gebhart/patrepeval huggingface dataset:
Close packing of spheres (1987)

The local environment of an ‘‘origin’’ sphere in an assembly of spheres may be represented by a Voronoi polyhedron or by a polyhedron of simplicial lines. These figures may be projected on to a spherical surface of contacts1 and this representation is used here to examine the number of spheres of one diameter which can be packed regularly in contact with an origin sphere of the same or other diameters. The restriction that in the packings the spheres contacting the origin sphere also make contact with all their neighbor spheres in the contacting shell allows only 15 configurations in the range of radius K (radius of origin sphere/radius of contacting sphere), 0.225&amp;lt;K&amp;lt;8.8. The relationship of two of these configurations and the possible structure of the C60 molecule is examined. The reason why a previous model of random close packing produced answers which agreed well with experimental values only for some values of K is revealed.
Intravenous Platelet Blockade with Cangrelor during PCI (2009)

The use of periprocedural cangrelor during PCI was not superior to placebo in reducing the primary end point. The prespecified secondary end points of stent thrombosis and death were lower in the cangrelor group, with no significant increase in the rate of transfusion. Further study of intravenous ADP blockade with cangrelor may be warranted. (ClinicalTrials.gov number, NCT00385138.)
Antimicrobial peptides are expressed and produced in healthy and inflamed human synovial membranes (2002)

The objective of this study was to determine the expression and production of antimicrobial peptides by healthy and inflamed human synovial membranes. Deposition of the antimicrobial peptides lysozyme, lactoferrin, secretory phospholipase A(2) (sPA(2)), matrilysin (MMP7), human neutrophil alpha-defensins 1-3 (HNP 1-3), human beta-defensin 1 (HBD-1), and human beta-defensin 2 (HBD-2) was determined by immunohistochemistry. Expression of mRNA for the antimicrobial peptides bactericidal permeability-increasing protein (BPI), heparin binding protein (CAP37), human cationic antimicrobial protein (LL37), human alpha-defensin 5 (HD5), human alpha-defensin 6 (HD6), HBD-1, HBD-2, and human beta-defensin 3 (HBD-3) was analysed by reverse transcription polymerase chain reaction (RT-PCR). RT-PCR revealed CAP37 and HBD-1 mRNA in samples of healthy synovial membrane. Additionally, HBD-3 and/or LL37 mRNA was detected in synovial membrane samples from patients with pyogenic arthritis (PA), osteoarthritis (OA) or rheumatoid arthritis (RA). BPI, HD5, HD6, and HBD-2 mRNAs were absent from all samples investigated. Immunohistochemistry identified lysozyme, lactoferrin, sPA(2), and MMP7 in type A synoviocytes of all samples. HBD-1 was only present in type B synoviocytes of some of the samples. Immunoreactive HBD-2 peptide was only visible in some inflamed samples. HNP1-3 was detected in both healthy and inflamed synovial membranes. The data suggest that human synovial membranes produce a broad spectrum of antimicrobial peptides. Under inflammatory conditions, the expression pattern changes, with induction of HBD-3 in PA (LL37 in RA; HBD-3 and LL37 in OA) as well as down-regulation of HBD-1. HBD-3 holds therapeutic potential in PA as it has a broad spectrum of antimicrobial activity and accelerates epithelial healing. However, caution is appropriate since defensins also promote fibrin formation and cell proliferation - key elements in joint infection. Clarification of the role of antimicrobial peptides in OA and RA will require further investigation.
Growth inhibition of human breast carcinoma and leukemia/lymphoma cell lines by recombinant interferon-beta 2. (1988)

Recombinant human interferon-beta 2 was produced in Escherichia coli by direct expression of cDNA encoding the mature protein sequence. At concentrations that stimulate DNA synthesis and growth in B-cell hybridomas and plasmacytomas, the cytokine was found to exert a strong inhibition on the growth of a number of carcinoma and leukemia/lymphoma cell lines. This antigrowth effect was observed in clonogenic assays and by measurements of cell number and thymidine incorporation in growing cultures. The effect was blocked by antibodies to a synthetic peptide from the N terminus of the molecule. Normal diploid fibroblasts were inhibited at concentrations higher than those needed for breast carcinoma cells.
Evaluation of a 30-Gene Paclitaxel, Fluorouracil, Doxorubicin, and Cyclophosphamide Chemotherapy Response Predictor in a Multicenter Randomized Trial in Breast Cancer (2010)

Gene expression profiling for prospective response prediction was feasible in this international trial. The 30-gene predictor can identify patients with greater than average sensitivity to T/FAC chemotherapy. However, it captured molecular equivalents of clinical phenotype. Next-generation predictive markers will need to be developed separately for different molecular subsets of breast cancers.
Combination of Photodynamic Therapy with Anti-Cancer Agents (2008)

Degenerative diseases such as cancer usually involve more than one pathological process. Therefore, attempts to combat such diseases with monotherapeutic approaches may not always do so efficiently. For this reason, the use of combination therapy with modalities that target different disease pathways represents an alternative strategy. Photodynamic therapy (PDT) has already been established as an alternative therapy for the treatment of various types of malignant disorders, including oesophageal, lung and bladder cancer as well as other degenerative diseases. This technique involves the administration of a tumor localizing photosensitizer followed by its activation with light of a specific wavelength. In the presence of tissue oxygen, the photoactive sensitizer triggers a series of photochemical and photobiological processes that may lead to direct cancer cell damage, tumor microvascular occlusion and host immune response. Due to these multiple actions, PDT has increasingly gained recognition as a potential adjuvant for conventional cancer treatments. Several preclinical studies and some clinical trials suggest that the use of PDT in combination with established treatments or with newly-developed modalities may be of benefit as compared to the individual modalities. In this review, we briefly introduce the reader to the main photobiological aspects of PDT, and then discuss the use of PDT in combination with other pharmacological approaches for the treatment of cancer.
Secretion and ion transport in airways during inflammation (1987)

Water and secretions interact in airways to produce the sol and gel layers that allow for entrapment of foreign materials and subsequent clearance by ciliary movement and by cough. Active Cl ion transport produces fluid, and this process is activated by products of mast cells (leukotrienes), eosinophils (major basic protein), and by other inflammatory mediators (prostaglandins, bradykinin). Gland secretions produce the bulk of the volume of secretions. Airway irritation stimulates gland secretion reflexly via vagal muscarinic pathways. Recently, the sensory nerves have been discovered to release substance P and other neuropeptides when the airways are irritated. The stimulatory effects of neuropeptides on gland secretion (and on other inflammatory sites) are modulated by enkephalinase a membrane-bound enzyme that cleaves neuropeptides and thereby inactivates them. Up- or down-regulation of enkephalinase is predicted to change the degree of inflammatory response to neuropeptides. Finally, the cell surface of airway epithelial cells have been discovered to secrete large molecular weight glycoconjugates; these secreted products are increased markedly by a series of proteinases produced by inflammatory cells (neutrophils, mast cells) and by bacteria. Their exact physiologic roles are still unknown but they may contribute to the bulk and viscoelastic properties of airway secretions, and they may serve an important role in bacterial, viral and inflammatory cell adhesion.
Antisense oligonucleotides to the p65 subunit of NF-kappa B block CD11b expression and alter adhesion properties of differentiated HL-60 granulocytes (1993)

NF-kappa B is a pleiotropic regulator of a variety of genes implicated in the cellular response to injury. This function has been attributed to the coordinated binding of subunits of NF-kappa B to distinct regions of the promoter elements of numerous genes, including cytokines, growth factor receptors, and adhesion molecules. Antisense phosphorothioate oligonucleotides to the p50 and p65 subunits of the NF-kappa B complex were used to define the physiologic role of this transcription factor in resting and stimulated granulocytes. A reduction in the expression of p65 was produced by treatment with the phosphorothioate antisense oligodeoxynucleotide. This reduction was accompanied by rapid changes in the cellular adhesion of dimethyl sulfoxide-differentiated HL-60 leukemia cells stimulated by 12-O-tetradecanoylphorbol 13-acetate (TPA). These effects were characterized by a marked reduction in CD11b integrin expression on the surface of treated cells. Furthermore, the p65 antisense oligomer effectively abolished an upregulation of CD11b that was produced by formyl-met-leu-phe and TPA. However, the p65 antisense phosphorothioate oligodeoxynucleotide had no significant effect on the production of reactive oxygen intermediates or on phagocytosis by these cells. These findings indicate that antisense oligomers to p65 can be used to define the role of NF-kappa B in the activation pathways of neutrophils.
Automatic Segmentation of Intracochlear Anatomy in Conventional CT (2011)

Cochlear implant surgery is a procedure performed to treat profound hearing loss. Clinical results suggest that implanting the electrode in the scala tympani, one of the two principal cavities inside the cochlea, may result in better hearing restoration. Segmentation of intracochlear cavities could thus aid the surgeon to choose the point of entry and angle of approach that maximize the likelihood of successful implant insertion, which may lead to more substantial hearing restoration. However, because the membrane that separates the intracochlear cavities is too thin to be seen in conventional in vivo imaging, traditional segmentation techniques are inadequate. In this paper, we circumvent this problem by creating an active shape model with micro CT (μCT) scans of the cochlea acquired ex vivo. We then use this model to segment conventional CT scans. The model is fitted to the partial information available in the conventional scans and used to estimate the position of structures not visible in these images. Quantitative evaluation of our method, made possible by the set of μCTs, results in Dice similarity coefficients averaging 0.75. Mean and maximum surface errors average 0.21 and 0.80 mm.
How Does Nonpenetrating Glaucoma Surgery Work? Aqueous Outflow Resistance and Glaucoma Surgery (2001)

Histologic, experimental, and theoretical studies of the aqueous outflow pathways point toward the juxtacanalicular region and inner wall of Schlemm's canal as the likely site of aqueous outflow resistance in the normal eye. At least 50% of the aqueous outflow resistance in the normal eye and the bulk of the pathologically increased resistance in the glaucomatous eye resides in the trabecular meshwork and the inner wall of Schlemm's canal. The uveoscleral, or uveovortex, pathway, which accounts for perhaps 10% of the aqueous drainage in the healthy aged human eye, can become a major accessory route for aqueous drainage after pharmacologic treatment. Surgeries designed to incise or remove the abnormal trabecular meshwork of glaucoma address the pathologic problem of the disease. Surgeries that unroof Schlemm's canal or expand the canal, such as viscocanalostomy, probably cause inadvertent ruptures of the inner wall and juxtacanalicular tissue, thus relieving the abnormal outflow resistance of glaucoma. This review is a summary of current thought on the pathophysiology of aqueous outflow resistance in glaucoma and, in light of this, provides an interpretation of the mechanism of pressure reduction created by these new surgeries.
Mutations of the neurofibromatosis type 2 gene and lack of the gene product in vestibular schwannomas (1994)

Schwannomas are common tumors of the nervous system and are frequently found in patients with neurofibromatosis (NF) 2. Although loss of heterozygosity in NF2 tumors suggests that the NF2 gene functions as a tumor suppressor gene, the NF2 gene shows amino acid sequence homology to structural proteins in one of which dominantly acting mutations have been described. We performed a mutational analysis in 30 vestibular schwannomas and examined the effect of mutations on the NF2 protein. We detected 18 mutations in 30 vestibular schwannomas of which seven contained loss or mutation of both NF2 alleles. Most mutations were predicted to result in a truncated protein. Mutational hot spots were not identified. Immunocytochemical studies using antibodies to the NF2 protein showed complete absence of staining in tumor Schwann cells, whereas staining was observed in normal vestibular nerve. These data indicate that loss of NF2 protein function is a necessary step in schwannoma pathogenesis and that the NF2 gene functions as a recessive tumor suppressor gene.
Temperature modulation of the optical transitions involving the Fermi surface in Ag: Theory (1974)

The thermomodulation mechanism for optical transitions originating or terminating near the Fermi surface in noble metals has been investigated. Detailed thermoderivative line shapes of $\ensuremath{\Delta}{\ensuremath{\epsilon}}_{2}$ for both inter-conduction-band transitions and transitions from the $d$ bands to the Fermi surface have been calculated for Ag. The calculation also gives the temperature dependence of the joint density of states for these transitions.
Six newly recognized types of Streptococcus pneumoniae (1995)

The serological properties of six new pneumococcal capsular types are described. A table listing all 90 pneumococcal types and their cross-reactions is included.
Granulocyte-macrophage colony-stimulating factor regulates the functional adhesive state of very late antigen-4 expressed by eosinophils (1997)

As very late antigen-4 (VLA-4) can exist in different functional states, we have sought to determine whether a cytokine expressed by inflamed endothelium (i.e., granulocyte-macrophage CSF (GM-CSF)) could regulate the functional state of VLA-4 expressed by eosinophils. Using a micropipette single cell adhesion assay able to measure the strength of adhesion forces, eosinophils exhibited low levels of basal adhesion to unstimulated endothelium (separation force, 0.022 +/- 0.003 mdynes). In contrast, individual eosinophils bound to IL-1beta-stimulated endothelium (0.49 +/- 0.02 mdynes), TNF-stimulated endothelium (0.62 +/- 0.05 mdynes), or IL-4-stimulated endothelium (0.11 +/- 0.01 mdynes) with increased avidity as assessed by separation force. Eosinophil binding to IL-4-stimulated endothelium was significantly inhibited by neutralizing Abs to either vascular cell adhesion molecule (VCAM) or VLA-4. The strength of eosinophil adhesion to VCAM (0.31 +/- 0.02 mdynes) or to connecting segment-1 (CS-1) (0.18 mdynes) was greater than the strength of eosinophil adhesion to unstimulated endothelium (0.02 mdynes), but was less than the strength of eosinophil adhesion to IL-1beta-stimulated endothelium (0.49 +/- 0.02 mdynes). After incubating eosinophils for 30 min with GM-CSF, the mean adhesion strength of eosinophils to CS-1 and VCAM increased significantly by 84 and 54%, respectively, compared with that of controls. This increased binding of eosinophils to VCAM or CS-1 was not due to alterations in VLA-4 receptor number (assessed by FACS analysis) or alterations in VLA-4 receptor distribution (assessed by confocal microscopy). These studies suggest that endothelial-derived cytokines such as GM-CSF have the potential to alter the functional state of eosinophil-expressed VLA-4 from a low affinity state to a high affinity state.
Genetics of Parkinson's disease (1997)

For the past 40 years, research into Parkinson's disease (PD) has been predominantly the province of epidemiologists interested in pursuing the connection between the disease and environmental factors such as viral infection or neurotoxins. Hereditary influences were actually discounted because of a high monozygotic twin discordance rate found in studies that were later shown to be inadequate and inconclusive. There has recently been a resurgence of interest in investigating hereditary factors in PD when it became more and more apparent that a positive family history was a major risk factor for the disease. Meanwhile, it also became increasingly apparent from neuropathological studies that the common, idiopathic form of Parkinson's disease had, in fact, a pathological correlate, i.e., the existence of Lewy bodies, an eosinophilic cytoplasmic inclusion body, distributed diffusely throughout the substantia nigra, hypothalamus, hippocampus, autonomic ganglia and olfactory tracts. Although candidate gene approaches to linkage in PD families have not been rewarding, a genome wide scan mapped PD to 4q21-23 in one large family with PD with diffuse Lewy bodies, where a candidate gene, alpha-synuclein, resides. This gene encodes a presynaptic protein of which a peptide fragment is known to be a constituent of Alzheimer's disease plaques. The identification of a missense mutation in the alpha-synuclein gene in four independent PD families suggests that at least some fraction of familial PD with diffuse Lewy bodies is the result of an abnormal protein that interferes with normal protein degradation leading to the development of inclusions and ultimately neuronal cell death. There may be common pathogenetic mechanisms involved in alpha-synuclein mutations in PD and beta-amyloid and presenilin gene mutations in Alzheimer's disease.
Titration of Power Output During Radiofrequency Catheter Ablation of Atrioventricular Nodal Reentrant Tachycardia (1993)

Radiofrequency lesions in the anterior, superior aspect of the tricuspid annulus result in selective elimination of fast pathway function in patients with typical atrioventricular (AV) nodal reentry tachycardia. This technique is simple and effective, but has been associated with a significant risk of inadvertent complete AV block. The purpose of this study was to compare the safety and effectiveness of two different techniques for radiofrequency catheter ablation of the fast AV nodal pathway. Initially, a fixed power output was used at each target site. This method was compared retrospectively to a newer technique where power output was gradually incremented at each site. Radiofrequency power was initially applied at 10 watts for 10-15 seconds. If no junctional ectopy or a change in PR interval was seen, power output was incremented by 2 to 4 watts every 10 to 15 seconds up to a maximum of 30 watts. Thirty seven of 38 (96%) patients treated using this incremental power output were cured of their AV nodal reentry tachycardia. None of these patients developed inadvertent complete AV block. In contrast, 92% of historic controls treated with a fixed power output between 20 and 30 watts achieved a primary success and nine of these 89 (10%) historic controls developed inadvertent complete AV block (P = 0.04). There was no difference in the amplitudes of atrial, His, or ventricular electrograms at the effective sites between the two groups.(ABSTRACT TRUNCATED AT 250 WORDS)
[Phase III randomized clinical trial of intratumoral injection of E1B gene-deleted adenovirus (H101) combined with cisplatin-based chemotherapy in treating squamous cell cancer of head and neck or esophagus]. (2004)

Intratumoral H101 injection showed a distinct efficacy in patients with squamous cell cancer of head and neck or esophagus,and was relatively safe.
Posterior spinal fusion using internal fixation with the Daab plate (1984)

The results of posterior spinal fusion, supplemented by internal fixation with the Daab plate in 43 patients, are presented. The Daab plate is a quadruped implant placed longitudinally in the coronal plane and fixed by simply pinching it around the spinous processes. The cause of the instability necessitating fusion was acute trauma in eight patients, late posttraumatic condition in 11, pure degenerative process in seven and spondylolisthesis in nine patients. In addition, there were solitary cases of tuberculous spondylitis, pyogenic spondylitis and metastatic destruction of the vertebral body. The fusion site was cervical in three, thoracic in eight, thoracolumbar in 12 and lumbar or lumbosacral in 20 cases. The mean follow-up time was 19 months. The consolidation of the fused area could, apart from radiographs, ultimately be evaluated at removal of the implant in 39 patients. The fusion was successful in 37 patients. Compared with previous reports, this result must be considered satisfactory when the severity of the cases in this series is noted. Internal fixation in connection with posterior fusion is needed only exceptionally, but in complicated cases the Daab plate seems to afford a simple method of securing the position of the segments for the first postoperative months.
Chiral OS-dialkyl phosphoramidothioates: their preparation, absolute configuration, and stereochemistry of their reactions in acid and base (1979)

With amines, the cis- and trans-isomers of 2-chloro-1,3,2-oxazaphospholidine-2-thiones, derived from (–)ephedrine, afford the corresponding 2-amino-derivatives which on sequential treatment with acidic alcohol, sodium hydroxide, and alkyl iodide are converted into OS-dialkyl phosphoramidothioates which are usually enantiomerically pure. In methanolic hydrogen chloride the phosphoramidothioates give the corresponding OS-dialkyl methylphosphorothioates with preponderant inversion of configuration whereas with isopropyl alcohol and hydrogen chloride OS-dialkyl isopropylphosphorothioates are formed with preponderant retention of configuration. With ethanolic hydrogen chloride, whether the P–N bond in the phosphoramidothioates is cleaved with inversion or retention of configuration is a function of the acid strength and of the substituents on nitrogen. Reactions which proceed with retention of configuration proceed by double displacements, initial formation of chloridates being followed by displacements with alcohol. Reactions of alkoxides with OS-dialkyl phosphoramidothioates, irrespective of the degree of substitution on nitrogen, proceed with preponderant inversion of configuration to afford OO-dialkyl phosphoramidates.