gebhart/patrepeval huggingface dataset:
CISUS: an integrated 3D ultrasound system for IGT using a modular tracking API (2004)

Ultrasound has become popular in clinical/surgical applications, both as the primary image guidance modality and also in conjunction with other modalities like CT or MRI. Three dimensional ultrasound (3DUS) systems have also demonstrated usefulness in image-guided therapy (IGT). At the same time, however, current lack of open-source and open-architecture multi-modal medical visualization systems prevents 3DUS from fulfilling its potential. Several stand-alone 3DUS systems, like Stradx or In-Vivo exist today. Although these systems have been found to be useful in real clinical setting, it is difficult to augment their functionality and integrate them in versatile IGT systems. To address these limitations, a robotic/freehand 3DUS open environment (CISUS) is being integrated into the 3D Slicer, an open-source research tool developed for medical image analysis and surgical planning. In addition, the system capitalizes on generic application programming interfaces (APIs) for tracking devices and robotic control. The resulting platform-independent open-source system may serve as a valuable tool to the image guided surgery community. Other researchers could straightforwardly integrate the generic CISUS system along with other functionalities (i.e. dual view visualization, registration, real-time tracking, segmentation, etc) to rapidly create their medical/surgical applications. Our current driving clinical application is robotically assisted and freehand 3DUS-guided liver ablation, which is fully being integrated under the CISUS-3D Slicer. Initial functionality and pre-clinical feasibility are demonstrated on phantom and ex-vivo animal models.
Bedside Catheterization of the Pulmonary Artery: Risks Compared with Benefits (1988)

The decision to use bedside pulmonary artery catheterization for managing patients must involve a careful assessment of the risks compared to the benefits. Complications can be minimized by following specific guidelines for catheter insertion and maintenance. Pulmonary artery catheterization has been shown to be more accurate than clinical assessment alone in critically ill patients for determining the cause of shock (hypovolemic, cardiogenic, or septic) or for assessing the cause of severe pulmonary edema (cardiogenic or noncardiogenic). The diagnosis of cardiac failure in medical or surgical patients with invasive hemodynamic monitoring provides physiologic data that guide pharmacologic treatment that may favorably influence preload and afterload in the failing or ischemic heart. Managing hemodynamics with the aid of pulmonary artery catheterization in patients with the adult respiratory distress syndrome has received considerable attention, but a contribution to better patient outcome has not been established. Similarly, although clinical management of hemodynamic instability in septic shock is facilitated by pulmonary artery catheterization, the mortality remains very high because of the lack of specific therapy to reverse the sepsis syndrome. Adequate volume resuscitation and improved tissue oxygenation are universally accepted goals, but specific hemodynamic endpoints are controversial and direct measurements of tissue oxygenation are not possible. Prospective studies to define the clinical value of pulmonary artery catheterization are needed, but must be designed very carefully in order to identify unequivocally the effect of pulmonary artery catheterization on outcome in critically ill patients.
Activation of the kallikrein-kinin system in arthritis and enterocolitis in genetically susceptible rats: modulation by a selective plasma kallikrein inhibitor. (1997)

We have developed models of acute and chronic inflammatory arthritis and enterocolitis using peptidoglycan-polysaccharide injected intraperitoneally or subserosally (intramurally) into the distal ileum and cecum. Acute inflammation occurs in both Buffalo and Lewis rats, characterized by inflammation of the injected areas of the intestine. However, only the genetically susceptible Lewis rat develops chronic synovitis and joint erosion or adhesions and granulomatous enterocolitis. In the Lewis rat but not the Buffalo rat, these changes are accompanied by a decrease in plasma prekallikrein and high-molecular-weight kininogen, reflecting activation of the kallikrein-kinin system. Pretreatment with a specific plasma kallikrein inhibitor modulates the acute and chronic arthritis. The same inhibitor partially abrogates the acute changes characteristic of enterocolitis, and preliminary data suggest similar results in the chronic model. The results of these studies indicate that the kallikrein-kinin system plays an important role in arthritis and enterocolitis induced by bacterial products and that kallikrein inhibitors are potential therapeutic agents for inflammatory arthritis and inflammatory bowel disease.
Anti-B4-blocked ricin: a phase I trial of 7-day continuous infusion in patients with B-cell neoplasms. (1993)

Anti-B4-bR can be administered safely by 7-day continuous infusion with tolerable, reversible toxicities to patients with relapsed B-cell neoplasms. Although occasional responses were seen, future trials will use anti-B4-bR in patients with lower tumor burdens to circumvent the obstacle of immunotoxin delivery to bulk disease.
Synthesis of mixed‐donor azaoxathia macrocyclic tetraamides, acyclic polyether di/and tetraamides and their C‐pivot lariat derivatives (2007)

Abstract magnified image The macrocyclic tetraamides 11a‐e and 15‐hydroxy macrocyclic tetraamides 23a‐c were prepared in good yields by the nucleophilic reaction of the potassium salts of the bis‐phenoles 10a‐c with the appropriate dihalo compounds 5a‐d and 15. Moreover, the acyclic diamides 7, 9, 17‐21 and bis‐acyclic tetraamide 22 were obtained in high yields by the reaction of the appropriate dichloro compounds with different phenoxides and secondary amines. Acylation of 23a‐c with different acid chlorides gave the corresponding esters 24a‐c. Compounds 24a‐c reacted with different secondary amines to afford the corresponding novel lariat macrocycles 25a‐d in high yields.
Physical and Biological Barriers to Viral Vector–mediated Delivery of Genes to the Airway Epithelium (2004)

A gene therapy for cystic fibrosis (CF) lung disease by intralumenal delivery of therapeutic transgenes into the lung is a logical treatment strategy if efficient gene transfer can be achieved without detrimental effects to the patient. Indeed, pioneering work in the late 1980s showed that genetically engineered viruses could deliver the CF corrective transgene to cultured cells from patients with CF. However, after many attempts to deliver the corrective gene to the lungs of patients with CF in vivo and with the luxury of 20/20 hindsight, it is realized that although logical, the strategy to accomplish this task did not appreciate the evolution of the lung to resist invasion by pathogens such as viruses. It is now apparent that several levels of barriers exist that restrict exogenous gene delivery to the airway epithelium by commonly used viral vectors. Components of the innate and cell-mediated immune system collectively limit both the access to and duration of gene transfer vectors to the airway epithelium. Alternative viral vectors that have evolved to circumvent these barriers will require further development if gene transfer is ever to be considered a therapy for CF lung disease.
DOUBLE CLAD HIGH BRIGHTNESS Nd FIBER LASER PUMPED BY GaAlAs PHASED ARRAY (1989)

We report on the most recent improved version of the double clad configuration for efficient pumping of a single mode fiber laser with a multi-mode pump1 In the earlier report, the first and second claddings were substantially fused slica and the core containing Nd was offset from the center of the fiber axis, as shown in Fig. (1,a).
Thyroid hormones and thyroid hormone receptors: effects of thyromimetics on reverse cholesterol transport. (2010)

Reverse cholesterol transport (RCT) is a complex process which transfers cholesterol from peripheral cells to the liver for subsequent elimination from the body via feces. Thyroid hormones (THs) affect growth, development, and metabolism in almost all tissues. THs exert their actions by binding to thyroid hormone receptors (TRs). There are two major subtypes of TRs, TRα and TRβ, and several isoforms (e.g. TRα1, TRα2, TRβ1, and TRβ2). Activation of TRα1 affects heart rate, whereas activation of TRβ1 has positive effects on lipid and lipoprotein metabolism. Consequently, particular interest has been focused on the development of thyromimetic compounds targeting TRβ1, not only because of their ability to lower plasma cholesterol but also due their ability to stimulate RCT, at least in pre-clinical models. In this review we focus on THs, TRs, and on the effects of TRβ1-modulating thyromimetics on RCT in various animal models and in humans.
Mutants in the S. cerevisiae PKC1 gene display a cell cycle-specific osmotic stability defect. (1992)

The PKC1 gene of Saccharomyces cerevisiae encodes a homologue of the Ca(2+)-dependent isozymes of mammalian protein kinase C (Levin, D.cE., F. O. Fields, R. Kunisawa, J. M. Bishop, and J. Thorner. 1990. Cell. 62:213-224). Cells depleted of the PKC1 gene product display a uniform phenotype, a behavior indicating a defect in the cell division cycle (cdc). These cells arrest division after DNA replication, but before mitosis. Unlike most cdc mutants, which continue to grow in the absence of cell division, PKC1-depleted cells arrest growth with small buds. We created conditional alleles of PKC1 to explore the nature of this unusual cdc defect. In contrast to PKC1-depleted cells, all of the conditional pkc1 mutants isolated were suppressed by the addition of CaCl2 to the medium, suggesting that the mutant enzymes could be activated by Ca2+. Arrest of growth and cell division in the conditional mutants was accompanied by cessation of protein synthesis, rapid loss of viability, and release of cellular material into the medium, suggesting cell lysis. This conclusion was supported by the observation that a pkc1 deletion mutant was capable of proliferation in osmotically stabilized medium, but underwent rapid cell lysis when shifted to hypo-osmotic medium. We have incorporated these observations into a model to explain the cdc-specific arrest of pkc1 mutants.
Study on the Surface Energy of Graphene by Contact Angle Measurements (2014)

Because of the atomic thinness of graphene, its integration into a device will always involve its interaction with at least one supporting substrate, making the surface energy of graphene critical to its real-life applications. In the current paper, the contact angle of graphene synthesized by chemical vapor deposition (CVD) was monitored temporally after synthesis using water, diiodomethane, ethylene glycol, and glycerol. The surface energy was then calculated based on the contact angle data by the Fowkes, Owens-Wendt (extended Fowkes), and Neumann models. The surface energy of fresh CVD graphene grown on a copper substrate (G/Cu) immediately after synthesis was determined to be 62.2 ± 3.1 mJ/m(2) (Fowkes), 53.0 ± 4.3 mJ/m(2) (Owens-Wendt) and 63.8 ± 2.0 mJ/m(2) (Neumann), which decreased to 45.6 ± 3.9, 37.5 ± 2.3, and 57.4 ± 2.1 mJ/m(2), respectively, after 24 h of air exposure. The ellipsometry characterization indicates that the surface energy of G/Cu is affected by airborne hydrocarbon contamination. G/Cu exhibits the highest surface energy immediately after synthesis, and the surface energy decreases after airborne contamination occurs. The root cause of intrinsically mild polarity of G/Cu surface is discussed.
Kinetics and Energetics of Trehalose Transport in Saccharomyces cerevisiae (1996)

Cells of Saccharomyces cerevisiae are able to transport trehalose against a concentration gradient, without efflux or counterflow of the labeled substrate. Uptake was inhibited by uncouplers, acetic acid, and organic mercury compounds. The addition of trehalose resulted in alkalinization of the medium. The ratio of H+ depletion to trehalose uptake by yeast cells was approximately 1:1, which indicates the existence of a trehalose-H+ symporter in these cells. The optimum pH for this active H+-trehalose symport was 5.0, and both the Km and the Vmax were negatively affected by increasing or decreasing the extracellular pH from its optimum value. Kinetic studies showed the existence of at least two different trehalose transport activities in yeast cells: a high-affinity H+-trehalose symporter (Km = 4 mM), and a low-affinity transport activity (Km > 100 mM) that could be a facilitated diffusion process. The high-affinity H+-trehalose symporter was repressed by glucose, whereas the low-affinity uptake was constitutively expressed in S. cerevisiae.
AACR-FDA-NCI Cancer Biomarkers Collaborative Consensus Report: Advancing the Use of Biomarkers in Cancer Drug Development (2010)

Recent discoveries in cancer biology have greatly increased our understanding of cancer at the molecular and cellular level, but translating this knowledge into safe and effective therapies for cancer patients has proved to be challenging. There is a growing imperative to modernize the drug development process by incorporating new techniques that can predict the safety and effectiveness of new drugs faster, with more certainty, and at lower cost. Biomarkers are central to accelerating the identification and adoption of new therapies, but currently, many barriers impede their use in drug development and clinical practice. In 2007, the AACR-FDA-NCI Cancer Biomarkers Collaborative stepped into the national effort to bring together disparate stakeholders to clearly delineate these barriers, to develop recommendations for integrating biomarkers into the cancer drug development enterprise, and to set in motion the necessary action plans and collaborations to see the promise of biomarkers come to fruition, efficiently delivering quality cancer care to patients.
New phase I trial methodology. (1997)

Phase I trial design is constantly evolving to adapt to deficiencies in traditional methods and to accommodate newer rationally designed agents. This article discusses some of the important aspects of the design of phase I studies with particular reference to identifying new methods of safer but rapid dose escalation and reproducible end points such as maximum tolerated dose and recommended phase II dose. Given the explosion of rationally designed drugs capable of pathway specific inhibition, we also discuss potential strategies in designing trials with these agents. It is hoped that future strategies incorporate the existing methodologies with newer dose titration examples to complete phase I trials in a rapid and timely fashion.
Drosophila short gastrulation induces an ectopic axis in Xenopus: evidence for conserved mechanisms of dorsal-ventral patterning (1995)

The Spemann organizer has long been recognized as a major source of patterning signals during the gastrula stage of amphibian embryogenesis. More recent evidence has suggested that the ventral side of the embryo also plays an important role in dorsal-ventral patterning during gastrulation through the action of signaling factors such as BMP-4. Bmp-4 is closely related to the Drosophila decapentaplegic (dpp) gene, and like Bmp-4, dpp is excluded from the neurogenic region. Recently we showed that Bmp-4 functions in an analogous role to that of dpp in Drosophila, suggesting that the mechanism of dorsal-ventral patterning in Xenopus and Drosophila embryos may be conserved. To further test this hypothesis, RNA of the Drosophila short gastrulation (sog) gene was injected into Xenopus embryos, since sog has been shown genetically to be an antagonist of dpp function. Overexpression of sog RNA in Xenopus dorsalizes the embryo by expanding neurogenic and dorsal paraxial tissue. When ectopically expressed on the ventral side of the embryo, sog induces a partial secondary axis. In addition, sog partially rescues embryos ventralized by ultraviolet irradiation. Since sog induces many similar changes in gene expression to that caused by truncated BMP receptors, we suggest that sog functions in part by opposing BMP-4 signaling. The recent identification of a possible Xenopus sog homolog, chordin, in conjunction with these results supports the hypothesis that dorsal-ventral patterning mechanisms are conserved between these two species.
The bulk of endogenously produced IgG2a is eliminated from the serum of adult C57BL/6 mice with a half‐life of 6–8 days (1986)

The concentration of IgG2a in the serum of C57BL/6 mice suppressed for the production of IgG2a was measured over a period of 3 months after suppression. The elimination of a minimum of 96% of the endogenous IgG2a molecules from the serum follows an exponential decay with a half-life of 6-8 days. A monoclonal IgG2a antibody injected into suppressed or normal mice is eliminated from the serum in the same fashion. We conclude that there are few, if any, "long-lived" IgG2a molecules present in the serum of C57BL/6 mice under physiological conditions.
Intratracheal Administration of Umbilical Cord Blood-Derived Mesenchymal Stem Cells in a Patient with Acute Respiratory Distress Syndrome (2014)

Umbilical cord blood (UCB)-derived mesenchymal stem cells (MSCs) have been introduced as a possible therapy in acute lung injury and acute respiratory distress syndrome (ARDS). This case history is reported of a 59-yr-old man who was treated with MSCs in the course of ARDS and subsequent pulmonary fibrosis. He received a long period of mechanical ventilation and weaning proved difficult. On hospital day 114, he underwent the intratracheal administration of UCB-derived MSCs at a dose of 1 × 10(6)/kg. After cell infusion, an immediate improvement was shown in his mental status, his lung compliance (from 22.7 mL/cmH2O to 27.9 mL/cmH2O), PaO2/FiO2 ratio (from 191 mmHg to 334 mmHg) and his chest radiography over the course of three days. Even though he finally died of repeated pulmonary infection, our current findings suggest the possibility of using MSCs therapy in an ARDS patient. It is the first clinical case of UCB-derived MSCs therapy ever reported.
Mesenchymal Stem Cells: In Vitro Differentiation among Bone and Cartilage Cell Lineages (2007)

Received: 1/May/2007, Accepted: 5/Jul/2007The capacity of mesenchymal stem cells (MSCs) to differentiate amongskeletal cell lineages and to undergo extensive proliferation in vitro rendersthem an appropriate source for cell-replacement therapy to heal defects ofbone and cartilage tissue.It is argued that in bone and cartilage defects,MSCs would better be transplanted as fully-differentiated cells otherwise theymay produce non-specific cells in defect sites. This notion may emphasizethe importance of the studies considering in vitro bone and cartilagedifferentiation of MSCs. Indeed, the capacity of producing osteoblastic andchondrocytic cell lineage is among the earliest differentiation potentials ofMSCs, being reported at first isolation of the cells. Recent studies, howeverindicate that MSCs could differentiate into more cell lineages than expected.The present study provides evidence for, in vitro potential of MSCs todifferentiate into bone and cartilage cell lineages. As an introduction tothe differentiation, the characteristics of MSCs have been described andMSCs differentiation reviewed. The culture condition for bone and cartilagedifferentiation, molecular regulation of the differentiation, signaling pathwayinvolved during the differentiation, and the genes up-regulated upon boneand cartilage differentiation have also been described.
Elimination of hepatitis C virus RNA in infected human hepatocytes by adenovirus-mediated expression of ribozymes (1996)

Hepatitis C virus (HCV), a positive-strand RNA virus, is the major infectious agent responsible for causing chronic hepatitis. Currently, there is no vaccine for HCV infection, and the only therapy for chronic hepatitis C is largely ineffective. To investigate new genetic approaches to the management of HCV infection, six hammerhead ribozymes directed against a conserved region of the plus strand and minus strand of the HCV genome were isolated from a ribozyme library, characterized, and expressed from recombinant adenovirus vectors. The expressed ribozymes individually or in combination were efficient at reducing or eliminating the respective plus- or minus-strand HCV RNAs expressed in cultured cells and from primary human hepatocytes obtained from chronic HCV-infected patients. This study demonstrates the potential utility of ribozyme therapy as a strategy for the treatment of hepatitis C virus infection.
Identification of a Regulatory T Cell Specific Cell Surface Molecule that Mediates Suppressive Signals and Induces Foxp3 Expression (2008)

Regulatory T (T(reg)) cells control immune activation and maintain tolerance. How T(regs) mediate their suppressive function is unclear. Here we identified a cell surface molecule, called GARP, (or LRRC32), which within T cells is specifically expressed in T(regs) activated through the T cell receptor (TCR). Ectopic expression of GARP in human naïve T (T(N)) cells inhibited their proliferation and cytokine secretion upon TCR activation. Remarkably, GARP over-expression in T(N) cells induced expression of T(reg) master transcription factor Foxp3 and endowed them with a partial suppressive function. The extracellular but not the cytoplasmic region of GARP, was necessary for these functions. Silencing Foxp3 in human T(reg) cells reduced expression of GARP and attenuated their suppressive function. However, GARP function was not affected when Foxp3 was downregulated in GARP-overexpressing cells, while silencing GARP in Foxp3-overexpressing cells reduced their suppressive activity. These findings reveal a novel cell surface molecule-mediated regulatory mechanism, with implications for modulating aberrant immune responses.
HOME TREATMENT OF SKIN CANCER AND SOLAR KERATOSES (1988)

S ummary Participants in a community survey of skin cancer and solar keratoses were asked about their use of home remedies for these lesions. There were 164 persons aged between 20 and 69 years at high risk who said they treated these lesions themselves (7.8% of those surveyed). Half of the agents used were naturopathic and of these Euphorbia peplus was unanimously considered an effective treatment. Aloe vera was the most popular remedy and paw paw and creams such as lanolin were also popular despite their generally perceived lack of efficacy. Most of the self‐treaters were at high risk of skin cancer and thus the danger of this home treatment is the likely failure to recognize invasive disease. Close medical supervision of the treatment of actinic lesions remains essential.
Thermal conductivity reduction in GaAs-AlAs distributed Bragg reflectors (1998)

Self-heating of vertical-cavity laser diodes is strongly affected by the thermal conductivity of the distributed Bragg reflectors (DBRs). Binary GaAs-AlAs DBRs are expected to be good heat conductors, but investigations of GaAs-AlAs superlattices indicate strong interface scattering of phonons. For the first time, we present direct thermal conductivity measurements of separated GaAs-AlAs DBRs with a quarter-wave layer thickness of more than 100 nm (tuned to 1.55-μm wavelength). Using an ac calorimetric method and finite element analysis, we measure about 50% thermal conductivity reduction compared to the average bulk value. GaAs-AlAs DBR's for shorter wavelengths are expected to show an even lower thermal conductivity.