cssi/SciSciGPT-SciSciNet huggingface dataset:
Duplex auditory distance assessment in a small passerine bird (Pipilo erythrophthalmus)

Eastern towhees, Pipilo erythrophthalmus, (Emberizidae, Passeriformes) in Florida estimate source sound-pressure level (SPL; i.e., sound amplitude) and often misjudge speaker distance in the field when vocalization source SPL is varied experimentally. Sound frequencies below ~3.5 kHz attenuate reliably with distance in comparison with higher sound frequencies in Florida scrub habitat. As a result, I predicted that towhees should use SPL as an auditory distance cue when they hear stimuli produced with sound frequencies below ~3.5 kHz but use another cue when they hear stimuli produced with sound frequencies above ~3.5 kHz. Subjects often misjudged speaker distance when approaching playbacks of SPL-altered stimuli produced with sound frequencies below ~3.5 kHz but rarely misjudged speaker distance when played SPL-altered stimuli produced with sound frequencies above ~3.5 kHz. I discuss the possibility that towhees employ a duplex sound localization strategy.
High Knudsen Number Thermal Flows with the D2Q13 Lattice Boltzmann Model

Lattice Boltzmann models have been successfully utilized to simulate conditions in rarefied flows. To further improve the characterization of transition flow expected in nano-scale channels, we explore implementing two wall-distance functions based on the integral of probability distribution functions to a D2Q13 model. A series of tests are performed to determine model performance in capturing the flow characteristics of highly rarefied conditions. The resulting model is validated using numerical data. The results show that the modified model is capable of simulating rarefied flow conditions, extending to the high end of the transition regime, up to Kn ∼ 5, representing a significant improvement over existing models.
Adenoviral-mediated gene transfer induces sustained pericardial VEGF expression in dogs: effect on myocardial angiogenesis.

Objective: Angiogenic peptides like VEGF (vascular endothelial growth factor) and bFGF (basic fibroblast growth factor) have entered clinical trials for coronary artery disease. Attempts are being made to devise clinically relevant means of delivery and to effect site-specific delivery of these peptides to the cardiac tissue, in order to limit systemic side-effects. We characterized the response of the pericardium to delivery of a replication-deficient adenovirus carrying the cDNA for AdCMV.VEGF , and assessed the effect of 165 pericardial VEGF on myocardial collateral development in a canine model of progressive coronary occlusion. Methods: Ameroid 165 9 constrictors were placed on the proximal left circumflex coronary artery of mongrel dogs. Ten days later, 6 310 pfu AdCMV.165 (n59), AdRSV.b-gal (n59), or saline (n57) were injected through an indwelling pericardial catheter. Transfection efficiency was assessed by X-gal staining. Pericardial and serum VEGF levels were measured serially by ELISA. Maximal myocardial collateral perfusion was quantified with radiolabeled or fluorescent microspheres 28 days after treatment. Results: In AdRSV.b-gal-treated dogs, there was extensive b-gal staining in the pericardium and epicardium, with minimal b-gal staining in the mid-myocardium and endocardium. Pericardial delivery of AdCMV.VEGF resulted in sustained (8-14 day) pericardial transgene expression, with VEGF 165
Inhibition of antiskin allograft immunity induced by infusions with photoinactivated effector T lymphocytes (PET cells). Is in vivo cell transferrable

We previously reported producing donor-specific tolerance to alloantigens by intravenous exposure to pretreated antidonor T cells. The current study extends that work by adoptively transferring the donor-specific tolerance into naive syngeneic recipients. Eight days after BALB/c mice received histoincompatible CBA/j skin grafts, their splenocytes which included an expanded population of cells mediating rejection were treated with 100 ng/ml 8-methoxypsoralen (8-MOP) photoactivated by 1 Joule/cm2 of ultraviolet A (UVA) light prior to infusion into naive BALB/c recipients. Whereas 8-MOP itself is biologically inert, photoactivated 8-MOP crosslinks DNA by covalently binding to pyrimidine bases. Recipient BALB/c mice which had been previously demonstrated to be hyporesponsive to CBA/j alloantigens in mixed leukocyte culture (MLC), cytotoxicity (CTL) and in vivo delayed type hypersensitivity (DTH) assays were the donors of spleen cells for the adoptive transfer experiments. Fifty to one hundred million viable spleen cells from these pretreated BALB/c mice were transferred into naive syngeneic recipients which then were tested for DTH response and allograft survival to the relevant and irrelevant antigens. The radiosensitivity of this transferrable suppression was evaluated by exposing the adoptively transferred cell population to 3200 rads of C-irradiation prior to cell transfer. The phenotype of the cells transferring this suppressive response was performed by depleting specific populations of cells with monoclonal antibodies prior to cell transfer. In vivo the DTH response of the pretreated BALB/c mice was specifically suppressed to the relevant alloantigen, correlating with retention of CBA/j skin grafts for up to 42 days post engraftment without visual evidence of rejection, in comparison to control mice complete rejection of the skin graft in less than 8 days. In vitro, splenocytes from BALB/c recipients of pretreated syngeneic splenocytes containing large numbers of BALB/c anti-CBA/j T cells proliferated less in MLC and generated lower cytotoxic T cell responses to CBA/j alloantigens than did controls and suppressed the naive and sensitized BALB/c MLC and CTL responses to CBA/j alloantigen. This specific suppressive response to alloantigen was optimally transferred into syngeneic naive recipients when the adoptive transfer was performed on the sixth day after the last infusion received by the spleen cell donor mice. The adoptive transfer of this suppressive response was abrogated by the prior X-irradiation of the donor spleen cells and significantly abolished by the depletion of Thy-1+, Lyt-2+, L3T4- T lymphocytes.(ABSTRACT TRUNCATED AT 400 WORDS)
Analytical approximation of complex band structures for band-to-band tunneling models

A unified analytical expression is developed to accurately describe the complex band structures in commonly used diamond and zinc-blende semiconductors. Fitting the model to the numerical complex band structures shows a significantly improved accuracy as compared with the effective mass approximation. The model is used to study the band-to-band tunneling in Si, Ge, GaAs and GaSb, with a maximum error of &#60;1.4% compared to the numerical band structures.
A prospective open-label study of mycophenolate mofetil for the treatment of diffuse systemic sclerosis

Objective. To evaluate the efficacy and safety of mycophenolate mofetil for the treatment of SSc. Methods. We recruited 15 patients with dcSSc to take part in an open-label study using mycophenolate mofetil to treat their disease over a 12-month period. The primary outcome measure was the modified Rodnan skin score (mRSS), whereas secondary outcomes included the Medsger severity score, pulmonary function studies, 2D echocardiograms and the Short Form Health Survey (SF)-36 questionnaire. Results. The mRSS significantly improved in those patients who tolerated the medication for >3 months (P < 0.0001), and there was a statistically significant improvement in the Medsger severity scores of the general (P ¼ 0.05), peripheral vascular involvement (P ¼ 0.05) and skin (P ¼ 0.0003) scores. The SF-36 scores improved (P ¼ 0.05) and the pulmonary function studies showed a trend towards improvement, though not of statistical significance. The mean pulmonary artery pressure by 2D echocardiography did not change. Conclusions. In this prospective open-label study of mycophenolate mofetil for the treatment of dcSSc, we observed significant improvements in skin scores, peripheral vascular involvement and patient-perceived health status. Pulmonary function studies did not worsen as expected, but instead showed a trend towards improvement. Controlled trials are needed to further investigate this trend for improved pulmonary function studies.
Core-Shell Nanowire Optical Antennas Fed by Slab Waveguides

A method of realizing nanoantenna systems at optical frequencies is suggested wherein a plasmonic nanowire is placed near a slab waveguide operating near the plasmonic resonant frequency of the nanowire. The polarizability of a nano-sized concentric cylindrical structure with the core made of an ordinary dielectrics and the shell made of a plasmonic material is calculated using Mie scattering theory. When such a core-shell nanowire is placed near a slab waveguide, the transverse magnetic (TM) surface wave guided by the waveguide can interact with the nanowire, and thus part of its energy is scattered into the open space. By reciprocity, under TM wave incidence, the induced dipole on the nanowire will launch a guided mode in the slab waveguide, thus converting part of the incident energy into the guided mode energy. A rigorous analytical treatment of the problem using the Green function of a dipole near a planar slab waveguide is developed, and the properties of such an optical antenna system are studied in detail. The finite element method is also utilized to demonstrate the idea directly.
Visualizing Loops Using a Game-Like Instructional Module

Loops are one of the most challenging concepts for students who are new to programming. This paper presents a game-like instructional module titled "Iterative Dungeon" that was designed to help students visualize the looping process. This module visualizes and reinforces the for loop, nested for loop and while loop. It has been used and evaluated in the CSC1310 Computer Programming I class during Fall 2012 at Winston-Salem State University (WSSU). To evaluate the impact of this module, a pre-test, a post-test, a survey, and interviews were conducted. Promising results, positive feedback and favorable comments from students show that this game module has positive impact on student learning.
Differential onset of median nerve block: randomized, double-blind comparison of mepivacaine and bupivacaine in healthy volunteers

We have compared the delay in onset of 1% mepivacaine and 0.33% bupivacaine in different nerve fibre types in 10 volunteers undergoing median nerve blocks, in a randomized, double-blind, crossover study. Hot, cold, pinprick and light touch sensations, compound motor action potentials (CMAP), sensory nerve action potentials (SNAP) and skin temperature were recorded at 2-min intervals. Hot, cold, pinprick, light touch sensations, SNAP and CMAP were significantly inhibited, and skin temperature was significantly increased after administration of both agents. The first noticeable reduction in cold sensation was detected later after bupivacaine compared with mepivacaine, but after a delay similar to that of other nerve functions. Bupivacaine and mepivacaine inhibited SNAP and CMAP with a similar time delay to steady-state. Bupivacaine produced steady-state inhibition of hot and cold sensations significantly later than mepivacaine; nevertheless, the sequence that sensory modalities failed, with few exceptions, and the extent of anaesthesia at 40 min were similar for both agents. Our technique provides a novel, multi-modal method of comparing local anaesthetics and related agents over time.
Distributed multi-pole model for motion simulation of PM-based spherical motors

Design and control of multi degrees of freedom (DOF) electromagnetic actuators require a good understanding of the magnetic fields, and involve real-time calculation of magnetic forces. This paper presents a new method to derive closed-form solutions for characterizing the magnetic field of permanent magnets (PM), and their uses in modeling the magnetic torque of a PM-based spherical motor. The method, referred here as distributed multi-pole (DMP) model, inherits many advantages of the dipole model originally conceptualized in the context of physics, but provides an effective means to account for the shape and magnetization of the physical magnet. The DMP models have been validated by comparing the calculated fields and magnetic forces against numerical and experimental results. The comparisons show excellent agreement. We also illustrate the application of the DMP model in developing an accurate torque model to faithfully simulate the transient response of a spherical motor, and as a basis for deriving a closed-form inverse torque model for its real-time current optimization. While developed in the context of a spherical motor, the modeling techniques presented in this paper are applicable to other PM-based actuator and sensing systems.
Do Time, Heterochromatin, NORs, or Chromosomal Rearrangements Correlate with Distribution of Interstitial Telomeric Repeats in Sigmodon (Cotton Rats)?

We studied the chromosomal distribution of telomere repeats (TTAGGG)n in 8 species of Sigmodon (cotton rats) using chromosome paints fluorescent in situ hybridization (FISH) from Sigmodon hispidus. In 2 species with the proposed primitive karyotype for the genus, telomere repeats were restricted to telomeric sites. But in the other 6 species that include 3 with proposed primitive karyotypes and 3 with highly rearranged karyotypes, telomere repeats were found on both telomeric sites and within interstitial telomeric sites (ITSs). To explain the distribution of ITS in Sigmodon, we gather data from C-bands, silver nitrate staining, G-bands, and chromosomal paint data from previous published studies. We did find some correlation with ITS and heterochromatin, euchromatic chromosomal rearrangements, and nucleolar organizing regions. No one type of chromosomal structure explains all ITS in Sigmodon. Multiple explanations and mechanisms for movement of intragenomic sequences are required to explain ITS in this genus. We rejected the hypothesis that age of a lineage correlates with the presence of ITS using divergence time estimate analyses. This multigene phylogeny places species with ITS (S. arizonae, S. fulviventer, S. hispidus, S. mascotensis, S. ochrognathus, and S. toltecus) in the clade with a species without ITS (S. hirsutus). Lineages with ITS (S. arizonae and S. mascotensis) arose independently from a lineage absent of ITS (S. hirsutus) around 0.67 to 0.83 Ma. The rearranged karyotypes of S. mascotensis and S. arizonae appear to be an independently derived autapomorphic characters, supporting a fast rate of chromosomal changes that vary among species.
H2B Ubiquitylation Plays a Role in Nucleosome Dynamics during Transcription Elongation

The monoubiquitylation of histone H2B has been associated with transcription initiation and elongation, but its role in these processes is poorly understood. We report that H2B ubiquitylation is required for efficient reassembly of nucleosomes during RNA polymerase II (Pol II)-mediated transcription elongation in yeast. This role is carried out in cooperation with the histone chaperone Spt16, and in the absence of H2B ubiquitylation and functional Spt16, chromatin structure is not properly restored in the wake of elongating Pol II. Moreover, H2B ubiquitylation and Spt16 play a role in each other's regulation. H2B ubiquitylation is required for the stable accumulation of Spt16 at the GAL1 coding region, and Spt16 regulates the formation of ubiquitylated H2B both globally and at the GAL1 gene. These data provide a mechanism linking H2B ubiquitylation to Spt16 in the regulation of nucleosome dynamics during transcription elongation.
What Good Are Positive Emotions

This article opens by noting that positive emotions do not fit existing models of emotions. Consequently, a new model is advanced to describe the form and function of a subset of positive emotions, including joy, interest, contentment, and love. This new model posits that these positive emotions serve to broaden an individual's momentary thought-action repertoire, which in turn has the effect of building that individual's physical, intellectual, and social resources. Empirical evidence to support this broadenand-build model of positive emotions is reviewed, and implications for emotion regulation and health promotion are discussed. Even though research on emotions has this new perspective are featured. My hope is flourished in recent years, investigations that that this article will unlock scientific curiosity expressly target positive emotions remain few and far between. Any review of the psychological literature on emotions will show that psychologists have typically favored negative emotions in theory building and hypothesis testing. In so doing, psychologists have inadvertently marginalized the emotions, such as joy, about positive emotions, not only to test the ideas presented here, but also to build other new models that might illuminate the nature and value of positive emotions. Psychology sorely needs more studies on positive emotions, not simply to level the uneven knowledge bases between negative and positive emotions, but interest, contentment, and love, that share a more critically, to guide applications and pleasant subjective feel. To date, then, psychology's knowledge base regarding positive emotions is so thin that satisfying answers to the question "What good are positive emotions?" have yet to be articulated. This is unfortunate. Experiences of positive emotion are central to human nature and contribute richly to the quality of people's lives (Diener & Larsen,
Enhanced biclustering on expression data

Microarrays are one of the latest breakthroughs in experimental molecular biology, which provide a powerful tool by which the expression patterns of thousands of genes can be monitored simultaneously and are already producing huge amount of valuable data. The concept of bicluster was introduced by Cheng and Church (2000) to capture the coherence of a subset of genes and a subset of conditions. A set of heuristic algorithms were also designed to either find one bicluster or a set of biclusters, which consist of iterations of masking null values and discovered biclusters, coarse and fine node deletion, node addition, and the inclusion of inverted data. These heuristics inevitably suffer from some serious drawback. The masking of null values and discovered biclusters with random numbers may result in the phenomenon of random interference which in turn impacts the discovery of high quality biclusters. To address this issue and to further accelerate the biclustering process, we generalize the model of bicluster to incorporate null values and propose a probabilistic algorithm (FLOC) that can discover a set of k possibly overlapping biclusters simultaneously. Furthermore, this algorithm can easily be extended to support additional features that suit different requirements at virtually little cost. Experimental study on the yeast gene expression data shows that the FLOC algorithm can offer substantial improvements over the previously proposed algorithm.
Webcams in context: web interfaces to create live 3D environments

Web services supporting deep integration between video data and geographic information systems (GIS) empower a large user base to build on popular tools such as Google Earth and Google Maps. Here we extend web interfaces designed explicitly for novice users to integrate streaming video with 3D GIS, and work to dramatically simplify the task of retexturing 3D scenes from live imagery. We also derive and implement constraints to use corresponding points to calibrate popular pan-tilt-zoom webcams with respect to GIS applications, so that the calibration is automatically updated as web users adjust the camera zoom and view direction. These contributions are demonstrated in a live web application implemented on the Google Earth Plug-in, within which hundreds of users have already geo-registered streaming cameras in hundreds of scenes to create live, updating textures in 3D scenes.
Signal-Dependent Protein Synthesis by Activated Platelets: New Pathways to Altered Phenotype and Function

New biologic activities of platelets continue to be discovered, indicating that concepts of platelet function in hemostasis, thrombosis, and inflammation require reconsideration as new paradigms evolve. Studies done over 3 decades ago demonstrated that mature circulating platelets have protein synthetic capacity, but it was thought to be low level and inconsequential. In contrast, recent discoveries demonstrate that platelets synthesize protein products with important biologic activities in a rapid and sustained fashion in response to cellular activation. This process, termed signal-dependent translation, uses a constitutive transcriptome and specialized pathways, and can alter platelet phenotype and functions in a fashion that can have clinical relevance. Signal-dependent translation and consequent protein synthesis are examples of a diverse group of posttranscriptural mechanisms in activated platelets that are now being revealed.
Viscous effects in droplet-ejecting capillary waves

Surface waves produced by parametric excitation experience a transition between simply connected waves and droplet-ejecting waves when the applied forcing exceeds a threshold level. Our measurements on a number of different fluids indicate that low-viscosity fluids have threshold accelerations which depend on only surface tension and forcing frequency while high viscosity fluids have thresholds which depend on only viscosity and forcing frequency. Models for the transition based on the condition that the wavelength, waveheight ratio approaches a fixed value at the transition are consistent with our observations.
An analysis of surface/wire currents and charges of commercially available passive UHF RFID tag antennas

An analysis of surface currents and charges, as well as wire current variations in passive UHF RFID tags are presented to illuminate differences in tag antenna designs. Surface and wire current or charge distributions are known to be important parameters in distinguishing the radiation pattern of passive tags in the far field, and has been shown recently to have severe consequences on directivity patterns of passive UHF tags on products containing non-RF translucent materials. Commercially available passive tags are used to study the variations of these parameters, where a detail comparison is performed with the typical UHF RFID dipole tag antenna. Issues regarding segment currents are also introduced in order to initiate discussions regarding the physical variations of tags, such as deformities due to curvatures.
Density functional theory and molecular dynamics studies of the energetics and kinetics of electroactive polymers: PVDF and P(VDF-TrFE)

We used first principles methods to study static and dynamical mechanical properties of the ferroelectric polymer poly(vinylidene fluoride) (PVDF) and its copolymer with trifluoro ethylene (TrFE). We use density functional theory [within the generalized gradient approximation (DFT-GGA)] to calculate structure and energetics for various crystalline phases for PVDF and P(VDF-TrFE). We find that the lowest energy phase for PVDF is a nonpolar crystal with a combination of trans (T) and gauche (G) bonds; in the case of the copolymer the role of the extra (bulkier) F atoms is to stabilize T bonds. This leads to the higher crystallinity and piezoelectricity observed experimentally. Using the MSXX first principles-based force field (FF) with molecular dynamics (MD), we find that the energy barrier necessary to nucleate a kink (gauche pairs separated by trans bonds) in an all-T crystal is much lower (14.9 kcal/mol) in P(VDF-TrFE) copolymer than in PVDF (24.8 kcal/mol). This correlates with the observation that the polar phase of the copolymer exhibits a solid-solid transition to a nonpolar phase under heating while PVDF directly melts. We also studied the mobility of an interface between polar and nonpolar phases under uniaxial stress; we find a lower threshold stress and a higher mobility in the copolymer as compared with PVDF. Finally, considering plastic deformation under applied shear, we find that the chains for P(VDF-TrFE) have a very low resistance to sliding, particularly along the chain direction. The atomistic characterization of these "unit mechanisms" provides essential input to mesoscopic or macroscopic models of electro-active polymers.
A Pathwise Algorithm for Covariance Selection

Covariance selection seeks to estimate a covariance matrix by maximum likelihood while restricting the number of nonzero inverse covariance matrix coefficients. A single penalty parameter usually controls the tradeoff between log likelihood and sparsity in the inverse matrix. We describe an efficient algorithm for computing a full regularization path of solutions to this problem.
Playing with Butler and Foucault: Bisexuality and Queer Theory

Scholars writing on the topic of bisexual identity frequently lament the lack of bisexual representation in works of queer theorists. However, though the problem has been noted, it has yet to be addressed within the main body of queer theory. The seminal works of this theoretical school, written by authors such as Michel Foucault, Judith Butler, Diana Fuss and Eve Sedgwick, all bypassed bisexuality as a topic of inquiry even while writing against binary, biological models of gender and sexuality. Works written within the last 15 years, often in response to or building off of these early works, have for the most part continued to ignore the numerous questions posed by bisexuality. I argue that queer theory would be strengthened by turning the lens onto bisexual subjects and realities. To show the utility of such an addition, this article will take on two of queer theories most cited works, Foucault's The History of Sexuality (1978) and Butler's Gender Trouble (1990/2006). By writing bisexuality into these ...
Priority inheritance protocols: an approach to real-time synchronization

An investigation is conducted of two protocols belonging to the priority inheritance protocols class; the two are called the basic priority inheritance protocol and the priority ceiling protocol. Both protocols solve the uncontrolled priority inversion problem. The priority ceiling protocol solves this uncontrolled priority inversion problem particularly well; it reduces the worst-case task-blocking time to at most the duration of execution of a single critical section of a lower-priority task. This protocol also prevents the formation of deadlocks. Sufficient conditions under which a set of periodic tasks using this protocol may be scheduled is derived. >
First place winner

Nutritional rickets is a serious disease that is infrequently encountered in the United States today because of the fortification of infant formulas and dairy products with vitamin D. We report a case of undiagnosed nutritional rickets presenting with recurrent febrile seizures. Febrile seizures, a common and usually benign presenting complaint, are not among the symptoms generally known to be associated with rickets. Therefore, the disease was uncovered only after a careful history and physical examination prompted a more thorough investigation into an underlying cause for recurrent seizures. The diagnosis was subsequently confirmed by quantitative laboratory testing. We review the historical and cultural factors, symptoms, and physical findings suggestive of this potentially serious yet easily treatable disease.
Composition and occurrence of electrum at the Morning Star Deposit, San Bernardino County, California; evidence for remobilization of gold and silver

Electrum, acanthite and uytenbogaardtite have been examined from six depths within the tabular quartz+ or -calcite stockwork and breccia-filled veins in the fault-zone-hosted Morning Star deposit of the northeastern Mojave Desert, California. Six distinct types of electrum have been identified on the basis of mineral association, grain morphology and composition. Two types, (1) pyrite-hosted and (2) quartz-hosted electrum, occur with acanthite after argentite and base-metal sulfide minerals in unoxidized portions of the orebody; the remaining four types, (3) goethite-hosted electrum, (4) electrum cores, (5) electrum rims and (6) wire electrum, are associated with assemblages of supergene minerals in its oxidized portions. Pyrite-hosted, quartz-hosted and goethite-hosted electrum range in composition from 61 to 75 wt.% Au and have uniform textures and no zoning. In lower portions of the oxidized ore zone, electrum seems to replace goethite and occurs as small grains on surfaces of the goethite. Textural evidence favors supergene remobilization of Au and Ag, which were deposited as electrum on or replacing goethite. This type of electrum is identical in appearance and composition to primary electrum. In the upper portions of the oxidized zone, secondary electrum occurs as a gold-rich rim on a core of electrum and as wire-like grains, both with acanthite and uytenbogaardtite. Such secondary electrum contains from 78 to 93 wt.% Au. Textural relations and associated minerals suggest that the primary electrum was hydrothermally deposited and partially remobilized by supergene processes.
CUDAMPF: a multi-tiered parallel framework for accelerating protein sequence search in HMMER on CUDA-enabled GPU

HMMER software suite is widely used for analysis of homologous protein and nucleotide sequences with high sensitivity. The latest version of hmmsearch in HMMER 3.x, utilizes heuristic-pipeline which consists of MSV/SSV (Multiple/Single ungapped Segment Viterbi) stage, P7Viterbi stage and the Forward scoring stage to accelerate homology detection. Since the latest version is highly optimized for performance on modern multi-core CPUs with SSE capabilities, only a few acceleration attempts report speedup. However, the most compute intensive tasks within the pipeline (viz., MSV/SSV and P7Viterbi stages) still stand to benefit from the computational capabilities of massively parallel processors. A Multi-Tiered Parallel Framework (CUDAMPF) implemented on CUDA-enabled GPUs presented here, offers a finer-grained parallelism for MSV/SSV and Viterbi algorithms. We couple SIMT (Single Instruction Multiple Threads) mechanism with SIMD (Single Instructions Multiple Data) video instructions with warp-synchronism to achieve high-throughput processing and eliminate thread idling. We also propose a hardware-aware optimal allocation scheme of scarce resources like on-chip memory and caches in order to boost performance and scalability of CUDAMPF. In addition, runtime compilation via NVRTC available with CUDA 7.0 is incorporated into the presented framework that not only helps unroll innermost loop to yield upto 2 to 3-fold speedup than static compilation but also enables dynamic loading and switching of kernels depending on the query model size, in order to achieve optimal performance. CUDAMPF is designed as a hardware-aware parallel framework for accelerating computational hotspots within the hmmsearch pipeline as well as other sequence alignment applications. It achieves significant speedup by exploiting hierarchical parallelism on single GPU and takes full advantage of limited resources based on their own performance features. In addition to exceeding performance of other acceleration attempts, comprehensive evaluations against high-end CPUs (Intel i5, i7 and Xeon) shows that CUDAMPF yields upto 440 GCUPS for SSV, 277 GCUPS for MSV and 14.3 GCUPS for P7Viterbi all with 100 % accuracy, which translates to a maximum speedup of 37.5, 23.1 and 11.6-fold for MSV, SSV and P7Viterbi respectively. The source code is available at https://github.com/Super-Hippo/CUDAMPF .
Integration host factor assembly at the cohesive end site of the bacteriophage lambda genome: implications for viral DNA packaging and bacterial gene regulation.

Integration host factor (IHF) is an Escherichia coli protein involved in (i) condensation of the bacterial nucleoid and (ii) regulation of a variety of cellular functions. In its regulatory role, IHF binds to a specific sequence to introduce a strong bend into the DNA; this provides a duplex architecture conducive to the assembly of site-specific nucleoprotein complexes. Alternatively, the protein can bind in a sequence-independent manner that weakly bends and wraps the duplex to promote nucleoid formation. IHF is also required for the development of several viruses, including bacteriophage lambda, where it promotes site-specific assembly of a genome packaging motor required for lytic development. Multiple IHF consensus sequences have been identified within the packaging initiation site (cos), and we here interrogate IHF–cos binding interactions using complementary electrophoretic mobility shift (EMS) and analytical ultracentrifugation (AUC) approaches. IHF recognizes a single consensus sequence within co...
Rationale for and Methods of Splenic Preservation Following Trauma

The best way to prevent overwhelming postsplenectomy sepsis is to preserve as much viable splenic tissue as possible in its normal location. Conservative management of splenic injuries can be successful, especially in children. In adults, there are many technical procedures that make repair of splenic injury practical. If splenectomy cannot be avoided, deliberate autotransplantation of fragments of splenic tissue, combined with pneumococcal vaccine prophylaxis, has been reported to be effective experimentally. Patients who require splenectomy for trauma should be immunized with polyvalent pneumococcal vaccine.
Active search and bandits on graphs using sigma-optimality

Many modern information access problems involve highly complex patterns that cannot be handled by traditional keyword based search. Active Search is an emerging paradigm that helps users quickly find relevant information by efficiently collecting and learning from user feedback. We consider active search on graphs, where the nodes represent the set of instances users want to search over and the edges encode pairwise similarity among the instances. Existing active search algorithms are either short of theoretical guarantees or inadequate for graph data. Motivated by recent advances in active learning on graphs, namely the Σ-optimality selection criterion, we propose new active search algorithms suitable for graphs with theoretical guarantees and demonstrate their effectiveness on several real-world datasets. We relate our active search setting to multi-armed bandits whose rewards are binary values indicating search hits or misses and arms cannot be pulled more than once. We also discussed theoretical guarantees for applying Σ-optimality as the exploration term for bandits on graphs.
Persistent Clocks for Batteryless Sensing Devices

Sensing platforms are becoming batteryless to enable the vision of the Internet of Things, where trillions of devices collect data, interact with each other, and interact with people. However, these batteryless sensing platforms—that rely purely on energy harvesting—are rarely able to maintain a sense of time after a power failure. This makes working with sensor data that is time sensitive especially difficult. We propose two novel, zero-power timekeepers that use remanence decay to measure the time elapsed between power failures. Our approaches compute the elapsed time from the amount of decay of a capacitive device, either on-chip Static Random-Access Memory (SRAM) or a dedicated capacitor. This enables hourglass-like timers that give intermittently powered sensing devices a persistent sense of time. Our evaluation shows that applications using either timekeeper can keep time accurately through power failures as long as 45s with low overhead.
Structures of the kinetically trapped i-motif DNA intermediates

In the present work, the conformational dynamics and folding pathways of i-motif DNA were studied in solution and in the gas-phase as a function of the solution pH conditions using circular dichroism (CD), photoacoustic calorimetry analysis (PAC), trapped ion mobility spectrometry-mass spectrometry (TIMS-MS), and molecular dynamics (MD). Solution studies showed at thermodynamic equilibrium the existence of a two-state folding mechanism, whereas during the pH = 7.0 → 4.5 transition a fast and slow phase (ΔHfast + ΔHslow = 43 ± 7 kcal mol−1) with a volume change associated with the formation of hemiprotonated cytosine base pairs and concomitant collapse of the i-motif oligonucleotide into a compact conformation were observed. TIMS-MS experiments showed that gas-phase, kinetically trapped i-motif DNA intermediates produced by nanoESI are preserved, with relative abundances depending on the solution pH conditions. In particular, a folded i-motif DNA structure was observed in nanoESI-TIMS-MS for low charge states in both positive and negative ion mode (e.g., z = ±3 to ±5) at low pH conditions. As solution pH increases, the cytosine neutralization leads to the loss of cytosine–cytosine+ (C·CH+) base pairing in the CCC strands and in those conditions we observe partially unfolded i-motif DNA conformations in nanoESI-TIMS-MS for higher charge states (e.g., z = −6 to −9). Collisional induced activation prior to TIMS-MS showed the existence of multiple local free energy minima, associated with the i-motif DNA unfolding at z = −6 charge state. For the first time, candidate gas-phase structures are proposed based on mobility measurements of the i-motif DNA unfolding pathway. Moreover, the inspection of partially unfolded i-motif DNA structures (z = −7 and z = −8 charge states) showed that the presence of inner cations may or may not induce conformational changes in the gas-phase. For example, incorporation of ammonium adducts does not lead to major conformational changes while sodium adducts may lead to the formation of sodium mediated bonds between two negatively charged sides inducing the stabilization towards more compact structures in new local, free energy minima in the gas-phase.
Brain transcriptomes of harbor seals demonstrate gene expression patterns of animals undergoing a metabolic disease and a viral infection

Diseases of marine mammals can be difficult to diagnose because of their life history and protected status. Stranded marine mammals have been a particularly useful resource to discover and comprehend the diseases that plague these top predators. Additionally, advancements in high-throughput sequencing (HTS) has contributed to the discovery of novel pathogens in marine mammals. In this study, we use a combination of HTS and stranded harbor seals (Phoca vitulina) to better understand a known and unknown brain disease. To do this, we used transcriptomics to evaluate brain tissues from seven neonatal harbor seals that expired from an unknown cause of death (UCD) and compared them to four neonatal harbor seals that had confirmed phocine herpesvirus (PhV-1) infections in the brain. Comparing the two disease states we found that UCD animals showed a significant abundance of fatty acid metabolic transcripts in their brain tissue, thus we speculate that a fatty acid metabolic dysregulation contributed to the death of these animals. Furthermore, we were able to describe the response of four young harbor seals with PhV-1 infections in the brain. PhV-1 infected animals showed a significant ability to mount an innate and adaptive immune response, especially to combat viral infections. Our data also suggests that PhV-1 can hijack host pathways for DNA packaging and exocytosis. This is the first study to use transcriptomics in marine mammals to understand host and viral interactions and assess the death of stranded marine mammals with an unknown disease. Furthermore, we show the value of applying transcriptomics on stranded marine mammals for disease characterization.
Sensing on ubiquitous surfaces via vibration signals: poster

This work explores vibration-based sensing to determine the location of a touch on extended surface areas as well as identify the object touching the surface leveraging a single sensor. It supports a broad array of applications through either passive or active sensing using only a single sensor. In the passive sensing, the received vibration signals are determined by the location of the touch impact. This allows location discrimination of touches precise enough to enable emerging applications such as virtual keyboards on ubiquitous surfaces for mobile devices. Moreover, in the active mode, the received vibration signals carry richer information of the touching object's characteristics (e.g., weight, size, location and material). This further enables our work to match the signals to the trained profiles and allows it to differentiate personal objects in contact with any surface. We evaluated extensively in the use cases of localizing touches (i.e., virtual keyboards), object localization and identification. Our experimental results demonstrate that the proposed vibration-based solution can achieve high accuracy, over 95%, in all these use cases.
Pulsed Nano-ESI Atmospheric-Pressure Ion Mobility Mass Spectrometry with Enhanced Ion Sampling.

Ion mobility-mass spectrometry (IM-MS) has gained considerable attention for detection of clusters and weakly bound species created by electrospray ionization (ESI). Atmospheric-pressure (AP) IM-MS offers an advantage in these studies compared to its low-pressure counterpart, owing to soft introduction of ions into the mobility cell with minimal ion activation. Here, we report new approaches to improve the sensitivity and soft ion introduction in AP-IM-MS. For the former, we demonstrate enhanced aerodynamic sampling of ions from the mobility cell into the MS using pulsed-field sampling. In this approach, ions are driven toward the MS, and the field is shut down once the ions reach the vicinity of the MS inlet orifice. The pulsed-field operation provides arrival times without the need for an exit ion gate in the mobility cell and leads to improvements in sensitivity of up to 1 order of magnitude. For soft ion generation, we report a pulsed nano-ESI source to introduce a packet of ions into the room-tempera...
Using the breast reconstruction risk assessment (BRA) score: An individualized risk calculator to assist expectation management and reconstructive decision making in the mastectomy patient

Breast reconstructive surgery carries tremendous psychosocial benefit to women who have undergone mastectomy. Over 100,000 of these reconstructive operations are performed every year in the United States alone. A plethora of literature exists to delineate pros, cons, risks, and benefits of the various autologous and prosthetic techniques in a reconstructive surgeon’s arsenal. However, this information can be difficult to assimilate in the context an individual patient with her unique combination of clinical and demographic characteristics. Risk calculators have made promising steps toward individualized care and decision-making. The Breast Reconstruction Risk Assessment (BRA) Score, is an online and mobile app that assists the patient and surgeon in the postmastectomy reconstructive decision. By estimating a patient’s risk of complications, given her preoperative information, the BRA Score provides an easy-to-use tool for a more individualized, patient-centered cancer care plan.
A 42-Year-Old Woman With Anemia, Shock, and Ischemic Stroke After Lung Transplantation

Case Presentation A 42-year-old woman with mixed connective tissue disease-associated interstitial lung disease underwent bilateral lung transplantation. She had an uneventful surgery and was extubated 3 h later. Induction immunosuppression therapy included methylprednisolone 500 mg intraoperatively, basiliximab (anti-IL-2 monoclonal antibody) on days 0 and 4 after transplantation, and methylprednisolone 125 mg intravenously bid for 2 days following surgery. Maintenance immunosuppression therapy consisted of prednisone 20 mg daily, mycophenolate mofetil 750 mg bid, and enteral tacrolimus 0.5 mg bid. Both the donor and the recipient were seropositive for cytomegalovirus. Infectious disease prophylaxis consisted of valganciclovir, trimethoprim-sulfamethoxazole, and voriconazole.
Existence of classical sonic-supersonic solutions for the pseudo steady Euler equations

We construct the sonic-supersonic solution for the two dimensional isentropic Euler equations in the self-similar plane, given the location of the sonic curve and the prescribed flow angle and speed along it. The system is degenerate and loses the hyperbolicity on the sonic curve. Singular terms also come in there. With these features, we perform a novel coordinate change and set up a proper function space with weighted metric, which yield the contraction of the solution scheme and prove the existence.
Physician Payment Reform - Progress to Date.

This Health Policy Report describes major reforms to physician payment that are under way in the United States as a result of the Affordable Care Act and the Medicare Access and CHIP Reauthorization ACT of 2015.
Black silicon as a multifunctional material for medical implants: First demonstrated use in in-vivo intraocular pressure sensing

We report the first in vivo demonstrated use of multifunctional black silicon (b-Si) on medical implants. B-Si is integrated onto the surface of a highly miniaturized sub-mm implantable intraocular pressure (IOP) sensor. This integration has significantly improved sensor signal-to-noise ratio (SNR) through the suppression of background noise as well as durability through minimized device biofouling. The incorporation of b-Si has enabled the use of a slit-lamp, the most widely used clinical ophthalmic microscope, for real-time IOP measurements on fully awake rabbits at a world-record 12-cm readout distance. Furthermore, b-Si has shown remarkable antifouling properties during a 6-month in vivo study by minimizing tissue proliferation and encapsulation on the ocular implant, promising much improved long-term implant serviceability.
Abstracting resource effects

In developing secure programs, reasoning about effects on resources can be hindered by obscure changes in program state. Effect systems mitigate this difficulty by describing these changes, but may require large amounts of low-level effect annotations, and create obstacles for reasoning. To reduce overhead, we propose an effect system, with a focus on system resources, that supports effect abstraction. It is being implemented in Wyvern, a capability-safe language.
OCCULT PAGET'S DISEASE OF THE ANUS: REPORT OF A CASE.

A unique case of Paget’s disease of the anus is presented. The condition was entirely asymptomatic, produced no gross changes in the skin, and was associated with a polypoid adenocarcinoma of the anorectal junction. ThePaget cells persisted for more than a year after apparently complete removal of the tumor. Several histologic stains showed a close relationship between the tumor and the abnormal cells. Various concepts regarding the etiology of these mucus-producing cells are outlined, and an important reason for recognizing them in tissue sections is suggested.
Pelvic Tuberculosis Diagnosed during Operative Laparoscopy for Suspected Ovarian Cancer.

Background. While the combination of a pelvic mass, very high serum level of CA-125, chest adenopathy, and ascites is concerning for advanced-stage ovarian cancer, the etiology of such a presentation can be due to disseminated pelvic tuberculosis. Case. A 67-year-old para 2 African-American woman presented with abdominal pain and shortness of breath. Subsequent CT and MR imaging demonstrated chest adenopathy, a pelvic mass, omental caking, and ascites. The patient underwent diagnostic laparoscopy with biopsy revealing noncaseating granulomas and subsequent tissue culture revealed Mycobacterium tuberculosis. The patient was diagnosed with disseminated pelvic tuberculosis and multidrug therapy was initiated. Conclusion. Pelvic tuberculosis can mimic advanced-stage ovarian cancer; thus obtaining a tissue sample may be beneficial to more appropriately direct treatment and planning for neoadjuvant therapies given the ineffectiveness of extensive surgical procedures in treating pelvic tuberculosis commonly employed in the treatment of advanced-stage ovarian cancer.