Developing Open Source Software using Version Control Systems: An Introduction to the Git Language for Documenting Your Computational Research

Version control systems track the history of code as it is committed (saved) by any number of developers. Have you made a coding error and cannot debug it? Version control systems allow for resetting code back to when it worked, and show what code has changed since previous commits. The contents of this lecture provide an introduction to the git version control language, GitHub for cloud hosting open source code repositories, and tutorials that demonstrate common and useful git and GitHub practices. This lecture is intended to be coupled with a discussion on creating reproducible computational research.The zipped folder contains: 1. pre-meeting software installation instructions, 2. references for discussion on reproducibility, coding best practices, and legal issues, and 3. slideshow with tutorial. Commands needed for the tutorial are in the slide notes. Links to additional video tutorials are provided in a slide. Combined, the presentation + reproducibility discussion + tutorial are designed to take about 50 minutes to complete. If used in a course, the tutorial information on the hidden slides could be used as part of a student assignment

Interhemispheric claustral circuits coordinate sensory and motor cortical areas that regulate exploratory behaviors

The claustrum has a role in the interhemispheric transfer of certain types of sensorimotor information. Whereas the whisker region in rat motor (M1) cortex sends dense projections to the contralateral claustrum, the M1 forelimb representation does not. The claustrum sends strong ipsilateral projections to the whisker regions in M1 and somatosensory (S1) cortex, but its projections to the forelimb cortical areas are weak. These distinctions suggest that one function of the M1 projections to the contralateral claustrum is to coordinate the cortical areas that regulate peripheral sensor movements during behaviors that depend on bilateral sensory acquisition. If this hypothesis is true, then similar interhemispheric circuits should interconnect the frontal eye fields (FEF) with the contralateral claustrum and its network of projections to vision-related cortical areas. To test this hypothesis, anterograde and retrograde tracers were placed in physiologically-defined parts of the FEF and primary visual cortex (V1) in rats. We observed dense FEF projections to the contralateral claustrum that terminated in the midst of claustral neurons that project to both FEF and V1. While the FEF inputs to the claustrum come predominantly from the contralateral hemisphere, the claustral projections to FEF and V1 are primarily ipsilateral. Detailed comparison of the present results with our previous studies on somatomotor claustral circuitry revealed a well-defined functional topography in which the ventral claustrum is connected with visuomotor cortical areas and the dorsal regions are connected with somatomotor areas. These results suggest that subregions within the claustrum play a critical role in coordinating the cortical areas that regulate the acquisition of modality-specific sensory information during exploration and other behaviors that require sensory attention

U.S. Political Corruption and Firm Financial Policies

Using a large panel of U.S. firms from 1980-2009, I examine the association between corruption on the part of political officials in a federal judicial district and the financial policies of public firms headquartered in that district. I find that corruption is negatively related to cash holdings, directly related to leverage, and that these relations are economically significant. These results are robust to firm fixed effects, an instrumental variable framework, the use of an alternative survey measure of corruption, and, further, are largest among firms who operate mainly around their headquarters. I also find that firm value tends to be lower when corruption is higher. Overall, the evidence suggests that firms reduce their capacity to pay bribes by managing liquidity down-ward and debt obligations upward when faced with a corrupt political environment. In other words, the local political environment plays a part in shaping financial policy

The Effectiveness of Grade 5 Mobilizations vs. Grade 1-4 Mobilizations on Mechanical Neck Pain: A Clinically Appraised Topic

• From 2000 to 2010, mechanical neck pain (MNP) prevalence ranged from 30% to 50% in adults. Other data suggests that 46% to 54% of every adult will experience some form of neck pain during their lives. • Non-thrust mobilizations (NTM) and Thrust mobilizations (TM) are among the common interventions used in manual therapy in treatment of MNP. • The evidence accumulated for this clinically appraised topic (CAT) suggests high clinical variability among the effectiveness in NTM and TM among adults with mechanical neck pain

Statistical mechanics of sum frequency generation spectroscopy for the liquid-vapor interface of dilute aqueous salt solutions

We demonstrate a theoretical description of vibrational sum frequency generation (SFG) at the boundary of aqueous electrolyte solutions. This approach identifies and exploits a simple relationship between SFG lineshapes and the statistics of molecular orientation and electric field. Our computer simulations indicate that orientational averages governing SFG susceptibility do not manifest ion-specific shifts in local electric field, but instead, ion-induced polarization of subsurface layers. Counterbalancing effects are obtained for monovalent anions and cations at the same depth. Ions held at different depths induce an imbalanced polarization, suggesting that ion-specific effects can arise from weak, long ranged influence on solvent organization

Toward a simple molecular understanding of sum frequency generation at air-water interfaces

Second-order vibrational spectroscopies successfully isolate signals from interfaces, but they report on intermolecular structure in a complicated and indirect way. Here we adapt a perspective on vibrational response developed for bulk spectroscopies to explore the microscopic fluctuations to which sum frequency generation (SFG), a popular surface-specific measurement, is most sensitive. We focus exclusively on inhomogeneous broadening of spectral susceptibilities for OH stretching of HOD as a dilute solute in D{sub 2}O. Exploiting a simple connection between vibrational frequency shifts and an electric field variable, we identify several functions of molecular orientation whose averages govern SFG. The frequency-dependence of these quantities is well captured by a pair of averages, involving alignment of OH and OD bonds with the surface normal at corresponding values of the electric field. The approximate form we obtain for SFG susceptibility highlights a dramatic sensitivity to the way a simulated liquid slab is partitioned for calculating second-order response

The effects of dissolved halide anions on hydrogen bonding in liquid water

Abstract: It is widely believed that the addition of salts to water engenders structural changes in the hydrogen-bond network well beyond the adjacent shell of solvating molecules. Classification of many ions as "structure makers" and "structure breakers" has been based in part on corresponding changes in the vibrational spectra (Raman and IR). Here we show that changes in O-H vibrational spectra induced by the alkali halides in liquid water result instead from the actions of ions' electric fields on adjacent water molecules. Computer simulations that accurately reproduce our experimental measurements suggest that the statistics of hydrogen-bond strengths are only weakly modified beyond this first solvation shell

Real-Time Identification of Serious Infection in Geriatric Patients Using Clinical Information System Surveillance

To develop and characterize an automated syndromic surveillance mechanism for early identification of older emergency department (ED) patients with possible life-threatening infection. DESIGN : Prospective, consecutive-enrollment, single-site observational study. SETTING : A large university medical center with an annual ED census of 75,273. PARTICIPANTS : Patients aged 70 and older admitted to the ED and having two or more systemic inflammatory response syndrome (SIRS) criteria during their ED stay. MEASUREMENTS : A search algorithm was developed to screen the census of the ED through its clinical information system. A study coordinator confirmed all patients electronically identified as having a probable infectious explanation for their visit. RESULTS : Infection accounted for 28% of ED and 34% of final hospital diagnoses. Identification using the software tool alone carried a 1.63 relative risk of infection (95% confidence interval CI=1.09–2.44) compared with other ED patients sufficiently ill to require admission. Follow-up confirmation by a study coordinator increased the risk to 3.06 (95% CI=2.11–4.44). The sensitivity of the strategy overall was modest (14%), but patients identified were likely to have an infectious diagnosis (specificity=98%). The most common SIRS criterion triggering the electronic notification was the combination of tachycardia and tachypnea. CONCLUSION : A simple clinical informatics algorithm can detect infection in elderly patients in real time with high specificity. The utility of this tool for research and clinical care may be substantial.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/66036/1/j.1532-5415.2008.02094.x.pd

The pUL37 tegument protein guides alphaherpesvirus retrograde axonal transport to promote neuroinvasion

A hallmark property of the neurotropic alpha-herpesvirinae is the dissemination of infection to sensory and autonomic ganglia of the peripheral nervous system following an initial exposure at mucosal surfaces. The peripheral ganglia serve as the latent virus reservoir and the source of recurrent infections such as cold sores (herpes simplex virus type I) and shingles (varicella zoster virus). However, the means by which these viruses routinely invade the nervous system is not fully understood. We report that an internal virion component, the pUL37 tegument protein, has a surface region that is an essential neuroinvasion effector. Mutation of this region rendered herpes simplex virus type 1 (HSV-1) and pseudorabies virus (PRV) incapable of spreading by retrograde axonal transport to peripheral ganglia both in culture and animals. By monitoring the axonal transport of individual viral particles by time-lapse fluorescence microscopy, the mutant viruses were determined to lack the characteristic sustained intracellular capsid motion along microtubules that normally traffics capsids to the neural soma. Consistent with the axonal transport deficit, the mutant viruses did not reach sites of latency in peripheral ganglia, and were avirulent. Despite this, viral propagation in peripheral tissues and in cultured epithelial cell lines remained robust. Selective elimination of retrograde delivery to the nervous system has long been sought after as a means to develop vaccines against these ubiquitous, and sometimes devastating viruses. In support of this potential, we find that HSV-1 and PRV mutated in the effector region of pUL37 evoked effective vaccination against subsequent nervous system challenges and encephalitic disease. These findings demonstrate that retrograde axonal transport of the herpesviruses occurs by a virus-directed mechanism that operates by coordinating opposing microtubule motors to favor sustained retrograde delivery of the virus to the peripheral ganglia. The ability to selectively eliminate the retrograde axonal transport mechanism from these viruses will be useful in trans-synaptic mapping studies of the mammalian nervous system, and affords a new vaccination paradigm for human and veterinary neurotropic herpesviruses