cssi/SciSciGPT-SciSciNet huggingface dataset:
A Numerical Method for Estimating Tendon Slack Length

Forces generated by muscle are transferred to bone via tendon. Since muscle force cannot be measured directly, computer modeling is a useful tool to enhance our understanding of normal and pathological movement. Hill-type muscle models have been used to estimate force based on information about a muscle’s architecture, activation and kinematics (Delp et al., 1995; Manal et al., 2002). Architectural parameters include optimal fiber length (l o m ), tendon slack length (l s t ), pennation angle (α), and maximum isometric force (Fmax ). In addition, musculotendon length (l mt ) and activation (a) are required inputs when estimating isometric muscle force (Equation I). Fm = f(lmt, lom, lst, Fmax, α, a) (1) Musculotendon length can be determined from MR images (Arnold et al., 2000), and activation recorded from EMGs (Manal, et al., 2002). Optimal fiber length and pennation angle can be measured experimentally (Murray, 2002), while Fmax can be estimated from the muscle’s physiologic cross-sectional area. Tendon slack length however cannot be measured readily, and therefore few estimates of l s t can be found in the literature. In this paper we present a numerical method for estimating tendon slack from subject specific muscle parameters and musculotendon lengths. An advantage of this method is that it yields subject specific estimates of tendon slack length.Copyright © 2003 by ASME
Vivisecting YouTube: An active measurement study

We deduce key design features behind the YouTube video delivery system by building a distributed active measurement infrastructure, and collecting and analyzing a large volume of video playback logs, DNS mappings and latency data. We find that the design of YouTube video delivery system consists of three major components: a “flat” video id space, multiple DNS namespaces reflecting a multi-layered logical organization of video servers, and a 3-tier physical cache hierarchy. We also uncover that YouTube employs a set of sophisticated mechanisms to handle video delivery dynamics such as cache misses and load sharing among its distributed cache locations and data centers.
The Put' of Perekovka: Transforming Lives at Stalin's White Sea‐Baltic Canal

As a highly propagandized Gulag project, the construction of Stalin's White Sea-Baltic Canal (Belomorsko-Baltiiskii kanal im. Stalina) produced a plethora of cultural products. While scholars have explored at length many of the official texts concerning the Canal, narratives written by the prisoners themselves remain largely unexamined. The present article uses unpublished, convict-composed autobiographies and short stories from the period of the Canal's construction to explore the various approaches to and interpretations of perekovka (re-forging), the ideological backbone of the Gulag project. These archival materials offer a fresh perspective on what has become one of the most infamous projects of the Soviet Gulag, and demonstrate how prisoner rhetoric often imitated official parlance. The notion of put' (pathway) is an essential component in these texts–not only as the road to socialist labor but also as the path to a life of crime, which further complicates the analysis of these texts while addressing Soviet self-fashioning and the potential for identity construction through writing.
AJR teaching file: Solitary pulmonary nodule with enhancing rim sign.

Clinical History An 84-year-old man presents with a recent cough but does not have fever or chills. On chest radiography, a solitary pulmonary nodule is identified. Because previous chest radiographs are not available for comparison, the lesion is studied with CT. Radiologic Description An axial CT image through a solitary pulmonary nodule acquired before the administration of IV contrast material (Fig. 1A) shows homogeneous soft-tissue density. After administration of IV contrast material (Fig. 1B), the nodule rim enhances more intensely than the central portion. The center of the nodule enhanced 17 H. Differential Diagnosis The differential diagnosis includes granuloma, metastasis, bronchogenic carcinoma, and round atelectasis. Diagnosis The diagnosis in this patient is benign granuloma. Commentary Solitary pulmonary nodules are commonly encountered in clinical practice. Distinguishing benign from malignant processes with imaging can be a challenge. Contrast-enhanced CT can help characterize solitary pulmonary nodules [1-3]. After the IV administration of iodinated contrast material, enhancement of 15 H or less is a strong predictor of benignancy [4]. In a study of 111 nodules that enhanced 15 H or less, 107 (96%) were benign. Of the 245 nodules that enhanced more than 15 H, 167 (68%) were malignant [4]. Using the technique described by Swensen et al. [1], a new finding has been observed in some benign solitary pulmonary nodules. This has been termed the "enhancing rim sign" because it refers to a rim of enhancing soft tissue at the periphery of a solitary pulmonary nodule that surrounds a homogeneous lower.
β-Adrenergic Regulation of Synaptic NMDA Receptors by cAMP-Dependent Protein Kinase

To identify the protein kinases regulating synaptic NMDA receptors, as well as the conditions favoring enhancement of NMDA receptor-mediated excitatory postsynaptic currents (EPSCs) by phosphorylation, we studied the effects of kinase activation and inhibition in hippocampal neurons. Inhibition of cAMP-dependent protein kinase (PKA) prevented recovery of NMDA receptors from calcineurin-mediated dephosphorylation induced by synaptic activity, suggesting that tonically active PKA phosphorylates receptors during quiescent periods. Conversely, elevation of PKA activity by forskolin, cAMP analogs, or the beta-adrenergic receptor agonists norepinephrine and isoproterenol overcame the ability of calcineurin to depress the amplitude of NMDA EPSCs. Thus, stimulation of beta-adrenergic receptors during excitatory synaptic transmission can increase charge transfer and Ca2+ influx through NMDA receptors.
Optical Constants of Beryllium from Photoabsorption Measurements for X-Ray Optics Applications

Beryllium (Be) has been recently receiving considerable attention as the key material for a range of potential applications in the extreme ultraviolet (EUV) and x-ray region. Most notably, it has been successfully implemented as the spacer material in beryllium-based multilayer mirrors for EUV lithography, achieving experimental reflectivities of about 70% at wavelengths around 11.4 nm. Knowledge of the absorptive and dispersive properties of this material thus becomes important for the modeling of these optics. Experimental photoabsorption results in the region 40-250 eV, derived from transmission measurements on free-standing beryllium foils, are presented in this work. The measured absorption in the region extending a few tens eV below the K edge (111.7 eV) appears to be significantly (up to 50%) lower than the tabulated values. Fine structure above the K edge is also demonstrated in the measurements. These data are incorporated in an updated set for the atomic scattering factors of beryllium, obtained in the range 0.1-30,000 eV. Finally, the Bragg reflectivity of MO/Be multilayer optics is modeled using the new experimental results.
Stochastic Inference to Sediment and Fluvial Hydraulics

This forum, supposedly serving as an introduction to the collected stochastic hydraulics papers appearing in this issue, is actually a follow-up of the forum by Dr. Thanos Papanicolaou in the December 1999 issue of this journal, in which a succinct definition of the word stochastic is given. A more extended discussion on the definition of stochastic can be found in Yen ~1988a!. Loosely, a stochastic process may be regarded as a random process that involves space and/or time, or it may be considered as a spatial or temporal process that involves probability. Stochastic hydraulics refers to hydraulic phenomena that are subject to stochastic processes. It is distinctly different from stochastic hydrology, which treats the phenomena without explicitly considering hydraulic principles. There is no shortage of examples of stochastic hydraulic processes: turbulence; flow induced vibration or fluctuation; hydraulic jump; mass; momentum or energy transport and dispersion; safety of hydraulic structures; sediment movement in flow; bed form migration; and stream morphology, just to name a few. Some stochastic perspectives of well known hydraulic problems have been discussed in Yen ~1992!. Traditionally, these problems have been treated in a deterministic manner. As indicated in Table 1, an observed stochastic process can be the product of a deterministic system or deterministic input. With the numerous scientific and popular books and articles on chaos published in the past 2 decades, it is now easy to understand that a system governed by deterministic physical laws, for example, Newton’s second law or the Navier-Stokes equation, can produce stochastic results. Not to mention that even such ‘‘basic’’ laws can themselves be subject to probabilistic analysis ~Chiu 1991!, for example, based on Boltzmann’s concept ~Ghidaoui et al. 2001!. Recasting hydraulic phenomena through the lens of stochastic perspectives can provide a number of benefits, such as: 1. Clarify the physical concept 2. Derive new theoretical concepts 3. Provide a link between stochastic reality and deterministic treatment of hydraulic problems 4. Provide additional or new information for improved design 5. Suggest alternatives to existing hydraulic methods 6. Provide a scientific basis for rational decision making in operational, planning, or management alternatives 7. Serve as a tool in data management for effective planning of data collection and appropriate measurement accuracy
Dynamic graphs and continuous Boolean networks, I: A hybrid model for gene regulation

In this paper we propose a new theoretical framework for describing continuous Boolean networks, which is based on dynamic graphs. It is shown that mathematical representations of this type allow for a broad range of interactions between the discrete and continuous variables in the system. Since the form of these interactions determines the dynamic properties of the network, the number of possible configurations can be significantly expanded in this way. In the context of gene regulation, this added flexibility can be used to formulate models that better reflect the physical nature of the underlying biochemical processes.
Proinflammatory Responses Induced by CD40 in Retinal Endothelial and Müller Cells are Inhibited by Blocking CD40-Traf2,3 or CD40-Traf6 Signaling

Purpose The cell surface receptor CD40 is required for the development of retinopathies induced by diabetes and ischemia/reperfusion. The purpose of this study was to identify signaling pathways by which CD40 triggers proinflammatory responses in retinal cells, since this may lead to pharmacologic targeting of these pathways as novel therapy against retinopathies. Methods Retinal endothelial and Muller cells were transduced with vectors that encode wild-type CD40 or CD40 with mutations in sites that recruit TNF receptor associated factors (TRAF): TRAF2,3 (ΔT2,3), TRAF6 (ΔT6), or TRAF2,3 plus TRAF6 (ΔT2,3,6). Cells also were incubated with CD40-TRAF2,3 or CD40-TRAF6 blocking peptides. We assessed intercellular adhesion molecule-1 (ICAM-1), CD40, monocyte chemoattractant protein-1 (MCP-1), VEGF, and prostaglandin E₂ (PGE₂) by fluorescence-activated cell sorting (FACS), ELISA, or mass spectrometry. Mice (B6 and CD40(-/-)) were made diabetic using streptozotocin. The MCP-1 mRNA was assessed by real-time PCR. Results The CD40-mediated ICAM-1 upregulation in endothelial and Muller cells was markedly inhibited by expression of CD40 ΔT2,3 or CD40 ΔT6. The CD40 was required for MCP-1 mRNA upregulation in the retina of diabetic mice. The CD40 stimulation of endothelial and Muller cells enhanced MCP-1 production that was markedly diminished by CD40 ΔT2,3 or CD40 ΔT6. Similar results were obtained in cells incubated with CD40-TRAF2,3 or CD40-TRAF6 blocking peptides. The CD40 ligation upregulated PGE₂ and VEGF production by Muller cells, that was inhibited by CD40 ΔT2,3 or CD40 ΔT6. All cellular responses tested were obliterated by expression of CD40 ΔT2,3,6. Conclusions Blockade of a single CD40-TRAF pathway was sufficient to impair ICAM-1, MCP-1, PGE₂, and VEGF upregulation in retinal endothelial and/or Muller cells. Blockade of CD40-TRAF signaling may control retinopathies.
Redefining tactical operations for MER using cloud computing

The Mars Exploration Rover Mission (MER) includes the twin rovers, Spirit and Opportunity, which have been performing geological research and surface exploration since early 2004. The rovers' durability well beyond their original prime mission (90 sols or Martian days) has allowed them to be a valuable platform for scientific research for well over 2000 sols, but as a by-product it has produced new challenges in providing efficient and cost-effective tactical operational planning. ***
Building systems to support development of drugs for biodefense

The mission of the National Institute of Allergy and Infectious Diseases (NIAID), Division of Microbiology and Infectious Diseases (DMID), is to support research and product development that addresses the control and prevention of infectious diseases. This mission includes the development of new drugs to mitigate illness, suffering, and death resulting from an expanding spectrum of naturally emerging diseases and potential biological weapons. DMID has established new resources and additional infrastructure to address these challenges. In addition, DMID plans to transition to a new paradigm for research and development approaches based on three concepts that comprise a broad spectrum approach: products with broad spectrum activity; broad spectrum technology that can be applied to improve specific drug characteristics (e.g., shelf life); and broad spectrum platforms that will reduce the time and cost to manufacture and evaluate products. Drug Dev Res 68:183–185, 2007. © 2007 Wiley-Liss, Inc.
The function of hairy-related bHLH repressor proteins in cell fate decisions

Hairy-related proteins are a distinct subfamily of basic helix-loop-helix (bHLH) proteins that generally function as DNA-binding transcriptional repressors. These proteins act in opposition to bHLH transcriptional activator proteins such as the proneural and myogenic proteins; together, the activator and repressor genes that encode these proteins have co-evolved as a regulatory gene "cassette" or "module" for controlling cell fate decisions. In the development of the Drosophila peripheral nervous system, Hairy-related genes function at multiple steps during neurogenesis, for example, as positional information genes that establish the "prepattern" that controls where "proneural cluster" equivalence groups will form, and later as nuclear effectors of the Notch signaling pathway to "single out" individual precursor cells within the equivalence group. Hairy-related genes also function in the establishment and restriction of other types of equivalence groups, such as those for muscle and Malphigian tubule precursors. This general function in cell fate specification has been conserved from Drosophila to vertebrates and has implications for human disease pathogenesis.
A Compact Quantum-Mechanical Model for Double-Gate MOSFET

A bias-dependent QM correction for surface potential calculation is derived for DG MOSFETs. The QM-corrected surface potential agrees with the 2D simulation results well. This indicates that both Vth shift in the subthreshold and strong inversion regions and gate capacitance degradation in the strong inversion region due to QM are predicted simultaneously. The model can predict the complicated QM effect dependence on various device parameters, such as Nbody, Tsi, Tox, etc
A new acoustic tailbeat transmitter for fishes

A new acoustic transmitter for monitoring the tailbeat frequency of free-swimming fishes and sharks is described. The transmitter is externally mounted on the fish's caudal peduncle and produces an acoustic pulse with every lateral movement of the tail. Field tests on obligate-swimming juvenile scalloped hammerhead sharks (Sphyrna lewini) show these transmitters accurately telemeter tailbeat deflections from free-swimming sharks. Tests in a flume show sharks with transmitters work harder and swim slower than sharks without transmitters, but these laboratory data can be used to correct for instrument artifacts on free-swimming sharks. A shark tracked with a tailbeat-sensing transmitter exhibited similar movement and activity patterns to shark pups tracked with smaller, orally inserted internal transmitters. The similarity of tracks indicate that the shark equipped with the tailbeat transmitter behaved normally. Thus, this new transmitter design offers a cost-effective, minimally intrusive method for accurately measuring activity rate and energy consumption of active fishes and sharks in the field.
IMPACCT: Methodology and Tools for Power-Aware Embedded Systems

Power-aware systems are those that must exploit a widerange of power/performance trade-offs in order to adapt to the power availabilityand application requirements. They require the integration of many novel powermanagement techniques, ranging from voltage scaling to subsystem shutdown.However, those techniques do not always compose synergistically with eachother; in fact, they can combine subtractively and often yield counterintuitive,and sometimes incorrect, results in the context of a complete system. Thiscan become a serious problem as more of these power aware systems are beingdeployed in mission critical applications. To address the problem of technique integration for power-aware embedded systems, we propose a new design tool framework called IMPACCT and the associated design methodology. The system modeling methodology includes application model for capturing timing/powerconstraints and mode dependencies at the system level. The tool performs power-awarescheduling and mode selection to ensure that all timing/power constraintsare satisfied and that all overhead is taken into account. IMPACCT then synthesizesthe implementation targeting a symmetric multiprocessor platform. Experimentalresults show that the increased dynamic range of power/performance settingsenabled a Mars rover to achieve significant acceleration while using lessenergy. More importantly, our tool correctly combines the state-of-the-arttechniques at the system level, thereby saving even experienced designersfrom many pitfalls of system-level power management.
Is there an elephant in the room? Addressing rival approaches to the interpretation of growth perturbations and small size.

Two interpretations of growth perturbation and small size are commonly applied in human biology: an adaptationist approach in which small size is considered to be an a relatively beneficial adjustment to environmental stressors, and a biomedical approach in which small size is considered nonadaptive, a sign of dysfunction or pathology. These two inter- pretations conflict, but are used without acknowledging or addressing the conflict. This article reviews the strengths and weaknesses of the two. This exercise does not prove the indisputable superiority of either approach. Considerations of epistemology show that biologists will never be faced with a decisive test of either, much as they might like such clear cut evidence. Never- theless, it is possible that a gradual decrease in the productivity of one approach will become a sufficient reason to abandon it. Alternatively, if specific areas of application can be distin- guished, each approach might continue to be productive in its own domain. Am. J. Hum. Biol.
Reducing power with performance constraints for parallel sparse applications

Sparse and irregular computations constitute a large fraction of applications in the data-intensive scientific domain. While every effort is made to balance the computational workload in such computations across parallel processors, achieving sustained near machine-peak performance with close-to-ideal load balanced computation-to-processor mapping is inherently difficult. As a result, most of the time, the loads assigned to parallel processors can exhibit significant variations. While there have been numerous past efforts that study this imbalance from the performance viewpoint, to our knowledge, no prior study has considered exploiting the imbalance for reducing power consumption during execution. Power consumption in large-scale clusters of workstations is becoming a critical issue as noted by several recent research papers from both industry and academia. Focusing on sparse matrix computations in which underlying parallel computations and data dependencies can be represented by trees, this paper proposes schemes that save power through voltage/frequency scaling. Our goal is to reduce overall energy consumption by scaling the voltages/frequencies of those processors that are not in the critical path; i.e., our approach is oriented towards saving power without incurring performance penalties.
Solid-state polymerization of diacetylene: 1,11,13,23-tetracosatetrayne

The solid-state polymerization of a diacetylene, 1,11,13,23-tetracosatetrayne, was studied using x-ray powder diffraction and electron diffraction. It is shown that the material exhibits polymorphism. Thermochromic transitions, which are generally observed for diacetylenes, are related to the particular crystalline phase using x-ray powder diffraction. The unit cell dimensions and space group of one polymorph were determined by electron diffraction analysis: a = 20.83 A, b = 4.84 A, c = 10.08 A, β = 92.4°, space group: P21/n. © 1995 John Wiley & Sons, Inc.
Characterization of Cl-HCO3 exchange in basolateral membrane of rat distal colon

Sodium-independent Cl movement (i.e., Cl-anion exchange) has not previously been identified in the basolateral membranes of rat colonic epithelial cells. The present study demonstrates Cl-HCO3 exch...
Homocysteine Inhibits Retinoic Acid Synthesis: A Mechanism for Homocysteine-Induced Congenital Defects

Hyperhomocysteinemia is frequently associated with congenital defects of the heart and neural tube and is a suspected pathogenic factor in atherosclerosis and neoplasia. Results in the present report show homocysteine treatment disrupts normal development of avian embryos; and this effect is prevented by retinoic acid. Based on this, we hypothesize that homocysteine may exert its teratogenic effects by disrupting retinoic acid signaling during development. A reporter cell line transfected with a retinoic acid response element (RARE) linked to a lacZ reporter gene was used to identify the site of retinoid inhibition. Using this reporter cell line, we show that homocysteine inhibits the oxidation of retinal to retinoic acid with concentrations of homocysteine that are in the pathophysiological range (.05 to 0.5 mM). In contrast, homocysteine concentrations as high as 5 mM are unable to inhibit the induction of lacZ by retinoic acid. We show that cellular uptake of homocysteine is sensitive to the specific L-system transport inhibitor, bicycloheptane, and bicycloheptane blocks the inhibition of retinoic acid synthesis by homocysteine, demonstrating that this inhibition occurs intracellularly. These results suggest that homocysteine-induced congenital defects are due to the specific ability of homocysteine to inhibit conversion of retinal to retinoic acid.
An Assessment of the Economics of Future Electric Power Generation Options and the Implications for Fusion

This study examines the potential range of electric power costs for some major alternatives to fusion electric power generation when it is ultimately deployed in the middle of the 21st century and, thus, offers a perspective on the cost levels that fusion must achieve to be competitive. The alternative technologies include coal burning, coal gasification, natural gas, nuclear fission, and renewable energy. The cost of electricity (COE) from the alternatives to fusion should be in a 30 to 53 mills/kW.h (1999 dollars) range if carbon sequestration is not needed, 30 to 61 mills/kW.h if sequestration is required, or as high as 83 mills/kW.h for the worst-case scenario for cost uncertainty. The reference COE range for fusion was estimated at 65 to 102 mills/kW.h for 1- to 1.3-GW(electric) scale power plants, based on the tokamak concept. Tokamak fusion costs will have to be reduced and/or cost-effective alternative nontokamak concepts devised before fusion will be competitive with the alternatives for the future production of electricity. Fortunately, there are routes to achieve this goal. Recent results from fusion experiments and developments in technology and engineering solutions indicate that lower cost fusion power plants are possible at the 1-GW(electric) level. Another general route formore » fusion to reduce costs is to go to large plant sizes [multigigawatts (electric)].« less
Turbulence Structure of the Hurricane Boundary Layer between the Outer Rainbands

As part of the Coupled Boundary Layers Air‐Sea Transfer (CBLAST)-Hurricane program, flights were conducted to directly measure turbulent fluxes and turbulence properties in the high-wind boundary layer of hurricanes between the outer rainbands. For the first time, vertical profiles of normalized momentum fluxes, sensible heat and humidity fluxes, and variances of three-dimensional wind velocities and specific humidity are presented for the hurricane boundary layer with surface wind speeds ranging from 20 to 30 m s 21 . The turbulent kinetic energy budget is estimated, indicating that the shear production and dissipation are the major source and sink terms, respectively. The imbalance in the turbulent kinetic energy budget indicates that the unmeasured terms, such as horizontal advection, may be important in hurricane boundary layer structure and dynamics. Finally, the thermodynamic boundary layer height, estimated based on the virtual potential temperature profiles, is roughly half of the boundary layer height estimated from the momentum flux profiles. The latter height where momentum and humidity fluxes tend to vanish is close to that of the inflow layer and also of the maximum in the tangential velocity profiles.
Measuring permanence of CO2 storage in saline formations: the Frio experiment

If CO2 released from fossil fuel during energy production is returned to the subsurface, will it be retained for periods of time significant enough to benefit the atmosphere? Can trapping be assured in saline formations where there is no history of hydrocarbon accumulation? The Frio experiment in Texas was undertaken to provide answers to these questions. One thousand six hundred metric tons of CO2 were injected into the Frio Formation, which underlies large areas of the United States Gulf Coast. Reservoir characterization and numerical modeling were used to design the experiment, as well as to interpret the results through history matching. Closely spaced measurements in space and time were collected to observe the evolution of immiscible and dissolved CO2 during and after injection. The high-permeability, steeply dipping sandstone allowed updip flow of supercritical CO2 as a result of the density contrast with formation brine and absence of a local structural trap. The front of the CO2 plume moved more quickly than had been modeled. By the end of the 10-day injection, however, the plume geometry in the plane of the observation and injection wells had thickened to a distribution similar to the modeled distribution. As expected, CO2 dissolved rapidly into brine, causing pH to fall and calcite and metals to be dissolved. Postinjection measurements, including time-lapse vertical seismic profiling transects along selected azimuths, cross-well seismic topography, and saturation logs, show that CO2 migration under gravity slowed greatly 2 months after injection, matching model predictions that significant CO2 is trapped as relative permeability decreases.
SenSay: a context-aware mobile phone

SenSay is a context-aware mobile phone that adapts to dynamically changing environmental and physiological states. In addition to manipulating ringer volume, vibration, and phone alerts, SenSay can provide remote callers with the ability to communicate the urgency of their calls, make call suggestions to users when they are idle, and provide the caller with feedback on the current status of the SenSay user. A number of sensors including accelerometers, light, and microphones are mounted at various points on the body to provide data about the user’s context. A decision module uses a set of rules to analyze the sensor data and manage a state machine composed of uninterruptible, idle, active and normal states. Results from our threshold analyses show a clear delineation can be made among several user states by examining sensor data trends. SenSay augments its contextual knowledge by tapping into applications such as electronic calendars, address books, and task lists.
Lambda red recombineering in Escherichia coli occurs through a fully single-stranded intermediate.

The phage lambda-derived Red recombination system is a powerful tool for making targeted genetic changes in Escherichia coli, providing a simple and versatile method for generating insertion, deletion, and point mutations on chromosomal, plasmid, or BAC targets. However, despite the common use of this system, the detailed mechanism by which lambda Red mediates double-stranded DNA recombination remains uncertain. Current mechanisms posit a recombination intermediate in which both 5′ ends of double-stranded DNA are recessed by λ exonuclease, leaving behind 3′ overhangs. Here, we propose an alternative in which lambda exonuclease entirely degrades one strand, while leaving the other strand intact as single-stranded DNA. This single-stranded intermediate then recombines via beta recombinase-catalyzed annealing at the replication fork. We support this by showing that single-stranded gene insertion cassettes are recombinogenic and that these cassettes preferentially target the lagging strand during DNA replication. Furthermore, a double-stranded DNA cassette containing multiple internal mismatches shows strand-specific mutations cosegregating roughly 80% of the time. These observations are more consistent with our model than with previously proposed models. Finally, by using phosphorothioate linkages to protect the lagging-targeting strand of a double-stranded DNA cassette, we illustrate how our new mechanistic knowledge can be used to enhance lambda Red recombination frequency. The mechanistic insights revealed by this work may facilitate further improvements to the versatility of lambda Red recombination.
The Economic Impact of Rent Seeking and Military Expenditures: A Comparison of Third World Military and Civilian Regimes

. The general stereotype of modern Third World military regimes is that of ultra-conservativism combined with military force to dismantle organizations of popular expression. These organizations through their rent-seeking activities are assumed to have reduced overall rates of economic growth. Empirically, the paper does find some support for this line of argument. However, it is apparent that the traditional stereotypes are inappropriate. The two regime types differ largely in terms of contrasting styles of economic management. Military regimes create an environment where military expenditures tend to have a positive overall impact on economic growth Civilian regimes having less control over rent seeking groups do not appear to be able to combine rent seeking activities and military expenditures in a manner conducive to overall economic growth.
The Schematics of Balance of Forces in the Planetary Boundary Layer.

Abstract It is pointed out that in a rotating frame of reference, the friction force on a fluid element may not be parallel and opposite to the velocity vector, as commonly depicted in textbook schematics of the force balance in the friction layer. A better schematic representation of the same is suggested here.
Scrotal temperature and semen quality in men with and without varicocele.

The exact role of varicocele in human male infertility remains controversial. Fifty-five male partners of infertile couples randomly selected and 17 fertile semen donors were evaluated for semen quality, scrotal temperature, and presence of varicocele using clinical palpation and Doppler ultrasound. The incidence of varicocele was 42% in male partners of infertile couples and 41% in fertile semen donors. Left scrotal temperature was significantly (p less than .001) higher in infertile males with varicocele as compared to all groups. No significant differences were observed in the percentage of morphologically normal sperm in semen of males with and without varicocele. However, the incidence of tapered, elongated, and immature sperm was significantly higher in the infertile patient population with a varicocele. Measurement of scrotal temperature and assessment of sperm morphology may be used as predictors of the presence and deleterious effect of varicocele.
DISSECT Method Using PNA-LNA Clamp Improves Detection of EGFR T790m Mutation

Non-small cell lung cancer (NSCLC) patients treated with small molecule EGFR inhibitors, such as gefitinib, frequently develop drug resistance due to the presence of secondary mutations like the T790M mutation on EGFR exon 20. These mutations may originate from small subclonal populations in the primary tumor that become dominant later on during treatment. In order to detect these low-level DNA variations in the primary tumor or to monitor their progress in plasma, it is important to apply reliable and sensitive mutation detection methods. Here, we combine two recently developed methodologies, Differential Strand Separation at Critical Temperature (DISSECT), with peptide nucleic acid-locked nucleic acid (PNA-LNA) polymerase chain reaction (PCR) for the detection of T790M EGFR mutation. DISSECT pre-enriches lowabundance T790M EGFR mutations from target DNA prior to implementing PNA-LNA PCR, a method that can detect 1 mutant allele in a background of 100–1000 wild type alleles. The combination of DISSECT and PNA-LNA PCR enables the detection of 1 mutant allele in a background of 10,000 wild type alleles. The combined DISSECT-PNA-LNA PCR methodology is amenable to adaptation for the sensitive detection of additional emerging resistance mutations in cancer.
Cap-Dependent Protein Translation Initiation in Multiple Myeloma: An Attractive Target for Therapy

It has been shown that overexpression and/or activation of eukaryotic initiation factor 4E (eIF4E) induces a malignant phenotype by regulating oncogenic protein synthesis. Aberrant control of protein synthesis contributes to lymphoma genesis, opening up possibilities of innovative therapeutics by targeting the translational machinery. In multiple myeloma (MM), understanding the mechanisms that control protein synthesis is emerging as an exciting new research area with significant potential for developing innovative therapies. Recently, eIF4E has been discovered as a critical regulator in protein synthesis. This review will summarize the role and regulatory mechanism of eIF4E in multiple myeloma, discuss the potential usage of mRNA translation controlling drugs for multiple myeloma treatment, and provide new leads for novel strategies of MM therapy.
The Experience of Online Counseling

In this qualitative study, the authors outline the experiences of 5 research participants who engaged in online chat-based counseling sessions. Participants discussed their experiences related to technological barriers, connecting with their counselor, interacting without visual or verbal feedback, receiving counseling in a personal space, and the flow and pace of the online sessions. The authors provide recommendations for the implementation of online counseling, including discussion of the limitations and benefits of this type of therapeutic conversation.
Single DNA imaging and length quantification through a mobile phone microscope

The development of sensitive optical microscopy methods for the detection of single DNA molecules has become an active research area which cultivates various promising applications including point-of-care (POC) genetic testing and diagnostics. Direct visualization of individual DNA molecules usually relies on sophisticated optical microscopes that are mostly available in well-equipped laboratories. For POC DNA testing/detection, there is an increasing need for the development of new single DNA imaging and sensing methods that are field-portable, cost-effective, and accessible for diagnostic applications in resource-limited or field-settings. For this aim, we developed a mobile-phone integrated fluorescence microscopy platform that allows imaging and sizing of single DNA molecules that are stretched on a chip. This handheld device contains an opto-mechanical attachment integrated onto a smartphone camera module, which creates a high signal-to-noise ratio dark-field imaging condition by using an oblique illumination/excitation configuration. Using this device, we demonstrated imaging of individual linearly stretched λ DNA molecules (48 kilobase-pair, kbp) over 2 mm2 field-of-view. We further developed a robust computational algorithm and a smartphone app that allowed the users to quickly quantify the length of each DNA fragment imaged using this mobile interface. The cellphone based device was tested by five different DNA samples (5, 10, 20, 40, and 48 kbp), and a sizing accuracy of <1 kbp was demonstrated for DNA strands longer than 10 kbp. This mobile DNA imaging and sizing platform can be very useful for various diagnostic applications including the detection of disease-specific genes and quantification of copy-number-variations at POC settings. © (2016) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE). Downloading of the abstract is permitted for personal use only.
Compensation for acoustic heterogeneities in photoacoustic computed tomography using a variable temporal data truncation reconstruction method

Photoacoustic computed tomography (PACT) is an emerging computed imaging modality that exploits optical contrast and ultrasonic detection principles to form images of the absorbed optical energy density within tissue. If the object possesses spatially variant acoustic properties that are unaccounted for by the reconstruction algorithm, the estimated image can contain distortions. While reconstruction algorithms have recently been developed for compensating for this effect, they generally require the objects acoustic properties to be known a priori. To circumvent the need for detailed information regarding an objects acoustic properties, we have previously proposed a half-time reconstruction method for PACT. A half-time reconstruction method estimates the PACT image from a data set that has been temporally truncated to exclude the data components that have been strongly aberrated. In this approach, the degree of temporal truncation is the same for all measurements. However, this strategy can be improved upon it when the approximate sizes and locations of strongly heterogeneous structures such as gas voids or bones are known. In this work, we investigate PACT reconstruction algorithms that are based on a variable temporal data truncation (VTDT) approach that represents a generalization of the half-time reconstruction approach. In the VTDT approach, the degree of temporal truncation for each measurement is determined by the distance between the corresponding transducer location and the nearest known bone or gas void location. Reconstructed images from a numerical phantom is employed to demonstrate the feasibility and effectiveness of the approach.
Specimen radiography--a mandatory adjunct to mammography.

The surgical specimens from 400 consecutive breast biopsies performed at the Virginia Mason Medical Center, Seattle, Washington, were radiographically examined, and the results were correlated with preoperative mammograms as well as clinical findings. Mammography was performed on 88.5% of the cases, and a total of 54 biopsies (13.5%) were performed because of suspicious radiographic microcalcifications without a palpable clinical mass. Specimen radiography was essential in these situations in order to document the adequacy of the biopsy and to localize the suspicious area for histologic examination. Fourteen (3.5%) clinically occult carcinomas were demonstrated in this manner. Seven of these were of microscopic size and most surely would have been missed had it not been for this procedure. Radiographic examination of the remaining 346 biopsy specimens yielded one additional microscopic occult carcinoma containing calcifications visible by specimen radiography but not mammographically. The application of this procedure in the pathology laboratory is discussed, and its essential relationship to preoperative mammography is stressed.
Effective Network Graphic Design

Achieving effective network graphic design is not that different from any other type of information graphic. As Edward Tufte pointed out in his seminal The Visual Display of Quantitative Information, “Graphical excellence is that which gives to the viewer the greatest number of ideas in the shortest time with the least ink in the smallest space.” Network graphics actually start out with an important advantage in that they typically have a high information/ink ratio.
Epidemiology Survey of Paragonimiasis in Several Counties of Zhejiang Province During 2000～2005

Objective To provide scientific basis for planning of prevention and control through the understanding of the prevalence of paragonimiasis in Zhejiang Province.Methods The crab eating habits of the inhabitants were studied by in- vestigation table.We dissected the crab to determine the situation of the crab infected by metacercaria.Intradermal test and ELISA were used to examine part of the population in nine villages.Result Eating raw crab rate was 37.66% according to the investigation table,metacercaria infection rate was 7,93% in dissected crabs.Positive rates of intradermal test were 15.94% and 2.27%,and antibody(Ab)positive rates of the population were 0.80% and 2.27% respectively in the counties of Qingyuan and Jingning.Ab positive rates of the population were 0 and 14.29% in the counties of Tiantai and Shaoxing. Conclusion The prevalence situation has changed in the old prevailing area of Zhejiang Province.Regular check-up and surveillance of epidemiology should be warranted.
Learning Cluster Analysis through Experience.

The field of machine learning is constantly developing useful new techniques for data analysis, but they are often ignored by researchers outside the field due to unfamiliarity and the difficulty of keeping up with a large body of work. We propose a methodology for training researchers how algorithms work through experience, such that they gain an implicit, rather than explicit, understanding of their function. Thus we combine theory from discovery learning with advanced software and a more educated target population to foster such understanding. We have developed an open source application for exploratory data analysis called Divvy that lets users quickly and visually interact with a range of data analysis techniques. Using a simplified version of Divvy, we find that undergraduate subjects are generally able to learn machine learning concepts through experience, though they have only partial success in applying them.
Tracking Blade Tip Vortices for Numerical Flow Simulations of Hovering Rotorcraft

Blade tip vortices generated by a helicopter rotor blade are a major source of rotor noise and airframe vibration. This occurs when a vortex passes closely by, and interacts with, a rotor blade. The accurate prediction of Blade Vortex Interaction (BVI) continues to be a challenge for Computational Fluid Dynamics (CFD). Though considerable research has been devoted to BVI noise reduction and experimental techniques for measuring the blade tip vortices in a wind tunnel, there are only a handful of post-processing tools available for extracting vortex core lines from CFD simulation data. In order to calculate the vortex core radius, most of these tools require the user to manually select a vortex core to perform the calculation. Furthermore, none of them provide the capability to track the growth of a vortex core, which is a measure of how quickly the vortex diffuses over time. This paper introduces an automated approach for tracking the core growth of a blade tip vortex from CFD simulations of rotorcraft in hover. The proposed approach offers an effective method for the quantification and visualization of blade tip vortices in helicopter rotor wakes. Keywords: vortex core, feature extraction, CFD, numerical flow visualization
Engineering Defined Motor Ensembles with DNA Origami

Many cytoskeletal motors function in groups to coordinate the spatial and temporal positioning of cellular cargo. While methods to study the biophysical properties of single motors are well established, methods to understand how multiple motors work synergistically or antagonistically are less well developed. Here, we describe a three-dimensional synthetic cargo structure made using DNA origami, which can be used to template defined numbers and types of cytoskeletal motors with programmable geometries and spacing. We describe methods for building the DNA origami structure, covalently attaching motors to DNA, forming the motor-DNA origami structure complex, and single-molecule assays to examine the motile properties of motor ensembles.
Nontherapeutic research, minimal risk, and the Kennedy Krieger lead abatement study.

rom 1993 through 1995, the Kennedy-Krieger Institute (KKI) conducted research that examined the effectiveness of three different methods of reducing environmental lead in older homes-each of which had already been demonstrated to reduce lead dust levels significantly (by 8o%) in affected homes. Funded in part by the Environmental Protection Agency (EPA), the "Lead-Based Paint Abatement and Repair and Maintenance Study" was intended to help landlords take advantage of state loan programs to make one of three lead reduction improvements. Environmental lead levels were measured using two different methods, one standard and the other experimental. In addition, blood lead levels of the young children living in the homes were monitored. Elevated blood lead levels in the chil-
Analog of the Riesz Theorem and the Basis Property in L p of a System of Root Functions of a Differential Operator : I

An ordinary differential operator of arbitrary order is considered. We find necessary conditions for the Riesz property of systems of normalized root functions, prove an analog of the Riesz theorem, and use it to obtain sufficient conditions for the basis property of a system of root functions of this operator in Lp.