bluuebunny/crossref_metadata_2025 huggingface dataset:
Taking Action With Data: Improving Environmental Public Health at the Community Level
Authors: Camponeschi Jenny , Vogt Christy M. , Creswell Paul D. , Mueller Meridith , Christenson Megan , Werner Mark A.
Published: August 2017

Context:

The Wisconsin Environmental Public Health Tracking Program (Wisconsin Tracking) compiles and provides data on health endpoints and related environmental exposures as a resource to local health departments, tribes, academia, and other stakeholders. The goal of providing these data is that stakeholders use them to develop projects that improve environmental health in their communities—that is, moving from “data to action.”

Objective:

To encourage use of Wisconsin Tracking data, we developed a minigrants program and issued a funding opportunity to local health departments and tribes. The opportunity requested proposals for small projects using our data, with the goal of making public health improvements in those communities. Wisconsin Tracking evaluated the minigrants program after its completion.

Design/Setting:

Eight local health departments in Wisconsin were awarded up to $10 500 to develop and implement projects over a 9-month period.

Methods:

Wisconsin Tracking created a funding opportunity announcement requiring utilization of our data to develop projects by local health departments in Wisconsin. We reviewed and scored applications, evaluating proposals on a range of criteria. During the 9-month project period, Wisconsin Tracking staff members provided a variety of technical assistance to grantees. An evaluation of the overall program followed.

Results:

Funded communities used Wisconsin Tracking data to improve public health infrastructure, leverage partnerships, establish new initiatives, respond to emergencies, improve communication with stakeholders and residents, and make a variety of public health improvements in their communities.

Conclusions:

Efforts to increase use of our data catalyzed development of small-scale environmental health projects. This minigrants program was successful at building relationships between local health departments and Wisconsin Tracking, increasing awareness of Wisconsin Tracking data and resources, and contributing to numerous documented public health improvements throughout Wisconsin.
Estimating the Public Health Impact of Air Pollution for Informing Policy in the Twin Cities: A Minnesota Tracking Collaboration
Authors: Johnson Jean E. , Bael David L. , Sample Jeannette M. , Lindgren Paula G. , Kvale Dorian L.
Published: August 2017

Objective:

The Minnesota Department of Health and the Minnesota Pollution Control Agency used local air pollution and public health data to estimate the impacts of particulate matter and ozone on population health, to identify disparities, and to inform decisions that will improve health.

Setting:

While air quality in Minnesota currently meets federal standards, urban communities are concerned about the impact of air pollution on their health. The Twin Cities (Minneapolis–St Paul) metropolitan area includes 7 counties where fine particulate levels and rates of asthma exacerbations are elevated in some communities.

Design:

We used the Environmental Protection Agency's BenMAP (Environmental Benefits Mapping and Analysis Program) software, along with local PM2.5 (fine particulate) and ozone ambient concentrations, census and population health data, to calculate impacts for 2008 at the zip code level. The impacts were summed across all zip codes for area-wide estimates. American Community Survey data were used to stratify zip codes by poverty and race for assessment of disparities.

Main Outcome Measures:

Attributable fraction, attributable rate and counts for all-cause mortality, asthma and chronic obstructive pulmonary disease hospitalizations, asthma emergency department (ED) visits, and cardiovascular disease hospitalizations.

Results:

In the Twin Cities (2008), air pollution was a contributing cause for an estimated 2% to 5% of respiratory and cardiovascular hospitalizations and ED visits and between 6% and 13% of premature deaths. The elderly (aged 65+ years) experienced the highest air pollution–attributable rates of death and respiratory hospitalizations; children experienced the highest asthma ED visit rates. Geographical and demographic differences in air pollution–attributable health impacts across the region reflected the differences in the underlying morbidity and mortality rates.

Conclusions:

Method was effective in demonstrating that changes in air quality can have quantifiable health impacts across the Twin Cities. Key messages and implications from this work were shared with the media, community groups, legislators and the public. The results are being used to inform initiatives aimed at reducing sources of air pollution and to address health disparities in urban communities.
CDC's National Environmental Public Health Tracking Program in Action: Case Studies From State and Local Health Departments
Authors: Eatman Shana , Strosnider Heather M.
Published: August 2017

The Centers for Disease Control and Prevention's (CDC's) National Environmental Public Health Tracking Program (Tracking Program) is a multidisciplinary collaboration that involves the ongoing collection, integration, analysis, interpretation, and dissemination of data from environmental hazard monitoring, human exposure surveillance, and health effects surveillance. With a renewed focus on data-driven decision-making, the CDC's Tracking Program emphasizes dissemination of actionable data to public health practitioners, policy makers, and communities. The CDC's National Environmental Public Health Tracking Network (Tracking Network), a Web-based system with components at the national, state, and local levels, houses environmental public health data used to inform public health actions (PHAs) to improve community health. This article serves as a detailed landscape on the Tracking Program and Tracking Network and the Tracking Program's leading performance measure, “public health actions.” Tracking PHAs are qualitative statements addressing a local problem or situation, the role of the state or local Tracking Program, how the problem or situation was addressed, and the action taken. More than 400 PHAs have been reported by funded state and local health departments since the Tracking Program began collecting PHAs in 2005. Three case studies are provided to illustrate the use of the Tracking Program resources and data on the Tracking Network, and the diversity of actions taken. Through a collaborative network of experts, data, and tools, the Tracking Program and its Tracking Network are actively informing state and local PHAs. In a time of competing priorities and limited funding, PHAs can serve as a powerful tool to advance environmental public health practice.
Economic Valuation of Selected Illnesses in Environmental Public Health Tracking
Authors: Zhou Ying , Nurmagambetov Tursynbek , McCord Matthew , Hsu Wan-Hsiang
Published: August 2017

Background:

In benefit-cost analysis of public health programs, health outcomes need to be assigned monetary values so that different health endpoints can be compared and improvement in health can be compared with cost of the program. There are 2 major approaches for estimating economic value of illnesses: willingness to pay (WTP) and cost of illness (COI). In this study, we compared these 2 approaches and summarized valuation estimates for 3 health endpoints included in the Centers for Disease Control and Prevention's National Environmental Public Health Tracking Network—asthma, carbon monoxide (CO) poisoning, and lead poisoning.

Method:

First, we compared results of WTP and COI estimates reported in the peer-reviewed literature when these 2 methods were applied to the same study participants. Second, we reviewed the availability and summarized valuations using these 2 approaches for 3 health endpoints.

Result:

For the same study participants, WTP estimates in the literature were higher than COI estimates for minor and moderate cases. For more severe cases, with substantial portion of the costs paid by the third party, COI could exceed WTP. Annual medical cost of asthma based on COI approach ranged from $800 to $3300 and indirect costs ranged from $90 to $1700. WTP to have no asthma symptoms ranged from $580 to $4200 annually. We found no studies estimating WTP to avoid CO or lead poisoning. Cost of a CO poisoning hospitalization ranged from $14 000 to $17 000. For patients who sustained long-term cognitive sequela, lifetime earnings and quality-of-life losses can significantly exceed hospitalization costs. For lead poisoning, most studies focused on lead exposure and cognitive ability, and its impact on lifetime earnings.

Conclusion:

For asthma, more WTP studies are needed, particularly studies designed for conditions that involve third-party payers. For CO poisoning and lead poisoning, WTP studies need to be conducted so that more comprehensive economic valuation estimates can be provided. When COI estimates are used alone, it should be clearly stated that COI does not fully capture the nonmarket cost of illness, such as pain and suffering, which highlights the need for WTP estimates.
Late respiratory effects of cancer treatment
Authors: Harris Clare , Sander Clare R.
Published: August 2017

Purpose of review

The aim of this article is to examine significant advances in our understanding of the late respiratory effects of cancer treatment, including surgery, radiotherapy, chemotherapy, biological therapies and haematopoietic stem cell transplant, and to provide a framework for assessing such patients.

Recent findings

Oncology therapies have advanced considerably over recent years but pulmonary toxicity remains a concern. Advances have been made in our understanding of the risk factors, including genetic ones that lead to toxicity from radiotherapy and chemotherapy and risk stratification models are being developed to aid treatment planning. Targeted biological treatments are continuously being developed and consequently the Pneumotox database of pulmonary toxicity continues to be an essential resource. Early detection of bronchiolitis obliterans in haematopoietic stem cell transplant patients has been found to be critical, with some positive results from intervention trials.

Pulmonary toxicity is a common unwanted consequence of life enhancing or saving cancer treatments which remain difficult to treat. Developments in these fields are mainly in the areas of prevention, early detection and monitoring of unwanted side effects. We discuss some of these developments within this review.
The Power of Symbolic Play in Emotional Development Through the DIR Lens
Authors: Wieder Serena
Published: August 2017

Symbolic play is a powerful vehicle for supporting emotional development and communication. It embraces all developmental capacities. This article describes how symbols are formed and how emotional themes are symbolized whereby children reveal their understanding of the world, their feelings and relationships, and how they see themselves in the symbols they choose in play. The DIR (Developmental, Individual Difference, Relationship) model provides the framework and context for understanding the unique profiles of all children, including those with autism, and the importance of elevating feelings and impulses to the level of symbolic ideas that support emotional and behavioral regulation. Children need play where interactive relationships with parents and caregivers help them climb the symbolic–emotional ladder, even when development is uneven, as in autism spectrum disorders. Examples illustrate children solving emotional challenges, exploring the range of emotions, developing reality testing, and reaching abstract levels of thought and empathy through symbolic play and conversations unifying emotions and intellect in early childhood development.
What Exactly Is Play, and Why Is It Such a Powerful Vehicle for Learning?
Authors: Gray Peter
Published: August 2017

“Play” is a word used commonly to refer to children's preferred activities and to some adult activities, and it is often said that play promotes learning. But what is play exactly, and what and how do children learn through play? This essay begins with a description of an evolutionary, practice theory of play by German philosopher and naturalist, Karl Groos, followed by a system of categorizing play according to the kinds of skills most obviously practiced: physical/locomotor play, constructive play, language play, fantasy play, social play, and play with formal rules. Play is then defined as activity that (1) is self-chosen and self-directed, (2) is motivated by means more than ends, (3) is guided by mental rules, and (4) includes a strong element of imagination. These characteristics are elaborated upon to show how each contributes to play's developmental value. Two final sections describe the special developmental value of age-mixed play and deleterious changes in children's well-being that have accompanied the decline of play in recent decades.
Adult sex ratios and reproductive strategies: a critical re-examination of sex differences in human and animal societies
Authors: Schacht Ryan , Kramer Karen L. , Székely Tamás , Kappeler Peter M.
Published: August 2017

It is increasingly recognized that the relative proportion of potential mates to competitors in a population impacts a range of sex-specific behaviours and in particular mating and reproduction. However, while the adult sex ratio (ASR) has long been recognized as an important link between demography and behaviour, this relationship remains understudied. Here, we introduce the first inter-disciplinary collection of research on the causes and consequences of variation in the ASR in human and animal societies. This important topic is relevant to a wide audience of both social and biological scientists due to the central role that the relative number of males to females in a population plays for the evolution of, and contemporary variation in, sex roles across groups, species and higher taxa. The articles in this theme issue cover research on ASR across a variety of taxa and topics. They offer critical re-evaluations of theoretical foundations within both evolutionary and non-evolutionary fields, and propose innovative methodological approaches, present new empirical examples of behavioural consequences of ASR variation and reveal that the ASR plays a major role in determining population viability, especially in small populations and species with labile sex determination. This introductory paper puts the contributions of the theme issue into a broader context, identifies general trends across the literature and formulates directions for future research.

This article is part of the themed issue ‘Adult sex ratios and reproductive decisions: a critical re-examination of sex differences in human and animal societies'.
Not all sex ratios are equal: the Fisher condition, parental care and sexual selection
Authors: Jennions Michael D. , Fromhage Lutz
Published: August 2017

The term ‘sex roles’ encapsulates male–female differences in mate searching, competitive traits that increase mating/fertilization opportunities, choosiness about mates and parental care. Theoretical models suggest that biased sex ratios drive the evolution of sex roles. To model sex role evolution, it is essential to note that in most sexually reproducing species (haplodiploid insects are an exception), each offspring has one father and one mother. Consequently, the total number of offspring produced by each sex is identical, so the mean number of offspring produced by individuals of each sex depends on the sex ratio (Fisher condition). Similarly, the total number of heterosexual matings is identical for each sex. On average, neither sex can mate nor breed more often when the sex ratio is even. But equally common inwhichsex ratio? The Fisher condition only applies to some reproductive measures (e.g. lifetime offspring production or matings) for certain sex ratios (e.g. operational or adult sex ratio; OSR, ASR). Here, we review recent models that clarify whether a biased OSR, ASR or sex ratio at maturation (MSR) have a causal or correlational relationship with the evolution of sex differences in parental care and competitive traits—two key components of sex roles. We suggest that it is more fruitful to understand the combined effect of the MSR and mortality rates while caring and competing than that of the ASR itself. In short, we argue that the ASR does not have a causal role in the evolution of parental care. We point out, however, that the ASR can be a cue for adaptive phenotypic plasticity in how each sex invests in parental care.

This article is part of the themed issue ‘Adult sex ratios and reproductive decisions: a critical re-examination of sex differences in human and animal societies’.
Adult sex ratio and social status predict mating and parenting strategies in Northern Ireland
Authors: Uggla Caroline , Mace Ruth
Published: August 2017

Evidence from animal species indicates that a male-biased adult sex ratio (ASR) can lead to higher levels of male parental investment and that there is heterogeneity in behavioural responses to mate scarcity depending on mate value. In humans, however, there is little consistent evidence of the effect of the ASR on pair-bond stability and parental investment and even less of how it varies by an individual's mate value. In this paper we use detailed census data from Northern Ireland to test the association between the ASR and pair-bond stability and parental investment by social status (education and social class) as a proxy for mate value. We find evidence that female, but not male, cohabitation is associated with the ASR. In female-biased areas women with low education are less likely to be in a stable pair-bond than highly educated women, but in male-biased areas women with the lowest education are as likely to be in a stable pair-bond as their most highly educated peers. For both sexes risk of separation is greater at female-biased sex ratios. Lastly, our data show a weak relationship between parental investment and the ASR that depends on social class. We discuss these results in the light of recent reformulations of parental investment theory.

This article is part of the themed issue ‘Adult sex ratios and reproductive decisions: a critical re-examination of sex differences in human and animal societies’.
Sex roles and adult sex ratios: insights from mammalian biology and consequences for primate behaviour
Authors: Kappeler Peter M.
Published: August 2017

Theoretical models and empirical studies in various taxa have identified important links between variation in sex roles and the number of adult males and females (adult sex ratio (ASR)) in a population. In this review, I examine these relationships in non-human primates. Because most existing theoretical models of the evolution of sex roles focus on the evolutionary origins of sex-biased behaviour, they offer only a general scaffold for predicting variation in sex roles among and within species. I argue that studies examining sex role variation at these more specific levels need to take social organization into account to identify meaningful levels for the measurement of ASR and to account for the fact that ASR and sex roles mutually influence each other. Moreover, taxon-specific life-history traits can constrain sex role flexibility and impact the operational sex ratio (OSR) by specifying the minimum length of female time outs from reproduction. Using examples from the primate literature, I highlight practical problems in estimating ASR and OSR. I then argue that interspecific variation in the occurrence of indirect forms of paternal care might indeed be linked to variation in ASR. Some studies also indicate that female aggression and bonding, as well as components of inter-sexual relationships, are sensitive to variation in ASR. Thus, links between primate sex roles and sex ratios merit further study, and such studies could prompt the development of more specific theoretical models that make realistic assumptions about taxon-specific life history and social organization.

This article is part of the themed issue ‘Adult sex ratios and reproductive decisions: a critical re-examination of sex differences in human and animal societies’.
Optimization of drying conditions of Cudrania tricuspidata using response surface methodology
Authors: Park Jong-Jin , Park Dae-Hee , Jung Gayoung , Shin Eunju , Do Seon-Gil , Lee Wonyoung
Published: August 2017

This study was conducted to obtain the optimal conditions of hot air drying for Cudrania tricuspidata by response surface methodology (RSM). The independent variables were blanching time (60, 120, 240 sec), drying temperature (40, 60, 80°C) and drying time (12, 24, 36 h). The dependant variables were total polyphenol content (TPC), total flavonoid content (TFC), DPPH radical scavenging activity (DPPH), and color difference (ΔE). Viable cell colony was counted according to changes of blanching time. It was confirmed that microorganisms gradually decreased with increasing blanching time. From RSM results, the predicted values of TPC, TFC, DPPH, and ΔE were 8.62 mg GAE/g, 56.65 mg RE/g, 40.26% and 11.69, respectively. Experimental values within the optimal range (240sec, blanching time; 60°C, drying temperature; 24 h, drying time) were 10.06 mg GAE/g, 49 mg RE/g, 44.99% and 10.53, respectively. The predicted values were similar to the experimental values. Comparing drying tendency according to changes of blanching time, moisture reduction was bigger in the blanched sample than that in control at 40°C. However, the differences between blanched and control decreased with increase of drying temperature. Viable cell gradually decreased as increasing blanching time.
Effect of lotus leaf on the quality characteristics and antioxidant properties of bread
Authors: Park La-Young
Published: August 2017

This study was carried out to investigate the quality characteristics and antioxidative activity of bread containing lotus leaf powder (in ratios of 0, 1, 2, and 3% of the total flour). The pH of dough and bread were decreased as the concentration of lotus leaf powder increased. The volume of dough during fermentation did not show significant difference between 1% lotus leaf powder containing dough and control. The weight of bread increased by addition of lotus leaf powder. The volume, specific volume and baking loss rate of the bread decreased as lotus leaf powder levels increased. Redness and yellowness of the inner crumb were decreased by the addition of lotus leaf powder, but lightness was increased. 2,2-diphenyl-1-picrylhydrazyl-radical scavenging activity and total polyphenol contents were increased significantly as the concentration of lotus leaf powder increased. The overall acceptability of bread containing 1% lotus leaf powder showed no significant difference compared with control. The result exhibited that adding the lotus leaf powder into the bread increased antioxidant activity, and the highest quality improvement was obtained by incorporating 1% (w/w) lotus leaf powder into the bread formula.
Biological activities of isolated phenolic compounds from Trachelospermum asiaticum var. intermedium nakai
Authors: Yun Ui-Tea , Cho Ju-Young , Jeong Eun-Young , Jo Jae-Bum , Lee Eun-Ho , Kim Byung-Oh , Cho Young-Je
Published: August 2017

This study provided the evidence activity for biological of phenolic compounds from Trachelospermum asiaticum var. intermedium nakaier as a beauty food. The contents of phenolic compounds in water and 70% ethanol extracts were 16.8 mg/g and 38.1 mg/g, respectively. DPPH free radical scavenging activities of water and ethanol extracts at 100 μg/mL of phenolic concentration were 80.9% and 83.1%, respectively. ABTS radical decolorization activity was 95.0% in water extracts and 95.8% in ethanol extracts at 200 μg/mL phenolic concentration. Antioxidant protection factor (PF) was determined to 2.43 and 2.45 PF in water extracts and ethanol extracts at 100 μg/mL phenolic concentration. TBARs of water and ethanol extracts were 89.9% and 89.3% each at 200 μg/mL phenolic concentration. The inhibitory effect of ethanol extracts at 200 μg/mL phenolic concentration on xanthine oxidase was 50.5%. The inhibitory activity of a-glucosidase was 92.6% in ethanol extracts at 200 μg/mL phenolic concentration. As a result, this study will provide valuable information as a functional material with antioxidant activity, inhibitory activities of xanthin oxidase and α-glucosidase.
Quality characteristics and antioxidant activity of sponge cake with cabbage powder
Authors: Kim Sook-Young , Kim Ki-Ju
Published: August 2017

The purpose of this study was to investigate the quality characteristics, antioxidant activities and sensory properties of sponge cake with cabbage powder (CP). Physicochemical and sensory properties of sponge cake with different amount (0%, 5%, 10%, and 15%) of CP were examined. As the increase in the amount of CP addition, the specific gravity and baking loss rate were increased, whereas the color of the cake crumb and crust, volume index and specific volume were decreased (p<0.05). The symmetry and uniformity index of the sponge cake were not affected by the addition of CP (5-15%) (p<0.05). The hardness was significantly increased while by CP addition cohesiveness was decreased (p<0.05). The springiness, gumminess and brittleness were not changed by CP addition (p<0.05). The total polyphenolic, DPPH radical scavenging activities and reducing power were significantly increased by addition of CP at high concentrations (p<0.05). In the sensory evaluation, addition of CP significantly degraded the panel preference related to the color, flavor and texture of the sponge cake. However, the highest point were given to sponge cakes containg 5-10% of CP in taste and overall acceptance (p<0.05). These data suggested that adding 5% of CP is the optimal concentration overall for making sponge cake. However, the sponge cake with 10% of CP is recommended in order to maximize antioxidant activity, the sponge cake was the best when contained 5% CP and the sponge cake prepared with the addition of 10% CP was recommended to use due to its advantages in functional property.
Euplotid: A quantized geometric model of the eukaryotic cell
Authors: Borges-Rivera Diego
Published: August 2017

Life continues to shock and amaze us, reminding us that truth is far stranger than fiction. http://Euplotid.io is a quantized, geometric model of the eukaryotic cell, an attempt at quantifying the incredible complexity that gives rise to a living cell by beginning from the smallest unit, a quanta. Starting from the very bottom we are able to build the pieces which when hierarchically and combinatorially combined produce the emergent complex behavior that even a single celled organism can show. Euplotid is composed of a set of quantized geometric 3D building blocks and constantly evolving dockerized bioinformatic pipelines enabling a user to build and interact with the local regulatory architecture of every gene starting from DNA-interactions, chromatin accessibility, and RNA-sequencing. Reads are quantified using the latest computational tools and the results are normalized, quality-checked, and stored. The local regulatory architecture of each gene is built using a Louvain based graph partitioning algorithm parameterized by the chromatin extrusion model and CTCF-CTCF interactions. Cis-Regulatory Elements are defined using chromatin accessibility peaks which are mapped to Transcriptional Start Sites based on inclusion within the same neighborhood. Deep Neural Networks are trained in order to provide a statistical model mimicking transcription factor binding, giving the ability to identify all Transcription Factors within a given chromatin accessibility peak. By in-silico mutating and re-applying the neural network we are able to gauge the impact of a transition mutation on the binding of any transcription factor. The annotated output can be visualized in a variety of 1D, 2D, 3D and 4D ways overlaid with existing bodies of knowledge such as GWAS results or PDB structures. Once a particular CRE of interest has been identified a Base Editor mediated transition mutation can then be performed in a relevant model for further study.
Are allocentric spatial reference frames compatible with theories of Enactivism?
Authors: König Sabine U. , Goeke Caspar , Meilinger Tobias , König Peter
Published: August 2017

Theories of Enactivism propose an action-oriented approach to understand human cognition. So far, however, empirical evidence supporting these theories has been sparse. Here, we investigate whether spatial navigation based on allocentric reference frames that are independent of the observer’s physical body can be understood within an action-oriented approach. Therefore, we performed three experiments testing the knowledge of the absolute orientation of houses and streets towards north, the relative orientation of two houses and two streets, respectively, and the location of houses towards each other in a pointing task. Our results demonstrate that under time pressure, the relative orientation of two houses can be retrieved more accurately than the absolute orientation of single houses. With infinite time for cognitive reasoning, the performance of the task using house stimuli increased greatly for the absolute orientation and surpassed the slightly improved performance in the relative orientation task. In contrast, with streets as stimuli participants performed under time pressure better in the absolute orientation task. Overall, pointing from one house to another house yielded the best performance. This suggests, firstly, that orientation and location information about houses are primarily coded in house-to-house relations, whereas cardinal information is deduced via cognitive reasoning. Secondly, orientation information for streets is preferentially coded in absolute orientations. Thus, our results suggest that spatial information about house and street orientation is coded differently and that house orientation and location is primarily learned in an action-oriented way, which is in line with an enactive framework for human cognition.
Using competition assays to quantitatively model cooperative binding by transcription factors and other ligands
Authors: Peacock Jacob , Jaynes James B.
Published: August 2017

BACKGROUND

The affinities of DNA binding proteins for target sites can be used to model the regulation of gene expression. These proteins can bind to DNA cooperatively, strongly impacting their affinity and specificity. However, current methods for measuring cooperativity do not provide the means to accurately predict binding behavior over a wide range of concentrations.

METHODS

We use standard computational and mathematical methods, and develop novel methods as described in Results.

RESULTS

We explore some complexities of cooperative binding, and develop an improved method for relatingin vitromeasurements toin vivofunction, based on ternary complex formation. We derive expressions for the equilibria among the various complexes, and explore the limitations of binding experiments that model the system using a single parameter. We describe how to use single-ligand binding and ternary complex formation in tandem to determine parameters that have thermodynamic relevance. We develop an improved method for finding both single-ligand dissociation constants and concentrations simultaneously. We show how the cooperativity factor can be found when only one of the single-protein dissociation constants can be measured.

CONCLUSIONS

The methods that we develop constitute an optimized approach to accurately model cooperative binding.

GENERAL SIGNIFICANCE

The expressions and methods we develop for modeling and analyzing DNA binding and cooperativity are applicable to most cases where multiple ligands bind to distinct sites on a common substrate. The parameters determined using these methods can be fed into models of higher-order cooperativity to increase their predictive power.

HIGHLIGHTS

Hill plots remain prominent in biology, but can mask cooperativity

Effective modeling of binding by two ligands requires the use of 3 parameters

We develop novel ways to find these parameters for two cooperating ligands

We show how they can be used to enhance the power of established methods

We describe how this framework can be extended to multiple cooperating ligands
Identification of single pair of interneurons for bitter taste processing in theDrosophilabrain
Authors: Bohra Ali Asgar , Kallman Benjamin R , Reichert Heinrich , VijayRaghavan K.
Published: August 2017

Drosophilahas become an excellent model system for investigating the organization and function of the gustatory system due to the relatively simple neuroanatomical organization of its brain and the availability of powerful genetic and transgenic technology. Thus, at the molecular and cellular level, a great deal of insight into the peripheral detection and coding of gustatory information has already been attained. In contrast, much less is known about the central neural circuits that process this information and induce behaviorally appropriate motor output. Here we combine functional behavioral tests with targeted transgene expression through specific driver lines to identify a single bilaterally homologous pair of bitter sensitive interneurons that are located in the subesophageal zone of the brain. Anatomical and functional data indicate that these interneurons receive specific synaptic input from bitter sensitive gustatory receptor neurons. Targeted transgenic activation and inactivation experiments show that these bitter sensitive interneurons can largely suppress the proboscis extension reflex to appetitive stimuli such as sugar and water. These functional experiments together with calcium-imaging studies indicate that these first order local interneurons play an important role in the inhibition of the proboscis extension reflex that occurs in response to bitter tastants. Taken together, our studies present a cellular identification and functional characterization of a key gustatory interneuron in the bitter sensitive gustatory circuitry of the adult fly.
Lymphopenic community acquired pneumonia, an unnoticed phenotype associated to mortality in non immuno-suppressed patients: a retrospective cohort study
Authors: Bermejo-Martin Jesus F , Cilloniz Catia , Mendez Raul , Almansa Raquel , Gabarrus Albert , Ceccato Adrian , Torres Antoni , Menendez Rosario ,   for the NEUMONAC group
Published: August 2017

Background

The role of neutrophil and lymphocyte counts as predictors of prognosis in Community Acquired Pneumonia (CAP) has not been appropriately studied.

Methods

This was a retrospective study to evaluate by multivariate regression analysis, the association between neutrophil and lymphocyte counts with mortality at 30-days post discharge in two large cohorts of hospitalized patients with CAP and no prior immunosupression: a multicentric with 1550 patients recruited at 14 hospitals in Spain and a unicentric with 2840 patients recruited at the Hospital Clinic-Barcelona.

Findings

The unicentric cohort accounted with a higher proportion of critically ill patients: 586 (20·6%) vs 131 (8·5%) and non survivors 245 (8·6%) vs 74 (4·8%). Lymphopenia (< 1000 lymphocytes/mm3) was present in the 52·8% of the patients in both cohorts. A sub-group of lymphopenic patients, those with lymphocyte counts below decil 3 (677 lymphocytes/mm3in the multicentric cohort and 651 lymphocytes/mm3in the unicentric one), showed > 2-fold increase in the risk of mortality, independently of the CURB-65 score, critical illness and receiving an appropriated antibiotic treatment: (OR [CI95%],p) (2·18 [1·21- 3·92], 0·009) and (2·33 [1·61-3·33], <0·001) respectively. Neutrophil counts were not associated with mortality risk.

Interpretation

Lymphopenia is present in a half of the patients with CAP needing of hospitalization, in absence of antecendents of immunosupression. Lymphopenic CAP with lymphocyte counts < 664 lymphocytes/mm3constitutes a particular immunological phenotype of the disease which is associated to an increased risk of mortality.

Funding

CibeRes, 2009 Support to Research Groups of Catalonia 911, IDIBAPS, SEPAR, SVN
Refresh my memory: Episodic memory reinstatements intrude on working memory maintenance
Authors: Hoskin Abigail N. , Bornstein Aaron M. , Norman Kenneth A. , Cohen Jonathan D.
Published: August 2017

A fundamental question in memory research is how different forms of memory interact. Previous research has shown that people rely on working memory (WM) in short-term recognition tasks; a common view is that episodic memory (EM) only influences performance on these tasks when WM maintenance is disrupted. However, retrieval of memories from EM has been widely observed during brief periods of quiescence, raising the possibility that EM retrievals during maintenance-critically, before a response can be prepared-might affect short-term recognition memory performance even in the absence of distraction. We hypothesized that this influence would be mediated by the lingering presence of reactivated EM content in WM. We obtained support for this hypothesis in three experiments, showing that delay-period EM reactivation introduces incidentally-associated information (context) into WM, and that these retrieved associations negatively impact subsequent recognition, leading to substitution errors (Experiment 1) and slowing of accurate responses (Experiment 2). fMRI pattern analysis showed that slowing is mediated by the content of EM reinstatement (Experiment 3). These results expose a previously hidden influence of EM on WM, raising new questions about the adaptive nature of their interaction.
Probe Efficient Feature Representation of Gapped K-mer Frequency Vectors from Sequences using Deep Neural Networks
Authors: Cao Zhen , Zhang Shihua
Published: August 2017

How to extract informative features from genome sequence is a challenging issue. Gapped k-mers frequency vectors (gkm-fv) has been presented as a new type of features in the last few years. Coupled with support vector machine (gkm-SVM), gkm-fvs have been used to achieve effective sequence-based predictions. However, the huge computation of a large kernel matrix prevents it from using large amount of data. And it is unclear how to combine gkm-fvs with other data sources in the context of string kernel. On the other hand, the high dimensionality, colinearity and sparsity of gkm-fvs hinder the use of many traditional machine learning methods without a kernel trick. Therefore, we proposed a flexible and scalable framework gkm-DNN to achieve feature representation from high-dimensional gkm-fvs using deep neural networks (DNN). We first proposed a more concise version of gkm-fvs which significantly reduce the dimension of gkm-fvs. Then we implemented an efficient method to calculate the gkm-fv of a given sequence at the first time. Finally, we adopted a DNN model with gkm-fvs as inputs to achieve efficient feature representation and a prediction task. Here, we took the transcription factor binding site prediction as an illustrative application. We applied gkm-DNN onto 467 small and 69 big human ENCODE ChIP-seq datasets to demonstrate its performance and compared it with the state-of-the-art method gkm-SVM. We demonstrated that gkm-DNN can not only improve the limitations of high dimensionality, colinearity and sparsity of gkm-fvs, but also make comparable overall performance compared with gkm-SVM using the same gkm-fvs. In addition, we used gkm-DNN to explore the representation power of gkm-fvs and provided more explanation on how gkm-fvs work.
Mapping Quantitative Trait Loci in Yeast
Authors: Liti Gianni , Warringer Jonas , Blomberg Anders
Published: August 2017

Natural Saccharomyces strains isolated from the wild differ quantitatively in molecular and organismal phenotypes. Quantitative trait loci (QTL) mapping is a powerful approach for identifying sequence variants that alter gene function. In yeast, QTL mapping has been used in designed crosses to map functional polymorphisms. This approach, outlined here, is often the first step in understanding the molecular basis of quantitative traits. New large-scale sequencing surveys have the potential to directly associate genotypes with organismal phenotypes, providing a broader catalog of causative genetic variants. Additional analysis of intermediate phenotypes (e.g., RNA, protein, or metabolite levels) can produce a multilayered and integrated view of individual variation, producing a high-resolution view of the genotype–phenotype map.
Precipitation of DNA with Isopropanol
Authors: Green Michael R. , Sambrook Joseph
Published: August 2017

DNA is less soluble in solutions containing isopropanol than in solutions containing ethanol. In contrast to precipitation with ethanol, which requires 2–3 volumes of alcohol, precipitation with isopropanol is performed with 0.6–0.7 volume of alcohol. Isopropanol is often the better choice when precipitating DNA from large volumes of solution. Precipitation with isopropanol, described here, is performed at room temperature to lessen the risk that solutes like sucrose or sodium chloride will be coprecipitated with the DNA.
Creation of Recombinant Antibodies: Using 5′-RACE to Amplify Immunoglobulin Sequences
Authors: Dasch James R. , Dasch Amy L.
Published: August 2017

Modern molecular biology techniques have been applied to the production of therapeutic antibodies. Nonetheless, recombinant antibodies remain the exception rather than the rule for the antibodies used in most research and diagnostic applications. The lack of penetration of recombinant antibodies into the research arena can be attributed largely to the fact that the Ig gene families are large and the variable region gene segments are, indeed, variable, precluding the use of polymerase chain reaction (PCR) with two simple primers to amplify the heavy and light chain gene segments. Because of the complexity of the V gene family and the number of possible sequences for amplification, there may be a distinct advantage to using a PCR method that does not require a specific 5′ primer to amplify the gene segment. 5′-RACE is just such a method. In the original 5′-RACE method, mRNA served as a template for cDNA synthesis using either oligo(dT) priming or a gene-specific primer. Terminal deoxynucleotide transferase (TdT) was used to tail the first strand with a region of known sequence, such as poly(A). Once tailed, the second strand can be amplified using poly(T). This 5′-RACE protocol uses the TdT activity of reverse transcriptase, which allows nontemplated addition of nucleotides to the end of the nascently made cDNA first strand.
RNA-Seq: RNA Conversion to cDNA and Amplification
Authors: Mardis Elaine , McCombie W. Richard
Published: August 2017

The Ovation RNA-Seq Kit provides a fast and simple method for preparing amplified cDNA from total RNA. Amplification is initiated both at the 3′ ends of the transcripts and across the entire range of transcribed sequences; thus, this approach is ideal for next-generation sequencing, because the reads are distributed across the transcript types. The amplified cDNA produced in this protocol is used to create libraries optimized for use in the Illumina Genome Analyzer II platform. A procedure for removing small degraded RNAs before the sample is processed into cDNA is also included.
Budding Yeast Strains and Genotype–Phenotype Mapping
Authors: Liti Gianni , Warringer Jonas , Blomberg Anders
Published: August 2017

A small number of well-studied laboratory strains of Saccharomyces cerevisiae, mostly derived from S288C, are used in yeast research. Although powerful, studies for understanding S288C do not always capture the phenotypic essence or the genetic complexity of S. cerevisiae biology. This is particularly problematic for multilocus phenotypes identified in laboratory strains because these loci have never been jointly exposed to natural selection and the corresponding phenotypes do not represent optimization for any particular purpose or environment. Isolation and sequencing of new natural yeast strains also reveal that the total sequence diversity of the S. cerevisiae global population is poorly sampled in common laboratory strains. Here we discuss methodologies required for using the natural genetic variation in yeast to complete a genotype–phenotype map.
A protocol for searching the most probable phase-retrieved maps in coherent X-ray diffraction imaging by exploiting the relationship between convergence of the retrieved phase and success of calculation
Authors: Sekiguchi Yuki , Hashimoto Saki , Kobayashi Amane , Oroguchi Tomotaka , Nakasako Masayoshi
Published: August 2017

Coherent X-ray diffraction imaging (CXDI) is a technique for visualizing the structures of non-crystalline particles with size in the submicrometer to micrometer range in material sciences and biology. In the structural analysis of CXDI, the electron density map of a specimen particle projected along the direction of the incident X-rays can be reconstructed only from the diffraction pattern by using phase-retrieval (PR) algorithms. However, in practice, the reconstruction, relying entirely on the computational procedure, sometimes fails because diffraction patterns miss the data in small-angle regions owing to the beam stop and saturation of the detector pixels, and are modified by Poisson noise in X-ray detection. To date, X-ray free-electron lasers have allowed us to collect a large number of diffraction patterns within a short period of time. Therefore, the reconstruction of correct electron density maps is the bottleneck for efficiently conducting structure analyses of non-crystalline particles. To automatically address the correctness of retrieved electron density maps, a data analysis protocol to extract the most probable electron density maps from a set of maps retrieved from 1000 different random seeds for a single diffraction pattern is proposed. Through monitoring the variations of the phase values during PR calculations, the tendency for the PR calculations to succeed when the retrieved phase sets converged on a certain value was found. On the other hand, if the phase set was in persistent variation, the PR calculation tended to fail to yield the correct electron density map. To quantify this tendency, here a figure of merit for the variation of the phase values during PR calculation is introduced. In addition, a PR protocol to evaluate the similarity between a map of the highest figure of merit and other independently reconstructed maps is proposed. The protocol is implemented and practically examined in the structure analyses for diffraction patterns from aggregates of gold colloidal particles. Furthermore, the feasibility of the protocol in the structure analysis of organelles from biological cells is examined.
(10R,13R)-17-(6-Hydroxy-5-methylheptan-2-yl)-10,13-dimethyl-2,3,4,7,8,9,10,11,12,13,14,15,16,17-tetradecahydro-1H-cyclopenta[a]phenanthren-3-ol hemihydrate: a bioactive steroid isolated from the Indian herbArtemisia reticulata
Authors: Bauri A. K. , Foro Sabine , Nguyen Do Nhu Quynh
Published: August 2017

The title tetracyclic steroidal compound, C27H46O2·0.5H2O, crystallized as a monohydrate with two independent molecules (1and2) in the asymmetric unit. In both molecules, the conformations of the three cyclohexane rings (A,BandC) are chair, half-chair and chair, respectively. The fourth ring,D, has a twisted conformation on the bond linking theDandCrings. The crystal structure is stabilized by hydrogen bonding with the two independent molecules being linked through the solvent water moleculeviavarious O—H...O hydrogen bonds, forming layers parallel to (-101).