gebhart/patrepeval huggingface dataset:
A Novel Gene Delivery System Using Urothelial Tissue Engineered Neo-Organs (1997)

Successful gene transfer can be achieved using biodegradable polymer scaffolds as a urothelial cell delivery vehicle. The transfected cell-polymer scaffold forms an organ-like structure with functional expression of the transfected genes. This study demonstrates that urothelial tissue engineered gene transfer is safe and effective.
The low HDL cholesterol/high triglyceride trait. (1993)

In 748 probands and 3,283 first-degree relatives from the Collaborative Lipid Research Clinics (LRC) Family Study, our specific aim was to examine the degree to which low (bottom decile) high density lipoprotein cholesterol (HDL-C, hypoalpha) and high (top decile) triglyceride (TG, hyperTG) levels occur conjointly (CT) and the extent to which these characteristics were shared within families. To control for family size and permit a comparison with the proband percentages, mean familial percentages of HDL-C/TG abnormalities were calculated. Concurrent low HDL-C and high TG levels were present in 2.7% of the probands, a value that was enriched to 12.7% (p = 0.003) of their associated first-degree relatives. If the proband had a low HDL-C value, 7.7% (p = 0.013) of relatives had CT. Familial (proband and at least one first-degree family member share the same lipoprotein/lipid phenotype) hypoalpha was observed in 2.4% of families while familial hyperTG was observed in 4.1%. Familial CT was seen in approximately 0.7%. If the proband had CT, 80% of their families had at least one other first-degree member with an HDL-C/TG abnormality, whereas the corresponding percentage for families associated with probands with only hypoalpha was 64% and for those with hyperTG alone, 54%. A broadly shared environmental factor cannot easily explain the familial association of hypoalpha, hyperTG, and CT. In probands with low HDL-C values alone or the conjoint low-HDL-C/high-TG trait, family screening is extremely valuable because low HDL-C/high TG is enriched in the respective family members, a conjoined trait closely associated with increased coronary heart disease risk.
Nanoscaled MOSFET Transistors on Strained Si, SiGe, Ge Layers: Some Integration and Electrical Properties Features (2006)

We have studied the integration process and the electrical properties of TiN/metal gate transistors with high k dielectrics for various strained substrates: Strained SOI, Strained SiGeOI, and Strained Ge. Substrate approaches enable (i)higher strain levels (additive with process induced strain), (ii)the co-integration of opposite strained layers for nMOS and PMOS, (iii)V T engineering for metal gates. Those features make the substrate approach a very promising solution for ultimate CMOS integration.
A Reagent for Selective Deprotection of Alkyl Acetates (1996)

The use of magnesium methoxide for selective deprotection of alkyl esters is described. By adjusting the equivalents of the magnesium methoxide reagent, it is possible to selectively cleave primary acetate in the presence of secondary and tertiary acetate and to cleave secondary acetate in the presence of tertiary acetate. A high selectivity can also be obtained for the same primary acetates if the β-positions of the acetates render a different steric bulkiness. This mild reagent has been successfully applied to the selective deprotection of many natural-occurring molecules including hydroxycitronnellol diacetate, trans-sobrerol diacetate, betulin diacetate, and baccatin III.
Volume sculpting (1995)

We present a modeling technique based on the metaphor of interactively sculpting complex 3D objects from a solid material, such as a block of wood or marble. The 3D model is represented in a 3D raster of voxels where each voxel stores local material property information such as color and texture. Sculpting is done by moving 3D voxel-based tools within the model. The affected regions are indicated directly on the 2D projected image of the 3D model. By reducing the complex operations between the 3D tool volume and the 3D model down to primitive voxel-by-voxel operations, coupled with the utilization of a localized ray casting for image updating, our sculpting tool achieves real-time interaction. Furthermore, volume sampling techniques and volume manipulations are employed to ensure that the process of sculpting does not introduce aliasing into the models.
Combining the predictions of multiple classifiers: using competitive learning to initialize neural networks (1995)

The primary goal of inductive learning is to generalize well -- that is, induce a function that accurately produces the correct output for future inputs. Hansen and Salamon showed that, under certain assumptions, combining the predictions of several separately trained neural networks will improve generalization. One of their key assumptions is that the individual networks should be independent in the errors they produce. In the standard way of performing backpropagation this assumption may be violated, because the standard procedure is to initialize network weights in the region of weight space near the origin. This means that backpropagation&amp;apos;s gradient-descent search may only reach a small subset of the possible local minima. In this paper we present an approach to initializing neural networks that uses competitive learning to intelligently create networks that are originally located far from the origin of weight space, thereby potentially increasing the set of reachable local minima....
Long-term expression of murine activated factor VII is safe, but elevated levels cause premature mortality (2008)

Intravenous infusion of recombinant human activated Factor VII (FVIIa) has been used for over a decade in the successful management of bleeding episodes in patients with inhibitory antibodies to Factor VIII or Factor IX. Previously, we showed that expression of murine FVIIa (mFVIIa) from an adeno-associated viral (AAV) vector corrected abnormal hemostatic parameters in hemophilia B mice. To pursue this as a therapeutic approach, we sought to define safe and effective levels of FVIIa for continuous expression. In mice transgenic for mFVIIa or injected with AAV-mFVIIa, we analyzed survival, expression levels, in vitro and in vivo coagulation tests, and histopathology for up to 16 months after birth/mFVIIa expression. We found that continuous expression of mFVIIa at levels at or below 1.5 microg/ml was safe, effective, and compatible with a normal lifespan. However, expression levels of 2 microg/ml or higher were associated with thrombosis and early mortality, with pathologic findings in the heart and lungs that were rescued in a low-factor X (low-FX) mouse background, suggesting a FX-mediated effect. The findings from these mouse models of continuous FVIIa expression have implications for the development of a safe gene transfer approach for hemophilia and are consistent with the possibility of thromboembolic risk of continuously elevated FVIIa levels.
The influence of stromal contraction in a wound model system on corneal epithelial stratification. (2001)

These studies showed that the contracted state of fibroblast-seeded gels enhanced the development of well-organized, stratified corneal epithelium.
Performance analysis of the IEEE 802.11 distributed coordination function (2000)

The IEEE has standardized the 802.11 protocol for wireless local area networks. The primary medium access control (MAC) technique of 802.11 is called the distributed coordination function (DCF). The DCF is a carrier sense multiple access with collision avoidance (CSMA/CA) scheme with binary slotted exponential backoff. This paper provides a simple, but nevertheless extremely accurate, analytical model to compute the 802.11 DCF throughput, in the assumption of finite number of terminals and ideal channel conditions. The proposed analysis applies to both the packet transmission schemes employed by DCF, namely, the basic access and the RTS/CTS access mechanisms. In addition, it also applies to a combination of the two schemes, in which packets longer than a given threshold are transmitted according to the RTS/CTS mechanism. By means of the proposed model, we provide an extensive throughput performance evaluation of both access mechanisms of the 802.11 protocol.
Characterization of Neuroprotection from Excitotoxicity by Moderate and Profound Hypothermia in Cultured Cortical Neurons Unmasks a Temperature-Insensitive Component of Glutamate Neurotoxicity (1998)

Although profound hypothermia has been used for decades to protect the human brain from hypoxic or ischemic insults, little is known about the underlying mechanism. We therefore report the first characterization of the effects of moderate (30 degrees C) and profound hypothermia (12 degrees to 20 degrees C) on excitotoxicity in cultured cortical neurons exposed to excitatory amino acids (EAA; glutamate, N-methyl-D-aspartate [NMDA], AMPA, or kainate) at different temperatures (12 degrees to 37 degrees C). Cooling neurons to 30 degrees C and 20 degrees C was neuroprotective, but cooling to 12 degrees C was toxic. The extent of protection depended on the temperature, the EAA receptor agonist employed, and the duration of the EAA challenge. Neurons challenged briefly (5 minutes) with all EAA were protected, as were neurons challenged for 60 minutes with NMDA, AMPA, or kainate. The protective effects of hypothermia (20 degrees and 30 degrees C) persisted after rewarming to 37 degrees C, but rewarming from 12 degrees C was deleterious. Surprisingly, however, prolonged (60 minutes) exposures to glutamate unmasked a temperature-insensitive component of glutamate neurotoxicity that was not seen with the other, synthetic EAA; this component was still mediated via NMDA receptors, not by ionotropic or metabotropic non-NMDA receptors. The temperature-insensitivity of glutamate toxicity was not explained by effects of hypothermia on EAA-evoked [Ca2+]i increases measured using high- and low-affinity Ca2+ indicators, nor by effects on mitochondrial production of reactive oxygen species. This first characterization of excitotoxicity at profoundly hypothermic temperatures reveals a previously unnoticed feature of glutamate neurotoxicity unseen with the other EAA, and also suggests that hypothermia protects the brain at the level of neurons by blocking, rather than slowing, excitotoxicity.
Four proline-rich sequences of the guanine-nucleotide exchange factor C3G bind with unique specificity to the first Src homology 3 domain of Crk (1994)

The widely expressed cellular Crk protein has the domain structure SH2-SH3-SH3. We have previously demonstrated that the more N-terminal SH3 domain of Crk (CrkSH3(N)) specifically binds several cytoplasmic proteins. A cDNA encoding one of these proteins was isolated and found to have two different splice forms. The sequence is virtually identical to C3G, a guanine-nucleotide exchange factor. The center region of the 145-155-kDa protein contains four similar proline-rich sequences which are capable of binding individually to the SH3(N) domains of c-Crk and v-Crk. Comparison of these sequences in C3G to proline-rich sequences in other Crk-binding proteins suggests that positively charged amino acids following the prolines play an important role in the binding to the CrkSH3(N) domain. The endogenous C3G could be coprecipitated with Crk from cell lysates of cells expressing high levels of c-Crk or v-Crk, suggesting high binding affinity and a possible interaction in vivo. Unlike many other SH3-binding proteins which interact with multiple SH3 domains, C3G from cell lysates binds preferentially to the CrkSH3(N) domain. This unique binding specificity supports the idea that C3G plays an important role in Crk signaling pathways.
On Catalytic Reduction of 4-Acylaminoisoquinolines (1967)

Catalytic reductions of 4-amino-, 4-acetamido-, and 4-benzamidoisoquinoline under several conditions were examined. Reduction of 4-acetamido- and 4-benzamidoisoquinoline over Adams catalyst in acetic acid or over Raney nickel in ethanol afforded the corresponding 1, 2, 3, 4-tetrahydro derivatives ; whereas their reduction over Adams catalyst in acetic acidsulfuric acid gave the corresponding 5, 6, 7, 8-tetrahydro derivatives. 4-Aminoisoquinoline was reduced to 5, 6, 7, 8-tetrahydro derivative either over Adams catalyst in acetic acid or over Raney nickel in ethanol.
Efficient tracking and querying for coordinated uncertain mobile objects (2013)

Accurately estimating the current positions of moving objects is a challenging task due to the various forms of data uncertainty (e.g. limited sensor precision, periodic updates from continuously moving objects). However, in many cases, groups of objects tend to exhibit similarities in their movement behavior. For example, vehicles in a convoy or animals in a herd both exhibit tightly coupled movement behavior within the group. While such statistical dependencies often increase the computational complexity necessary for capturing this additional structure, they also provide useful information which can be utilized to provide more accurate location estimates. In this paper, we propose a novel model for accurately tracking coordinated groups of mobile uncertain objects. We introduce an exact and more efficient approximate inference algorithm for updating the current location of each object upon the arrival of new (uncertain) location observations. Additionally, we derive probability bounds over the groups in order to process probabilistic threshold range queries more efficiently. Our experimental evaluation shows that our proposed model can provide 4X improvements in tracking accuracy over competing models which do not consider group behavior. We also show that our bounds enable us to prune up to 50% of the database, resulting in more efficient processing over a linear scan.
Growth hormone (GH) binding protein and GH interactions in vivo in the guinea pig (1992)

GH binding proteins (GHBPs) are present in the blood of several species and by complexing with circulating GH may alter its clearance and distribution. The actions of human GHBP (hGHBP) have hitherto been studied indirectly via their effects on the clearance of hGH. In the present experiments, recombinant preparations of hGHBP and a shorter variant lacking exon 3 (delta 3hGHBP) were tested in vivo, either alone or after preincubation with recombinant hGH, recombinant 20K methionyl-hGH, or rat GH. Multiple serial blood sampling was performed in conscious chronically cannulated guinea pigs and both GHBP and GH variants monitored in the same samples by specific RIAs, unaffected by endogenous activities in this species. hGHBP, delta 3hGHBP, hGH, and 20K met-hGH (10-40 micrograms) were all cleared rapidly when injected alone (t1/2 = 11-20 min). However, when the same amounts of hGHBP and hGH were incubated together for 60 min and then injected, the clearance of both proteins was greatly prolonged (t1/2 hGHBP = 75-94 min, hGH = 80-137 min). Similar results were obtained for hGH complexed with delta 3hGHBP, and over a range of GH:GHBP ratios from 0.3:1 to 4:1. The effect was specific for 22K hGH; neither rat GH nor 20K met-hGH altered hGHBP clearance, nor were their clearances slowed by preincubation with hGHBP. Rapid complex formation also could be demonstrated in vivo. Injections of hGH 30 min after delta 3hGHBP, or vice versa, altered the established plasma disappearance curve of hGHBP, and hGH clearance was slowed in parallel. During a continuous infusion of hGH to steady state, injections of delta 3hGHBP increased plateau hGH concentrations by forming a delta 3hGHBP/hGH complex in the circulation. These experiments show that the conscious chronically cannulated guinea pig provides a useful model in which the in vivo interaction between hGHBP and hGH can be studied dynamically. The results imply that the location, extent, and rate of complex formation between GHBP and GH may be an important determinant of the passage of GH between the intra- and extravascular compartments, which could affect the pattern of tissue exposure to GH.
Inhibin and activin production and subunit expression in human placental cells cultured in vitro (2000)

Inhibins and activins are dimeric proteins, with each subunit being one of three related protein subunits (alpha, betaA or betaB). The mRNA levels of these subunits were studied quantitatively during in-vitro differentiation of human cytotrophoblast cells into syncytium, using Northern blot analysis and semi-quantitative reverse transcription-polymerase chain reaction (RT-PCR) analysis. The corresponding protein concentrations were determined by specific enzyme-linked immunosorbent assays for inhibin A, B, pro alphaC and activin A in cellular protein extracts and culture medium (n = 5). Immunofluorescence studies showed syncytium formation after 48 h. The alpha subunit was present before plating and increased at 48 h (P<0.001) while the betaA subunit was weak before plating and increased at 24 h. The betaB subunit was not detected. With respect to corresponding protein synthesis, inhibin A (alpha + betaA) had risen after 48 h in cellular protein extract and after 72 h in culture medium, while activin A (betaA + betaB) was detected after 24 h, with no significant variations in culture medium. There was a good correlation between inhibin A and alpha subunit expression (r = 0.736, P<0.001), as well as between activin A and betaA subunit expression (r = 0.755, P<0.001). This study showed that mRNA expression parallels protein synthesis of inhibin and activin in trophoblast cells. Inhibin A synthesis appears to be dependent on alpha subunit mRNA expression, rather than on the betaA subunit which controls activin A synthesis. This study has also shown that isolated cytotrophoblast cells do not produce dimeric inhibin. However, during the transformation of cytotrophoblast cells into syncytium, betaA subunit mRNA expression may be an indicator of cell aggregation, while alpha subunit mRNA expression may be an indicator of cell fusion.
Enhancement of sortase A-mediated protein ligation by inducing a β-hairpin structure around the ligation site (2011)

A Staphylococcus aureus transpeptidase, sortase A (SrtA), catalyzes selective peptide/protein ligations that have been applied to cell imaging and protein engineering, while the ligations do not proceed to completion due to their reversibility. We successfully enhanced SrtA-mediated protein ligation through the formation of a β-hairpin around the ligation site.
Ooplasmic transfer in mature human oocytes (1998)

Ooplasmic transplantation aimed at restoring normal growth in developmentally compromised oocytes and embryos was evaluated in seven couples (eight cycles) with multiple implantation failures. Two approaches were investigated to transfer ooplasm from donor eggs at metaphase II (MII) stage into patient MII eggs: (i) electrofusion of a ooplasmic donor fragment into each patient egg (three cycles), and (ii) direct injection of a small amount of ooplasm from a donor egg into each patient egg (five cycles). Some donor eggs were used multiple times. Donor eggs were divided into two groups, one being used for ooplasmic extraction and the other one for egg donation. Cleaved embryos resulting from the latter were cryopreserved, where numbers and satisfactory development permitted. A second control group consisted of embryos derived from patient eggs after intracytoplasmic sperm injection without ooplasmic transfer. This was performed when sufficient number of eggs were available (n = 5). Donor eggs (n = 40) were evaluated cytogenetically after micromanipulation in order to confirm the presence of chromosomes. One egg was anuclear and the recipient embryos were not transferred. Normal fertilization was significantly higher after injection of ooplasm (63%) in comparison with fusion (23%). Pronuclear anomalies appeared enhanced after fusion with ooplasts. Embryo morphology was not improved in the three cycles with electrofusion and patients did not become pregnant. An improvement in embryo morphology was noted in two patients after injection of ooplasm and both became pregnant, but one miscarried. A third pregnancy was established in the repeat patient, without obvious embryo improvement. One baby was born and the third pregnancy is ongoing with a normal karyotype. Two other patients with male factor infertility had poor embryos after ooplasmic injection, but the donor embryo controls were also poor. The patients did not become pregnant and had no donor embryos frozen. Ooplasmic transfer at the MII stage may be promising in patients with compromised embryos; however, evaluation of ooplasmic anomalies and optimization of techniques will require further investigation prior to widescale application.
Increasing cellulose accessibility is more important than removing lignin: A comparison of cellulose solvent‐based lignocellulose fractionation and soaking in aqueous ammonia (2010)

While many pretreatments attempt to improve the enzymatic digestibility of biomass by removing lignin, this study shows that improving the surface area accessible to cellulase is a more important factor for achieving a high sugar yield. Here we compared the pretreatment of switchgrass by two methods, cellulose solvent- and organic solvent-based lignocellulose fractionation (COSLIF) and soaking in aqueous ammonia (SAA). Following pretreatment, enzymatic hydrolysis was conducted at two cellulase loadings, 15 filter paper units (FPU)/g glucan and 3 FPU/g glucan, with and without BSA blocking of lignin absorption sites. The hydrolysis results showed that the lignin remaining after SAA had a significant negative effect on cellulase performance, despite the high level of delignification achieved with this pretreatment. No negative effect due to lignin was detected for COSLIF-treated substrate. SEM micrographs, XRD crystallinity measurements, and cellulose accessibility to cellulase (CAC) determinations confirmed that COSLIF fully disrupted the cell wall structure, resulting in a 16-fold increase in CAC, while SAA caused a 1.4-fold CAC increase. A surface plot relating the lignin removal, CAC, and digestibility of numerous samples (both pure cellulosic substrates and lignocellulosic materials pretreated by several methods) was also developed to better understand the relative impacts of delignification and CAC on glucan digestibility.