subject to thermal fluctuations, but the effect of these on cell functions is unknown. Here, we form nanotubes from liposomes using an optically trapped bead adhering to the liposome membrane. From the power spectral density of this bead, we study the nanotube fluctuations in the range of membrane tensions measured in vivo. We show that an actin sleeve covering the nanotube damps its high-frequency fluctuations because of the network viscoelasticity. Our work paves the way for further studies of the effect of nanotube fluctuations on cellular functions.

Actin modulates shape and mechanics of tubular membranes

The actin cytoskeleton shapes cells and also organizes internal membranous compartments. In particular, it interacts with membranes for intracellular transport of material in mammalian cells, yeast, or plant cells. Tubular membrane intermediates, pulled along microtubule tracks, are formed during this process and destabilize into vesicles. While the role of actin in tubule destabilization through scission is suggested, literature also provides examples of actin-mediated stabilization of membranous structures. To directly address this apparent contradiction, we mimic the geometry of tubular intermediates with preformed membrane tubes. The growth of an actin sleeve at the tube surface is monitored spatiotemporally. Depending on network cohesiveness, actin is able to entirely stabilize or locally maintain membrane tubes under pulling. On a single tube, thicker portions correlate with the presence of actin. These structures relax over several minutes and may provide enough time and curvature geometries for other proteins to act on tube stability.

Report on the CCT Supplementary comparison S2 on thermal conductivity measurements of insulating materials by guarded hot plate

Seven National Metrology Institutes (NMIs) from France, United States, United Kingdom, Russia, Mexico, China and Germany participated in an inter-laboratory comparison on thermal conductivity measurements by the Guarded Hot Plate method. This action was part of a series of supplementary inter-laboratory comparisons (including infrared spectral emittance and thermal diffusivity) sponsored by the Consultative Committee on Thermometry (CCT) Task Group on Thermophysical Quantities (TG-ThQ). The objective of this collaborative work was to strengthen the consistency of thermal conductivity measurements carried out worldwide on low conductive materials. Measurements were conducted successively by all participants on the same sets of specimens of insulating materials (mineral wool and expanded polystyrene) at temperatures ranging from 10 °C to 40 °C, according to the International Standard ISO 8302. This protocol aimed to minimize issues of material variability by circulating the same pairs of specimens among the laboratories following the strict format of a round-robin test program. More than 120 data points (combinations of material, thickness and temperature) were compared. 92 % of the data points were in agreement, with differences to weighted mean values less than the expanded uncertainties calculated from the individual NMI uncertainties and uncertainties related to the comparison process.

Fluctuations of a membrane nanotube revealed by high-resolution force measurements

Pulling membrane nanotubes from liposomes presents a powerful method to gain access to membrane mechanics. Here we extend classical optical tweezers studies to infer membrane nanotube dynamics with high spatial and temporal resolution. We first validate our force measurement setup by accurately measuring the bending modulus of EPC membrane in tube pulling experiments. Then we record the position signal of a trapped bead when it is connected, or not, to a tube. We derive the fluctuation spectrum of these signals and find that the presence of a membrane nanotube induces higher fluctuations, especially at low frequencies (10-1000 Hz). We analyse these spectra by taking into account the peristaltic modes of nanotube fluctuations. This analysis provides a new experimental framework for a quantitative study of the fluctuations of nanotubular membrane structures that are present in living cells, and now classically used for in vitro biomimetic approaches.

Prolonged outbreak of adenovirus A31 in allogeneic stem cell transplant recipients

BACKGROUND

An outbreak of human adenovirus (HAdV) A31 occurred from December 2011 to March 2012 at the Center for Allogeneic Stem Cell Transplantation (CAST), Karolinska University Hospital in Sweden. We analyzed the outbreak, the routes of transmission, and report the medical consequences.

METHODS

The medical records of all patients admitted to CAST during the outbreak period were studied. Phylogenetic analysis of the patient HAdV strains was performed by sequencing the hexon gene and the more variable E3 gene.

RESULTS

We identified 9 cases of HAdV A31. Hygiene measures were implemented, but transmission continued for 2 months. All 9 patients had been admitted to the ward, but 2 had no connection in time to other known HAdV A31 cases. DNA sequencing of the patient strains strongly suggested nosocomial transmission. Transplantation was postponed and then cancelled in 1 patient, and 5 patients were treated with cidofovir because of high levels of viremia. In 7 patients, concomitant graft-versus-host disease (GVHD) grade II-V complicated the clinical picture, as it was difficult to distinguish symptoms of GVHD from those of HAdV infection.

CONCLUSION

An outbreak of HAdV in HSCT recipients can be difficult to control. Although none of the patients had severe disease, the medical consequences were significant. It is possible that unidentified cases with mild symptoms may have caused continuous transmission at the unit. Regular testing of all patients several weeks beyond the last case identified may be an important measure to control transmission.

Development and Evaluation of a Loop-Mediated Isothermal Amplification Assay for the Detection of Adenovirus 40 and 41

Human adenoviruses (hAdVs) of subgroup F (enteric serotypes 40 and 41) display characteristic gut tropism, in vivo, fastidious growth characteristics in cell culture, and are estimated to be associated with 5-20% worldwide of acute gastroenteritis cases among infants and young children. Adequate hAdV gastroenteritis case management requires laboratory-based diagnosis. The present study aimed to the development and evaluation of a simple and cost-effective, one-step, single-tube adenovirus type 40/41 specific loop-mediated isothermal amplification (LAMP) assay for the detection of hAdV40/41 DNA in environmental and/or clinical samples, since no LAMP assay has previously been reported for the detection of these virus types. The assay targeted the hexon gene and had the advantages of being rapid, simple, specific, and sensitive. Results could be obtained within 60 min, under isothermal conditions at 69 °C. The detection limits for hAdV genomes were between 50 and 100 copies/reaction for hAdV40 and hAdV41, and no cross-reactions with other selected viruses, were found. The assay was evaluated with clinical as well as environmental samples. The developed assay is expected to provide a potential molecular tool in obtaining greater knowledge of the hAdV40/41 importance in the epidemiology and clinical manifestations of gastroenteritis.

Follicle development in cryopreserved bitch ovarian tissue grafted to immunodeficient mouse

The present study evaluated: (1) in vivo follicular development in canine ovarian tissue after slow freezing and xenotransplantation; and (2) the use of erythropoietin (EPO) as an angiogenic factor to optimise the transplantation procedure. Frozen-thawed ovarian tissue from five bitches was grafted into severe combined immunodeficient (SCID) mice (n=47) treated with or without EPO (500 IU kg(-1), once daily for 3 days) (Groups A and B, respectively) and analysed after 0, 1, 8 or 16 weeks. Follicle grade, follicle density, follicle morphology and stromal cells density were assessed by histological analysis, whereas vascularisation of the graft was quantified by immunohistochemistry with anti-α-smooth muscle actin antibody. Despite a massive loss of follicles after grafting, secondary follicle density was higher at 8 and 16 weeks than at 1 week regardless of EPO treatment. EPO significantly improved early follicle morphology and stromal cell density after 8 weeks and blood vessel density at 16 weeks after transplantation (P<0.05). Intact secondary follicles with more than three granulosa cells layers were observed 16 weeks after transplantation. The results suggest that canine ovarian tissue can be successfully preserved by our slow-freezing protocol because the tissue showed follicular growth after xenotransplantation. EPO treatment did not lessen the massive loss of follicles after transplantation.

Control of the estrous cycle in guinea-pig (Cavia porcellus)

The aim of this work was to look for a simple method to obtain synchronized ovulation in guinea pigs under farming conditions while respecting animal welfare. The luteolytic activity of three different prostaglandins F2alpha (PGF2α) analogs (D-cloprostenol, D,L-cloprostenol and luprostiol) and a daily treatment with oral progestagen (altrenogest) was tested successively at different stages of the estrous cycle on the same group of females during a period of 8 mo. The estrous cycle length was not modified by the administration of PGF2α analogs, whatever the stage of the estrous cycle when the treatment was initiated. Our results led us to reject the use of PGF2α analog to induce practical synchronization of the estrus in this species. In females (n = 29), given 15 days with altrenogest (0.1 mL po once a day), ovulation occurred 4.43 ± 0.13 days after the end of the treatment. Altrenogest treatment was followed by mating. No negative impacts of the treatment on the pregnancy rates, delivery rates and litter sizes were observed. This standard method of guinea-pig estrus synchronization is less stressful for the animals compared to techniques using progesterone tubing.

115 FIRST SUCCESSFUL PREGNANCY AFTER EMBRYO TRANSFER INTO SYNCHRONIZED FEMALES IN GUINEA PIG (CAVIA PORCELLUS)

The guinea pig (Cavia porcellus) has been used as a laboratory animal since the late 18th century and still remains essential in many research areas. It also plays an important role in the Andes societies as a source of protein for many low-income highlanders and as part of rituals and traditional medicines. Thus, the conservation of genetic diversity is a long-term issue that must be considered. To establish an embryo cryobank, it is necessary to develop a method of embryo transfer. Up to now no pregnancies after surgical embryo transfer into synchronized females have been reported in guinea pigs. The aim of this work was to design a standard embryo transfer method in this species. Eight normally cycling female guinea pigs from the Maria-Marcela Farm (Puente Piedra, Peru), weighing from 1 to 1.5 kg, were used in this study. Females were housed under farming conditions and fed on commercial pellets and tap water ad libitum. Three donor females were superovulated using 15 IU of human menopausal gonadotrophin (hMG, Massone®, Buenos Aires, Argentina) and mated as soon as the vagina opened. Copulatory plug was observed and vaginal smears were taken to guarantee successful mating. Thirty-eight embryos were collected between Days 3.5 and 4.5 after ovulation at the morula and early blastocyst stages. Five recipient females were synchronized by a daily 0.1-mL dose of altrenogest (Regumate® Equine, Intervet, France) per os by means of a syringe for 15 days. Two embryos were transferred into each uterine horn by laparotomy at Day 3.5 and 4.5 after ovulation. Two types of pipettes were tested for embryo transfer: pulled glass pipettes approximately 0.3 mm in diameter in 2 female recipients and plastic open pulled straws (OPS, Minitüb®, Germany) in 3 recipients. Pregnancy diagnosis was detected by observation of no return to oestrus at Day 16 and confirmed by ultrasonography. None of the 3 OPS-transferred females were pregnant. One of the 2 pulled glass pipette–transferred females was diagnosed as pregnant and delivered 2 stillbirths (one per uterine horn). There were no postsurgical complications and the females undergoing embryo transfer returned to normal reproduction. We demonstrated that a classic surgical embryo transfer method is possible under field conditions to obtain pregnancy in this species. We suggest further studies using glass pipettes, which allow a more precise embryo deposition. Future experiments will incorporate the transfer of frozen-thawed embryos on a larger scale.

Postoperative spondylodiscitis due to Kytococcus schroeteri in a diabetic woman

Kytococcus schroeteri, a Gram-positive coccus, is usually regarded as part of the human skin flora. It has been described in prosthetic valve endocarditis but never as being involved in osteoarticular infections. We report here the first case of a spondylodiscitis due to K. schroeteri identified by 16S rRNA gene sequencing.

Enteric adenoviruses

The 41 serotypes of human adenoviruses are classified into six subgenera (A-F) with different tropisms. Enteric infections are caused in children by serotypes Ad40 and Ad41 of subgenus F. Serotypes Ad40 and Ad41 transform embryonic cells but cannot induce tumours in newborn hamsters. They differ from all other (established) human adenoviruses by being unable to replicate in conventional cell cultures. Ad40 and Ad41 grow in 293 cells (human embryonic kidney cells immortalized by transfection with the E1A, E1B regions of Ad5). In spite of the difficulty of isolating Ad40 and Ad41 they can be directly identified in stools by enzyme-linked immunosorbent assay (ELISA) and solid-phase immuno-electron microscopy. The amount of viral DNA in stool preparations is sufficient for identification by DNA restriction or dot-blot analysis. Adenoviruses have been associated with 7-17% of cases of diarrhoea in children. Ad40 and Ad41 cause diarrhoea throughout the year. Clinical features are watery stools, vomiting and moderately elevated temperature; respiratory symptoms are infrequent. The diarrhoea is protracted (mean 8.6 and 12.2 days for Ad40 and Ad41 respectively). Children with rotavirus diarrhoea vomited more frequently and had a higher temperature and diarrhoea of shorter duration. The impact of enteric adenoviruses in the aetiology of diarrhoea world-wide is not known but is accessible to investigation.

Sézary syndrome in a patient receiving infliximab for ankylosing spondylitis

Infliximab, a tumour necrosis factor (TNF)-alpha antagonist, has shown striking efficacy in the treatment of chronic inflammatory rheumatological diseases such as rheumatoid arthritis and ankylosing spondylitis. However, long-term follow-up studies support that treatment with infliximab is associated with an increased risk of non-Hodgkin lymphoma. So far, few cases of cutaneous lymphoma have been reported in patients receiving TNF-alpha-blocking agents. We report a patient who developed Sézary syndrome 17 months after the onset of infliximab therapy for ankylosing spondylitis. Cutaneous lesions partially remitted following infliximab withdrawal and methotrexate treatment. Although the causal link between infliximab and the emergence of Sézary syndrome is uncertain, the present case raises the need for exhaustive long-term registries of malignancies, including primary cutaneous lymphomas, in patients receiving TNF-alpha-blocking agents.

No link between viral findings in the prostate and subsequent cancer development

In an investigation of 201 prostate tissue samples from patients with benign prostate hyperplasia that later progressed to prostate cancer and 201 matched controls that did not, there were no differences in the prevalence of adenovirus, herpesvirus, papilloma virus, polyoma virus and Candida albicans DNA.

A dual RF resonator system for high-field functional magnetic resonance imaging of small animals

A new apparatus has been developed that integrates an animal restrainer arrangement for small animals with an actively tunable/detunable dual radio-frequency (RF) coil system for in vivo anatomical and functional magnetic resonance imaging of small animals at 4.7 T. The radio-frequency coil features an eight-element microstrip line configuration that, in conjunction with a segmented outer copper shield, forms a transversal electromagnetic (TEM) resonator structure. Matching and active tuning/detuning is achieved through fixed/variable capacitors and a PIN diode for each resonator element. These components along with radio-frequency chokes (RFCs) and blocking capacitors are placed on two printed circuit boards (PCBs) whose copper coated ground planes form the front and back of the volume coil and are therefore an integral part of the resonator structure. The magnetic resonance signal response is received with a dome-shaped single-loop surface coil that can be height-adjustable with respect to the animal's head. The conscious animal is immobilized through a mechanical arrangement that consists of a Plexiglas body tube and a head restrainer. This restrainer has a cylindrical holder with a mouthpiece and position screws to receive and restrain the head of the animal. The apparatus is intended to perform anatomical and functional magnetic resonance imaging in conscious animals such as mice, rats, hamsters, and marmosets. Cranial images acquired from fully conscious rats in a 4.7 T Bruker 40 cm bore animal scanner underscore the feasibility of this approach and bode well to extend this system to the imaging of other animals.

Probing Norwalk-like virus presence in shellfish, using artificial neural networks

A database was examined using artificial neural network (ANN) models to investigate the efficacy of predicting PCR-identified Norwalk-like virus presence and absence in shellfish. The relative importance of variables in the model and the predictive power obtained by application of ANN modelling methods were compared with previously developed logistic regression models. In addition, two country-specific datasets were analysed separately with ANN models to determine if the relative importance of the input variables was similar for geographically diverse regions. The results of this analysis found that ANN models predicted Norwalk-like virus presence and absence in shellfish with equivalent, and better, precision than logistic regression models. For overall classification performance, ANN modelling had a rate of 93%, vs 75% for the logistic regression. ANN models were able to illuminate the site-specific relationships between indicators and pathogens.

Rapid typing of human adenoviruses by a general PCR combined with restriction endonuclease analysis

We have developed a system for rapid typing of adenoviruses (Ads) based on a combination of PCR and restriction endonuclease (RE) digestion (PCR-RE digestion). Degenerated consensus primers were designed, allowing amplification of DNA from all 51 human Ad prototype strains and altogether 44 different genome variants of Ad serotypes 1, 3, 4, 5, 7, 11, 19, 40, and 41. The 301-bp amplimer of 22 prototype strains representing all six subgenera and the genome variant was selected as a target for sequencing to look for subgenus and genome type variabilities. The sequences obtained were used to facilitate the selection of specific REs for discrimination purposes in a diagnostic assay by following the concept of cleavage or noncleavage of the 301-bp amplimer. On the basis of these results, a flowchart was constructed, allowing identification of subgenus B:2 and D serotypes and almost complete distinction of subgenus A, B:1, C, E, and F serotypes. Application of the PCR-RE digestion system to clinical samples allowed typing of 34 of 40 clinical samples positive for Ad. The genome type determined by this method was identical to that obtained by traditional RE typing of full-length Ad DNA. The remaining six samples were positive only after a nested PCR. Therefore, to reduce the risk of false-negative results, samples scored negative by the PCR-RE digestion system should be evaluated by the described nested PCR. Used in combination, the PCR-RE digestion method and the nested PCR provide a reliable and sensitive system that can easily be applied to all kinds of clinical samples when rapid identification of adenoviruses is needed.

High prevalence of Chlamydia pneumoniae DNA in peripheral blood mononuclear cells in patients with cardiovascular disease and in middle-aged blood donors

Nested polymerase chain reaction (nPCR) demonstrated the presence of Chlamydia pneumoniae-specific DNA in peripheral blood mononuclear cells (PBMC). PBMC samples were obtained from 103 consecutive patients (62 male, 41 female) aged 22-85 years (mean, 64) admitted for coronary angiography because of suspected coronary heart disease and from 52 blood donors (43 male, 9 female) aged 40-64 years (mean, 49). Of the 101 evaluable patients, 60 (59%) were identified by nPCR assay as C. pneumoniae DNA carriers; C. pneumoniae-specific microimmunofluorescence (MIF) serology confirmed exposure to the bacterium in 57 (95%) of the 60 nPCR-positive patients. Among the 52 blood donors, the nPCR assay identified 24 (46%) C. pneumoniae DNA carriers, all of whom were positive by C. pneumoniae-specific serology. Thirty-two patients (32%) and 23 blood donors (44%) were MIF antibody-positive but repeatedly nPCR-negative; Bartonella henselae- or Bartonella quintana-specific antibodies were not detected among any of these subjects. In this study, C. pneumoniae DNA was common in PBMC of patients with coronary heart disease and in middle-aged blood donors.

Rapid diagnosis of respiratory Chlamydia pneumoniae infection by nested touchdown polymerase chain reaction compared with culture and antigen detection by EIA

Chlamydia pneumoniae is a common cause of respiratory tract infection and community-acquired pneumonia. During an extensive outbreak of C. pneumoniae in northern Sweden, 319 respiratory samples from 129 persons were collected. Sputum, throat, and nasopharyngeal samples were obtained and analyzed by nested touchdown polymerase chain reaction (PCR), EIA, and culture in Hep-2 and McCoy cells. Serology was performed by complement fixation and microimmunofluorescence tests. By PCR, 30 patients were diagnosed with C. pneumoniae compared with 26 positive by EIA and 23 by culture. The finding of C. pneumoniae in the respiratory samples was accompanied by serology indicating acute infection in 26 (96%) of 27 patients for whom adequate sera were available. Nested PCR was sensitive and reliable for diagnosing acute respiratory C. pneumoniae infection. Sputum samples had the highest diagnostic efficacy, and the nested type of PCR was superior to one-step PCR. EIA and culture were less sensitive than nested PCR.

Simple procedure for discrimination and typing of enteric adenoviruses after detection by polymerase chain reaction

A procedure was developed for specific discrimination and typing of the enteric human adenoviruses, Ad40 and Ad41, after polymerase chain reaction (PCR) amplification of a sequence in the hexon gene highly conserved among all 47 serotypes recognised. By Taq I restriction of the 300 bp amplimers, subgenus F DNA could be discriminated from DNAs of adenoviruses belonging to all other subgenera. Discrimination between Ad40 and Ad41 was subsequently achieved by cleavage with either Cfo I, HinP I, Mae III, Mvn I, and/or Rsa I. Thus, PCR detection of viral DNA combined with restriction analysis of amplified products provides a valuable tool for use in epidemiological studies of diarrhoea of adenoviral aetiology.

Detection of adenoviruses and enteroviruses in polluted waters by nested PCR amplification

A procedure has been developed for the rapid detection of enteroviruses and adenoviruses in environmental samples. Several systems for virus concentration and extraction of nucleic acid were tested by adding adenovirus type 2 and poliovirus type 1 to different sewage samples. The most promising method for virus recovery involved the concentration of viruses by centrifugation and elution of the virus pellets by treatment with 0.25 N glycine buffer, pH 9.5. Nucleic acid extraction by adsorption of RNA and DNA to silica particles was the most efficient. One aliquot of the extracted nucleic acids was used for a nested two-step PCR, with specific primers for all adenoviruses; and another aliquot was used to synthesize cDNA for a nested two-step PCR with specific primers for further detection of seeded polioviruses or all enteroviruses in the river water and sewage samples. The specificity and sensitivity were evaluated, and 24 different enterovirus strains and the 47 human adenovirus serotypes were recognized by the primers used. The sensitivity was estimated to be between 1 and 10 virus particles for each of the species tested. Twenty-five samples of sewage and polluted river water were analyzed and showed a much higher number of positive isolates by nested PCR than by tissue culture analysis. The PCR-based detection of enteroviruses and adenoviruses shows good results as an indicator of possible viral contamination in environmental wastewater.

Detection of adenoviruses in stools from healthy persons and patients with diarrhea by two-step polymerase chain reaction

The use of the polymerase chain reaction (PCR) for detection of human adenoviruses in diluted stool samples was investigated. Two sets of nested primers, including primers specific for the hexon-coding region and for the E1B region of enteric adenoviruses (EAd), were assessed by two-step amplification. The primers constitute two different PCR systems designed for the detection of adenoviruses belonging to all six subgenera (A-F), and the two EAds Ad40 and Ad41, respectively. In a two-step PCR mediated amplification a single virus particle was detected when the two sets of general hexon primers or EAd specific primers were used. Earlier results from PCR detection of adenoviruses in stool from children suffering from diarrhea gave indications that adenovirus particles are commonly shed in stools without being identified as the cause of illness [Allard et al.: Journal of Clinical Microbiology 28:2659-2667, 1990]. Therefore, the general and the EAd specific PCR assays were assessed on 150 stool specimens from three groups including 50 healthy children, 50 healthy adults, and 50 adults suffering from diarrhea. When the two sets of general hexon primers were used, 25 of the 50 specimens from the healthy children (mean age 21 months) were found positive by two-step PCR amplification. Nine of the 50 specimens from the healthy adults (mean age 32 years) were found positive whereas 12 of the 50 specimens from sick adults (mean age 31 years) gave amplification products, using the two sets of general hexon primers in a nested fashion. None of the 150 specimens were found to be positive by two-step PCR amplification using the two sets of EAd-specific primers.(ABSTRACT TRUNCATED AT 250 WORDS)

The E1B transcription map of the enteric adenovirus type 41

Enteric adenovirus type 41 (Ad41) is defective for growth in conventional established cell lines. Ad41 is dependent on the Ad5 early regions E1A/E1B since it cannot grow in HEK cells but only in 293 HEK cells transformed by Ad5 E1 region. However, Hep-2 cells have also been shown to support the growth of Ad41 to some extent. The nucleotide sequence of the E1B region of the Ad41 strain D389 has been determined. When compared to the corresponding region of the Ad41 prototype strain (Tak) the degree of homology in the DNA sequences was close to 100%. The mRNAs from the E1B region of the Ad41 strain D389 have been studied by Northern blot, primer extension, and polymerase chain reaction-cDNA analysis. E1B transcripts corresponding to Ad2 14 S, 22 S, and 9 S mRNAs were identified but no 13 S mRNA equivalent was detected, a pattern similar to that seen in the Ad40 and Ad12 transcription maps. However, the Ad41 E1B 14S mRNA equivalent has one additional small exon of 23 nucleotides, created by a donor and an acceptor splice site located at positions not seen in other E1B transcripts of human adenoviruses analyzed so far. The coding potential for E1B 19K, 55K, and 15K proteins and for pIX is retained in the Ad41 transcripts. In contrast to other adenoviruses, except for the closely related Ad40, the ORF of pIX starts in the intron of the 22 S mRNA.

Polymerase chain reaction for detection of adenoviruses in stool samples

The usefulness of the polymerase chain reaction (PCR) method for diagnosing adenovirus infections was investigated. Several primers, including primers specific for the hexon-coding region and for enteric adenovirus types 40 and 41, were evaluated. The PCR method was validated against cell culturing in routine diagnostic work and against restriction enzyme analysis of viral DNA. Sixty diagnostic specimens were selected for evaluation by the PCR method. Twenty of the 60 specimens were found positive on the basis of cytopathic effects and latex agglutination (Adenolex [Orion Diagnostica, Helsinki, Finland]), and 16 were identified and typed as adenoviruses by polyacrylamide gel electrophoresis. PCR was performed on all 60 specimens in parallel directly on diluted stool samples and on viral DNA extracted from cells inoculated with the same stool samples. When the general hexon primers were used 51 of the 60 specimens from infected cell cultures were found positive by PCR, whereas only 13 specimens were found positive when PCR was performed directly on stool samples. With the use of selective primers for enteric adenoviruses 16 of the 60 cell cultures were found to exhibit amplification products by PCR, whereas 4 were detected in stool samples. None of the 60 specimens were found positive by PCR when an adenovirus type 40-specific primer pair was used. PCR was found to be a fast, sensitive, and reliable method for the detection of adenoviruses in diarrheal disease, provided the amplifications were performed directly on diluted stool samples.

Studies of immunologic tolerance to host minor histocompatibility antigens following allogeneic bone marrow transplantation in mice

We showed previously that transplantation of 10(7) unmanipulated C57BL/6 marrow cells to irradiated LP mice yields healthy (B6-LP) chimeras showing no signs of rejection or graft-versus-host disease (GVHD). The aim of this work was to gain more insight into the mechanism(s) responsible for tolerance to host minor histocompatibility antigens following allogeneic bone marrow transplantation (BMT). (B6-LP) chimeras showed very good immune reconstitution when studied in vitro for proliferative response to mitogens and alloantigens and generation of T cell cytotoxic activity. In co-culture experiments their spleen cells showed no natural suppressor activity. When used as cell donors, their capacity to initiate GVHD in four strains of mice presenting H-2 differences was normal when compared to C57BL/6 donors. However, they provoked no GVHD in the three strains of H-2 compatible mice studied. Re-irradiated (B6-LP) chimeras rapidly died of GVHD following injection of C57BL/6 marrow + spleen cells. (B6-LP.R111) chimera cells appeared tolerant to LP minor antigens presented in the context of H-2r or H-2b. No anamnestic anti-idiotypic suppressor response was noted when stable (B6-LP) chimeras were stimulated with naive C57BL/6 cells. These findings suggest that in BMT chimeras transplanted across minor histocompatibility barriers: (1) both host and donor-derived antigen-presenting cells can present host antigens to donor T cells whose numbers in the marrow inoculum will determine if GVHD or tolerance will ensue, (2) GVHD can be triggered by only a limited number of 'dominant' minor antigens, and (3) we found no evidence for the presence of natural suppressors, veto cells or anti-idiotypic suppressor T cells.

The mechanism of graft-host-tolerance in murine radiation chimeras transplanted across minor histocompatibility barriers

A better understanding of the mechanism(s) involved in graft-host-tolerance following allogeneic bone marrow transplantation is needed to develop new strategies to prevent graft-versus-host disease (GVHD). Based on previous studies, mainly in MHC-mismatched donor-recipient pairs, three hypotheses have been proposed: clonal deletion, active suppression and lack of adequate antigen-presenting cells. Our goal was to identify the mechanism(s) by which tolerance is achieved and maintained in radiation chimeras transplanted across minor histocompatibility barriers. Healthy (B6----LP) chimeras were obtained following injection of 10(7) C57BL/6 marrow cells to irradiated (9.5 Gy) LP hosts and used experimentally 100 days after chimerization. The tolerance state of (B6----LP) chimeras could not be abrogated after i.v. transfer of 5 x 10(7) donor-type spleen cells alone or with repeated i.p. injection of host-type antigen-presenting cells. No GVHD was observed when 10(7) marrow cells plus 5 x 10(7) spleen cells from (B6----LP) chimeras were injected to irradiated LP recipients. Chimera spleen cells suppressed GVHD when adoptively transferred to LP recipients of a C57BL/6 graft. These results suggest that in this model the presence of suppressor cells is both necessary and sufficient to maintain graft-host-tolerance.

Physical organization of the enteric adenovirus type 41 early region 1A

Enteric adenovirus types 40 and 41 (Ad40 and Ad41), representing subgenus F, differ from all other human adenoviruses by being so fastidious that productive replication does not occur in conventional established cell lines. They are dependent of the Ad5 early regions E1A and E1B since they can not grow in HEK cells, only in 293 HEK cells transformed by Ad5 E1. The overall genetic organization of Ad41 E1A is similar to the E1A region of other characterized human adenoviruses but it is slightly shorter, comprising 1350 bp. The inverted terminal repeat (ITR) at the 5' end of both Ad40 and AD41 consists of 163 nucleotides, being similar to the ITR of Ad12 (subgenus A) and longer than the ITRs of adenoviruses of subgenera B, C, and E. The early mRNA products (12 and 13 S) can be translated into a 222-amino acid (aa) and a 251-aa tentative protein, respectively. In a comparison of the Ad41 251-aa protein with corresponding peptides of Ad12, Ad7, Ad5, and Ad4, three conserved amino acid sequences CS1-CS3 can be found. In the second conserved domain CS2, which is particularly acidic, the homology is very high within all five serotypes compared. Only one among eight conserved amino acids differs in the Ad41 251-aa protein. Within CS1 and CS3 which exhibit a hydrophilic and a hydrophobic character, respectively, the amino acid composition of the Ad41 protein is less conserved than the corresponding regions in all other analyzed adenovirus types. Ten of 16 conserved amino acids in CS1 are shared by Ad41 and 18 of 23 conserved amino acids in CS3 are shared by Ad41.

Detection of adenoviruses in stool specimens by nucleic acid spot hybridization

Nucleic acid hybridization was used for the detection of adenovirus DNA in stool specimens, and the results were compared with those obtained by a radioimmunoassay (RIA) for adenovirus hexon antigen. DNA from 40 specimens, 18 of which were positive by RIA, were spotted onto nitrocellulose filters and analyzed by hybridization using radioactively labeled adenovirus-2 DNA or a cloned DNA fragment from enteric adenovirus-41 as probes. With the adenovirus-2 DNA probe, 15 of the 18 RIA-positive specimens were also positive in the hybridization assay, and one of the RIA negative specimens was also scored as positive. The cloned adenovirus-41 fragment gave a positive signal with five specimens, all of which were also detected with the adenovirus-2 DNA probe. The results show that hybridization is an alternative method for detection of adenovirus in stool specimens. The sensitivity of the assay is comparable to that of the RIA.