gebhart/patrepeval huggingface dataset:
Robotic-aided 3D TRUS guided intraoperative prostate brachytherapy (2004)

We have developed a robotic aided 3D transrectal ultrasound (TRUS) guided, intraoperative prostate brachytherapy. This system allows brachytherapy needles to be inserted into the prostate along various trajectories including oblique to avoid pubic arch interference. We unified the robotic coordinate system with the 3D TRUS image coordinate system. In addition, we also hdeveloped the method to automatically detect the needle in TRUS images for oblique insertion. We have evaluated our prototype system using prostate phantoms in terms of different needle insertion depths and the distances of the needle from the TRUS transducer. We have shown that our robotic aided 3D TRUS guided system was capable of placing the needle tip with approximately 0.74 mm ± 0.24 mm accuracy at a target identified in the 3D TRUS image. Brachytherapy accuracy was tested by dropping 0.8 mm beads into prostate phantoms via various angles up to ± 20°. Our results showed that the bead-dropping accuracy was 2.59 mm ± 0.76 mm with the error due to the needle deflection caused by the needle's bevel.
Immunogenicity of a non-repetitive sequence of Plasmodium falciparum circumsporozoite protein in man and mice. (1988)

In the present work, the hypothesis that individuals naturally exposed to Plasmodium falciparum malaria infection in endemic areas produce antibodies directed against non-repetitive epitopes of the circumsporozoite protein was investigated. Using a synthetic peptide reproducing the non-repetitive group-conserved region I sequence, we have shown that specific anti-region I antibodies are detectable in sera from endemic countries. Of these sera, 87% also had antibodies against the immunodominant repetitive epitope (Asn-Ala-Asn-Pro, NANP) of P. falciparum. In order to study the immunogenicity of this non-repetitive epitope, a synthetic peptide consisting of both region I and three (NANP) repeats [RI-(NANP)3] was used to immunize inbred strains of mice. H-2b mice produced antibodies against both the repetitive and the non-repetitive epitope. These antibodies were specific for each epitope, recognized P. falciparum sporozoites in immunofluorescence, and inhibited sporozoite penetration into human liver cells in vitro. Non-H-2b mice were completely unresponsive. Lymph node cells from H-2b mice immunized with RI-(NANP)3 peptide proliferated in the presence of RI-(NANP)3 and of (NANP)4 peptide, but never in the presence of RI peptide alone. These findings demonstrate that in the configuration used (i) the non-repetitive epitope region I does not carry T-helper epitopes; (ii) the (NANP) repetitive epitope may act as a carrier for the immune response to region I in mice; and (iii) therefore, immune response to region I in man probably depends on the recognition of T-cell epitopes similar to those involved in the anti-NANP response: i.e. such a T epitope may be NANP itself in responding individuals or another, not yet recognized, sporozoite T-cell epitope.
Remote regions: a simple abstraction for remote memory (2018)

We propose an intuitive abstraction for a process to export its memory to remote hosts, and to access the memory exported by others. This abstraction provides a simpler interface to RDMA and other remote memory technologies compared to the existing verbs interface. The key idea is that a process can export parts of its memory as files, called remote regions, that can be accessed through the usual file system operations (read, write, memory map, etc). We built this abstraction in the Linux kernel, and evaluated it. We show that remote regions are easy to use and perform close to RDMA. We demonstrate it via micro-benchmarks and by adapting two in-memory single-host applications to use remote memory: R and Metis. With R, using remote regions requires no changes to the code and allows R to run with remote memory that exceeds the physical memory of a host. With Metis, the modifications amount to ≈100 lines of code and they allow Metis to scale its performance across 8 hosts.
Thoracic Epidural Catheter Placement Via the Caudal Approach in Infants by Using Electrocardiographic Guidance (2002)

We examined the success of inserting epidural catheters via the caudal route in infants by using electrocardiographic guidance. A case series of 20 patients with thoracic epidural analgesia was studied. After the induction of general anesthesia, an 18-gauge IV catheter was inserted into the caudal space to allow threading of a 20-gauge epidural catheter. The electrocardiogram (ECG) tracings via the epidural catheter, as well as the surface ECG at the target spine level, were recorded simultaneously with a modified two-channel five-lead ECG system. The epidural catheter was advanced from the caudal space until the tip reached the target level as demonstrated by a match in the configuration of the epidural ECG tracing to that of the surface ECG tracing at the target level. The catheter tip location was verified by postoperative radiographs. All catheter tips were located within two vertebrae of the target level, and satisfactory intraoperative epidural anesthesia was achieved in all subjects.
Processing polymeric powders (1989)

The concept of uniformly and continuously depositing and sinter-fusing nominal 0.1 to 40 microns dimensioned electrostatically charged polymer powder particles onto essentially uniformly spread 5 to 20 micron grounded continuous fiber tow to produce a respoolable thermoplastic composite two-preg was formulated at NASA Langley. The process was reduced to practice under a NASA grant at the University of Akron this spring. The production of tow-preg is called phase 1. The production of ultrafine polymer powders from 5 to 10 percent (wt) polymer solids in solvent is considered. This is phase 0 and is discussed. The production of unitape from multi tow-pregs was also considered. This is phase 2 and is also discussed. And another approach to phase 1, also proposed last summer, was scoped. This is phase 1A and is also discussed.
Correction: Neutralization-guided design of HIV-1 envelope trimers with high affinity for the unmutated common ancestor of CH235 lineage CD4bs broadly neutralizing antibodies (2019)

[This corrects the article DOI: 10.1371/journal.ppat.1008026.].
New infrared transparent oxide glasses (2005)

Glass materials based on rare earth oxides and aluminum oxide can provide a combination of infrared transparency, strength, hardness, and environmental stability in a formable material. This article describes a new family of rare earth oxide-aluminum oxide glass materials that can be made by casting from melts formed in platinum crucibles. The glasses transmit light in the wavelength range from 0.3 to 5 μm in sections of ~0.3 cm, they have a Vickers hardness of 800-1000, and exhibit excellent environmental stability typical of refractory oxide materials. The composition of the glass can be adjusted to achieve refractive indices in the range 1.7-1.8 and Abbe numbers of 30-60. The materials are promising candidates for passive optical elements or as a host for optically active ions such as Yb or Nd that provide laser action or absorb at laser line wavelengths.
A patch testing and cross‐sensitivity study of carbamazepine‐induced severe cutaneous adverse drug reactions (2012)

Drug patch testing is a safe and useful method for the identification of CBZ as the culprit drug of SJS/TEN as well as DRESS. Testing of chemically or pharmacologically related AEDs may provide information on cross-reactivity for these patients.
<i>Helicobacter pylori hspA‐hspB</i> heat‐shock gene cluster: nucleotide sequence, expression, putative function and immunogenicity (1994)

All Helicobacter pylori isolates synthesize a 54 kDa immunodominant protein that was reported to be associated with the nickel-dependent urease of H. pylori. This protein was recently recognized as a homologue of the heat-shock protein of the GroEL class. The gene encoding the GroEL-like protein of H. pylori (HspB) was cloned (pILL689) and was shown to belong to a bicistronic operon including the hspA and hspB genes. In Escherichia coli, the constitutive expression of the hspA and hspB genes was initiated from a promoter located within an IS5 insertion element that mapped upstream to the two open reading frames (ORFs). IS5 was absent from the H. pylori genome, and was thus acquired during the cosmid cloning process. hspA and hspB encoded polypeptides of 118 and 545 amino acid residues, corresponding to calculated molecular masses of 13.0 and 58.2 kDa, respectively. Amino acid sequence comparison studies revealed that, although H. pylori HspA and HspB proteins were highly similar to their bacterial homologues, the H. pylori HspA featured a striking motif at the C-terminus. This unique motif consists of a series of cysteine and histidine residues resembling a nickel-binding domain, which is not present in any of the other bacterial GroES homologues so far characterized. When the pILL689 recombinant plasmid was introduced together with the H. pylori urease gene cluster (pILL763) into an E. coli host strain, an increase of urease activity was observed. This suggested a close interaction between the HspA and HspB proteins and the urease enzyme, and a possible role for HspA in the chelation of nickel ions. The genes encoding each of the HspA and HspB polypeptides were cloned, expressed independently as proteins fused to the maltose-binding protein (MBP) and purified in large scale. The MBP-HspA and MBP-HspB fusion proteins were shown to retain their antigenic properties. Both HspA and HspB represent antigens that are specifically recognized by the sera from H. pylori-infected patients. Whereas HspB was known to be immunogenic in humans, this is the first demonstration that HspA per se is also immunogenic.
Electrochemical Sensing of Ethylene Employing a Thin Ionic-Liquid Layer (2011)

We introduce an electrochemical ethylene sensor that employs a thin layer of ionic liquid as electrolyte. Ethylene is oxidized in a potential window starting ∼600 mV before the onset of the gold working electrode oxidation, which inhibits the ethylene oxidation at high applied potential. The current amplitude and sensor response time depend on the ionic-liquid film thickness, relative humidity, and applied potential, in agreement with a theoretical model based on diffusion. A detection limit of 760 ppb and a linear response up to 10 ppm were achieved. As illustrated by the detection of ethylene, ionic liquids could serve as an alternative electrolyte for many electrochemical gas sensors that heretofore relied on a strongly acidic electrolyte.
The equivalence of linear spherical deconvolution and model-free linear transform methods for diffusion MRI (2013)

This work provides a theoretical analysis of linear spherical deconvolution methods in diffusion MRI, building off of a theoretical framework that was previously developed for model-free linear transforms of the Fourier 2-sphere. It is demonstrated that linear spherical deconvolution methods have an equivalent representation as model-free linear transform methods. This perspective is used to study the characteristics of linear spherical deconvolution from the point of view of the diffusion propagator. Practical results are shown with experimental brain MRI data.
<scp>D</scp>-Phenylalanine Biosynthesis Using <i>Escherichia Coli:</i> Creation of a New Metabolic Pathway (2001)

D-Amino acids are being increasingly used in the rational design of chiral drugs such as anti-cancer compounds and viral inhibitors. In common with the commercial manufacture of L-amino acids, both chemo-enzymatic resolution approaches and direct single isomer syntheses have been undertaken in the production of D-amino acids and their derivatives. We have developed a fermentation route to the synthesis of D-phenylalanine in Escherichia coli K12 using metabolic engineering. The key enzymes used in this system are a DAHP synthase and the chorismate mutase-prephenate dehydratase from E. coli in conjunction with an operon of D-amino acid aminotransferase (Bacillus sphaericus), L-amino acid deaminase (Proteus myxofaciens) and alanine racemase (Salmonella typhimurium). These enzymes form a pathway, which deregulates L-phenylalanine synthesis and subsequently converts the L-phenylalanine into its D-isomer. Due to the broad specificity of both the L-amino acid deaminase and the D-amino acid aminotransferase, this system, with slight modifications, can be used to synthesize a wide variety of D-amino acids.
TRB: Tag Replication Buffer for Enhancing the Reliability of the Cache Tag Array (2010)

Protecting the on-chip cache memories against soft errors has become an increasing challenge in designing new generation reliable microprocessors. Previous efforts have mainly focused on improving the reliability of the cache data arrays. Due to its crucial importance to the correctness of cache accesses, the tag array demands high reliability against soft errors while the data array is fully protected. Exploiting the address locality of memory accesses, we propose to duplicate most recently accessed tag entries in a small Tag Replication Buffer (TRB) thus to protect the information integrity of the tag array in the data cache with low performance, energy and area overheads. A Selective-TRB scheme is further proposed to protect only tag entries of dirty cache lines. The experimental results show that the Selective-TRB scheme achieves a higher access-with-replica (AWR) rate of 97.4% for the dirty-cache line tags. To provide a comprehensive evaluation of the tag-array reliability, we also conduct an architectural vulnerability factor (AVF) analysis for the tag array and propose a refined metric, detected-without-replica-AVF (DOR-AVF), which combines the AVF and AWR analysis. Based on our DOR-AVF analysis, a TRB scheme with early write-back (EWB) is proposed, which achieves a zero DOR-AVF at a negligible performance overhead.
Molecular Understanding of Cellular Uptake by Arginine-Rich Cell Penetrating Peptides (2006)

A mechanistic hypothesis is presented for how water-soluble guanidinium-rich transporters attached to small cargos (MW ca. <3000) can migrate across the non-polar lipid membrane of a cell and enter the cytosol. Positively-charged and water soluble arginine oligomers can associate with negatively-charged, bidentate hydrogen bond acceptor groups of endogenous membrane constituents, leading to the formation of membrane soluble ion pair complexes. The resultant less polar, ion pair complexes partition into the lipid bilayer and migrate in a direction, and with a rate, influenced by the membrane potential. The complex dissociates on the inner leaf of the membrane and the transporter conjugate enters the cytosol. This mechanism could also be involved in the translocation of guanidinium-rich molecules that are endocytosed due to their size or the conditions of the assay, across the endosomal membrane.
Degradable Adhesives for Surgery and Tissue Engineering (2017)

This review highlights the research on degradable polymeric tissue adhesives for surgery and tissue engineering. Included are a comprehensive listing of specific uses, advantages, and disadvantages of different adhesive groups. A critical evaluation of challenges affecting the development of next generation materials is also discussed, and insights into the outlook of the field are explored.
A process for producing ultraclean gasoline by coupling efficient hydrodesulfurization and directional olefin conversion (2012)

To solve the contradiction between ultradeep hydrodesulfurization (HDS) and octane recovery in clean gasoline production, this article proposes a novel two‐stage fluid catalytic cracking (FCC) gasoline hydro‐upgrading process with the selective HDS catalyst in the first reactor and the complemental HDS and octane recovery catalyst in the second reactor. The process achieved the relayed removal of sulfur‐containing compounds with different natures, providing itself with excellent HDS performance, and the hydroisomerization and aromatization of olefins in the second stage endowed the process with superior octane recovery ability and high product yield while remarkably reducing the olefin content of FCC gasoline. The process was also featured by low hydrogen consumption due to the low first‐stage olefin saturation and the balanced second‐stage hydrogenation and dehydrogenation. The two‐stage process developed here sheds a light for efficiently producing ultralow sulfur gasoline from the poor‐quality FCC gasoline of high olefin and sulfur contents. © 2012 American Institute of Chemical Engineers AIChE J, 59: 571–581, 2013
Single-Step Delamination of a MWW Borosilicate Layered Zeolite Precursor under Mild Conditions without Surfactant and Sonication (2013)

Layered borosilicate zeolite precursor ERB-1P (Si/B = 11) is delaminated via isomorphous substitution of Al for B using a simple aqueous Al(NO3)3 treatment. Characterization by PXRD shows loss of long-range order, and TEM demonstrates transformation of rectilinear layers in the precursor to single and curved layers in the delaminated material. N2 physisorption and base titration confirm the expected decrease of micropore volume and increase in external surface area for delaminated materials relative to their calcined 3D zeolite counterpart, whereas FTIR and multinuclear NMR spectroscopies demonstrate synthesis of Brønsted acid sites upon delamination. Comparative synthetic studies demonstrate that this new delamination method requires (i) a borosilicate layered zeolite precursor, in which boron atoms can be isomorphously substituted by aluminum, (ii) neutral amine pore fillers instead of rigid and large quaternary amine SDAs, and (iii) careful temperature control, with the preferred temperature window being around 135 °C for ERB-1P delamination. Acylation of 2-methoxynaphthalene was used as a model reaction to investigate the catalytic benefits of delamination. A partially dealuminated delaminated material displays a 2.3-fold enhancement in its initial rate of catalysis relative to the 3D calcined material, which is nearly equal to its 2.5-fold measured increase in external surface area. This simple, surfactant- and sonication-free, mild delamination method is expected to find broad implementation for the synthesis of delaminated zeolite catalysts.
Difluoromethyl Phenyl Sulfone, a Difluoromethylidene Equivalent: Use in the Synthesis of 1,1‐Difluoro‐1‐alkenes (2004)

A nucleophilic substitution–elimination reaction strategy in which difluoromethyl phenyl sulfone is used as a selective difluoromethylidene equivalent allows the facile synthesis of 1,1-difluoro-1-alkenes from primary alkyl halides (see scheme).
Hydrogel-based transparent soils for root phenotyping in vivo (2019)

Root phenotypes are increasingly explored as predictors of crop performance but are still challenging to characterize. Media that mimic field conditions (e.g., soil, sand) are opaque to most forms of radiation, while transparent media do not provide field-relevant growing conditions and phenotypes. We describe here a "transparent soil" formed by the spherification of hydrogels of biopolymers. It is specifically designed to support root growth in the presence of air, water, and nutrients, and allows the time-resolved phenotyping of roots in vivo by both photography and microscopy. The roots developed by soybean plants in this medium are significantly more similar to those developed in real soil than those developed in hydroponic conditions and do not show signs of hypoxia. Lastly, we show that the granular nature and tunable properties of these hydrogel beads can be leveraged to investigate the response of roots to gradients in water availability and soil stiffness.
Closing the loop in webpage understanding (2008)

Little work has been done towards an integrated statistical model for understanding webpage structures and processing natural language sentences within the HTML elements. This paper proposed a novel framework called WebNLP which enables bidirectional integration of page structure understanding and text understanding in an iterative manner. Experiments show that the WebNLP framework achieved significantly better performance.
Control of Oxygen Precipitation in Silicon by Infrared Laser Irradiation (2005)

We have investigated the effect of infrared laser irradiation on the oxygen precipitation in silicon crystals during the heat-treatments. The laser light of the wave numbers of 1085 cm-1 was adopted, which is close to the wave number of the infrared absorption by oxygen in silicon (Si-O-Si) at high temperature. We have found that for the high-temperature anneals around 1200 °C for 1-2 h, the infrared laser irradiation during the anneals significantly (almost completely) suppresses the oxygen precipitation.
Photoinduced electron transfer in a symmetrical diporphyrin–fullerene triad (2004)

Two triad molecules consisting of either two zinc, or two free-base porphyrins symmetrically joined to a fullerene via phenyleneethynylene-containing linkages have been synthesized, and their photochemistry investigated. In the zinc form of the triad, PZn–C60–PZn, excitation of a zinc porphyrin in 2-methyltetrahydrofuran solution is followed by photoinduced electron transfer to the fullerene with a time constant of 20 ps. The resulting PZn˙+–C60˙−–PZn charge-separated state is formed with a quantum yield of 98% and has a lifetime of 820 ps. The first excited singlet state of the free-base analog gives the P2H˙+–C60˙−–P2H charge-separated state with a time constant of 200 ps and a yield of 98%. The charge-separated state decays with a lifetime of 2.8 ns. The difference in the rates of photoinduced electron transfer is consistent with reaction in the normal region of the Marcus–Hush relationship of transfer rate and driving force, and charge recombination is consistent with Marcus–Hush inverted behavior. The presence of the two porphyrin electron donors in these triads enhances the absorption cross section for light collection, and the molecular framework employed could be used to prepare molecules with enhanced energy conversion or optoelectronic properties.
Association between Protection against Clinical Malaria and Antibodies to Merozoite Surface Antigens in an Area of Hyperendemicity in Myanmar: Complementarity between Responses to Merozoite Surface Protein 3 and the 220-Kilodalton Glutamate-Rich Protein (2003)

We performed a longitudinal clinical and parasitological follow-up study in OoDo, a village in southeast Asia in which malaria is hyperendemic, in order to assess the association between protection against malaria attacks and antibodies to three currently evaluated vaccine candidates, merozoite surface protein 1 (MSP1), MSP3, and the 220-kDa glutamate-rich protein (GLURP) from Plasmodium falciparum. Our results showed that the levels of cytophilic immunoglobulin G3 (IgG3) antibodies against conserved regions of MSP3 and GLURP were significantly correlated with protection against clinical P. falciparum malaria. In contrast, the levels of noncytophilic IgG4 antibodies against GLURP increased with the number of malaria attacks. Furthermore, we observed a complementary effect of the MSP3- and GLURP-specific IgG3 antibodies in relation to malaria protection. In the individuals that did not respond to one of the antigens, a strong response to the other antigen was consistently detected and was associated with protection, suggesting that induction of antibodies against both MSP3 and GLURP could be important for the development of protective immunity. The complementarity of the responses to the two main targets of antibody-dependent cellular inhibition identified to date provides the first rational basis for combining these two antigens in a hybrid vaccine formulation.