Miracle-dz/UniFAR-FTUs huggingface dataset:
Pull-out strength of cemented solid versus fenestrated pedicle screws in osteoporotic vertebrae

Objectives Cement augmentation of pedicle screws could be used to improve screw stability, especially in osteoporotic vertebrae. However, little is known concerning the influence of different screw types and amount of cement applied. Therefore, the aim of this biomechanical in vitro study was to evaluate the effect of cement augmentation on the screw pull-out force in osteoporotic vertebrae, comparing different pedicle screws (solid and fenestrated) and cement volumes (0 mL, 1 mL or 3 mL). Materials and Methods A total of 54 osteoporotic human cadaver thoracic and lumbar vertebrae were instrumented with pedicle screws (uncemented, solid cemented or fenestrated cemented) and augmented with high-viscosity PMMA cement (0 mL, 1 mL or 3 mL). The insertion torque and bone mineral density were determined. Radiographs and CT scans were undertaken to evaluate cement distribution and cement leakage. Pull-out testing was performed with a material testing machine to measure failure load and stiffness. The paired t-test was used to compare the two screws within each vertebra. Results Mean failure load was significantly greater for fenestrated cemented screws (+622 N; p ⩽ 0.001) and solid cemented screws (+460 N; p ⩽ 0.001) than for uncemented screws. There was no significant difference between the solid and fenestrated cemented screws (p = 0.5). In the lower thoracic vertebrae, 1 mL cement was enough to significantly increase failure load, while 3 mL led to further significant improvement in the upper thoracic, lower thoracic and lumbar regions. Conclusion Conventional, solid pedicle screws augmented with high-viscosity cement provided comparable screw stability in pull-out testing to that of sophisticated and more expensive fenestrated screws. In terms of cement volume, we recommend the use of at least 1 mL in the thoracic and 3 mL in the lumbar spine. Cite this article: C. I. Leichtle, A. Lorenz, S. Rothstock, J. Happel, F. Walter, T. Shiozawa, U. G. Leichtle. Pull-out strength of cemented solid versus fenestrated pedicle screws in osteoporotic vertebrae. Bone Joint Res 2016;5:419–426.
EaseDB: a cache-oblivious in-memory query processor

We propose to demonstrate EaseDB, the first cache-oblivious queryprocessor for in-memory relational query processing. The cache-oblivious notion from the theory community refers to the property that no parameters in an algorithm or a data structure need to be tuned for a specific memory hierarchy for optimality. As a result, EaseDB automatically optimizes the cache performance as well as the overall performance of query processing on any memory hierarchy. We have developed a visualization interface to show the detailed performance of EaseDB in comparison with its cache-conscious counterpart, with both the parameters in the cache-conscious algorithms and the hardware platforms varied.
Switching DNA-binding specificity by unnatural amino acid substitution

The specificity of protein–nucleic acid recognition is believed to originate largely from hydrogen bonding between protein polar atoms, primarily side-chain and polar atoms of nucleic acid bases. One way to design new nucleic acid binding proteins of novel specificity is by structure-guided alterations of the hydrogen bonding patterns of a nucleic acid–protein complex. We have used cI repressor of bacteriophage λ as a model system. In the λ-repressor–DNA complex, the ɛ-NH2 group (hydrogen bond donor) of lysine-4 of λ-repressor forms hydrogen bonds with the amide carbonyl atom of asparagine-55 (acceptor) and the O6 (acceptor) of CG6 of operator site OL1. Substitution of lysine-4 (two donors) by iso-steric S-(2-hydroxyethyl)-cysteine (one donor and one acceptor), by site-directed mutagenesis and chemical modification, leads to switch of binding specificity of λ-repressor from C:G to T:A at position 6 of OL1. This suggests that unnatural amino acid substitutions could be a simple way of generating nucleic acid binding proteins of altered specificity.
Ecosystem management and land conservation can substantially contribute to California’s climate mitigation goals

Significance Combatting climate change will require using all available tools, especially those that contribute to other societal and economic goals, such as natural resource protection and energy security. Conserving and managing natural and agricultural lands to retain and absorb greenhouse gasses (GHGs) are tools that have not been widely integrated into climate policy. Our analysis provides a quantification of potential climate benefits from multiple land-based activities for a jurisdiction with an emissions reduction target (up to 13.3% of the cumulative reductions needed to meet the 2050 target, or nearly three-fourths of a billion metric tons of GHGs). This approach provides a model that other jurisdictions can use to evaluate emissions reductions that might be achieved from conserving and restoring natural lands. Modeling efforts focused on future greenhouse gas (GHG) emissions from energy and other sectors in California have shown varying capacities to meet the emissions reduction targets established by the state. These efforts have not included potential reductions from changes in ecosystem management, restoration, and conservation. We examine the scale of contributions from selected activities in natural and agricultural lands and assess the degree to which these actions could help the state achieve its 2030 and 2050 climate mitigation goals under alternative implementation scenarios. By 2030, an Ambitious implementation scenario could contribute as much as 147 MMTCO2e or 17.4% of the cumulative reductions needed to meet the state’s 2030 goal, greater than the individual projected contributions of four other economic sectors, including those from the industrial and agricultural sectors. On an annual basis, the Ambitious scenario could result in reductions as high as 17.9 MMTCO2e⋅y−1 or 13.4% of the state’s 2030 reduction goal. Most reductions come from changes in forest management (61% of 2050 projected cumulative reductions under the Ambitious scenario), followed by reforestation (14%), avoided conversion (11%), compost amendments to grasslands (9%), and wetland and grassland restoration (5%). Implementation of a range of land-based emissions reduction activities can materially contribute to one of the most ambitious mitigation targets globally. This study provides a flexible, dynamic framework for estimating the reductions achievable through land conservation, ecological restoration, and changes in management regimes.
SimpleFit: A Framework for Analyzing Design Trade-Offs in Raw Architectures

The semiconductor industry roadmap projects that advances in VLSI technology will permit more than one billion transistors on a chip by the year 2010. The MIT Raw microprocessor is a proposed architecture that strives to exploit these chip-level resources by implementing thousands of tiles, each comprising a processing element and a small amount of memory, coupled by a static two-dimensional interconnect. A compiler partitions fine-grain instruction-level parallelism across the tiles and statically schedules intertile communication over the interconnect. Because Raw microprocessors fully expose their internal hardware structure to the software, they can be viewed as a gigantic FPGA with coarse-grained tiles in which software orchestrates communication over static interconnections. One open challenge in Raw architectures is to determine their optimal grain size and balance. The grain size is the area of each tile and the balance is the proportion of area in each tile devoted to memory, processing, communication, and off-chip global I/O. If the total chip area is fixed, higher processing power per tile requires large tiles and hence reduces the total number of tiles on the chip. This paper presents SimpleFit, a novel analytical framework that designers can use to reason about the design space of Raw microprocessors. Our model is also generalizable to multiprocessors on a chip. Based on an architectural model, an application model, and a VLSI cost analysis, the framework computes the performance of applications and uses an optimization process to identify designs that will execute these applications most cost-effectively, Although the optimal machine configurations obtained vary for different applications, problem sizes, and budgets, the general trends for various applications are similar. Accordingly, for the applications studied, assuming a one billion logic transistor equivalent area, we recommend building a Raw chip with approximately 1,000 tiles, 30 words/cycle global I/O, 20 Kbytes of local memory per tile, three to four words/cycle local communication bandwidth, and single-issue processors. This configuration will give performance near the global optimum for most applications.
Monodromy in Hamiltonian Floer theory

Schwarz showed that when a closed symplectic manifold (M,ω) is symplectically aspherical (i.e. the symplectic form and the first Chern class vanish on π2(M)) then the spectral invariants, which are initially defined on the universal cover of the Hamiltonian group, descend to the Hamiltonian group Ham(M,ω). In this note we describe less stringent conditions on the Chern class and quantum homology of M under which the (asymptotic) spectral invariants descend to Ham(M,ω). For example, they descend if the quantum multiplication of M is undeformed and H2(M) has rank > 1, or if the minimal Chern number is at least n+ 1 (where dimM = 2n) and the even cohomology of M is generated by divisors. The proofs are based on certain calculations of genus zero Gromov–Witten invariants. As an application, we show that the Hamiltonian group of the one point blow up of T 4 admits a Calabi quasimorphism. Moreover, whenever the (asymptotic) spectral invariants descend it is easy to see that Ham(M,ω) has infinite diameter in the Hofer norm. Hence our results establish the infinite diameter of Ham in many new cases. We also show that the area pseudonorm — a geometric version of the Hofer norm — is nontrivial on the (compactly supported) Hamiltonian group for all noncompact manifolds as well as for a large class of closed manifolds.
On the Tip-of-the-Tongue: Neural Correlates of Increased Word-finding Failures in Normal Aging

Tip-of-the-tongue (TOT) experiences are frustrating word-finding failures where people are temporarily unable to produce a word they are certain they know. TOT frequency increases with normal aging during adulthood, and behavioral evidence suggests that the underlying deficit is in retrieving the complete phonology of the target word during production. The present study investigated the neural correlates of this phonological retrieval deficit. We obtained 3-D T1-weighted structural magnetic resonance images (MRI) for healthy participants between 19 and 88 years old and used voxel-based morphometry to measure gray matter density throughout the brain. In a separate session, participants named celebrities cued by pictures and descriptions, indicating when they had a TOT, and also completed Raven's Progressive Matrices (RPM), a task that does not involve phonological production. The number of TOTs increased with age and also with gray matter atrophy in the left insula, an area implicated in phonological production. The relation between TOTs and left insula atrophy cannot be attributed to the correlation of each variable with age because TOTs were related to insula atrophy even with age effects removed. Moreover, errors on the RPM increased with age, but performance did not correlate with gray matter density in the insula. These results provide, for the first time, an association between a region in the neural language system and the rise in age-related word-finding failures and suggest that age-related atrophy in neural regions important for phonological production may contribute to age-related word production failures.
Dynorphin Opioid Peptides Enhance Acid-Sensing Ion Channel 1a Activity and Acidosis-Induced Neuronal Death

Acid-sensing ion channel 1a (ASIC1a) promotes neuronal damage during pathological acidosis. ASIC1a undergoes a process called steady-state desensitization in which incremental pH reductions desensitize the channel and prevent activation when the threshold for acid-dependent activation is reached. We find that dynorphin A and big dynorphin limit steady-state desensitization of ASIC1a and acid-activated currents in cortical neurons. Dynorphin potentiation of ASIC1a activity is independent of opioid or bradykinin receptor activation but is prevented in the presence of PcTx1, a peptide which is known to bind the extracellular domain of ASIC1a. This suggests that dynorphins interact directly with ASIC1a to enhance channel activity. Inducing steady-state desensitization prevents ASIC1a-mediated cell death during prolonged acidosis. This neuroprotection is abolished in the presence of dynorphins. Together, these results define ASIC1a as a new nonopioid target for dynorphin action and suggest that dynorphins enhance neuronal damage following ischemia by preventing steady-state desensitization of ASIC1a.
Two-stage compression for fast volume rendering of time-varying scalar data

This paper presents a two-stage compression method for accelerating GPU-based volume rendering of time-varying scalar data. Our method aims at reducing transfer time by compressing not only the data transferred from disk to main memory but also that from main memory to video memory. In order to achieve this reduction, the proposed method uses packed volume texture compression (PVTC) and Lempel-Ziv-Oberhumer (LZO) compression as a lossy compression method on the GPU and a lossless compression method on the CPU, respectively. This combination realizes efficient compression exploiting both temporal and spatial coherence in time-varying data. We also present experimental results using scientific and medical datasets. In the best case, our method produces 56% more frames per second, as compared with a single-stage (GPU-based) compression method. With regard to the quality of images, we obtain permissible results ranging from approximately 30 to 50 dB in terms of PSNR (peak signal-to-noise ratio).
The Bistable Behaviour of Pseudomonas putida KT2440 during PHA Depolymerization under Carbon Limitation

Poly(hydroxyalkanoates) (PHAs) are bacterial polyesters offering a biodegradable alternative to petrochemical plastics. The intracellular formation and degradation of PHAs is a dynamic process that strongly depends on the availability of carbon and other nutrients. Carbon excess and nitrogen limitation are considered to favor PHA accumulation, whereas carbon limitation triggers PHA depolymerization when all other essential nutrients are present in excess. We studied the population dynamics of Pseudomonas putida KT2440 at the single cell level during different physiological conditions, favoring first PHA polymerization during growth on octanoic acid, and then PHA depolymerization during carbon limitation. PHAs accumulate intracellularly in granules, and were proposed to separate preferentially together with nucleic acids, leading to two daughter cells containing approximately equal amounts of PHA. However, we could show that such P. putida KT2440 cells show bistable behavior when exposed to carbon limitation, and separate into two subpopulations: one with high and one with low PHA. This suggests an asymmetric PHA distribution during cell division under carbon limitation, which has a significant influence on our understanding of PHA mobilization.
Gap Junctional Coupling and Patterns of Connexin Expression among Neonatal Rat Lumbar Spinal Motor Neurons

Interneuronal gap junctional coupling is a hallmark of neural development whose functional significance is poorly understood. We have characterized the extent of electrical coupling and dye coupling and patterns of gap junction protein expression in lumbar spinal motor neurons of neonatal rats. Intracellular recordings showed that neonatal motor neurons are transiently electrically coupled and that electrical coupling is reversibly abolished by halothane, a gap junction blocker. Iontophoretic injection of Neurobiotin, a low molecular weight compound that passes across most gap junctions, into single motor neurons resulted in clusters of many labeled motor neurons at postnatal day 0 (P0)–P2, and single labeled motor neurons after P7. The compact distribution of dye-labeled motor neurons suggested that, after birth, gap junctional coupling is spatially restricted. RT-PCR, in situ hybridization, and immunostaining showed that motor neurons express five connexins, Cx36, Cx37, Cx40, Cx43, and Cx45, a repertoire distinct from that expressed by other neurons or glia. Although all five connexins are widely expressed among motor neurons in embryonic and neonatal life, Cx36, Cx37, and Cx43 continue to be expressed in many adult motor neurons, and expression of Cx45, and in particular Cx40, decreases after birth. The disappearance of electrical and dye coupling despite the persistent expression of several gap junction proteins suggests that gap junctional communication among motor neurons may be modulated by mechanisms that affect gap junction assembly, permeability, or open state.
Colonization of barley roots by endophytic fungi and their reduction of take-all caused by Gaeumannomyces graminis var. tritici.

Fungal root endophytes obtained from natural vegetation were tested for antifungal activity in dual culture tests against the root pathogen Gaeumannomyces graminis var. tritici. Fifteen isolates, including Acremonium blochii, Acremonium furcatum, Aspergillus fumigatus, Cylindrocarpon sp. , Cylindrocarpon destructans, Dactylaria sp. , Fusarium equiseti, Phoma herbarum, Phoma leveillei, and a sterile mycelium, selected based on the dual culture test, were inoculated on barley roots in growth tubes under axenic conditions, both in the absence and presence of G. graminis var. tritici. All isolates colonized the rhizosphere and very often the root cortex without causing disease symptoms and without affecting plant growth. Eight isolates significantly reduced the symptoms caused by G. graminis var. tritici, and 6 of them reduced its presence in the roots.
Snake Cathelicidin NA-CATH and Smaller Helical Antimicrobial Peptides Are Effective against Burkholderia thailandensis

Burkholderia thailandensis is a Gram-negative soil bacterium used as a model organism for B. pseudomallei, the causative agent of melioidosis and an organism classified category B priority pathogen and a Tier 1 select agent for its potential use as a biological weapon. Burkholderia species are reportedly “highly resistant” to antimicrobial agents, including cyclic peptide antibiotics, due to multiple resistance systems, a hypothesis we decided to test using antimicrobial (host defense) peptides. In this study, a number of cationic antimicrobial peptides (CAMPs) were tested in vitro against B. thailandensis for both antimicrobial activity and inhibition of biofilm formation. Here, we report that the Chinese cobra (Naja atra) cathelicidin NA-CATH was significantly antimicrobial against B. thailandensis. Additional cathelicidins, including the human cathelicidin LL-37, a sheep cathelicidin SMAP-29, and some smaller ATRA peptide derivatives of NA-CATH were also effective. The D-enantiomer of one small peptide (ATRA-1A) was found to be antimicrobial as well, with EC50 in the range of the L-enantiomer. Our results also demonstrate that human alpha-defensins (HNP-1 & -2) and a short beta-defensin-derived peptide (Peptide 4 of hBD-3) were not bactericidal against B. thailandensis. We also found that the cathelicidin peptides, including LL-37, NA-CATH, and SMAP-29, possessed significant ability to prevent biofilm formation of B. thailandensis. Additionally, we show that LL-37 and its D-enantiomer D-LL-37 can disperse pre-formed biofilms. These results demonstrate that although B. thailandensis is highly resistant to many antibiotics, cyclic peptide antibiotics such as polymyxin B, and defensing peptides, some antimicrobial peptides including the elapid snake cathelicidin NA-CATH exert significant antimicrobial and antibiofilm activity towards B. thailandensis.
THE ECONOMETRICS OF FINANCIAL MARKETS

This book is an ambitious effort by three well-known and well-respected scholars to fill an acknowledged void in the literature—a text covering the burgeoning field of empirical finance. As the authors note in the preface, there are several excellent books covering financial theory at a level suitable for a Ph.D. class or as a reference for academics and practitioners, but there is little or nothing similar that covers econometric methods and applications. Perhaps the closest existing text is the recent addition to the Wiley Series in Financial and Quantitative Analysis. written by Cuthbertson (1996). The major difference between the books is that Cuthbertson focuses exclusively on asset pricing in the stock, bond, and foreign exchange markets, whereas Campbell, Lo, and MacKinlay (henceforth CLM) consider empirical applications throughout the field of finance, including corporate finance, derivatives markets, and market microstructure. The level of anticipation preceding publication can be partly measured by the fact that at least three reviews (including this one) have appeared since the book arrived. Moreover, in their reviews, both Harvey (1998) and Tiso (1998) comment on the need for such a text, a sentiment that has been echoed by numerous finance academics.
Mechanical characteristics of hollow shear connectors under direct shear force

The steel-concrete composite decks have high fatigue durability and deformability in comparison with ordinary RC slabs. Withal, the steel-concrete composite deck is mostly heavier than the RC slabs. We have proposed herein a new type of steel-concrete composite deck which is lighter than the typical steel-concrete composite decks. This can be achieved by arranging hollow sectional members as shear connectors, namely, half-pipe or channel shear connectors. The present study aims to experimentally investigate mechanical characteristics of the half-pipe shear connectors under the direct shear force. The shear bond capacity and deformability of the half-pipe shear connectors are strongly affected by the thickness-to-diameter ratio. Additionally, the shear strengths of the hollow shear connectors (i.e., the half-pipe and the channel shear connectors) are compared. Furthermore, shear capacities of the hollow shear connectors equivalent to headed stud connectors are also discussed.