gebhart/patrepeval huggingface dataset:
Colorectal carcinomas: Diagnostic implications of their changing frequency and anatomic distribution (1989)

This retrospective review included 1,694 consecutive cases of colorectal carcinoma diagnosed at the University of Chicago Medical Center during a 25-year period (1960 through 1984). The number and percentage of tumors occurring within 7 anatomic segments of the large bowel were determined. The statistical data for a recent 5-year interval were then compared with those of the 2 preceding decades. There was a 10.2% increase in the frequency of cancers originating in the cecum or ascending colon, while rectal and rectosigmoid carcinomas declined by 15.8% during the same study period. These data provide further evidence for a progressive left-to-right shift in cancer distribution within the colon during the past quarter century. Currently, the most proximal and distal 20-25 cm segments of the large bowel (cecum or ascending colon versus rectum and rectosigmoid) each harbor approximately 25% of the tumors. Therefore, the classic medical teaching that over 50% of colorectal cancers would be detectable by digital examination and/or proctosigmoidoscopy is no longer accurate. This documented increase in proximal colon cancers and redistribution of lesions within various large bowel segments indicate the growing importance of barium enema and colonoscopy as the optimal techniques for detection of colorectal neoplasms.
Size and shape determination of spheroidal scatterers using two-dimensional angle resolved scattering (2010)

We demonstrate accurate determination of the size and shape of spherical and spheroidal scatterers through inverse analysis of two-dimensional solid-angle and depth resolved backscattered light intensities. Intensity of scattered light is measured over a wide range of solid angles using a novel scanning fiber optic interferometer from both individual and ensembles of scatterers. T-matrix based inverse analysis of these two-dimensional angular measurements yields completely unique size and aspect ratio determinations with subwavelength precision over a large range of possible scatterer geometries.
Strain-Specific Association of Cytotoxic Activity and Virulence of ClinicalStaphylococcus aureusIsolates (2003)

Staphylococcus aureus has been shown to invade and induce the death of various cell types. Here we investigate whether the cytotoxicity of intracellular S. aureus is a general feature or rather characteristic of individual S. aureus strains. The majority of 23 randomly collected clinical S. aureus isolates were killed inside keratinocytes and fibroblasts, indicating that the uptake of S. aureus represents an important mechanism of cell-autonomous host defense. However, seven independent S. aureus isolates survived intracellularly and induced significant cytotoxicity for their host cells. Subcloning analysis revealed that the ability or inability to kill host cells is a stable, apparently genetically determined trait of a given S. aureus isolate. We show that noncytotoxic strains but not cytotoxic strains colocalize with the lysosomal marker LAMP-1, suggesting that only cytotoxic strains escape degradation by the endolysosomal pathway. In a mouse septicemic model, cytotoxic S. aureus isolates produce significantly greater lethality (96%) compared to noncytotoxic strains (41%), which corresponds to 23-, 63-, and 30,000-fold increases of bacterial loads in the liver, spleen, and kidney, respectively. Finally, cytotoxic S. aureus strains produce clinically apparent arthritis in mice at a greater frequency than compared to noncytotoxic S. aureus strains. The results of our study unravel a previously unrecognized dichotomy of cytotoxic and noncytotoxic S. aureus isolates, which may play an important role in the dissemination of, and mortality induced by, S. aureus infection.
Burkholderia cepacia Produces a Hemolysin That Is Capable of Inducing Apoptosis and Degranulation of Mammalian Phagocytes (1998)

Burkholderia cepacia is an opportunistic pathogen that has become a major threat to individuals with cystic fibrosis (CF). In approximately 20% of patients, pulmonary colonization with B. cepacia leads to cepacia syndrome, a fatal fulminating pneumonia sometimes associated with septicemia. It has been reported that culture filtrates of clinically derived strains of B. cepacia are hemolytic. In this study, we have characterized a factor which contributes to this hemolytic activity and is secreted from B. cepacia J2315, a representative of the virulent and highly transmissible strain belonging to the recently described genomovar III grouping. Biochemical data from the described purification method for this hemolysin allows us to hypothesize that the toxin is a lipopeptide. As demonstrated for other lipopeptide toxins, the hemolysin from B. cepacia was surface active and lowered the surface tension of high-pressure liquid chromatography-grade water from 72.96 to 29.8 mN m(-1). Similar to reports for other pore-forming cytotoxins, low concentrations of the hemolysin were able to induce nucleosomal degradation consistent with apoptosis in human neutrophils and the mouse-derived macrophage-type cell line J774.2. Exposure of human neutrophils to higher concentrations of toxin resulted in increased activities of the neutrophil degranulation markers cathepsin G and elastase. Based on the results obtained in this study, we suggest a role that allows B. cepacia to thwart the immune response and a model of the events that may contribute to the severe inflammatory response in the lungs of CF patients.
Implantable Biohybrid Artificial Organs (1995)

Biohybrid artificial organs encompass all devices which substitute for an organ or tissue function and incorporate both synthetic materials and living cells. This review concerns implantable immunoisolation devices in which the tissue is protected from immune rejection by enclosure within a semipermeable membrane. Two critical areas are discussed in detail: (i) Device design and performance as it relates to maintenance of cell viability and function. Attention is focussed on oxygen supply limitation and how it is affected by tissue density and the development of materials that induce neovascularization at the host tissue-membrane interface; and (ii) Protection from immune rejection. Our current knowledge of the mechanisms that may be operative in immune rejection in the presence of a semipermeable membrane barrier is limited. Nonetheless, recent studies shed light on the role played by membrane properties in preventing immune rejection, and many studies demonstrate substantial progress towards clinically useful implantable immunoisolation devices.
Synthesis of 1′-Deoxypsicofuranosyl-deoxynucleosides as Potential Anti-HIV Agents (1992)

Abstract Various routes to the targets 1, 2, 3, 1-deoxy-psicofuranosyl nucleoside analogues related to anti-HIV agents, are reported. Two routes afforded their 6′-benzylated derivatives 9, 10 and 15. Only the epoxide 12 and deoxynucleosides 19 and 22 were able to be deprotected leading in the first case to 16 and its ring opening derivative 17 and in the second case to 20 and to the target 3.
Genes and psychosis: old wine in new bottles? (1995)

Despite initial setbacks, linkage studies with DNA markers continue to occupy center stage in psychiatric research. Advances in molecular and statistical techniques have revived the search for disease genes, leading to a new harvest of findings. Most interest in recent years has focused on potential linkages between schizophrenia and chromosomes X-Y (the pseudoautosomal region) and 22q12-13.1, and between bipolar affective disorder and chromosomes 18 (pericentromeric region) and 21q22.3. This article provides a critical evaluation of theses studies, with implications for future research. Concerns over earlier linkage trials make this scrutiny current and topical.
AAV-Mediated CRISPR/Cas Gene Editing of Retinal Cells In Vivo (2016)

Thy1-YFP transgenic mice were used as a rapid quantifiable means to assess the efficacy of CRISPR/Cas-based retinal gene modification in vivo. We demonstrate that genomic modification of cells in the adult retina can be readily achieved by viral-mediated delivery of CRISPR/Cas.
Inversions between ribosomal RNA genes of Escherichia coli. (1981)

It might be anticipated that the presence of redundant but oppositely oriented sequences in a chromosome could allow inversion of the intervening material through homologous recombination. For example, the ribosomal RNA gene rrnD of Escherichia coli has the opposite orientation fro rrnB and rrnE and is separated from these genes by roughly 20% of the chromosome. Starting with a derivative of Cavalli Hfr, we have constructed mutants that have an inversion of the segment between rrnD and either rrnB or rrnE. These mutants are generally quite viable but do exhibit a slight reduction in growth rate relative to the parental strain. A major line of laboratory E. coli, W3110 and its derivatives, also has an inversion between rrnD and rrnE, probably created directly by a recombinational event between these highly homologous genes.
Molten ionic oxides for CO2 capture at medium to high temperatures (2019)

Molten ionic oxides based on sodium borate and mixed alkali-metal borates show remarkably fast sorption kinetics and intrinsic regenerability as <italic>liquid</italic> absorbents for CO<sub>2</sub> capture at medium to high temperatures
Regression of established pulmonary metastases and subcutaneous tumor mediated by the systemic administration of high-dose recombinant interleukin 2. (1985)

Incubation of resting lymphoid cells with recombinant interleukin 2 (IL-2) in vitro leads to the generation of lymphokine activated killer (LAK) cells capable of lysing fresh tumor cell suspensions in short-term chromium-release assays. Our previous studies (7) have demonstrated that the injection of LAK cells plus low doses of recombinant IL-2 were capable of inhibiting the growth of pulmonary metastases. We have now explored the ability of high doses of recombinant IL-2, administered systemically, to generate LAK cells in vivo, and to mediate antitumor effects directly. Administration of increasing doses of recombinant IL-2 intraperitoneally resulted in the generation of LAK cells in the spleens of recipient mice. Doses of 100,000 U recombinant IL-2 administered intraperitoneally approximately every 8 h for 5 d were capable of dramatically inhibiting established 3-d pulmonary metastases from the MCA-105 and MCA-106 syngeneic sarcomas and the syngeneic B16 melanoma in C57BL/6 mice. Grossly visible metastases present at 10 d after tumor injection also underwent regression following IL-2 therapy. Surprisingly, established 10 d pulmonary metastases were more susceptible to the effects of IL-2 than were the smaller 3 d pulmonary metastases. All antitumor effects of the systemic administration of recombinant IL-2 were eliminated if mice received prior treatment with 500 rad total body irradiation. The administration of high doses of recombinant IL-2 was also capable of inhibiting the growth of 3-d established subcutaneous tumors from the MCA-105 sarcoma, and of mediating the inhibition of growth and regression of established palpable subcutaneous MCA-105 sarcomas. Lymphocytes, which appeared morphologically to be activated, were present at the site of regressing tumor, and it appears that the mechanism of the antitumor effect of recombinant IL-2 administered systemically is via the generation of LAK cells in vivo, although this hypothesis remains to be proven. The ready availability of high doses of recombinant human IL-2, and the demonstration of antitumor effects seen in animal models have led us to the initiation of the clinical trials of recombinant IL-2 in humans.
Vascular Response in the Femoropopliteal Segment after Implantation of an ePTFE Balloon-Expandable Endovascular Graft: An Intravascular Ultrasound Study (2000)

Following endograft placement, luminal changes within the endograft, at the endograft edges, and at the remote arterial segments were minimal. Intimal hyperplasia was not observed in the endograft. The distinct LA increase at the anastomotic segments was determined by the extent of VA and PLA change.
Formatted anti–tumor necrosis factor α VHH proteins derived from camelids show superior potency and targeting to inflamed joints in a murine model of collagen‐induced arthritis (2006)

These data suggest that because of the flexibility of their format, camelid anti-TNF VHH proteins can be converted into potent therapeutic agents that can be produced and purified cost-effectively.
Transcriptional activation of the interleukin‐8 gene by platelet‐activating factor in human peripheral blood monocytes (1997)

Interleukin-8 (IL-8) is a member of the chemokine family and a potent neutrophil chemoattractant and activator. It is produced by a variety of cell types during inflammation. In the present work, we examined the regulation of IL-8 gene expression in monocytes by the pro-inflammatory lipid mediator, platelet-activating factor (PAF). Stimulation of human peripheral blood monocytes with PAF augmented their release of IL-8. The enhancement of IL-8 secretion was associated with an increase in IL-8 mRNA expression. PAF induced a concentration- and time-dependent augmentation of IL-8 mRNA accumulation. The response was maximal at PAF concentrations of 10-100 nM. The increased mRNA expression was evident after 1.5 hr of stimulation and persisted for 6 hr. Stimulation of monocytes with PAF, followed by arrest of de novo transcription with actinomycin D, indicated that PAF only marginally increased the stability of IL-8 mRNA. However, in vitro nuclear transcription demonstrated that the enhancement of IL-8 mRNA expression occurred mainly at the transcriptional level. The PAF-induced increase in IL-8 mRNA levels could be blocked with a PAF receptor antagonist. These results show, for the first time, that IL-8 gene expression and protein production can be upregulated by PAF. This interaction could be important in the development and amplification of the inflammatory response.
Biodegradable nanoparticles for local drug delivery (2000)

To reduce restenosis after balloon angioplasty, local drug administration has the intuitive appeal of a higher site-specificity with lower drug doses needed than in the case of systemic administration. Whereas free drug administered locally diffuses out within a couple of minutes after restoration of blood circulation [1,2], the use of nanoparticles as drug carriers increases the drug uptake and the residence time considerably. In the preparation of these nanoparticles, a stabilizer is usually employed. However, 90–95% of the stabilizer is washed away during purification, which may be a drawback when further surface modification is anticipated. To obtain biodegradable nanoparticles that allow further surface modification, particles were prepared from poly(ethylene oxide)-poly(DL-lactic-co-glycolic acid) (PEO-PLGA) block copolymers. In aqueous environment the hydrophilic PEO-block may serve as a stabilizer, whereas the PEO-endgroup offers possibilities for nanoparticle surface modification. Moreover, drug-loaded particles were prepared and the drug loading efficiency was determined. Probucol was chosen as a drug, as it has an anti-restenosis activity [3]. Since drug release from the nanoparticles takes place by diffusion from and degradation of the matrix, the in vitro degradation of the PEO-PLGA nanoparticles was studied. The in vitro characteristics of these particles were compared with conventionally stabilized poly(DL-lactic acid) (PDLLA) and PLGA nanoparticles.
A gene activated in mouse 3T3 cells by serum growth factors encodes a protein with "zinc finger" sequences. (1988)

We have recently identified by cDNA cloning a set of genes that are rapidly activated in mouse 3T3 cells by serum or purified growth factors. Here we report that the cDNA (clone 268) derived from one of these immediate early genes (zif/268) encodes a protein with three tandem "zinc finger" sequences typical of a class of eukaryotic transcription factors. The mRNA of zif/268 is present in many organs and tissues of the mouse and is especially abundant in the brain and thymus tissue. The 5' genomic flanking sequence of zif/268 has sequences related to binding sites for known regulatory proteins, including four sequences that resemble the core of the serum response elements (SREs) upstream of the c-fos and actin genes. The SRE-like sequences could be responsible for the coordinate activation of zif/268 and fos after serum stimulation of 3T3 cells.
Polymer-Caged Lipsomes:  A pH-Responsive Delivery System with High Stability (2007)

Polymer-incorporated liposomes were prepared from preformed liposomes and a cholesterol-functionalized poly(acrylic acid) additive via a simple drop-in procedure. These modified liposomes possess surface-active carboxylate groups that can be cross-linked with telechelic 2,2‘-(ethylenedioxy)bis(ethylamine) linkers, resulting in polymer-caged liposomes (PCLs) that are highly stable and have tunable pH-sensitive responses.
Enhanced viewing-angle integral imaging by multiple-axis telecentric relay system (2007)

One of the main limitations of integral imaging is the narrow viewing angle. This drawback comes from the limited field of view of microlenses during the pickup and display. We propose a novel all-optical technique which allows the substantial increase of the field of view of any microlens and therefore of the viewing angle of integral-imaging displays.
Inhibition of Herpes Simplex Virus Replication by Antisense Oligo-2'-O-methylribonucleoside Methylphosphonates (1995)

Antisense oligonucleoside methylphosphonates complementary to the 12 nucleotides found at the intron/exon junction of the splice acceptor site of herpes simplex virus type 1 (HSV-1) immediate early mRNAs 4 and 5 were synthesized. The methylphosphonate oligomers contained either 2'-deoxyribose nucleosides, d-OMPs, or 2'O-methylribose nucleosides, mr-OMPs. At 37 degrees C, the affinity of the mr-OMP for a complementary 12-mer RNA target was approximately four times higher than that of the corresponding d-OMP as measured by a constant activity gel electrophoresis mobility shift assay. An mr-OMP whose sequence contained two mismatched bases did not bind to the RNA target under these conditions. The mr-OMP also showed improved ability to inhibit HSV-1 replication in HSV-1 infected Vero cells in culture. Thus the IC50 of the mr-OMP was five times less than that of the d-OMP. No inhibition was observed by the mismatched mr-OMP, and no inhibition of herpes simplex virus type 2 (HSV-2) replication was observed with any of the oligomers. These results demonstrate a direct correlation between oligomer binding affinity and antisense activity in cell culture and suggest that oligo-2'-O-methylribonucleoside methylphosphonates are promising candidates for development of effective antisense reagents.
Genetic and Immunological Properties of Phage-Displayed Human Anti-Rh(D) Antibodies: Implications for Rh(D) Epitope Topology (1998)

Understanding anti-Rh(D) antibodies on a molecular level would facilitate the genetic analysis of the human immune response to Rh(D), lead to the design of therapeutically useful reagents that modulate antibody binding, and provide relevant information regarding the structural organization of Rh(D) epitopes. Previously, we described a Fab/phage display-based method for producing a large array of anti-Rh(D) antibodies from the peripheral blood lymphocytes of a single alloimmunized donor. In the current study, we present a detailed analysis of 83 randomly selected clones. Sequence analysis showed the presence of 28 unique gamma1 heavy chain and 41 unique light chain gene segments. These paired to produce 53 unique Fabs that had specificity for at least half of the major Rh(D) epitopes. Surprisingly, despite this diversity, only 4 closely related heavy chain germline genes were used (VH3-30, VH3-30.3, VH3-33, and VH3-21). Similarly, nearly all Vkappa light chains (15/18) were derived from one germline gene (DPK9). lambda light chains showed a more diverse VL gene usage, but all (23/23) used the identical Jlambda2 gene. Several Fabs that differed in epitope specificity used identical heavy chains but different light chains. In particular, 2 such clones differed by only 3 residues, which resulted in a change from epD2 to epD3 specificity. These results suggest a model in which footprints of anti-Rh(D) antibodies are essentially identical to one another, and Rh(D) epitopes, as classically defined by panels of Rh(D) variant cells, are not discrete entities. Furthermore, these data imply that the epitope specificity of an anti-Rh(D) antibody can change during the course of somatic mutation. From a clinical perspective, this process, which we term epitope migration, has significance for the design of agents that modulate antibody production and for the creation of mimetics that block antibody binding in the settings of transfusion reactions and hemolytic disease of the newborn.
Characterization by Fourier Transform Infrared Spectroscopy (FT-IR) and 2D IR Correlation Spectroscopy of PAMAM Dendrimer (2006)

FT-IR and 2D correlation spectroscopy were employed to study the microstructural changes occurring during phase transitions of a liquid crystal poly(amidoamine) codendrimer (PAMAM (L1)16(L2)16) generation 3, functionalized on the terminal groups by one-chain promesogenic calamitic units (4-(4'-decyloxybenzoyloxy)salicylaldehyde (L1)) and two-chain promesogenic calamitic units (4-(3',4'-didecyloxybenzoyloxy)salicylaldehyde (L2)). Spectral modifications associated with molecular conformation rearrangements allowing for molecular shape change on going from a liquid-crystalline organization to another were found. The transition temperatures were calculated, and they are in good agreement with the DSC data. Spectral analysis gives evidence of the LC phase transitions and to an additional transition associated with the existence of conformers. Various types of hydrogen bonding have been established.
Rules for DNA target-site recognition by a lactococcal group II intron enable retargeting of the intron to specific DNA sequences (2000)

Group II intron homing occurs primarily by a mechanism in which the intron RNA reverse splices into a DNA target site and is then reverse transcribed by the intron-encoded protein. The DNA target site is recognized by an RNP complex containing the intron-encoded protein and the excised intron RNA. Here, we analyzed DNA target-site requirements for the Lactococcus lactis Ll.LtrB group II intron in vitro and in vivo. Our results suggest a model similar to yeast mtDNA introns, in which the intron-encoded protein first recognizes a small number of nucleotide residues in double-stranded DNA and causes DNA unwinding, enabling the intron RNA to base-pair with the DNA for reverse splicing. Antisense-strand cleavage requires additional interactions between the protein and 3' exon. Key nucleotide residues are recognized directly by the intron-encoded protein independent of sequence context, and there is a stringent requirement for fixed spacing between target site elements recognized by the protein and RNA components of the endonuclease. Experiments with DNA substrates containing GC-clamps or "bubbles" indicate a requirement for DNA unwinding in the 3' exon but not the distal 5' exon region. Finally, by applying the target-site recognition rules, we show that the L1.LtrB intron can be modified to insert at new sites in a plasmid-borne thyA gene in Escherichia coli. This strategy should be generally applicable to retargeting group II introns and to delivering foreign sequences to specific sites in heterologous genomes.