gebhart/patrepeval huggingface dataset:
Pf155/RESA protein influences the dynamic microcirculatory behavior of ring-stage Plasmodium falciparum infected red blood cells (2012)

Proteins exported by Plasmodium falciparum to the red blood cell (RBC) membrane modify the structural properties of the parasitized RBC (Pf-RBC). Although quasi-static single cell assays show reduced ring-stage Pf-RBCs deformability, the parameters influencing their microcirculatory behavior remain unexplored. Here, we study the dynamic properties of ring-stage Pf-RBCs and the role of the parasite protein Pf155/Ring-Infected Erythrocyte Surface Antigen (RESA). Diffraction phase microscopy revealed RESA-driven decreased Pf-RBCs membrane fluctuations. Microfluidic experiments showed a RESA-dependent reduction in the Pf-RBCs transit velocity, which was potentiated at febrile temperature. In a microspheres filtration system, incubation at febrile temperature impaired traversal of RESA-expressing Pf-RBCs. These results show that RESA influences ring-stage Pf-RBCs microcirculation, an effect that is fever-enhanced. This is the first identification of a parasite factor influencing the dynamic circulation of young asexual Pf-RBCs in physiologically relevant conditions, offering novel possibilities for interventions to reduce parasite survival and pathogenesis in its human host.
A new voting based hardware data prefetch scheme (2002)

The dramatic increase in the processor memory gap in recent years has led to the development of techniques like data prefetching that hide the latency of cache misses. Two such hardware techniques are the stream buffer and the stride predictor. They have dissimilar architectures, are effective for different kinds of memory access patterns and require different amounts of extra memory bandwidth. We compare the performance of these two techniques and propose a scheme that unifies them. Simulation studies on six benchmark programs confirm that the combined scheme is more effective in reducing the average memory access time (AMAT) than either of the two individually.
Directional 3-D interpolation technique for volume rendering (2002)

A 3-D interpolation method is proposed as the preprocessing step for 3-D visualization to compensate the poor interslice resolution in 3-D medical imaging. The proposed method uses the surface information which is obtained at each voxel using local gradients. If the voxel to be interpolated is found on a surface or in its vicinity, interpolation is performed along the direction parallel to the surface; otherwise interpolation is done along the vertical z-direction. Since the method uses correlation information inherent in 3-D data effectively, it can provide the interpolated image which preserves the surface smoothness and also reduces the interpolation error near the surface. As experimental results, volume rendering and cut-view images of interpolated 3-D medical data are presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Replication Kinetics for a Reporter Merkel Cell Polyomavirus (2022)

Merkel cell polyomavirus (MCV) causes one of the most aggressive human skin cancers, but laboratory studies on MCV replication have proven technically difficult. We report the first recombinase-mediated MCV minicircle (MCVmc) system that generates high levels of circularized virus, allowing facile MCV genetic manipulation and characterization of viral gene expression kinetics during replication. Mutations to Fbw7, Skp2, β-TrCP and hVam6p interaction sites, or to the stem loop sequence for the MCV-encoded miRNA precursor, markedly increase viral replication, whereas point mutation to an origin-binding site eliminates active virus replication. To further increase the utility of this system, an mScarlet fusion protein was inserted into the VP1 c-terminus to generate a non-infectious reporter virus for studies on virus kinetics. When this reporter virus genome is heterologously expressed together with MCV VP1 and VP2, virus-like particles are generated. The reporter virus genome is encapsidated and can be used at lower biosafety levels for one-round infection studies. Our findings reveal that MCV has multiple, self-encoded viral restriction mechanisms to promote viral latency over lytic replication, and these mechanisms are now amenable to examination using a recombinase technology.
New perspective on conceptus estrogens in maternal recognition and pregnancy establishment in the pig† (2019)

The proposed signal for maternal recognition of pregnancy in pigs is estrogen (E2), produced by the elongating conceptuses between days 11 to 12 of pregnancy with a more sustained increase during conceptus attachment and placental development on days 15 to 30. To understand the role of E2 in porcine conceptus elongation and pregnancy establishment, a loss-of-function study was conducted by editing aromatase (CYP19A1) using CRISPR/Cas9 technology. Wild-type (CYP19A1+/+) and (CYP19A1-/-) fibroblast cells were used to create embryos through somatic cell nuclear transfer, which were transferred into recipient gilts. Elongated and attaching conceptuses were recovered from gilts containing CYP19A1+/+ or CYP19A1-/- embryos on day 14 and 17 of pregnancy. Total E2 in the uterine flushings of gilts with CYP19A1-/- embryos was lower than recipients containing CYP19A1+/+ embryos with no difference in testosterone, PGF2α, or PGE2 on either day 14 or 17. Despite the loss of conceptus E2 production, CYP19A1-/- conceptuses were capable of maintaining the corpora lutea. However, gilts gestating CYP19A1-/- embryos aborted between days 27 and 31 of gestation. Attempts to rescue the pregnancy of CYP19A1-/- gestating gilts with exogenous E2 failed to maintain pregnancy. However, CYP19A1-/- embryos could be rescued when co-transferred with embryos derived by in vitro fertilization. Endometrial transcriptome analysis revealed that ablation of conceptus E2 resulted in disruption of a number biological pathways. Results demonstrate that intrinsic E2 conceptus production is not essential for pre-implantation development, conceptus elongation, and early CL maintenance, but is essential for maintenance of pregnancy beyond 30 days .
Random Forest Classification For P300 Based Brain Computer Interface Applications (2013)

Publication in the conference proceedings of EUSIPCO, Marrakech, Morocco, 2013
Microbiological impact of atrazine pollution in river sediment and soil (2004)

Atrazine is a frequently detected pollutant in agricultural soils, groundwater and surface waters. Microbial degradation was confirmed in soils, and recently several atrazine-degrading bacteria have been isolated. Degradation in aquifers, however, is not well understood, and to date, atrazine degraders have not been isolated from water. In the present study, the impact of atrazine was assessed in agricultural soil and river sediment and the composition of the atrazine-degrading bacterial community in the soil and sediment was compared. Atrazine pollution increased the number and diversity of the endogenous atrazine degraders in both environments. Proteobacteria were predominant atrazine degraders in soils, whereas the community of atrazine-degrading bacteria in sediment consisted mostly of coryneforms.
Report from the Annual Conference of the British Society of Echocardiography, November 2016, Queen Elizabeth II Conference Centre, LondonForewordNational Invited Lecture 2016Echo Research and Practice sessionAbstract 1: Left ventricular mechano-temporal alterations during the apparent recovery of acute stress-induced (Tako-tsubo) cardiomyopathyAbstract 2: Right ventricular structure and function in veteran ultrarunners: is there evidence for chronic maladaptation?Abstract 3: Feasibility, efficacy and safety of physiologist-led stress echocardiography in a rapid access chest pain settingAbstract 4: Prognostic value of simultaneous stress echocardiography and carotid ultrasound in patients with suspected coronary artery diseaseAbstract 5: Long-term echocardiographic follow-up in transcatheter aortic valve implantationAbstract 6: The CHA2DS2VASc risk score appropriately risk stratifies patients prior to atrial fibrillation ablation and reduces the requirement for trans-esophageal echocardiographyAbstract 7: The role of speckle tracking strain imaging in assessing left ventricular response to cardiac resynchronization therapy in responders and non-responders (2017)

Peer reviewed
Heterogeneous integration of ultra-narrow linewidth lasers on silicon for microwave photonics (2022)

Heterogeneous integration provides the capability of integrating III-V gain material with ultra-low-loss silicon photonic circuits on a monolithic silicon substrate. This integration results in the dramatic reduction of optical loss of the laser cavity and thus extends the photon lifetime and narrows the linewidth of semiconductor lasers beyond what is achieved with monolithic III-V integration. Recent progress includes widely-tunable III-V/silicon lasers with ultra-wide tuning range and lasers on silicon nitride with narrow linewidth that is comparable with fiber lasers. These lasers will play a critical role in ultra low noise microwave photonics.
Review of On-Chip Inductor Structures With Magnetic Films (2009)

A comparison of on-chip inductors with magnetic materials from previous studies is presented and examined. Results from on-chip inductors with magnetic material integrated into a 90 nm CMOS processes are presented. The inductors use copper metallization and amorphous Co-Zr-Ta magnetic material. Inductance densities of up to 1700 nH/mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> were obtained thanks to inductance increases of up to 31 times, significantly greater than previously published on-chip inductors. With such improvements, the effects of eddy currents, skin effect, and proximity effect become clearly visible at higher frequencies. Co-Zr-Ta was chosen for its good combination of high permeability, good stability at high temperature (> 250degC), high saturation magnetization, low magnetostriction, high resistivity, minimal hysteretic loss, and compatibility with silicon technology. The Co-Zr-Ta alloy can operate at frequencies up to 9.8 GHz, but trade-offs exist between frequency, inductance, and quality factor. Our inductors with thick copper and thicker magnetic films have dc resistances as low as 0.04 Omega, and quality factors of up to 8 at frequencies as low as 40 MHz.
The First Case of Biological Therapy Discontinuation After a Complete Remission Induced by Maintenance Therapy With Adalimumab for Refractory Ulcerative Colitis (2014)

A 43-year-old woman, diagnosed with ulcerative colitis (UC) at age of 30, received outpatient treatment with corticosteroids. However, flare-up occurred, and adalimumab (ADA) treatment commenced in July 2009. A complete remission with mucosal healing was achieved by 32 weeks after initiation of ADA therapy. Because of progressive skin eruptions, ADA maintenance was discontinued at 124 weeks. Regardless, complete remission with mucosal healing was maintained until 176 weeks. We concluded that ADA is an effective therapy to achieve a complete remission in a patient with steroid-refractory UC, and that long-term complete remission may be an important indication to discontinue biological therapy.
Regional comparison of tumor vascularity and permeability parameters measured by albumin‐GD‐DTPA and GD‐DTPA (1995)

Sequential albumin-Gd-DTPA and Gd-DTPA dynamic enhancement studies were performed in an animal tumor model for the comparison of regional vascularity and permeability parameters measured by these two different sizes of contrast agents. The early albumin-Gd-DTPA enhancement arises from the vascular compartment, and the averaged signal enhancement derived from the first 3 to first 6 images postinjection can be reliably used to assess vascularity. The signal intensity in the images during the period of 5-10 min post-albumin-Gd-DTPA injection shows a steady linear variation. The intercept of the linear relationship is another indicator of the vascularity and the slope represents the tumor permeability to albumin-Gd-DTPA. The Gd-DTPA enhancement study was analyzed by a two-compartmental pharmacokinetic model to calculate the regional vascularity and permeability. The permeability parameters measured from albumin-Gd-DTPA and Gd-DTPA show an excellent correlation. The vascularity parameters measured from albumin-Gd-DTPA show good linear correlation with the low vascularity groups measured by Gd-DTPA, but show saturation for the high vascularity groups. The enhancement mechanisms for both contrast agents are discussed to relate the imaging parameters to the physiological variables.
Mycolic acids, a promising mycobacterial ligand for targeting of nanoencapsulated drugs in tuberculosis (2015)

The appearance of drug-resistant strains of Mycobacterium tuberculosis (Mtb) poses a great challenge to the development of novel treatment programmes to combat tuberculosis. Since innovative nanotechnologies might alleviate the limitations of current therapies, we have designed a new nanoformulation for use as an anti-TB drug delivery system. It consists of incorporating mycobacterial cell wall mycolic acids (MA) as targeting ligands into a drug-encapsulating Poly dl-lactic-co-glycolic acid polymer (PLGA), via a double emulsion solvent evaporation technique. Bone marrow-derived mouse macrophages, either uninfected or infected with different mycobacterial strains (Mycobacterium avium, Mycobacterium bovis BCG or Mtb), were exposed to encapsulated isoniazid-PLGA nanoparticles (NPs) using MA as a targeting ligand. The fate of the NPs was monitored by electron microscopy. Our study showed that i) the inclusion of MA in the nanoformulations resulted in their expression on the outer surface and a significant increase in phagocytic uptake of the NPs; ii) nanoparticle-containing phagosomes were rapidly processed into phagolysosomes, whether MA had been included or not; and iii) nanoparticle-containing phagolysosomes did not fuse with non-matured mycobacterium-containing phagosomes, but fusion events with mycobacterium-containing phagolysosomes were clearly observed.
Dynamic range improvement through balanced detection for SBS-based high resolution OSAs (2014)

An out-of-band signal components cancellation scheme through balanced detection is proposed for SBS-based OSAs. Accompanied with the nonlinear distortion compensation, the dynamic range of the measured spectra can be improved from around10 dB to >50 dB.
Anatomy and white matter connections of the inferior frontal gyrus (2019)

The superior frontal gyrus (SFG) is an important region implicated in a variety of tasks including motor movement, working memory, resting-state, and cognitive control. A detailed understanding of the subcortical white matter of the SFG could improve postoperative morbidity related to surgery around this gyrus. Through DSI-based fiber tractography validated by gross anatomical dissection, we characterized the fiber tracts of the SFG based on their relationships to other well-known neuroanatomic structures. Diffusion imaging from the Human Connectome Project from 10 healthy adult subjects was used for fiber tractography. We evaluated the SFG as a whole based on its connectivity with other regions. All tracts were mapped in both hemispheres, and a lateralization index was calculated based on resultant tract volumes. Ten cadaveric dissections were then performed using a modified Klingler technique to delineate the location of major tracts integrated within the SFG. We identified four major SFG connections: the frontal aslant tract connecting to the inferior frontal gyrus; the inferior fronto-occipital fasciculus connecting to the cuneus, lingual gyrus, and superior parietal lobule; the cingulum connecting to the precuneus and parahippocampal gyrus/uncus; and a callosal fiber bundle connecting the SFG bilaterally. The functional networks of the SFG involve a complex series of white matter tracts integrated within the gyrus, including the FAT, IFOF, cingulum, and callosal fibers. Postsurgical outcomes related to this region may be better understood in the context of the fiber-bundle anatomy highlighted in this study. Clin. Anat. 33:823-832, 2020. © 2019 Wiley Periodicals, Inc.
Regulation of OmpA Translation and Shigella dysenteriae Virulence by an RNA Thermometer (2019)

RNA thermometers are <i>cis</i>-acting riboregulators that mediate the posttranscriptional regulation of gene expression in response to environmental temperature. Such regulation is conferred by temperature-responsive structural changes within the RNA thermometer that directly result in differential ribosomal binding to the regulated transcript. The significance of RNA thermometers in controlling bacterial physiology and pathogenesis is becoming increasingly clear. This study combines <i>in silico</i>, molecular genetics, and biochemical analyses to characterize both the structure and function of a newly identified RNA thermometer within the <i>ompA</i> transcript of <i>Shigella dysenteriae</i> First identified by <i>in silico</i> structural predictions, genetic analyses have demonstrated that the <i>ompA</i> RNA thermometer is a functional riboregulator sufficient to confer posttranscriptional temperature-dependent regulation, with optimal expression observed at the host-associated temperature of 37°C. Structural studies and ribosomal binding analyses have revealed both increased exposure of the ribosomal binding site and increased ribosomal binding to the <i>ompA</i> transcript at permissive temperatures. The introduction of site-specific mutations predicted to alter the temperature responsiveness of the <i>ompA</i> RNA thermometer has predictable consequences for both the structure and function of the regulatory element. Finally, <i>in vitro</i> tissue culture-based analyses implicate the <i>ompA</i> RNA thermometer as a bona fide <i>S. dysenteriae</i> virulence factor in this bacterial pathogen. Given that <i>ompA</i> is highly conserved among Gram-negative pathogens, these studies not only provide insight into the significance of riboregulation in controlling <i>Shigella</i> virulence, but they also have the potential to facilitate further understanding of the physiology and/or pathogenesis of a wide range of bacterial species.
Supplemental Figure Legend from LIGHT Elevation Enhances Immune Eradication of Colon Cancer Metastases (2023)

Supplemental Figure Legend from LIGHT Elevation Enhances Immune Eradication of Colon Cancer Metastases
Design Study of a Humidification Tower for the Advanced Humid Air Turbine System (2005)

The advanced humid air turbine (AHAT) system, which can be equipped with a heavy-duty, single-shaft gas turbine, aims at high efficiency equal to that of the HAT system. Instead of an intercooler, a WAC (water atomization cooling) system is used to reduce compressor work. The characteristics of a humidification tower (a saturator), which is used as a humidifier for the AHAT system, were studied. The required packing height and the exit water temperature from the humidification tower were analyzed for five virtual gas turbine systems with different capacities (1, 3.2, 10, 32, and 100MW) and pressure ratios (π=8, 12, 16, 20, and 24). Thermal efficiency of the system was compared with that of a simple cycle and a recuperative cycle with and without the WAC system. When the packing height of the humidification tower was changed, the required size varied for the three heat exchangers around the humidification tower (a recuperator, an economizer, and an air cooler). The packing height with which the sum total of the size of the packing and these heat exchangers became a minimum was 1m for the lowest pressure ratio case, and 6m for the highest pressure ratio case.
Endovascular and open surgical treatment of brachiocephalic arterial disease. (1998)

The treatment of occlusive lesions in the innominate, subclavian, and axillary arteries has, until recently, been entirely surgical. Recently, advances in endovascular technologies have provided an alternative means of therapy. The advent of balloon angioplasty has resulted in some turmoil between medical specialties regarding patient selection and acceptable applications. Innovations in imaging, guidewire, catheter, stent, and balloon technology allow one to obtain percutaneous access and perform therapeutic procedures in a relatively safe manner. However, the excellent and time-tested results of surgery remain a standard for developing new procedures. Despite the appeal of less invasive techniques, the morbidity, mortality, and durability of novel treatments must equal or exceed those standards set by surgical procedures. Proponents of the endovascular options must familiarize themselves with advantages and disadvantages of surgical procedures. In a similar manner, surgeons have an obligation to understand the less invasive technologies as well. The clinician must uphold the best interests of the patient as a fundamental factor in the determination of a particular form of therapy. This paradox is well illustrated by consideration of occlusive lesions in the upper extremity.
Automated quantification of steatosis: agreement with stereological point counting (2017)

The results suggest that the new method can be a suitable automated replacement for SPC. Before further improvements can be verified, it is necessary to thoroughly assess the variability of SPC between human observers.
RETRACTED: Gadolinium-Free Cardiac MR Stress T1-Mapping to Distinguish Epicardial From Microvascular Coronary Disease (2018)

CMR stress T1 mapping accurately detected and differentiated between obstructive epicardial CAD and microvascular dysfunction, without contrast agents or radiation.
ASSURE (2009)

Software failures in server applications are a significant problem for preserving system availability. We present ASSURE, a system that introduces rescue points that recover software from unknown faults while maintaining both system integrity and availability, by mimicking system behavior under known error conditions. Rescue points are locations in existing application code for handling a given set of programmer-anticipated failures, which are automatically repurposed and tested for safely enabling fault recovery from a larger class of (unanticipated) faults. When a fault occurs at an arbitrary location in the program, ASSURE restores execution to an appropriate rescue point and induces the program to recover execution by virtualizing the program's existing error-handling facilities. Rescue points are identified using fuzzing, implemented using a fast coordinated checkpoint-restart mechanism that handles multi-process and multi-threaded applications, and, after testing, are injected into production code using binary patching. We have implemented an ASSURE Linux prototype that operates without application source code and without base operating system kernel changes. Our experimental results on a set of real-world server applications and bugs show that ASSURE enabled recovery for all of the bugs tested with fast recovery times, has modest performance overhead, and provides automatic self-healing orders of magnitude faster than current human-driven patch deployment methods.
Inhibition of Herpesvirus Replication and Herpesvirus-Induced Deoxyribonucleic Acid Polymerase by Phosphonoformate (1978)

Phosphonoformate was found to be an inhibitor of the deoxyribonucleic acid polymerase induced by the herpesvirus of turkeys. The apparent inhibition constants were 1 to 3 muM. Phosphonoformate was also able to block the replication in cell culture of Marek's disease herpesvirus, the herpesvirus of turkeys, and herpes simplex virus. It was as effective as phosphonoacetate. Phosphonoformate was not an effective inhibitor of a phosphonoacetate-resistant mutant of the herpesvirus of turkeys nor of its induced deoxyribonucleic acid polymerase.