gebhart/patrepeval huggingface dataset:
Blocking of monocyte-associated B7-H1 (CD274) enhances HCV-specific T cell immunity in chronic hepatitis C infection (2007)

The establishment of a chronic hepatitis C (CHC) infection is associated with defective HCV-specific T cell responses. Recent studies suggest that negative T cell regulators such as programmed death 1 (PD-1) contribute to the impairment of virus-specific T cell functions in chronic viral infections. However, the implication of peripheral monocytes from CHC patients in the inhibition of HCV-specific T cell responses is only partially defined. In this study, we found that B7-H1, a ligand of PD-1, was significantly up-regulated on monocytes of CHC patients. Proliferation of T cells in response to anti-CD3 antibody was directly suppressed by B7-H1+CD14+ monocytes, and this suppression was reversed by addition of antagonistic B7-H1 mAb. Furthermore, blocking of monocyte-associated B7-H1 (moB7-H1) significantly enhanced the frequency of IFN-gamma-producing, HCV-specific CD4+ and CD8+ effector T cells and the production of Th1 cytokines, such as IL-2 but not Th2 cytokines, including IL-4 and IL-10. Upon B7-H1 blockade, production of perforin was also increased in CD8+ T cells stimulated with HCV peptides. Our findings suggest that moB7-H1 inhibits HCV-specific CD4+ and CD8+ T lymphocyte proliferation and suppresses Th1 cytokine production and perforin secretion. Blockade of the B7-H1 pathway thus represents an attractive approach in the treatment of chronic HCV infection.
Creating the Sydney York Morphological and Acoustic Recordings of Ears Database (2013)

This paper introduces the process for creating the Sydney York Morphological and Acoustic Recordings of Ears (SYMARE) database. The SYMARE database supports research exploring the relationship between the morphology of human outer ears and their acoustic filtering properties-a relationship that is viewed by many as holding the key to human spatial hearing and the future of 3D personal audio. The SYMARE database is comprised of acoustically measured head-related impulse responses for 61 listeners (48 male/13 female), multiple high-resolution surface mesh models (upper torso, head and ears) for these listeners obtained from magnetic resonance imaging (MRI) data, and the corresponding simulated HRIR data for these listeners generated using the Fast Multipole Boundary Element Method (FM-BEM). In this work, we compare acoustically measured HRIR data for 61 listeners with the listeners' corresponding simulated HRIR data generated using the FM-BEM.
Gold Nanoparticle Chemiresistor Sensor Array that Differentiates between Hydrocarbon Fuels Dissolved in Artificial Seawater (2010)

Gold nanoparticle films (Au(NPF)) functionalized with a range of hydrophobic and hydrophilic thiols were assembled in chemiresistor sensor arrays that were used to differentiate between complex mixtures of analytes in the aqueous phase. A chemiresistor array sampled a simple system of linear alcohols (methanol, ethanol, propan-1-ol, and butan-1-ol) dissolved in water over a range of concentrations. Discriminant analysis confirmed that the response patterns of the array could be used to successfully distinguish between the different alcohol solutions at concentrations above 20 mM for all of the alcohols except methanol, which was distinguished at concentrations above 200 mM. Alcohol solutions more dilute than these concentrations had response patterns that were not consistently recognizable and failed cross validation testing. This defined the approximate limit of discrimination for the system, which was close to the limits of detection for the majority of the individual sensors. Another Au(NPF) chemiresistor array was exposed to, and successfully identified crude oil, diesel, and three varieties of gasoline dissolved in artificial seawater at a fixed concentration. This work is a demonstration that the pattern of responses from an array of differently functionalized Au(NPF) sensors can be used to distinguish analytes in the aqueous phase.
Cell cycle and apoptosis deregulation in classical Hodgkin lymphomas. (2005)

Classical Hodgkin lymphomas (cHL) have now been recognized as B-cell lymphomas with some exceptional cases of T-cell origin. In recent years, there has been accumulating evidence that Hodgkin and Reed-Sternberg (H/RS) cells, the presumed neoplastic-cell population in cHL, are characterized by a profound disturbance of the cell cycle and apoptosis regulation. The constitutive activation of the nuclear factor (NF)-kappaB pathway, which is considered to be involved in the proliferation and survival of H/RS cells. Moreover, substantial evidence that H/RS cells have defective cell cycle and apoptosis regulation has been provided by studies showing that these cells are characterized, in a large proportion of cases, by alterations of the p53, Rb and p27 tumor suppressor pathways, overexpression of cyclins involved in the G1/S and G2/M transition such as cyclins E, D2, D3, A and B1, overexpression of cyclin-dependent kinases such as CDK1, 2 and 6 and overexpression of anti-apoptotic proteins such as c-FLIP, bcl-xl, c-IAP2, X-linked I4P and survivin. Recent studies suggest that interleukin 13 (IL-13) is an important growth and survival factor in H/RS cells. Furthermore, the Epstein-Barr Virus (EBV), which is present in H/RS cells in about 30-50% of cHL, has been shown to affect the cell cycle and apoptosis regulation in cHL. The present review summarizes data with respect to the cell cycle and apoptosis deregulation in cHL.
Least-squares design of IIR filters with prescribed magnitude and phase responses and a pole radius constraint (2000)

This paper presents a method for the frequency domain design of infinite impulse response (IIR) digital filters. The proposed method designs filters approximating prescribed magnitude and phase responses. IIR filters of this kind can have approximately linear-phase responses in their passbands, or they can equalize magnitude and phase responses of given systems. In many cases, these filters can be implemented with less memory and with fewer computations per output sample than equivalent finite impulse response (FIR) digital filters. An important feature of the proposed method is the possibility to specify a maximum radius for the poles of the designed rational transfer function. Consequently, stability can be guaranteed, and undesired effects of implementations using fixed-point arithmetic can be alleviated by restricting the poles to keep a prescribed distance from the unit circle. This is achieved by applying Rouche's theorem in the proposed design algorithm. We motivate the use of IIR filters with an unequal number of poles and zeros outside the origin of the complex plane. In order to satisfy simultaneous specifications on magnitude and phase responses, it is advantageous to use IIR filters with only a few poles outside the origin of the z-plane and an arbitrary number of zeros. Filters of this type are a compromise between IIR filters with optimum magnitude responses and phase-approximating FIR filters. We use design examples to compare filters designed by the proposed method to those obtained by other methods. In addition, we compare the proposed general IIR filters with other popular more specialized structures such as FIR filters and cascaded systems consisting of frequency-selective IIR filters and phase-equalizing allpass filters.
Expression and functional characterization of FOXP3+CD4+ regulatory T cells in ulcerative colitis (2006)

There is an expansion of FOXP3+CD4+ T cells in mucosal lymphoid tissues in UC. CD4+CD25+ isolated from UC MLN express FOXP3 and display features of TR cells in spite of active mucosal inflammation. These data suggest that their suppressor activity may be abrogated in vivo or they are unable to counterbalance the chronic mucosal inflammation in UC.
Improving effects of the mushroom Yamabushitake (Hericium erinaceus) on mild cognitive impairment: a double‐blind placebo‐controlled clinical trial (2008)

A double-blind, parallel-group, placebo-controlled trial was performed on 50- to 80-year-old Japanese men and women diagnosed with mild cognitive impairment in order to examine the efficacy of oral administration of Yamabushitake (Hericium erinaceus), an edible mushroom, for improving cognitive impairment, using a cognitive function scale based on the Revised Hasegawa Dementia Scale (HDS-R). After 2 weeks of preliminary examination, 30 subjects were randomized into two 15-person groups, one of which was given Yamabushitake and the other given a placebo. The subjects of the Yamabushitake group took four 250 mg tablets containing 96% of Yamabushitake dry powder three times a day for 16 weeks. After termination of the intake, the subjects were observed for the next 4 weeks. At weeks 8, 12 and 16 of the trial, the Yamabushitake group showed significantly increased scores on the cognitive function scale compared with the placebo group. The Yamabushitake group's scores increased with the duration of intake, but at week 4 after the termination of the 16 weeks intake, the scores decreased significantly. Laboratory tests showed no adverse effect of Yamabushitake. The results obtained in this study suggest that Yamabushitake is effective in improving mild cognitive impairment.
PSMA-Targeted Radionuclide Therapy of Metastatic Castration-Resistant Prostate Cancer with 177Lu-Labeled PSMA-617 (2016)

(177)Lu-PSMA-617 is a promising new option for therapy of mCRPC and deserves more attention in larger prospective trials.
Evaluating the Effects of Culture and Etiquette on Human-Computer Interaction and Human Performance. (2009)

We claim that ideas of etiquette can be expanded and util-ized to facilitate, inform, and predict human-computer in-teraction and perceptions. By expanding on the qualitative model of etiquette proposed by Brown and Levinson we created a quantitative, computational model of etiquette that allows a machine to interpret and display politeness. This model was then embedded into a testbed and a series of experiments involving human task performance were completed to test various hypotheses related to the model. Relevant compliance data (e.g., accuracy, response time, attitudes, etc.) were obtained as dependent variables. The results show that the variables included in our model have important effects on subjects ’ decision making and per-formance in our experimental tasks. The results also dem-onstrate that variations in etiquette can result in objective, measurable consequences in human+machine performance.
Mechanism of plasmid delivery by hydrodynamic tail vein injection. II. Morphological studies (2006)

Our studies suggest an alternative or additional pathway for naked DNA into hepatocytes besides direct entry via membrane pores. It may be difficult to prove which of these pathways lead to gene expression, but the membrane pore hypothesis alone appears insufficient to explain why expression happens preferentially in hepatocytes. Further study is needed to delineate the importance of each of these putative pathways and their interrelationship in enabling oligonucleotide (siRNA) activity and pDNA expression.
Regulation of Adult Bone Mass by the Zinc Finger Adapter Protein Schnurri-3 (2006)

Genetic mutations that disrupt osteoblast function can result in skeletal dysmorphogenesis or, more rarely, in increased postnatal bone formation. Here we show that Schnurri-3 (Shn3), a mammalian homolog of the Drosophila zinc finger adapter protein Shn, is an essential regulator of adult bone formation. Mice lacking Shn3 display adult-onset osteosclerosis with increased bone mass due to augmented osteoblast activity. Shn3 was found to control protein levels of Runx2, the principal transcriptional regulator of osteoblast differentiation, by promoting its degradation through recruitment of the E3 ubiquitin ligase WWP1 to Runx2. By this means, Runx2-mediated extracellular matrix mineralization was antagonized, revealing an essential role for Shn3 as a central regulator of postnatal bone mass.
Loss of RD1 contributed to the attenuation of the live tuberculosis vaccines Mycobacterium bovis BCG and Mycobacterium microti (2002)

Although large human populations have been safely immunized against tuberculosis with two live vaccines, Mycobacterium bovis BCG or Mycobacterium microti, the vole bacillus, the molecular basis for the avirulence of these vaccine strains remains unknown. Comparative genomics has identified a series of chromosomal deletions common to both virulent and avirulent species but only a single locus, RD1, that has been deleted from M. bovis BCG and M. microti. Restoration of RD1, by gene knock-in, resulted in a marked change in colonial morphology towards that of virulent tubercle bacilli. Three RD1-encoded proteins were localized in the cell wall, and two of them, the immunodominant T-cell antigens ESAT-6 and CFP-10, were also found in culture supernatants. The BCG::RD1 and M. microti::RD1 knock-ins grew more vigorously than controls in immunodeficient mice, inducing extensive splenomegaly and granuloma formation. Increased persistence and partial reversal of attenuation were observed when immunocompetent mice were infected with the BCG::RD1 knock-in, whereas BCG controls were cleared. Knocking-in five other RD loci did not affect the virulence of BCG. This study describes a genetic lesion that contributes to safety and opens new avenues for vaccine development.
Biomarkers in early breast neoplasia (1993)

Early breast neoplasia may be defined in many ways. Any non-invasive or invasive but nonmetastatic breast cancer qualifies as early neoplasia in the sense that they are non-lethal. Before we can prevent lethal breast cancer, we must gain a better understanding of the biological abnormalities underlying its development and progression. Many studies into the mechanisms of breast cancer evolution have evaluated potential precursor lesions (e.g., proliferative disease without atypia [PDWA], atypical ductal hyperplasia [ADH], and ductal carcinoma in situ [DCIS]) for genetic alterations known to occur in fully developed invasive carcinomas. This approach has shed some light on events which may be important in early malignant transformation, including the observations that overexpression of the c-erbB-2 oncogene and mutations of the p53 tumor suppressor gene are present in significant subsets of DCIS, but not PDWA or ADH. This approach is limited by our incomplete knowledge of cancer genetics. However, there is more to learn by evaluating known cancer-associated genes in potential precursor lesions using established techniques such as immunohistochemistry and in situ hybridization. Until recently, technology could not detect unknown genetic abnormalities in microscopic lesions such as PDWA, ADH, or DCIS. Now, PCR-based techniques have the theoretical ability to detect novel tumor promoter and suppressor genes in clinical samples of these very small lesions. For example, suppressor-type genes may be detected using comprehensive mapping probes to identify loss of heterozygosity in PCR-amplified DNA extracted from a few hundred cells microdissected from either fresh or archival tissue.(ABSTRACT TRUNCATED AT 250 WORDS)
Iron species in iron homeostasis and toxicity (1995)

Iron homeostasis in prokaryotic cells appears to be regulated essentially at the level of the genome by the Fur protein. When iron is in short supply the uptake and assimilation pathways are de-repressed and siderophores are synthesized together with the outer, inner (plasma) membrane, periplasmic and cytosolic components necessary for the uptake of ferri-siderophores. When iron is no longer limiting the Fe2+ the Fur complex acts as a transcriptional repressor, and shuts down the synthesis of all the components of iron assimilation. In euykarotic cells, iron homeostasis is dependent upon the iron regulatory factor (IRF), a cytoplasmic protein that can bind to specific stem loops, iron responsive elements (IREs) on the messenger ribonucleic acid molecules (mRNAs) of proteins involved in iron storage (ferritin), utilization (erythroid delta-aminolaevulinate synthase, AIS), and uptake (transferrin receptor). During ion depletion the IRE is in a high affinity form, which, by binding strongly to the corresponding mRNAs, down regulates iron storage and utilization, while up-regulating transferrin receptor expression. When the cells are iron replete, IRF binding to IREs is weak, allowing transferrin receptor mRNA to be degraded. In this paper it is shown that in physiological conditions of iron overload and depletion, IRF functions in vivo in the manner already described for in vitro models. The nature and the speciation of the various iron species within the low molecular weight pool of eukaryotic cells remains unclear.
Demonstration of Inhibition of Mediator Release From Human Mast Cells by Azatadine Base (1986)

In vitro experimentation using dispersed human lung mast cells demonstrated that azatadine base, a compound with known H1-antihistamine properties, inhibited anti-IgE-induced release of histamine and leukotriene C4 by 45% and 85%, respectively. To assess the clinical relevance of these findings and to compare in vitro mast cell data with results obtained in vivo, nasally instilled azatadine was tested in a double-blind, placebo-controlled clinical trial in which nasal challenges with antigen were performed on eight allergic individuals. Pretreatment with azatadine significantly suppressed the number of sneezes following antigen challenge and inhibited the associated elevations in histamine, kinins, and enzyme(s) hydrolyzing the artificial substrate N-alpha-tosyl-L-arginine-methyl-ester in nasal secretions, whereas placebo was inactive. Hence, we showed agreement between our in vitro and in vivo experimental models of the allergic reaction. Topical application of azatadine base has the potential to become an effective antiallergic treatment.
Electron mobilities in gallium, indium, and aluminum nitrides (1994)

Electron mobilities in GaN and InN are calculated, by variational principle, as a function of temperature for carrier concentrations of 1016, 1017, and 1018 cm−3 with compensation ratio as a parameter. Both GaN and InN have maximum mobilities between 100 and 200 K, depending on the electron density and compensation ratio, with lower electron density peaking at lower temperature. This is due to the interplay of piezoelectric acoustic phonon scattering at low carrier concentrations and ionized impurity scattering at higher carrier concentrations. Above 200 K, polar mode optical phonon scattering is the mobility limiting process. The 300 and 77 K electron and Hall mobilities as functions of carrier concentration in the range of 1016–1020 cm−3 and compensation ratio are also calculated. The theoretical maximum mobilities in GaN and InN at 300 K are about 1000 and 4400 cm2 V−1 s−1, respectively, while at 77 K the limits are beyond 6000 and 30 000 cm2 V−1 s−1, respectively. We compare the results with experimental data and find reasonable correlation, but with evidence that structural imperfection and heavy compensation play important roles in the material presently available. Only phonon limited scattering processes are considered in the calculation of the mobility in AlN since it is an insulator of extremely low carrier concentration. We find a phonon limited electron mobility of about 300 cm2 V−1 s−1 at 300 K.
Integrated modeling of clinical and gene expression information for personalized prediction of disease outcomes (2004)

We describe a comprehensive modeling approach to combining genomic and clinical data for personalized prediction in disease outcome studies. This integrated clinicogenomic modeling framework is based on statistical classification tree models that evaluate the contributions of multiple forms of data, both clinical and genomic, to define interactions of multiple risk factors that associate with the clinical outcome and derive predictions customized to the individual patient level. Gene expression data from DNA microarrays is represented by multiple, summary measures that we term metagenes; each metagene characterizes the dominant common expression pattern within a cluster of genes. A case study of primary breast cancer recurrence demonstrates that models using multiple metagenes combined with traditional clinical risk factors improve prediction accuracy at the individual patient level, delivering predictions more accurate than those made by using a single genomic predictor or clinical data alone. The analysis also highlights issues of communicating uncertainty in prediction and identifies combinations of clinical and genomic risk factors playing predictive roles. Implicated metagenes identify gene subsets with the potential to aid biological interpretation. This framework will extend to incorporate any form of data, including emerging forms of genomic data, and provides a platform for development of models for personalized prognosis.
The Cervical Sympathetic Nerves in Surgery of the Neck (1991)

The otolaryngologist-head and neck surgeon is aware that the cervical sympathetic nerves lie behind the carotid artery and should be avoided during neck surgery. To render this sketchy dictum more tangible, relevant anatomy and physiology of the autonomic supply to the head and neck is reviewed, as are aspects of site-of-lesion testing, with respect to Horner's syndrome. Examples of neck operations during which the cervical sympathetic chain--from the base of skull to the root of the neck--may be injured are illustrated.
Enzymatic digestibility and pretreatment degradation products of AFEX‐treated hardwoods (Populus nigra) (2009)

There is a growing need to find alternatives to crude oil as the primary feed stock for the chemicals and fuel industry and ethanol has been demonstrated to be a viable alternative. Among the various feed stocks for producing ethanol, poplar (Populus nigra x Populus maximowiczii) is considered to have great potential as a biorefinery feedstock in the United States, due to their widespread availability and good productivity in several parts of the country. We have optimized AFEX pretreatment conditions (180 degrees C, 2:1 ammonia to biomass loading, 233% moisture, 30 minutes residence time) and by using various combinations of enzymes (commercical celluloses and xylanases) to achieve high glucan and xylan conversion (93 and 65%, respectively). We have also identified and quantified several important degradation products formed during AFEX using liquid chromatography followed by mass spectrometry (LC-MS/MS). As a part of degradation product analysis, we have also quantified oligosaccharides in the AFEX water wash extracts by acid hydrolysis. It is interesting to note that corn stover (C4 grass) can be pretreated effectively using mild AFEX pretreatment conditions, while on the other hand hardwood poplar requires much harsher AFEX conditions to obtain equivalent sugar yields upon enzymatic hydrolysis. Comparing corn stover and poplar, we conclude that pretreatment severity and enzymatic hydrolysis efficiency are dictated to a large extent by lignin carbohydrate complexes and arabinoxylan cross-linkages for AFEX.