gebhart/patrepeval huggingface dataset:
Radiation Absorbed Dose to the Embryo/Fetus from Radiopharmaceuticals (1997)

Radiation protection practice requires the knowledge of estimated absorbed radiation doses to aid in the understanding of the potential detriment of various exposures. In nuclear medicine, the radiation doses to the internal organs of the subject are commonly calculated using the MIRD methods and equations. The absorbed dose to the embryo or fetus has long been an area of concern. The recent release of the pregnant female phantom series, and its incorporation into the MIRDOSE 3 computer software, has made possible the estimation of absorbed doses from radionuclides in the body to the fetus in early pregnancy and at 3, 6, and 9 mo gestation. A survey of several major medical institutions was made to determine the radiopharmaceuticals which might be given, whether intentionally or not, to women of childbearing years. Biokinetic data for these radiopharmaceuticals were gathered from various documents and other resources, and the absorbed doses to the embryo and fetus at these different stages of gestation from radiations originating within the mother's organs were estimated. In addition, information about activity distributed within the placenta and fetus was included where quantitative data were available. These absorbed dose estimates can be used to evaluate the risk associated with the use of different radiopharmaceuticals so that a more informed evaluation of the risks and benefits of the different procedures may be made. Further research is needed into the mechanisms and quantitative aspects of the placental transfer of many radiopharmaceuticals.
Rule-based filtering for Java applets (2002)

Java has been designed with a sophisticated security model that prevents applets downloaded from an untrusted network to attack the local system. However, malicious applets could exploit bugs in the virtual machine in order to gain access to system resources to perform unauthorized operations. The paper discusses the problem of intercepting such applets through a set of filtering rules that can be applied before a fixed version of the virtual machine is released. Moreover, we present an implementation of a filtering tool that can be used either as a firewall extension or as a virtual machine extension.
Heterogeneous Cross-Linking of Chitosan Gel Beads:  Kinetics, Modeling, and Influence on Cadmium Ion Adsorption Capacity (1997)

Chitosan, a linear biopolymer of glucosamine residues, selectively adsorbs transition-metal ions such as cadmium from dilute solution. In order to process chitosan into a more durable form, a 5 wt % chitosan solution was cast into spherical gel beads of 3 mm diameter and then reacted with glutaraldehyde at free amine sites to form imine cross-links between linear chitosan chains. The rate processes of the heterogeneous cross-linking reaction and the effect of cross-linking on the cadmium ion adsorption capacity were determined. The cross-linking reaction was complete within 48 h at 27 °C, and the final extent of cross-linking ranged from 0.07 to 2.40 mol of glutaraldehyde consumed/mol of amine. Heterogeneous cross-linking was modeled as a shrinking core process where the molecular diffusion of glutaraldehyde through the cross-linked shell of the gel bead limited the overall rate of glutaraldehyde consumption. The effective diffusion coefficient of glutaraldehyde through the cross-linked layer was 4.7 × 10-8 cm2/s. The saturation adsorption capacity of cadmium ions on the cross-linked gel beads exponentially decreased from 250 to 100 mg of Cd/g of chitosan as the extent of cross-linking increased from 0 to 1.3 mol of glutaraldehyde consumed/mol of amine. At higher extents of cross-linking, the saturation adsorption capacity remained at 100 mg of Cd/g of chitosan. Highly porous chitosan beads formed by freeze-drying of cross-linked gel beads had the same cadmium ion adsorption capacity as the cross-linked gel beads over the same extents of cross-linking.
Topology for Computing (2005)

The emerging field of computational topology utilizes theory from topology and the power of computing to solve problems in diverse fields. Recent applications include computer graphics, computer-aided design (CAD), and structural biology, all of which involve understanding the intrinsic shape of some real or abstract space. A primary goal of this book is to present basic concepts from topology and Morse theory to enable a non-specialist to grasp and participate in current research in computational topology. The author gives a self-contained presentation of the mathematical concepts from a computer scientist's point of view, combining point set topology, algebraic topology, group theory, differential manifolds, and Morse theory. He also presents some recent advances in the area, including topological persistence and hierarchical Morse complexes. Throughout, the focus is on computational challenges and on presenting algorithms and data structures when appropriate.
Latchup in merged triple well structure (2005)

In advanced CMOS, RF CMOS, and RF BiCMOS, structures which allow the separation of the p-well from the low doped p- substrate to form an "isolated MOSFET" are advantageous; this technology is also referred to as "triple well" technology. As practiced today, circuit designers desire to re-map dual-well structures to triple well implementations without a change in the on-chip design, ground-rules, or p+/n+ spacing rules. As a result, "triple well" is being practiced not as isolated regions but "merged triple well" where the n-well and associated isolating buried layers are integrated. This paper compares latchup measurements with standard dual-well implementation to a merged triple well implementation in a high resistivity p- substrate wafer. The results are shown with standard dual-well structures, and the merged triple well structures in a BiCMOS SiGe technology. Physical models are developed to explain the enhancement and reduction effects of latchup in merged triple well technology.
A Lentivirus Packaging System Based on Alternative RNA Transport Mechanisms To Express Helper and Gene Transfer Vector RNAs and Its Use To Study the Requirement of Accessory Proteins for Particle Formation and Gene Delivery (1999)

A lentivirus-based packaging system was designed to reduce the chance of recombination between helper and gene transfer vector sequences by using the constitutive transport element (CTE) derived from Mason-Pfizer monkey virus for expression of the viral proteins and the Rev-Rev response element (RRE) combination for expression of the gene transfer vector. Using this approach, we evaluated a series of human immunodeficiency virus type 1 packaging constructs that express one or more accessory proteins (Vif, Vpr, and Vpu), in addition to the Gag and Pol proteins, for particle formation and virus stock production for gene transfer. Constructs that also express Vpr or both Vpr and Vpu produced more particles, as measured by a p24 assay, than did plasmids that did not contain these sequences. Transactivation experiments showed that the packaging plasmids that encode Vpr or both Vpr and Vpu also expressed a functional single-exon Tat protein. For these constructs, high-titer virus stocks could be prepared in the absence of a cotransfected Tat-expressing plasmid. Amphotropic-envelope-pseudotyped virus stocks prepared with all of the packaging constructs, irrespective of whether any of the accessory proteins were coexpressed, were equally efficient in transducing growth-arrested HeLa cells. The combination/mixed packaging system was compared to systems that were based on either the CTE alone or Rev and RRE for expression of both the packaging plasmid as well as the gene transfer vector. The combination/mixed packaging system was comparable to the other systems for production of virus stocks, suggesting that this design may prove to be safer for the eventual deployment of lentivirus vectors for therapeutic purposes.
Renaissance (2012)

Résumé Redonner un sens à sa vie après le cataclysme d’un déni de grossesse. Comprendre ce silence pour ressurgir et accepter l’enfant. Renaître au monde en donnant la vie.
A systematic survey of the Cys2His2 zinc finger DNA-binding landscape (2015)

Cys2His2 zinc fingers (C2H2-ZFs) comprise the largest class of metazoan DNA-binding domains. Despite this domain's well-defined DNA-recognition interface, and its successful use in the design of chimeric proteins capable of targeting genomic regions of interest, much remains unknown about its DNA-binding landscape. To help bridge this gap in fundamental knowledge and to provide a resource for design-oriented applications, we screened large synthetic protein libraries to select binding C2H2-ZF domains for each possible three base pair target. The resulting data consist of >160 000 unique domain-DNA interactions and comprise the most comprehensive investigation of C2H2-ZF DNA-binding interactions to date. An integrated analysis of these independent screens yielded DNA-binding profiles for tens of thousands of domains and led to the successful design and prediction of C2H2-ZF DNA-binding specificities. Computational analyses uncovered important aspects of C2H2-ZF domain-DNA interactions, including the roles of within-finger context and domain position on base recognition. We observed the existence of numerous distinct binding strategies for each possible three base pair target and an apparent balance between affinity and specificity of binding. In sum, our comprehensive data help elucidate the complex binding landscape of C2H2-ZF domains and provide a foundation for efforts to determine, predict and engineer their DNA-binding specificities.
Transcervical Carotid Stenting with Flow Reversal for Neuroprotection: Technique, Results, Advantages, and Limitations (2006)

Carotid angioplasty and stenting are progressively earning a role as a less invasive alternative in the treatment of carotid occlusive disease. The most common approach for carotid artery stenting involves transfemoral access and use of a filter or balloon device for neuroprotection. This approach has limitations related to both the site of access and the method of neuroprotection. Specifically, an aortoiliac segment with advanced occlusive or aneurysmal disease or an anatomically unfavorable or atheromatous arch and arch branches can significantly limit the safety of the retrograde transfemoral pathway to the carotid bifurcation. Additionally, data provided by the use of transcranial Doppler monitoring and diffusion-weighted magnetic resonance imaging in patients undergoing filter- or balloon-protected carotid artery stenting demonstrate that currently available devices are associated with a considerable incidence of cerebral embolization. To address these limitations, we, along with others, have employed a direct transcervical approach for carotid artery stenting that incorporates the principle of flow reversal for neuroprotection. The technique bypasses all of the anatomic limitations of transfemoral access and simplifies the application of flow reversal, which is one of the safest neuroprotection techniques. The purpose of this review is to describe our method of transcervical carotid artery stenting, review the accumulating outcomes data, and discuss the clinical advantages of and indications for this increasingly popular technique.
Four viral genes independently contribute to attenuation of live influenza A/Ann Arbor/6/60 (H2N2) cold-adapted reassortant virus vaccines (1988)

Clinical studies previously demonstrated that live influenza A virus vaccines derived by genetic reassortment from the mating of influenza A/Ann Arbor/6/60 (H2N2) cold-adapted (ca) donor virus with epidemic wild-type influenza A viruses are reproducibly safe, infectious, immunogenic, and efficacious in the prevention of illness caused by challenge with virulent wild-type virus. These influenza A reassortant virus vaccines also express the ca and temperature sensitivity (ts) phenotypes in vitro, but the genes of the ca virus parent which specify the ca, ts, and attenuation (att) phenotypes have not adequately been defined. To identify the genes associated with each of these phenotypes, we isolated six single-gene substitution reassortant viruses, each of which inherited only one RNA segment from the ca parent virus and the remaining seven RNA segments from the A/Korea/1/82 (H3N2) wild-type virus parent. These were evaluated in vitro for their ca and ts phenotypes and in ferrets, hamsters, and seronegative adult volunteers for the att phenotype. We found that the polymerase PA gene of the ca parent specifies the ca phenotype and that the PB2 and PB1 genes independently specify the ts phenotype. The PA, M, PB2, and PB1 genes of the ca donor virus each contribute to the att phenotype. The finding that four genes of the ca donor virus contribute to the att phenotype provides a partial explanation for the observed phenotypic stability of ca reassortant viruses following replication in humans.
MGMT Promoter Methylation and Field Defect in Sporadic Colorectal Cancer (2005)

Some colorectal cancers arise from a field defect defined by epigenetic inactivation of MGMT. Detection of this abnormality may ultimately be useful in risk assessment for colorectal cancer.
Optical modulation of terahertz pulses in a parallel plate waveguide (2008)

In this work we present a technique for optically modulating a terahertz pulse inside a parallel plate waveguide. A novel semiconductor filled waveguide is formed by coating both sides of a thin, high resistivity silicon slab with a transparent conducting oxide. While the waveguide is intrinsically lossy due to the low conductivity of the oxides, it permits photoexcitation through the plates, generating free carriers within the silicon that modulates the terahertz pulse transmission. We demonstrate this modulation by observing the Drude response of photoexcited carriers within the silicon in a narrow strip inside the waveguide.
Thermal Cracking of Canola Oil:  Reaction Products in the Presence and Absence of Steam (1996)

The product distribution obtained from the thermal cracking of canola oil was studied at atmospheric pressure in a fixed-bed reactor in the temperature range 300−500 °C and gas hourly space velocity (GHSV) in the range 3.3−640 h-1 over inert materials and in the presence and absence of steam. Results showed that canola oil conversions were high (54−100 wt %) and depended strongly on the operating variables. Products essentially consisted of C4 and C5 hydrocarbons, aromatic and C6+ aliphatic hydrocarbons, and C2-C4 olefins, as well as a diesel-like fuel fraction and hydrogen. GC−MS analyses showed that product distribution as well as the lengths of the carbon chain of hydrocarbons and oxygenated hydrocarbons depended strongly not only on the cracking temperature and space velocity but also on whether cracking was conducted in the presence or absence of steam. On the other hand, cracking over inert materials showed that both conversion and product distribution were completely independent of morphology of the cracking surface. A reaction scheme has been proposed to account for the product distribution obtained from the thermal cracking of canola oil. The observed changes in both canola oil conversion and product distribution with changes in the operating variables were found to be consistent with the reaction scheme.
Characterization and isolation of thyroid microsomal antigen. (1987)

We investigated the structure of the 107-kD thyroid protein recognized as microsomal antigen. Solubilized microsomes were incubated with affinity gels consisting of IgG, from thyroiditis patients or controls, linked to Reacti-gel. Eluates were analyzed by SDS polyacrylamide electrophoresis and Western blot. 107- and 101-kD proteins were augmented in eluates from gels containing patient IgG and had microsomal antigenicity. In a Western blot of microsomes run under unreduced conditions, poorly defined large proteins were identified by antibody. When eluted electrophoretically and reanalyzed in reducing conditions, they demonstrated the 107-kD antigen. The 107-kD protein identified in reducing conditions was extracted and reanalyzed under nonreducing conditions. Large molecular mass proteins were then observed. On two-dimensional electrophoresis, a 107-kD antigen was isolated with isoelectric point of 7.0. The microsomal antigen may be complexes or multimers of a 107-kD peptide with isoelectric point of 7.0.
Input shaper designs for minimizing the expected level of residual vibration in flexible structures (1997)

The method of input shaping has been shown to yield good performance in the control of flexible structures while being insensitive to modeling errors. However, previous studies do not take into account the distributions of the parameter variations. We develop an input shaping method that allows the ranges of system parameter values to be weighted according to the expected modeling errors. Comparisons with previously proposed input shaper designs in terms of shaper length, frequency insensitivity, and expected level of residual vibration are presented, illustrating the qualities of the new input shaper design method.
The genetic basis of tissue responses to ionizing radiation (2007)

The response of mammalian cells to ionizing radiation can be directly influenced by genetics, and mouse strains can be identified that differ in their cellular radiosensitivity. The C57BL/6 radiation resistant and DBA/2 radiation susceptible mouse strains were utilized to aid the elucidation of the mechanisms involved in the early response to ionizing radiation. Investigation of the p53 pathway revealed differences in the expression and activity of p53 and its downstream targets between these mouse strains. The radiation resistant C57BL/6 strain showed an early p53 response and preferentially upregulated pro-apoptotic Bax, whereas the radiation sensitive DBA/2 strain exhibited a later, more prolonged p53 response and a greater expression of the cyclin dependent kinase inhibitor p21. These two mouse strains also showed significantly different levels of splenic radiation-induced apoptosis, the radiation resistant C57BL/6 scoring twofold more apoptotic cells than its radiation sensitive counterpart. These data provided a quantitative endpoint for an apoptosis genetic linkage analysis. The preliminary results of the linkage analysis indicated that three distinct loci may be involved in driving the different apoptosis phenotypes exhibited by the mouse strains. Moreover, we ascertained whether the mechanisms involved in the response to ionizing radiation may work in a tissue-specific fashion. In the linkage analysis, comparison of apoptosis scores in the colon and small intestine with data from the spleen showed little correlation suggesting that levels of apoptosis are tissue-specific. Tissue-specificity in the colon and small intestine was further illustrated by work with a 2D gel electrophoresis system. This revealed different patterns of p53 phosphorylation between the intestinal tissues both before and after exposure to ionizing radiation. The data discussed here will aid our understanding of the genes and mechanisms involved in radiation responses.
Magnesium therapy for nephrolithiasis. (2005)

Clinical trial evidence does not justify the use of MgO or Mg(OH)2 as a sole therapy for calcium oxalate kidney stones in a general patient population. However, the addition of magnesium to potassium citrate therapy improves outcomes. Clinical trials should focus on patients who are likely to be Mg deficient.
Spectral modulation detection and vowel and consonant identifications in cochlear implant listeners (2009)

Speech understanding by cochlear implant listeners may be limited by their ability to perceive complex spectral envelopes. Here, spectral envelope perception was characterized by spectral modulation transfer functions in which modulation detection thresholds became poorer with increasing spectral modulation frequency (SMF). Thresholds at low SMFs, less likely to be influenced by spectral resolution, were correlated with vowel and consonant identifications [Litvak, L. M. et al. (2008). J. Acoust. Soc. Am. 122, 982-991] for the same listeners; while thresholds at higher SMFs, more likely to be affected by spectral resolution, were not. Results indicate that the perception of broadly spaced spectral features is important for speech perception.
Towards Scene Understanding: Unsupervised Monocular Depth Estimation With Semantic-Aware Representation (2019)

Monocular depth estimation is a challenging task in scene understanding, with the goal to acquire the geometric properties of 3D space from 2D images. Due to the lack of RGB-depth image pairs, unsupervised learning methods aim at deriving depth information with alternative supervision such as stereo pairs. However, most existing works fail to model the geometric structure of objects, which generally results from considering pixel-level objective functions during training. In this paper, we propose SceneNet to overcome this limitation with the aid of semantic understanding from segmentation. Moreover, our proposed model is able to perform region-aware depth estimation by enforcing semantics consistency between stereo pairs. In our experiments, we qualitatively and quantitatively verify the effectiveness and robustness of our model, which produces favorable results against the state-of-the-art approaches do.
Cetuximab plus Irinotecan as third line chemotherapy for metastatic colorectal cancer (2008)

14623 Background: Cetuximab combined with irinotecan has shown progression free and overall survival benefits in metastatic colorectal cancer as third line chemotherapy. We evaluate the outcome of this treatment given to patients in South Wales, UK. Methods: Metastatic colorectal cancer patients who received cetuximab and irinotecan were identified. Data was collected from patient records. Cetuximab was given 400 mg/m2 first dose followed by 250 mg/m2 weekly thereafter. Irinotecan was given 350 mg/m2 every 3 weeks or 180 mg/m2 fortnightly. The response status was evaluated with CT scan according to RECIST after 6 weeks of treatment. Time to progression (TTP) was defined as time from treatment start date to documented disease progression or death whichever is earlier. Overall survival (OS) is defined as time from treatment start date to death from any cause. Results: Total of 42 patients were treated between October 2004 and January 2007. Male =23; median age =63 (range = 42–84); PFS 0–1 =42; previous oxaliplatin =38; liver metastases =37; >3 metastatic sites = 9; EGFR status Positive = 13, Negative =3, unknown =27. Median treatment duration: 12 weeks (range: 1 - 71). PR = 9 (21.4%), SD = 10 (23.8%), PD =23 (54.7%). Two patients with negative EGFR expression showed PR. At analysis all patients had disease progression and 37 patients had died. Median TTP =16 weeks (1–74 weeks), median OS =30 weeks (1 - 130 weeks). Reasons for stopping treatment are: radiological disease progression = 28, poor PFS = 4, break from treatment = 7, side effects = 2 (rash and tiredness each) and CVA = 1. Patients who achieved PR or SD on CT scan after 6 weeks treatment had significantly longer median survival compared to those who did not achieve this (17 vs. 51 weeks; p = 0.001). Median OS after stopping cetuximab was longer for those patients with PR/SD compared to those with PD. Conclusions: Our median TTP and OS are comparable to those of BOND trial (4.1 and 8.6 months). Response to cetuximab and irinotecan could be seen in tumours with negative EGFR expression by current IHC method. Novel treatment options are needed for those whose disease progressed on cetuximab and irinotecan treatment as they have significantly shorter survival compared to those who achieve PR or SD. The PD status after 6 weeks treatment is predictive of shorter survival. No significant financial relationships to disclose.