gebhart/patrepeval huggingface dataset:
Improving Insulin Therapy: Achievements and Challenges (1994)

Microvascular complications of diabetes can be forestalled by effective glycemic control. However, the inherent limitations of standard subcutaneous insulins reduce their ability to control glycemia without risk of significant hypoglycemia and hyperinsulinemia. Hypoglycemia is unacceptable for most patients and may be dangerous. Hyperinsulinemia is undesirable because it causes weight gain and it has a putative association with atherosclerosis. This paper summarizes the major historical improvements in insulin therapy, and calls attention to the fact that none of the presently available commercial preparations in any combination is capable of simulating the profile of normal insulin secretion--the latter being regarded as the most effective means of normalizing glycemia. For this reason, a variety of new approaches to simulating the pharmacokinetics or glucodynamics of insulin secretion are under investigation. Fast-acting insulin analogues suitable for subcutaneous injection have been developed and appear to mimic the physiological insulin response more closely than standard insulins. Less progress has been made with basal insulins. Intravenous insulin has pharmacodynamic advantages but practical disadvantages of administration. Nasal insulin would be an attractive treatment modality only if its bioavailability could be significantly increased and its safety assured. Other interventions which improve glucose metabolism without necessarily simulating normal insulin secretion are under investigation. These include biosynthetic human C-peptide, insulin-like growth factor-1 and glucagon-like peptide 1 (7-36 amide).
LPA protects intestinal epithelial cells from apoptosis by inhibiting the mitochondrial pathway (2003)

We previously showed (Gastroenterology 123: 206-216, 2002) that lysophosphatidic acid (LPA) protects and rescues rat intestinal epithelial cells (IEC-6) from apoptosis. Here, we provide evidence for the LPA-elicited inhibition of the mitochondrial apoptotic pathway leading to attenuation of caspase-3 activation. Pretreatment of IEC-6 cells with LPA inhibited campothecin-induced caspase-9 and caspase-3 activation and DNA fragmentation. A caspase-9 inhibitor peptide mimicked the LPA-elicited antiapoptotic activity. LPA elicited ERK1/ERK2 and PKB/Akt phosphorylation. The LPA-elicited antiapoptotic activity and inhibition of caspase-9 activity were abrogated by pertussis toxin, PD 98059, wortmannin, and LY 294002. LPA reduced cytochrome c release from mitochondria and prevented activation of caspase-9. LPA prevented translocation of Bax from cytosol to mitochondria and increased the expression of the antiapoptotic Bcl-2 mRNA and protein. LPA had no effect on Bcl-xl, Bad, and Bak mRNA or protein expression. These data indicate that LPA protects IEC-6 cells from camptothecin-induced apoptosis through G(i)-coupled inhibition of caspase-3 activation mediated by the attenuation of caspase-9 activation due to diminished cytochrome c release, involving upregulation of Bcl-2 protein expression and prevention of Bax translocation.
Electromagnetic Heating of Breast Tumors in Interventional Radiology: In Vitro and in Vivo Studies in Human Cadavers and Mice (2001)

Magnetic heating of breast tumors is a promising technique for future interventional radiologic treatments.
Terahertz time-domain spectroscopy characterization of carbon nanostructures embedded in polymer (2017)

This work presents results of terahertz time-domain spectroscopy (THz-TDS) investigations of two types of polymer-based nanocomposites, consisting of bulk samples of graphene nanoflakes embedded in a polymer matrix and thin films where single-walled carbon nanotubes (SWCNTs) with a chiral index (7,5) were wrapped in single strains of a polymer. Our THz-TDS setup is a room-temperature system with a frequency range of 0.1 to 3.5 THz, based on photoconductive switches as both the emitter and detector, excited by 100-fs-wide optical pulses. We have studied THz spectra of both types of samples and compared them to the ones obtained for the pure polymer reference specimens and fitted the experimental complex conductivity data to the Drude–Smith model. The Drude–Smith model fits our data well, demonstrating that graphene nanoflakes and SWCNTs, exhibit highly localized intra grain/tube electron backscattering with a femtosecond relaxation time.
Barley alpha-amylase genes. Quantitative comparison of steady-state mRNA levels from individual members of the two different families expressed in aleurone cells. (1988)

We have cloned and sequenced two barley alpha-amylase genes belonging to the high pI isozyme family, one of which, Amy6-4, corresponds to a cDNA previously characterized by our laboratory. A 750-base pair probe from Amy6-4, representing primarily the promoter/upstream sequences cross-hybridizes on genomic Southern blots under stringent conditions to five other genes or pseudogenes; this demonstrates that the promoter/upstream region in these different members of the gene family is highly conserved. In contrast, this probe hybridizes very poorly to the genomic fragment containing the other cloned high pI gene, Amy46, a finding consistent with substantial divergence of sequence about 200 base pairs upstream from the TATA box of each. We compared steady-state mRNA levels from these individual genes to levels for mRNAs from two low pI alpha-amylase genes and from the single copy gene for aleurain, a thiol protease, using quantitative S1 nuclease protection assays. We found, in RNA from aleurone cells treated with gibberellic acid for 19-24 h, that the two low pI alpha-amylase mRNAs are each about five times more abundant than Amy6-4 or aleurain, which are, in turn, about 10 times more abundant than Amy46. These results indicate that as many as seven closely related high pI genes are needed to provide mRNA levels approaching those from the two low pI genes. We speculate that the substantially lower level of expression of Amy46 may be related to its divergent sequence upstream from the promoter.
A prospective, randomized trial of gonadotropin-releasing hormone agonist plus estrogen-progestin or progestin "add-back" regimens for women with leiomyomata uteri. (1993)

Treatment of women with myomas with GnRH agonists (GnRH-a) for 3-6 months will result in profound hypoestrogenism, a significant but temporary reduction in uterine volume, and menstrual suppression. Long-term (i.e. > 6 months) treatment with a GnRH-a is not recommended because of accelerated bone resorption and the presence of hypoestrogenic symptoms. In this 2-yr study, women with myomas were treated with GnRH-a plus one of two steroid "add-back" regimens to minimize adverse sequelae of chronic hypoestrogenism. Fifty-one premenopausal women with large, symptomatic uterine myomas all received the GnRH-a, leuprolide acetate depot (LAD), every 4 weeks for 12 weeks at which time the women were randomized to receive LAD plus either an estrogen-progestin or progestin-only add-back regimen for an additional 92 weeks. Efficacy parameters assessed included serial uterine volumes, hemoglobin concentrations, and hematocrits; safety parameters evaluated included serial bone mineral density measurements, lipid profiles, and medication-related symptoms. This report analyzes the first 52 weeks of study data. Mean uterine volume decreased to 64% of pretreatment size at 12 weeks of LAD treatment in both groups. The estrogen-progestin add-back group had no significant regrowth of uterine volume, which was 75% of pretreatment size at treatment week 52; in contrast, the progestin add-back group had a mean uterine volume of 92% of pretreatment size by treatment week 52. Both groups demonstrated significant improvements in mean hemoglobin concentrations and hematocrits. The progestin add-back group had a significant decline in mean high density lipoprotein-cholesterol concentration, which was not seen in the estrogen-progestin add-back group. Finally, after a significant 3% bone loss during the first 12 weeks of treatment, bone mineral density stabilized in both add-back regimen groups. GnRH-a/steroid add-back regimens provide a useful long-term treatment strategy in women with large, symptomatic uterine myomas and may obviate the need for surgical intervention in selected cases. The estrogen-progestin add-back regimen was superior or equal to the progestin add-back regimen in all efficacy and safety parameters assessed.
Unusual N-glycosylation of a recombinant human erythropoietin expressed in a human lymphoblastoid cell line does not alter its biological properties (2000)

Erythropoietin (Epo) is a 166 amino acids protein containing three N-glycosylation sites (Asn-24, Asn-38, and Asn-83) and 1 O- glycosylation site (Ser-126) and involved in the regulation of the level of red blood cells. Today, only one recombinant human Epo (rHuEpo), produced in CHO cell line, is extensively used in therapy to cure severe anemia. The structure of the glycan chains of this rHuEpo slightly differ of those of the urinary human Epo (uHuEpo), considered as the natural Epo molecule. In an attempt to produce a rHuEpo as close as possible to the uHuEpo, Epo gene was expressed in a human lymphoblastoid cell line, named RPMI 1788. In order to fully characterize the Epo-RPMI, structural characterizations of the protein skeleton as well as glycan chains were undergone. As expected, the amino acid sequence of the Epo-RPMI conformed to that of uHuEpo. Surprisingly, the structure of some N-glycan chains, as mainly determined by ESI-MS, revealed some unusual characteristics. Thus, 80% of N-glycans possess a bisecting GlcNAc residue, 25% bear a second fucose residue which is present, in a large part, in a sialyl Le(x)motif, and 13% contain more than three LacNAc repeats (up to five per molecule). Despite these unusual structural characteristics, the data concerning the in vitro and in vivo biological activities were not impaired when compared to Epo-CHO and uHuEpo.
Characteristics of Candida albicans adherence to mouse tissues (1990)

An ex vivo binding assay originally described for determining lymphocyte homing receptors was adapted for studying Candida albicans-host cell interactions in unfixed tissue sections. BALB/cByJ mice were sacrificed, and various organs were removed, rapidly frozen on dry ice, and sectioned. C. albicans yeast cells were suspended to 1.5 x 10(8) cells per ml in Dulbecco modified Eagle medium supplemented with 5% newborn calf serum, and 100 microliters of the suspension was added to tissue sections for 15 min with rotation at 4 degrees C or at 22 to 24 degrees C. The sections were then fixed in glutaraldehyde, washed, and examined. Stationary-phase yeast cells adhered better than log-phase cells, and adherence characteristics were similar at 4 degrees C and 22 to 24 degrees C. Yeast cells from nine strains of C. albicans showed similar tissue specificity. Adherence to lymph node tissue was confined to subcapsular spaces and trabecular sinuses. In the spleen, yeast cells bound to the marginal zones. In both tissues, an association of yeast cells with tissue macrophages was suggested by results with macrophage-specific monoclonal antibodies and fluorescent or immunoperoxidase staining techniques. C. albicans adhered to convoluted tubules, glomeruli, and the tunica media of arterioles in the kidney. During experimentally induced fungemia in mice, C. albicans yeast cells associated with the same tissue sites as in the ex vivo assay, except that binding to renal arterioles was not seen in the in vivo test. A strain of Saccharomyces cerevisiae showed some adherence patterns in common with C. albicans, which indicates that tissue adherence is not sufficient for virulence. Mechanisms of attachment were not determined, but strains of C. albicans varied quantitatively in their ability to attach, and binding was inhibited by chelators of divalent cations.
Video coding using compressive sensing for wireless communications (2011)

A new video coding method based on compressive sampling is proposed, in which a video is coded using compressive measurements on video cubes. Video reconstruction is based on minimizing the total variation (TV) of the pixelwise DCT coefficients along temporal direction. The reconstruction algorithm is an efficient TV minimization algorithm based on the augmented Lagrangian method and an alternating minimization technique.
Refined structure of monomelic diphtheria toxin at 2.3 Å resolution (1994)

The structure of toxic monomeric diphtheria toxin (DT) was determined at 2.3 A resolution by molecular replacement based on the domain structures in dimeric DT and refined to an R factor of 20.7%. The model consists of 2 monomers in the asymmetric unit (1,046 amino acid residues), including 2 bound adenylyl 3'-5' uridine 3' monophosphate molecules and 396 water molecules. The structures of the 3 domains are virtually identical in monomeric and dimeric DT; however, monomeric DT is compact and globular as compared to the "open" monomer within dimeric DT (Bennett MJ, Choe S, Eisenberg D, 1994b, Protein Sci 3:0000-0000). Detailed differences between monomeric and dimeric DT are described, particularly (1) changes in main-chain conformations of 8 residues acting as a hinge to "open" or "close" the receptor-binding (R) domain, and (2) a possible receptor-docking site, a beta-hairpin loop protruding from the R domain containing residues that bind the cell-surface DT receptor. Based on the monomeric and dimeric DT crystal structures we have determined and the solution studies of others, we present a 5-step structure-based mechanism of intoxication: (1) proteolysis of a disulfide-linked surface loop (residues 186-201) between the catalytic (C) and transmembrane (T) domains; (2) binding of a beta-hairpin loop protruding from the R domain to the DT receptor, leading to receptor-mediated endocytosis; (3) low pH-triggered open monomer formation and exposure of apolar surfaces in the T domain, which insert into the endosomal membrane; (4) translocation of the C domain into the cytosol; and (5) catalysis by the C domain of ADP-ribosylation of elongation factor 2.
Ribosome Degradation and the Degradation Products in Starved Escherichia coli (1972)

The properties of the abnormal ribonucleoprotein particles produced by Escherichia coli Q-13 starved for glucose were studied. Smaller species of these partially deproteinized particles separable to six distinct sizes contained partially degraded ribonucleic acids. The mode of ribosome degradation under this condition is discussed in terms of differential appearance of these intermediate particles.
Convolution on Splash 2 (2002)

Convolution is a fundamental operation in many signal and image processing applications. Since the computation and communication pattern in a convolution operation is regular, a number of special architectures have been designed and implemented for this operator. The Von Neumann architectures cannot meet the real-time requirements of applications that use convolution as an intermediate step. We combine the advantages of systolic algorithms with the low cost of developing application specific designs using field programmable gate arrays (FPGAs) to build a scalable convolver for use in computer vision systems. The performance of the systolic algorithm of (Kung et al., 1981) is compared theoretically and experimentally with many other convolution algorithms reported in the literature. The implementation of a convolution operation on Splash 2, an attached processor based on Xilinx 4010 FPGAs, is reported with impressive performance gains.
Technical terminology: some linguistic properties and an algorithm for identification in text (1995)

Abstract This paper identifies some linguistic properties of technical terminology, and uses them to formulate an algorithm for identifying technical terms in running text. The grammatical properties discussed are preferred phrase structures: technical terms consist mostly of noun phrases containing adjectives, nouns, and occasionally prepositions; rerely do terms contain verbs, adverbs, or conjunctions. The discourse properties are patterns of repetition that distinguish noun phrases that are technical terms, especially those multi-word phrases that constitute a substantial majority of all technical vocabulary, from other types of noun phrase. The paper presents a terminology indentification algorithm that is motivated by these linguistic properties. An implementation of the algorithm is described; it recovers a high proportion of the technical terms in a text, and a high proportaion of the recovered strings are vaild technical terms. The algorithm proves to be effective regardless of the domain of the text to which it is applied.
Determination of the nucleotide conformation in the productive enzyme‐substrate complexes of RNA‐depolymerases (1997)

The aim of this work is to determine the conformation of the nucleobase adjacent to the cleavable phosphodiester bond in the productive enzyme-substrate complex of RNA-depolymerizing enzymes. To this end the kinetic parameters of hydrolysis of UpA, 2'-C-Me- and 3'-C-Me-UpA were determined for RNase A, RNase Pb2, nuclease S1 and snake venom phosphodiesterase. In these derivatives the ranges of the allowed orientation of uridine residues are restricted due to the substitution of methyl groups for the ribose hydrogen atoms. The results described demonstrate that the proposed method is of general value for the estimation of the nucleotide glycoside angles in the productive enzyme-substrate complexes.
Chimeric CD19 antibody mediates cytotoxic activity against leukemic blasts with effector cells from pediatric patients who received T-cell–depleted allografts (2004)

Relapse is a major problem after transplantation in children with acute B-lineage leukemias, and new therapies are needed to increase graft-versus-leukemia (GvL) effects without inducing graft-versus-host disease (GvHD). Here, we studied the ability of effector cells recovered from patients after transplantation with positive-selected stem cells from alternative donors to induce antibody-dependent cellular cytotoxicity (ADCC). For this purpose, a chimeric CD19 antibody, CD19-4G7chim, was generated. This antibody efficiently mediated ADCC against primary acute lymphoblastic leukemia (ALL) blasts by using purified natural killer (NK) cells from healthy donors or mononuclear cells from patients as effector cells. Increased lysis was obtained after stimulation of effector cells with interleukin-2 (IL-2). ADCC was not prevented by inhibitory effects mediated by HLA class I. We propose that treatment with chimeric CD19 antibodies leading to ADCC by donor-derived NK cells may become a therapeutic option for the post-transplantation treatment of minimal residual B-lineage ALLs.
Wherefore art thou r3579x? (2007)

In a social network, nodes correspond topeople or other social entities, and edges correspond to social links between them. In an effort to preserve privacy, the practice of anonymization replaces names with meaningless unique identifiers. We describe a family of attacks such that even from a single anonymized copy of a social network, it is possible for an adversary to learn whether edges exist or not between specific targeted pairs of nodes.
Use of polysialic acid in repair of the central nervous system (2006)

Polysialic acid (PSA), a large cell-surface carbohydrate that regulates cell interactions, is used during vertebrate development to promote precursor cell migration and axon path-finding. The induction of PSA expression in damaged adult CNS tissues could help them to rebuild by creating conditions permissive for architectural remodeling. This possibility has been explored in two contexts, the regeneration of axons and the recruitment of endogenous neural precursors to a lesion. Glial scars that form at CNS injury sites block axon regeneration. It has been found that transfection of scar astrocytes by a viral vector encoding polysialyltransferase leads to sustained expression of high levels of PSA. With this treatment, a substantial portion of severed corticospinal tract axon processes were able to grow through a spinal injury site. In the studies of precursor cell migration to a cortical lesion, it was found that induced PSA expression in a path extending from the subventricular zone to a lesion near the cortical surface increased recruitment of BrdU/nestin-positive cells along the path and into the injury site. These displaced precursors were able to differentiate in a regionally appropriate manner. These findings suggest that induced PSA expression can be used as a strategy for promoting tissue repair involving both replacement of cells and rebuilding of neural connections.
Vaccines based on the cell surface carbohydrates of pathogenic bacteria (2005)

Glycoconjugate vaccines, in which a cell surface carbohydrate from a micro-organism is covalently attached to an appropriate carrier protein are proving to be the most effective means to generate protective immune responses to prevent a wide range of diseases. The technology appears to be generic and applicable to a wide range of pathogens, as long as antibodies against surface carbohydrates help protect against infection. Three such vaccines, against Haemophilus influenzae type b, Neisseria meningitidis Group C and seven serotypes of Streptococcus pneumoniae, have already been licensed and many others are in development. This article discusses the rationale for the development and use of glycoconjugate vaccines, the mechanisms by which they elicit T cell-dependent immune responses and the implications of this for vaccine development, the role of physicochemical methods in the characterisation and quality control of these vaccines, and the novel products which are under development.
“Molded” Macroporous Poly(glycidyl methacrylate-co-trimethylolpropane trimethacrylate) Materials with Fine Controlled Porous Properties:  Preparation of Monoliths Using Photoinitiated Polymerization (1997)

A model system has been developed for in situ photopolymerization of glycidyl methacrylate and trimethylolpropane trimethacrylate, leading to macroporous monolithic sorbents. This model system allows the preparation of continuous porous objects intended for applications such as detection, separation, and catalysis. The ease of the preparation, the short time needed for reaction, and the possibility of running the reaction at a low temperature are some of the main advantages of the photoinitiated in situ polymerization compared to a thermally initiated polymerization. Important system variables acting upon the porous properties and flow characteristics of the monoliths have been investigated in an experimental 23 full factorial design. The porous properties of the monoliths are a direct consequence of the quality of the porogenic solvent, as well as the percentage of cross-linking monomer and the ratio between the monomer and porogen phases. The presence of interactive effects between these reaction conditions were verified using multivariate analysis. It was concluded that the pore formation mechanism in an in situ photopolymerization follows rules similar to those found earlier for thermally initiated in situ polymerization of poly(glycidyl methacrylate-co-ethylenedimethacrylate) and poly(styrene-co-divinylbenzene).
Self-assembled Ge nanostructures on polymer-coated silicon: Growth and characterization (2000)

Self-assembled Ge nanoparticles have been grown on polymer-coated Si substrates by thermal evaporation under high vacuum utilizing the nonwetting condition given by the surface free-energy relation σGe≫σpolymer. The nanostructures have been characterized by Raman spectroscopy, atomic-force microscopy (AFM), and optical microscopy. Raman spectrum shows a prominent Ge–Ge vibration peak at 302 cm−1. AFM and optical microscopy show the formation of isolated Ge islands (≲100 nm base, ≲25 nm height), nanowires (160 nm base, 25 nm height), and islands in linear chains. The possibility of embedding such nanostructures in waveguide structures are discussed.