bluuebunny/crossref_metadata_2025 huggingface dataset:
Stable isotope analyses reveal previously unknown trophic mode diversity in the Hymenochaetales
Authors: Korotkin Hailee B. , Swenie Rachel A. , Miettinen Otto , Budke Jessica M. , Chen Ko‐Hsuan , Lutzoni François , Smith Matthew E. , Matheny P. Brandon
Published: October 2018

Premise of the Study

The Hymenochaetales are dominated by lignicolous saprotrophic fungi involved in wood decay. However, the group also includes bryophilous and terricolous taxa, but their modes of nutrition are not clear. Here, we investigate patterns of carbon and nitrogen utilization in numerous non‐lignicolous Hymenochaetales and provide a phylogenetic context in which these non‐canonical ecological guilds arose.

Methods

We combined stable isotope analyses of δ13C and δ15N and phylogenetic analyses to explore assignment and evolution of nutritional modes. Clustering procedures and statistical tests were performed to assign trophic modes to Hymenochaetales and test for differences between varying ecologies. Genomes of Hymenochaetales were mined for presence of enzymes involved in plant cell wall and lignin degradation and sucrolytic activity.

Key Results

Three different trophic clusters were detected – biotrophic, saprotrophic, and a second biotrophic cluster including many bryophilous Hymenochaetales and mosses. Non‐lignicolous Hymenochaetales are generally biotrophic. All lignicolous Hymenochaetales clustered as saprotrophic and most terricolous Hymenochaetales clustered as ectomycorrhizal. Overall, at least 15 species of Hymenochaetales are inferred as biotrophic. Bryophilous species ofRickenellacan degrade plant cell walls and lignin, and cleave sucrose to glucose consistent with a parasitic or endophytic life style.

Conclusions

Most non‐lignicolous Hymenochaetales are biotrophic. Stable isotope values of many bryophilous Hymenochaetales cluster as ectomycorrhizal or in a biotrophic cluster indicative of parasitism or an endophytic life style. Overall, trophic mode diversity in the Hymenochaetales is greater than anticipated, and non‐lignicolous ecological traits and biotrophic modes of nutrition are evolutionarily derived features.
The Multilevel Relationships of HIV‐Related Stigma to Child and Caregiver Mental Health among HIV‐Affected Households in South Africa
Authors: Williams Leslie D. , Aber J. Lawrence ,   SIZE Research Group
Published: October 2018

HIV/AIDS‐related (HAR) stigma is still a prevalent problem in Sub‐Saharan Africa, and has been found to be related to mental health of HIV‐positive individuals. However, no studies in the Sub‐Saharan African context have yet examined the relationship between HAR stigma and mental health among HIV‐negative, HIV‐affected adults and families; nor have any studies in this context yet examined stigma as an ecological construct predicting mental health outcomes through supra‐individual (setting level) and individual levels of influence. Multilevel modeling was used to examine multilevel, ecological relationships between HAR stigma and mental health among child and caregiver pairs from a systematic, community‐representative sample of 508 HIV‐affected households nested within 24 communities in KwaZulu‐Natal, South Africa. Two distinct dimensions of HAR stigma were measured: individual stigmatizing attitudes, and perceptions of community normative stigma. Findings suggest that individual‐level HAR stigma significantly predicts individual mental health (depression and anxiety) among HIV‐affected adults; and that community‐level HAR stigma significantly predicts both individual‐level mental health outcomes (anxiety) among HIV‐affected adults, and mental health outcomes (PTSD and externalizing behavior scores) among HIV‐affected children. Differentiated patterns of relationships were found using the two different stigma measures. These findings of unique relationships identified when utilizing two conceptually distinct stigma measures, at two levels of analysis (individual and community) suggest that HAR stigma in this context should be conceptualized as a multilevel, multidimensional construct. These findings have important implications both for mental health interventions and for interventions to reduce HAR stigma in this context.
Brown adipose tissue, energy expenditure, and biomarkers of cardio‐metabolic health among the Yakut (Sakha) of northeastern Siberia
Authors: Levy Stephanie B. , Klimova Tatiana M. , Zakharova Raisa N. , Federov Afanasiy I. , Fedorova Valentina I. , Baltakhinova Marina E. , Leonard William R.
Published: October 2018

Objectives

This study provides the first investigation of non‐shivering thermogenesis (NST) and brown adipose tissue (BAT) activity among an indigenous circumpolar population, the Yakut of northeastern Siberia. The study also examines the health significance of BAT activity in this population by testing the relationships between BAT thermogenesis and biomarkers of cardio‐metabolic disease risk, such as percent body fat and blood glucose and cholesterol levels.

Methods

Data were collected in the Sakha Republic (Yakutia) for 31 men and 43 women. Change in energy expenditure and BAT thermogenesis were quantified after a 30‐minute mild cooling condition. Anthropometric dimensions, blood glucose, and lipid levels were also collected.

Results

On average, the skin temperature of the supraclavicular area was constant after cooling while the skin temperature of a point on the sternum dropped significantly (P < .001), thus suggesting the presence of active supraclavicular BAT among Yakut adults. Participants with evidence of greater BAT thermogenesis exhibited a larger percent change in energy expenditure (% ΔEE) and an increase in respiratory quotient (RQ) after cooling (P ≤ .05). While there was no relationship between BAT activity and blood lipid levels, BAT thermogenesis was positively associated with blood glucose levels (P < .01).

Conclusions

Yakut adults exhibit evidence of active BAT deposits. Given that there is a significant relationship between BAT activity and % ΔEE, it is possible that BAT plays a role in NST among Yakut adults. While the relationship between BAT and body composition is inconclusive, participants with greater BAT seemed to preferentially utilize glucose during cold stress exposure.
Does a man's testosterone “rebound” as dependent children grow up, or when pairbonds end? A test in Cebu, Philippines
Authors: Rosenbaum Stacy , Gettler Lee T. , McDade Thomas W. , Bechayda Sonny S. , Kuzawa Christopher W.
Published: October 2018

Objective

Cross‐culturally, men's T declines in response to pairbonding and fatherhood, but less is known about what happens to T during and after life history transitions that theoretically lead to renewed mating effort. We tested whether men's T rises (or declines less with age) as their children age, or when pairbonds end, independent of changes in fatherhood‐related variables such as co‐residence with children.

Methods

We used demographic, behavioral, and salivary hormone data (waking and pre‐bed T) collected in 2009 and 2014 for the Cebu Longitudinal Health and Nutrition Survey (n = 571 men).

Results

Fathers with older children tended to have attenuated decline in pre‐bedtime T between 2009 and 2014 compared to men with younger children, after controlling for pairbonding (ß = 1.58, SE = 0.88, P = 0.074). Separated men had higher pre‐bedtime T than pairbonded men, controlling for fatherhood‐related variables (ß = 11.74, SE = 4.33, P = 0.007). Change in T did not significantly differ for men who separated between the two surveys, relative to men who remained pairbonded throughout.

Conclusion

We found modest support for the prediction that men experience less of an age‐related drop in T as their youngest child ages, a trend that might strengthen as children age further. We also replicate the finding that separated men have higher T, although longitudinal changes in the hormone were not significantly different in these men. Our data suggest that, of two life history transitions that may predict renewed mating effort, pair bond loss is more strongly endocrine mediated than potential mating effort shifts related to the aging of children.
Severe bleeding with subclinical oculocutaneous albinism in a patient with a novel HPS6 missense variant
Authors: Han Chen G. , O'Brien Kevin J. , Coon Lea M. , Majerus Julie A. , Huryn Laryssa A. , Haroutunian Sara G. , Moka Nagabhishek , Introne Wendy J. , Macnamara Ellen , Gahl William A. , Malicdan May Christine V. , Chen Dong , Krishnan Koyamangalath , Gochuico Bernadette R.
Published: October 2018

Heřmanský–Pudlák syndrome (HPS), a rare autosomal recessive disorder, manifests with oculocutaneous albinism and a bleeding diathesis. However, severity of disease can be variable and is typically related to the genetic subtype of HPS; HPS type 6 (HPS‐6) is an uncommon subtype generally associated with mild disease. A Caucasian adult female presented with a history of severe bleeding; ophthalmologic examination indicated occult oculocutaneous albinism. The patient was diagnosed with a platelet storage pool disorder, and platelet whole mount electron microscopy demonstrated absent delta granules. Genome‐wide SNP analysis showed regions of homozygosity that included the HPS1 and HPS6 genes. Full length HPS1 transcript was amplified by PCR of genomic DNA. Targeted next‐generation sequencing identified a novel homozygous missense variant in HPS6 (c.383 T > C; p.V128A); this was associated with significantly reduced HPS6 mRNA and protein expression in the patient's fibroblasts compared to control cells. These findings highlight the variable severity of disease manifestations in patients with HPS, and illustrate that HPS can be diagnosed in patients with excessive bleeding and occult oculocutaneous albinism. Genetic analysis and platelet electron microscopy are useful diagnostic tests in evaluating patients with suspected HPS.

Clinical Trial registration:

Registrar: ClinicalTrials.gov

Website: www.clinicaltrials.gov

Registration Numbers: NCT00001456 and NCT00084305.
Incisor tooth wear and age determination in mountain gorillas from Volcanoes National Park, Rwanda
Authors: Galbany Jordi , Muhire Thadée , Vecellio Veronica , Mudakikwa Antoine , Nyiramana Aisha , Cranfield Michael R. , Stoinski Tara S. , McFarlin Shannon C.
Published: October 2018

Objectives

Ecological factors, but also tooth‐to‐tooth contact over time, have a dramatic effect on tooth wear in primates. The aim of this study is to test whether incisor tooth wear changes predictably with age and can thus be used as an age estimation method in a wild population of mountain gorillas (Gorilla beringei beringei) from Volcanoes National Park, Rwanda.

Materials and methods

In mountain gorillas of confidently known chronological age (N = 24), we measured the crown height of all permanent maxillary and mandibular incisors (I1, I1, I2, I2) as a proxy for incisal macrowear. Linear and quadratic regressions for each incisor were used to test whether age can be predicted by crown height. Using these models, we then predicted age at death of two individual mountain gorillas of probable identifications, based on their incisor crown height.

Results

Age decreased significantly with incisor height for all teeth, but the upper first incisors (I1) provided the best results, with the lowest Akaike's Information Criterion corrected for small sample size (AICc) and lowest Standard Error of the Estimate (SEE). When the best age equations for each sex were applied to gorillas with probable identifications, the predicted ages differed 1.58 and 3.33 years from the probable ages of these individuals.

Conclusions

Our findings corroborate that incisor crown height, a proxy for incisal wear, varies predictably with age. This relationship can be used to estimate age at death of unknown gorillas in the skeletal collection, and in some cases, to corroborate the identity of individual gorillas recovered from the forest postmortem at an advanced state of decomposition. Such identifications help fill gaps in the demographic database and support research that requires individual‐level data.
Measurement of the Ratio between g‐Factors of the Ground States of 87Rb and 85Rb
Authors: Mora Jason , Cobos Aracely , Fuentes Dominic , Jackson Kimball Derek F.
Published: October 2018

The ratio between the Landé g‐factors of the Rb and Rb ground‐state hyperfine levels is experimentally measured to be , consistent with previous measurements. The g‐factor ratio is determined by comparing the Larmor frequencies of overlapping ensembles of Rb and Rb atoms contained within an evacuated, antirelaxation‐coated vapor cell. The atomic spins are polarized via synchronous optical pumping and the Larmor frequencies are measured by off‐resonant probing using optical rotation of linearly polarized light. The accuracy of this measurement of exceeds that of previous measurements by a factor of ≈50 and is sensitive to effects related to quantum electrodynamics.
Methane Hydration‐Shell Structure and Fragility
Authors: Wu Xiangen , Lu Wanjun , Streacker Louis M. , Ashbaugh Henry S. , Ben‐Amotz Dor
Published: October 2018

The influence of oily molecules on the structure of liquid water is a question of importance to biology and geology and many other fields. Previous experimental, theoretical, and simulation studies of methane in liquid water have reached widely conflicting conclusions regarding the structure of hydrophobic hydration‐shells. Herein we address this question by performing Raman hydration‐shell vibrational spectroscopic measurements of methane in liquid water from −10 °C to 300 °C (at 30 MPa, along a path that parallels the liquid‐vapor coexistence curve). We show that, near ambient temperatures, methane's hydration‐shell is slightly more tetrahedral than pure water. Moreover, the hydration‐shell undergoes a crossover to a more disordered structure above ca. 85 °C. Comparisons with the crossover temperature of aqueous methanol (and other alcohols) reveal the stabilizing influence of an alcohol OH head‐group on hydrophobic hydration‐shell fragility.
Tribological behavior prediction of friction materials for ultrasonic motors using Monte Carlo‐based artificial neural network
Authors: Li Song , Shao Mingchao , Duan Chunjian , Yan Yingnan , Wang Qihua , Wang Tingmei , Zhang Xinrui
Published: October 2018

In this article, the relationship of complexity, diversity, and uncertainty between components and tribological properties of friction materials based on a Monte Carlo‐based artificial neural network (MC‐ANN) model was predicted precisely. Meanwhile, the grey relational analysis was applied to figure out weight of factors, optimize formulation design, and calculate nonlinear dependency of ingredients. The accuracy of model was studied by comparing experimental and simulated values on the basis of statistical methods (root‐mean‐squared error). It was found that the model exhibited an excellent performance in predicting and fitting effect. Moreover, comprehensive analysis of weight indicated that nano‐SiO2and mica exerted a significant role in improving the friction stability and wear resistance. According to different contents of each ingredient, the corresponding friction coefficient and specific wear rate could be obtained by virtue of a well‐trained MC‐ANN model without experiments, which saved a lot of time and money. It can be expected that the results of this work will extend the current research and pave a route for further in‐depth studies of friction materials. © 2018 Wiley Periodicals, Inc. J. Appl. Polym. Sci.2019,136, 47157.
Do Bony Orbit Dimensions Predict Diel Activity Pattern in Sciurid Rodents?
Authors: Smith Stephanie M. , Angielczyk Kenneth D. , Schmitz Lars , Wang Steve C.
Published: October 2018

Diel activity pattern (DAP) is a key aspect of an animal's ecology, but it is difficult to infer when behavior cannot be directly observed, as in the fossil record. Various anatomical correlates have therefore been used to attempt to classify DAP. Eyeball dimensions are good predictors of DAP because they relate directly to light sensitivity of the eye. Osteological characters, such as scleral ring dimensions, are also reliable proxies, but bony orbit dimensions alone have proven less reliable because soft tissues other than the eyeball can affect orbit size and shape. However, it would be useful if bony orbit dimensions could be used to determine DAP, particularly for mammals, which have no scleral ring, and nonmammalian synapsids, which infrequently preserve scleral rings. We investigated the possibility of predicting DAP in sciurids (Mammalia: Rodentia: Sciuridae) using orbit measurements and other cranial dimensions, and a variety of quantitative methods, including phylogenetic flexible discriminant analysis, classification trees, and logistic regression. The latter two methods do not require a priori assignment of DAP and therefore reflect the situation in a fossil data set. We find that although there are some interfering phylogenetic factors, nocturnal and non‐nocturnal sciurids can be differentiated from one another with over 80% accuracy using all methods investigated here; attempts to differentiate crepuscular animals from nocturnal and diurnal species proved much less successful. Our results indicate that these analyses offer several viable options for predicting DAP in the fossil record, but such analyses should be conducted in a phylogenetic context whenever possible. Anat Rec, 301:1774–1787, 2018. © 2018 Wiley Periodicals, Inc.
The Influence of Leaping Frequency on Secondary Bone in Cercopithecid Primates
Authors: Lad Susan E. , Pampush James D. , Mcgraw W. Scott , Daegling David J.
Published: October 2018

Bone remodeling is at least partially mediated by the mechanical environment created by an animal's behavior. Here, we test the hypothesis that bone remodeling is primarily induced by high magnitude loads, likely encountered during leaping/bounding behaviors. Osteon population density (OPD), osteon cross‐sectional area (On.Ar), and relative osteonal area (%HAV) were measured from femoral and humeral midshaft thin sections of four cercopithecids (N = 5 per species) from Taï Forest, Côte d'Ivoire:Colobus polykomos,Piliocolobus badius,Cercopithecus diana, andCercocebus atys. All species are generalized quadrupeds but vary in leaping frequency and overall activity budget. Differences between taxa with high (C. polykomosandP. badius) and low leaping frequency (C. dianaandC. atys) were assessed via a phylogenetically informed generalized linear mixed model using Markov Chain Monte Carlo methods. Femoral OPD and %HAV are greater in the high frequency leapers than in low frequency leapers, suggesting that frequent high magnitude loads engender remodeling, however, there is no similar pattern in the humerus, which presumably also experiences high magnitude loads during leaping. Additionally, OPD and %HAV are greater in the humerus than the femur, despite load magnitude being presumably higher in the femur. These results provide conflicting support for hypotheses about load magnitude and load frequency as they relate to bone remodeling activity. Future work is proposed to parse out the respective effects of load magnitude and frequency on bone remodeling. Anat Rec, 302:1116–1126, 2019. © 2018 Wiley Periodicals, Inc.
TET2‐Mediated Spatiotemporal Changes of 5‐Hydroxymethylcytosine During Organogenesis in the Late Mouse Fetus
Authors: Li Xiangjun , Xie Fangfang , Jin Junfeng , Wu Yuqiong , Luo Ziwei , Zhang Fengxue , Zhang Saixia , Chen Dongfeng , Liu Aijun
Published: October 2018

Genomic DNA demethylation is important for mammalian embryonic development and organ function. 5‐Hydroxymethylcytosine (5hmC) is considered a novel epigenetic marker. Ten‐eleven translocation (TET) enzymes convert 5‐methylcytosine (5mC) to 5hmC. To explore the dynamic changes of epigenetic modifications during organogenesis in the late mouse fetus, the regional distribution and histological localization of 5hmC and TET enzymes was investigated by immunohistochemical method. The liver of mouse fetus gradually matured from embryonic day (E) 12.5 to E18.5.5mC was positive in developing liver at E16.5 and E18.5. 5hmC, TET2 and TET3 were strongly positive in hepatocytes and oval cells at E18.5. The small intestinal villi were formed at E16.5. The striate border and goblet cells appeared at E18.5. 5mC was detectable from E12.5 to E18.5. 5hmC and TET2 were positive in small intestine at E12.5, E14.5, and E18.5. The alveolar was formed at E18.5. 5mC and 5hmC were detectable from E12.5 to E18.5. Only TET2 was positive in the lung of the late Kunming mouse fetus. For vertebra, mesenchymal cells formed hyaline cartilage at E15.5 and then ossify at E16.5 and E18.8. 5mC, 5hmC, and TET2 were detectable in chondrocytes and osteocytes during the late Kunming mouse fetal; TET1 expressed from E14.5 to E16.5 and TET3 expressed in bone matrix at E18.5. In summary, TET2 was strongly expressed in liver, small intestinal, lung, and vertebra in the late Kunming mouse fetus. These findings suggested that TET2 may play a more critical role than TET1 and TET3 during organogenesis in the late stage of Kunming mouse embryo. Anat Rec, 302:954–963, 2019. © 2018 Wiley Periodicals, Inc.
Areas of Cartilaginous and Osseous Metaplasia After Experimental Myocardial Infarction in Rats
Authors: Manole Catalin Gabriel , Marinescu Bogdan Gabriel , Marta Daciana , Nicolescu Mihnea Ioan
Published: October 2018

The presence of hyaline cartilage has been previously documented in heart tissue of different vertebrates, ranging from birds to superior mammals. However, there is scarce published data regarding the appearance of focal deposits of hyaline‐like cartilage within the hearts of laboratory rats. Few mechanisms that could trigger the appearance of this type of cartilage in heart were hypothesized (e.g., mechanical stress, ageing). Using different microscopy techniques this report confirms the presence of hyaline cartilage and bone in Wistar rats, which underwent left anterior coronary artery ligation for experimental myocardial infarction. The presented (ultra)structural evidence of focal chondroid metaplasia in the papillary muscles and close to the insertion point in the ventricular mass of the infarcted heart suggests a structural adaptation of cardiac myocardium to the newly acquired kinetics of left ventricular wall, after experimental myocardial infarction. Specific cartilaginous matrix proteins are known to mediate cardiac extracellular matrix remodeling, and this study provides evidence of a complete transition to a cartilaginous pattern in postinfarcted heart, which may nonetheless constitute a supplemental risk factor of a further heart failure condition. Moreover, for heart focal chondrogenesis, we also presume the involvement of the cellular and molecular inflammatory milieu that dominates the first 24 hr border zone landscape of the experimental myocardial infarction lesion. Anat Rec, 302:947–953, 2019. © 2018 Wiley Periodicals, Inc.
Remarkable Enhancement in Boron Uptake Within Glioblastoma Cells With Carboranyl–Indole Carboxamides
Authors: Narlawar Rajeshwar , Austin Christopher J. D. , Kahlert Jan , Selleri Silvia , Da Pozzo Eleonora , Martini Claudia , Werry Eryn L. , Rendina Louis M. , Kassiou Michael
Published: October 2018

Novel boron‐rich, carboranyl–indole carboxamide ligands were prepared and found to effectively target the 18 kDa translocator protein (TSPO), an upregulated mitochondrial membrane‐bound protein which has been observed in variety of tumor cell lines and its expression appears to be proportional to the degree of tumorigenicity, emphasizing a key role in cancer cell proliferation. Both boronated compounds displayed remarkably high affinities for the TSPO. In addition, the in vitro uptake of these compounds into T98G human glioma cells was found to be 25‐ to 100‐fold greater than that of clinical boron neutron capture therapy (BNCT) agents.
State Estimation For An Agonistic‐Antagonistic Muscle System
Authors: Nguyen Thang Tien , Warner Holly , La Hung , Mohammadi Hanieh , Simon Dan , Richter Hanz
Published: October 2018

Research on assistive technology, rehabilitation, and prosthetics requires the understanding of human machine interaction, in which human muscular properties play a pivotal role. This paper studies a nonlinear agonistic‐antagonistic muscle system based on the Hill muscle model. To investigate the characteristics of the muscle model, the problem of estimating the state variables and activation signals of the dual muscle system is considered. In this work, parameter uncertainty and unknown inputs are taken into account for the estimation problem. Three observers are presented: a high gain observer, a sliding mode observer, and an adaptive sliding mode observer. Theoretical analysis shows the convergence of the three observers. Numerical simulations reveal that the three observers are comparable and provide reliable estimates.
Conceptual design of a dedicated‐crop biorefinery for Jatropha curcas using a systematic sustainability evaluation
Authors: Navarro‐Pineda Freddy S. , Handler Robert , Sacramento Rivero Julio C.
Published: October 2018

The sustainability of two scenarios for the exploitation of Jatropha curcas biomass was assessed using a suitable sustainability framework. The first scenario, or base case (BC), was set up as a traditional biodiesel process with crude glycerin as the only co‐product. The second scenario was a biorefinery plant (BR) that builds on the BC by including thermochemical transformations of lignocellulosic biomass into bio‐oil, bio‐char, and heat and power for internal consumption. The process lifecycle was divided in two stages: cultivation and transformation. The BC scenario was only sustainable in the Renewability category. Expanding the system to a biorefinery (BR scenario) improved performance on all other indicators. The biorefinery was also sustainable in the Economics, Community development, and Mitigation categories. None of the scenarios was sustainable in the fossils‐based products Displacement category. The main areas for improvement were the use of water for irrigation, and the high inputs of agrochemicals (fertilizers, pesticides, insecticides, and herbicides). Seed yield is a critical variable that affects most sustainability indicators. The capital investment would be recovered after year 10 in the current economic context. The cultivation stage is largely responsible for the impacts of both cases as it contributes the most to the production costs (62–77%), environmental impacts, non‐renewable energy consumption (66–68%), and freshwater consumption (97–98%). Hence, even though diversifying the products portfolio improves the values of all sustainability indicators, it is clear that optimizing the agronomic stage is crucial for attaining the sustainability of the overall system. © 2018 Society of Chemical Industry and John Wiley & Sons, Ltd
Framing learning entanglement in innovative learning spaces: Connecting theory, design and practice
Authors: Carvalho Lucila , Yeoman Pippa
Published: October 2018

Innovative learning spaces have emerged in response to the influx of educational technologies and new social practices associated with twenty‐first‐century learning. Whilst dominant narratives of change often suggest that alterations in the designed environment for learning will result in changed practice, on the ground educators are struggling to align their pedagogical models with new spaces for learning, direct instruction is still common, and technologically deterministic narratives mask a failure to engage with the materiality of learning. This article argues for a non‐deterministic theory of things in educational research and calls for a deeper understanding of the flows of matter, information and human–thing dependence, which will render visible the heterogeneous entanglements characteristic of innovative spaces for learning. It highlights that educational designers (e.g. teachers, space planners, architects, instructional designers) are in pressing need of analytical tools capable of supporting their work in ways that promote correspondence between (a) pedagogy, place and people and (b) theory, design and practice. In response, we introduce an analytical approach to framing learning entanglement that accounts for the artefacts, resources and tools available to learners; the choice of tasks and pedagogical models and the social roles and divisions of labour governing any given learning situation. Finally, we practically demonstrate how this approach aids in identifying correspondence or dissonance across dimensions of design and scale levels, in both the analysis and design of complex environments for learning.
Addition of high load of lysophosphatidic acid to standard and high‐fat chows causes no significant changes of its circulating and peripheral tissue levels but affects body weight and visceral fat mass of mice
Authors: Inoue Manami , Okamoto Yoko , Atsumi Yuta , Shiojiri Masatoshi , Hidaka Mayumi , Tanaka Tamotsu , Tsutsumi Toshihiko , Shirasaka Naoki , Tokumura Akira
Published: October 2018

Oral administration of lysophosphatidic acid (LPA), a critical intercellular lipid mediator, exerts wound healing and antiulcer effects on gastrointestinal system. To evaluate effects of food‐derived LPA on body homeostasis, we measured LPA levels by liquid chromatography–tandem mass spectrometry in chows, feces, plasma, liver, and visceral fat of mice fed a normal or high‐fat chow supplemented with or without LPA‐rich soybean phospholipids for 30 days. Reductions in daily body weight gains and visceral fat mass were mainly related to lower chow intake by mice fed the LPA‐rich high‐fat chow, whereas reduced body weight gains and fat mass were mainly related to decreased intestinal triacylglycerol absorption in mice fed LPA‐rich chow. Our results showed no significant increase in plasma, liver, or adipose LPA levels, even if a quite high LPA concentration (2.0%) in chows was ingested daily, suggesting limited effects of food‐derived LPA on the lumen side of the digestive tract. © 2018 BioFactors, 44(6):548–557, 2018
Amino acid modifications for conformationally constraining naturally occurring and engineered peptide backbones: Insights from the Protein Data Bank
Authors: Di Costanzo Luigi , Dutta Shuchismita , Burley Stephen K.
Published: October 2018

Extensive efforts invested in understanding the rules of protein folding are now being applied, with good effect, in de novo design of proteins/peptides. For proteins containing standard α‐amino acids alone, knowledge derived from experimentally determined three‐dimensional (3D) structures of proteins and biologically active peptides are available from the Protein Data Bank (PDB), and the Cambridge Structural Database (CSD). These help predict and design protein structures, with reasonable confidence. However, our knowledge of 3D structures of biomolecules containing backbone modified amino acids is still evolving. A major challenge in de novo protein/peptide design concerns the engineering of conformationally constrained molecules with specific structural elements and chemical groups appropriately positioned for biological activity. This review explores four classes of amino acid modifications that constrain protein/peptide backbone structure. Systematic analysis of peptidic molecule structures (eg, bioactive peptides, inhibitors, antibiotics, and designed molecules), containing these backbone‐modified amino acids, found in the PDB and CSD are discussed. The review aims to provide structure–function insights that will guide future design of proteins/peptides.
An inquiry‐based exercise in medicinal chemistry: Synthesis of a molecular library and screening for potential antimalarial and anti‐inflammatory compounds
Authors: Hall David J. , Martin Charles G. , Welford Michael , Debbert Stefan L.
Published: October 2018

The development of new medicines holds particular fascination for chemistry, biochemistry, and biology students interested in a career in medicine or the life sciences. The identification and refinement of lead compounds to treat diseases requires researchers to be facile in a number of different disciplines including organic synthesis, biochemistry, cell biology, and molecular biology. We have developed an interdisciplinary, inquiry‐based laboratory spanning both organic chemistry and biochemistry classes that acquaints students with research in medicinal chemistry. The first part of the exercise takes place in the second semester of organic chemistry, where pairs of students design and execute their own multistep synthesis of a novel compound with anti‐inflammatory and/or antimalarial potential. Later, in first semester biochemistry, many of the same students then test these synthesized compounds for cytotoxicity, inhibition of the enzyme nitric oxide synthase, and inhibition of the transcription factor NF‐kB. Learning outcomes, measured by the Classroom Undergraduate Research Experience (CURE) survey, suggest that students participating in both classes had higher gains than an average student. © 2018 International Union of Biochemistry and Molecular Biology, 46(5):424–434, 2018.
Student difficulties during structure–function problem solving
Authors: Halmo Stephanie M. , Sensibaugh Cheryl A. , Bhatia Kush S. , Howell Alexandra , Ferryanto Ersta P. , Choe Bryant , Kehoe Kaitlin , Watson Morgan , Lemons Paula P.
Published: October 2018

Protein structure–function is a key concept in biochemistry. We used the perspective of domain‐specific problem‐solving to investigate students’ solutions to a well‐defined protein structure–function problem. We conducted think‐aloud interviews with 13 undergraduate students and performed qualitative content analysis to examine the differences in the domain‐general and domain‐specific knowledge among correct and incorrect solutions. Our work revealed that students used domain‐general and domain‐specific knowledge in their problem solving. We also identified difficulties for students with the amino acid backbone, amino acid categorization, and causal mechanisms of noncovalent interactions. Using the identified difficulties, we make recommendations for the design of instructional materials targeted to improve protein structure–function problem solving in the biochemistry classroom. © 2018 International Union of Biochemistry and Molecular Biology, 46(5):453–463, 2018.
Assessing stakeholder perceptions of the american society for biochemistry and molecular biology accreditation program for baccalaureate degrees
Authors: Dean Diane M. , Martin Debra , Carastro L. Michael , Kennelly Peter J. , Provost Joseph J. , Tansey John T. , Wolfson Adele J.
Published: October 2018

The American Society for Biochemistry and Molecular Biology (ASBMB) began an accreditation program in 2013. The criteria for accreditation of undergraduate programs include sufficient infrastructure ‐ number and expertise of faculty, physical space and equipment, support for faculty and students ‐ and incorporation of core concepts in the curriculum ‐ structure and function of biomolecules; information storage; energy transfer; and quantitative skills. Students in accredited programs are able to have their degrees ASBMB certified by taking an exam focused on knowledge or skills across the four core concept areas. Members of the accreditation committees administered a survey to key stakeholders in the BMB community: undergraduate programs, both those that have applied for accreditation and those that have not; alumni/ae of accredited programs; graduate and professional programs; and employers. The goals of the study were to gauge the success of the program and determine necessary areas of improvement. The results indicate that the major benefits of applying for accreditation are the impetus to gather data and analysis not generally collected, and access to assessment data via the exam. However, stakeholders outside of the undergraduate community showed little awareness of the accreditation program. Additionally, the application process itself was seen to be very time consuming. This feedback will be used to improve the process and engage in further outreach. © 2018 International Union of Biochemistry and Molecular Biology, 46(5):464–471, 2018.
Developing a three‐dimensional animation for deeper molecular understanding of michaelis–menten enzyme kinetics
Authors: Florjanczyk Ursula , Ng Derek P. , Andreopoulos Stavroula , Jenkinson Jodie
Published: October 2018

The mathematical models that describe enzyme kinetics are invaluable predictive tools in numerous scientific fields. However, the daunting mathematical language used to describe kinetic behavior can be confusing for life science students; they often struggle to conceptualize and relate the mathematical representations to the molecular phenomena occurring at both macroscopic and microscopic levels. Students with less developed abstract and mathematical thinking skills may benefit from a visual learning approach. The paucity of visual resources for enzyme kinetics makes this a fertile field for developing novel learning media. We discuss developing a three‐dimensional animation aimed at introducing key concepts of Michaelis–Menten enzyme kinetics to undergraduate life science students. This animation uses both realistic and metaphoric depictions of the underlying molecular players, environments, and interactions in enzyme kinetics to contextualize and explain the relationship between the mathematical models and underlying molecular systems. The animation can be viewed at bit.ly/michaelis‐menten. © 2018 International Union of Biochemistry and Molecular Biology, 46(5):561–565, 2018.
Design and implementation of structural bioinformatics projects for biological sciences undergraduate students
Authors: Oke Muse , Agbalajobi Ramon , Osifeso Mowaninuwuraola , Muhammad Babagana , Lawal Halimat , Mai Muhammad , Adegunle Quadri
Published: October 2018

Contemporary biology is currently undergoing a revolution, driven by the availability of high‐throughput technologies and a wide variety of bioinformatics tools. However, bioinformatics education and practice is still in its infancy in most of the African continent. Consequently, concerted efforts have been made in recent years to incorporate bioinformatics modules into biological sciences curriculum of African Universities. Despite this, one aspect of bioinformatics that is yet to be incorporated is structural bioinformatics. In this article, we report on a structural bioinformatics project carried out by final year project students in a Nigerian university. The target protein was the thermoacidophilic Sulfolobus islandicus rod‐shaped virus 1 (SIRV1) Rep protein, which was further characterized using various free, user‐friendly and online sequence‐based and structure‐based bioinformatics tools. This exercise gave students the opportunity to generate new data, interpret the data, and acquire collaborative research skills. In this report, emphasis is placed on analysis of the data generated to further encourage analytical skills. By sharing this experience, it is anticipated that other similar institutions would adopt parallel strategies to expose undergraduate students to structural biology, and increase awareness of freely available bioinformatics tools for tackling pertinent biological questions. © 2018 International Union of Biochemistry and Molecular Biology, 46(5):547–554, 2018.
WeChat: An applicable and flexible social app software for mobile teaching
Authors: Tu Shuo , Yan Xiaohua , Jie Kemin , Ying Muying , Huang Chunhong
Published: October 2018

The rapid development and popularization of smart phones and mobile internet has created a new social lifestyle, and correspondingly prompts the transformation of network teaching from desktop computer to mobile teaching. This article has compared the pros and cons of Tsinghua Education Online and WeChat official account (WOA) in fulfilling teaching functions. We also described the construction of WOA platform with the example of WOA‐based teaching in biochemistry and molecular biology. The platform can establish nearly 75 menu catalogs and 2,250 items, which is capable for the publication of any types of teaching materials and information. The WOA teaching is well accepted and becomes popular in China due to the free, interactive, attractive, adaptable, portable, sustainable, and more participatory teaching styles. © 2018 International Union of Biochemistry and Molecular Biology, 46(5):555–560, 2018.
“Test‐enhanced” focused self‐directed learning after the teaching modules in biochemistry
Authors: Bobby Zachariah , Meiyappan Kavitha
Published: October 2018

Focused self‐directed learning is very much essential at present in medical education to catch‐up with the increasing information load. Cognitive psychology laboratory studies show that repeated testing of information produces superior retention relative to repeated study. The overall goal of this intervention was to evaluate the effectiveness of “Test enhanced learning” in the form of “Open book examination” as a formative assessment in Biochemistry when compared to “Self‐study.” Three exercises were carried out after the regular teaching sessions on different topics in biochemistry for the first year MBBS students. A multiple choice questions based pretest was conducted after the regular lecture classes on a topic but before the revision exercise. The students were subjected “Open book examination” with short answer questions for a period of 1 hour. A posttest was done with the same set of MCQs after the revision exercises. The gain score of “Open book examination” was compared with that of “Self study.” Feedback from the students was taken. The isolated results from each of the three exercises conducted and their combined results supported the hypothesis that “Test enhanced learning” in the form of open book examination is a superior form of learning process than self‐study for assimilation of knowledge. Most of the students opined that the “Open book examination” enhanced their self directed focused learning process. The students felt that “Open book examination” is more beneficial than “Self study” in reinforcing the learning concepts after regular didactic lectures. © 2018 International Union of Biochemistry and Molecular Biology, 46(5):472–477, 2018.
User‐friendly tool kits for protein gel electrophoresis techniques: A training program for high school students
Authors: Maurye Praveen , Basu Arpita , Sen Sohini , Biswas Jayanta Kumar , Bandyopadhyay Tapas Kumar , Naskar Malay
Published: October 2018

Recent advancements in biochemical sciences have helped the researchers to explore the molecular logic of life inclusive of its multifarious expressions and explain many facts about the structure and functions of cellular macromolecules. Due to its simple and cost‐effective nature, polyacrylamide gel electrophoresis (PAGE) has become the most favored technique for qualitative and quantitative examination of macromolecules. Major drawbacks of such modifications are the cost and operational complexities faced by naïve students. Many interlinking laboratory equipment are needed in the school laboratories for the conduct of even simple scientific experiment. Some of these costly modern equipment are inaccessible for students of small laboratories, and their alternatives are not easily available. Many of these laboratory equipment required for routine gel electrophoresis technique can be fabricated in their simplest form using off‐the‐shelf components. A short term biochemistry training program was executed for high school students to provide them “hands‐on” training using newly modified equipment, which was proved to be an exciting way of learning biochemical gel separation techniques. © 2018 International Union of Biochemistry and Molecular Biology, 46(5):566–577, 2018.
Anticipated learning outcomes for a biochemistry course‐based undergraduate research experience aimed at predicting protein function from structure: Implications for assessment design
Authors: Irby Stefan M. , Pelaez Nancy J. , Anderson Trevor R.
Published: October 2018

Several course‐based undergraduate research experiences (CUREs) have been published in the literature. However, only limited attempts have been made to rigorously identify the discovery‐type research abilities that students actually develop during such experiences. Instead, there has been a greater focus on technical or procedural‐type knowledge or general CURE skills that are too comprehensive to effectively assess. Before the extent of discovery‐type learning outcomes can be established in students (termed verified learning outcomes or VLOs), it is important to rigorously identify the anticipated learning outcomes (ALOs) and to then develop student assessments that target each ALO to reveal the nature of such student learning. In this article we present a matrix of 43 ALOs, or course‐based undergraduate research abilities (CURAs), that instructors anticipate students will develop during a recently‐developed biochemistry CURE focusing on the prediction of protein function from structure. The CURAs were identified using the process for identifying course‐based undergraduate research abilities (PICURA) and classified into seven distinct themes that enabled the characterization of the CURE and a comparison to other published inventories of research competencies and CURE aspects. These themes and the CURE protocols aligning to the CURAs were used to form the ALO matrix that was, in turn, used to inform the design of an assessment that revealed evidence that a student had developed some of the targeted CURAs. Future research will focus on further assessment development that targets other identified CURAs. This approach has potential applications to other CUREs both in biochemistry and other science disciplines. © 2018 International Union of Biochemistry and Molecular Biology, 46(5):478–492, 2018.
Localized and adaptive soft sensor based on an extreme learning machine with automated self‐correction strategies
Authors: Poerio Dominic V. , Brown Steven D.
Published: October 2018

A novel, nonlinear soft sensor based on a localized, adaptive single‐layer feedforward neural network with random hidden layer weights, also called an extreme learning machine, combined with the recursive partial least squares algorithm to update the linear output layer weights, is explored. The soft sensor is highly adaptive with minimal operator input, and automated mechanisms are included to self‐correct numerous aspects of the underlying model. For instance, mechanisms are put in place to automatically select an optimized local model region describing the current process dynamics from the historical data when the current prediction error reaches an adaptively computed threshold. Additionally, the new soft sensor simultaneously employs an ensemble of models with diverse recursive partial least squares forgetting factors with automated and adaptive reweighting of the models in the ensemble, thus enabling real‐time model memory adjustment. The validity of the method is shown by comparison with numerous other soft sensor methods for the prediction of the activity of a polymerization catalyst.
Cancer stem cells in esophageal cancer and response to therapy
Authors: Harada Kazuto , Pool Pizzi Melissa , Baba Hideo , Shanbhag Namita D. , Song Shumei , Ajani Jaffer A.
Published: October 2018

Cancer stem cells can be characterized by unique biomarkers; however, there exists an immense complexity of changing characteristics driven by tumor evolution and exposure to therapy. Attempts to target cancer stem cells are ongoing, but more in‐depth research is necessary.