gebhart/patrepeval huggingface dataset:
Repair of articular surfaces by allografts of articular and growth-plate cartilage (1986)

Allografts of intact cartilage, isolated chondrocytes and cultured chondrocytes taken from the epiphysial growth-plate and from the articular surface of immature rabbits were inserted into full thickness defects in the tibial articular surface of 160 mature rabbits. In the contralateral knees, which were used as controls, similar defects were made but no grafts were inserted. Grafts were followed up for periods of up to one year after transplantation. Both intact articular and intact growth-plate grafts produced significantly better repair than that seen in control ungrafted defects in normal joints (P less than 0.01 and P less than 0.05 respectively) and in arthritic joints (P less than 0.01). Cultured chondrocytes cut to a precise fit also produced significantly better repair than ungrafted defects in arthritic joints (P less than 0.05).
Expression of genes for microphthalmia isoforms, Pax3 and MSG1, in human melanomas. (1999)

Microphthalmia (MITF) gene product, a transcription factor of the basic-helix-loop-helix type, is thought to play a role in the regulation of genes encoding the enzymes necessary for melanogenesis. These include tyrosinase, TRP-1 and TRP-2. Melanocyte-specific isoform of microphthalmia, MITF-M, is expressed in normal and malignant melanocytes. The presence of two other isoforms of microphthalmia, MITF-A and MITF-H, which differ from MITF-M in the amino-terminus, was demonstrated also in some non-melanocytic lineages. Here we have analyzed the presence of all three known isoforms of MITF mRNA in a panel of 17 human melanoma cell lines by a reverse transcriptase-polymerase chain reaction using isoform-specific primers. While, as expected, the predominant form in melanoma cell lines was MITF-M, low amounts of MITF-A mRNA was found in almost all melanomas, as well as in most of 20 tumor cell lines of the non-melanocyte origin (lung and colon carcinomas, osteosarcomas and neuroblastomas). The expression of MITF-H was not detected, with a few exceptions, in the tested cell lines. Pax3 transcription factor was reported earlier to regulate positively the melanocyte-specific promoter of the MITF gene. We found here that the Pax 3 mRNA was expressed in all melanoma cell lines, even in those that had repressed the MITF-M and were amelanotic. This suggests that additional factors, besides Pax3, are required for the MITF expression. The MSG1 (melanocyte-specific gene 1), a gene originally isolated from melanocytes and containing a strong transcription activation domain, was also found expressed in all melanomas and most non-melanocyte tumor cell lines. Together, these data indicate that the MITF-M isoform is the major type of MITF mRNA present in human melanoma cell lines and show that the expression of the isoform MITF-A and the MSG1 is not restricted to malignant melanocytes and occurs in a wide range of tumor cell lines.
Pharmacologic prophylaxis of acute graft-versus-host disease after allogeneic marrow transplantation. (1993)

The immunology, pathophysiology, incidence, clinical manifestations, grading, and prevention of acute graft-versus-host disease (GVHD) are reviewed. GVHD occurs after allogeneic marrow transplantation when immunologically competent T lymphocytes in the donor marrow identify the host's antigens as foreign and attempt to reject host tissues. Acute GVHD occurs within three months after marrow transplantation and may affect the skin, gastrointestinal tract, liver, and immune system. Even with prophylactic immunosuppression, acute GVHD occurs in 20% to 80% of patients. Moderate to severe GVHD (grades II-IV) is a major cause of morbidity and mortality after allogeneic bone marrow transplantation. Conventional GVHD prophylaxis consists of immunosuppressives such as corticosteroids, methotrexate, and cyclosporine. Methotrexate and cyclosporine are equally effective in preventing GVHD. A combination of both drugs is better than either drug alone and results in an improved survival rate. The addition of corticosteroids to methotrexate, cyclosporine, or antithymocyte globulin is also more effective than single-drug therapy. Serial administration of intravenous immune globulin may contribute additional protection against acute GVHD. There is conflicting evidence concerning the prophylactic efficacy of pentoxifylline. Elimination of T lymphocytes from the donor marrow before transplantation has been associated with less GVHD but a higher incidence of graft failure. Total elimination of GVHD in patients with leukemia may cause loss of a graft-versus-leukemia effect, resulting in increased relapse rates and decreased long-term survival. Promising experimental prophylactic agents include thalidomide, zolimomab aritox, tacrolimus, antibodies to cytokines involved in the pathogenesis of GVHD, and monoclonal antibodies against cytokine receptors on T lymphocytes. Current research efforts are also directed toward eliminating GVHD without compromising the graft-versus-leukemia effect.
A statistical perspective on gene expression data analysis (2003)

Rapid advances in biotechnology have resulted in an increasing interest in the use of oligonucleotide and spotted cDNA gene expression microarrays for medical research. These arrays are being widely used to understand the underlying genetic structure of various diseases, with the ultimate goal to provide better diagnosis, prevention and cure. This technology allows for measurement of expression levels from several thousands of genes simultaneously, thus resulting in an enormous amount of data. The role of the statistician is critical to the successful design of gene expression studies, and the analysis and interpretation of the resulting voluminous data. This paper discusses hypotheses common to gene expression studies, and describes some of the statistical methods suitable for addressing these hypotheses. S-plus and SAS codes to perform the statistical methods are provided. Gene expression data from an unpublished oncologic study is used to illustrate these methods.
Kinetostatic Analysis and Design Optimization of the Tricept Machine Tool Family (2002)

Selecting a mechanism for a machine tool that will best suit the needs of a forecast set of rigidities can be a difficult and costly exercise. This problem can now be addressed using a kinetostatic modeling method. In this paper, a kinetostatic model for the Tricept machine tool family is established based on lumped flexibilities. This model can be used to analyze the effect of link flexibility on the machine tool’s global stiffness and the platform positioning precision. The Tricept machine tool is a new type of parallel mechanism with prismatic actuators whose degree of freedom is dependent on a passive constraining leg connecting the base and the platform. The geometric model and the mechanical design of the Tricept machine tool is first recalled. Then, a lumped kinetostatic model is proposed in order to account for joint and link compliances. It is shown that the link flexibility has a significant effect on the machine tool’s precision and that it is necessary to take the link flexibility into account. Additionally, the inverse kinematics and velocity equations are given for both rigid-link and flexible-link mechanisms. Finally, the optimization of the stiffness is addressed using a genetic algorithm.
Histidylated Polylysine as DNA Vector:  Elevation of the Imidazole Protonation and Reduced Cellular Uptake without Change in the Polyfection Efficiency of Serum Stabilized Negative Polyplexes (2000)

We have reported that polylysine substituted with histidyl residues (His) was suited to make complexes with plasmid DNA (pDNA) and to transfect cells in vitro in the presence of serum. The present study was performed to determine whether the acetylation of the alpha-amino group of histidyl residues (AcHis) had an influence on the size and the charge of polyplexes and on their transfection efficiency. We found that the presence of free alpha-amino groups allowed the formation of smaller polyplexes but did not modify the zeta potential of +17 mV. At a physiological salt concentration, the adsorption of many serum proteins on His- and AcHis-polyplexes reduced their size below 100 nm, inhibited their aggregation, and reversed their zeta potential to -25 mV. The acetylation of the alpha-amino groups reduced slightly the adsorption of serum proteins. The presence of the alpha-amino groups increased the pK of the imidazole protonation of histidine bound to polylysine from pH 5.8 to 6.9; in addition, the protonation was further elevated in the presence of pDNA. Serum stabilized negative histidylated polyplexes were less taken up by cells but their transfection efficiency did not decrease; depending on the cell line, His-polyplexes were more efficient than AcHis-polyplexes. The results indicate that (i) the alpha-amino groups of histidyl residues bound to polylysine favorably influence the size and the transfection efficiency of polyplexes, (ii) the alpha-amino groups also elevate the imidazole protonation of His-polyplexes, which is suited to destabilize the membrane of early endocytic vesicles in order to favor pDNA delivery in the cytosol, and (iii) the absorption of selective serum proteins on His-polyplexes could be a way for in vivo gene targeting.
A 16-mW, 120-dB linear switched-capacitor delta-sigma modulator with dynamic biasing (1999)

A high-resolution, fourth-order /spl Delta//spl Sigma/ analog-to-digital converter is presented. Power-reduction techniques have been applied across many aspects of the design. A class-A amplifier was designed with bias currents optimized according to the expected activity in each clock phase. The modulator achieves a 122 dB dynamic range over a 400-Hz bandwidth, -123-dB total harmonic distortion, and 16-mW power consumption from a single 5-V supply. It is implemented in a 0.6-/spl mu/m double-polysilicon CMOS process and has an active area of 2 mm/sup 2/.
Requirements for noncovalent binding of vaccinia topoisomerase I to duplex DNA (1994)

Vaccinia DNA topoisomerase binds duplex DNA and forms a covalent adduct at sites containing a conserved sequence element 5'(C/T)CCTT decreases in the scissile strand. Distinctive aspects of noncovalent versus covalent interaction emerge from analysis of the binding properties of Topo(Phe-274), a mutated protein which is unable to cleave DNA, but which binds DNA noncovalently. Whereas DNA cleavage by wild type enzyme is most efficient with 'suicide' substrates containing fewer than 10 base pairs distal to the scissile bond, optimal noncovalent binding by Topo(Phe-274) requires at least 10-bp of DNA 3' of the cleavage site. Thus, the region of DNA flanking the pentamer motif serves to stabilize the noncovalent topoisomerase-DNA complex. This result is consistent with the downstream dimensions of the DNA binding site deduced from nuclease footprinting. Topo(Phe-274) binds to duplex DNA lacking the consensus pentamer with 7-10-fold lower affinity than to CCCTT-containing DNA.
Intrathyroidal cytokine gene expression in Hashimoto's thyroiditis (1996)

Hashimoto's thyroiditis (HT) is an organ-specific autoimmune disease in which cytokines are likely to have a role in the initiation and perpetuation of the disease. Using the reverse transcription-polymerase chain reaction (RT-PCR) we analysed the cytokine profile in four HT tissue samples. Furthermore, cell fractionation was carried out on two tissue samples and cytokine profile was studied in CD4+ and CD8+ T cells, in addition to the residual cellular infiltrate composed of CD4- and CD8- cells. Our results showed IL-1 beta, IL-4 and IL-6 mRNA expression in three out of four tissue samples, whereas IL-1 alpha, IL-2, IL-8, IL-10, interferon-gamma (IFN-gamma) and tumour necrosis factor-alpha (TNF-alpha) were expressed in all tissue samples studied. Expression of IL-1 alpha and IL-1 beta was absent in both CD4+ and CD8+ subsets. However, IL-2, IL-4, IL-6, IL-8, IFN-gamma and TNF-alpha mRNA were detected in both CD4+ and CD8+ subsets. IL-10 was expressed in the CD4+ subset in one sample, whereas it was negative in both CD8+ fractions. All the cytokines studied were expressed in the residual infiltrate. These results suggest a mixed Th1 and Th2 response in HT, both of which may have an important role in the pathophysiology of the thyroid destructive process through cell-mediated cytotoxicity, and/or humoral autoimmunity manifested by autoantibody production.
Crystalline monoclonal antibodies for subcutaneous delivery (2003)

Therapeutic applications for mAbs have increased dramatically in recent years, but the large quantities required for clinical efficacy have limited the options that might be used for administration and thus have placed certain limitations on the use of these agents. We present an approach that allows for s.c. delivery of a small volume of a highly concentrated form of mAbs. Batch crystallization of three Ab-based therapeutics, rituximab, trastuzumab, and infliximab, provided products in high yield, with no detectable alteration to these proteins and with full retention of their biological activity in vitro. Administration s.c. of a crystalline preparation resulted in a remarkably long pharmacokinetic serum profile and a dose-dependent inhibition of tumor growth in nude mice bearing BT-474 xenografts (human breast cancer cells) in vivo. Overall, this approach of generating high-concentration, low-viscosity crystalline preparations of therapeutic Abs should lead to improved ease of administration and patient compliance, thus providing new opportunities for the biotechnology industry.
Antigenicity of Polypeptides (Poly Amino Acids): Immunogenicity of Chemically Modified Polymers. II (1970)

It has been shown that chemical modification of the negatively charged carboxyl groups of synthetic polymers of amino acids via introduction of neutral determinants tends to reduce immunogenic properties of the respective polymer.
SCISOR: extracting information from on-line news (1990)

The future of natural language text processing is examined in the SCISOR prototype. Drawing on artificial intelligence techniques, and applying them to financial news items, this powerful tool illustrates some of the future benefits of natural language analysis through a combination of bottom-up and top-down processing.
Crystal structure of the tyrosine kinase domain of the hepatocyte growth factor receptor c-Met and its complex with the microbial alkaloid K-252a (2003)

The protooncogene c-met codes for the hepatocyte growth factor receptor tyrosine kinase. Binding of its ligand, hepatocyte growth factor/scatter factor, stimulates receptor autophosphorylation, which leads to pleiotropic downstream signaling events in epithelial cells, including cell growth, motility, and invasion. These events are mediated by interaction of cytoplasmic effectors, generally through Src homology 2 (SH2) domains, with two phosphotyrosine-containing sequence motifs in the unique C-terminal tail of c-Met (supersite). There is a strong link between aberrant c-Met activity and oncogenesis, which makes this kinase an important cancer drug target. The furanosylated indolocarbazole K-252a belongs to a family of microbial alkaloids that also includes staurosporine. It was recently shown to be a potent inhibitor of c-Met. Here we report the crystal structures of an unphosphorylated c-Met kinase domain harboring a human cancer mutation and its complex with K-252a at 1.8-A resolution. The structure follows the well established architecture of protein kinases. It adopts a unique, inhibitory conformation of the activation loop, a catalytically noncompetent orientation of helix alphaC, and reveals the complete C-terminal docking site. The first SH2-binding motif (1349YVHV) adopts an extended conformation, whereas the second motif (1356YVNV), a binding site for Grb2-SH2, folds as a type II Beta-turn. The intermediate portion of the supersite (1353NATY) assumes a type I Beta-turn conformation as in an Shc-phosphotyrosine binding domain peptide complex. K-252a is bound in the adenosine pocket with an analogous binding mode to those observed in previously reported structures of protein kinases in complex with staurosporine.
In Vitro Transcription of Long RNA Containing Modified Nucleosides (2012)

The in vitro synthesis of long RNA can be accomplished using phage RNA polymerase and template DNA. However, the in vitro synthesized RNA, unlike those transcribed in vivo in cells, lacks nucleoside modifications. Introducing modified nucleosides into in vitro transcripts is important because they reduce the potential of RNA to activate RNA sensors and translation of such nucleoside-modified RNA is increased in cell lines, primary cells, and after in vivo delivery. Here, we describe the in vitro synthesis of nucleoside-modified RNA with enhanced translational capacity and reduced ability to activate immune sensors.
Complete sequence of the staphylococcal gene encoding protein A. A gene evolved through multiple duplications. (1984)

The gene coding for protein A from Staphylococcus aureus has been isolated by molecular cloning, and a subclone containing an 1.8-kilobase insert was found to give a functional protein A in Escherichia coli. The complete nucleotide sequence of the insert, including the structural gene and the 5' and 3' flanking sequences, has been determined. Starting from a TTG initiator codon, an open reading frame comprising 1527 nucleotides gives a preprotein of 509 amino acids and a predicted Mr = 58,703. The structural gene is flanked on both sides by palindromic structures followed by a stretch of T residues, suggesting transcriptional termination signals. Thus, it appears that protein A is translated from a monocistronic mRNA. The sequence reveals extensive internal homologies involving a 58-amino acid unit, responsible for IgG binding, repeated 5 times and an 8-amino acid unit, possibly responsible for binding to the cell wall of S. aureus, repeated 12 times. Comparisons between the repeated regions show a marked preference for silent mutations, indicating an evolutionary pressure to keep the amino acid sequence preserved. The structure of the gene also suggests how the gene has evolved.
RNA Processing and Degradation inBacillus subtilis (2003)

This review focuses on the enzymes and pathways of RNA processing and degradation in Bacillus subtilis, and compares them to those of its gram-negative counterpart, Escherichia coli. A comparison of the genomes from the two organisms reveals that B. subtilis has a very different selection of RNases available for RNA maturation. Of 17 characterized ribonuclease activities thus far identified in E. coli and B. subtilis, only 6 are shared, 3 exoribonucleases and 3 endoribonucleases. Some enzymes essential for cell viability in E. coli, such as RNase E and oligoribonuclease, do not have homologs in B. subtilis, and of those enzymes in common, some combinations are essential in one organism but not in the other. The degradation pathways and transcript half-lives have been examined to various degrees for a dozen or so B. subtilis mRNAs. The determinants of mRNA stability have been characterized for a number of these and point to a fundamentally different process in the initiation of mRNA decay. While RNase E binds to the 5' end and catalyzes the rate-limiting cleavage of the majority of E. coli RNAs by looping to internal sites, the equivalent nuclease in B. subtilis, although not yet identified, is predicted to scan or track from the 5' end. RNase E can also access cleavage sites directly, albeit less efficiently, while the enzyme responsible for initiating the decay of B. subtilis mRNAs appears incapable of direct entry. Thus, unlike E. coli, RNAs possessing stable secondary structures or sites for protein or ribosome binding near the 5' end can have very long half-lives even if the RNA is not protected by translation.
Acute effects of hindlimb unweighting on satellite cells of growing skeletal muscle (1994)

The proliferative behavior of satellite cells in growing rat soleus and extensor digitorum longus muscles was examined at short periods after initiation of hindlimb unweighting. Mitotic activity of satellite cells in both muscles decreased below weight-bearing control levels within 24 h of initiation of hindlimb unweighting. This satellite cell response was > or = 48 h before any atrophic morphological changes that take place in the muscles. Suppression of mitotic activity was most severe in the soleus muscle where continuous infusion of label demonstrated that virtually all mitotic activity was abolished between 3 and 5 days. The results of this study suggest that satellite cell mitotic activity is a sensitive indicator of primary atrophic changes occurring in growing myofibers and may be a predictor of future morphological changes.
Adeno-associated virus general transduction vectors: analysis of proviral structures (1988)

We used two kinds of adeno-associated virus (AAV) vectors to transduce the neomycin resistance gene into human cells. The first of these (dl52-91) retains the AAV rep genes; the second (dl3-94) retains only the AAV terminal repeats and the AAV polyadenylation signal (428 base pairs). Both vectors could be packaged into AAV virions and produced proviral structures that were essentially the same. Thus, the AAV sequences that are required in cis for packaging (pac), integration (int), rescue (res), and replication (ori) of viral DNA are located within a 284-base-pair sequence that includes the terminal repeat. Most of the G418r cell lines (73%) contained proviruses which could be rescued (Res+) when the cells were superinfected with the appropriate helper viruses. Some produced high yields of viral DNA; other rescued at a 50-fold lower level. Most of the lines that were Res+ (79%) contained a tandem repeat of the AAV genome (2 to 20 copies) which was integrated randomly with respect to cellular DNA. Junctions between two consecutive AAV copies in a tandem array contained either one or two copies of the AAV terminal palindrome. Junctions between AAV and cellular sequences occurred predominantly at or within the AAV terminal repeat, but in some cases at internal AAV sequences. Two lines were seen that contained free episomal copies of AAV DNA. Res+ clones contained deleted proviruses or tandem repeats of a deleted genome. Occasionally, flanking cellular DNA was also amplified. There was no superinfection inhibition of AAV DNA integration. Our results suggest that AAV sequences are amplified by DNA replication either before or after integration and that the mechanism of replication is different from the one used during AAV lytic infections. In addition, we have described a new AAV general transduction vector, dl3-94, which provides the maximum amount of room for insertion of foreign DNA and integrates at a high frequency (80%).
The VR Book: Human-Centered Design for Virtual Reality (2015)

Virtual reality (VR) can provide our minds with direct access to digital media in a way that seemingly has no limits. However, creating compelling VR experiences is an incredibly complex challenge. When VR is done well, the results are brilliant and pleasurable experiences that go beyond what we can do in the real world. When VR is done badly, not only is the system frustrating to use, but it can result in sickness. There are many causes of bad VR; some failures come from the limitations of technology, but many come from a lack of understanding perception, interaction, design principles, and real users. This book discusses these issues by emphasizing the human element of VR. The fact is, if we do not get the human element correct, then no amount of technology will make VR anything more than an interesting tool confined to research laboratories. Even when VR principles are fully understood, the first implementation is rarely novel and almost never ideal due to the complex nature of VR and the countless possibilities that can be created. The VR principles discussed in this book will enable readers to intelligently experiment with the rules and iteratively design towards innovative experiences.