gebhart/patrepeval huggingface dataset:
Ray tracing on programmable graphics hardware (2005)

Recently a breakthrough has occurred in graphics hardware: fixed function pipelines have been replaced with programmable vertex and fragment processors. In the near future, the graphics pipeline is likely to evolve into a general programmable stream processor capable of more than simply feed-forward triangle rendering.In this paper, we evaluate these trends in programmability of the graphics pipeline and explain how ray tracing can be mapped to graphics hardware. Using our simulator, we analyze the performance of a ray casting implementation on next generation programmable graphics hardware. In addition, we compare the performance difference between non-branching programmable hardware using a multipass implementation and an architecture that supports branching. We also show how this approach is applicable to other ray tracing algorithms such as Whitted ray tracing, path tracing, and hybrid rendering algorithms. Finally, we demonstrate that ray tracing on graphics hardware could prove to be faster than CPU based implementations as well as competitive with traditional hardware accelerated feed-forward triangle rendering.
Purification and molecular cloning of the APO-1 cell surface antigen, a member of the tumor necrosis factor/nerve growth factor receptor superfamily. Sequence identity with the Fas antigen. (1992)

The APO-1 antigen as defined by the mouse monoclonal antibody anti-APO-1 was previously found to be expressed on the cell surface of activated human T and B lymphocytes and a variety of malignant human lymphoid cell lines. Cross-linking of the APO-1 antigen by anti-APO-1 induced programmed cell death, apoptosis, of APO-1 positive cells. To characterize the APO-1 cell surface molecule and to better understand its role in induction of apoptosis, the APO-1 protein was purified to homogeneity from membranes of SKW6.4 B lymphoblastoid cells by solubilization with sodium deoxycholate, affinity chromatography with anti-APO-1 antibody, and reversed phase high performance liquid chromatography. Each purification step was followed by an APO-1-specific solid phase enzyme-linked immunosorbent assay using the monoclonal antibody anti-APO-1. In sodium dodecyl sulfate-polyacrylamide gel electrophoresis, the APO-1 antigen was found to be a membrane glycoprotein of 48-kDa. Endoproteinase-cleaved peptides of the APO-1 protein were subjected to amino acid sequencing, and corresponding oligonucleotides were used to identify a full-length APO-1 cDNA clone from an SKW6.4 cDNA library. The deduced amino acid sequence of APO-1 showed sequence identity with the Fas antigen, a cysteine-rich transmembrane protein of 335 amino acids with significant similarity to the members of the tumor necrosis factor/nerve growth factor receptor superfamily. The APO-1 antigen was expressed upon transfection of APO-1 cDNA into BL60-P7 Burkitt's lymphoma cells and conferred sensitivity towards anti-APO-1-induced apoptosis to the transfectants.
Problems in the investigational study and clinical use of cancer immunotherapy (1990)

The last decade has witnessed a veritable explosion in the investigational study and clinical use of immunotherapy for the treatment of cancer. Although this is an exciting development, the promise of cancer immunotherapy has not yet been fulfilled. Why is there an apparent discrepancy between the theory of cancer immunotherapy and the actual results from clinical studies? Michael Osband and Susan Ross suggest that there are several basic problems with the clinical study and therapeutic use of immunotherapy that must be overcome before it can be considered a viable treatment for a broad range of tumors. The purpose of this article is to describe some of the more important of these problems.
Costimulation Signals for Memory CD8+ T Cells During Viral Infections (2009)

Costimulation signals have been recognized as critical for optimal T-cell responses and result from important interactions between receptors on the surface of T cells and their ligands on antigen-presenting cells. Two families of receptors, the CD28 family and the tumor necrosis factor receptor (TNFR) family, have been found to be major players in providing costimulation to CD8+ T cells. Recent studies using viral infection models have highlighted the importance of CD28 costimulation signals during memory responses against viruses. Programmed death-1 (PD-1), another member of the CD28 family, may contribute to functional defects of helpless memory CD8+ T cells. Members of the TNFR family, such as CD27, 4-1BB, CD40, TRAIL (tumor necrosis factor-related apoptosis-inducing ligand), and OX40, have also been implicated in the survival, generation, maintenance, and quality of virus-specific memory CD8+T cells. The delivery of costimulatory molecules such as CD28, 4-1BB, and OX40 can help boost the generation and function of virus-specific memory CD8+ T cells. The use of costimulatory molecules as adjuvants, along with viral antigens in vaccines, may facilitate the generation of effective antigen-specific memory CD8+ T-cell responses. Understanding the costimulatory requirements of memory CD8+ T cells, therefore, may lead to improved vaccines that target anti-viral CD8+ T-cell memory.
A Nonenzymatic RNA Polymerase Model (1983)

Polynucleotide templates containing C (cytidine) as the major component facilitate the synthesis of oligonucleotides from mixtures of the activated mononucleotide derivatives (as indicated by structure 1 in the text). A nucleotide is incorporated into oligomeric products if and only if its complement is present in the template. The reaction has a high fidelity and produces products with mean chain lengths of six to ten nucleotides. Bases other than guanosine are incorporated within oligomers or at their 3' termini, but rarely at their 5' termini.
Über chemisch markierte Antigene. III. Mitteilung. Zur Einführung von vielkernigen Ringsystemen in Proteine (1940)

Article Über chemisch markierte Antigene. III. Mitteilung. Zur Einführung von vielkernigen Ringsystemen in Proteine was published on January 1, 1940 in the journal Biological Chemistry (volume 267, issue 1-2).
Berkeley DB (1999)

Berkeley DB is an Open Source embedded database system with a number of key advantages over comparable systems. It is simple to use, supports concurrent access by multiple users, and provides industrial-strength transaction support, including surviving system and disk crashes. This paper describes the design and technical features of Berkeley DB, the distribution, and its license.
Nanoporous Plasmonic Metamaterials (2008)

Abstract We review different routes for the generation of nanoporous metallic foams and films exhibiting well‐defined pore size and short‐range order. Dealloying and templating allows the generation of both 2D and 3D structures that promise a plasmonic response determined by material constituents and porosity. Viewed in the context of metamaterials, the ease of fabrication of samples covering macroscopic dimensions is highly promising, and suggests more in‐depth investigations of the plasmonic and photonic properties of this material system for photonic applications.
Integrin α4β1–VCAM-1–mediated adhesion between endothelial and mural cells is required for blood vessel maturation (2005)

Neovascularization depends on vascular cell proliferation and on the stabilization of vessels by association of vascular smooth muscle-like pericytes with ECs. Here we show that integrin alpha4beta1 (VLA-4) and VCAM-1 promote close intercellular adhesion between ECs and pericytes and that this interaction is required for blood vessel formation. Integrin alpha4beta1 is expressed by proliferating but not quiescent ECs, while its ligand VCAM-1 is expressed by proliferating but not quiescent mural cells. Antagonists of this integrin-ligand pair block the adhesion of mural cells to proliferating endothelia in vitro and in vivo, thereby inducing apoptosis of ECs and pericytes and inhibiting neovascularization. These studies indicate that integrin alpha4beta1 and VCAM-1 facilitate a critical cell-cell adhesion event required for survival of endothelial and mural cells during vascularization.
The Selective Protection and Deprotection of Ambident Nucleophiles with Parent and Substituted Triarylmethyls (2002)

N-triphenylmethyl and N-4,4&amp;amp;apos;-dimethoxytriphenylmethyl of o-aminophenol, m-aminophenol, and p-aminophenol compounds were easily prepared from triphenylmethyl chloride and 4,4&amp;amp;apos;-dimethoxytriphenyl- methyl chloride. S-triphenylmethyl-2-mercapto ethanol was also selectively synthesized using the triphenylmethyl chloride and 2-mercapto ethanol. The reactivity of nitrogen and sulfur versus oxygen in the protection reactions was compared. In principle, the protection of aminophenols and 2-mercapto ethanol with triarylmethyls (trityls) may take place on the oxygen. However, in this framework, we discuss the different reactivities of oxygen, nitrogen and sulfur towards triphenylmethyl chloride (TrCl) and 4,4&amp;amp;apos;-dimethoxytriphenylmethyl chloride (DMTrCl) and find that nitrogen and sulfur are more reactive than oxygen.
Mapping Microvasculature with Acoustic Angiography Yields Quantifiable Differences between Healthy and Tumor-bearing Tissue Volumes in a Rodent Model (2012)

Vascular network quantification by using high-spatial-resolution acoustic angiographic images is feasible. Data suggest that the angiogenic processes associated with tumor development in the models studied result in higher instances of vessel tortuosity near the tumor site.
Serum Lipid Profile in Colorectal Cancer Patients with and without Synchronous Distant Metastases (2005)

Elevated serum lipid levels may facilitate the development of distant metastasis in CRC patients.
Hollow-waveguide-based nanosecond, near-infrared pulsed laser ablation of tissue (2005)

With near-infrared, nanosecond laser pulses delivered through a cyclic-olefin-polymer-coated silver hollow waveguide, efficient and sharp ablation of myocardial tissue can be achieved, suggesting the usefulness of the hollow waveguide as a new flexible delivery system for high-intensity laser pulses.
Spontaneous Isopeptide Bond Formation as a Powerful Tool for Engineering Site-Specific Antibody-Drug Conjugates (2016)

Spontaneous isopeptide bond formation, a stabilizing posttranslational modification that can be found in gram-positive bacterial cell surface proteins, has previously been used to develop a peptide-peptide ligation technology that enables the polymerization of tagged-proteins catalyzed by SpyLigase. Here we adapted this technology to establish a novel modular antibody labeling approach which is based on isopeptide bond formation between two recognition peptides, SpyTag and KTag. Our labeling strategy allows the attachment of a reporting cargo of interest to an antibody scaffold by fusing it chemically to KTag, available via semi-automated solid-phase peptide synthesis (SPPS), while equipping the antibody with SpyTag. This strategy was successfully used to engineer site-specific antibody-drug conjugates (ADCs) that exhibit cytotoxicities in the subnanomolar range. Our approach may lead to a new class of antibody conjugates based on peptide-tags that have minimal effects on protein structure and function, thus expanding the toolbox of site-specific antibody conjugation.
THE CARRIER STATE IN PERTUSSIS1 (1968)

Journal Article THE CARRIER STATE IN PERTUSSIS Get access CALVIN C. LINNEMANN, JR, CALVIN C. LINNEMANN, JR Search for other works by this author on: Oxford Academic PubMed Google Scholar JAMES W. BASS, JAMES W. BASS Search for other works by this author on: Oxford Academic PubMed Google Scholar MARGARET H. D. SMITH MARGARET H. D. SMITH Search for other works by this author on: Oxford Academic PubMed Google Scholar American Journal of Epidemiology, Volume 88, Issue 3, November 1968, Pages 422–427, https://doi.org/10.1093/oxfordjournals.aje.a120903 Published: 01 November 1968 Article history Received: 23 February 1968 Published: 01 November 1968
MicroRNA Expression Profiles in Serous Ovarian Carcinoma (2008)

Our results indicate that dysregulation of microRNAs is involved in ovarian carcinogenesis and associated with the prognosis of serous ovarian carcinoma.
Lymphocytes : a practical approach (2000)

Preface Preparation of lymphocytes and idenfication of lymphocyte subpopulations Immunohistochemistry of lymphoid organs T and B-cell hybridomas Murine T-cell culture Human CD4+ T-cell culture Human Cytotoxic T-cell culture Limiting dilution analysis for quantification of antigen-specific T-cells HLA -peptide tetrameric complexes Expansion of human T-cells for immunotheraphy HLA typing Characterisation of lymphocyte surface markers Apoptosis assays for lymphocytes Thymic organ culture Index
The cell-bound fructosyltransferase of Streptococcus salivarius: the carboxyl terminus specifies attachment in a Streptococcus gordonii model system (1993)

The ftf gene, coding for the cell-bound beta-D-fructosyltransferase (FTF) of Streptococcus salivarius ATCC 25975, has been analyzed, and its deduced amino acid sequence has been compared with that of the secreted FTF of Streptococcus mutans and the levansucrases (SacBs) of Bacillus species. A unique proline-rich region detected at the C terminus of the FTF of S. salivarius preceded a hydrophobic terminal domain. This proline-rich region was shown to possess strong homology to the product of the prgC gene from pCF10 in Enterococcus faecalis, which encodes a pheromone-responsive protein of unknown function, as well as homology to the human proline-rich salivary protein PRP-4. A series of 3'-OH deletions of the S. salivarius ftf gene expressed in Streptococcus gordonii Challis LGR2 showed that the C terminus was required for cell surface attachment in this heterologous organism, as only the complete gene product was cell bound. This cell-bound activity was released in the presence of sucrose, suggesting that the mode of attachment and release of the S. salivarius FTF in S. gordonii was similar to that in its native host.
Distinct Recognition of Non-Clade B Human Immunodeficiency Virus Type 1 Epitopes by Cytotoxic T Lymphocytes Generated from Donors Infected in Africa (1999)

We present detailed studies of human immunodeficiency virus (HIV)-specific cytotoxic T-lymphocyte (CTL) responses to clade A or C HIV type 1 in three donors infected in East Africa. We define several novel non-clade B CTL epitopes, including some restricted by HLA alleles common in Africans. Although cross-clade CTL recognition of these epitopes does occur, recognition can also be highly clade specific.
“Superhumanized” Antibodies: Reduction of Immunogenic Potential by Complementarity-Determining Region Grafting with Human Germline Sequences: Application to an Anti-CD28 (2002)

Humanized Abs are created by combining, at the genetic level, the complementarity-determining regions of a murine mAb with the framework sequences of a human Ab variable domain. This leads to a functional Ab with reduced immunogenic side effects in human therapy. In this study, we report a new approach to humanizing murine mAbs that may reduce immunogenicity even further. This method is applied to humanize the murine anti-human CD28 Ab, 9.3. The canonical structures of the hypervariable loops of murine 9.3 were matched to human genomic V gene sequences whose hypervariable loops had identical or similar canonical structures. Framework sequences for those human V genes were then used, unmodified, with the 9.3 complementarity-determining regions to construct a humanized version of 9.3. The humanized 9.3 and a chimeric 9.3 control were expressed in Escherichia coli as Fab. The humanized Fab showed a moderate loss in avidity in a direct binding ELISA with immobilized CD28-Ig fusion protein (CD28-Ig). Humanized 9.3 blocked ligation of CD28-Ig to cells expressing the CD28 receptor CD80. Lastly, the humanized 9.3 showed biological activity as an immunosuppressant by inhibiting a MLR.
Stability of capillary gels for automated sequencing of DNA (1992)

Recent interest in capillary gel electrophoresis has been fueled by the Human Genome Project and other large-scale sequencing projects. Advances in gel polymerization techniques and detector design have enabled sequencing of DNA directly in capillaries. Efforts to exploit this technology have been hampered by problems with the reproducibility and stability of gels. Gel instability manifests itself during electrophoresis as a decrease in the current passing through the capillary under a constant voltage. Upon subsequent microscopic examination, bubbles are often visible at or near the injection (cathodic) end of the capillary gel. Gels have been prepared with the polyacrylamide matrix covalently attached to the silica walls of the capillary. These gels, although more stable, still suffer from problems with bubbles. The use of actual DNA sequencing samples also adversely affects gel stability. We examined the mechanisms underlying these disruptive processes by employing polyacrylamide gel-filled capillaries in which the gel was not attached to the capillary wall. Three sources of gel instability were identified. Bubbles occurring in the absence of sample introduction were attributed to electroosmotic force; replacing the denaturant urea with formamide was shown to reduce the frequency of these bubbles. The slow, steady decline in current through capillary sequencing gels interferes with the ability to detect other gel problems. This phenomenon was shown to be a result of ionic depletion at the gel-liquid interface. The decline was ameliorated by adding denaturant and acrylamide monomers to the buffer reservoirs. Sample-induced problems were shown to be due to the presence of template DNA; elimination of the template allowed sample loading to occur without complications.(ABSTRACT TRUNCATED AT 250 WORDS)
Inkjet printed bandpass filters and filtennas using silver nanoparticle ink on flexible substrate (2015)

This paper presents an inkjet printed CPW filtenna designed at 5.8 GHz. The proposed structure consists of a CPW pseudo-interdigital bandpass filter and a CPW inset-fed antenna. The bandpass filter is fabricated using inkjet printing technology. The structure is printed on flexible Kapton substrate with polyimide film using silver nanoparticle ink. The filter is then used to suppress the spurious harmonics of the antenna. Measurements from the fabrication confirm the accuracy of the design method and the simulation results.
Severe combined immunodeficiency mouse-human skin chimeras: a unique animal model for the study of psoriasis and cutaneous inflammation (2001)

Elucidation of the molecular and cellular mechanisms responsible for the pathogenesis of psoriasis had been significantly handicapped due to lack of an ideal animal model. To overcome this hurdle several investigators have developed a number of animal models for psoriasis. Recent establishment of the SCID-human skin chimeras with transplanted psoriasis plaques has opened new vistas to study the molecular complexities involved in psoriasis. This model also offers a unique opportunity to investigate various key biological events such as cell proliferation, angiogenesis, homing in of T cells in target tissues, neurogenic inflammation and cytokine/chemokine cascades involved in an inflammatory reaction. The SCID mouse model will be of immense help to target the cellular and molecular events associated with these pathogenic processes and develop novel drugs for psoriasis and other inflammatory diseases. In this article we have reviewed the prospects and the limitations of the SCID mouse model of psoriasis.
Inspiratory duty cycle responses to flow limitation predict nocturnal hypoventilation (2009)

Upper airway obstruction (UAO) can elicit neuromuscular responses that mitigate and/or compensate for the obstruction. It was hypothesised that flow-limited breathing elicits specific timing responses that can preserve ventilation due to increases in inspiratory duty cycle rather than respiratory rate. By altering nasal pressure during non-rapid eye movement (non-REM) sleep, similar degrees of UAO were induced in healthy males and females (n = 10 each). Inspiratory duty cycle, respiratory rate and minute ventilation were determined for each degree of UAO during non-REM sleep and compared with the baseline nonflow-limited condition. A dose-dependent increase in the inspiratory duty cycle and respiratory rate was observed in response to increasing severity of UAO. Increases in the inspiratory duty cycle, but not respiratory rate, helped to acutely maintain ventilation. Heterogeneity in these responses was associated with variable degrees of ventilatory compensation, allowing for the segregation of individuals at risk for hypoventilation during periods of inspiratory airflow limitation. Upper airway obstruction constitutes a unique load on the respiratory system. The inspiratory duty cycle, but not the respiratory rate, determine the individual's ability to compensate for inspiratory airflow limitation during sleep, and may represent a quantitative phenotype for obstructive sleep apnoea susceptibility.
Validation of Cell-Cycle Arrest Biomarkers for Acute Kidney Injury Using Clinical Adjudication (2014)

Urinary [TIMP-2]·[IGFBP7] greater than 0.3 (ng/ml)(2)/1,000 identifies patients at risk for imminent AKI. Clinical trial registered with www.clinicaltrials.gov (NCT 01573962).
Is working memory training effective? A meta-analytic review. (2012)

It has been suggested that working memory training programs are effective both as treatments for attention-deficit/hyperactivity disorder (ADHD) and other cognitive disorders in children and as a tool to improve cognitive ability and scholastic attainment in typically developing children and adults. However, effects across studies appear to be variable, and a systematic meta-analytic review was undertaken. To be included in the review, studies had to be randomized controlled trials or quasi-experiments without randomization, have a treatment, and have either a treated group or an untreated control group. Twenty-three studies with 30 group comparisons met the criteria for inclusion. The studies included involved clinical samples and samples of typically developing children and adults. Meta-analyses indicated that the programs produced reliable short-term improvements in working memory skills. For verbal working memory, these near-transfer effects were not sustained at follow-up, whereas for visuospatial working memory, limited evidence suggested that such effects might be maintained. More importantly, there was no convincing evidence of the generalization of working memory training to other skills (nonverbal and verbal ability, inhibitory processes in attention, word decoding, and arithmetic). The authors conclude that memory training programs appear to produce short-term, specific training effects that do not generalize. Possible limitations of the review (including age differences in the samples and the variety of different clinical conditions included) are noted. However, current findings cast doubt on both the clinical relevance of working memory training programs and their utility as methods of enhancing cognitive functioning in typically developing children and healthy adults.