Miracle-dz/UniFAR-FTUs huggingface dataset:
Intra- and Intersubtype Alternative Pak2-Activating Structural Motifs of Human Immunodeficiency Virus Type 1 Nef

ABSTRACT The design of antiviral strategies against human immunodeficiency virus type 1 (HIV-1) has been largely derived from studies of subtype B viruses, although they constitute only 12% of infections worldwide. At 50% of all HIV-1 infections worldwide, subtype C viruses are the most predominant. Here, we present evidence that subtype C Nefs display functional Pak2-activating motifs that differ from those found in subtype B and E Nefs. The identification of multiple Pak2-activating structural motifs that singly affect one Nef activity revealed a functional plasticity that has implications for future drug and vaccine design aimed at HIV-1 Nef and its effects on the deregulation of the immune system.
Lack of an effect of sodium zeolite A on rat tibia histomorphometry

Cell culture studies suggest that the aluminum silicate polymer sodium Zeolite A (SZA) increases bone cell proliferation and extracellular matrix production. This study in rats investigated the short‐term (2 weeks) and long‐term (18 weeks) in vivo effects of SZA on growth rate (weight gain) and tibia histomorphometry. In separate short‐term experiments, female (experiment 1) or male (experiment 2) Sprague‐Dawley rats grown and maintained on normal calcium diets were gavaged daily during a 2 week treatment period with 30 mg/kg, 100 mg/kg, or 500 mg of SZA/kg of rat body weight. In the long‐term study (experiment 3) ovariectomized (OVX) rats were fed a low calcium diet containing 0, 1.80, and 9.00 g of SZA/kg of diet (0, 125, and 617 mg/kg of body weight, respectively). Short‐ and long‐term treatment of growing rats with SZA resulted in a dose‐dependent increase in bone aluminum. In the first experiment, growing intact female rats showed no significant SZA dose‐dependent response in growth rate (weight gain) or histomorphometry of cortical bone in the tibial diaphysis or cancellous bone in the secondary spongiosa of the tibial metaphysis. In the second experiment, growing male rats, with right hind limbs immobilized by unilateral sciatic neurotomy, showed no SZA dose‐dependent response in growth rate. The longitudinal growth of cancellous bone in the tibia of the denervated limb and the intact contralateral limb were not influenced by sciatic neurectomy and/or by treatment with SZA. Histomorphometry demonstrated that cortical bone mass and formation was reduced in the sciatic‐sectioned limb when compared with the contralateral intact limb of vehicle‐treated rats, as evidenced by significant reductions in static measurements of cortical bone area (‐8.5%) and cross‐sectional area (‐4.8%) and in calculations of the periosteal formation rate (‐33.8%) and mineral apposition rate (‐31.6%), and the endocortical formation rate (‐35.5%) and mineral apposition rate (‐37.9%). The cancellous bone mass of denervated limbs of vehicle‐treated rats was also deficient, as evidenced by decreased cancellous bone area (‐39.1%) and perimeter (‐31.9%). The bone mineral apposition rate was decreased (‐26.7%) indicating reduced osteoblast activity. Treatment with SZA did not influence these indices in the tibiae of either sciatic‐sectioned limbs or contralateral intact limbs. In the long‐term experiment, OVX resulted in a dramatic 88% decrease in cancellous bone volume which was prevented by treatment with 17/β‐estradiol and not influenced by treatment with Zeolite A. The increases in osteoblast and osteoclast number following OVX were not influenced by SZA. The results indicate that SZA treatment has no anabolic effect on cortical and cancellous bone formation and mass in normal growing female rats and that this compound does not protect against osteopenia due to reduced load bearing in the growing male rat or gonadal hormone deficiency in adult female rats.
Author ' s personal copy Life cycle energy analysis of fiber-reinforced composites

Life cycle assessment is a technique to assess environmental aspects associated with a product or process by identifying energy, materials, and emissions over its life cycle. The energy analysis includes four stages of a life cycle: material production phase, manufacturing phase, use phase, and end-of-life phase. In this study, the life cycle energy of fiber-reinforced composites manufactured by using the pultrusion process was analyzed. For more widespread use of composites, it is critical to estimate how much energy is consumed during the lifetime of the composites compared to other materials. In particular, we evaluated a potential for composite materials to save energy in automotive applications. A hybrid model, which combines process analysis with economic input–output analysis, was used to capture both direct and indirect energy consumption of the pultrusion process in the material production and manufacturing stages. 2009 Elsevier Ltd. All rights reserved.
Anatomical study of the final common pathway for vocalization in the cat

Vocalization, the nonverbal production of sound, can be elicited in many vertebrates by stimulation in several regions of the limbic system but most easily in the caudal periaqueductal gray (PAG). This study shows that a specific cell group in the lateral part of the caudal PAG and in the tegmentum just lateral to it projects bilaterally to the nucleus retroambiguus (NRA) in the caudal medulla oblongata. Similar but much weaker projections are derived from the dorsal PAG. Neurons in the NRA in turn project via a contralateral pathway through the ventral funiculus of the spinal cord to motoneuronal cell groups, innervating intercostal and abdominal muscles. These projections are stronger on the contralateral side, although at lower thoracic and upper lumbar levels, many fibers recross to terminate in the ipsilateral motoneuronal cell groups. In the brainstem NRA neurons project to the motoneuronal cell groups innervating mouth‐opening and perioral muscles as well as to motoneurons innervating the pharynx, soft palate, and tongue, and probably to the larynx. All these muscles are active in vocalization. The present anatomical results, combined with the physiological results of others, indicate that the projections from PAG via NRA to vocalization motoneurons from the final common pathway in vocalization. The role of this pathway in the total framework of emotional behavior is discussed.
Infectious mononucleosis: detection of herpeslike virus and reticular aggregates of small cytoplasmic particles in continuous lymphoid cell lines derived from peripheral blood.

Although an etiologic agent has not been isolated and identified, infectious mononucleosis has long been suspected to be an infectious disease, presumably of viral etiology. This concept is further supported by certain epidemiological features of the disease and by the nature of the acute illness. Recently, cytomegalovirus,l myxovirus,2 and the herpeslike virus (HLV)3 have all been implicated in the pathogenesis of this disease in man. In ultrastructural studies of circulating atypical lymphocytes from patients with infectious mononucleosis4 and of lymphoblastoid cells derived from bone marrow cultures of infectious mononucleosis patients,5 viral particles could not be demonstrated. Recent reports from several laboratories have revealed that circulating cells from the peripheral blood of patients with infectious mononucleosis have the potential for long-term proliferation in vitro.6 In this laboratory, 16 suspension cultures from nine patients with heterophile-positive infectious mononucleosis have been obtained in continuous culture. These established cell lines have been shown to synthesize immunoglobulin,7 to produce interferon,8 and to have chromosomal abnormalities similar to those consistently found in cultured cells derived from Burkitt's lymphoma.9 In the course of studying the fine structural features of these cell lines, viruslike particles have been detected and identified. In the present communication the results of these findings will be reported. Materials and Methods. -Sixteen continuous suspension cultures were established from nine patients with heterophile-positive infectious mononucleosis (Table 1) by means of techniques which have been described previously.6 Samples of cell suspensions were examined periodically for the presence of microbial agents. 0 In each instance, cell lines were found to be free of detectable viruses, bacteria, fungi, mycoplasma, and endotoxins. From nine patients with infectious mononucleosis, 14 cultures were processed for electron microscopy (Table 2). As controls, other continuous cultures from peripheral blood were processed collaterally-one from a patient with lymphoblastic leukemia and another from a patient with leukocytosis of unknown etiology. In addition, thoracic duct and peripheral blood cultures from. a patient with hyperglobulinemia of unknown etiology, buffy coats from the peripheral blood of six patients with infectious mononucleosis, and those from three clinically healthy individuals were also examined. Four of the contin-
Joint formation in dissimilar Al alloy/steel and Mg alloy/steel friction stir spot welds

The microstructural features and overlap shear strength properties of friction stir spot welds made between Al 6111 and low carbon steel, and between Mg alloy AM60 and DP600 dual phase steel, are investigated. When Al 6111 is the upper sheet in the dissimilar sandwich, completed spot welds show evidence of intermetallic layer formation and cracking. Increasing tool pin penetration into the lower sheet provided increased mechanical interlocking of the sheets due to clinching. However, increasing penetration also promoted intermetallic formation and cracking in completed welds. However, dissimilar AM60/DP600 steel friction stir spot welds produced with AM60 as the upper sheet in the dissimilar sandwich do not show evidence of intermetallic formation and cracking may be avoided by removing the zinc coating on the DP600 steel before the friction stir spot welding operation.
Sintering theory and practice

Sintering Measurement Techniques. Solid-State Sintering Fundamentals. Microstructure and Processing Relations in Solid-State Sintering. Solid-State Sintering of Mixed Powders. Liquid-Phase Sintering. Pressure-Assisted Sintering. Novel Sintering Techniques. Sintering Atmospheres. Sintering Practice. Future Directions. Appendix. Index.
LIBRUS: combined machine learning and homology information for sequence-based ligand-binding residue prediction

MOTIVATION Identifying residues that interact with ligands is useful as a first step to understanding protein function and as an aid to designing small molecules that target the protein for interaction. Several studies have shown that sequence features are very informative for this type of prediction, while structure features have also been useful when structure is available. We develop a sequence-based method, called LIBRUS, that combines homology-based transfer and direct prediction using machine learning and compare it to previous sequence-based work and current structure-based methods. RESULTS Our analysis shows that homology-based transfer is slightly more discriminating than a support vector machine learner using profiles and predicted secondary structure. We combine these two approaches in a method called LIBRUS. On a benchmark of 885 sequence-independent proteins, it achieves an area under the ROC curve (ROC) of 0.83 with 45% precision at 50% recall, a significant improvement over previous sequence-based efforts. On an independent benchmark set, a current method, FINDSITE, based on structure features achieves an ROC of 0.81 with 54% precision at 50% recall, while LIBRUS achieves an ROC of 0.82 with 39% precision at 50% recall at a smaller computational cost. When LIBRUS and FINDSITE predictions are combined, performance is increased beyond either reaching an ROC of 0.86 and 59% precision at 50% recall. AVAILABILITY Software developed for this study is available at http://bioinfo.cs. umn.edu/supplements/binf2009 along with Supplementary data on the study.
Data Layout Transformation for Enhancing Data Locality on NUCA Chip Multiprocessors

With increasing numbers of cores, future CMPs (Chip Multi-Processors) are likely to have a tiled architecture with a portion of shared L2 cache on each tile and a bank-interleaved distribution of the address space. Although such an organization is effective for avoiding access hot-spots, it can cause a significant number of non-local L2 accesses for many commonly occurring regular data access patterns. In this paper we develop a compile-time framework for data locality optimization via data layout transformation. Using a polyhedral model, the program's localizability is determined by analysis of its index set and array reference functions, followed by non-canonical data layout transformation to reduce non-local accesses for localizable computations. Simulation-based results on a 16-core 2D tiled CMP demonstrate the effectiveness of the approach. The developed program transformation technique is also useful in several other data layout transformation contexts.
Short-term memory and working memory as indices of children's cognitive skills

In the current literature, empirical and conceptual distinctions have been drawn between a more or less passive short-term memory (STM) system and a more dynamic working memory (WM) system. Distinct tasks have been developed to measure their capacity and research has generally shown that, for adults, WM, and not STM, is a reliable predictor of general cognitive ability. However, the locus of the differences between the tasks has received little attention. We present data from children concerning measures of matrices reasoning ability, reading, and numerical skill along with forward and backward order serial recall of WM, STM, and STM with articulatory suppression tasks. As indices of children's cognitive skills, STM and WM are shown to be rather similar in terms of memory per se. Neither the opportunity for rehearsal nor task complexity provides satisfactory explanations for differences between memory tests.
Cyclic changes in carbohydrate concentrations during hibernation in the arctic ground squirrel.

GALSTER, WILLIAM A. , AND PETER MORRISON. Cyclic changes in carbohydrate concentrations during hibernation in the arctic ground squirrel. Am. J. Physiol. 218(4): 1228-1232. 1970. -Blood samples from right ventricular cannulas and tissues were collected from arctic ground squirrels during summer and winter. Average plasma glucose (mg/ml) and tissue glycogen (mg/g) values from ‘Cunexcited” fasted ground squirrels in summer (plasma, 0.85; liver, 17.8; thigh muscle, 4.5; kidney, 0.2; heart, 0.8; and brown fat, 0.1) were not significantly different from values in nonhibernating squirrels during winter. Results in hibernating squirrels were correlated with the time in hibernation since the previous arousal. In the first one-fifth of each hibernation period, average values for liver glycogen did not change, but values in the other tissues and plasma glucose were doubled. Plasma glucose, and glycogen in liver and thigh muscle declined steadily during each hibernation period, but glycogen concentrations in kidney, brown fat, and heart did not change. Values at the end of the hibernation period approached 0.5 mg/ml (plasma), 5.0 mg/g (liver) and 4.0 mg/g (thigh muscle). These tissues appear to represent a glucose “pool,” one-half of which is utilized during each of the hibernation periods and restored during each active period. It is suggested that these declines, and particularly that in plasma glucose, may directly initiate arousal in this species.
A probabilistic approach to buffer insertion

This work presents a formal probabilistic approach for solving optimization problems in design automation. Prediction accuracy is very low especially at high levels of design flow. This can be attributed mainly to unawareness of low level layout information and variability in fabrication process. Hence a traditional deterministic design automation approach where each cost function is represented as a fixed value becomes obsolete. A new approach is gaining attention in which the cost functions are represented as probability distributions and the optimization criteria is probabilistic too. This design optimization philosophy is demonstrated through the classic buffer insertion problem. Formally, we capture wirelengths as probability distributions (as compared to the traditional approach which considers wirelength as fixed values) and present several strategies for optimizing the probabilistic criteria. During the course of this work many problems are proved to be NP-Complete. Comparisons are made with the Van-Ginneken "optimal under fixed wire-length" algorithm. Results show that the Van-Ginneken approach generated delay distributions at the root of the fanout wiring tree which had large probability (0.91 in the worst case and 0.55 on average) of violating the delay constraint. Our algorithms could achieve 100% probability of satisfying the delay constraint with similar buffer penalty. Although this work considers wirelength prediction inaccuracies, our probabilistic strategy could be extended trivially to consider fabrication variability in wire parasitics.
The Cactus Worm: Experiments with Dynamic Resource Discovery and Allocation in a Grid Environment

The ability to harness heterogeneous, dynamically available grid resources is attractive to typically resource-starved computational scientists and engineers, as in principle it can increase, by significant factors, the number of cycles that can be delivered to applications. However, new adaptive application structures and dynamic runtime system mechanisms are required if we are to operate effectively in grid environments. To explore some of these issues in a practical setting, the authors are developing an experimental framework, called Cactus, that incorporates both adaptive application structures for dealing with changing resource characteristics and adaptive resource selection mechanisms that allow applications to change their resource allocations (e.g., via migration) when performance falls outside specified limits. The authors describe the adaptive resource selection mechanisms and describe how they are used to achieve automatic application migration to “better” resources following performance degradation. The results provide insights into the architectural structures required to support adaptive resource selection. In addition, the authors suggest that the Cactus Worm affords many opportunities for grid computing.
Recent Advances in Chiral Nematic Structure and Iridescent Color of Cellulose Nanocrystal Films

One unique property of cellulose nanocrystals (CNC) is their property of forming suspensions with chiral nematic order. This order can be preserved in films cast from the suspensions, raising the possibility of applications as photonic materials and templates. However, it has proved difficult to generate uniform, well-ordered chiral nematic materials from CNC. Recently, the importance of kinetic arrest due to gel formation in the later stages of evaporation has been recognized as a key step in film formation. In this brief review, recent developments regarding the structure of chiral nematic suspensions and films as monitored by polarized light microscopy are outlined, and attention is drawn to the importance of shear forces on the self-organization process.
Properties of rapidly dissolving eutectic mixtures of poly(ethylene glycol) and fenofibrate: the eutectic microstructure.

Poly(ethylene glycol) or PEG is an ideal inactive component for preparing simple binary eutectic mixtures because of its low entropy of fusion ( approximately 0.0076 J/mol-K), lower melting point (approximately 62 degrees C) compared to most pharmaceuticals, miscibility with drugs at elevated temperatures, and its covalent crystalline lattice. Implication of these physicochemical properties on eutectic crystallization and size reduction of the drug is discussed. Enhancement of the dissolution rate of a poorly soluble compound through the formation of PEG-drug eutectics was investigated using fenofibrate. Solid dispersions of PEG-fenofibrate when characterized, revealed that PEG and fenofibrate form a simple eutectic mixture containing 20-25%(w/w) fenofibrate at the eutectic point. Eutectic crystallization led to the formation of an irregular microstructure in which fenofibrate crystals were found to be less than 10 microm in size. Dissolution rate improvement of fenofibrate correlated with the phase diagram, and the amount of fenofibrate released from the dispersions that contained fenofibrate as a eutectic mixture was at least 10-fold higher compared to untreated fenofibrate. On aging, the dissolution rate of the dispersion containing 15%(w/w) fenofibrate in PEG remained unaltered. The results indicate that PEG-drug eutectic formation is a valuable option for particle size reduction and subsequent dissolution rate improvement.
Navigating with landmarks: computing goal locations from places codes

A computer model of rodent navigation, based on coupled mechanisms for place recognition, path integration, and maintenance of head direction, o ers a way to operationally combine constraints from neurophysiology and behavioral observation. We describe how one such model reproduces a variety of experiments by Collett, Cartwright, and Smith [6] in which gerbils learn to nd a hidden food reward, guided by an array of visual landmarks in an open arena. We also describe some neurophysiological predictions of the model; these may soon be veri ed experimentally. Portions of the model have been implemented on a mobile robot.
An analogue of Serre's conjecture for Galois representations and Hecke eigenclasses in the mod p$ co

The conjecture of Serre referred in the title is the one about modularity of odd Galois representations into GL(2,F) where F is a finite field of characteristic p. We present an analogous conjecture where GL(2) is replaced by GL(n). We explain the analogue of "oddness. " We then present some theoretical and experimental evidence for the conjecture, primarily when n = 3. Our conjecture does not require the Galois representation to be irreducible. Our most interesting examples involve the sum of an irreducible even 2-dimensional representation and a 1-dimensional representation.
Keep Calm and Carry On: Exploring the Social Determinants of Indoor Environment Quality

Poor Indoor Environment Quality (IEQ) in office environments leads to worker discomfort and lost productivity. This paper provides a unique perspective into the specifically social determinants of IEQ in naturally ventilated offices and our work toward designing technology that might improve it. Based on 15 qualitative interviews we explore the rituals, practices and negotiations involved in opening windows and thermostat adjustment. We find that a wish to maintain status quo results in workers putting up with discomfort with IEQ factors well before requesting a change. In closing, we introduce our future design work aimed at drawing attention to existing office practices and encouraging a broader participation in negotiations around IEQ factors in the workplace.