gebhart/patrepeval huggingface dataset:
Enhancing immune responses for cancer therapy. (2007)

Although the immune system possesses the means to respond to cancer, it often fails to control the spread of malignancy. Nonetheless, equipping endogenous immunity to release a strong antitumor response has significant advantages over conventional therapies. This review explores some of the options available to accomplish this, focusing first on vaccinations with tumor antigens to stimulate the immune system and empower stronger antitumor responses. We then compare and contrast the so-far limited clinical success of vaccination with the well-documented curative potential of adoptive therapy using T lymphocytes transfer. Finally, we highlight novel approaches using T cell receptor (TCR) gene transfer strategy to exploit allogeneic T cell repertoires in conjunction with receptors selected in vitro for defined MHC/peptide combinations, as a basis for antigen-specific gene therapy of cancers.
Mutations in a Protein Tyrosine Phosphatase Gene ( <i>PTP2</i> ) and a Protein Serine/Threonine Phosphatase Gene ( <i>PTC1</i> ) Cause a Synthetic Growth Defect in <i>Saccharomyces cerevisiae</i> (1993)

Two protein tyrosine phosphatase genes, PTP1 and PTP2, are known in Saccharomyces cerevisiae. However, the functions of these tyrosine phosphatases are unknown, because mutations in either or both phosphatase genes have no clear phenotypic effects. In this report, we demonstrate that although ptp2 has no obvious phenotype by itself, it has a profound effect on cell growth when combined with mutations in a novel protein phosphatase gene. Using a colony color sectoring assay, we isolated 25 mutants in which the expression of PTP1 or PTP2 is required for growth. Complementation tests of the mutants showed that they have a mutation in one of three genes. Cloning and sequence determination of one of these gene, PTC1, indicated that it encodes a homolog of the mammalian protein serine/threonine phosphatase 2C (PP2C). The amino acid sequence of the PTC1 product is approximately 35% identical to PP2C. Disruption of PTC1 indicated that the PTC1 function is nonessential. In contrast, ptc1 ptp2 double mutants showed a marked growth defect. To examine whether PTC1 encodes an active protein phosphatase, a glutathione S-transferase (GST)-PTC1 fusion gene was constructed and expressed in Escherichia coli. Purified GST-PTC1 fusion protein hydrolyzed a serine phosphorylated substrate in the presence of the divalent cation Mg2+ or Mn2+. GST-PTC1 also had weak (approximately 0.5% of its serine phosphatase activity) protein tyrosine phosphatase activity.
Dialysis unit and patient characteristics associated with reuse practices and mortality (1998)

The diverse patient and dialysis unit characteristics in the United States pose challenges for assessing the safety and efficacy of reuse practices. A 10% random sample of period-prevalent hemodialysis patients from units practicing conventional dialysis (<25% of patients with high-efficiency/high-flux dialysis) were analyzed. The data included 13,926 patient observations in 1989-1990 and 20,422 in 1991-1993. Centers for Disease Control and Prevention and Health Care Financing Administration facility survey Medicare data were analyzed with a Cox regression model, evaluating the risk of reuse compared with no reuse and adjusting for comorbidity, unit characteristics, and profit status. In 1989-1990, freestanding and hospital-based units that did not reuse dialyzers were not significantly different from each other in mortality rates. In 1991-1993, however, no-reuse, freestanding, for-profit units had higher risks (relative risk [RR] = 1.23, P = 0.003) compared with no-reuse, hospital-based, nonprofit units. No-reuse, hospital-based, for-profit units, in contrast, were associated with a lower mortality risk (RR = 0.70, P = 0.0001). An isolated higher risk associated with peracetic acid manual reuse in freestanding units (1989-1990) was identified in for-profit units only. In the 1991-1993 period, an increased mortality risk was noted in hospital-based, nonprofit units practicing formaldehyde automatic reuse, and in freestanding, for-profit units using glutaraldehyde, which accounted for <5% of all units. All other interactions of reuse germicide and technique were not different from no-reuse. The varying mortality rates identified in both no-reuse and reuse units using conventional dialysis suggest that other factors, such as dialysis therapy and anemia correction (both known predictors of patient survival), have a greater influence on U.S. mortality than reuse germicides and techniques.
Virtual-physical registers (2002)

A novel dynamic register renaming approach is proposed in this work. The key idea of the novel scheme is to delay the allocation of physical registers until a late stage in the pipeline, instead of doing it in the decode stage as conventional schemes do. In this way, the register pressure is reduced and the processor can exploit more instruction-level parallelism. Delaying the allocation of physical registers require some additional artifact to keep track of dependences. This is achieved by introducing the concept of virtual-physical registers, which do not require any storage location and are used to identify dependences among instructions that have not yet allocated a register to its destination operand. Two alternative allocation strategies have been investigated that differ in the stage where physical registers are allocated: issue or write-back. The experimental evaluation has confirmed the higher performance of the latter alternative. We have performed all evaluation of the novel scheme through a detailed simulation of a dynamically scheduled processor. The results show a significant improvement (e.g., 19% increase in IPC for a machine with 64 physical registers in each file) when compared with the traditional register renaming approach.
Use of state diagrams to engineer communications software (1978)

This paper presents our experience with a variation on the use of state diagrams in the development of a communications system. The following techniques are described:- State diagram notation functions as the design language used to describe the functional specification of major program modules.- These modules are coded in a high-level language using the state diagrams as the program structure and specification.- The actual programs are used as input to a simulator which performs a structured walk-through.- Automatically produced state diagrams from final software serve as documentation and act as a check on meeting initial system requirements.
RSS item ranking based on implicit feedback (2010)

Really Simple Syndication(RSS) has been widely used in our daily lives, but RSS doesn't always collect interesting articles, user has to sift through every subscription for articles they like. The ranking of unread RSS articles has the potential power to release user from this heavy burden. Although user preferences can be learned from explicit feedbacks such as rating or tagging, implicit feedback techniques which collect information by monitoring users' natural behavior instead of asking them to explicitly give feedbacks become more attractive. There are several implicit feedbacks including scrolling and gazing, however, some of them may not be effective or require special equipments. In this article, we present a model-based approach for ranking unread RSS items and make recommendations via implicit behavior analysis. Since time spent on reading has been proved to be a useful measurement for user modelling, the approach aims at learning predictive models of user preferences from their implicit feedback of reading time only. User preference are expressed by latent semantic classes, and Bayesian inference with a set of heuristics is used to reveal the probability that an article may attract the user. Experimental evaluation shows substantial improvements over existing methods.
A facile route to N-fused pyrrole lactams (2003)

Institute of Natural Drug of Yunnan Baiyao Group Co., Ltd., Kunming 650032, P.R. China<br> <em>E-mail</em> : yangzhijd@sina.com.cn <em> Fax</em>: 86-0871-4101463<br> <em>Department of Basic Courses of Shenyang Pharmaceutical University, Shenyang 110016, P.R. China</em><br> <em>Manuscript received 19 August 2002, revised 11 February 2003, accepted 1 April 2003</em> <em>N</em>-Fused pyrrole lactams (la-d) were prepared by substitution and cyclization of methyl 1-(2-bromoethane)pyrrole carboxylate in one-pot. The latter was obtained by treatment of methyl pyrrole-2-carboxylate with excess 1,2-dibromoethane containing NaOH in the presences of PTC.
Primary hyperparathyroidism in 29 dogs: diagnosis, treatment, outcome and associated renal failure (2005)

Primary hyperparathyroidism cases with high total calcium were more likely to develop renal failure in this group of dogs; however, the calcium phosphate product did not seem to be a useful predictor. Ultrasound-guided chemical ablation seemed to have limited advantage over surgery.
Air turbine drives: Performance and limitations (1956)

THE practice in modern jet aircraft of using axial-flow jet engine compressors has decreased the number of engine pads available for driving accessories. This, coupled with the presence of a high-pressure air supply as a source of power, has brought about the introduction of the air turbine as a prime mover. Since the energy level of the jet engine bleed air is dependent upon the engine setting, which is in turn dependent upon the airplane flight condition, the design of the turbine drive will be dictated by, first, the flight condition which results in a minimum energy supply to the prime mover and, second, the power that must be developed by the prime mover. These factors will influence the performance of the unit at the airplane cruise condition where air consumption is most critical. The first section of this discussion is concerned with the imposed requirements at the design point, and the penalty involved from the standpoint of performance, at the cruise condition. Subsequent sections will deal with the turbine configuration and the turbine control system response rate.
Ultra trace analysis and electrical characterization of Cu diffusion through thin quasi-amorphous Ta-N-O barriers (1997)

Besides the advantages of Cu-based metallization systems, like lower electrical resistivity and higher electromigration resistance, they have one major drawback-Cu is a fast diffuser into Si and SiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> . Hence, a diffusion or drift barrier is necessary between Cu and Si or SiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> respectively, in order to prevent deterioration of the devices. Many refractory metals and their compounds have been studied, with Ta-based diffusion barriers being among the most promising. Unfortunately, most of these barriers are polycrystalline and provide inadequate protection because they contain grain boundaries that may serve as active diffusion paths for Cu. Depositing an amorphous-like film even very thin (<50 nm) barriers can be used without any danger for the integrity of future ULSI devices. This work focuses on the microanalytical and electrical characterization of 5 to 50 nm thin quasi-amorphous Ta-N-O diffusion barriers in the Cu/Si contact system.
Requirement of Multiple Basic Helix-Loop-Helix Genes for Retinal Neuronal Subtype Specification (2004)

Retinal precursor cells give rise to six types of neurons and one type of glial cell during development, and this process is controlled by multiple basic helix-loop-helix (bHLH) genes. However, the precise mechanism for specification of retinal neuronal subtypes, particularly horizontal neurons and photoreceptors, remains to be determined. Here, we examined retinas with three different combinations of triple bHLH gene mutations. In retinas lacking the bHLH genes Ngn2, Math3, and NeuroD, horizontal neurons as well as other neurons such as bipolar cells were severely decreased in number. In the retina lacking the bHLH genes Mash1, Ngn2, and Math3, horizontal and other neurons were severely decreased, whereas ganglion cells were increased. In the retina lacking the bHLH genes Mash1, Math3, and NeuroD, photoreceptors were severely decreased, whereas ganglion cells were increased. In all cases, glial cells were increased. The increase and decrease of these cells were the result of cell fate changes and cell death and seem to be partly attributable to the remaining bHLH gene expression, which also changes because of triple bHLH gene mutations. These results indicate that multiple bHLH genes cross-regulate each other, cooperatively specify neuronal subtypes, and regulate neuronal survival in the developing retina.
Neuroendocrine-Immune Surveillance of Osteosarcoma: Emerging Hypothesis (2003)

Osteosarcoma is a bone-forming cancer predominantly found in children and adolescents more often than in adults. Osteosarcoma of the gnathic apparatus is relatively rare in the young population, and this condition becomes a concern of clinical dentists for predominantly the middle-aged and aging patient groups. Osteosarcomas are invaded by lymphocytes, which exhibit signs of activation. The immune processes that are engaged within the malignant bone matrix involve the production of cytokines, which regulate the process of apoptotic programmed cell death. This paper discusses the mechanisms by which apoptosis of osteosarcoma cells is modulated by the neuroendocrine-immune system, and potential physiological implications.
Transparent resistive random access memory and its characteristics for nonvolatile resistive switching (2008)

This report covers the fabrication of a fully transparent resistive random access memory (TRRAM) device based on an ITO (indium tin oxide)/ZnO/ITO capacitor structure and its resistive switching characteristics. The fabricated TRRAM has a transmittance of 81% (including the substrate) in the visible region and an excellent switching behavior under 3V. The retention measurement suggests that the memory property of the TRRAM device could be maintained for more than 10years. We believe that the TRRAM device presented in this work could be a milestone of future see-through electronic devices.
Expression of p75<sup>NGFR</sup> trkA, and trkB mRNA in rat C6 glioma and type I astrocyte cultures (1992)

Using a quantitative reverse transcription-polymerase chain reaction (RT-PCR) we have investigated the expression of the neurotrophin receptors p75NGFR, trkA, and trkB mRNAs in cultures of rat pup type I astrocytes and in the C6 rat glioma cell line. All three neurotrophin receptor mRNAs are expressed in both C6 cells and in type I astrocytic cultures. p75NGFR mRNA levels are increased by either cycloheximide or nerve growth factor (NGF) treatment of C6 cells as measured using RT-PCR. Type I astrocyte cultures also expressed p75NGFR mRNA and NGF treatment increased p75NGFR mRNA levels in these cultures. TrkB mRNA levels were increased by cycloheximide treatment of type I astrocyte cultures but not by NGF treatment. Using RT-PCR, trkA mRNA was detected in astrocytic cultures as well as in the rat C6 and PC-12 cell lines. We conclude that cultures of type I astrocytes express active NGF receptors and that glia can elicit a response to NGF as seen by an increase in p75NGFR mRNA levels following exposure to NGF.
The Broad Spectrum of Celiac Disease and Gluten Sensitive Enteropathy (2016)

The celiac disease is an immune chronic condition with genetic transmission, caused by the intolerance to gluten. Gluten is a protein from cereals containing the following soluble proteins: gliadine, which is the most toxic, and the prolamins. The average prevalence is about 1% in USA and Europe, but high in Africa: 5.6% in West Sahara. In the pathogenesis several factors are involved: gluten as external trigger, genetic predisposition (HLA, MYO9B), viral infections, abnormal immune reaction to gluten. Severity is correlated with the number of intraepithelial lymphocytes, cryptic hyperplasia and villous atrophy, as well as with the length of intestinal involvement. The severity is assessed according to the Marsh-Oberhuber staging. Diagnostic criteria are: positive serological tests, intestinal biopsy, the reversal after gluten free diet (GFD). Beside refractory forms, new conditions have been described, like the non celiac gluten intolerance. In a time when more and more people adhere to GFD for nonscientific reasons, practitioners should be updated with the progress in celiac disease knowledge.
Simplified-Traditional Chinese Character Conversion based on Multi- Data Resources: Towards a Fused Conversion Algorithm (2011)

In recent years, communication between Chinese communities in different parts of the world has been on a constant increase. However, between the traditional Chinese character used in Taiwan, Hong Kong and Macao, and the simplified Chinese character used in mainland China and Singapore, extensive differences in both formation and usage may result in unexpected hindrance in verbal communications. Though there are already a lot of conversion methods from researchers and industry companies, the precisions are still not high enough for professional usage especially on one-to-many cases. To solve this seemingly technical but actually linguistically-related problem, this paper proposes a new priority-based multi-data resources management model. With this model, conversion can be more context-sensitive, human controllable, and thus more reliable. A new algorithm called Fused Conversion Algorithm from Multi-Data resources (FCMD) is also presented. This algorithm incorporates the advantages of reverse maximum matching and N-Gram-based statistical model to render the system more responsive to contextual nuances. After parameter training on a huge LDC corpus, the conversion precision of the proposed method reaches 90.2% on one-to-many cases, which are the most difficult part in Chinese character conversion, with an overview precision rate at 99.7%. Its experimental performance in terms of precision and efficiency promises a significant improvement over the state-of-the-art models.
Probabilistic estimation of short sequence expression using RNA-Seq data and the “positional bootstrap” (2016)

Abstract When estimating expression of a transcript or part of a transcript using RNA-seq data, it is commonly assumed that reads are generated uniformly from positions within the transcript. While this assumption is acceptable for long transcript sequences where reads from many positions are averaged, it frequently leads to large errors for short sequences, e.g ., less than 100 bp. Analysis of short sequences, such as when studying splice junctions and microRNAs, is increasingly important and necessitates addressing errors in short-sequence expression estimation. Indeed, when we examined RNA-seq data from diverse studies, we found that large errors are introduced by variations in RNA-seq coverage due to sequence content, experimental conditions and sample preparation. We developed a technique that we call the positional bootstrap, which quantifies the level of uncertainty in expression induced by non-uniform coverage. Unlike methods that attempt to correct for biases in coverage, but do so by making strong assumptions about the form of those biases, the positional bootstrap can quantify the noise induced by all types of bias, including unknown ones. Results obtained using independently generated RNA-seq datasets show that the positional bootstrap increases the accuracy of estimates of alternative splicing levels, tissue-differential alternative splicing and tissue differential expression, by a factor of up to 10. A Python implementation of the algorithm to quantify splicing levels is freely available from github.com/PSI-Lab/BENTO-Seq.
A Monoclonal Antibody to α1β1 Blocks Antigen-induced Airway Responses in Sheep (2003)

The integrin alpha1beta1 (very late antigen-1; CD49a/CD29) is a major adhesion receptor for collagen I, IV, and VI, and its induced expression on activated monocytes and lymphocytes plays a central role in their retention and activation at inflammatory sites in autoimmune pathologies. However, the role of alpha1beta1 in allergic settings has not been explored. In this study, we show that a single 45-mg dose of aerosolized monoclonal antibody AQC2 to the alpha1 chain of human and sheep very late antigen-1, given 30 minutes before challenge, blocks both the allergen-induced late response and the associated airway hyperresponsiveness, functional indicators of allergen-induced inflammation, in sheep. AQC2 does not affect the early response. Consistent with these effects, AQC2 tended to reduce the cell response associated with local antigen instillation. An isotype-matched control antibody had no protective effects. Two humanized versions of AQC2, a wild-type IgG1 and an aglycosyl form of the same monoclonal antibody, which has reduced Fc receptor-mediated effector functions, are equally effective in blocking the antigen-induced late response and airway hyperresponsiveness in the sheep model. These data suggest that mononuclear leukocyte adhesion-dependent pathologies contribute to allergic lung disease and provide proof-of-concept that antagonists of alpha1 integrins may be useful in preventing these events.
On the cutting edge of semiconductor sensors: towards intelligent X-ray detectors (2012)

De breedte van de ongevoelige rand van kristallijne halfgeleidersensoren kan waarschijnlijk gereduceerd worden tot minder dan één pixel. Dit blijkt uit het onderzoek van Marten Bosma. State-of-the-art pixeldetectoren anno 2012 combineren geavanceerde signaalverwerkingselektronica met hoogwaardige kristallijne halfgeleidersensoren. Deze detectoren kunnen daardoor, in vergelijking met hedendaagse medische-radiografiesystemen, met gebruik van een lagere stralingsdosis scherpere röntgenfoto’s maken. Zelfs is het mogelijk om kleurenröntgenfoto’s te maken, hetgeen de diagnostische waarde van een foto significant kan verhogen. Het gelimiteerde oppervlak van de detectoren vormt echter een grote uitdaging om een concurrerend radiodiagnostisch systeem te realiseren. Een getegeld oppervlak van deze relatief kleine detectoren zou daarvoor de oplossing kunnen bieden. Om naden in het uiteindelijke beeld te voorkomen, dienen de afzonderlijke detectormodules gevoelig te zijn over hun volledige oppervlak. Een significante verkleining van de ongevoelige rand van de sensoren draagt bij aan de realisatie van zo’n module en is daarom een stap in de richting naar toekomstige intelligente en dosisefficiënte radiografiesystemen van groot formaat.