Observing many researchers using the same data and hypothesis reveals a hidden universe of uncertainty

This study explores how researchers' analytical choices affect the reliability of scientific findings. Most discussions of reliability problems in science focus on systematic biases. We broaden the lens to emphasize the idiosyncrasy of conscious and unconscious decisions that researchers make during data analysis. We coordinated 161 researchers in 73 research teams and observed their research decisions as they used the same data to independently test the same prominent social science hypothesis: that greater immigration reduces support for social policies among the public. In this typical case of social science research, research teams reported both widely diverging numerical findings and substantive conclusions despite identical start conditions. Researchers' expertise, prior beliefs, and expectations barely predict the wide variation in research outcomes. More than 95% of the total variance in numerical results remains unexplained even after qualitative coding of all identifiable decisions in each team's workflow. This reveals a universe of uncertainty that remains hidden when considering a single study in isolation. The idiosyncratic nature of how researchers' results and conclusions varied is a previously underappreciated explanation for why many scientific hypotheses remain contested. These results call for greater epistemic humility and clarity in reporting scientific findings.

Tissue plasminogen activator (rt-PA) in acute ischemic stroke: Outcomes associated with ambulation

PURPOSE

Several clinical trials have highlighted general favorable outcomes of intravenous tissue type plasminogen activator (rt-PA) in acute ischemic stroke using different measures including, National Institutes of Health Stroke Scale (NIHSS) and modified Rankin Scale (mRS). Findings from most of these measures indicate that the benefits of rt-PA are time dependent, thus, supporting intensive efforts to fast-track hospital thrombolytic treatment in patients with stroke. Despite the widespread benefits of rt-PA, the effectiveness of this therapy on specific functions such as ambulatory performance of the recovering stroke patient is not fully investigated. We aim to investigate this issue in the current study.

METHODS

We analyzed data from a retrospective cohort of acute ischemic stroke patients admitted to Greenville Health System (GHS) between 2010-2013. We identified patients who received rt-PA within a 4.5 hour time frame following the onset of acute ischemic stroke symptoms. Our analysis compared ambulatory variables and hospital-level characteristics in proportions of patients receiving rt-PA with those not receiving rt-PA. This analysis determined whether early treatment with rt-PA is associated with favorable changes in ambulatory status from admission to discharge following acute ischemic stroke.

RESULTS

Among 663 patients with ischemic stroke who were eligible to receive rt-PA, 241 patients received rt-PA and 422 patients did not due to several risk factors. We found a statistically significant difference (P < 0.001) for changes in ambulation status from hospital admission to discharge between patients receiving rt-PA and patients who did not receive rt-PA. Among patients who received rt-PA, 27.8% improved in their ambulation status, 41.9% saw no change in their ambulation status, 0.4% worsened in their ambulation status, and 29.9% were unable to be determined. Of the patients who did not receive rt-PA, 20.1% improved in their ambulation status, 61.8% saw no change in their ambulation status, 1.4% worsened in their ambulation status, and 16.6% were unable to be determined.

CONCLUSION

Our current study indicates that early treatment with rt-PA may be associated with favorable changes in ambulatory status from admission to discharge following acute ischemic stroke.

Are Cortical Spreading Depression and Headache in Migraine Causally Linked?

During the past few decades, much controversy has surrounded the pathophysiology of migraine. Cortical spreading depression (CSD) is widely accepted as the neuronal process underlying visual auras. It has been proposed that CSD can also cause the headaches, at least in migraine with aura. We describe three patients, each fulfilling the International Headache Society criteria for migraine with aura, who suffered from headaches 6–10 days per month. Two patients were treated with flunarizine and the third patient with topiramate for the duration of 4 months. All patients reported that aura symptoms resolved completely, whereas the migraine headache attacks persisted or even increased. These observations question the theory that CSD (silent or not) is a prerequisite for migraine headaches.

Antibodies to Aqx toxin of Actinobacillus equuli in horses and foals

Actinobacillus equuli is found in the normal oral flora of horses, but has been associated with several diseases, and particularly with the usually fatal septicaemia in neonatal foals which is thought to be associated with a failure of the passive transfer of immunoglobulins via the colostrum. The Aqx protein of A equuli, belonging to the RTX family of pore-forming toxins, is also cytotoxic to horse lymphocytes. The presence of antibodies to Aqx was investigated in sera from individual horses from different regions; the sera from adult horses and foals 24 hours after birth reacted with Aqx, and sera from foals sampled shortly after an intake of colostrum also reacted with Aqx, but sera from foals taken before an intake of colostrum did not react with Aqx.

Opsonic capacity of foal serum for the two neonatal pathogens Escherichia coli and Actinobacillus equuli

Two of the most commonly isolated foal pathogens are Escherichia coli and Actinobacillus equuli. The hypothesis tested in this study was that young foals carry a lower opsonic capacity for these bacteria compared to adult horses. A flow-cytometric method for the phagocytosis of these by equine neutrophils was established. The opsonic capacity of serum from healthy foals from birth to age 6 weeks was evaluated and related to the concentrations of IgGa and IgGb. Phagocytosis of yeast was used as a control. Serum was required for phagocytosis, with higher concentrations for E. coli than for A. equuli. Ingestion of colostrum led to a significantly higher serum opsonic capacity. After that, there was no consistent age-related trend for opsonic capacity for the different microbes. Foal serum showed similar or higher opsonisation of E. coli and A. equuli compared to serum from mature individuals. During the studied period, the predominance among IgG subisotypes switched from IgGb to IgGa. Although the overall correlation between concentrations of IgG subisotypes and serum opsonic capacity was poor, sera with IgGb levels below 1.9 mg/ml induced lower opsonisation of E. coli and yeast, but not of A. equuli. Complement activation was important for opsonisation of all tested microbes. The results of this study are significant to the understanding of a key immunological facet in the pathophysiology of equine neonatal septicaemia in clinical practice.

Sows intramammarily inoculated with Escherichia coli influence of time of infection, hormone concentrations and leucocyte numbers on development of disease

The aim of this study was to identify factors that influence the development of disease in sows inoculated with Escherichia coli in the mammary gland. Ten cross-bred primiparous sows were intramammarily inoculated with living E. coli bacteria at different time points before parturition: seven sows within 48 h before parturition and three sows approximately 96 h before parturition. Before and after inoculation, blood samples and mammary gland biopsy specimens were collected and clinical observations were made. All seven sows inoculated close to parturition developed a rectal temperature of >39.5 degrees C during the first 48 h post-partum and two of them also showed other signs of clinical disease. In the sows inoculated 4 days before parturition, the rectal temperature never exceeded 39.5 degrees C during the first 48 h post-partum and none of them showed any other sign of clinical discase. There was a tendency (P < 0.1) that histological signs of mastitis were more frequent in the sows inoculated close to parturition. There were no overall differences between the two groups of sows in plasma concentrations of cortisol, oestradiol-17beta and 15-ketodihydro-PGF2alpha before inoculation. Before inoculation, the number of neutrophils in the blood was overall higher (P < 0.05) in the group of sows that were inoculated close to parturition. In comparison, the number of lymphocytes before inoculation had a tendency (P < 0.1) to be lower in that group. The data suggest that the time of infection of the mammary gland relative to parturition and the number of circulating neutrophils at the time of infection influence the development of chinical coliform mastitis in the sow.

The use of medications for cognitive enhancement

OBJECTIVE

To provide Canadian physicians and allied health care professionals with the evidence they need to help them make treatment decisions in the management of patients with Alzheimer's disease or other dementias.

OPTIONS

The full range and quality of diagnostic and therapeutic modalities available to Canadian physicians for the management of dementia.

OUTCOMES

Improvement in the treatment of dementias, leading to reduced suffering, increased functional capacity and decreased economic burden. EVIDENCE AND VALUES: The creation of these evidence-based consensus statements involved literature reviews of the subject by the authors; comparison of alternative clinical pathways and description of the methods whereby published data were analyzed; definition of the level of evidence for data in each case; evaluation and revision in a conference setting (involving primary care physicians, neurologists, psychiatrists, geriatricians, psychologists, consumers and other interested parties); insertion of tables showing key variables and data from various studies and tables of data with recommendations; and reassessment by all authors.

BENEFITS, HARMS, AND COSTS

A rational plan for the therapy of dementias is likely to lead to substantial benefits in both human and economic terms.

RECOMMENDATIONS

Treatment decisions should be made taking into account the severity or stage of the disease, the availability of caregivers, the presence of disease affecting other bodily systems and the ability of the subject to pay the cost of the medications. Donepezil is considered to have positive effects upon certain tests of neuropsychological function and may produce some improvement in Alzheimer's disease of mild to moderate severity as measured by rating scales. Its ability to improve quality of life remains uncertain. No other drug treatments (apart from symptomatic therapies) are at present approved for the treatment of Alzheimer's disease*.

VALIDATION

These recommendations were created by a writing committee, evaluated and revised at a consensus conference and further reviewed and revised by the writing committee prior to publication.

Specific immune response of mares and their newborn foals to Actinobacillus spp. present in the oral cavity

Oral swab samples, serum and colostrum was taken from 15 mares and 14 of their foals, within 24 h of birth. The presence of antibody against Actinobacillus spp. isolated from the oral cavity was investigated using agar gel immunodiffusion. Antibodies against 48 out of the 77 Actinobacillus isolates from all horses in the study were present in the respective sera of 13 mares and 9 foals. In 11 mother-foal pairs, the antibody content of the foal serum was similar to that of the mare, and in 9 cases this was reflected in the antibody content of colostrum from the mare. The results indicate that an immune response to Actinobacillus spp. colonising the oral cavity is present in many adult horses and that this immune response can be transferred from mother to foal via colostrum.

Separate modifiability, mental modules, and the use of pure and composite measures to reveal them

How can we divide a complex mental process into meaningful parts? In this paper, I explore an approach in which processes are divided into parts that are modular in the sense of being separately modifiable. Evidence for separate modifiability is provided by an instance of selective influence: two factors F and G (usually experimental manipulations) such that part A is influenced by F but invariant with respect to G, while part B is influenced by G but invariant with respect to F. Such evidence also indicates that the modules are functionally distinct. If we have pure measures MA and MB, each of which reflects only one of the parts, we need to show that MA is influenced by F but not G, while MB is influenced by G but not F. If we have only a composite measure MAB of the entire process, we usually also need to confirm a combination rule for how the parts contribute to MAB. I present a taxonomy of separate-modifiability methods, discuss their inferential logic, and describe several examples in each category. The three categories involve measures that are derived pure (based on different transformations of the same data; example: separation of sensory and decision processes by signal detection theory), direct pure (based on different data; example: selective effects of adaptation on spatial-frequency thresholds), and composite (examples: the multiplicative-factor method for the analysis of response rate; the additive-factor method for the analysis of reaction time). Six of the examples concern behavioral measures and functional processes, while four concern brain measures and neural processes. They have been chosen for their interest and importance; their diversity of measures, species, and combination rules; their illustration of different ways of thinking about data; the questions they suggest about possibilities and limitations of the separate-modifiability approach; and the case they make for the fruitfulness of searching for mental modules.

Antimicrobial susceptibility of equine isolates of Actinobacillus spp. and identification of beta-lactamases in some strains

A total number of 149 Actinobacillus strains isolated from clinical samples (73 strains) and from the oral cavity of healthy horses (76 strains) were tested for their susceptibility to 17 antimicrobial substances. The antibiograms were generally very similar between the various strains and no differences could be clearly correlated to either phenotype or source of isolates. However, when tested against penicillin, ampicillin, trimethoprim-sulfa, and streptomycin, small groups of strains with what appeared to be acquired resistance could be identified. Eight of the penicillin-resistant strains were found to produce beta-lactamase. The beta-lactamases appeared to be bound tightly to the cell wall, thereby frustrating further characterization by isoelectric focusing. Plasmids of approximately 3 kb were found in four out of seven beta-lactamase-producing strains submitted to plasmid analysis.

Effects of Actinobacillus equuli culture supernatants on equine neutrophil functions and survival

After exposure of equine granulocytes from both foals and adult horses to culture supernatants from clinical isolates of Actinobacillus equuli, phagocytic capacity and respiratory burst was examined by flow-cytometry and a chemiluminescence assay, respectively. One haemolytic isolate of an equine Actinobacillus was also included in the study. An average decrease of 22% in total number of granulocytes, in the flow cytometric assay (P < 0.01), and an average decrease of 26% in light emission, in the chemiluminescence assay (P < 0.001), was seen after exposure to bacterial culture supernatants of A. equuli, indicating that the supernatants contained leukotoxic bacterial products. Supernatants from the haemolytic isolate appeared to contain a higher amount or more potent leukotoxic metabolites when haemolysis was expressed, causing a decrease in total number of granulocytes of 44% (P < 0.01) and a decrease in light emission of 52% (P < 0.01). Evaluation of the stability of the methods used revealed that within-method variation was far less than the observed results. The leukotoxic effects of A. equuli culture supernatants were mainly reflected in the decreased survival of neutrophils and not in neutrophil functions.

General covariance and harmonic maps

The principle of general covariance is used to derive the conditions for a map to be harmonic. Modification to the harmonic map equations due to the presence of a Yang-Mills field is described.

Biochemical fingerprinting and ribotyping of isolates of Actinobacillus equuli from healthy and diseased horses

A total of 112 isolates of Actinobacillus equuli, including both clinical isolates and isolates from the oral cavity of healthy horses, were included in this study. All isolates were ribotyped and 92 of the isolates were also typed biochemically, with the commercially available Pheneplate (PhP) system, which includes 48 different substrates. As expected, ribotyping was more sensitive than biochemical fingerprinting in detecting differences between the isolates. The correlation between the two methods used was poor. It was not possible to distinguish clinical isolates from normal flora isolates by either of the two methods used.

The Weyl character formula, the half-spin representations, and equal rank subgroups

Let B be a reductive Lie subalgebra of a semi-simple Lie algebra F of the same rank both over the complex numbers. To each finite dimensional irreducible representation Vlambda of F we assign a multiplet of irreducible representations of B with m elements in each multiplet, where m is the index of the Weyl group of B in the Weyl group of F. We obtain a generalization of the Weyl character formula; our formula gives the character of Vlambda as a quotient whose numerator is an alternating sum of the characters in the multiplet associated to Vlambda and whose denominator is an alternating sum of the characters of the multiplet associated to the trivial representation of F.

Isolation of Actinobacillus equuli from the oral cavity of healthy horses and comparison of isolates by restriction enzyme digestion and pulsed-field gel electrophoresis

Swab samples were collected from the oral cavity of 174 horses in 10 farms and cultured selectively for Actinobacillus equuli. A. equuli could be isolated from 37% of all samples, varying between 12 and 88% in the different farms. Eight horses were sampled repeatedly for several days, with a variation in isolation frequency between 50 and 88%. Isolates were compared by restriction enzyme digestion and Pulsed-Field Gel Electrophoresis. A high degree of strain variability was found within each horse population as well as some variability over time between strains isolated from the same horse.

Aeromonas hydrophila septicaemia in a grey seal (Halichoerus grypus) from the Baltic Sea: a case study

Aeromonas hydrophila septicaemia in a grey seal (Halichoerus grypus) from the Swedish part of the Baltic Sea is reported. The pathogen was isolated from both lung and spleen specimens. All of the A. hydrophila isolates produced haemolysin and Vero active cytotoxin. The aerolysin gene was found in all tested isolates as evidenced by the polymerase chain reaction (PCR) technique. Also, all isolates tested showed identical patterns of biochemical and antibiotic resistance. As Aeromonas spp. commonly occur in aquatic environments, we suggest that organisms from this genus may also play an important role as opportunistic pathogens in morbillivirus infected seals.

Biochemical modulation of tumor cell energy in vivo: II. A lower dose of adriamycin is required and a greater antitumor activity is induced when cellular energy is depressed

A quadruple drug combination--consisting of a triple-drug combination of N-(phosphonacetyl)-L-aspartate (PALA) + 6-methylmercaptopurine riboside (MMPR) + 6-amino-nicotinamide (6-AN), designed to primarily deplete cellular energy in tumor cells, + Adriamycin (Adria)--yielded significantly enhanced anticancer activity (i.e., tumor regressions) over that produced by either Adria alone at maximum tolerated dose (MTD) or by the triple-drug combination, against large, spontaneous, autochthonous murine breast tumors. The adenosine triphosphate (ATP)-depleting triple-drug combination administered prior to Adria resulted in a 100% tumor regression rate (12% complete regression; 88% partial regression) of spontaneous tumors. Histological examination of treated tumors demonstrated that the treatment-induced mechanism of cancer cell death was by apoptosis. The augmented therapeutic results (100% tumor regressions) were obtained with approximately one-half the MTD of Adria as a single agent and suggest the potential clinical benefit of longer, more effective, and safer treatment by low doses of Adria when combined with the triple-drug combination. Two likely mechanisms of action are discussed: (1) prevention of DNA repair; (2) complementary disruption of biochemical pathways by both the triple-drug combination and the biochemical cascade of apoptosis that is induced by a DNA-damaging anticancer agents such as Adria.

On the London equations

The classical London equations for superconductors are written in differential form notation and recast in relativistic form, where they yield the Proca equation. In particular, the field itself acts as its own charge carrier.

Superconnections and internal supersymmetry dynamics

In previous papers we proposed a theory of internal supersymmetry using the superalgebra su(n/1) to give rise to a unified structure that included quarks and leptons in 2n-5 generations. In the present paper we suggest that the notion of superconnections as introduced by Quillen provides a natural setting for the dynamics of an internally supersymmetric theory with the Higgs field occurring as the "zero-th order part" of the superconnection. The Higgs mechanism enters quadratically into the curvature of the superconnection and hence quartically into the Lagrangian. The supercovariant derivative gives a coupling of the Higgs field to the matter field similar to that put in "by hand" in the Lagrangian of the Weinberg-Salam theory.

Douglas' solution of the Plateau problem

Using ideas suggested by some recent developments in string theory, we give here an elementary demonstration of one of the key steps in Douglas' celebrated proof of the existence of solutions of the Plateau problem in n dimensions.

On the automorphism group of the conformal superalgebra

There is no automorphism of the conformal superalgebra that induces PT (parity and time reversal) on space time. Those conformal transformations that induce PT must change the sign of the odd brackets. In particular, in any implementation of conformal supersymmetry, CP can preserve but CPT must (at best) reverse the sign of the odd brackets (C, charge conjugation).

A monoclonal antibody which detects a 125 kd glycoprotein on embryonal carcinoma cells and is mitogenic for murine spleen cells

The isolation and characterisation of a monoclonal antibody (2H9), selected for reactivity against murine teratocarcinoma stem cells, is described. This antibody recognizes one major glycoprotein on the surface of embryonal carcinoma (EC) cells but detects multiple glycoprotein species on various murine or human derived cell types. The binding of the antibody to cells is abolished by treatment with periodate or neuraminidase. These results suggest that 2H9 antibody detects a carbohydrate determinant; this is apparently distinct from other anti-EC reactive monoclonal antibodies and a variety of lectins. These antibodies are mitogenic for a population of lymphocytes in murine spleen. The antibodies recognize numerous cell surface glycoproteins on the surface of the spleen cells.

Perception, production, and imitation of time ratios by skilled musicians

We have described our exploration of the judgment, production, and imitation of fractions of a beat by skilled musicians, illustrating our findings with data from violinist and conductor Paul Zukofsky. For small fractions we found systematic and substantial errors. In the judgment task small stimulus fractions are associated with names that are too large (overestimation). In both production and imitation tasks the fractions produced were too large (overproduction, overimitation). A summary of our findings and of the expectations they violate is provided in Figure 7. The temporal patterns we used are perhaps the simplest that qualify as rhythms, incorporating just a beat interval and a fraction. The phenomena we discovered in relation to these simple patterns, and their implications for underlying mechanisms, must be considered in attempts to understand the perception and production of more complex rhythms, as in actual music. We explored and rejected several plausible explanations for the overestimation and overproduction of small fractions. Although we have as yet no satisfactory explanations of the errors themselves, relations among the errors have powerful implications for human timing mechanisms. The relation between the errors in judgment and production requires us to reject a feedback model of production, in which a subject uses the same processes as in the judgment task to evaluate and adjust his performance in the production task. An explanation of the inconsistency between judgment and production seems most likely to lie in a change in time perception induced by the production task. Together with the existence of systematic errors in judgment, the equality of the errors in production and imitation argues that imitation is not accomplished by concatenating all the processes used in judgment and production. Our results are instead consistent with a model containing four internal transformation processes, in which judgment and production share no process, but do involve the same internal-fraction representation, and in which imitation shares one process with judgment and another with production.

Internal supersymmetry and unification

We construct a family of finite-dimensional representations of the superalgebra sl(n/m) that depend on an integer parameter for m > 1 and on a complex parameter, b, for m = 1. We describe some models of elementary particles for sl(2/1), sl(3/1), and sl(5/1). This involves the choice of the parameter b and the choice of the operators I(3) (the third component of the weak left-handed isospin) and U (the weak hypercharge). These must commute, and are related to the electric charge by the usual formula Q = I(3) + (1/2)U. In particular, taking I(3) to be in its standard form in su(2) subset sl(5) subset sl(5/1) and requiring that U commute with color su(3) subset sl(5) subset sl(5/1) leaves three free parameters, two for the choice of U and one for the choice of b. We show that there are just two possible choices of these parameters yielding exactly all 32 quark and lepton charges: the Georgi-Glashow U in su(5), corresponding to U(1,-(2/3)) and arbitrary b and U(0,(1/3)) negated set membership su(5), with b = 2. We provide a general construction of representations of sl(n/1) consisting exactly of sequences of generations of quarks and leptons.