Stimulus Onset Hub: an Open-Source, Low Latency, and Opto-Isolated Trigger Box for Neuroscientific Research Replicability and Beyond.

Accurate stimulus onset timing is critical to almost all behavioral research. Auditory, visual, or manual response time stimulus onsets are typically sent through wires to various machines that record data such as: eye gaze positions, electroencephalography, stereo electroencephalography, and electrocorticography. These stimulus onsets are collated and analyzed according to experimental condition. If there is variability in the temporal accuracy of the delivery of these onsets to external systems, the quality of the resulting data and scientific analyses will degrade. Here, we describe an approximately 200 dollar Arduino based system and associated open-source codebase that achieved a maximum of 4 microseconds of delay from the inputs to the outputs while electrically opto-isolating the connected external systems. Using an oscilloscope, the device is configurable for the different environmental conditions particular to each laboratory (e.g., light sensor type, screen type, speaker type, stimulus type, temperature, etc). This low-cost open-source project delivered electrically isolated digital stimulus onset Transistor-Transistor Logic triggers with an input/output delay of 4 µs, and was successfully tested with seven different external systems that record eye and neurological data.

Microsaccades during high speed continuous visual search.

Here, we provide an analysis of the microsaccades that occurred during continuous visual search and targeting of small faces that we pasted either into cluttered background photos or into a simple gray background. Subjects continuously used their eyes to target singular 3-degree upright or inverted faces in changing scenes. As soon as the participant's gaze reached the target face, a new face was displayed in a different and random location. Regardless of the experimental context (e.g. background scene, no background scene), or target eccentricity (from 4 to 20 degrees of visual angle), we found that the microsaccade rate dropped to near zero levels within only 12 milliseconds after stimulus onset. There were almost never any microsaccades after stimulus onset and before the first saccade to the face. One subject completed 118 consecutive trials without a single microsaccade. However, in about 20% of the trials, there was a single microsaccade that occurred almost immediately after the preceding saccade's offset. These microsaccades were task oriented because their facial landmark targeting distributions matched those of saccades within both the upright and inverted face conditions. Our findings show that a single feedforward pass through the visual hierarchy for each stimulus is likely all that is needed to effectuate prolonged continuous visual search. In addition, we provide evidence that microsaccades can serve perceptual functions like correcting saccades or effectuating task-oriented goals during continuous visual search.

High Resolution Human Eye Tracking During Continuous Visual Search.

While several studies have shown human subjects' impressive ability to detect faces in individual images in paced settings (Crouzet et al., 2010), we here report the details of an eye movement dataset in which subjects rapidly and continuously targeted single faces embedded in different scenes at rates approaching six face targets each second (including blinks and eye movement times). In this paper, we describe details of a large publicly available eye movement dataset of this new psychophysical paradigm (Martin et al., 2018). The paradigm produced high-resolution eye-tracking data from an experiment on continuous upright and inverted 3° sized face detection in both background and no-background conditions. The new "Zapping" paradigm allowed large amounts of trials to be completed in a short amount of time. For example, our three studies encompassed a total of 288,000 trials done in 72 separate experiments, and yet only took approximately 40 hours of recording for the three experimental cohorts. Each subject did 4000 trials split into eight blocks of 500 consecutive trials in one of the four different experimental conditions: {upright, inverted} × {scene, no scene}. For each condition, there are several covariates of interest, including: temporal eye positions sampled at 1250 hz, saccades, saccade reaction times, microsaccades, pupil dynamics, target luminances, and global contrasts.

Zapping 500 faces in less than 100 seconds: Evidence for extremely fast and sustained continuous visual search.

A number of studies have shown human subjects' impressive ability to detect faces in individual images, with saccade reaction times starting as fast as 100 ms after stimulus onset. Here, we report evidence that humans can rapidly and continuously saccade towards single faces embedded in different scenes at rates approaching 6 faces/scenes each second (including blinks and eye movement times). These observations are impressive, given that humans usually make no more than 2 to 5 saccades per second when searching a single scene with eye movements. Surprisingly, attempts to hide the faces by blending them into a large background scene had little effect on targeting rates, saccade reaction times, or targeting accuracy. Upright faces were found more quickly and more accurately than inverted faces; both with and without a cluttered background scene, and over a large range of eccentricities (4°-16°). The fastest subject in our study made continuous saccades to 500 small 3° upright faces at 4° eccentricities in only 96 seconds. The maximum face targeting rate ever achieved by any subject during any sequence of 7 faces during Experiment 3 for the no scene and upright face condition was 6.5 faces targeted/second. Our data provide evidence that the human visual system includes an ultra-rapid and continuous object localization system for upright faces. Furthermore, these observations indicate that continuous paradigms such as the one we have used can push humans to make remarkably fast reaction times that impose strong constraints and challenges on models of how, where, and when visual processing occurs in the human brain.

Targeting of the purine biosynthesis host cell pathway enhances the activity of tenofovir against sensitive and drug-resistant HIV-1.

BACKGROUND: Targeting host-cell pathways to increase the potency of nucleoside/nucleotide analog reverse transcriptase inhibitors (NRTIs) is an important strategy for clinical investigation. Resveratrol is a natural product that inhibits cellular ribonucleotide reductase, prolonging the S phase of the cell cycle and preferentially lowering dATP levels. METHODS: We performed in vitro evaluation of resveratrol on the antiviral activity of adenosine analog tenofovir (TFV) against sensitive and drug-resistant human immunodeficiency virus type 1 (HIV-1), from subtypes B and C, in primary cells. RESULTS: Resveratrol enhanced the antiviral activity of TFV by up to 10-fold and restored susceptibility of TFV-resistant viruses. Resveratrol prevented wild-type HIV-1 from developing phenotypic resistance to TFV. Notably, resveratrol enhanced TFV activity against sensitive and resistant HIV-1 from both subtypes B and C. CONCLUSIONS: Prolonged wide-scale use of thymidine analogs in the setting of viral failure has limited the efficacy of second-line NRTI-based regimens in Africa. Moreover, the extensive use of ddI and d4T has led to high frequencies of the K65R mutation, further compromising TFV efficacy. In light of increasing resistance to commonly used NRTIs in global HIV treatment programs, targeting nucleoside biosynthesis with resveratrol, or derivatives with improved bioavailabilities, is a potential strategy to maintain, enhance, and restore susceptibility of commonly used NRTIs.

Impact of age, gender, and race on circulating γδ T cells.

A major subset of human peripheral blood γδ T cells expresses the Vγ2Vδ2 T cell receptor and responds to malignant or infectious diseases. We noted significant differences in the numbers of Vγ2Vδ2 T cells in blood samples from healthy Caucasian CA or African American (AA) donors. On average, CA donors had 3.71% ± 4.37% Vδ2 cells (as a percentage of total lymphocytes) compared with 1.18% ± 2.14% Vδ2 cells for AA donors (p < 0.0001). Age and race had the greatest impact on Vδ2 cell levels; the effect of age was similar for both racial groups. The Vδ2 cell population was dominated, for both donor groups, by cells expressing the Vγ2-Jγ1.2 Vδ2 T cell receptor, an apparent result of strong positive selection and there was substantial overlap in the public Vγ2 clonotypes from both racial groups. Mechanisms for selection and amplification of Vδ2 cells are nearly identical for both groups, despite the significant difference in baseline levels. These data show that appropriate controls, matched for age and race, may be required for clinical studies of Vγ2Vδ2 T cells in infectious disease or cancer and raise important questions about the mechanisms regulating the levels of circulating Vδ2 cells.

Viral load decay in antiretroviral-naïve patients receiving once-daily tenofovir and emtricitabine plus twice-daily nevirapine.

PURPOSE: The once-daily nucleoside reverse transcriptase inhibitor backbone of tenofovir and emtricitabine has been proven effective in combination with efavirenz and protease inhibitors in large clinical trials. This study evaluated tenofovir and emtricitabine in combination with nevirapine. METHODS: Viral load was assessed at baseline, Day 3, and Day 7 in addition to Weeks 2, 4, 8, 12, 16, 24, 32, 40, 48, 60, 72, and 84 in 10 antiretroviral-naïve patients participating in an open-label clinical trial of tenofovir and emtricitabine once daily in combination with nevirapine twice daily. RESULTS: All patients achieved viral decay with this combination. Two patients discontinued prior to virologic suppression, one with a viral load of 55 copies/mL. Virologic suppression (<50 copies/mL) was achieved by Week 24 in the remaining 8 patients. An undetectable viral load was maintained during > or =60 weeks follow-up. CONCLUSION: In this study of treatment-naïve patients, the combination of tenofovir and emtricitabine plus twice-daily nevirapine produced sustained viral load decay in patients including those with a high baseline viral load.

Impacts of HIV infection on Vgamma2Vdelta2 T cell phenotype and function: a mechanism for reduced tumor immunity in AIDS.

HIV infection causes rapid and lasting defects in the population of Vgamma2Vdelta2 T cells. To fully describe the impact of HIV, we examined PBMC samples from HIV+ patients receiving highly active antiretroviral therapy, who had displayed prolonged viral control and CD4 counts above 300 cells/mm3. We observed lower frequencies of CD27-/CD45RA- Vgamma2Vdelta2 cells in HIV+ individuals when compared with controls, coupled with an increased proportion of CD45RA+ cells. These changes were common among 24 HIV+ patients and were not related to CD4 cell count or viral RNA burden. Vgamma2 cells from HIV+ individuals had lower expression of Granzyme B and displayed reduced cytotoxicity against Daudi targets after in vitro stimulation. There was increased expression of FasR (CD95) on Vgamma2 cells from HIV+ PBMC that may be a mechanism for depletion of Vgamma2 cells during disease. In addition to the well-characterized defects in the Vgamma2 repertoire and functional responses to phosphoantigen, the proportion of CD27-/CD45RA- Vgamma2Vdelta2 T cells after isopentenyl pyrophosphate stimulation was reduced sharply in HIV+ donors versus controls. Thus, HIV infection has multiple impacts on the circulating Vgamma2Vdelta2 T cell population that combine to reduce the potential effector activity in terms of tumor cytotoxicity. Changes in Vgamma2Vdelta2 T cells, along with concomitant effects on NK and NKT cells that also contribute to tumor surveillance, may be important factors for elevating the risk of malignancy during AIDS.

Tenofovir and abacavir combination therapy: lessons learned from an urban clinic population.

Regimens containing abacavir (ABC), tenofovir (TDF), and lamivudine (3TC) have recently been demonstrated to have high failure rates. This poses a clinical dilemma of how to manage patients currently being treated with other regimens containing tenofovir/abacavir. We evaluated the outcomes of tenofovir/abacavir regimens in our clinical practice through a retrospective review of 2655 charts. Two hundred patients (7%) were on a tenofovir/abacavir-containing regimen. Fifty-nine patients met the criteria for analysis and were grouped into three groups: (1) antiretroviral naïve, (2) virally suppressed patients switched to TDF/ABC, and (3) patients with failure of their first antiretroviral regimen. Rates of viral suppression in the naïve, switch, and first-failure groups were 95%, 86%, and 46%, respectively. In the first-failure group, viral suppression was 66% without and 18% with a preexisting M184V. A composite analysis of the groups revealed a success rate of 86% when the regimen contained zidovudine (ZDV) and 62% when it did not. No K65R mutations were noted. These findings support continued caution in the use of TDF/ABC in combination. However, these data suggest that this combination may be successfully used in selected situations such as in combination with ZDV. In patients already virally suppressed on a TDF/ABC-containing regimen, considerations include continuing the regimen or adding zidovudine, in the attempt to protect against the development of a K65R mutation and/or virologic failure, versus changing a stable regimen.

Brucellosis in San Diego: epidemiology and species-related differences in acute clinical presentations.

Although aggressive public health measures have greatly reduced the number of brucellosis cases in the United States, there is a resurgence of interest in this worldwide zoonosis because of its potential as a bioweapon and its 8-fold higher incidence in California, Texas, and the other borderlands between the United States and Mexico compared with the national rate. Accordingly, we reviewed the clinical records of 28 patients diagnosed at a university hospital in San Diego, CA, between 1979 and 2002 to look for new epidemiologic trends and to test the hypothesis that there are species-specific differences in clinical presentations. In contrast to the latest California-wide study completed in 1992, Brucella abortus infections were more common (73%) than Brucella melitensis after 1992, and women were more commonly infected (77% compared with 39%) than men. Major risk factors remained Hispanic ethnicity, travel to Mexico, and ingestion of nonpasteurized dairy products. Analysis of diagnostic procedures suggested that the traditional practice of prolonged incubation of blood cultures increased their sensitivity for Brucella, even in automated radiometric systems. Direct comparison of the clinical manifestations of infections with B. abortus and B. melitensis strongly supported differences in acute presentations. B. melitensis presented more acutely as fevers of unknown origin with statistically significant higher rates of abdominal tenderness, hepatomegaly, splenomegaly, thrombocytopenia, pancytopenia, and hepatic dysfunction. These results suggest that the epidemiology of brucellosis in California may be evolving, and they show, to our knowledge for the first time in a single series, that species-specific differences in presentations may account for some of the protean manifestations of brucellosis. Familiarity with manifestations of brucellosis and the optimal laboratory techniques for its diagnosis could help physicians protect the public against this reemerging, under-recognized zoonosis.

The effect of moving to a new hospital facility on the prevalence of methicillin-resistant Staphylococcus aureus.

BACKGROUND: The influence of hospital design on nosocomial transmission of methicillin-resistant Staphylococcus aureus (MRSA) is unknown. Our hospital's relocation to a new building with radically different ward design allowed us to study this question. Our old hospital facility had open bay wards and intensive care units, and few poorly located sinks for handwashing (bed:sink ratio 4:1). Our new hospital facility had optimized hand-washing geography and distribution of ward beds into mostly single or double rooms (bed:sink ratio 1.3:1). METHODS: We compared the prevalence of MRSA in the 2 institutions by obtaining nasal swabs from all patients on 8 selected wards and intensive care units at 2 time points both before and after the move. In addition, passive surveillance rates of MRSA for all hospitalized patients for 2 years both before and after the move were compared. Hand hygiene practices, although unrelated to the study periods, were directly observed. RESULTS: Eight of 123 patients cultured before the move were MRSA positive, compared to 5 of 138 patients cultured after the move (P=NS). MRSA prevalence determined by passive surveillance of all hospitalized patients before and after the move was also unchanged. An insignificant increase in the frequency of hand-hygiene performance following the move (20% to 23%) was observed. CONCLUSION: Radical facility design changes, which would be permissive of optimal infection control practices, were not sufficient, by themselves, to reduce the nosocomial spread of MRSA in our institution.

Association between longer duration of HIV-suppressive therapy and partial recovery of the V gamma 2 T cell receptor repertoire.

Human immunodeficiency virus (HIV) infection alters the function and repertoire of peripheral blood gamma delta T cells expressing the V gamma 2/V delta 2 T cell receptor (TCR). A cross-sectional comparison of the V gamma 2 TCR repertoire was performed for 56 HIV-infected subjects, 51 of whom were receiving highly active antiretroviral therapy (HAART), to measure changes in the V gamma 2 TCR repertoire. Longer durations of HAART were associated with partial recovery of the normal TCR repertoire, and recovery was greatest in subjects with complete virus suppression. Changes in the V gamma 2 TCR repertoire are sensitive measures for the effects of HAART and of residual HIV replication.