gebhart/patrepeval huggingface dataset:
Immune Checkpoint Blockade in Human Cancer Therapy: Lung Cancer and Hematologic Malignancies (2016)

Tumor immune evasion is one of the hallmarks of cancer, and expression of the B7 family of immune checkpoints (PD-L1, PD-L2, B7-H3, B7x and HHLA2) is one mechanism of immune evasion by tumors to suppress T-cell function. Antibodies blocking these interactions of B7-1/B7-2/CTLA-4 and PD-L1/PD-L2/PD-1 have had remarkable clinical success in several cancers and are less toxic than traditional chemotherapy. Even though only a small proportion of patients respond to checkpoint blockade, the duration of such responders due to immunological memory is remarkable and is longer than would be expected with any other agent in refractory disease. In this article, we review the therapeutic trials of blocking these pathways in human lung cancer and hematological malignancies.
Analytical Chemistry of Bacillus thuringiensis (1990)

This article presents a review of the analytical chemistry of Bacillus thuringiensis and an introduction to the remaining chapters in this book. Included are critical evaluations of the appropriate analytical targets, sample preparation and determination by bioassay, immunoassay, electrophoresis and chromatography. Issues of purifying reference standards are also discussed.
Naturally transmitted segmented filamentous bacteria segregate with diabetes protection in nonobese diabetic mice (2011)

Vertebrates typically harbor a rich gastrointestinal microbiota, which has coevolved with the host over millennia and is essential for several host physiological functions, in particular maturation of the immune system. Recent studies have highlighted the importance of a single bacterial species, segmented filamentous bacteria (SFB), in inducing a robust T-helper cell type 17 (Th17) population in the small-intestinal lamina propria (SI-LP) of the mouse gut. Consequently, SFB can promote IL-17-dependent immune and autoimmune responses, gut-associated as well as systemic, including inflammatory arthritis and experimental autoimmune encephalomyelitis. Here, we exploit the incomplete penetrance of SFB colonization of NOD mice in our animal facility to explore its impact on the incidence and course of type 1 diabetes in this prototypical, spontaneous model. There was a strong cosegregation of SFB positivity and diabetes protection in females, but not in males, which remained relatively disease-free regardless of the SFB status. In contrast, insulitis did not depend on SFB colonization. SFB-positive, but not SFB-negative, females had a substantial population of Th17 cells in the SI-LP, which was the only significant, repeatable difference in the examined T-cell compartments of the gut, pancreas, or systemic lymphoid tissues. Th17-signature transcripts dominated the very limited SFB-induced molecular changes detected in SI-LP CD4(+) T cells. Thus, a single bacterium, and the gut immune system alterations associated with it, can either promote or protect from autoimmunity in predisposed mouse models, probably reflecting their variable dependence on different Th subsets.
Early experience with in situ saphenous vein bypass for distal arterial reconstruction. (1986)

During a 36-month period 74 patients underwent infrainguinal in situ saphenous vein bypass to the popliteal or tibial vessels. The first 54 operations were performed with standard valvulotomes and valve-cutting scissors, while in the last 20 operations a new intraluminal valve-cutting device was used to incise the valves. Ninety-four percent of bypasses were performed for limb salvage, 80% of all operations were done to the tibial vessels, and 31% of bypasses were done to the ankle vessels. The operation was attempted in 81 patients and completed in 74 patients, for a vein utilization rate of 91%. Fifty-five percent of all veins had a distal diameter of less than 4 mm (average 3.6 mm). The patency rates were 92% at 3 months and 90% at 12 and 36 months for all grafts. There were six failed grafts, all within the first 6 months, and eight diabetic patients required reoperation, two for missed valve leaflets, and three needed revision of the distal anastomosis; however, all these grafts were patent at the time of reexploration. There were four perioperative deaths and two patients had nonfatal postoperative myocardial infarctions. This study demonstrates that in situ saphenous vein grafting provides for a high vein utilization rate and suggests that the technique provides for higher graft patency and limb salvage rates than do more traditional types of procedures.
Multichannel Bin-Wise Robust Frequency-Domain Adaptive Filtering and Its Application to Adaptive Beamforming (2007)

Least-squares error (LSE) or mean-squared error (MSE) optimization criteria lead to adaptive filters that are highly sensitive to impulsive noise. The sensitivity to noise bursts increases with the convergence speed of the adaptation algorithm and limits the performance of signal processing algorithms, especially when fast convergence is required, as for example, in adaptive beamforming for speech and audio signal acquisition or acoustic echo cancellation. In these applications, noise bursts are frequently due to undetected double-talk. In this paper, we present impulsive noise robust multichannel frequency-domain adaptive filters (MC-FDAFs) based on outlier-robust M-estimation using a Newton algorithm and a discrete Newton algorithm, which are especially designed for frequency bin-wise adaptation control. Bin-wise adaptation and control in the frequency-domain enables the application of the outlier-robust MC-FDAFs to a generalized sidelobe canceler (GSC) using an adaptive blocking matrix for speech and audio signal acquisition. It is shown that the improved robustness leads to faster convergence and to higher interference suppression relative to nonrobust adaptation algorithms, especially during periods of strong interference
Palmitoylation of Intracellular Signaling Proteins: Regulation and Function (2004)

Protein S-palmitoylation is the thioester linkage of long-chain fatty acids to cysteine residues in proteins. Addition of palmitate to proteins facilitates their membrane interactions and trafficking, and it modulates protein-protein interactions and enzyme activity. The reversibility of palmitoylation makes it an attractive mechanism for regulating protein activity, and this feature has generated intensive investigation of this modification. The regulation of palmitoylation occurs through the actions of protein acyltransferases and protein acylthioesterases. Identification of the protein acyltransferases Erf2/Erf4 and Akr1 in yeast has provided new insight into the palmitoylation reaction. These molecules work in concert with thioesterases, such as acyl-protein thioesterase 1, to regulate the palmitoylation status of numerous signaling molecules, ultimately influencing their function. This review discusses the function and regulation of protein palmitoylation, focusing on intracellular proteins that participate in cell signaling or protein trafficking.
Dual role of macrophages in tumor growth and angiogenesis (2006)

During the neoplastic progression, macrophages as well as dendritic and NK cells are attracted into the tumor site and initiate the immune response against transformed cells. They activate and present tumor antigens to T cells, which are then activated to kill tumor cells. However, tumor cells are often capable of escaping the immune machinery. As the immune surveillance is not sufficient anymore, tumor-associated macrophages contribute to tumor progression. It is notable that tumor-associated macrophages promote the proliferation of tumor cells directly by secreting growth factors. They also participate in tumor progression by acting on endothelial cells and thus promoting the neovascularization of the tumor. Tumor-associated macrophages are indeed key protagonists during angiogenesis and promote each step of the angiogenesis cascade.
Continuous Monitoring of Intrathoracic Impedance and Right Ventricular Pressures in Patients With Heart Failure (2010)

Decompensated HF develops based on hemodynamic derangements and is preceded by significant changes in intrathoracic impedance and right ventricular pressures during the month prior to a major clinical event. Impedance and pressure changes are moderately correlated. Future research may establish the complementary contribution of both parameters to guide diagnosis and management of patients with HF by implantable devices.
A low complexity joint equalizer and decoder for 1000Base-T Gigabit Ethernet (2002)

A VLSI architecture for low complexity joint decoding and equalization for 1000Base-T Gigabit Ethernet is presented. A one-tap parallel decision-feedback decoder jointly decodes the trellis and cancels the ISI due to the first tap of the post-cursor channel impulse response. The one-dimensional branch metrics are precomputed in a look-ahead fashion to meet the speed requirements. The less significant tail of the channel impulse response is canceled with a simple decision-feedback prefilter. The design has been implemented in 3.3 V, 0.25 /spl mu/m standard cell CMOS process for operation at 125 MHz.
An Improved Least-Laxity-First Scheduling Algorithm of Variable Time Slice for Periodic Tasks (2007)

The LLF (least laxity first) scheduling algorithm assigns a priority to a task according to its executing urgency. The smaller the laxity value of a task is, the sooner it needs to be executed. However it leads to switch frequently among tasks, which causes the overhead of a system and restricts its application. The least switch and laxity first scheduling algorithm is proposed in the paper, which improves the least laxity first algorithm for periodic task by searching out an appropriate common divisor.
A Case Study (2011)

This chapter addresses the design and procedural variables of creating a bilingual Web site information portal for an audience of culturally diverse immigrants. A Web site developed as a resource for a diverse Somali community (http://www.somaliresource. net) is used as a case study for this chapter. The Somali community, which includes immigrants, refugees, and asylees, faces difficulties associated with language barriers. They struggle with the adjustment of life in a completely new system in Minnesota. The aim of this resource is to address some of the Somali’s informational needs in the form of a one-stop bilingual Web site. It is our goal to describe our design process, and offer recommendations on design and procedural variables for working with the Somali cultural group. We envision that graphic designers and other researchers will find it useful to reference this material when they address design issues related to different cultural groups.Request access from your librarian to read this chapter's full text.
Synthetic infrared spectra (1997)

We have designed, microfabricated, and characterized a diffractive optical element that reproduces the infrared spectrum of HF from 3600 to 4300 cm(-1) . The reflection-mode diffractive optic consists of 4096 lines, each 4.5mum wide, at 16 discrete depths relative to the substrate from 0 to 1.2 mum and was fabricated upon a silicon wafer by anisotropic reactive ion-beam etching in a four-mask-level process. We envisage the use of diffractive optical elements of this type as the basis for a new class of miniaturized, remote chemical sensor systems based on correlation spectroscopy.
Making artificial antibodies: A format for phage display of combinatorial heterodimeric arrays (1999)

The gene VII protein (pVII) and gene IX protein (pIX) are associated closely on the surface of filamentous bacteriophage that is opposite of the end harboring the widely exploited pIII protein. We developed a phagemid format wherein antibody heavy- and light-chain variable regions were fused to the amino termini of pVII and pIX, respectively. Significantly, the fusion proteins interacted to form a functional Fv-binding domain on the phage surface. Our approach will be applicable to the display of generic peptide and protein libraries that can form combinatorial heterodimeric arrays. Consequently, it represents a first step toward artificial antibodies and the selection of novel biological activities.
High-power coherent GaAs-based monolithic semiconductor lasers (2001)

Stable-beam operation to high coherent powers from large aperture devices can only be obtained from active-photonic- lattice (APL) structures of large built-in index step. Resonant phase-locked arrays of antiguides, so called ROW array, have provided 1.6W CW coherent power from 200micrometers - wide apertures. Two-dimensional surface-emitting APLs combining ROW arrays and DFB-DBR structures with central (pi) phase-shift are capable of providing coherent powers in the multi-watt range. ARROW-type devices, simpler APL structures, hold the potential for emitting 1W single-mode CW power reliability in stable beam patterns.
Tamoxifen for Prevention of Breast Cancer: Report of the National Surgical Adjuvant Breast and Bowel Project P-1 Study (1998)

Tamoxifen decreases the incidence of invasive and noninvasive breast cancer. Despite side effects resulting from administration of tamoxifen, its use as a breast cancer preventive agent is appropriate in many women at increased risk for the disease.
APRIL, a New Ligand of the Tumor Necrosis Factor Family, Stimulates Tumor Cell Growth (1998)

Members of the tumor necrosis factor (TNF) family induce pleiotropic biological responses, including cell growth, differentiation, and even death. Here we describe a novel member of the TNF family designated APRIL (for a proliferation-inducing ligand). Although transcripts of APRIL are of low abundance in normal tissues, high levels of mRNA are detected in transformed cell lines, and in human cancers of colon, thyroid, and lymphoid tissues in vivo. The addition of recombinant APRIL to various tumor cells stimulates their proliferation. Moreover, APRIL-transfected NIH-3T3 cells show an increased rate of tumor growth in nude mice compared with the parental cell line. These findings suggest that APRIL may be implicated in the regulation of tumor cell growth.
Local Immune Responses Correlate with Presentation and Outcome in Tuberculosis (1998)

Local cellular immune responses may affect presentation and outcome in tuberculosis (TB). To investigate this hypothesis, we performed bronchoalveolar lavage (BAL) on 30 patients with untreated pulmonary tuberculosis and assessed the type of cellular inflammatory response and cytokine production. We then correlated BAL findings and cytokine production with clinical findings. We also performed BAL on a subset of patients to examine changes in cytokine production by BAL cells over time. We found that at presentation patients with less clinically and radiographically advanced TB (smear-negative, noncavitary disease) had a local immune response characterized by a predominance of lymphocytes. Furthermore, BAL cells from these patients secreted interferon (IFNgamma), and not Interleukin-4, suggesting a Th 1-type lymphocytic response. In patients with smear-positive and/or cavitary disease, macrophages or polymorphonuclear leukocytes were the predominant BAL cell type, but with treatment and clinical improvement these patients went on to recruit IFNgamma producing cells to the lung. We conclude that the type of cellular immune response that occurs locally in the lung may affect presentation and outcome in pulmonary TB, and an understanding of the development of this response may lead to insights into pathogenesis and novel therapies for TB.
Modulation of Bacillus subtilis levansucrase gene expression by sucrose and regulation of the steady-state mRNA level by sacU and sacQ genes (1986)

In Bacillus subtilis, the extracellular enzyme levansurcrase is synthesized in the presence of sucrose. A termination structure between the transcription start site and the structural gene was the apparent site for regulation by sucrose of transcription into the structural gene. Sequence analysis of the sacB leader region from two strains constitutive for levansucrase synthesis showed a single base change in the stem of this termination structure. This single base change also led to the constitutive synthesis of a sacB'-'lacZ fusion, whereas the wild-type sacB'-'lacZ fusion was induced by the addition of sucrose. S1 nuclease mapping of sacB transcripts with probes labeled either within the termination structure or 3' to the termination structure showed that sucrose did not increase the number of transcripts extending into the termination structure; however, sucrose did increase the number of transcripts extending past the termination structure. Two pleiotropic mutations which affect the expression of levansucrase, sacQ36 hyperproducing [sacQ36(Hy)] and sacU32(Hy), were separately introduced into the strain carrying the sacB'-'lacZ fusion. These mutations each increased the expression levels of the sacB'-'lacZ fusion. S1 mapping showed increased levels of transcript initiating at the sacB promoter in strains with the sacQ36(Hy) and sacU32(Hy) mutations. This increased transcription appeared to be independent of the sucrose-regulated transcription termination, suggesting the existence of at least two different mechanisms for the regulation of sacB expression.
Reconstruction of Patellar Articular Cartilage with Free Autologous Perichondrial Grafts: An Experimental Study in Dogs (1979)

The cartilaginous potential of the perichondrium has earlier been utilized to reconstruct articular cartilage in unloaded joints in adult rabbits. The present work in adult dogs has been performed to find out if the perichondrium can be used for the same purpose in joints subjected to pressure. In 13 knee joints the articular cartilage of the patella was excised completely and the resected surface was covered with an autologous perichondrial graft taken from the rib cartilage. After 3 weeks of immobilization the dogs were allowed to run freely until sacrifice 2 to 17 months later. In all 13 cases regeneration of cartilage took place. Within 8 months the regenerated cartilage showed no or only very slight degenerative signs but from 12 months and later such changes were common. In control cases where the resected surface was left without any graft no cartilage at all was found. Conclusively cartilage formation from grafted rib perichondrium is achieved in the knee joints of adult dogs, but it does not resist considerable pressure forces.
Pancreatic Cancer Stem Cells (2008)

Cellular heterogeneity in cancer was observed decades ago by studies in mice which showed that distinct subpopulations of cells within a tumor mass are capable of driving tumorigenesis. Conceptualized from this finding was the stem-cell hypothesis for cancer, which suggests that only a specific subset of cancer cells within each tumor is responsible for tumor initiation and propagation, termed tumor initiating cells or cancer stem cells (CSCs). Recent data has been provided to support the existence of CSCs in human blood cell-derived cancers and solid organ tumors of the breast, brain, prostate, colon, and skin. Study of human pancreatic cancers has also revealed a specific subpopulation of cancer cells that possess the characteristics of CSCs. These pancreatic cancer stem cells express the cell surface markers CD44, CD24, and epithelial-specific antigen, and represent 0.5% to 1.0% of all pancreatic cancer cells. Along with the properties of self-renewal and multilineage differentiation, pancreatic CSCs display upregulation of important developmental genes that maintain self-renewal in normal stem cells, including Sonic hedgehog (SHH) and BMI-1. Signaling cascades that are integral in tumor metastasis are also upregulated in the pancreatic CSC. Understanding the biologic behavior and the molecular pathways that regulate growth, survival, and metastasis of pancreatic CSCs will help to identify novel therapeutic approaches to treat this dismal disease.
Turnover of Inositol Phospholipids and Signal Transduction (1984)

Various extracellular informational signals such as those from a group of hormones and some neurotransmitters appear to be passed from the cell surface into the cell interior by two routes, protein kinase C activation and Ca2+ mobilization. Both routes usually become available as the result of an interaction of a single ligand and a receptor and act synergistically to evoke subsequent cellular responses such as release reactions. The signal-dependent breakdown of inositol phospholipids, particularly phosphatidylinositol bisphosphate, now appears to be a key event for initiating these processes.
Facile electron-beam lithography technique for irregular and fragile substrates (2014)

A facile technique is presented which enables high-resolution electron beam lithography on irregularly-shaped, non-planar or fragile substrates such as the edges of a silicon chip, thin and narrow suspended beams and bridges, or small cylindrical wires. The method involves a spin-free dry-transfer of pre-formed uniform-thickness polymethyl methacrylate, followed by conventional electron beam writing, metal deposition, and lift-off. High-resolution patterning is demonstrated for challenging target substrates. The technique should find broad application in micro- and nano-technology research arenas.
MicroRNAs Regulate Ocular Neovascularization (2008)

In this study, we used ischemia-induced retinal neovascularization (NV) as a model to investigate the possible role of microRNAs in a clinically important disease process. Microarray analysis demonstrated seven microRNAs (miR-106a, -146, -181, -199a, -214, -424, and -451) that were substantially increased and three microRNAs (miR-31, -150, and -184) that were substantially decreased in ischemic retina. Potential targets for the upregulated microRNAs were not identified, but bioinformatic analysis suggested target genes for the downregulated microRNAs, and these were confirmed using a luciferase reporter assay. Real-time reverse transcriptase PCR confirmed that the substantial levels of miR-31, -150, and -184 present in normal retina were significantly reduced in ischemic retina. Interestingly, constitutive levels of miR-31 and -184 are high in the cornea and lens, two avascular tissues. Intraocular injection of pre-miR-31, -150, or -184 significantly reduced ischemia-induced retinal NV, and injection of pre-miR-31 or -150 also significantly reduced choroidal NV. These data suggest that alteration of microRNA levels contributes to two types of ocular NV, and that injection or enhanced expression of microRNAs is a potential therapeutic strategy.