gebhart/patrepeval huggingface dataset:
Novel agents for pancreatic ductal adenocarcinoma: emerging therapeutics and future directions (2018)

A poor prognosis of pancreatic ductal adenocarcinoma (PDAC) associated with chemoresistance has not changed for the past three decades. A multidisciplinary diagnosis followed by surgery and chemo(radiation)therapy is the main treatment approach. However, gemcitabine- and 5-fluorouracil-based therapies did not present satisfying outcomes. Novel regimens targeting pancreatic cancer cells, the tumor microenvironment, and immunosuppression are emerging. Biomarkers concerning the treatment outcome and patient selection are being discovered in preclinical or clinical studies. Combination therapies of classic chemotherapeutic drugs and novel agents or novel therapeutic combinations might bring hope to the dismal prognosis for PDAC patients.
Most tumors in transgenic mice with human c-Ha-ras gene contained somatically activated transgenes. (1990)

Two independent transgenic mouse lines carrying human hybrid c-Ha-ras genes with their own promoter region encoding prototype products, were established. In these lines, about 50% of transgenic offspring had tumors within 18 months. The tumors developed in restricted tissues and about 60% of affected mice had angiosarcomas. The transgenes were expressed both in the tumors and in all normal tissues. However, somatic mutational activation was detected only in the transgenes of the tumors. The point mutation at the 61st codon, from CAG(Gln) to CTG(Leu), was detected in all angiosarcomas (22/22), some lung adenocarcinomas (3/11) and Harderian gland adenocarcinomas (4/7) in both lines. The other point mutation at the 12th codon from GGC(Gly) to GTC(Val) was detected in two of the four skin papillomas. No mutations on these codons were detected in normal tissues of transgenic mice. Nontransgenic littermates had no tumors at all. From these results, it was strongly suggested that the mouse tumors do not develop only by the expression of the transgenes, and that definite somatic point mutation of the human c-Ha-ras transgenes in certain cell types may be a causative event in tumorigenesis in these transgenic mice.
Performance of real-time source-location estimators for a large-aperture microphone array (2005)

A large array of microphones is being studied as a possible means of acquiring data in offices, conference rooms, and auditoria without requiring close-talking microphones. An array that surrounds all possible sources has a large aperture and such arrays have attractive properties for accurate spatial resolution and significant signal-to-noise enhancement. For the first time, this paper presents all the details of a real-time, source-location algorithm (LEMSalg) based on time-of-arrival delays derived from a phase transform applied to the generalized cross-power spectrum. It is being used successfully in a representative environment where microphone SNRs are below 0 dB. We have found that many small features are required to make a useful location estimating algorithm work and work well in real-time. We present an experimental evaluation of the current algorithm's performance using data taken with the Huge Microphone Array (HMA) system, which has 448 microphones in a noisy, reverberant environment. Using off-line computation, we also compared the LEMSalg to two alternative methods. The first of these adds local beamforming to the preprocessing of the base algorithm, increasing performance significantly at modest additional computational cost. The second algorithm maximizes the total steered-response power in the same phase transform. While able to derive good position estimates from shorter data runs, this method is two orders of magnitude more computationally expensive and is not yet suitable for real-time use.
Cloud Points: Can We Measure or Model Them? (2003)

Abstract The terminology "cloud point" has been traditionaly adopted by the American Society for Testing and Materials (ASTM) D2500 to refer to the temperature at which "cloudiness" of a relatively transparent petroleum fluid is observed upon cooling. The cloudiness forms as a "finite and detectable" amount of wax and/or paraffins precipitates from the test fluid contained in a 1½-in (˜30 mm) diameter glass tube. Nowadays, more sophisticated techniques of differing measurement principles and varying degrees of sensitivity have been developed to measure cloud points of petroleum fluids including opaque hydrocarbon systems (dark oils). Alternative terminologies like wax appearance temperature (WAT) and wax precipitation temperature (WPT), amongst a few others, have also emerged and are used interchangeably. Meanwhile, numerous characterization and modeling efforts have been made to simulate "measured" cloud points of petroleum fluids. The goals of this paper are to provide an objective review of the concept of "cloud point" and to illucidate the adequacy and limitations of the measurement techniques and modeling approaches.
Computational complexity of a problem in molecular structure prediction (1992)

The computational task of protein structure prediction is believed to require exponential time, but previous arguments as to its intractability have taken into account only the size of a protein's conformational space. Such arguments do not rule out the possible existence of an algorithm, more selective than exhaustive search, that is efficient and exact. (An efficient algorithm is one that is guaranteed, for all possible inputs, to run in time bounded by a function polynomial in the problem size. An intractable problem is one for which no efficient algorithm exists.) Questions regarding the possible intractability of problems are often best answered using the theory of NP-completeness. In this treatment we show the NP-hardness of two typical mathematical statements of empirical potential energy function minimization of macromolecules. Unless all NP-complete problems can be solved efficiently, these results imply that a function minimization algorithm can be efficient for protein structure prediction only if it exploits protein-specific properties that prohibit the simple geometric constructions that we use in our proofs. Analysis of further mathematical statements of molecular structure prediction could constitute a systematic methodology for identifying sources of complexity in protein folding, and for guiding development of predictive algorithms.
Isolates of human immunodeficiency virus type 1 from the brain may constitute a special group of the AIDS virus. (1989)

The biologic, serologic, and molecular properties of isolates of human immunodeficiency virus type 1 (HIV-1) from the central nervous system (CNS) were determined and compared to those of isolates from peripheral blood and lymph nodes. Among these were pairs of CNS and blood isolates obtained from six infected individuals. The data show that HIV-1 isolates from the CNS can be distinguished from peripheral blood isolates by their (i) relative inability to infect established T-cell lines, (ii) reduced cytopathogenicity, (iii) inability to modulate CD4 antigen expression on infected cells, (iv) efficient replication in peripheral blood macrophages, and (v) insensitivity to serum neutralization. Paired CNS and peripheral blood isolates from the same individual also display some differences in cellular tropism. The blood isolates replicate better in T-cell lines and glioma cell lines, whereas the paired CNS isolates replicate more efficiently in primary macrophages. These results suggest that viruses isolated from the CNS of infected individuals may represent a specific HIV-1 subgroup.
Cytogenetic stability of aneuploid maize tissue cultures (1986)

Monosomic maize tissue cultures might be used to select recessive mutations of cellular traits. This strategy would avoid some of the problems encountered with haploid cultures such as lack of vigor, sterility of regenerated plants, and uncontrolled diploidization. Monosomic and other aneuploid plants were selected among progeny of W22 R/r-x1 crossed with genetic stocks containing recessive markers. The r-x1 allele induces aneuploidy at a frequency of about 15%. Immature tassels of selected plants were used to initiate totipotent tissue cultures. Plants were regenerated from the cultures over a period of 3 to 17 months after culture initiation. Meiotic karyotypes of microsporocytes and pollen sterility were analyzed in regenerated plants. At least 40% of the 161 plants regenerated from aneuploid cultures had altered karyotypes. This frequency was not related to culture age. Most alterations involved chromosome breakage rather than changes in chromosome number. Types of alterations included heteromorphic pairs (18.1%), translocations (12.5%), addition (10.6%) or loss (1.4%) of chromosomes, and genomic doubling (2.8%). Four euploid cultures, including one with a translocation, were equally unstable (49% with alterations among 115 plants). Euploid cultures gave rise to plants with translocations (12.3%), heteromorphic pairs (8.8%), and genomic doubling (29.2%), but no single chromosome additions or losses. Plants that shared a common distinctive karyotype, such as a specific translocation, were probably derived from a common cell line. Tassels with sectors of two different karyotypes were frequent in plants regenerated from aneuploid (20%) or euploid (33%) cultures. Coenocytic microsporocytes, which lacked cell walls between nuclei, were found in plants from monosomic-2, deficient-2L, and monosomic-6 cultures. Another aberration (23% of 144 regenerants) was lack of cell wall formation after the first and (or) second meiotic division, which was often followed by nuclear fusion. Karyotypic changes observed in this study rarely involved the monosomic chromosome, which means that monosomic tissue cultures could be used to select recessive mutants. Further tests would be needed to demonstrate that the selected gene resides in the monosomic chromosome.Key words: Zea mays, monosomic, trisomic, chromosome, somaclonal variation, karyotype.
Effects of various adjuvants on efficacy of a vaccine against Streptococcus bovis and Lactobacillus spp in cattle (2000)

Results suggest that immunization of feedlot steers against S bovis and Lactobacillus spp with vaccines incorporating Freund adjuvant, QuilA, dextran, or alum as an adjuvant effectively induced high, long-lasting serum anti-S bovis and anti-Lactobacillus IgG concentrations. Of the adjuvants tested, dextran may be the most effective.
Apoptosis of tumor infiltrating effector TIM-3+CD8+ T cells in colon cancer (2015)

TIM-3 functions to enforce CD8+ T cell exhaustion, a dysfunctional state associated with the tolerization of tumor microenvironment. Here we report apoptosis of IFN-γ competent TIM-3+ population of tumor-infiltrating CD8+ T cells in colon cancer. In humans suffering from colorectal cancer, TIM-3+ population is higher in cancer tissue-resident relative to peripheral blood CD8+ T cells. Both the TIM-3+ and TIM-3- cancer tissue-resident CD8+ T cells secrete IFN-γ of comparable levels, although apoptotic cells are more in TIM-3+ compared to TIM-3- population. In mouse CT26 colon tumor model, majority of tumor-infiltrating CD8+ T cells express TIM-3 and execute cytolysis function with higher effector cytokine secretion and apoptosis in TIM-3+ compared to TIM-3- population. The tumor cells secrete galectin-9, which increases apoptosis of tumor-infiltrating CD8+ T cells. Galectin-9/TIM-3 signaling blockade with anti-TIM-3 antibody reduces the apoptosis and in addition, inhibits tumor growth in mice. The blockade increases therapeutic efficacy of cyclophosphamide to treat tumor in mice as well. These results reveal a previously unexplored role of TIM-3 on tumor-infiltrating CD8+ T cells in vivo.
Strain-sensing fabrics for wearable kinaesthetic-like systems (2003)

In recent years, an innovative technology based on polymeric conductors and semiconductors has undergone rapid growth. These materials offer several advantages with respect to metals and inorganic conductors: lightness, large elasticity and resilience, resistance to corrosion, flexibility, impact strength, etc. These properties are suitable for implementing wearable devices. In particular, a sensitive glove able to detect the position and the motion of fingers and a sensorized leotard have been developed. Here, the characterization of the strain-sensing fabric is presented. In the first section, the polymerization process used to realize the strain sensor is described. Then, the thermal and mechanical transduction properties of the strain sensor are investigated and a geometrical parameter to invariantly codify the sensor response during aging is proposed. Finally, a brief outline of ongoing applications is reported.
Induction of functional platelets from mouse and human fibroblasts by p45NF-E2/Maf (2012)

Determinant factors leading from stem cells to megakaryocytes (MKs) and subsequently platelets have yet to be identified. We now report that a combination of nuclear factor erythroid-derived 2 p45 unit (p45NF-E2), Maf G, and Maf K can convert mouse fibroblast 3T3 cells and adult human dermal fibroblasts into MKs. To screen MK-inducing factors, gene expressions were compared between 3T3 cells that do not differentiate into MKs and 3T3-L1 cells known to differentiate into MKs. 3T3 cells transfected with candidate factors were cultured in a defined MK lineage induction medium. Among the tested factors, transfection with p45NF-E2/MafG/MafK lead to the highest frequency of CD41-positive cells. Adult human dermal fibroblasts transfected with these genes were cultured in MK lineage induction medium. Cultured cells had megakaryocytic features, including surface markers, ploidy, and morphology. More than 90% of MK-sized cells expressed CD41, designated induced MK (iMK). Infusion of these iMK cells into immunodeficient mice led to a time-dependent appearance of CD41-positive, platelet-sized particles. Blood samples from iMK-infused into thrombocytopenic immunodeficient mice were perfused on a collagen-coated chip, and human CD41-positive platelets were incorporated into thrombi on the chip, demonstrating their functionality. These findings demonstrate that a combination of p45NF-E2, Maf G, and Maf K is a key determinant of both megakaryopoiesis and thrombopoiesis.
Estimating Road Traffic Congestion using Vehicle Velocity (2006)

This study investigates an alternative way to estimate degrees of road traffic congestion based on routine GPS measurements from main roads in urban areas of Bangkok, Thailand. We classify three levels of traffic congestion according to the weighted exponential moving averages of measured GPS speed. Human perception is used to obtain classification thresholds and evaluated the performance of the proposed method. The benefits of our proposed method over existing techniques is that it is simple, easy to understand, and compatible with existing traffic report systems in Bangkok
SafeMem: Exploiting ECC-Memory for Detecting Memory Leaks and Memory Corruption During Production Runs (2005)

Memory leaks and memory corruption are two major forms of software bugs that severely threaten system availability and security. According to the US-CERT vulnerability notes database, 68% of all reported vulnerabilities in 2003 were caused by memory leaks or memory corruption. Dynamic monitoring tools, such as the state-of-the-art Purify, are commonly used to detect memory leaks and memory corruption. However, most of these tools suffer from high overhead, with up to a 20 times slowdown, making them infeasible to be used for production-runs. This paper proposes a tool called SafeMem to detect memory leaks and memory corruption on-the-fly during production-runs. This tool does not rely on any new hardware support. Instead, it makes a novel use of existing ECC memory technology and exploits intelligent dynamic memory usage behavior analysis to detect memory leaks and corruption. We have evaluated SafeMem with seven real-world applications that contain memory leak or memory corruption bugs. SafeMem detects all tested bugs with low overhead (only 1.6%-14.4%), 2-3 orders of magnitudes smaller than Purify. Our results also show that ECC-protection is effective in pruning false positives for memory leak detection, and in reducing the amount of memory waste (by a factor of 64-74) used for memory monitoring in memory corruption detection compared to page-protection.
Adaptive Query Processing in the Looking Glass (2005)

A great deal of work on adaptive query processing has been done over the last few years: Adaptive query processing has been used to detect and correct optimizer errors due to incorrect statistics or simplified cost metrics; it has been applied to long-running continuous queries over data streams whose characteristics vary over time; and routing-based adaptive query processing does away with the optimizer altogether. Despite this large body of interrelated work, no unifying comparison of adaptive query processing techniques or systems has been attempted; we tackle this problem. We identify three families of systems (plan-based, CQ-based, and routingbased), and compare them in detail with respect to the most important aspects of adaptive query processing: plan quality, statistics monitoring and re-optimization, plan migration, and scalability. We also suggest two new approaches to adaptive query processing that address some of the shortcomings revealed by our in-depth analysis: (1) Proactive re-optimization, where the optimizer chooses query plans with the expectation of reoptimization; and (2) Plan logging, where optimizer decisions under different conditions are logged over time, enabling plan reuse as well as analysis of relevant statistics and benefits of adaptivity. 1
dRAM Design Using the Taper-Isolated Dynamic RAM Cell (1982)

The TI dRAM cell, a MOSFET with two dynamically programmable threshold states, is very attractive for VLSI dRAM's because of its potential 3X density advantage over the one-transistor and -capacitor (1-T) cell, 10X lower leakage at high temperatures compared to the 1-T cell, and its immunity to soft errors. Linear scaling of the 1-T cell by a factor k reduces the available signal by ~k/sup 3/, whereas the charging current for the TI RAM cell is invariant to scaling since the W/L ratio remains constant allowing it to scale to higher density. An experimental array (64 rows by 8 columns), representing a cross section of a 16K dRAM, with on-chip decoding and sensing has been fabricated using the TI RAM cell as the memory element, Using 4-spl mu/m design rules, the cell size was 204 /spl mu/m/sup 2/ due to pitch requirements for the decoder and sense amplifier. This compares with 170-200 /spl mu/m/sup 2/ for the 1-T cell using 2.5-/spl mu/m design rules being fabricated in the 64K dRAM's today. The array which is compatible with 5-V-only operation was designed to provide diagnostic capability rather than speed and shows the data can be accessed 85-100 ns after the CAS signal, In this paper, the physics of the TI RAM cell are discussed as well as circuit considerations for its implementation into an array.
Synthesis of Hydrophobic Derivatives of the G∧C Base for Rosette Nanotube Self-Assembly in Apolar Media (2008)

Eleven self-complementary G/\C derivatives bearing hydrophobic moieties were synthesized and characterized. One representative derivative from this family was shown to self-assemble into rosette nanotubes in hexane and form Langmuir-Blodgett films at the air-water interface.
Combinatorial control of muscle development by basic helix-loop-helix and MADS-box transcription factors. (1996)

Members of the MyoD family of muscle-specific basic helix-loop-helix (bHLH) proteins function within a genetic pathway to control skeletal muscle development. Mutational analyses of these factors suggested that their DNA binding domains mediated interaction with a coregulator required for activation of muscle-specific transcription. Members of the myocyte enhancer binding factor 2 (MEF2) family of MADS-box proteins are expressed at high levels in muscle and neural cells and at lower levels in several other cell types. MEF2 factors are unable to activate muscle gene expression alone, but they potentiate the transcriptional activity of myogenic bHLH proteins. This potentiation appears to be mediated by direct interactions between the DNA binding domains of these different types of transcription factors. Biochemical and genetic evidence suggests that MEF2 factors are the coregulators for myogenic bHLH proteins. The presence of MEF2 and cell-specific bHLH proteins in other cell types raises the possibility that these proteins may also cooperate to regulate other programs of cell-specific gene expression. We present a model to account for such cooperative interactions.
The immune-stimulating peptide WKYMVm has therapeutic effects against ulcerative colitis (2013)

In this study, we examined the therapeutic effects of an immune-stimulating peptide, WKYMVm, in ulcerative colitis. The administration of WKYMVm to dextran sodium sulfate (DSS)-treated mice reversed decreases in body weight, bleeding score and stool score in addition to reversing DSS-induced mucosa destruction and shortened colon. The WKYMVm-induced therapeutic effect against ulcerative colitis was strongly inhibited by a formyl peptide receptor (FPR) 2 antagonist, WRWWWW, indicating the crucial role of FPR2 in this effect. Mechanistically, WKYMVm effectively decreases intestinal permeability by stimulating colon epithelial cell proliferation. WKYMVm also strongly decreases interleukin-23 and transforming growth factor-β production in the colon of DSS-treated mice. We suggest that the potent immune-modulating peptide WKYMVm and its receptor FPR2 may be useful in the development of efficient therapeutic agents against chronic intestinal inflammatory diseases.
Influence of PCR Reagents on DNA Polymerase Extension Rates Measured on Real-Time PCR Instruments (2013)

Simple DNA extension rate assays can be performed on real-time PCR instruments. Activity is decreased by monovalent cations, DNA dyes, and most melting temperature depressors. Rational inclusion of PCR components on the basis of their effects on polymerase extension is likely to be useful in PCR, particularly rapid-cycle or fast PCR.
Statins reduce human blood–brain barrier permeability and restrict leukocyte migration: Relevance to multiple sclerosis (2006)

Our data parallel the previously reported magnetic resonance imaging-based radiological findings and suggest an effect of statins that could be beneficial in early MS, restricting the diffusion of molecular tracers and the migration of immune cells across the human BBB.
Noninvasive Method for Glucose Level Estimation by Saliva (2013)

Aims: Diagnostic devices available in the market to measure blood glucose level require blood as diagnostic body fluid. Hence, necessity arises to find some non-invasive diagnostic mean to measure body glucose level frequently without any discomfort to the patient. The present study was aimed at estimation of blood and salivary glucose level in diabetic and non diabetic subjects.