gebhart/patrepeval huggingface dataset:
A registration, tracking, and visualization system for image-guided surgery (1997)

Medical scans such as Magnetic Resonance (MR) and computed tomography (CT) are currently common diagnostic tools in surgical applications. Typically information contained in these medical scans is neither in the coordinate system of the patient as positioned in the world, nor does it reflect the viewpoint of the surgeon during an operation. Any correspondences between the medical images and the actual patient environment have to be drawn mentally by the surgeon during the procedure. The approach of medical image registration and tracking seeks to compute these correspondences automatically and then directly augment the real operating environment with the information contained in medical scans. Such an environment provides the surgeon with an enhanced ability to plan, navigate and localize throughout a surgical procedure. This thesis presents a registration, tracking, and visualization system for image-guided surgery. During a procedure, a patient&amp;apos;s internal scan is registered to his position in the world. The patient is then tracked throughout the procedure using a fixed trackable LEDs. A live image from an overhead video camera is blended with the registered internal structures to create an enhanced reality visualization. A trackable probe is also used as an interactive tool to relate positions in the world to those in the scan. As the probe is moved around the patient in the world, a virtual pointer appears in the corresponding position in the 3D model and orthogonal slices of the internal scan. The system has been used at the Brigham and Women&amp;apos;s Hospital for over 20 neurosurgical cases, and is currently being used routinely for 1-2 cases per week. The system has also been used for initial experiments in functional brain mapping using transcranial magnetic stimulation o...
High barrier height GaN Schottky diodes: Pt/GaN and Pd/GaN (1996)

Platinum (Pt) and palladium (Pd) Schottky diodes on n-type GaN grown by metalorganic chemical vapor deposition were achieved and investigated. Aluminum was used for ohmic contacts. Barrier heights were determined to be as high as ΦB=1.13 eV by the current–voltage (I–V) method and ΦB=1.27 eV by the capacitance–voltage (C–V) method for the Pt/GaN diode, and ΦB=1.11 eV, ΦB=0.96 eV, and ΦB=1.24 eV by I–V, activation energy (I–V–T), and C–V methods for the Pd/GaN diode, respectively. The ideality factors were obtained to be n∼1.10.
Aspects on interaction between multistage stabilization of polyacrylonitrile precursor and mechanical properties of carbon fibers (1995)

Abstract The progression of polyacrylonitrile (PAN) fibers on multistage stabilization stage has been monitored by following the variations in density, elemental composition, morphological aspect, and mechanical properties. The effects of various processing conditions during the multistage stabilization on the mechanical properties of final carbon fibers were evaluated in detail. To achieve an optimal extent of stabilization of PAN fibers is critical as the final mechanical properties of carbon fibers are concerned. This aim can be realized by adjusting and matching the temperatures in each step and the processing rates during multistage stabilization. Imposing stretching on multistage stabilization is beneficial to mechanical properties of carbon fibers. © 1995 John Wiley &amp; Sons, Inc.
Effect of anaemia and cardiovascular disease on surgical mortality and morbidity (1996)

A low preoperative haemoglobin or a substantial operative blood loss increases the risk of death or serious morbidity more in patients with cardiovascular disease than in those without. Decisions about transfusion should take account of cardiovascular status and operative blood loss as well as the haemoglobin concentration.
Thrombin modulates and reverses neuroblastoma neurite outgrowth. (1988)

Previous studies have shown that neuroblastoma cells and several types of primary neuronal cells in culture rapidly extend neurites when switched from serum-containing to serum-free medium. The present studies on cloned neuroblastoma cells show that thrombin blocked this spontaneous differentiation at 2 nM with a half-maximal potency of 50 pM. This required the catalytic activity of thrombin and was reversed upon thrombin removal. Thrombin also caused cells in serum-free medium to retract their neurites at equally low concentrations. Two other serine proteases, urokinase and plasmin, did not block or reverse neurite extension even at 100-fold higher concentrations. A specific assay for thrombin indicated that thrombin detected in serum-containing medium from neuroblastoma cultures was derived from serum and that it was likely responsible for much of the known capacity of serum to maintain neuroblastoma cells in a nondifferentiated state. This was supported by the finding that heparin addition reduced the thrombin concentration in serum-containing medium and stimulated neurite outgrowth from neuroblastoma cells in serum-containing medium. Studies on the ability of thrombin to modulate neurite outgrowth by other agents showed that it blocked and reversed the neurite outgrowth activity of two thrombin inhibitors: protease nexin-1 (which is identical to glial-derived neurite-promoting factor) and hirudin. Thrombin, however, did not block the neurite-promoting activity of dibutyryl cAMP or prostaglandin E1. These results suggest a specific role for thrombin in control of neurite outgrowth.
Oxidative Biaryl Coupling Reaction of Phenol Ether Derivatives Using a Hypervalent Iodine(III) Reagent (1998)

The hypervalent iodine(III)-induced intramolecular biaryl coupling reaction of phenol ether derivatives (nonphenolic derivatives) was investigated with the aim of preparing various dibenzo heterocyclic compounds. 1,3-Diarylpropanes (1a−e), N-benzyl-N-phenethylamines (2a−c) and N,N-dibenzylamines (3a−e) react with a hypervalent iodine reagent, phenyliodine(III) bis(trifluoroacetate) (PIFA), containing BF3·Et2O in CH2Cl2 to give the biaryl coupling products (4−6) in good yield. As an application of the reaction, we examined the synthesis of oxygen- and sulfur-containing dibenzoheterocyclic compounds (12−15), whose side chain moiety could be easily cleaved by the known method to give 2,2‘-substituted biphenyl compounds (16−18).
Electro-optic measurement of THz field pulses with a chirped optical beam (1998)

Using a linearly chirped optical probe pulse in free-space electro-optic measurements, a temporal wave form of a co-propagating THz field is linearly encoded onto the frequency spectrum of the optical probe pulse, and then decoded by dispersing the probe beam from a grating to a detector array. We achieve acquisition of picosecond THz field pulses without using mechanical time-delay device. We also demonstrate a single-shot electro-optic measurement of the temporal wave form of a THz pulse.
Sequencing-by-Hybridization at the Information-Theory Bound: An Optimal Algorithm (2000)

In a recent paper (Preparata et al., 1999) we introduced a novel probing scheme for DNA sequencing by hybridization (SBH). The new gapped-probe scheme combines natural and universal bases in a well-defined periodic pattern. It has been shown (Preparata et al., 1999) that the performance of the gapped-probe scheme (in terms of the length of a sequence that can be uniquely reconstructed using a given size library of probes) is significantly better than the standard scheme based on oligomer probes. In this paper we present and analyze a new, more powerful, sequencing algorithm for the gapped-probe scheme. We prove that the new algorithm exploits the full potential of the SBH technology with high-confidence performance that comes within a small constant factor (about 2) of the information-theory bound. Moreover, this performance is achieved while maintaining running time linear in the target sequence length.
Adipose Tissue‐Derived Mesenchymal Stem Cells Have In Vivo Immunosuppressive Properties Applicable for the Control of the Graft‐Versus‐Host Disease (2006)

Previous studies have shown the relevance of bone marrow-derived MSCs (BM-MSCs) in controlling graft-versus-host disease (GVHD) after allogeneic transplantation. Since adipose tissue-derived MSCs (Ad-MSCs) may constitute a good alternative to BM-MSCs, we have expanded MSCs derived from human adipose tissue (hAd-MSCs) and mouse adipose tissue (mAd-MSCs), investigated the immunoregulatory properties of these cells, and evaluated their capacity to control GVHD in mice. The phenotype and immunoregulatory properties of expanded hAd-MSCs were similar to those of human BM-MSCs. Moreover, hAd-MSCs inhibited the proliferation and cytokine secretion of human primary T cells in response to mitogens and allogeneic T cells. Similarly, ex vivo expanded mAd-MSCs had an equivalent immunophenotype and exerted immunoregulatory properties similar to those of hAd-MSCs. Moreover, the infusion of mAd-MSCs in mice transplanted with haploidentical hematopoietic grafts controlled the lethal GVHD that occurred in control recipient mice. These findings constitute the first experimental proof that Ad-MSCs can efficiently control the GVHD associated with allogeneic hematopoietic transplantation, opening new perspectives for the clinical use of Ad-MSCs.
An expanded genetic code with a functional quadruplet codon (2004)

With few exceptions the genetic codes of all known organisms encode the same 20 amino acids, yet all that is required to add a new building block are a unique tRNA/aminoacyl-tRNA synthetase pair, a source of the amino acid, and a unique codon that specifies the amino acid. For example, the amber nonsense codon, TAG, together with orthogonal Methanococcus jannaschii or Escherichia coli tRNA/synthetase pairs have been used to genetically encode a variety of unnatural amino acids in E. coli and yeast, respectively. However, the availability of noncoding triplet codons ultimately limits the number of amino acids encoded by any organism. Here, we report the design and generation of an orthogonal synthetase/tRNA pair derived from archaeal tRNA(Lys) sequences that efficiently and selectively incorporates an unnatural amino acid into proteins in response to the quadruplet codon, AGGA. Frameshift suppression with L-homoglutamine (hGln) does not significantly affect protein yields or cell growth rates and is mutually orthogonal with amber suppression, permitting the simultaneous incorporation of two unnatural amino acids, hGln and O-methyl-L-tyrosine, at distinct positions within myoglobin. This work suggests that neither the number of available triplet codons nor the translational machinery itself represents a significant barrier to further expansion of the genetic code.
BMS-345541 Is a Highly Selective Inhibitor of IκB Kinase That Binds at an Allosteric Site of the Enzyme and Blocks NF-κB-dependent Transcription in Mice (2003)

The signal-inducible phosphorylation of serines 32 and 36 of I kappa B alpha is critical in regulating the subsequent ubiquitination and proteolysis of I kappa B alpha, which then releases NF-kappa B to promote gene transcription. The multisubunit I kappa B kinase responsible for this phosphorylation contains two catalytic subunits, termed I kappa B kinase (IKK)-1 and IKK-2. BMS-345541 (4(2'-aminoethyl)amino-1,8-dimethylimidazo(1,2-a)quinoxaline) was identified as a selective inhibitor of the catalytic subunits of IKK (IKK-2 IC(50) = 0.3 microm, IKK-1 IC(50) = 4 microm). The compound failed to inhibit a panel of 15 other kinases and selectively inhibited the stimulated phosphorylation of I kappa B alpha in cells (IC(50) = 4 microm) while failing to affect c-Jun and STAT3 phosphorylation, as well as mitogen-activated protein kinase-activated protein kinase 2 activation in cells. Consistent with the role of IKK/NF-kappa B in the regulation of cytokine transcription, BMS-345541 inhibited lipopolysaccharide-stimulated tumor necrosis factor alpha, interleukin-1 beta, interleukin-8, and interleukin-6 in THP-1 cells with IC(50) values in the 1- to 5-microm range. Although a Dixon plot of the inhibition of IKK-2 by BMS-345541 showed a non-linear relationship indicating non-Michaelis-Menten kinetic binding, the use of multiple inhibition analyses indicated that BMS-345541 binds in a mutually exclusive manner with respect to a peptide inhibitor corresponding to amino acids 26-42 of I kappa B alpha with Ser-32 and Ser-36 changed to aspartates and in a non-mutually exclusive manner with respect to ADP. The opposite results were obtained when studying the binding to IKK-1. A binding model is proposed in which BMS-345541 binds to similar allosteric sites on IKK-1 and IKK-2, which then affects the active sites of the subunits differently. BMS-345541 was also shown to have excellent pharmacokinetics in mice, and peroral administration showed the compound to dose-dependently inhibit the production of serum tumor necrosis factor alpha following intraperitoneal challenge with lipopolysaccharide. Thus, the compound is effective against NF-kappa B activation in mice and represents an important tool for investigating the role of IKK in disease models.
Locating the anomalous scatterer substructures in halide and sulfur phasing (2002)

Improved data quality now makes it feasible to exploit the weak anomalous signal derived only from the sulfurs inherent to the protein or in particular from halide ions incorporated by soaking. The latter technique requires the location of a high number of partially occupied halide sites. This number appears to be roughly proportional to the exposed protein surface. This paper explores the application of dual-space ab initio methods as implemented in the program SHELXD to the location of substructures of sulfur in SAD experiments, bromide in SAD and MAD experiments and iodide using SAD and SIRAS to determine the anomalous-atom substructure. Sets of atoms consistent with the Patterson function were generated as a starting point for the dual-space recycling procedure in SHELXD. The substructure is then expanded to the full structure by maximum-likelihood phasing with SHARP and density modification with the program DM. Success in the location of the substructures and subsequent phasing depends critically on the quality of the data and on the extent of the anomalous signal. This varies with each crystal and soak, but for the same crystal the significance of the anomalous signal was found to be highly sensitive to the redundancy of the intensity measurements, which in some cases made all the difference. This is illustrated by the determination of the previously unknown structure of repeat 11 of the human mannose-6-phosphate/insulin-like growth factor II receptor (Man6P/IGFII-receptor), with 310 amino acids in the asymmetric unit, which was phased by soaking the crystals in a cryoprotectant solution containing halide anions.
The natural history of regional dysfunction in a canine preparation of chronic infarction. (1985)

We used a canine preparation of experimental infarction to study the natural course of echocardiographically defined regional wall motion abnormalities in the 6 weeks after acute coronary ligation. Eight dogs underwent serial short-axis echocardiographic evaluation and microsphere blood flow determinations at control, and 30 min, 48 hr, 1 week, 3 weeks, and 6 weeks after acute coronary artery ligation. Wall motion analysis and blood flow calculations were applied to 10 degree radial segments of the left ventricle (short axis) and correlated to the size and extent of infarction as defined histologically at 6 weeks. All animals had at least 50% transmural histologic infarction. The ratio of flow in infarcted tissue vs noninfarcted myocardium fell to 0.40 +/- 0.13 for endocardium and 0.56 +/- 0.13 for epicardium at 30 min after ligation, but recovered to 0.83 +/- 0.15 for endocardium and 1.12 +/- 0.11 for epicardium by 6 weeks. The maximum circumferential extent of abnormal regional wall motion was observed at 48 hr after infarction (mean circumferential extent = 51%), but was resolved to a significant extent by 6 weeks (circumferential extent = 21%, p less than .001). Four animals had virtually normal wall motion by 6 weeks after infarction. Segment-by-segment regional dysfunction correlated highly with the regional transmural reduction in blood flow of 20% )r = .89, p = .0001) for the experiment as a whole, but the echocardiogram tended to underestimate the size of the histologic infarct at 6 weeks.(ABSTRACT TRUNCATED AT 250 WORDS)
Aromatic-aromatic interactions: free energy profiles for the benzene dimer in water, chloroform, and liquid benzene (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAromatic-aromatic interactions: free energy profiles for the benzene dimer in water, chloroform, and liquid benzeneWilliam L. Jorgensen and Daniel L. SeveranceCite this: J. Am. Chem. Soc. 1990, 112, 12, 4768–4774Publication Date (Print):June 1, 1990Publication History Published online1 May 2002Published inissue 1 June 1990https://pubs.acs.org/doi/10.1021/ja00168a022https://doi.org/10.1021/ja00168a022research-articleACS PublicationsRequest reuse permissionsArticle Views4889Altmetric-Citations941LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Culture, Black Men, and Prostate Cancer: What is Reality? (2004)

Lack of discussion about the decision to screen for prostate cancer and general lack of culturally appropriate communication with healthcare providers has engendered distrust, created fear, fostered disconnect, and increased the likelihood of nonparticipation in prostate cancer screening among black men.
Human testicular aromatase: immunocytochemical and biochemical studies. (1995)

The location of the aromatase enzyme in the testes of human subjects ages 3 months to 72 yr was determined immunocytochemically using a monoclonal antibody specific to human aromatase. In addition, an assay was developed to measure aromatase activity in suspensions of cryosections in order to validate the presence and to quantitate the activity of aromatase in the sections. In mature testes, aromatase immunostain was always associated with Leydig cells and was absent from Sertoli cells. Aromatase activity ranged from 0.014-0.55 pmol estrogen per mg/h and was significantly correlated with the immunostain intensity (P < 0.02). Thus, the aromatase activity provided a semiquantitative estimate of the immunoreaction. Activity and immunostain intensity of aromatase did not correlate with increasing age. Rather, the highest levels were measured in four of six testes of men ages 18-20 yr, three of whom also had the strongest immunostain for aromatase. The Leydig cell clusters of these subjects were larger and more prominent than those in the other specimens. A low level of aromatase activity but no immunostain was detected in prepubertal testes. Aromatase was not detected by either method in normal tissue from the testis of a patient with testicular cancer.
Epidemiology and Prevention of Pancreatic Cancer (2004)

Pancreatic cancer is an uncommon tumor, but because the mortality rate approaches 100%, this form of cancer has now become a common cause of cancer mortality. In the United States it is the fourth most frequent cause of cancer mortality; in Japan it ranks as the fifth commonest cause of death from cancer. Smoking is the major known risk factor for pancreatic cancer, accounting for approximately 25-30% of all cases. Some of the time-dependent changes in the frequency of pancreatic cancer can be explained by smoking trends. Aggressive public health measures to control smoking would substantially reduce the burden of pancreatic cancer. Dietary factors are less important for pancreatic cancer than for other digestive tract tumors, but consumption of a diet with adequate quantities of fruits and vegetables, plus control of calories either by dietary measures or by exercise will help to prevent this lethal tumor. There are more than a dozen inherited germline mutations that increase the risk of pancreatic cancer. Of these, hereditary pancreatitis confers the greatest risk, while BRCA2 mutations are the commonest inherited disorder. In addition to germline defects, there are several common polymorphisms in genes that control detoxification of environmental carcinogens that may alter the risk of pancreatic cancer. More research will be needed in this area, to explain and to clarify the interaction between genes and environmental factors.
Dysphagia After Stroke (2005)

The high incidence for dysphagia and pneumonia is a consistent finding with stroke patients. The pneumonia risk is greatest in stroke patients with aspiration. These findings will be valuable in the design of future dysphagia research.
A Transient Receptor Potential Vanilloid 4-Dependent Mechanism of Hyperalgesia Is Engaged by Concerted Action of Inflammatory Mediators (2006)

The transient receptor potential vanilloid 4 (TRPV4) is a primary afferent transducer that plays a crucial role in neuropathic hyperalgesia for osmotic and mechanical stimuli, as well as in inflammatory mediator-induced hyperalgesia for osmotic stimuli. In view of the clinical importance of mechanical hyperalgesia in inflammatory states, the present study investigated the role of TRPV4 in mechanical hyperalgesia induced by inflammatory mediators and the second-messenger pathways involved. Intradermal injection of either the inflammogen carrageenan or a soup of inflammatory mediators enhanced the nocifensive paw-withdrawal reflex elicited by hypotonic or mechanical stimuli in rat. Spinal administration of TRPV4 antisense oligodeoxynucleotide blocked the enhancement without altering baseline nociceptive threshold. Similarly, in TRPV4(-/-) knock-out mice, inflammatory soup failed to induce any significant mechanical or osmotic hyperalgesia. In vitro investigation showed that inflammatory mediators engage the TRPV4-mediated mechanism of sensitization by direct action on dissociated primary afferent neurons. Additional behavioral observations suggested that multiple mediators are necessary to achieve sufficient activation of the cAMP pathway to engage the TRPV4-dependent mechanism of hyperalgesia. In addition, direct activation of protein kinase A or protein kinase C epsilon, two pathways that mediate inflammation-induced mechanical hyperalgesia, also induced hyperalgesia for both hypotonic and mechanical stimuli that was decreased by TRPV4 antisense and absent in TRPV4(-/-) mice. We conclude that TRPV4 plays a crucial role in the mechanical hyperalgesia that is generated by the concerted action of inflammatory mediators present in inflamed tissues.
Efficient Identification of Mutated Cancer Antigens Recognized by T Cells Associated with Durable Tumor Regressions (2014)

These findings suggest that the minigene screening approach can facilitate the antigen repertoire analysis of tumor reactive T cells, and lead to the development of new adoptive cell therapies with purified T cells that recognize candidate-mutated antigens derived from genes essential for the carcinogenesis.