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New facilities of the 2020s, such as the High Luminosity Large Hadron Collider (HL-LHC), will be relevant through at least the 2030s. This means that their software efforts and those that are used to analyze their data need to consider sustainability to enable their adaptability to new challenges, longevity, and efficiency, over at least this period. This will help ensure that this software will be easier to develop and maintain, that it remains available in the future on new platforms, that it meets new needs, and that it is as reusable as possible. This report discusses a virtual half-day workshop on "Software Sustainability and High Energy Physics" that aimed 1) to bring together experts from HEP as well as those from outside to share their experiences and practices, and 2) to articulate a vision that helps the Institute for Research and Innovation in Software for High Energy Physics (IRIS-HEP) to create a work plan to implement elements of software sustainability. Software sustainability practices could lead to new collaborations, including elements of HEP software being directly used outside the field, and, as has happened more frequently in recent years, to HEP developers contributing to software developed outside the field rather than reinventing it. A focus on and skills related to sustainable software will give HEP software developers an important skill that is essential to careers in the realm of software, inside or outside HEP. The report closes with recommendations to improve software sustainability in HEP, aimed at the HEP community via IRIS-HEP and the HEP Software Foundation (HSF)., Comment: A report from the "Sustainable Software in HEP" IRIS-HEP blueprint workshop: https://indico.cern.ch/event/930127

New facilities of the 2020s, such as the High Luminosity Large Hadron Collider (HL-LHC), will be relevant through at least the 2030s. This means that their software efforts and those that are used to analyze their data need to consider sustainability to enable their adaptability to new challenges, longevity, and efficiency, over at least this period. This will help ensure that this software will be easier to develop and maintain, that it remains available in the future on new platforms, that it meets new needs, and that it is as reusable as possible. This report discusses a virtual half-day workshop on "Software Sustainability and High Energy Physics" that aimed 1) to bring together experts from HEP as well as those from outside to share their experiences and practices, and 2) to articulate a vision that helps the Institute for Research and Innovation in Software for High Energy Physics (IRIS-HEP) to create a work plan to implement elements of software sustainability. Software sustainability practices could lead to new collaborations, including elements of HEP software being directly used outside the field, and, as has happened more frequently in recent years, to HEP developers contributing to software developed outside the field rather than reinventing it. A focus on and skills related to sustainable software will give HEP software developers an important skill that is essential to careers in the realm of software, inside or outside HEP. The report closes with recommendations to improve software sustainability in HEP, aimed at the HEP community via IRIS-HEP and the HEP Software Foundation (HSF)., Comment: A report from the "Sustainable Software in HEP" IRIS-HEP blueprint workshop: https://indico.cern.ch/event/930127

New facilities of the 2020s, such as the High Luminosity Large Hadron Collider (HL-LHC), will be relevant through at least the 2030s. This means that their software efforts and those that are used to analyze their data need to consider sustainability to enable their adaptability to new challenges, longevity, and efficiency, over at least this period. This will help ensure that this software will be easier to develop and maintain, that it remains available in the future on new platforms, that it meets new needs, and that it is as reusable as possible. This report discusses a virtual half-day workshop on "Software Sustainability and High Energy Physics" that aimed 1) to bring together experts from HEP as well as those from outside to share their experiences and practices, and 2) to articulate a vision that helps the Institute for Research and Innovation in Software for High Energy Physics (IRIS-HEP) to create a work plan to implement elements of software sustainability. Software sustainability practices could lead to new collaborations, including elements of HEP software being directly used outside the field, and, as has happened more frequently in recent years, to HEP developers contributing to software developed outside the field rather than reinventing it. A focus on and skills related to sustainable software will give HEP software developers an important skill that is essential to careers in the realm of software, inside or outside HEP. The report closes with recommendations to improve software sustainability in HEP, aimed at the HEP community via IRIS-HEP and the HEP Software Foundation (HSF)., Comment: A report from the "Sustainable Software in HEP" IRIS-HEP blueprint workshop: https://indico.cern.ch/event/930127

Evidence-based teaching is a highly complex skill, requiring repeated cycles of deliberate practice and feedback to master. Despite existing well-characterized frameworks for practice-based training in K-12 teacher education, the major principles of these frameworks have not yet been transferred to instructor development in higher educational contexts, including training of graduate teaching assistants (GTAs). We sought to determine whether a practice-based training program could help GTAs learn and use evidence-based teaching methods in their classrooms. We implemented a weekly training program for introductory biology GTAs that included structured drills of techniques selected to enhance student practice, logic development, and accountability and reduce apprehension. These elements were selected based on their previous characterization as dimensions of active learning. GTAs received regular performance feedback based on classroom observations. To quantify use of target techniques and levels of student participation, we collected and coded 160 h of video footage. We investigated the relationship between frequency of GTA implementation of target techniques and student exam scores; however, we observed no significant relationship. Although GTAs adopted and used many of the target techniques with high frequency, techniques that enforced student participation were not stably adopted, and their use was unresponsive to formal feedback. We also found that techniques discussed in training, but not practiced, were not used at quantifiable frequencies, further supporting the importance of practice-based training for influencing instructional practices.

Evidence-based teaching is a highly complex skill, requiring repeated cycles of deliberate practice and feedback to master. Despite existing well-characterized frameworks for practice-based training in K-12 teacher education, the major principles of these frameworks have not yet been transferred to instructor development in higher educational contexts, including training of graduate teaching assistants (GTAs). We sought to determine whether a practice-based training program could help GTAs learn and use evidence-based teaching methods in their classrooms. We implemented a weekly training program for introductory biology GTAs that included structured drills of techniques selected to enhance student practice, logic development, and accountability and reduce apprehension. These elements were selected based on their previous characterization as dimensions of active learning. GTAs received regular performance feedback based on classroom observations. To quantify use of target techniques and levels of student participation, we collected and coded 160 h of video footage. We investigated the relationship between frequency of GTA implementation of target techniques and student exam scores; however, we observed no significant relationship. Although GTAs adopted and used many of the target techniques with high frequency, techniques that enforced student participation were not stably adopted, and their use was unresponsive to formal feedback. We also found that techniques discussed in training, but not practiced, were not used at quantifiable frequencies, further supporting the importance of practice-based training for influencing instructional practices.

Opsins are photosensitive proteins catalyzing light-dependent processes across the tree of life. For both microbial (type 1) and metazoan (type 2) opsins, photosensing depends upon covalent interaction between a retinal chromophore and a conserved lysine residue. Despite recent discoveries of potential opsin homologs lacking this residue, phylogenetic dispersal and functional significance of these abnormal sequences have not yet been investigated. We report discovery of a large group of putatively non-retinal binding opsins, present in a number of fungal and microbial genomes and comprising nearly 30% of opsins in the Halobacteriacea, a model clade for opsin photobiology. We report phylogenetic analyses, structural modeling, genomic context analysis and biochemistry, to describe the evolutionary relationship of these recently described proteins with other opsins, show that they are expressed and do not bind retinal in a canonical manner. Given these data, we propose a hypothesis that these abnormal opsin homologs may represent a novel family of sensory opsins which may be involved in taxis response to one or more non-light stimuli. If true, this finding would challenge our current understanding of microbial opsins as a light-specific sensory family, and provides a potential analogy with the highly diverse signaling capabilities of the eukaryotic G-protein coupled receptors (GPCRs), of which metazoan type 2 opsins are a light-specific sub-clade.

Opsins are photosensitive proteins catalyzing light-dependent processes across the tree of life. For both microbial (type 1) and metazoan (type 2) opsins, photosensing depends upon covalent interaction between a retinal chromophore and a conserved lysine residue. Despite recent discoveries of potential opsin homologs lacking this residue, phylogenetic dispersal and functional significance of these abnormal sequences have not yet been investigated. We report discovery of a large group of putatively non-retinal binding opsins, present in a number of fungal and microbial genomes and comprising nearly 30% of opsins in the Halobacteriacea, a model clade for opsin photobiology. We report phylogenetic analyses, structural modeling, genomic context analysis and biochemistry, to describe the evolutionary relationship of these recently described proteins with other opsins, show that they are expressed and do not bind retinal in a canonical manner. Given these data, we propose a hypothesis that these abnormal opsin homologs may represent a novel family of sensory opsins which may be involved in taxis response to one or more non-light stimuli. If true, this finding would challenge our current understanding of microbial opsins as a light-specific sensory family, and provides a potential analogy with the highly diverse signaling capabilities of the eukaryotic G-protein coupled receptors (GPCRs), of which metazoan type 2 opsins are a light-specific sub-clade.

Opsins are photosensitive proteins catalyzing light-dependent processes across the tree of life. For both microbial (type 1) and metazoan (type 2) opsins, photosensing depends upon covalent interaction between a retinal chromophore and a conserved lysine residue. Despite recent discoveries of potential opsin homologs lacking this residue, phylogenetic dispersal and functional significance of these abnormal sequences have not yet been investigated. We report discovery of a large group of putatively non-retinal binding opsins, present in a number of fungal and microbial genomes and comprising nearly 30% of opsins in the Halobacteriacea, a model clade for opsin photobiology. Based on phylogenetic analyses, structural modeling, genomic context and biochemistry, we propose that these abnormal opsin homologs represent a novel family of sensory opsins which may be involved in taxis response to one or more non-light stimuli. This finding challenges current understanding of microbial opsins as a light-specific sensory family, and provides a potential analogy with the highly diverse signaling capabilities of the eukaryotic G-protein coupled receptors (GPCRs), of which metazoan type 2 opsins are a light-specific sub-clade.

Opsins are photosensitive proteins catalyzing light-dependent processes across the tree of life. For both microbial (type 1) and metazoan (type 2) opsins, photosensing depends upon covalent interaction between a retinal chromophore and a conserved lysine residue. Despite recent discoveries of potential opsin homologs lacking this residue, phylogenetic dispersal and functional significance of these abnormal sequences have not yet been investigated. We report discovery of a large group of putatively non-retinal binding opsins, present in a number of fungal and microbial genomes and comprising nearly 30% of opsins in the Halobacteriacea, a model clade for opsin photobiology. Based on phylogenetic analyses, structural modeling, genomic context and biochemistry, we propose that these abnormal opsin homologs represent a novel family of sensory opsins which may be involved in taxis response to one or more non-light stimuli. This finding challenges current understanding of microbial opsins as a light-specific sensory family, and provides a potential analogy with the highly diverse signaling capabilities of the eukaryotic G-protein coupled receptors (GPCRs), of which metazoan type 2 opsins are a light-specific sub-clade.

Organisms across the tree of life use a variety of mechanisms to respond to stress-inducing fluctuations in osmotic conditions. Cellular response mechanisms and phenotypes associated with osmoadaptation also play important roles in bacterial virulence, human health, agricultural production and many other biological systems. To improve understanding of osmoadaptive strategies, we have generated 59 high-quality draft genomes for the haloarchaea (a euryarchaeal clade whose members thrive in hypersaline environments and routinely experience drastic changes in environmental salinity) and analyzed these new genomes in combination with those from 21 previously sequenced haloarchaeal isolates. We propose a generalized model for haloarchaeal management of cytoplasmic osmolarity in response to osmotic shifts, where potassium accumulation and sodium expulsion during osmotic upshock are accomplished via secondary transport using the proton gradient as an energy source, and potassium loss during downshock is via a combination of secondary transport and non-specific ion loss through mechanosensitive channels. We also propose new mechanisms for magnesium and chloride accumulation. We describe the expansion and differentiation of haloarchaeal general transcription factor families, including two novel expansions of the TATA-binding protein family, and discuss their potential for enabling rapid adaptation to environmental fluxes. We challenge a recent high-profile proposal regarding the evolutionary origins of the haloarchaea by showing that inclusion of additional genomes significantly reduces support for a proposed large-scale horizontal gene transfer into the ancestral haloarchaeon from the bacterial domain. The combination of broad (17 genera) and deep (≥5 species in four genera) sampling of a phenotypically unified clade has enabled us to uncover both highly conserved and specialized features of osmoadaptation. Finally, we demonstrate the broad utility of such datasets, for meta

Organisms across the tree of life use a variety of mechanisms to respond to stress-inducing fluctuations in osmotic conditions. Cellular response mechanisms and phenotypes associated with osmoadaptation also play important roles in bacterial virulence, human health, agricultural production and many other biological systems. To improve understanding of osmoadaptive strategies, we have generated 59 high-quality draft genomes for the haloarchaea (a euryarchaeal clade whose members thrive in hypersaline environments and routinely experience drastic changes in environmental salinity) and analyzed these new genomes in combination with those from 21 previously sequenced haloarchaeal isolates. We propose a generalized model for haloarchaeal management of cytoplasmic osmolarity in response to osmotic shifts, where potassium accumulation and sodium expulsion during osmotic upshock are accomplished via secondary transport using the proton gradient as an energy source, and potassium loss during downshock is via a combination of secondary transport and non-specific ion loss through mechanosensitive channels. We also propose new mechanisms for magnesium and chloride accumulation. We describe the expansion and differentiation of haloarchaeal general transcription factor families, including two novel expansions of the TATA-binding protein family, and discuss their potential for enabling rapid adaptation to environmental fluxes. We challenge a recent high-profile proposal regarding the evolutionary origins of the haloarchaea by showing that inclusion of additional genomes significantly reduces support for a proposed large-scale horizontal gene transfer into the ancestral haloarchaeon from the bacterial domain. The combination of broad (17 genera) and deep (≥5 species in four genera) sampling of a phenotypically unified clade has enabled us to uncover both highly conserved and specialized features of osmoadaptation. Finally, we demonstrate the broad utility of such datasets, for meta

Nucleosomes, the basic repeat units of eukaryotic chromatin, have been suggested to influence the evolution of eukaryotic genomes, both by altering the propensity of DNA to mutate and by selection acting to maintain or exclude nucleosomes in particular locations. Contrary to the popular idea that nucleosomes are unique to eukaryotes, histone proteins have also been discovered in some archaeal genomes. Archaeal nucleosomes, however, are quite unlike their eukaryotic counterparts in many respects, including their assembly into tetramers (rather than octamers) from histone proteins that lack N- and C-terminal tails. Here, we show that despite these fundamental differences the association between nucleosome footprints and sequence evolution is strikingly conserved between humans and the model archaeon Haloferax volcanii. In light of this finding we examine whether selection or mutation can explain concordant substitution patterns in the two kingdoms. Unexpectedly, we find that neither the mutation nor the selection model are sufficient to explain the observed association between nucleosomes and sequence divergence. Instead, we demonstrate that nucleosome-associated substitution patterns are more consistent with a third model where sequence divergence results in frequent repositioning of nucleosomes during evolution. Indeed, we show that nucleosome repositioning is both necessary and largely sufficient to explain the association between current nucleosome positions and biased substitution patterns. This finding highlights the importance of considering the direction of causality between genetic and epigenetic change.

Nucleosomes, the basic repeat units of eukaryotic chromatin, have been suggested to influence the evolution of eukaryotic genomes, both by altering the propensity of DNA to mutate and by selection acting to maintain or exclude nucleosomes in particular locations. Contrary to the popular idea that nucleosomes are unique to eukaryotes, histone proteins have also been discovered in some archaeal genomes. Archaeal nucleosomes, however, are quite unlike their eukaryotic counterparts in many respects, including their assembly into tetramers (rather than octamers) from histone proteins that lack N- and C-terminal tails. Here, we show that despite these fundamental differences the association between nucleosome footprints and sequence evolution is strikingly conserved between humans and the model archaeon Haloferax volcanii. In light of this finding we examine whether selection or mutation can explain concordant substitution patterns in the two kingdoms. Unexpectedly, we find that neither the mutation nor the selection model are sufficient to explain the observed association between nucleosomes and sequence divergence. Instead, we demonstrate that nucleosome-associated substitution patterns are more consistent with a third model where sequence divergence results in frequent repositioning of nucleosomes during evolution. Indeed, we show that nucleosome repositioning is both necessary and largely sufficient to explain the association between current nucleosome positions and biased substitution patterns. This finding highlights the importance of considering the direction of causality between genetic and epigenetic change.

Author Posting. © The Oceanography Society, 2012. This article is posted here by permission of The Oceanography Society for personal use, not for redistribution. The definitive version was published in Oceanography 25, no. 1 (2012): 62–77, doi:10.5670/oceanog.2012.04., The Lau Integrated Study Site (ISS) has provided unique opportunities for study of ridge processes because of its back-arc setting in the southwestern Pacific. Its location allows study of a biogeographical province distinct from those of eastern Pacific and mid-Atlantic ridges, and crustal compositions along the ridge lie outside the range of mid-ocean ridge crustal compositions. The Lau ISS is located above a subduction zone, at an oblique angle. The underlying mantle receives water and other elements derived from the downgoing lithospheric slab, with an increase in slab influence from north to south. Water lowers the mantle melting temperature and leads to greater melt production where the water flux is greater, and to distinctive regional-scale gradients along the ridge. There are deeper faulted axial valleys with basaltic volcanism in the north and inflated axial highs with andesites in the south. Differences in igneous rock composition and release of magmatic volatiles affect compositions of vent fluids and deposits. Differences in vent fluid compositions and small-scale diffuse-flow regimes correlate with regional-scale patterns in microbial and megafaunal distributions. The interdisciplinary research effort at the Lau ISS has successfully identified linkages between subsurface processes and deep-sea biological communities, from mantle to microbe to megafauna., Support was provided by National Science Foundation grants OCE-1038135 to MKT, OCE-0732369 and OCE-0240985 to CRF, OCE-0732369 and OCE-0838107 to PRG, OCE-0242618 to CHL, OCE-0242902 and OCE-0752256 to PJM, OCE-0728391 and OCE-0937404 to A-LR, and a GRFP to RB.

Author Posting. © The Oceanography Society, 2012. This article is posted here by permission of The Oceanography Society for personal use, not for redistribution. The definitive version was published in Oceanography 25, no. 1 (2012): 62–77, doi:10.5670/oceanog.2012.04., The Lau Integrated Study Site (ISS) has provided unique opportunities for study of ridge processes because of its back-arc setting in the southwestern Pacific. Its location allows study of a biogeographical province distinct from those of eastern Pacific and mid-Atlantic ridges, and crustal compositions along the ridge lie outside the range of mid-ocean ridge crustal compositions. The Lau ISS is located above a subduction zone, at an oblique angle. The underlying mantle receives water and other elements derived from the downgoing lithospheric slab, with an increase in slab influence from north to south. Water lowers the mantle melting temperature and leads to greater melt production where the water flux is greater, and to distinctive regional-scale gradients along the ridge. There are deeper faulted axial valleys with basaltic volcanism in the north and inflated axial highs with andesites in the south. Differences in igneous rock composition and release of magmatic volatiles affect compositions of vent fluids and deposits. Differences in vent fluid compositions and small-scale diffuse-flow regimes correlate with regional-scale patterns in microbial and megafaunal distributions. The interdisciplinary research effort at the Lau ISS has successfully identified linkages between subsurface processes and deep-sea biological communities, from mantle to microbe to megafauna., Support was provided by National Science Foundation grants OCE-1038135 to MKT, OCE-0732369 and OCE-0240985 to CRF, OCE-0732369 and OCE-0838107 to PRG, OCE-0242618 to CHL, OCE-0242902 and OCE-0752256 to PJM, OCE-0728391 and OCE-0937404 to A-LR, and a GRFP to RB.

A follow-up study to their 2007 HARP evaluation, UCJC found that HARP has continued to fulfill its goals of diverting clients from jail and residential treatment into supportive housing. Compared to a similar supportive housing through The Road Home (TBRA), HARP has served a more criminal justice and treatment-involved population and, therefore, seen larger declines in uses of these services post-housing. At one year approximately 50% of both HARP and TBRA remained stably housed. The study also identifies factors related to successful housing exit and criminal recidivism for HARP clients.

The report examines 6 Utah Juvenile Drug Courts (JDCs) in Weber, Salt Lake, Tooele, Utah, Emery, and Grand counties, providing descriptive statistics on population served, services offered, and during and post-JDC juvenile recidivism. The four largest JDCs are compared to similar probationers on post-program juvenile and adult recidivism, with a 30 month follow-up period. There were no significant differences on alcohol/drug recidivism between probation and JDC after controlling for other significant factors; however, JDC had significantly less delinquency/criminal recidivism, even after controlling for other significant factors.

A follow-up study to their 2007 HARP evaluation, UCJC found that HARP has continued to fulfill its goals of diverting clients from jail and residential treatment into supportive housing. Compared to a similar supportive housing through The Road Home (TBRA), HARP has served a more criminal justice and treatment-involved population and, therefore, seen larger declines in uses of these services post-housing. At one year approximately 50% of both HARP and TBRA remained stably housed. The study also identifies factors related to successful housing exit and criminal recidivism for HARP clients.

The report examines 6 Utah Juvenile Drug Courts (JDCs) in Weber, Salt Lake, Tooele, Utah, Emery, and Grand counties, providing descriptive statistics on population served, services offered, and during and post-JDC juvenile recidivism. The four largest JDCs are compared to similar probationers on post-program juvenile and adult recidivism, with a 30 month follow-up period. There were no significant differences on alcohol/drug recidivism between probation and JDC after controlling for other significant factors; however, JDC had significantly less delinquency/criminal recidivism, even after controlling for other significant factors.

The Salt Lake County Adult Felony Drug Court received a three year grant from the Substance Abuse and Mental Health Services Administration (SAMHSA) to expand and enhance the drug court. Funding began in January 2003. The primary purposes of the grant were to increase the number of clients served, increase treatment slots, and enhance services provided in-house at Criminal Justice Services (CJS, the lead drug court agency). To accomplish this, funding was used to hire and/or retain case managers, therapists, and clerical support. In addition, with the SAMHSA funding CJS was able to reserve residential treatment slots at Salt Lake County Substance Abuse Services licensed providers and develop an in-house intensive outpatient (IOT) treatment program. The grant also included funds specifically set aside for evaluation of the enhancement and expansion and the overall effectiveness of the drug court. The objectives of this final evaluation report are to examine both process and outcome measures. Three interim reports were conducted during the grant period (March 2004, September 2004, and March 2005) that covered only process measures. This final report includes an update and expansion of the process evaluation covering the following: enhancement client characteristics at intake, treatment services received, judicial supervision, compliance, participation and retention, client satisfaction, during-program improvements in clients’ lives (such as living situation, employment, and health), and drug court professionals’ perspectives of the program. The outcome evaluation examines drug court’s impact on post-program recidivism, substance use, and quality of life, as well as the cost-benefit of the program.

The Salt Lake County Adult Felony Drug Court received a three year grant from the Substance Abuse and Mental Health Services Administration (SAMHSA) to expand and enhance the drug court. Funding began in January 2003. The primary purposes of the grant were to increase the number of clients served, increase treatment slots, and enhance services provided in-house at Criminal Justice Services (CJS, the lead drug court agency). To accomplish this, funding was used to hire and/or retain case managers, therapists, and clerical support. In addition, with the SAMHSA funding CJS was able to reserve residential treatment slots at Salt Lake County Substance Abuse Services licensed providers and develop an in-house intensive outpatient (IOT) treatment program. The grant also included funds specifically set aside for evaluation of the enhancement and expansion and the overall effectiveness of the drug court. The objectives of this final evaluation report are to examine both process and outcome measures. Three interim reports were conducted during the grant period (March 2004, September 2004, and March 2005) that covered only process measures. This final report includes an update and expansion of the process evaluation covering the following: enhancement client characteristics at intake, treatment services received, judicial supervision, compliance, participation and retention, client satisfaction, during-program improvements in clients’ lives (such as living situation, employment, and health), and drug court professionals’ perspectives of the program. The outcome evaluation examines drug court’s impact on post-program recidivism, substance use, and quality of life, as well as the cost-benefit of the program.