cssi/SciSciGPT-SciSciNet huggingface dataset:
Minimalist models for protein folding and design.

Abstract Protein folding research during the past decade has emphasized the dominant role of native state topology in determining the speed and mechanism of folding for small proteins; this has been illustrated by simulations using minimalist protein models. The advantages of minimalist protein models lie in their ability to rapidly collect meaningful statistics about folding pathways and kinetics, their ease of characterization with coarse-grained order parameters and their concentration on the essential physics of the problem to connect with experimental observables for a target protein. The maturation of experimental protein folding has driven the need for more quantitative protein simulations to better understand the balance between sequence details and fold topology. In the past year, we have seen the emergence of more complex minimalist models, ranging from all-atom G o potentials to coarse-grained bead models in which G o interactions are replaced or supplemented by more physically motivated potentials. The reduced computational cost at the coarse-grained level of abstraction will potentially enable both folding studies on a genomic scale and systematic application in protein design.
Optimum design for a two-stage CMOS I/O ESD protection circuit

In industry, the design of CMOS ESD (electrostatic discharge) protection devices and circuits has been approached empirically. In this work, we propose an optimization methodology for a typical two-stage CMOS I/O protection circuit based on simulation. We have identified two kinds of design, namely resistor-limited and NMOS-limited, and demonstrated that the isolation resistor design is the key to the circuit's protection level and performance.
Discontinuous Shear Thickening of Frictional Hard-Sphere Suspensions

Discontinuous shear thickening (DST) observed in many dense athermal suspensions has proven difficult to understand and to reproduce by numerical simulation. By introducing a numerical scheme including both relevant hydrodynamic interactions and granularlike contacts, we show that contact friction is essential for having DST. Above a critical volume fraction, we observe the existence of two states: a low viscosity, contactless (hence, frictionless) state, and a high viscosity frictional shear jammed state. These two states are separated by a critical shear stress, associated with a critical shear rate where DST occurs. The shear jammed state is reminiscent of the jamming phase of granular matter. Continuous shear thickening is seen as a lower volume fraction vestige of the jamming transition.
Occupational Therapy Students’ Perspectives on Occupation as an Agent That Promotes Healthful Lifestyles

OBJECTIVES This study was conducted to determine occupational therapy students' perspectives on occupation as an agent that promotes healthful lifestyles, what factors influence these perspectives, and the extent to which formal classroom instruction in occupation as a health-promoting agent influenced their perspective transformation. METHOD Through a precourse and postcourse survey, weekly log sheets, and audiotaped class discussions, data regarding attitudes and beliefs about health promotion were collected from 23 occupational therapy master's students enrolled in the course Wellness Through Occupation. The data were analyzed with a priori concept coding to determine whether perspective transformation occurred as a result of formal classroom instruction. RESULTS Participants indicated that family values, previous formal and informal instruction, and personal experience were the major factors that influenced their perspectives on occupation as an agent that promotes a healthful lifestyle. The results demonstrated that participants had a perspective transformation, which is the first step in the behavioral change process. CONCLUSION Formal classroom instruction can be a factor in promoting healthful lifestyles through occupation. Such instruction can be an important step in empowering people to take responsibility for their own health.
Exploiting Molecular Mimicry: Defining Rules of the Game

Molecular mimicry has been touted as a mean to develop new generation of vaccines to target carbohydrate antigens on pathogens and on tumor cells. Structural and immunological rules governing molecular mimicry require definition for its successful exploitation. Of interest are the kinds of structures that peptides adopt as carbohydrate mimics, the extent to which topological or sequence similarities among peptide mimeotopes define serum cross-reactivity to carbohydrate antigens and the extent to which peptide mimeotopes affect T-cell responses. Rational design concepts can be applied to define how a peptide may mimic carbohydrate antigens, similarities in binding affinities of antibodies for carbohydrate and for peptides, how peptides can mimic core structures on otherwise dissimilar carbohydrate antigens, and how peptide mimeotopes can be used to manipulate cellular responses not achievable by carbohydrate antigens.
The role of prior experience in language acquisition.

Learners exposed to an artificial language recognize its abstract structural regularities when instantiated in a novel vocabulary (e.g., Gomez, Gerken, & Schvaneveldt, 2000; Tunney & Altmann, 2001). We asked whether such sensitivity accelerates subsequent learning, and enables acquisition of more complex structure. In Experiment 1, pre-exposure to a category-induction language of the form aX bY sped subsequent learning when the language is instantiated in a different vocabulary. In Experiment 2, while naive learners did not acquire an acX bcY language, in which aX and bY co-occurrence regularities were separated by a c-element, prior experience with an aX bY language provided some benefit. In Experiment 3 we replicated this finding with a 24-hour delay between learning phases, and controlled for prior experience with the aX bY language's prosodic and phonological characteristics. These findings suggest that learners, and the structure they can acquire, change as a function of experience.
Using the intraoperative hand held probe without lymphoscintigraphy or using only dye correlates with higher sensory morbidity following sentinel lymph node biopsy in breast cancer: A review of the literature

There are no studies that have directly investigated the incremental reduction in sensory morbidity that lymphoscintigraphy images (LS) and triangulated body marking or other skin marking techniques provide during sentinel lymph node biopsy (SLNB) compared to using only the probe without LS and skin marking or using only dye. However, an indirect assessment of this potential for additional sensory morbidity reduction is possible by extracting morbidity data from studies comparing the morbidity of SLNB to that of axillary lymph node dissection. A literature search yielded 13 articles that had data on sensory morbidity at specific time points on pain, numbness or paresthesia from SLNB that used radiotracer and probe or used only dye as a primary method of finding the sentinel node (SN). Of these, 10 utilized LS, while 3 did not utilize LS. By matching the data in studies not employing LS to the studies that did, comparisons regarding the percentage of patients experiencing pain, numbness/paresthesia after SLNB could be reasonably attempted at a cutoff of 9 months. In the 7 studies reporting on pain after 9 months (> 9 months) that used LS (1347 patients), 13.8% of patients reported these symptoms, while in the one study that did not use LS (143 patients), 28.7% of patients reported these symptoms at > 9 months (P 9 months that used LS (601 patients), 12.5% of patients reported these symptoms, while in the 3 studies that did not use LS (229 patients), 23.1% of patients reported these symptoms at > 9 months (P = 0.0002). Similar trends were also noted for all these symptoms at ≤ 9 months. Because of variations in techniques and time of assessing morbidity, direct comparisons between studies are difficult. Nevertheless at a minimum, a clear trend is present: having the LS images and skin markings to assist during SLNB appears to yield more favorable morbidity outcomes for the patients compared to performing SLNB with only the probe or performing SLNB with dye alone. These results are extremely pertinent, as the main reason for performing SLNB itself in the first place is to achieve reduced morbidity.
Land Tenure and the Adoption of Conservation Practices

We use a logit adoption model with data on 941 U.S. corn producers from the 1996 Agricultural Resource Management Study to analyze the influence of land tenure on the adoption of conservation practices. We extend previous analyses by distinguishing renters according to lease type and by distinguishing practices according to the timing of costs and returns. We find that cash-renters are less likely than owner-operators to use conservation tillage, but share-renters are not. Both cash-renters and share-renters are less likely than owner-operators to adopt practices that provide benefits only over the longer term (grassed waterways, stripcropping, and contour farming).
THE ROLE OF NAD+ DEPLETION IN THE MECHANISM OF SULFUR MUSTARD-INDUCED METABOLIC INJURY

Results of our previous studies on the chemical warfare agent sulfur mustard (2,2'-dichlorodiethyl sulfide) suggested that mustard-induced inhibition of glycolysis is not solely a function of NAD+ depletion. To define the role of NAD+ in mustard-induced metabolic injury, we examined the effects of mustard+/-niacinamide on energy metabolism in cultured human keratinocytes. Sulfur mustard caused concentration-dependent decreases in viable cell number and ATP content at 24 hours, but not earlier, and time- and concentration-dependent glycolytic inhibition and NAD+ depletion as early as 4 hours. Niacinamide partially protected NAD+ levels at all time points, but did not prevent adverse effects on glycolysis, intracellular ATP, or viable cell number. These results support our earlier conclusions and suggest that sulfur mustard may inhibit glycolysis directly.
The theory and method of comparative area studies

Though many now downplay the tension between area studies and disciplinary political science, there has been little substantive guidance on how to accomplish complementarity between their respective approaches. This article seeks to develop the idea of comparative area studies (CAS) as a rubric that maintains the importance of regional knowledge while contributing to general theory building using inductive intra-regional, cross-regional, inter-regional comparison. Treating regions as theoretically-grounded analytical categories, rather than inert or innate geographical entities, can help inform both quantitative and qualitative attempts to build general theory.
The Function of Television in Childhood Aggression

Considerable focus has been placed on the issue of whether television programs in general, and specifically programs with a high content of violent behavior, play a causal role in the aggressive and violent behavior of children and adolescents. Put most simply, the issue has been: “Does T.V. cause aggression and violence?” For those who were convinced that T.V. causes aggression and/or violence, the next issue became delineating the psychological mechanisms which accounted for the assumed causal link. Modeling, disinhibition, imitation, vicarious reinforcement, activation, and habituation, were invoked in various combinations by different theoreticians (Bogart, 1980).
Distance guided selection of the best base classifier in an ensemble with application to cervigram image segmentation

We empirically evaluate a distance-guided learning method embedded in a multiple classifier system (MCS) for tissue segmentation in optical images of the uterine cervix. Instead of combining multiple base classifiers as in traditional ensemble methods, we propose a Bhattacharyya distance based metric for measuring the similarity in decision boundary shapes between a pair of statistical classifiers. By generating an ensemble of base classifiers trained independently on separate training images, we can use the distance metric to select those classifiers in the ensemble whose decision boundaries are similar to that of an unknown test image. In an extreme case, we select the base classifier with the most similar decision boundary to accomplish classification and segmentation on the test image. Our approach is novel in the way that the nearest neighbor is picked and effectively solves classification problems in which base classifiers with good overall performance are not easy to construct due to a large variation in the training examples. In our experiments, we applied our method and several popular ensemble methods to segmenting acetowhite regions in cervical images. The overall classification accuracy of the proposed method is significantly better than that of a single classifier learned using the entire training set, and is also superior to other ensemble methods including majority voting, STAPLE, Boosting and Bagging.
ATGL-Catalyzed Lipolysis Regulates SIRT1 to Control PGC-1α/PPAR-α Signaling

Sirtuin 1 (SIRT1), an NAD+-dependent protein deacetylase, regulates a host of target proteins, including peroxisome proliferator–activated receptor (PPAR)-γ coactivator-1α (PGC-1α), a transcriptional coregulator that binds to numerous transcription factors in response to deacetylation to promote mitochondrial biogenesis and oxidative metabolism. Our laboratory and others have shown that adipose triglyceride lipase (ATGL) increases the activity of the nuclear receptor PPAR-α, a PGC-1α binding partner, to promote fatty acid oxidation. Fatty acids bind and activate PPAR-α; therefore, it has been presumed that fatty acids derived from ATGL-catalyzed lipolysis act as PPAR-α ligands. We provide an alternate mechanism that links ATGL to PPAR-α signaling. We show that SIRT1 deacetylase activity is positively regulated by ATGL to promote PGC-1α signaling. In addition, ATGL mediates the effects of β-adrenergic signaling on SIRT1 activity, and PGC-1α and PPAR-α target gene expression independent of changes in NAD+. Moreover, SIRT1 is required for the induction of PGC-1α/PPAR-α target genes and oxidative metabolism in response to increased ATGL-mediated lipolysis. Taken together, this work identifies SIRT1 as a critical node that links β-adrenergic signaling and lipolysis to changes in the transcriptional regulation of oxidative metabolism.
Cooling and Roughness Effects on Transition on Nozzle Throats and Blunt Bodies

Observations of boundary-laye r transition in a supersonic wind-tunnel nozzle throat were made in the region where the local Mach number increased from 0.4 to 2. The wall temperature ranged from adiabatic to 0.66 times the stagnation temperature, and its surface was roughened with random sand-grain, weave-type, and wire-screen roughness. It was found that wall cooling accelerates transition markedly regardless of surface conditions and that for a given height the random sand-type roughness is generally the most effective transition trigger. Transition location was much less sensitive to weave-type roughness and its orientation, although a drastic transition Reynolds number decrease was noted when the weave wavelength increased. With the roughness small or absent, phenomena involving boundary-layer relaminarization were observed. A substantial portion of these data cannot be accounted for by existing blunt-body boundary-layer transition correlations.
Nopp 140 shuttles on tracks between nucleolus and cytoplasm

Nopp140 is a nucleolar phosphoprotein of 140 kd that we originally identified and purified as a nuclear localization signal (NLS)-binding protein. Molecular characterization revealed a 10-fold repeated motif of highly conserved acidic serine clusters that contain an abundance of phosphorylation consensus sites for casein kinase II (CK II). Indeed, Nopp140 is one of the most phosphorylated proteins in the cell, and NLS binding was dependent on phosphorylation. Nopp140 was shown to shuttle between the nucleolus and the cytoplasm. Shuttling is likely to proceed on tracks that were revealed by immunoelectron microscopy. These tracks extend from the dense fibrillar component of the nucleolus across the nucleoplasm to some nuclear pore complexes. We suggest that Nopp140 functions as a chaperone for import into and/or export from the nucleolus.
Analysis of Thermal Stress Resistance of Partially Absorbing Ceramic Plate Subjected to Asymmetric Radiation, II: Convective Cooling at Front Surface

Thermal stresses in a partially absorbing brittle ceramic plate asymmetrically heated by radiation and cooled by convection on the same surface with finite and infinite heat transfer coefficients are analyzed. Comparison of the results from this study with those obtained in Part I, where the plate is subjected to radiation heating in the front surface and cooled by convection at the rear surface, indicates that the magnitudes of the maximum steady-state tensile thermal stresses are nearly identical. Significant differences are found in the transient thermal stresses and the temperature distribution. The relative temperature levels in the present case are found to be significantly lower than those obtained in Part I. Implications of these results to the design and operation of engineering structures such as concentrated solar receivers are discussed.
Results of recent experiments on cosmic rays

The paper presented a synopsis of the methods used and results obtained by the author and his associates, I. S. Bowen, R. M. Otis, and G. H. Cameron, in the investigations on high-frequency rays of cosmic origin (1) in sounding balloon observations at extreme altitudes, (2) by mountain-peak and airplane observations, and (3) by measurements in snow-fed lakes at high altitudes. Discharge rate of an electroscope at altitudes from 5 to 15.5 km.—Four specially designed instruments, each comprising a recording electroscope, thermometer, and barometer and each weighing but 190 gr., were sent up with sounding balloons from Kelly Field, Texas. Three were recovered, and of these two had satisfactory records of their flight, during which they reached altitudes of 11.2 and 15.5 km., respectively. A comparison of the recorded electroscope reading at the 5-km. level during ascent, with the reading at the same level, during descent, shows that the average discharge rate of the electroscope while between the 5-km. level and the 15.5-km. level was about three times its discharge rate at the surface of the earth, and corresponded in this particular instrument to an average rate of production of ions of 46.2 ions per cc. per sec. This is only 25 per cent of the value to be expected from the observations of Hess and of Kolhorster, and constitutes definite proof that there exists no penetrating radiation of cosmic origin having an absorption coefficient as large as 0.57 per meter of water.
Register file write data gating techniques and break-even analysis model

Register Files account for 30% of 32nm Intel WSM Core dynamic power of which 25% is due to write data distribution. We analyze Register File data gating strategies used to reduce write bitline dynamic power by as much as 96%. We explore the tradeoff of various data gating topologies (Global, Midway, Local), logic implementations (NAND, NOR, Tri-State), and techniques (Stack-Forcing, State-Forcing) to reduce both dynamic and leakage power. We then present a simple and accurate data gating break-even analysis model. The model comprehends "Data" and "Enable" switching activity, signal probability, logic implementation overhead, demonstrating an average error range of ±5%.
Optimizing File Retrieval in Delay-Tolerant Content Distribution Community

In WiFi-based content distribution community infrastructure (CDCI), file servers are deployed in diverse locations around cities, caching popular files interesting to a community. They serve file download requests from mobile users in proximity via WiFi. In this paper, we study the optimal caching strategy for file servers in CDCI so that the mean file retrieval probability within deadline is maximized, subject to storage capacity constraints of each file server. The optimal caching strategy depends on many factors, such as users' mobility patterns, access point topology, file popularity, etc. We have formalized this content management problem as a mixed integer optimization problem. Because of NPhardness and a large variable space of this optimization problem, we propose a heuristic algorithm MobaSsign to allocate file blocks. Extensive experiments show that our heuristic caching strategy considering mobility patterns improves the file retrieval probability within deadline.
Segregated graphs and marginals of chain graph models

Bayesian networks are a popular representation of asymmetric (for example causal) relationships between random variables. Markov random fields (MRFs) are a complementary model of symmetric relationships used in computer vision, spatial modeling, and social and gene expression networks. A chain graph model under the Lauritzen-Wermuth-Frydenberg interpretation (hereafter a chain graph model) generalizes both Bayesian networks and MRFs, and can represent asymmetric and symmetric relationships together. As in other graphical models, the set of marginals from distributions in a chain graph model induced by the presence of hidden variables forms a complex model. One recent approach to the study of marginal graphical models is to consider a well-behaved supermodel. Such a supermodel of marginals of Bayesian networks, defined only by conditional independences, and termed the ordinary Markov model, was studied at length in [6]. In this paper, we show that special mixed graphs which we call segregated graphs can be associated, via a Markov property, with supermodels of marginals of chain graphs defined only by conditional independences. Special features of segregated graphs imply the existence of a very natural factorization for these supermodels, and imply many existing results on the chain graph model, and the ordinary Markov model carry over. Our results suggest that segregated graphs define an analogue of the ordinary Markov model for marginals of chain graph models. We illustrate the utility of segregated graphs for analyzing outcome interference in causal inference via simulated datasets.
The differential migration of sterol acetates on silica gels and its application to the fractionation of sterol mixtures

SUMMARY The retention volumes of 12 sterol acetates relative to cholesteryl acetate were determined on four well-characterized silica gels of different body structure. These values illustrate the contribution of silica gel structure to the chromatographic process and permit the selection of appropriate gels for a given separation. The application of these values to the fractionation of model and biological mixtures of sterol acetates is illustrated.
Effects of food addition on life history of Yellow-Bellied Marmots

We provided two social groups with supplemental food for several years (River Colony, June 1996–August 2000 and Marmot Meadow, June 1998–August 2000) to examine the effects of food addition on life history characteristics of female Yellow-bellied Marmots (Marmota flaviventris). We compared demographic and life history characteristics of supplemented females and reference females living within the same colony but adjacent home ranges. Supplemental food did not increase growth rates during gestation and lactation; however, growth rates of supplemented mothers increased after young were weaned. There was no clear effect of food addition on survival rates, female recruitment, age of first reproduction, or reproductive effort, such as increased litter size or weaning masses of young. Social structure of yellow-bellied marmots is most likely the main factor influencing life-history characteristics and the role of food availability is minor.
Effects of intermittent tendon pressure on alpha motoneuron excitability.

The purpose of this study was to test the effectiveness of intermittent tendon pressure on the depression of alpha motoneuron excitability. The excitability changes of the motoneurons were assessed by measuring changes in H-reflex amplitudes before, during, and after intermittent tendon pressure application. Twenty-six of 28 subjects with no known neurological deficit displayed an immediate decrease in H-reflex amplitudes during tendon pressure (X = 73% of control values), which reached a maximum depression (45% of controls) within 20 to 30 seconds of application. The analysis of variance revealed significant differences (p less than .05), and post-hoc t tests indicated that these differences were between control values (prepressure and postpressure) and those values obtained at times 0, 5, 10, 20, and 30 seconds of pressure application. These results suggest that a maintained reduction in muscle tone might be induced through intermittent tendon pressure. Because we found no carry-over effects after pressure application, the usefulness of this technique is limited to the time during which the stimulus is presented.
Maskless Lithography and in situ Visualization of Conductivity of Graphene using Helium Ion Microscopy

The remarkable mechanical and electronic properties of graphene make it an ideal candidate for next generation nanoelectronics. With the recent development of commercial-level single-crystal graphene layers, the potential for manufacturing household graphene-based devices has improved, but significant challenges still remain with regards to patterning the graphene into devices. In the case of graphene supported on a substrate, traditional nanofabrication techniques such as e-beam lithography (EBL) are often used in fabricating graphene nanoribbons but the multi-step processes they require can result in contamination of the graphene with resists and solvents. In this letter, we report the utility of scanning helium ion lithography for fabricating functional graphene nanoconductors that are supported directly on a silicon dioxide layer, and we measure the minimum feature size achievable due to limitations imposed by thermal fluctuations and ion scattering during the milling process. Further we demonstrate that ion beams, due to their positive charging nature, may be used to observe and test the conductivity of graphene-based nanoelectronic devices in situ.
Bat species diversity at an urban-rural interface: Dominance by one species in an urban area

To investigate urbanization impacts on a midwestern bat community, we used 9 years of mist-net captures from 10 urban and rural sites on the southwestern edge of Indianapolis, IN, where the percentage of urbanized groundcover within 1.3 km of a net site ranged from 0% to 26%. We used Pearson correlation statistics to examine the effect of urban groundcover on each species’ abundance, and the Shannon-Wiener diversity index to quantify species diversity at the study area. To test the effect of urbanization on diversity, we used the percentage of urban groundcover and year to construct linear mixed-models. Eptesicus fuscus (Big Brown Bat) was the dominant species at all sites, regardless of degree of urbanization. Percent of urban groundcover was negatively related to bat-species diversity, although 1 species, Myotis septentrionalis (Northern Long-eared Bat), showed a positive correlation with urban groundcover. Perimyotis subflavus (Tri-colored Bat) and Myotis lucifugus (Little Brown Bat) displayed significant negative correlations with the percentage of urban groundcover. Myotis sodalis (Indiana Bat) had a negative but statistically insignificant correlation. These data provide land managers with further insight when planning future bat-mitigation strategies.
Genetic Differentiation among Mountain Pine Beetle Populations from Lodgepole Pine and Ponderosa Pine in Northeast Utah

Isozyme comparisons were made among mountain pine beetles (Dendroctonus ponderosae Hopkins) from 4 sites in NE Utah. Genetic differentiation was more closely associated with host tree species—lodgepole pine (Pinus contorta var. latifolia Engelmann) vs. ponderosa pine ( P. ponderosa Lawson)—than with geographic distances among sites. Differences in average heterozygosity and frequencies at certain gene loci may be related to stage in the infestation cycle or environmental stress related to food quantity. Differences were small between males and females at any one site but among sites males showed greater differences than did females. A difference in gene frequencies between early- and late-emerging beetles was found at one site.
The D.C. Bottle Bill Initiative: A Casualty of the Reagan Era

The purpose of this article is to describe the bottle bill initiative that occurred in the District of Columbia in 1986-1987, including a description of the historical and political background of the bottle bill movement in general, and to offer an analysis of why the D.C. initiative failed. The lessons gained from the experience in D.C. offer insights in how to improve environmental policy entrepreneurship.
Fine Needle Aspiration of Metastases to the Thyroid Gland: A Detailed Retrospective Cytomorphologic Study of 12 Cases

Thyroid malignancies are rare compared to benign tumors. Metastases to thyroid (MTs) are even rarer, comprising 1.4%-3% of all thyroid malignancies. MTs have no specific clinicoradiologic features to distinguish them from primary tumors. The difference is important for management implications. Fine needle aspiration (FNA) is 90% accurate for primary thyroid malignancies, but much less accurate for MTs (74%). We retrospectively identified 12 FNA …
Arch structure is associated with unique joint work, relative joint contributions and stiffness during landing.

Abstract To examine lower extremity joint contributions to a landing task in high-(HA) and low-arched (LA) female athletes by quantifying vertical stiffness, joint work and relative joint contributions to landing. Methods Twenty healthy female recreational athletes (10 HA and 10 LA) performed five barefoot drop landings from a height of 30 cm. Three-dimensional kinematics (240 Hz) and ground reaction forces (960 Hz) were recorded simultaneously. Vertical stiffness, joint work values and relative joint work values were calculated using Visual 3D and MatLab. Results HA athletes had significantly greater vertical stiffness compared to LA athletes (p = 0.013). Though no differences in ankle joint work were observed (p = 0.252), HA athletes had smaller magnitudes of knee (p = 0.046), hip (p = 0.019) and total lower extremity joint work values (p = 0.016) compared to LA athletes. HA athletes had greater relative contributions of the ankle (p = 0.032) and smaller relative contributions of the hip (p = 0.049) compared to LA athletes. No differences in relative contributions of the knee were observed (p = 0.255). Conclusions These findings demonstrate that aberrant foot structure is associated with unique contributions of lower extremity joints to load attenuation during landing. These data may provide insight into the unique injury mechanisms associated with arch height in female athletes.
Responses to injured conspecifics and heterospecifics by water fleas, Chydorus sphaericus

AbstractCladocerans have been shown to exhibit a variety of responses to chemical stimuli associated with predation risk, including those from predators and injured conspecifics. In this study, we tested the hypothesis that individuals of Chydorus sphaericus would respond with avoidance behavior to chemical cues from both injured conspecifics and injured heterospecifics. Avoidance behavior was seen in response to cues from C. sphaericus and Daphnia magna. Responses to cues from Daphnia pulex were intermediate between those of the other cues and the water control. We propose that a concentration effect may be responsible for the mixed responses to heterospecific cues and speculate that responses to a broad range of cues may help explain the expansive range of C. sphaericus.
Spatial Mismatch: Understanding Differences in Income Mobility Between Cities

Why do some American cities appear to be havens of opportunity while others remain stratified? Recent studies illustrate large differences in intergenerational income mobility between American cities, especially for low-income individuals. These differences are difficult to explain through economic productivity alone – for example, some booming cities, like Atlanta, GA and Columbus, OH, exhibit low levels of income mobility. I argue that differences in city policy are at the root of disparities in income mobility. In particular, I examine the effect of accessible public transportation on income mobility. Drawing upon sociologist William Julius Wilson’s “spatial mismatch” hypothesis, I make a case that physical separation from jobs perpetuates intergenerational poverty, and that effective public transportation alleviates this separation. New data allows me to test this nationally. I conduct my analysis in two parts: First, a national statistical study of urban intergenerational income mobility from 1980 to 1996, using public transit accessibility as an explanatory variable. Second, a case study of the politics of public transportation in Columbus, OH, using elite interviews and historical sources. Synthesizing these two parts, I argue that public transit's social efficacy depends on the structure of local institutions: In cities with fewer veto points for regional planning and greater municipal fiscal autonomy, local governments are more likely to prioritize democratic goals in transit planning over technocratic ones. At the same time, citizen support is essential: City governments are more responsive to demands for public transit when there is a confluence of interests between social classes in its favor.
SOE Reform: Time for Serious Corporate Governance

This policy paper is motivated by the Government’s “Pakistan: Framework for Economic Growth (FEG) 2011” which places weak corporate governance at the top of the “software” constraints to growth. The efforts to reform the State-Owned Enterprises (SOEs) have stalled in Pakistan for almost five years—with significant negative implications not only in terms of fiscal losses, but also deteriorated and cost-ineffective service delivery. The paper suggests a number of urgent policy measures designed to improve the efficiency and effectiveness of SOEs. These include basic governance reforms, revamped commercialization processes and enhanced market regulations. The paper also provides some perspectives on international experience on SOE reforms combined with some suggestions on how the Government can move forward. The Policy Working Paper Series disseminates the findings of work in progress to encourage the exchange of ideas about development issues. An objective of the series is to get the findings out quickly, even if the presentations are less than fully polished. The papers carry the names of the authors and should be cited accordingly. The findings, interpretations, and conclusions expressed in this paper are entirely those of the authors. They do not necessarily represent the views of the International Bank for Reconstruction and Development / World Bank and its affiliated organizations, or those of the Executive Directors of the World Bank or the governments they represent. SOE Reform: Time for Serious Corporate Governance
Toll-like receptor 9 antagonizes antibody affinity maturation.

Key events in T cell–dependent antibody responses, including affinity maturation, are dependent on the B cell’s presentation of antigen to helper T cells at critical checkpoints in germinal-center formation in secondary lymphoid organs. Here we found that signaling via Toll-like receptor 9 (TLR9) blocked the ability of antigen-specific B cells to capture, process and present antigen and to activate antigen-specific helper T cells in vitro. In a mouse model in vivo and in a human clinical trial, the TLR9 agonist CpG enhanced the magnitude of the antibody response to a protein vaccine but failed to promote affinity maturation. Thus, TLR9 signaling might enhance antibody titers at the expense of the ability of B cells to engage in germinal-center events that are highly dependent on B cells’ capture and presentation of antigen. The presentation of antigen by germinal-center B cells to follicular T cells engenders the process of antibody affinity maturation and humoral memory. Pierce and colleagues show that TLR9 signaling in B cells antagonizes B cell–mediated antigen presentation, which leads to the enhanced generation of short-lived plasma cells and the production of lower-affinity antibodies.
Two important periods in the history of mechanochemistry

Some form of mechanochemical experience has existed from fine grinding of materials since prehistoric times, yet the first systematic investigations on the chemical effects of mechanical action were carried out only at the end of the nineteenth century. Walthere Spring studied the consolidation and reactions of powdered materials due to high pressure at the University of Liege, in order to understand the formation of minerals in the earth’s crust and M. Carey Lea carried out experiments on the decomposition of compounds by grinding in a mortar. In some of his experiments mechanical action produced distinctly different result from the effect of heat. The first part of this paper compares the circumstances and results of Spring and Lea. The other important period in the history of mechanochemistry was the 1960s, the time when the first dedicated conferences were organized and a broader community of mechanochemists formed. This happened in the Soviet Union and Eastern Europe where several groups were working on subjects related to mechanochemistry. In 1968, the first dedicated conference was organized as a special session of the yearly meeting of Soviet colloid chemists. An attempt is made to reconstruct the circumstances leading to that event and the roles played by Rebinder and Thiessen in bringing it together. The next conference on mechanochemistry was already a separate event and it started a yearly series. Extensions have led to the INCOME conferences, including this one in Kosice in 2017.
What are we missing? Scope 3 greenhouse gas emissions accounting in the metals and minerals industry

Metal and mineral companies have significant greenhouse gas emissions in their upstream and downstream value chains due to outsourced extraction, beneficiation and transportation activities, depending on a firm’s business model. While many companies move towards more transparent reporting of corporate greenhouse gas emissions, value chain emissions remain difficult to capture, particularly in the global supply chain. Incomplete reports make it difficult for companies to track emissions reductions goals or implement sustainable supply chain improvements, especially for commodity products that form the base of many other sector’s value chains. Using voluntarily-reported CDP data, this paper sheds light on hotspots in value chain emissions for individual metal and mineral companies, and for the sector as a whole. The state of value chain emissions reporting for the industry is discussed in general, with a focus on where emissions could potentially be underestimated and how estimates could be improved.
CHAPTER 13 – Economics and Market for Biosensors

Biosensors seem to offer tremendous potential in their application to different and ever-expanding areas. Both the academic and industrial sectors have realized this and are gradually putting more and more resources in this area. As in all research and development areas, one has to keep the economic aspects in focus. Universities with their culture of openness and their emphasis on research publish findings quickly in the open literature but tend to pay scant attention to economic aspects. Industrial organizations may be expected to undertake a careful and thorough evaluation of economic and other aspects before investing in biosensors. Such information is jealously guarded. In particular, economic forecasting organizations and trade groups which collect such information consider it a source of income. Thus very little reliable economic information on biosensors is available in the open literature. More information needs to be made available so that it can be used in the future development of biosensors.
Issues in the history of computing

It should be easy to do the history of computing. After all, computing began less than 50 years ago, and we have crowds of eye witnesses, mountains of documents, storerooms of original equipment, and the computer itself to process all the information those sources generate. What's so hard? What are we missing?
Special Considerations in Common GI Diseases, Obesity, and Following Bariatric Surgery

Contrary to popular belief, obesity is not good for bones nor is it protective against the development of osteoporosis. Common consequences of obesity such as type 2 diabetes mellitus, and several of the common medications used to treat elevated blood glucose significantly increase the risk of osteoporosis and fragility fracture.
Ruggedized peptide receptors for soldier health and performance monitoring

As the Army moves towards equipping the soldier with more advanced wearable sensing devices for real-time environmental, health, and performance monitoring, there is a significant need for the biological receptors integrated into such devices capable of consistent performance in multifaceted operational environments. The instability, long development times, and inconsistencies in production of monoclonal antibodies, the gold standard receptors for biological detection, has resulted in the advent of alternative antibody technologies to fill these technological gaps. Protein Catalyzed Capture (PCC) agent technology is capable of the bottom-up development of highly stable and tailorable receptors through iterative in situ ‘click’ chemistry cycles with one-bead-one-compound (OBOC) peptide libraries. Aside from the inherent thermal stability and binding performance comparable to, and oftentimes exceeding, monoclonal antibodies, the modularity of PCCs allows for easy integration into various detection platforms and assays. Capable of full receptor development in ~2 weeks, as highlighted in this proceeding, PCCs can fulfill the need for alternative antibodies by addressing critical gaps in adaptability, manufacturability, and stability.
Regulation of tau’s proline rich region by its N-terminal domain

Abstract Tau is an intrinsically disordered, microtubule-associated protein with a role in regulating microtubule dynamics. Despite intensive research, the molecular mechanisms of taumediated microtubule polymerization are poorly understood. Here we use single molecule fluorescence to investigate the role of tau’s N-terminal domain (NTD) and proline rich region (PRR) in regulating interactions of tau with soluble tubulin. Both full-length tau isoforms and truncated variants are assayed for their ability to bind soluble tubulin and stimulate microtubule polymerization. We describe a novel role for tau’s PRR as an independent tubulin-binding domain with polymerization capacity. In contrast to the relatively weak tubulin interactions distributed throughout the microtubule binding repeats (MTBR), resulting in heterogeneous tau:tubulin complexes, the PRR binds tubulin tightly and stoichiometrically. Moreover, we demonstrate that interactions between the PRR and MTBR are reduced by the NTD through a conserved conformational ensemble. Based on our data, we propose that tau’s PRR can serve as a core tubulin-binding domain, while the MTBR enhances polymerization capacity by increasing the local tubulin concentration. The NTD negatively regulates tubulin-binding interactions of both of these domains. This study draws attention to the central role of the PRR in tau function, as well as providing mechanistic insight into tau-mediated polymerization of tubulin. Significance Statement Tau is an intrinsically disordered, microtubule associated protein linked to a number of neurodegenerative disorders. Here we identify tau’s proline rich region as having autonomous tubulin binding and polymerization capacity, which is enhanced by the flanking microtubule binding repeats. Moreover, we demonstrate that tau’s N-terminal domain negatively regulates both binding and polymerization. We propose a novel model for tau-mediated polymerization whereby the proline rich region serves as a core tubulin-binding domain, while the microtubule binding repeats increase the local concentration. Our work draws attention to the importance of the proline rich region and N-terminal domain in tau function, and highlights the proline rich region as a putative target for the development of therapeutics.
A paradox or a challenge

Sepesi et al . (1) found in a large retrospective series that higher body mass index (BMI) was associated with improved overall survival in patients undergoing surgical resection of non-small cell lung cancer (NSCLC). Is this a paradox? “Paradox” is a rhetorical, not a scientific, term (2). Unfortunately, the term obesity paradox has entered into the medical vocabulary while simultaneously becoming less and less clearly defined. By now, the term is used to refer to almost anything that suggests improved outcomes associated with obesity. The underlying assumption is that any better outcome related to obesity is ipso facto surprising and counterintuitive and thus considered a “paradox”.
The Chloroprocaine Controversy: II. Is Chloroprocaine Neurotoxic?

The preceding report (page 124) indicated that the use of chloroprocaine (2CP) for epidural anesthesia is not excessively hazardous if certain precautions are observed. We find in this report that 2CP is a safe local anesthetic drug. Severe neurodysfunction occurs in the isolated nerve when exposed to Nesacaine, the commercial 2CP preparation, which contains the additive sodium bisulfite (as an antioxidant) at low pH. We ascribe nerve function failure to the low intracellular pH resulting from SO2 diffusion into the cell followed by hydration to H2SO3. The molecular SO2 is liberated from bisulfite at low pH. The SO2 concentration is dependent on the bisulfite concentration and the degree of pH depression. Application of the factors presented above, plus the factor of spinal compliance presented in the previous report, explains most of the paradoxical findings reported from other laboratories in the “chloroprocaine controversy.”
Reducing Time to Pain Medication Administration for Pediatric Patients with Long Bone Fractures in the Emergency Department.

Introduction Pain management is a critical aspect of effective long bone fracture treatment. Pediatric patients frequently report suboptimal pain management, which is an area of growing public concern. The purpose of this quality improvement project was to develop a protocol with the goal to administer pain medication to children presenting with suspected long bone fractures ≤47 minutes of emergency department arrival. Methods A multidisciplinary team developed a standardized protocol for pain management of patients presenting with musculoskeletal pain utilizing acetaminophen as the first-line agent under a nurse-initiated order. Following education and implementation, weekly reports generated using the International Classification of Diseases codes of fractures were reviewed to assess compliance with the protocol. This study evaluates the frequency of a second pain medication administration and reduction in vital signs and pain scores. Results Implementation of a pain management protocol reduced median time to pain medication administration to 26 minutes. Overall, 63% (n = 638) of patients required a second pain medication. Of these, 66.5% (348/523) who initially received acetaminophen and 59.7% (286/479) who initially received an opioid required a second pain medication. No significant changes in pre and posttreatment vital signs were found between groups. Patients who initially received opioids experienced a greater reduction in posttreatment pain scores. Conclusions Using a standardized pain management protocol in combination with comprehensive education effectively reduces median time to pain medication administration in pediatric patients with long bone fractures. Acetaminophen is a rapid and effective first-line agent for managing pain in this population.