gebhart/patrepeval huggingface dataset:
The representation of uncertainty in medical expert systems (1989)

The development of the rule-based expert system has provided important new techniques for the representation of knowledge. However, continued use of this representational scheme has highlighted some of its deficiencies. In particular, many within scientific and non-scientific fields attempting to use the rule-base design to describe natural phenomena often find it difficult to represent the complexities of the world as 'absolute' rules. For this reason, many investigators acknowledge the need to add an uncertainty mechanism to the rule-base construct. Such a facility would allow the quantification of accuracy or strength of association within individual rules Although agreement exists on the need for an uncertainty representation facility, the debate concerning the most appropriate methodology is far from resolved. The purpose of this paper is to provide a review and commentary on the current state of debate over the five most popular candidate uncertainty models: symbolic representation, MYCIN certainty factors, Bayesian, Dempster-Shafer and fuzzy set logic. The advantages and disadvantages of each uncertainty calculi will be presented and assessed with respect to their applicability to the medical expert systems domain.
Identification of regions in polyomavirus middle T and small t antigens important for association with protein phosphatase 2A (1995)

Two subunits of protein phosphatase 2A (PP2A) have been shown previously to bind to the small t and middle T antigens (ST and MT, respectively) of polyomavirus. To determine sequences important for binding of PP2A to ST and MT, we first constructed a series of ST mutants in regions known to be important for biological activity of ST and MT. Several mutations in two small regions just amino terminal to the Cys-X-Cys-X-X-Cys motifs of ST and MT abolished PP2A binding to ST in vitro. Parallel mutations were constructed in MT to investigate the role of PP2A binding in the function of polyomavirus MT. Wild-type and mutant MT proteins were stably expressed in NIH 3T3 cells and analyzed (i) for their ability to induce transformation and (ii) for associated cellular proteins and corresponding enzymatic activities previously described as associating with wild-type MT. A number of the mutant MTs were found to be defective in binding of PP2A as assayed by coimmunoprecipitation. In contrast, a deletion of the highly conserved stretch of amino acids 42 to 47 (His-Pro-Asp-Lys-Gly-Gly) in the ST-MT-large T antigen common region did not affect PP2A binding to MT. MT mutants defective for PP2A binding were also defective in transformation, providing further evidence that association with PP2A is important for the ability of MT to transform cells. All mutants which were impaired for PP2A binding were similarly or more dramatically impaired for associated protein and lipid kinase activities, supporting the possibility that PP2A binding is necessary for the formation and/or stability of an MT-pp60c-src complex.
Incidence of early pseudo‐progression in a cohort of malignant glioma patients treated with chemoirradiation with temozolomide (2008)

Up to 50% of malignant glioma patients treated with RT/TMZ and progression immediately after RT develop pseudo-progression. The current study data support the idea to continue TMZ in the case of progressive lesions immediately after RT/TMZ. Surgery should be considered in symptomatic cases. The inclusion of patients with progressive lesions developing directly after chemoradiation in studies regarding recurrent gliomas will lead to an overestimation of the results.
A functional antibody mutant with an insertion in the framework region 3 loop of the VH domain: implications for antibody engineering (1992)

We have studied the effects of a four residue insertion into the FR3 loop of the heavy chain variable region from the anti-NP antibody B1-8. The insertion mutant is obtained as secreted antibody without major defects in biosynthesis, indicating that antibody variable domains can accommodate length variation not only in complementarity determining regions (CDRs), but also in framework region (FR) loops. The B1-8 antigen binding site is not affected by the change in a neighbouring loop. FR3 insertions represent a new method of antibody engineering with a potential to obtain strong antigen binding by designing additional antigen contacting residues.
Molecular cloning of a novel member of the immunoglobulin gene superfamily homologous to the polymeric immunoglobulin receptor (1992)

The CMRF35 monoclonal antibody recognizes a cell membrane antigen present on the surface of monocytes, neutrophils, a proportion of peripheral blood T and B lymphocytes and lymphocytic cell lines. Initial studies with CMRF35 suggested an unusual pattern of serological reactivity which did not correspond to any of the known leukocyte differentiation antigen clusters. We describe here the cloning and sequencing of a cDNA encoding the CMRF35 antigen by means of expression in COS cells and immunoselection with the CMRF35 monoclonal antibody. The cDNA encodes a novel integral membrane glycoprotein of 224 amino acids that represents a new member of the immunoglobulin (Ig) gene superfamily. The molecule comprises (a) a single extracellular Ig variable domain remarkably similar to the Fc receptor for polymeric IgA and IgM, (b) a membrane-proximal domain containing a high proportion of proline, serine and threonine residues that was predicted to be heavily O-glycosylated, (c) an unusual transmembrane anchor that contained a glutamic acid and a proline residue and (d) a short cytoplasmic tail. Transcripts encoding the CMRF35 protein were detected in early monocytic cell lines, in peripheral blood T cells and in some B lymphoblastoid cell lines, confirming the results of immunocytological staining. However, the level of CMRF35 expression on peripheral blood T cells was shown to decrease in response to mitogenic stimulation. The likelihood that the CMRF35 antigen shares a common evolutionary ancestor with the poly Ig Fc receptor is discussed.
Three‐Dimensional Biochemical and Biomechanical Patterning of Hydrogels for Guiding Cell Behavior (2006)

The ability to spatially tailor material biomechanical and biochemical properties at the microscale and to create freeform 3D patterns and gradients within existing photoactive networks (see figure) is demonstrated. The ability of patterned substrates to guide cell migration is also shown.
Application of serum proteomics to the Women's Health Initiative conjugated equine estrogens trial reveals a multitude of effects relevant to clinical findings (2009)

ClinicalTrials.gov identifier: NCT00000611.
A CMOS transceiver analog front-end for gigabit ethernet over CAT-5 cables (2002)

As Fast Ethernet (100Base-T) proliferates and becomes the leading standard in local area networks (LAN), demand for gigabit ethernet increases rapidly. Although fiber-optic gigabit transceivers (1000FX) are available, the high cost of fiber modules and fiber cables limits deployment of 1000FX transceivers to switch uplinks and backbone connections. An integrated CMOS transceiver for gigabit ethernet over unshielded twisted pair (UTP) category-5 (CAT-5) cables significantly reduces cost while providing high data bandwidth at relatively low power consumption. A full-duplex transmission allows up to 2 Gb/s data throughput. Furthermore, compatibility with existing cabling infrastructure allows rapid deployment of 1000Base-T transceivers on desktop and laptop PCs.
A history of microarrays in biomedicine (2005)

The fundamental strategy of the current postgenomic era or the era of functional genomics is to expand the scale of biologic research from studying single genes or proteins to studying all genes or proteins simultaneously using a systematic approach. As recently developed methods for obtaining genome-wide mRNA expression data, oligonucleotide and DNA microarrays are particularly powerful in the context of knowing the entire genome sequence and can provide a global view of changes in gene expression patterns in response to physiologic alterations or manipulation of transcriptional regulators. In biomedical research, such an approach will ultimately determine biologic behavior of both normal and diseased tissues, which may provide insights into disease mechanisms and identify novel markers and candidates for diagnostic, prognostic and therapeutic intervention. However, microarray technology is still in a continuous state of evolution and development, and it may take time to implement microarrays as a routine medical device. Many limitations exist and many challenges remain to be achieved to help inclusion of microarrays in clinical medicine. In this review, a brief history of microarrays in biomedical research is provided, including experimental overview, limitations, challenges and future developments.
Detection of moving objects in natural scenes by a stochastic multi-feature analysis of video sequences (2002)

A new technique for the detection and description of moving objects in natural scenes is presented which is based on an object-oriented, statistical multi-feature analysis of video sequences. In most conventional schemes for the detection of moving objects, temporal differences of subsequent images from a video sequence are evaluated in a block based manner by so called change detection algorithms. These methods are based on the assumption that significant temporal changes of an image signal are caused by moving objects in the scene. However, as temporal changes of an image signal can as well be caused by many other sources (camera noise, varying illumination, small camera motion, trees in motion), such systems are afflicted with the dilemma of either causing many false alarms or failing to detect relevant events. To scope with this problem, the additional features texture and motion beyond temporal signal differences are extracted and evaluated in the new algorithm. Furthermore, these features are evaluated in an object-oriented instead of a block oriented fashion to increase the reliability of detection. The adaption of this method to normal fluctuations of the observed scene is performed by a time-recursive space-variant estimation of the temporal probability distributions of the different features (signal difference, texture and motion). Feature data which differ significantly from the estimated distributions are interpreted to be caused by moving objects.
Crystallographic studies of perovskite-like compounds. II. Rare earth alluminates (1956)

The aluminates of the trivalent ions of Gd, Eu, and Sm are isostructural with GdFeO 3. They belong to space group YD~-Pbnm with four distorted perovskite units in the true crystallographic cell. The aluminates of the trivalent ions of Nd, Pr and La are rhombohedral belonging to space group D~d--R3m with two formula units in the unit cell. These crystals bear a very close structural relationship to the orthorhombie ones.
Subatmospheric pressure wound therapy and the vacuum-assisted closure device: basic science and current clinical successes (2006)

This article reviews the development, current theories behind the mechanism of action and clinical use of subatmospheric pressure wound therapy with the vacuum-assisted closure device. An evolving list of indications for subatmospheric pressure therapy is discussed including its use in chronic wounds, traumatic wounds and orthopedic salvage, infected sternal wounds, management of the open abdomen, enterocutaneous fistulae, burn wounds, skin grafts and dermal substitutes, as well as systemic disease processes, such as myoglobinuria. The vacuum-assisted closure device Instill system is also reviewed, in which subatmospheric pressure therapy has been combined with the instillation of therapeutic solutions for the treatment of difficult infected wounds.
Range image acquisition with a single binary-encoded light pattern (1990)

The problem of strike identification in range image acquisition systems based on triangulation with periodically structured illumination is discussed. A coding scheme is presented based on a single fixed binary encoded illumination pattern, which contains all the information required to identify the individual strikes visible in the camera image. Every sample point indicated by the light pattern is made identifiable by means of a binary signature, which is locally shared among its closest neighbors. The applied code is derived from pseudonoise sequences, and it is optimized so that it can make the identification fault-tolerant to the largest extent. A prototype measurement system based on this coding principle is presented. Experimental results obtained with the measurement system are also presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A PDZ domain‐based assay for measuring HIV protease activity: Assay design considerations (2003)

We have recently described a biochemical detection method for peptide products of enzymatic reactions based on the formation of PDZ domain*peptide ligand complexes. The product sensor is based on using masked or cryptic PDZ domain peptide ligands as enzyme substrates. Upon enzymatic processing, a PDZ-binding motif is exposed, and the product sequence bound specifically by a Eu(3+)chelate-labeled GST-PDZ ([Eu(3+)]GST-PDZ). The practical applicability of this PDZ-based detection method is determined by the affinity of the PDZ domain*peptide ligand interaction, and the efficiency of the enzyme to process the masked peptide ligand. To expand the use of this PDZ-based detection strategy to a broader range of enzymatic assays, we have taken advantage of the plasticity in ligand recognition by the variety of PDZ domains found in nature. In the original work, the PDZ3 of PSD-95 was used, which preferentially recognizes the consensus sequence Ser-X-Val-COOH. Here, we show that NHERF PDZ1, which binds to the consensus sequence Thr/Ser-X-Leu-COOH, can be used to extend the flexibility in the recognition of the carboxy-terminal amino acid of the ligand, and monitor the enzymatic activity of HIV protease. The choices of detection format, for example, TRET or ALPHA, were also investigated and influenced assay design.
Absence of Ret Signaling in Mice Causes Progressive and Late Degeneration of the Nigrostriatal System (2007)

Support of ageing neurons by endogenous neurotrophic factors such as glial cell line-derived neurotrophic factor (GDNF) and brain-derived neurotrophic factor (BDNF) may determine whether the neurons resist or succumb to neurodegeneration. GDNF has been tested in clinical trials for the treatment of Parkinson disease (PD), a common neurodegenerative disorder characterized by the loss of midbrain dopaminergic (DA) neurons. BDNF modulates nigrostriatal functions and rescues DA neurons in PD animal models. The physiological roles of GDNF and BDNF signaling in the adult nigrostriatal DA system are unknown. We generated mice with regionally selective ablations of the genes encoding the receptors for GDNF (Ret) and BDNF (TrkB). We find that Ret, but not TrkB, ablation causes progressive and adult-onset loss of DA neurons specifically in the substantia nigra pars compacta, degeneration of DA nerve terminals in striatum, and pronounced glial activation. These findings establish Ret as a critical regulator of long-term maintenance of the nigrostriatal DA system and suggest conditional Ret mutants as useful tools for gaining insights into the molecular mechanisms involved in the development of PD.
Human Papillomavirus Infection and Cervical Cancer in Latin America (1989)

To evaluate a possible association between infection with human papillomavirus (HPV) and cervical cancer, we performed a multicenter case-control study in Latin America of 759 cases of invasive cervical cancer and 1467 randomly selected age-matched controls. Demographic, sexual, behavioral, and other clinical data were obtained by interview, and HPV DNA was assayed in cervical-swab specimens with use of filter in situ hybridization. Cervical infection with HPV 16 or 18 or both was strongly associated with cervical cancer. HPV DNA was detected in 62 percent of the cases but only 32 percent of the controls, and the relative risk of cancer increased from 2.1 (95 percent confidence interval, 1.6 to 2.8) to 9.1 (6.1 to 13.6) with hybridization reactions of increasing strength. Although the number of sexual partners, age at first intercourse, number of live births, and Pap-smear history were also significant risk factors, the strong associations between infection with HPV 16 or 18 or both and cervical cancer persisted after we adjusted for these variables. These observations are consistent with the hypothesis that genital infection with HPV 16 or 18 may have a role in the pathogenesis of cervical cancer. Other well-known risk factors were also identified in the study, but they did not affect the association between HPV and cervical cancer.
Four New Members Expand the Interleukin-1 Superfamily (2000)

We report here the cloning and characterization of four new members of the interleukin-1 (IL-1) family (FIL1delta, FIL1epsilon, FIL1zeta, and FIL1eta, with FIL1 standing for "Family of IL-1"). The novel genes demonstrate significant sequence similarity to IL-1alpha, IL-1beta, IL-1ra, and IL-18, and in addition maintain a conserved exon-intron arrangement that is shared with the previously known members of the family. Protein structure modeling also suggests that the FIL1 genes are related to IL-1beta and IL-1ra. The novel genes form a cluster with the IL-1s on the long arm of human chromosome 2.
Construction of Linear Polymers, Dendrimers, Networks, and Other Polymeric Architectures by Copper‐Catalyzed Azide‐Alkyne Cycloaddition “Click” Chemistry (2008)

DOI: 10.1002/marc.200800208 Unfortunately, an incorrect affiliation was processed. The correct version is shown below: We would like to apologize for any inconvenience this mistake may have caused!
Elevated blood pressure and enhanced myocardial contractility in mice with severe IGF-1 deficiency. (1996)

To circumvent the embryonic lethality of a complete deficiency in insulin-like growth factor 1 (IGF-1), we generated mice homozygous for a site-specific insertional event that created a mutant IGF-1 allele (igf1m). These mice have IGF-1 levels 30% of wild type yet survive to adulthood, thereby allowing physiological analysis of the phenotype. Miniaturized catheterization technology revealed elevated conscious blood pressure in IGF-1(m/m) mice, and measurements of left ventricular contractility were increased. Adenylyl cyclase activity was enhanced in IGF-1(m/m) hearts, without an increase in beta-adrenergic receptor density, suggesting that crosstalk between IGF-1 and beta-adrenergic signaling pathways may mediate the increased contractility. The hypertrophic response of the left ventricular myocardium in response to aortic constriction, however, was preserved in IGF-1(m/m) mice. We conclude that chronic alterations in IGF-1 levels can selectively modulate blood pressure and left ventricular function, while not affecting adaptive myocardial hypertrophy in vivo.
An integrated approach to holistic metrology qualification for multi-patterning process layers: AM: Advanced metrology (2016)

Multi-patterning lithography at the 10-nm and 7-nm nodes is driving an exponential increase of metrology complexity in the overlay and alignment tree. Coupled with the highly involved process stacks required to reach these nodes, the setup and verification of the metrology recipes have reached new levels of importance. With an all-encompassing holistic mindset the authors present four node-enabling technologies using production data from a leading logic customer. Firstly an optimized layout is defined using a metric that ranks the importance of available wafer coordinate positions based on the model to be use for lithographic apparatus actuation. Next to minimize influence of process induced target asymmetry on overlay, the authors define how to find the optimum wavelength and polarization settings for overlay metrology. Once the process has reached a high volume-manufacturing (HVM) environment, we propose a method of monitoring using a single point key performance indicator (KPI). In the last section all learning is applied with integrated metrology (IM) within HVM to realize improved correctable error in measured overlay.
P-Chiral Oligonucleotides in Biological Recognition Processes (2007)

Internucleotide phosphodiester linkages in non-modified oligonucleotides are quickly degraded by nucleolytic enzymes present in the cells and this feature practically eliminates natural DNA and RNA molecules from medical applications and from many structural and mechanistic studies. P-chiral oligonucleotide analogs, in which one of the non-bridging phosphate oxygen atoms is substituted with another heteroatom (e.g. S, Se) or a chemical group (e.g. CH3, BH3(-)), have significantly greater nuclease resistance and also offer important possibilities for detailed studies of interactions with other biomolecules at the molecular level. Notably, these substitutions do not disrupt hydrogen bonding between nucleobases and affect the overall geometry of the oligomers to only low or moderate extent, although important changes of hydration patterns and changes of interactions with metal ions are observed. Such the probes, including isotopomeric species labeled with a heavy oxygen isotope, possessing phosphorus atoms of selected absolute configurations, have been used for elucidation of the mode of action of many enzymes (nucleases, transferases, kinases), ribozymes and DNA-zymes, as well as for investigations on thermodynamic stability of nucleic acids complexes (duplexes, triplexes, i-motif) and for studies on a mechanism of conformational changes of B-Z type. They are also useful tools for analysis of interactions of the phosphoryl oxygen atoms in natural precursors with functional groups of proteins. The synthetic routes to stereodefined forms of selected types of P-chiral oligonucleotides are presented, as well as recently developed methods for their configurational analysis at micromolar concentration. Selected examples of application of diastereomerically pure P-chiral oligonucleotides for structural, biochemical and biological experiments are discussed.
Cutting Edge: IL-18-Transgenic Mice: In Vivo Evidence of a Broad Role for IL-18 in Modulating Immune Function (2001)

IL-18 has been shown to be a strong cofactor for Th1 T cell development. However, we previously demonstrated that when IL-18 was combined with IL-2, there was a synergistic induction of a Th2 cytokine, IL-13, in both T and NK cells. More recently, we and other groups have reported that IL-18 can potentially induce IgE, IgG1, and Th2 cytokine production in murine experimental models. Here, we report on the generation of IL-18-transgenic (Tg) mice in which mature mouse IL-18 cDNA was expressed. CD8+CD44high T cells and macrophages were increased, but B cells were decreased in these mice while serum IgE, IgG1, IL-4, and IFN-gamma levels were significantly increased. Splenic T cells in IL-18 Tg mice produced higher levels of IFN-gamma, IL-4, IL-5, and IL-13 than control wild-type mice. Thus, aberrant expression of IL-18 in vivo results in the increased production of both Th1 and Th2 cytokines.
Application of an Electric Field to Colloidal Particles Suspended in a Liquid-Crystal Solvent (2001)

We study the behavior of colloidal particles suspended in a thermotropic nematic solvent in the presence of an electric field. For normal boundary conditions of the nematic director at the particles' surface, we show experimentally that an electric field applied along the dipolar axis of an elastic dipole induces a transition to an elastic quadrupolar configuration. Turning the field off makes the system go back to the initial state. We also show that it is possible to directly evidence an elastic quadrupolar repulsion between droplets.