gebhart/patrepeval huggingface dataset:
FacetAtlas: Multifaceted Visualization for Rich Text Corpora (2010)

Documents in rich text corpora usually contain multiple facets of information. For example, an article about a specific disease often consists of different facets such as symptom, treatment, cause, diagnosis, prognosis, and prevention. Thus, documents may have different relations based on different facets. Powerful search tools have been developed to help users locate lists of individual documents that are most related to specific keywords. However, there is a lack of effective analysis tools that reveal the multifaceted relations of documents within or cross the document clusters. In this paper, we present FacetAtlas, a multifaceted visualization technique for visually analyzing rich text corpora. FacetAtlas combines search technology with advanced visual analytical tools to convey both global and local patterns simultaneously. We describe several unique aspects of FacetAtlas, including (1) node cliques and multifaceted edges, (2) an optimized density map, and (3) automated opacity pattern enhancement for highlighting visual patterns, (4) interactive context switch between facets. In addition, we demonstrate the power of FacetAtlas through a case study that targets patient education in the health care domain. Our evaluation shows the benefits of this work, especially in support of complex multifaceted data analysis.
A Novel Device for the Simple and Efficient Refinement of Liposuctioned Tissue (2001)

In short, our device allows a surgeon who is harvesting adipose tissue for autologous fat transplantation to immediately, easily, efficiently, and sterilely isolate adipose tissue from the unwanted waste components that are associated with primary liposuction effluent. It does so by "trapping" the fat tissue contained within raw liposuction effluent. Once the tissue fraction has been separated, the device design then allows for direct implantation or subsequent washing/rinsing of the tissue with saline/buffer of choice in preparation for tissue reimplantation.
High expression of L‐type amino‐acid transporter 1 (LAT1) in gastric carcinomas: Comparison with non‐cancerous lesions (2011)

Amino acid transporters are essential for maintenance and proliferation of both normal and transformed cells. In the present study, L-type amino-acid transporter 1 (LAT1) immunoreactive expression was investigated in gastric carcinomas, in comparison with gastric adenomas and non-neoplastic lesions, using our recently developed novel monoclonal antibody. In a total of 87 cases of advanced gastric cancer, high LAT1 expression was observed in carcinoma cells, predominantly at plasma membranes with greater intensity in non-scirrhous than scirrhous carcinomas. Gastric carcinoma cases with lymph node metastasis showed significantly higher LAT1 expression than cases without lymph node metastasis. A positive correlation with Ki-67 LI was observed and the highly expressing non-scirrhous carcinomas showed a significantly poorer prognosis than the low LAT1 group. Cox hazard test revealed that TNM stage and LAT1 expression were independent prognostic factors in non-scirrhous carcinoma group. Further, a significant poor prognosis was confirmed in high LAT1 expression group, when limited to undifferentiated carcinoma cases excluding scirrhous carcinoma. Lower levels were found in adenomas. In conclusion, LAT 1 expression may be linked with cell proliferation and prognosis of gastric carcinomas, and offers a potential target for future anticancer therapy by inhibitors.
Treponema innocens, a New Species of Intestinal Bacteria, and Emended Description of the Type Strain of Treponema hyodysenteriae Harris et al. (1979)

Twelve treponemes with serpentine morphology were isolated from pigs and dogs and were compared with strain B78, the type strain of Treponema hyodysenteriae Harris et al. Nine of the 12 were isolated from cases of swine dysentery, and these were similar in characteristics to strain B78. The three other isolates were not enteropathogenic for swine and could be differentiated from the aforementioned nine isolates on the basis of enteropathogenicity, hemolytic pattern, deoxyribonucleic acid homology, fructose fermentation, and indole production. The morphological and metabolic characters of the 12 isolates and an emended description of strain B78, the type strain of T. hyodysenteriae, are presented in this report. Based on these data, the nonpathogenic types are regarded as belonging to a new species, Treponema innocens. The type strain of T. innocens is strain B256 (=ATCC 29796).
Gentamicin-Loaded Hydraulic Calcium Phosphate Bone Cement as Antibiotic Delivery System (1997)

A hydraulic calcium phosphate cement made of beta-tricalcium phosphate [beta-Ca3(PO4)2], monocalcium phosphate monohydrate [Ca(H2PO4)2-H2O], and water was used as a delivery system for the antibiotic gentamicin sulfate (GS). GS, added as powder or as aqueous solution, was very beneficial to the physicochemical properties of the cement. The setting time increased from 2 to 4.5 min with 3% (w/w) GS and then slowly decreased to 3.75 min with 16% (w/w) GS. The tensile strength increased from 0.4 to 1.6 MPa with 16% (w/w) GS. These effects were attributed to the presence of sulfate ions in GS. The release of GS from the cement was measured in a pH 7.4 phosphate-buffered saline solution at 37 degrees C by USP paddle method. Factors such as cement porosity, GS content and presence of sulfate ions or polymeric additives were investigated. The amount of GS released was roughly proportional to the square root of time up to approximately 50% release. Afterwards, the release rate markedly slowed down to zero. In all but two cement formulations, the total dose of GS was released within 7 days, indicating that no irreversible binding occurred between the cement paste and the antibiotic. When small amounts of hydroxypropylcellulose or poly(acrylic acid) were added to the cement, the maximum fraction released was a few percent lower than the total GS dose, suggesting some binding between the polymer and GS. The GS release rate was strongly influenced by the presence of sulfate ions in the cement paste and by the cement porosity. The higher the sulfate ion content of the cement paste, the lowe the GS release rate. This influence was attributed to the finer cement micro-structure induced by the presence of sulfate ions. Furthermore, when the initial cement porosity was increased from 38 to 69%, the release rate almost tripled (0.16 to 0.45 h-1/2). Finally, the biological activity of GS in the cement was maintained, as measured by assaying the release medium.
Lapped transforms for efficient transform/subband coding (1990)

Two lapped transforms for subband/transform coding of signals are introduced: a version of the lapped orthogonal transform (LOT), which can be efficiently computed for any transform length; and the modulated lapped transform (MLT), which is based on a modulated quadrature mirror (QMF) bank. The MLT can also be efficiently computed by means of a type-IV discrete sine transform (DST-IV). The LOT and the MLT are both asymptotically optimal lapped transforms for coding an AR(1) signal with a high intersample correlation coefficient. The coding gains of the LOT and MLT of length M are higher than that of the discrete cosine transform (DCT) of the same length; they are actually close to the coding gains obtained with a DCT of length 2M. An MLT-based adaptive transform coder (ACT) for speech signals is simulated; the code is essentially free from frame rate noise and has a better spectral resolution that DCT-based ATC systems.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
The zinc finger transcriptional repressor Blimp1/Prdm1 is dispensable for early axis formation but is required for specification of primordial germ cells in the mouse (2005)

Blimp1, a zinc-finger containing DNA-binding transcriptional repressor, functions as a master regulator of B cell terminal differentiation. Considerable evidence suggests that Blimp1 is required for the establishment of anteroposterior axis formation and the formation of head structures during early vertebrate development. In mouse embryos, Blimp1 is strongly expressed in axial mesendoderm, the tissue known to provide anterior patterning signals during gastrulation. Here, we describe for the first time the defects caused by loss of Blimp1 function in the mouse. Blimp1 deficient embryos die at mid-gestation, but surprisingly early axis formation, anterior patterning and neural crest formation proceed normally. Rather, loss of Blimp1 expression disrupts morphogenesis of the caudal branchial arches and leads to a failure to correctly elaborate the labyrinthine layer of the placenta. Blimp1 mutant embryos also show widespread blood leakage and tissue apoptosis, and, strikingly, Blimp1 homozygous mutants entirely lack PGCs. At the time of PGC allocation around 7.25 days post coitum, Blimp1 heterozygous embryos exhibit decreased numbers of PCGs. Thus Blimp1 probably acts to turn off the default pathway that allows epiblast cells to adopt a somatic cell fate, and shifts the transcriptional program so that they become exclusively allocated into the germ cell lineage.
Detection of Pseudomonas aeruginosa from clinical and environmental samples by amplification of the exotoxin A gene using PCR (1994)

PCR was used to detect Pseudomonas aeruginosa from water samples by amplifying a 396-bp region of the exotoxin A (ETA) structural gene sequence. The identify of the amplified 396-bp fragment was confirmed by digesting it with PvuI restriction endonuclease, which produced the predicted 246- and 150-bp fragments. Specific primers amplified ETA-positive P. aeruginosa DNA, whereas other species of Pseudomonas and GC-rich bacteria did not yield any 396-bp fragment. The specificity and sensitivity of the assay were 100 and 96%, respectively, which confirms the assay's reliability for diagnostic and epidemiological studies. The assay can detect as few as 5 to 10 cells in a 10-ml water sample or 0.1 pg of P. aeruginosa DNA per reaction mixture (5 microliters) by ethidium bromide staining of an agarose gel. Ten-times-lower concentrations were detected by hybridization with a digoxigenin-labeled oligonucleotide probe internal to the PCR product. With this PCR method, ETA-positive P. aeruginosa was detected in animal cage water samples at a level of 40 cells per ml. This method is rapid and less cumbersome than other diagnostic methods for the identification of P. aeruginosa strains. The method described can be used to detect a low level of P. aeruginosa from environmental and clinical samples without the use of selective media or additional biochemical tests.
2-Pyridylsilyl Group: A Useful Multifunctional Group in Organic Synthesis (2006)

The utility of the 2-pyridylsilyl group as a multifunctional group in organic synthesis is described. The use of the 2-pyridylsilyl group as a removable directing group is a powerful synthetic strategy that circumvents the specificity-generality dilemma in metal-mediated organic synthesis. In addition, the utility of the 2-pyridylsilyl group as a phase tag for strategic separation and as a removable hydrophilic group for aqueous reactions is also described.
Viscoelastic Acoustic Response of Layered Polymer Films at Fluid-Solid Interfaces: Continuum Mechanics Approach (1999)

We have derived the general solution of a wave equation describing the dynamics of two-layere viscoelastic polymer materials of arbitrary thickness deposited on solid (quartz) surfaces in a fluid environment. Within the Voight model of viscoelastic element, we calculate the acoustic response of the system to an applied shear stress, i.e. we find the shift of the quartz generator resonance frequency and of the dissipation factor, and show that it strongly depends on the viscous loading of the adsorbed layers and on the shear storage and loss moduli of the overlayers. These results can readily be applied to quartz crystal acoustical measurements of the viscoelasticity of polymers, which conserve their shape under the shear deformations and do not flow, and layered structures such as protein films adsorbed from solution onto the surface of self-assembled monolayres.
Measurement and wireless transmission of embedded capacitive microsensor's output using ΣΔ conversion and radio frequency identification (RFID) technology (1997)

This article concerns the design and post-fabrication testing of a CMOS integrated circuit (IC) for the Remote- Queried Embedded Microsensor (RQEM) system. The IC may be coupled to capacitive microsensors to measure the output of the sensors, to digitize this measured output, and to condition and encode the digital data. Wireless transmission of the code to a commercial Radio Frequency Identification (RFID) system reader is implemented using Differential Phase Shift Keying of a low-frequency signal, which inductively couples the RQEM antenna coil to the receiving antenna of the RFID reader. The IC extracts its own operating power and digital clock signal from the interrogating signal, which is transmitted by the RFID reader. The IC uses switched- capacitor techniques for acquisition and for A/D conversion of data. A first-order Sigma-Delta ((Sigma) (Delta) ) A/D converter is used with an output transconductance amplifier (OTA) in the balancing integrator and the comparator. The same OTA is also used in the acquisition circuit, which is a sample-and-hold offset-free circuit. Several fabricated chips were tested with on-chip test capacitors, used to calibrate the IC's output.
Transforming growth factor beta as a virulence mechanism for Leishmania braziliensis. (1993)

Transforming growth factor beta (TGF-beta) has potent down-regulating effects on macrophages and is thus capable of influencing the fate of intramacrophage parasites, including leishmanias. We report the development of a mouse model for the study of the human pathogen Leishmania braziliensis and demonstrate, both in vitro and in vivo, a key regulatory role for TGF-beta in the pathogenesis of infection with this parasite. Recombinant TGF-beta added to cultures of murine peritoneal macrophages led to increased intracellular L. braziliensis replication, whereas addition of neutralizing anti-TGF-beta monoclonal antibody decreased levels of infection. Macrophages infected with L. braziliensis produced biologically active TGF-beta, with a direct correlation between amounts of TGF-beta induced by two parasite isolates and their relative virulence. In vivo, treatment with recombinant TGF-beta rendered avirulent parasites virulent and activated latent L. braziliensis infection. Activation of parasite replication was observed in mice which had been infected with L. braziliensis 15 weeks previously but had not developed lesions or had healed lesions, depending on the parasite isolate used to infect the mice. The exacerbation of L. braziliensis infection in vivo was associated with an increase of interleukin 10 mRNA in the draining lymph node. These results demonstrate that TGF-beta is able to alter the course of in vitro and in vivo infections with L. braziliensis, the latter being characterized by an increase in interleukin 10, an important Th2 helper-T-cell cytokine.
MCP-1 and RANTES Are Mediators of Acute and Chronic Inflammation (2001)

Regulation of leukocyte migration and activation by chemokines are recognized as potentially important functions in the induction of acute and chronic inflammatory reactions. Regulated upon activation normal T cell expressed and presumably secreted (RANTES), monocyte chemotactic protein-1 (MCP-1), and related molecules constitute the C-C class of the beta chemokine supergene family with inflammatory properties. Here we report that in experimental studies RANTES and MCP-1 provoke mast cell activation and increase histidine decarboxylase mRNA expression in a dose-dependent manner. Moreover, injections of RANTES and MCP-1 in the rat skin cause mast cell, eosinophil, and macrophage recruitment, and prostaglandin E2 (PGE2) generation. In a chronic inflammatory model MCP-1 was found to mediate the recruitment of mononuclear cells in calcified granulomas. In addition, MCP-1 mediated parasitic infections caused by Trichinella spiralis. In accordance with other studies, RANTES and MCP-1 were found to play an important role in the lung allergic inflammation, lung leukocyte infiltration, bronchial hyperresponsiveness, and the recruitment of eosinophils in the pathogenesis of asthma. Here for the first time we propose a new mechanism of pulmonary airway inflammation where RANTES and MCP-1 are deeply involved. We also studied the apparent role played by RANTES in the pathogenesis of relapsing-remitting multiple sclerosis enhancing the inflammatory response within the nervous system.
Physical Interaction with Yes-associated Protein Enhances p73 Transcriptional Activity (2001)

Specific protein-protein interactions are involved in a large number of cellular processes and are mainly mediated by structurally and functionally defined domains. Here we report that the nuclear phosphoprotein p73 can engage in a physical association with the Yes-associated protein (YAP). This association occurs under physiological conditions as shown by reciprocal co-immunoprecipitation of complexes from lysates of P19 cells. The WW domain of YAP and the PPPPY motif of p73 are directly involved in the association. Furthermore, as required for ligands to group I WW domains, the terminal tyrosine (Y) of the PPPPY motif of p73 was shown to be essential for the association with YAP. Unlike p73alpha, p73beta, and p63alpha, which bind to YAP, the endogenous as well as exogenously expressed wild-type p53 (wt-p53) and the p73gamma isoform do not interact with YAP. Indeed, we documented that YAP interacts only with those members of the p53 family that have a well conserved PPXY motif, a target sequence for WW domains. Overexpression of YAP causes an increase of p73alpha transcriptional activity. Differential interaction of YAP with members of the p53 family may provide a molecular explanation for their functional divergence in signaling.
Rolling Mechanical Imaging: A novel Approach for Soft Tissue Modelling and Identification during Minimally Invasive Surgery (2008)

This paper proposes a novel approach for the identification of the internal structure and mechanical properties of biological soft tissue using a force sensitive wheeled probe to generate a 'mechanical image' by rolling across the surface of a solid organ. Initially, a testing facility for validating the concept ex-vivo was developed. Preliminary validation tests were carried out on a silicone phantom with embedded abnormalities with the aim to link the derived 'mechanical image' with the known internal structure. Ex-vivo validation tests were also conducted on excised porcine livers. The data were analyzed in four parts: 1) the dynamic analysis of wheel-tissue interaction to validate that the measured parameters are representative of underlying tissue stiffness; 2) the development of a 'mechanical image' from the rolling data; 3) a comparison of standard 1-DOF indentation testing with 2-DOF rolling and 4) the characterization of the relationship between force and tissue deflection from the data contained within the mechanical image. The results show that the 'rolling mechanical image' is capable of capturing information relating to the underlying tissue stiffness distribution and characterizing the force-tissue deflection profile for a tissue sample. Examples of scenarios, where this information could potentially be used, include providing a surgeon with the ability to probe solid organs in-vivo during robot-assisted MIS or providing prior information for the modeling of tool-tissue interactions, such as steerable needles.
Selection of Endometrial Carcinomas for DNA Mismatch Repair Protein Immunohistochemistry Using Patient Age and Tumor Morphology Enhances Detection of Mismatch Repair Abnormalities (2009)

Women with hereditary nonpolyposis colorectal cancer (HNPCC) have a high risk for endometrial cancer (EC) and frequently present with a gynecologic cancer as their first or sentinel malignancy. Identification of these patients is important given their personal and family risk for synchronous and metachronous tumors. The revised Bethesda Guidelines provide screening criteria for HNPCC in colorectal cancers. However, there are currently no such screening recommendations for women with endometrial carcinoma. We applied some of the colorectal cancer screening criteria, including age and tumor morphology, to endometrial endometrioid carcinoma. The purpose of this study was to describe patient and tumor characteristics and to assess the ability of these criteria to enhance detection of mismatch repair (MMR) deficiency, and hence HNPCC in EC. Immunohistochemistry (IHC) for DNA mismatch repair (IHC-MMR) proteins was performed in a defined subset of patients with EC. This included women younger than 50 years of age and women >or=50 years whose tumors showed morphologic features suggestive of MMR deficiency (TM-MMR). The extent of IHC-MMR in the older patient group was compared with that in a comparison group of EC >or=50 years that was previously analyzed for microsatellite instability status. Seventy-one patients met the selection criteria for IHC testing; 32 (45%) showed abnormal results. The rate of IHC abnormality in the younger group was approximately 30% with a nearly equal distribution of MLH1/PMS2 and MSH2/MSH6 abnormalities. In the older age group, TM-MMR triggered IHC analysis in 31 of 34 cases. Of these, 18 cases showed loss of IHC-MMR (58% of cases), 7 with loss of MSH2/MSH6. In contrast, the rate of microsatellite instability in the comparison group was only 21%. The IHC abnormal group showed more frequent tumor infiltrating lymphocytes, dedifferentiated EC, more tumors centered in the lower uterine segment, and more frequent synchronous clear cell carcinomas of the ovary than tumors with a normal immunophenotype. Although many of the patients with loss of IHC-MMR showed personal and/or family history (13 of 32) of HNPCC-associated tumors, most did not. Tumor morphology (TM-MMR) along with IHC-MMR enhances the detection of EC patients at risk of HNPCC.
Aero-Sol−Gel Synthesis of Nanostructured Silica Powders (1997)

Nanostructured silica powders are synthesized by a nonpyrolytic, room-temperature aero-sol−gel process. Hydrolysis and condensation of tetraethoxysilane (TEOS) and tetramethoxysilane (TMOS) precursors produce nanosized silica powders that have specific surface areas greater than 400 m2/g. This paper reports on a novel synthetic approach and characterization of the morphology, particle growth process, surface area, and chemical composition using small-angle X-ray scattering (SAXS), N2 adsorption, and elemental analysis. Structural models for the morphology and growth process of the silica particles are suggested. The effects of reactant temperature and powder sintering on the specific surface area of silica are discussed.