gebhart/patrepeval huggingface dataset:
Tree indexing on solid state drives (2010)

Large flash disks, or solid state drives (SSDs), have become an attractive alternative to magnetic hard disks, due to their high random read performance, low energy consumption and other features. However, writes, especially small random writes, on flash disks are inherently much slower than reads because of the erase-before-write mechanism. To address this asymmetry of read-write speeds in tree indexing on the flash disk, we propose FD-tree, a tree index designed with the logarithmic method and fractional cascading techniques. With the logarithmic method, an FD-tree consists of the head tree -- a small B+-tree on the top, and a few levels of sorted runs of increasing sizes at the bottom. This design is write-optimized for the flash disk; in particular, an index search will potentially go through more levels or visit more nodes, but random writes are limited to a small area -- the head tree, and are subsequently transformed into sequential ones through merging into the lower runs. With the fractional cascading technique, we store pointers, called fences, in lower level runs to speed up the search. Given an FD-tree of n entries, we analytically show that it performs an update in O (log B n ) sequential I/Os and completes a search in O (log B n ) random I/Os, where B is the flash page size. We evaluate FD-tree in comparison with representative B+-tree variants under a variety of workloads on three commodity flash SSDs. Our results show that FD-tree has a similar search performance to the standard B+-tree, and a similar update performance to the write-optimized B+-tree variant. As a result, FD-tree dominates the other B+-tree index variants on the overall performance on flash disks as well as on magnetic disks.
Growth Control in Cultured Mouse Fibroblasts: Induction of the Pleiotypic and Mitogenic Responses by a Purified Growth Factor (1974)

Addition of serum to quiescent mouse fibroblasts induces a series of macromolecular changes (a pleiotypic response) followed by DNA synthesis and cell division. A new pituitary hormone, fibroblast growth factor, and hydrocortisone acting at physiological concentrations can completely replace exogenously added serum for the induction of these events in lines of BALB/c 3T3 cells. The induction of cell growth is specific for cultured fibroblasts; no stimulation is observed for mouse epithelial cells or virally transformed fibroblasts.
Variants of the Adiponectin (<emph type="ital">ADIPOQ</emph>) and Adiponectin Receptor 1 (<emph type="ital">ADIPOR1</emph>) Genes and Colorectal Cancer Risk (2008)

The SNP rs266729, which tags the 5' flanking region of the ADIPOQ gene, is associated with decreased colorectal cancer risk.
Recent progress in vision-based HCI (2010)

This talk will firstly introduce some recent progress in vision-based HCI area, including the “sixth sense” concept system by MIT media lab and the “Kinect” body controller developed by Microsoft. Based on them, some trends of the field are analyzed. The talk will then focus on face perception related progress, which is one of the main efforts of the lecturer. Demos will be shown and the techniques behind the demos will be briefly introduced.
Modelling of lateral bipolar devices in a CMOS process (2002)

In spite of the emergence of CMOS technology, the well-controlled characteristics of bipolar transistors retain many advantages over those of CMOS transistors for some critical analog applications. This is the reason why special technologies have been proposed to combine both types of transistors on the same chip. An inexpensive and widely applicable approach lies in using bipolars that are realisable with existing CMOS technologies. Bipolar transistors occur as parasitic devices in CMOS and it is not necessary to use additional processing steps in their manufacture. These bipolar transistors, therefore, provide cost effective devices which are relatively simple to fabricate. The extraction of a DC parameter set for the lateral device is more complicated than for a vertical device because of the presence of two parasitic vertical bipolar transistors which are formed by the emitter/collector, the base and the substrate regions. This paper proposes a method which involves the use of subcircuits incorporating three SPICE Gummel-Poon models. The development of this model, its implementation and the results obtained are outlined and discussed.
Evaluation of Gen-Probe Amplified Mycobacterium Tuberculosis Direct Test and PCR for direct detection of Mycobacterium tuberculosis in clinical specimens (1994)

The Gen-Probe Amplified Mycobacterium Tuberculosis Direct Test (AMTD) is a direct specimen assay for the identification of Mycobacterium tuberculosis from respiratory samples. rRNA is amplified, and the product is detected with a specific chemiluminescent probe. We performed a retrospective evaluation of three separate respiratory specimens from each of 250 patients by using the AMTD and compared the results with those of microscopy, culturing, and a patient chart review. From the latter results, 198 patients (594 specimens) were found negative for M. tuberculosis by culturing and clinical criteria. The overall specificity of the AMTD after discrepancy resolution was 98.5% (585 of 594). There were 52 patients with culture-proven and/or clinically diagnosed tuberculosis. Of these 156 specimens, the organism was cultured from 142 (91%), and acid-fast microscopy was positive for 105 (67.3%). The AMTD was positive for 142 (91%) specimens from these patients. Tuberculosis patient samples were tested by a PCR assay which uses primers for amplification of the IS6110 insertion sequence of the M. tuberculosis complex. The PCR assay detected 144 of the 156 (92.3%) specimens. Overall, when three specimens per patient were examined, the AMTD found all 52 patients positive for tuberculosis, while the PCR assay found 51 patients positive by agarose gel analysis and all 52 patients positive by Southern blot hybridization.
DOUBLE HEMIARTHROPLASTY OF THE KNEE IN RHEUMATOID ARTHRITIS (1973)

1. Of fifty consecutive double hemiarthroplasties of the knee for rheumatoid arthritis using Maclntosh prostheses, forty-six were available for detailed assessment in thirty-six patients after one to six years. 2. Two early deaths were related to the operation but two late deaths were not. Three knees required revision, one of them twice. 3. The late results were 87 per cent good and 13 per cent fair. No patients followed up were the same as previously or worse. Every patient stated that he would have the operation performed again. 4. In our experience this operation in carefully selected patients produces satisfactory results. It is essential that great care is given to the operative technique.
Selective expression of interleukin 10, interferon gamma, and granulocyte-macrophage colony-stimulating factor in ovarian cancer biopsies. (1992)

The variable clinical response seen with most cancer immunotherapy suggests that there is a large interindividual variation in immunologic response to tumors. One of the key functional parameters of an immune response is the local production of cytokines. As a method to survey the immune status of tumor-infiltrating cells, we have investigated the constitutive expression of cytokine mRNA in biopsies from epithelial ovarian carcinomas by using a PCR-assisted mRNA amplification assay. Using a set of cytokine-specific primers for 10 different cytokines, we have found selective expression of interleukin 10 (IL-10), granulocyte-macrophage colony-stimulating factor, and interferon gamma mRNA in ovarian tumor tissue as compared to normal ovaries and ovarian tumor cell lines. Such differences could not be explained by the extent of T-cell infiltration, since comparing samples with the same intensity of T-cell receptor (TCR) constant region alpha-chain product from the tumor and normal biopsies demonstrated different cytokine patterns. No IL-2 gene expression was detected in the tumor biopsies. IL-2 mRNA, however, became expressed after stimulation of the tumor-derived cells via the CD3 molecule but not after growth in recombinant IL-2 alone. Using the same methodology, we also analyzed the TCR variable region beta-chain gene repertoire. No restriction or biased expression of these genes was observed.
3-Hydroxy-3-methylglutaryl-coenzyme A reductase inhibitors. 5. 6-(Fluoren-9-yl)- and 6-(fluoren-9-ylidene)-3,5-dihydroxyhexanoic acids and their lactone derivatives (1986)

A limited study was conducted to determine the biological consequences of rendering the phenyl rings of the previously reported 7-(3,5-disubstituted [1,1'-biphenyl]-2-yl)-3,5-dihydroxy-6-heptenoic acids coplanar. Such constraint substantially diminished intrinsic HMG-CoA reductase inhibitory activity.
The transcriptional response of human cells to ionizing radiation (2004)

Genetic information must faithfully replicate itself and maintain its integrity in spite of the frequent occurrence of DNA damage. Improper DNA repair gives rise to mutations within the genome which can lead to tumorigenesis and malignant transformation. To counter genotoxic stresses such as ionizing radiation (IR), mammalian cells possess an elaborate set of countermeasures to maintain precise control over cell growth and assure DNA repair. The tumor suppressor p53 and the protein kinase ATM are vital components of proper IR response. Deficiencies in the function of either one of these proteins result in inadequate IR stress response and cancer susceptibility. In this thesis, we use high-throughput methods to thoroughly examine the IR response in human cells. In chapter 2, we used oligonucleotide microarrays to determine the temporal expression profiles of IR-responsive genes in lymphoblastoid cells. We also assessed effects of IR dose on this temporal pattern of expression. By combining dose response data with temporal profiles of expression, we identified sets of coordinately responding genes. In chapter 3, we identified IR-responsive genes whose gene expression change following irradiation is directly regulated by p53. We used genomic microarrays to detect regions in the genome that immunoprecipitated with p53 in response to IR stress. For a subset of newly identified potential p53 target genes, we located p53 binding motifs computationally and confirmed p53 binding with conventional chromatin immunoprecipitation assays. In addition, we show that the IR-responsive genes C12orf5, GPX1, PLK3, and PRKA81 contain p53 binding sites that possess functional p53-responsive elements. In chapter 4, we examined the differences in transcriptional response between ATM+/+ and ATM −/− cells. Again, we used expression microarrays to compare global gene expression patterns. We found that ATM −/− cells do not show complete absence of transcriptional changes as a result of IR exposure. Instead, these cells display delayed kinetics in activation of crucial pathways necessary for proper IR response, with one of these being p53 transactivation.
[Why do mutations cause disease--a protein chemical perspective]. (2001)

We argue that studies of the kinetic and thermodynamic stability of proteins are important in order to understand the effects of many mutations, and we describe such studies. Knowledge about native, denatured and aggregated forms of proteins is essential to the understanding of how mutations can affect protein stability. We conclude that much of our knowledge in this area is still rudimentary, but we expect that this field of research will evolve rapidly over the next few years.
APC Activation by IFN-α Decreases Regulatory T Cell and Enhances Th Cell Functions (2010)

Type I IFNs are central to a vast array of immunological functions. Their early induction in innate immune responses provides one of the most important priming mechanisms for the subsequent establishment of adaptive immunity. The outcome is either promotion or inhibition of these responses, but the conditions under which one or the other prevails remain to be defined. The main objective of the current study was to determine the involvement of IFN-alpha on murine CD4(+)CD25(-) Th cell activation, as well as to define the role played by this cytokine on CD4(+)CD25(+) regulatory T (Treg) cell proliferation and function. Although IFN-alpha promotes CD4(+)CD25(-) Th cells coincubated with APCs to produce large amounts of IL-2, the ability of these cells to respond to IL-2 proliferative effects is prevented. Moreover, in medium supplemented with IFN-alpha, IL-2-induced CD4(+)CD25(+) Treg cell proliferation is inhibited. Notably, IFN-alpha also leads to a decrease of the CD4(+)CD25(+) Treg cell suppressive activity. Altogether, these findings indicate that through a direct effect on APC activation and by affecting CD4(+)CD25(+) Treg cell-mediated suppression, IFN-alpha sustains and drives CD4(+)CD25(-) Th cell activation.
An intraventricular soft robotic pulsatile assist device for right ventricular heart failure (2014)

Due to its more complex geometry and motion, right ventricular heart failure (RVHF) is less understood than left ventricular heart failure and has fewer treatment options. There are currently no mechanical circulatory support devices designed specifically for the right ventricle. This work presents the design of a ventricular assist device (VAD) which leverages the specific geometry and lower pressure of the right ventricle (RV) in order to avoid the major pitfalls of current VADs. The device consists of a contracting linear actuator spanning the RV, bringing its walls together and assisting in the ejection of blood from the ventricle.
Attack of the killer microseconds (2017)

Microsecond-scale I/O means tension between performance and productivity that will need new latency-mitigating ideas, including in hardware.
Immunohistochemical study of lymphoid tissues in adjuvant arthritis (AA) by image analysis; relationship with synovial lesions (2000)

The aim of this study was to examine leucocyte populations in lymphoid organs during AA and to ascertain the relationship with lesions in synovial joints. Popliteal lymph nodes, spleen and knee synovial membranes were removed from both healthy and AA rats at intervals of 3-4 days over a 3-week period. Cryostat sections were stained with MoAbs directed against lymphocyte and macrophage subpopulations, and studied by image analysis. Throughout the arthritic period, high numbers of ED1+ and ED3+ macrophages were seen in both lymphoid compartments and intercellular adhesion molecule-1 (ICAM-1) expression also increased in some zones of lymph nodes and spleen. The percentages of CD4+ and CD8+ cells rose in the splenic zones studied but fell in the lymph node cortex. Very few natural killer (NK) cells were found in lymphoid tissues, but the number rose after AA induction. In synovia from AA rats, ED2+ macrophages proliferated but alpha/beta T cell infiltration was only occasionally observed, accompanied by ED1+ cells and ICAM-1 expression. In conclusion, synovitis developing after AA induction seems to be caused directly by macrophages and indirectly by lymphocytes placed both in popliteal lymph nodes and spleen.
Haemophilia B: impact on patients and economic burden of disease (2011)

Worldwide, haemophilia is the most common hereditary bleeding disorder. The incidence of haemophilia B, however, is considerably less than haemophilia A and consequently appears to have received less attention in the research literature. This article aims to summarise the available evidence documenting the patient and economic burden associated with haemophilia B and current methods of disease management. Both the immediate and long-term clinical consequences of haemophilia B can have significant implications for patients in terms of functional limitations and diminished health-related quality of life (HRQOL). Evidence demonstrates that primary prophylaxis is the optimal strategy for replacing missing clotting factor IX (FIX) and managing haemophilia B. Use of recombinant FIX (rFIX) over plasma-derived FIX (pd-FIX) is also generally preferred for safety reasons. Prophylaxis using currently available rFIX products, however, requires a demanding regimen of intravenous infusions 2-3 times a week which may have significant implications for adherence and ultimately the long-term efficacy of such regimens. Only limited assessments of the cost-effectiveness of prophylactic versus on-demand FIX treatment regimens have been conducted to date. Prophylaxis, however, is generally more costly as greater quantities of FIX are consumed. Any reduction in FIX replacement dosing frequency is expected to improve patient adherence and contribute to improved clinical outcomes, further supporting the cost-effectiveness of such interventions. Although a rare disease, as economic constraints for healthcare increase, generating further information regarding the key clinical, patient and economic outcomes associated with haemophilia B will be essential for supporting improvements in care for people with haemophilia B.
Design of Targeted B Cell Killing Agents (2011)

B cells play an important role in the pathogenesis of both systemic and organ-specific autoimmune diseases. Autoreactive B cells not only produce autoantibodies, but also are capable to efficiently present specific autoantigens to T cells. Furthermore, B cells can secrete proinflammatory cytokines and amplify the vicious process of self-destruction. B cell-directed therapy is a potentially important approach for treatment of various autoimmune diseases. The depletion of B cells by anti-CD20/19 monoclonal antibody Retuximab® used in autoimmune diseases therapy leads to systemic side effects and should be significantly improved. In this study we designed a repertoire of genetically engineered B cell killers that specifically affected one kind of cells carrying a respective B cell receptor. We constructed immunotoxins (ITs), fused with c-myc epitope as a model targeting sequence, based on barnase, Pseudomonas toxin, Shiga-like toxin E.coli and Fc domain of human antibody IgGγ1. C-MYC hybridoma cell line producing anti-c-myc IgG was chosen as a model for targeted cell depletion. C-myc sequence fused with toxins provided addressed delivery of the toxic agent to the target cells. We demonstrated functional activity of designed ITs in vitro and showed recognition of the fusion molecules by antibodies produced by targeted hybridoma. To study specificity of the proposed B cells killing molecules, we tested a set of created ITs ex vivo, using C-MYC and irrelevant hybridoma cell lines. Pseudomonas-containing IT showed one of the highest cytotoxic effects on the model cells, however, possessed promiscuous specificity. Shiga-like toxin construct demonstrated mild both cytotoxicity and specificity. Barnase and Fc-containing ITs revealed excellent balance between their legibility and toxic properties. Moreover, barnase and Fc molecules fused with c-myc epitope were able to selectively deplete c-myc-specific B cells and decrease production of anti-c-myc antibodies in culture of native splenocytes, suggesting their highest therapeutic potential as targeted B cell killing agents.
A drug-resistant mutation in the ribosomal DNA of Tetrahymena. (1985)

A mutation that confers resistance to the drug paromomycin is shown to be in the structural gene that codes for the ribosomal RNA in Tetrahymena. This observation was made by exploiting a variant of the ribosomal DNA that distorts amplification of this locus when a new somatic nucleus develops during conjugation. Because the allelic forms of this locus have a restriction endonuclease site polymorphism, it was possible to correlate drug resistance with presence of a specific allele. The genetic results have been confirmed by sequence analysis (presented elsewhere). Thus, the crosses presented here provide a unique opportunity to identify mutations in the ribosomal DNA.
Cannabinoids Inhibit the Vascular Endothelial Growth Factor Pathway in Gliomas (2004)

Cannabinoids inhibit tumor angiogenesis in mice, but the mechanism of their antiangiogenic action is still unknown. Because the vascular endothelial growth factor (VEGF) pathway plays a critical role in tumor angiogenesis, here we studied whether cannabinoids affect it. As a first approach, cDNA array analysis showed that cannabinoid administration to mice bearing s.c. gliomas lowered the expression of various VEGF pathway-related genes. The use of other methods (ELISA, Western blotting, and confocal microscopy) provided additional evidence that cannabinoids depressed the VEGF pathway by decreasing the production of VEGF and the activation of VEGF receptor (VEGFR)-2, the most prominent VEGF receptor, in cultured glioma cells and in mouse gliomas. Cannabinoid-induced inhibition of VEGF production and VEGFR-2 activation was abrogated both in vitro and in vivo by pharmacological blockade of ceramide biosynthesis. These changes in the VEGF pathway were paralleled by changes in tumor size. Moreover, intratumoral administration of the cannabinoid Delta9-tetrahydrocannabinol to two patients with glioblastoma multiforme (grade IV astrocytoma) decreased VEGF levels and VEGFR-2 activation in the tumors. Because blockade of the VEGF pathway constitutes one of the most promising antitumoral approaches currently available, the present findings provide a novel pharmacological target for cannabinoid-based therapies.
T cell transfer model of chronic colitis: concepts, considerations, and tricks of the trade (2008)

The inflammatory bowel diseases (Crohn's disease; ulcerative colitis) are idiopathic chronic inflammatory disorders of the intestine and/or colon. A major advancement in our understanding of the pathogenesis of these diseases has been the development of mouse models of chronic gut inflammation. One model that has been instrumental in delineating the immunological mechanisms responsible for the induction as well as regulation of intestinal inflammation is the T cell transfer model of chronic colitis. This paper presents a detailed protocol describing the methods used to induce chronic colitis in mice. Special attention is given to the immunological concepts that explain disease pathogenesis in this model, considerations and potential pitfalls in using this model, and finally different "tricks" that we have learned over the past 12 years that have allowed us to develop a more simplified version of this model of experimental IBD.
Low temperature growth of GaN single crystal films using ECR plasma excited metalorganic vapor phase epitaxy. (1987)

A low-temperature-growth technique for GaN single crystal films has been developed using electron cyclotron resonance (ECR) plasma excitation. GaN films were grown on sapphire substrates utilizing reaction of trimethylgallium (TMGa) with highly activated nitrogen produced by ECR excitation of ammonia. Growth conditions to obtain single crystals were studied. Single crystal growth of Zn-doped films can be obtained. Zn-doped films exhibit a luminescence band peaking at 430550 nm. Surface morphologies of both undoped and Zn-doped films are very smooth.
Antitumor and antimicrobial activities of lipid A-subunit analogue GLA-27. (1988)

Activities for enhancing nonspecific host resistance against microbial infections and growth inhibition against tumors by a lipid A-subunit analogue GLA-27 were investigated. GLA-27, a 4-O-phosphono-D-glucosamine derivative with 2-N-3-tetradecanoyloxytetradecanoyl and 3-O-tetradecanoyl group, inhibited significantly the growth of solid-type tumors RL male 1 lymphoma and Meth A fibrosarcoma. In the case of RL male 1 lymphoma, 2.5 micrograms of GLA-27 was needed to exhibit the activity, while for Meth A fibrosarcoma, 250 micrograms of GLA-27 was needed. On the other hand, tail lesions induced by intravenous inoculation with vaccinia virus were effectively suppressed in mice injected with 1 microgram of GLA-27 1 day before the viral injection. The antiviral activity of GLA-27 was 100 times higher than that of MDP by ED50. GLA-27 also showed nonspecific protective activity against Pseudomonas aeruginosa infection at a dose of 30 micrograms/mouse, although the activity was far less than that induced by lipid A. GLA-27 did not exhibit toxic activities such as pyrogenicity and Shwartzman reaction.