A standardized head-fixation system for performing large-scale, in vivo physiological recordings in mice

BACKGROUND

The Allen Institute recently built a set of high-throughput experimental pipelines to collect comprehensive in vivo surveys of physiological activity in the visual cortex of awake, head-fixed mice. Developing these large-scale, industrial-like pipelines posed many scientific, operational, and engineering challenges.

NEW METHOD

Our strategies for creating a cross-platform reference space to which all pipeline datasets were mapped required development of 1) a robust headframe, 2) a reproducible clamping system, and 3) data-collection systems that are built, and maintained, around precise alignment with a reference artifact.

RESULTS

When paired with our pipeline clamping system, our headframe exceeded deflection and reproducibility requirements. By leveraging our headframe and clamping system we were able to create a cross-platform reference space to which multi-modal imaging datasets could be mapped.

COMPARISON WITH EXISTING METHODS

Together, the Allen Brain Observatory headframe, surgical tooling, clamping system, and system registration strategy create a unique system for collecting large amounts of standardized in vivo datasets over long periods of time. Moreover, the integrated approach to cross-platform registration allows for multi-modal datasets to be collected within a shared reference space.

CONCLUSIONS

Here we report the engineering strategies that we implemented when creating the Allen Brain Observatory physiology pipelines. All of the documentation related to headframe, surgical tooling, and clamp design has been made freely available and can be readily manufactured or procured. The engineering strategy, or components of the strategy, described in this report can be tailored and applied by external researchers to improve data standardization and stability.

Experience shapes activity dynamics and stimulus coding of VIP inhibitory cells

Cortical circuits can flexibly change with experience and learning, but the effects on specific cell types, including distinct inhibitory types, are not well understood. Here we investigated how excitatory and VIP inhibitory cells in layer 2/3 of mouse visual cortex were impacted by visual experience in the context of a behavioral task. Mice learned a visual change detection task with a set of eight natural scene images. Subsequently, during 2-photon imaging experiments, mice performed the task with these familiar images and three sets of novel images. Strikingly, the temporal dynamics of VIP activity differed markedly between novel and familiar images: VIP cells were stimulus-driven by novel images but were suppressed by familiar stimuli and showed ramping activity when expected stimuli were omitted from a temporally predictable sequence. This prominent change in VIP activity suggests that these cells may adopt different modes of processing under novel versus familiar conditions.

A large-scale standardized physiological survey reveals functional organization of the mouse visual cortex

To understand how the brain processes sensory information to guide behavior, we must know how stimulus representations are transformed throughout the visual cortex. Here we report an open, large-scale physiological survey of activity in the awake mouse visual cortex: the Allen Brain Observatory Visual Coding dataset. This publicly available dataset includes the cortical activity of nearly 60,000 neurons from six visual areas, four layers, and 12 transgenic mouse lines in a total of 243 adult mice, in response to a systematic set of visual stimuli. We classify neurons on the basis of joint reliabilities to multiple stimuli and validate this functional classification with models of visual responses. While most classes are characterized by responses to specific subsets of the stimuli, the largest class is not reliably responsive to any of the stimuli and becomes progressively larger in higher visual areas. These classes reveal a functional organization wherein putative dorsal areas show specialization for visual motion signals.

Biological variation in the sizes, shapes and locations of visual cortical areas in the mouse

Visual cortex is organized into discrete sub-regions or areas that are arranged into a hierarchy and serves different functions in the processing of visual information. In retinotopic maps of mouse cortex, there appear to be substantial mouse-to-mouse differences in visual area location, size and shape. Here we quantify the biological variation in the size, shape and locations of 11 visual areas in the mouse, after separating biological variation and measurement noise. We find that there is biological variation in the locations and sizes of visual areas.

Fieldwork after conflict: contextualising the challenges of access and data quality

Despite sustained scholarly interest in post-conflict states, there has not been a thorough review and analysis of associated methodology and the challenges of conducting research in these contexts. Addressing this gap, this paper directs attention to the particular effects of these settings on access and data quality and their ramifications for the resulting scholarship. It assesses the intrinsic challenges of performing fieldwork in these environments, drawing on both relevant social science literature and the authors' experiences of carrying out research in Afghanistan and Timor-Leste. The study demonstrates that the post-conflict environment moulds research design and, consequently, influences how questions are answered as well as the questions asked. Moreover, it highlights ways to mitigate these issues. This work is of relevance to scholars planning to engage in field research and to researchers reflecting upon their work, as well as to policymakers who are considering undertaking programmes or commissioning research in post-conflict areas.

Aberrant Cortical Activity in Multiple GCaMP6-Expressing Transgenic Mouse Lines

Transgenic mouse lines are invaluable tools for neuroscience but, as with any technique, care must be taken to ensure that the tool itself does not unduly affect the system under study. Here we report aberrant electrical activity, similar to interictal spikes, and accompanying fluorescence events in some genotypes of transgenic mice expressing GCaMP6 genetically encoded calcium sensors. These epileptiform events have been observed particularly, but not exclusively, in mice with Emx1-Cre and Ai93 transgenes, of either sex, across multiple laboratories. The events occur at >0.1 Hz, are very large in amplitude (>1.0 mV local field potentials, >10% df/f widefield imaging signals), and typically cover large regions of cortex. Many properties of neuronal responses and behavior seem normal despite these events, although rare subjects exhibit overt generalized seizures. The underlying mechanisms of this phenomenon remain unclear, but we speculate about possible causes on the basis of diverse observations. We encourage researchers to be aware of these activity patterns while interpreting neuronal recordings from affected mouse lines and when considering which lines to study.

A comprehensive transcriptional map of primate brain development

The transcriptional underpinnings of brain development remain poorly understood, particularly in humans and closely related non-human primates. We describe a high-resolution transcriptional atlas of rhesus monkey (Macaca mulatta) brain development that combines dense temporal sampling of prenatal and postnatal periods with fine anatomical division of cortical and subcortical regions associated with human neuropsychiatric disease. Gene expression changes more rapidly before birth, both in progenitor cells and maturing neurons. Cortical layers and areas acquire adult-like molecular profiles surprisingly late in postnatal development. Disparate cell populations exhibit distinct developmental timing of gene expression, but also unexpected synchrony of processes underlying neural circuit construction including cell projection and adhesion. Candidate risk genes for neurodevelopmental disorders including primary microcephaly, autism spectrum disorder, intellectual disability, and schizophrenia show disease-specific spatiotemporal enrichment within developing neocortex. Human developmental expression trajectories are more similar to monkey than rodent, although approximately 9% of genes show human-specific regulation with evidence for prolonged maturation or neoteny compared to monkey.

Transcriptional landscape of the prenatal human brain

The anatomical and functional architecture of the human brain is largely determined by prenatal transcriptional processes. We describe an anatomically comprehensive atlas of mid-gestational human brain, including de novo reference atlases, in situ hybridization, ultra-high resolution magnetic resonance imaging (MRI) and microarray analysis on highly discrete laser microdissected brain regions. In developing cerebral cortex, transcriptional differences are found between different proliferative and postmitotic layers, wherein laminar signatures reflect cellular composition and developmental processes. Cytoarchitectural differences between human and mouse have molecular correlates, including species differences in gene expression in subplate, although surprisingly we find minimal differences between the inner and human-expanded outer subventricular zones. Both germinal and postmitotic cortical layers exhibit fronto-temporal gradients, with particular enrichment in frontal lobe. Finally, many neurodevelopmental disorder and human evolution-related genes show patterned expression, potentially underlying unique features of human cortical formation. These data provide a rich, freely-accessible resource for understanding human brain development.

[Authorization and reimbursement of orphan drugs in an international comparison]

BACKGROUND

This paper analyses schemes to promote the authorisation of and reimbursement for orphan drugs.

METHODS

8 countries - Australia, Canada, Germany, Great Britain, France, Netherlands, Switzerland, USA - were studied to compare specific regulations for orphan drugs regarding drug admission, health technology assessment (HTA), decision-making for reimbursement, and off-label and compassionate use. Information was obtained by reviewing published and grey literature. Expert interviews were also conducted.

RESULTS

The comparison of orphan drug legislation reveals that the EU and the USA offer the greatest incentives for the development of orphan drugs, whereas there is a tendency for Australia and Switzerland to profit from incentives in other countries. Although not explicitly stated, economic evaluation of orphan drugs takes the special circumstances for orphan drugs into account. In addition to common reimbursement practices, special schemes or programmes for the reimbursement of high-priced orphan drugs exist in all countries that were analysed. Therefore access to orphan drugs seems to be warranted. However, due to co-payments of 5%, the USA may form an exception.

CONCLUSION

On the one hand, the use of special criteria for drug admission, HTA, and reimbursement promotes R&D for orphan drugs. On the other hand, high opportunity costs arise, because huge efforts are made for a minority of patients. A solution for this moral dilemma may be the application of "rule of rescue" or of "no cure, no pay" programmes.

Clinical outcome of children presenting with a severe manifestation of acute disseminated encephalomyelitis

BACKGROUND

Acute disseminated encephalomyelitis (ADEM) is an acute, inflammatory-demyelinating disorder of the CNS with a favourable outcome in the majority of cases.

OBJECTIVE

The aim of this study was to examine the long-term outcome of children with an initially severe form of ADEM.

METHODS

Children with ADEM according to the criteria of the International Pediatric MS Study Group (IPMSSG) referred to the rehabilitation centre Vogtareuth were included. Neurological impairment was evaluated with a standardized telephone-based interview assessing the EDSS score. Neuropsychological outcome was assessed with review of the medical records and a standardized parental questionnaire (KOPKIJ).

RESULTS

Twelve children (1 year 9 months to 13 years of age) were included. All children had focal-neurological signs and changes in mental status at presentation and an MRI of the brain showing a range of white and gray matter lesions. 11/12 patients with a mean follow-up of 6.2 years (2-13.6 years) had a monophasic course of the disease. One child had a multiphasic ADEM. Two children had an EDSS score of 0, three an EDSS of 2, five an EDSS between 3 and 5 and two children had an EDSS score of 6 and 9. Results of a standardized parental questionnaire (KOPKIJ) revealed that 7 children had deficits in the categories alertness, memory, school performance, visual-spatial skills and/or impulse control.

CONCLUSION

The results of our study indicate that children with an initially severe manifestation of ADEM continue to have in the majority of cases neurological and neuropsychological handicaps.

Incidence of enteroviruses in Mamala Bay, Hawaii using cell culture and direct polymerase chain reaction methodologies

The consequence of point and nonpoint pollution sources, discharged into marine waters, on public recreational beaches in Mamala Bay, Hawaii was evaluated using virus cell culture and direct reverse transcriptase-polymerase chain reaction (RT-PCR). Twelve sites, nine marine, two freshwater (one stream and one canal), and one sewage, were assessed either quarterly or monthly for 1 year to detect the presence of human enteric viruses. Water samples were concentrated from initial volumes of 400 L to final volumes of 30 mL using Filterite electronegative cartridge filters and a modified beef extract elution procedure. Cell culture was applied using the Buffalo Green Monkey kidney cell line to analyze samples for enteroviruses. Positive samples were also evaluated by RT-PCR, using enterovirus-specific primers. Levels of RT-PCR inhibition varied with each concentrated sample. Resin column purification increased PCR detection sensitivity by at least one order of magnitude in a variety of sewage outfall and recreational marine water samples but not in the freshwater canal samples. Using cell culture, viable enteroviruses were found in 50 and 17% of all outfall and canal samples, respectively. Samples were positive at beaches 8% of the time. These data illustrate the potential public health hazard associated with recreational waters. Using direct PCR, viruses were detected at the outfall but were not found in any beach or canal samples, in part, owing to substances that inhibit PCR. Therefore, conventional cell culture is the most effective means of detecting low levels of infectious enteroviruses in environmental waters, whereas direct RT-PCR is rendered less effective by inhibitory compounds and low equivalent reaction volumes.

Aging effects on the organic base transporter and stereoselective renal clearance

OBJECTIVE

The organic base transporter is responsible for stereoselective renal excretion. Changes in activity of this system secondary to aging may affect the disposition of an organic base in a stereoselective manner.

METHODS

Eight young men (age range, 22 to 33 years) and seven elderly men (age range, 62 to 79 years) were given 10 mg pindolol twice daily, pindolol with 200 mg trimethoprim once daily (a known inhibitor of organic base secretion) and pindolol with 1.5 gm ammonium chloride (NH4Cl) four times daily for 3 days on three occasions. On day 4, urine and plasma were collected over 24 hours to determine renal clearance (CLR) values of pindolol isomers.

RESULTS

R(+)-Pindolol CLR values in young versus elderly men were 203 +/- 82 versus 150 +/- 87 ml/min, 128 +/- 51 versus 113 +/- 35 ml/min, and 480 +/- 248 versus 247 +/- 59 ml/min during the control, trimethoprim, and NH4Cl study phases, respectively. S(-)-Pindolol CLR values in young versus elderly were 279 +/- 81 versus 207 +/- 105 ml/min, 178 +/- 70 versus 136 +/- 42 ml/min, and 593 +/- 294 versus 276 +/- 49 ml/min during control, trimethoprim, and NH4Cl phases, respectively. NH4Cl increased R(+)-pindolol CLR by 138% (p < 0.05 versus pindolol alone) in young men, which was significantly greater than that observed in elderly subjects (66%; p < 0.05 versus pindolol alone; p = 0.016 young versus old). NH4Cl affected S(-)-pindolol CLR in a similar manner. Trimethoprim decreased R(+)-pindolol CLR in the young subjects by 37% (p < 0.05 versus pindolol alone), which was similar to that observed in the elderly subjects (26%; p < 0.05 versus pindolol alone; p = 0.94 young versus elderly). Trimethoprim affected S(-)-pindolol CLR in a similar manner. Stereoselective renal excretion of pindolol was unaffected by NH4Cl and trimethoprim, where the R(+)/S(-)-pindolol CLR ratio was unchanged (p = NS) from control in the young and elderly subjects. Comparison of the pindolol CLR isomer ratio between young and elderly groups showed no significant differences. Changes in pindolol clearance values resulted in significant changes in beta-blocking activity, assessed by isoproterenol (INN, isoprenaline) testing.

CONCLUSIONS

Trimethoprim and NH4Cl significantly affect pindolol renal and total clearance values. Aging does not alter renal excretion of pindolol except for the magnitude by which renal excretion can be stimulated.

Urine acidification affects the activity of the organic base transporter in a nonstereoselective manner

This investigation determined 1) the effect of urine acidification on renal clearance (Clrenal), total systemic clearance (Cltotal) and nonrenal clearance (Clnonrenal) of pindolol, 2) whether urine acidification affected the stereoselectivity of pindolol excretion and 3) the pharmacodynamic effects that may result from changes in the activity of the organic base transporter. The Clrenal, Cltotal and Clnonrenal values of pindolol isomers were determined during pindolol administration (10 mg twice daily; control phase) and during pindolol administration (10 mg twice daily) with NH4Cl, a systemic and urinary acidifier, (1.5 g every 6 hr). Eight healthy males (22-33 yr) randomly received this therapy for 3 days on two occasions. On day 4, urine and plasma were collected over 24 hr. R-(+) pindolol Clrenal values during control and NH4Cl were 203 +/- 82 and 480 +/- 248 ml/min, respectively (P = .03). S-(-) pindolol Clrenal values during control and NH4Cl were 279 +/- 81 and 593 +/- 294 ml/min, respectively (P = .005). NH4Cl increased R-(+) pindolol Clrenal by 173% +/- 136% (P = .003) and S-(-) pindolol Clrenal by 127% +/- 105% (P = .03). Stereoselective renal excretion of pindolol was unaffected by NH4Cl; the R(+)/S(-) pindolol Clrenal ratio was unchanged from control to NH4Cl (0.74 +/- 0.23 to 0.81 +/- 0.10, P = NS, respectively). NH4Cl, however, affected pindolol Clnonrenal in a stereoselective fashion; R-(+) pindolol Clnonrenal values increased (641 +/- 241 to 851 +/- 251 ml/min; P = .02), whereas S-(-) pindolol Clnonrenal values remained constant (354 +/- 116 vs. 370 +/- 213 ml/min). Changes in pindolol clearance values resulted in a significant reduction in beta-blocking activity assessed by isoproterenol testing. We conclude that increasing the urine proton gradient can increase the Clrenal value of organic bases by 2-fold in a manner that is not stereoselective. NH4Cl, however, did increase the Clnonrenal value of pindolol in a stereoselective manner. These data, therefore, indicate that the administration of a urine-acidifying agent can greatly enhance the elimination of organic bases and ultimately reduce the pharmacologic activity of the organic base.

Evaluation of lamellar body number density as the initial assessment in a fetal lung maturity test cascade

The objective of this study was to assess the sensitivity and specificity of lamellar body number density in the prenatal prediction of the respiratory distress syndrome. Seventy consecutive amniotic fluid specimens obtained by amniocentesis within 72 hours of delivery were assessed for lamellar body number density, optical absorbance at 650 nm, lecithin/sphingomyelin ratio and phosphatidylglycerol. A maturity criterion of > or = 46,000/microL for lamellar body number density yielded values for diagnostic sensitivity of 100% (7/7), specificity of 89% (49/55), positive predictive value of 54% (7/13) and negative predictive value of 100% (49/49). These values were also determined for the other analytes, with results similar to those reported elsewhere. Lamellar body number density is an effective and inexpensive first test for the rapid identification of the fetus at high risk for the respiratory distress syndrome. A cascade approach, using lamellar body number density as the first test and optical absorbance at 650 nm as the second test, improves the predictive value as compared to any single test of fetal lung maturity.

Cigarette smoking during pregnancy: acute effects on uterine flow velocity waveforms

OBJECTIVE

To determine the acute effects of smoking during pregnancy on selected characteristics of the flow velocity waveform of the uterine artery.

METHODS

We studied 19 chronic smokers at a mean (+/- standard error) gestational age of 28 +/- 1 weeks. After informed consent was given, the uterine artery was located using ultrasound imaging with color flow mapping. The characteristic waveform was imaged by pulsed Doppler ultrasonography. Maternal heart rate and blood pressure and the systolic-diastolic ratio (S/D) and resistance index of the uterine artery were measured before (-10 and -1 minutes), during (+5 and +10 minutes), and after (+20 and +30 minutes) smoking two standard cigarettes in succession.

RESULTS

Maternal heart rate increased 27%, systolic blood pressure increased 8%, and diastolic blood pressure increased 19% with smoking (P < .001). The uterine artery S/D and resistance index decreased from 2.33 to 2.02 and from 0.55 to 0.49, respectively (P < .001).

CONCLUSION

The acute effects of smoking on maternal systemic hemodynamics probably influence the flow velocity waveform of the uterine artery and preclude any definitive interpretation of acute changes in downstream resistance.

The role of real-time scanning in antenatal fetal surveillance

The additional value of real-time ultrasound scanning (RTBS) in antepartum assessment of fetal well-being was studied in 158 high-risk patients after a nonstress test (NST). Fetal breathing movements (FBM), fetal movements (FM), tonus (TON), and normal amniotic fluid volume (AFV) when present on RTBS were reliable signs of fetal well-being. These ultrasound markers of fetal well-being appeared to be as reliable indicators of good outcome as the reactive NST. Multiple indicators did not improve the accuracy of the prediction of normal outcome. All test results were normal in only about 50% of patients. In general, abnormal test results were poor indicators of poor outcome. Only when all parameters were abnormal were babies invariably affected. Five of six babies with major anomalies showed increased AFV, and seven of 13 growth-retarded or postmature babies demonstrated decreased AFV. The parameters obtained on RTBS appeared to be far more reliable than the contraction stress test (CST) in discriminating the truly abnormal fetus. Three babies with positive CST in this study had normal outcomes. These results, if confirmed in larger studies, suggest that RTBS after a nonreactive NST is an effective and potentially economical method of fetal assessment.