gebhart/patrepeval huggingface dataset:
Clinical Molecular Imaging in the Gastrointestinal Tract (2008)

Introduction – Greater sensitivity and specificity for the clinical detection of disease in the gastrointestinal tract, including esophagus, stomach, small bowel, and colon, may be achieved with use of exogenous probes that target molecular markers of neoplasia. These probes can be labeled with fluorescent dyes and detected endoscopically during routine screening, and guide tissue biopsy for early detection of cancer, assessment of sub-mucosal invasion, and monitoring response to therapy. There has been a great deal of research that demonstrates the use of molecular probes to target neoplasia. For example, monoclonal antibodies have been investigated for tumor detection and drug delivery because of their high specificity;1 however, their use in vivo has been limited by immunogenicity and challenges associated with reagent development and production in quantity. Recently, a number of near infrared fluorescent imaging probes have been developed to detect neoplasia with fluorescence endoscopy. The molecular targets for detection have included proteolytic enzymes, matrix metalloproteinases, endothelial-specific markers, and apoptosis reporters.2-5 Thus, methods of targeted detection are promising, and further development is needed to improve the detection rate for flat dysplasia that cannot be appreciated on standard white light endoscopy as well as for polypoid adenomas.
Measurements of spectra of clustered Barkhausen transitions in technical steel (1973)

Various measurements are performed to investigate the spectra of clustered Barkhausen transitions in technical steel. These spectra are formed by the discontinuous jumps of magnetization in the material, when the external magnetic field is changed with relatively high speed. The methods used include power, amplitude and autocorrelation spectra and their magnetization and temperature dependences. A differential correlation is shown to exist between the optically measured grain size and the different spectra, thus confirming the basic principle of a recently proposed electronic differential grain-size analyzer for technical steel.
Fusion of liposomes induced by a cationic protein from the acrosome granule of abalone spermatozoa (1986)

Lysin, a protein of Mr 16 000 from the acrosome granule of the abalone, is responsible for the dissolution of the egg vitelline layer. The primary structure of this cationic protein projects some hydrophobic domains in the secondary structure. Lysin was found to associate nonselectively with phospholipid bilayers and cause a spontaneous release of encapsulated carboxyfluorescein in liposomes. The association of lysin with phosphatidylcholine liposomes suggests that there is a hydrophobic interaction between lysin and lipid bilayers. Binding of lysin to phospholipid resulted in the aggregation of phosphatidylserine-containing liposomes, but aggregation was not observed in neutral phosphatidylcholine liposomes. Resonance energy transfer and dequenching of fluorescent 1-palmitoyl-2-cis-parinaroylphosphatidylcholine were both used to determine the fusogenic activity of lysin in aggregated liposomes. Results from both assays are consistent. Lysin-induced fusion was observed in all the phosphatidylserine-containing liposomes, and the general trend of fusion susceptibility was phosphatidylserine/phosphatidylcholine (1:2) approximately equal to phosphatidylserine/phosphatidylcholine/phosphatidylethanolamine (1:1:1) greater than phosphatidylserine/phosphatidylethanolamine (1:2). Cholesterol up to 30% did not affect the intrinsic fusion susceptibility. A hydrophobic penetration by protein molecules and the packing of phospholipid bilayers are used to interpret the fusion susceptibility. Lysin-induced liposome aggregation was highly independent of the state of self-association of lysin in ionic medium. However, the fusogenic activity of self-associated lysin was found to be much less than the monodispersed one. Liposomes preincubated with Ca2+ did not fuse initially as readily as those without Ca2+ treatment.(ABSTRACT TRUNCATED AT 250 WORDS)
Efficient models of polymerization applied to FtsZ ring assembly in Escherichia coli (2018)

High protein concentrations complicate modeling of polymer assembly kinetics by introducing structural complexity and a large variety of protein forms. We present a modeling approach that achieves orders of magnitude speed-up by replacing distributions of lengths and widths with their average counterparts and by introducing a hierarchical classification of species and reactions into sets. We have used this model to study FtsZ ring assembly in <i>Escherichia coli</i> The model's prediction of key features of the ring formation, such as time to reach the steady state, total concentration of FtsZ species in the ring, total concentration of monomers, and average dimensions of filaments and bundles, are all in agreement with the experimentally observed values. Besides validating our model against the in vivo observations, this study fills some knowledge gaps by proposing a specific structure of the ring, describing the influence of the total concentration in short and long kinetics processes, determining some characteristic mechanisms in polymer assembly regulation, and providing insights about the role of ZapA proteins, critical components for both positioning and stability of the ring.
Claudin 19-based familial hypomagnesemia with hypercalciuria and nephrocalcinosis in a sibling pair (2016)

Although rare, FHHNC should be suspected in patients who present with nephrocalcinosis in the setting of congenital eye anomalies..
Detection of loss of heterozygosity in formalin-fixed paraffin-embedded tumor specimens by the polymerase chain reaction. (1991)

A polymerase chain reaction-based procedure was used for the detection of DNA length polymorphisms generated by naturally occurring genetic deletions or insertions of known sequence. This method consists of a simple one-step assay that does not require any restriction enzyme analysis or Southern blot hybridization, allowing identification in ethidium bromide-stained gels. The procedure described here was used to detect loss of heterozygosity at various loci, including the Hbb beta-globin gene cluster, in chemically induced mouse skin tumors, using a variety of tissue preparations, including microdissection of formalin-fixed, paraffin-embedded specimens, short-term cultures, and fluorescence-activated cell sorting of epithelial populations. This approach may be useful in detecting tumor-specific reduction to homozygosity at polymorphic chromosomal loci, allowing the mapping of putative tumor-suppressor loci involved in carcinogenesis.
Molecular Epidemiology and Evolution of European Bat Lyssavirus 2 (2018)

Bat rabies cases in Europe are mainly attributed to two lyssaviruses, namely European Bat Lyssavirus 1 (EBLV-1) and European Bat Lyssavirus 2 (EBLV-2). Prior to the death of a bat worker in Finland in 1985, very few bat rabies cases were reported. Enhanced surveillance in the two subsequent years (1986-1987) identified 263 cases (more than a fifth of all reported cases to date). Between 1977 and 2016, 1183 cases of bat rabies were reported, with the vast majority (>97%) being attributed to EBLV-1. In contrast, there have been only 39 suspected cases of EBLV-2, of which 34 have been confirmed by virus typing and presently restricted to just two bat species; <i>Myotis daubentonii</i> and <i>Myotis dasycneme</i>. The limited number of EBLV-2 cases in Europe prompted the establishment of a network of European reference laboratories to collate all available viruses and data. Despite the relatively low number of EBLV-2 cases, a large amount of anomalous data has been published in the scientific literature, which we have here reviewed and clarified. In this review, 29 EBLV-2 full genome sequences have been analysed to further our understanding of the diversity and molecular evolution of EBLV-2 in Europe. Analysis of the 29 complete EBLV-2 genome sequences clearly corroborated geographical relationships with all EBLV-2 sequences clustering at the country level irrespective of the gene studied. Further geographical clustering was also observed at a local level. There are high levels of homogeneity within the EBLV-2 species with nucleotide identities ranging from 95.5-100% and amino acid identities between 98.7% and 100%, despite the widespread distribution of the isolates both geographically and chronologically. The mean substitution rate for EBLV-2 across the five concatenated genes was 1.65 × 10<sup>-5</sup>, and evolutionary clock analysis confirms the slow evolution of EBLV-2 both between and within countries in Europe. This is further supported by the first detailed EBLV-2 intra-roost genomic analysis whereby a relatively high sequence homogeneity was found across the genomes of three EBLV-2 isolates obtained several years apart (2007, 2008, and 2014) from <i>M. daubentonii</i> at the same site (Stokesay Castle, Shropshire, UK).
Event-plane-dependent dihadron correlations with harmonicvnsubtraction in Au + Au collisions atsNN=200GeV (2014)

STAR measurements of dihadron azimuthal correlations ($\ensuremath{\Delta}\ensuremath{\phi}$) are reported in midcentral (20--60%) Au + Au collisions at $\sqrt{{s}_{{}_{\mathit{NN}}}}=200$ GeV as a function of the trigger particle's azimuthal angle relative to the event plane, ${\ensuremath{\phi}}_{s}=|{\ensuremath{\phi}}_{t}\ensuremath{-}{\ensuremath{\psi}}_{\mathrm{EP}}|$. The elliptic (${v}_{2}$), triangular (${v}_{3}$), and quadratic (${v}_{4}$) flow harmonic backgrounds are subtracted using the zero yield at minimum (ZYAM) method. The results are compared to minimum-bias d + Au collisions. It is found that a finite near-side ($|\ensuremath{\Delta}\ensuremath{\phi}|&lt;\ensuremath{\pi}/2$) long-range pseudorapidity correlation (ridge) is present in the in-plane direction (${\ensuremath{\phi}}_{s}\ensuremath{\sim}0$). The away-side ($|\ensuremath{\Delta}\ensuremath{\phi}|&gt;\ensuremath{\pi}/2$) correlation shows a modification from d + Au data, varying with ${\ensuremath{\phi}}_{s}$. The modification may be a consequence of path-length-dependent jet quenching and may lead to a better understanding of high-density QCD.
Diversity in Guanosine 3′,5′-Bisdiphosphate (ppGpp) Sensitivity among Guanylate Kinases of Bacteria and Plants (2014)

The guanosine 3',5'-bisdiphosphate (ppGpp) signaling system is shared by bacteria and plant chloroplasts, but its role in plants has remained unclear. Here we show that guanylate kinase (GK), a key enzyme in guanine nucleotide biosynthesis that catalyzes the conversion of GMP to GDP, is a target of regulation by ppGpp in chloroplasts of rice, pea, and Arabidopsis. Plants have two distinct types of GK that are localized to organelles (GKpm) or to the cytosol (GKc), with both enzymes being essential for growth and development. We found that the activity of rice GKpm in vitro was inhibited by ppGpp with a Ki of 2.8 μM relative to the substrate GMP, whereas the Km of this enzyme for GMP was 73 μM. The IC50 of ppGpp for GKpm was ∼10 μM. In contrast, the activity of rice GKc was insensitive to ppGpp, as was that of GK from bakers' yeast, which is also a cytosolic enzyme. These observations suggest that ppGpp plays a pivotal role in the regulation of GTP biosynthesis in chloroplasts through specific inhibition of GKpm activity, with the regulation of GTP biosynthesis in chloroplasts thus being independent of that in the cytosol. We also found that GKs of Escherichia coli and Synechococcus elongatus PCC 7942 are insensitive to ppGpp, in contrast to the ppGpp sensitivity of the Bacillus subtilis enzyme. Our biochemical characterization of GK enzymes has thus revealed a novel target of ppGpp in chloroplasts and has uncovered diversity among bacterial GKs with regard to regulation by ppGpp.
Immunotherapy with CpG‐ODN in neoplastic meningitis: A phase I trial (2015)

TLR-9 agonists are immunostimulating agents that have antitumor effects in animal models. A phase I trial was conducted to define the safety profile of subcutaneous injections, combined with intrathecally administration of CpG-28, a TRL 9 agonist, in patients with neoplastic meningitis (NM). Cohorts of 3-6 patients with NM were treated for 5 weeks with escalating doses of CpG-28. The primary endpoint was tolerance. Secondary endpoints were progression free survival (PFS) and overall survival (OS). Twenty-nine patients were treated with CpG-28. The primary cancers were malignant glioma, lung carcinoma, breast cancer, melanoma or melanocytoma, ependymoma, and colorectal cancer. The median age was 56 years and median Karnovsky Performance status (KPS) was 70%. The treatment was well tolerated. Adverse effects that were possibly or probably related to the studied drug were grade 2 lymphopenia, anemia and neutropenia, local erythema at injection sites, fever and seizure. There were five serious adverse events: two confusions, two infections of ventricular devices and one grade 4 thrombopenia and neutropenia. The median PFS was 7 weeks and median OS was 15 weeks. Interestingly, the median survival was slightly (but not significantly) higher in the eight patients who were concomitantly treated with bevacizumab (19 weeks vs 15 weeks; P = 0.11). CpG-28 was well tolerated at doses up to 0.3 mg/kg subcutaneously and 18 mg intrathecally. Additional trials are warranted.
Thr 94 and Wat2b Effect Protonation of the Retinal Chromophore in Rhodopsin (2003)

Only with the help from (little) “friends” is it possible for the 11-cis-retinal Schiff base to compete successfully against Glu 113 for a proton (see picture). A strategically placed amino acid, Thr 94, plus a water molecule are sufficient to reduce the basicity of the glutamate and stabilize the protonated chromophore—this is the result of ab initio optimization and molecular-dynamic study of the retinal binding site in rhodopsin.
Red blood cell lipid peroxidation in predialysis chronic renal failure. (1987)

In hemodialysis patients the pentose-phosphate shunt activity is deficient. As a consequence, the lipid peroxidation of the erythrocyte membranes is increased as shown by the increase in malonyldialdehyde concentrations and is accompanied by a decrease of the level of vitamin E in RBC. In the present study we have found that increased lipid peroxidation of the erythrocyte membranes is present also in chronic renal failure patients in the predialysis state, provided that the serum creatinine levels are higher than 5 mg/dl.
Synthesis and secretion of extracellular enzymes by bacilli. (1985)

Bacillus spp. possess well characterized excretion mechanisms for enzymes such as alpha-amylase and serine protease. The physiological basis of this protein excretion is reviewed and the potential for secretion of foreign proteins outlined in this review.
Demographic characteristics of smoldering multiple myeloma patients: A hospital-based study including 11,643 patients. (2019)

e13064 Background: SMM is the requisite asymptomatic phase that precedes Multiple Myeloma (MM). Observation until progression to MM has been the standard of care. However, the improvement in risk assessment and utility of chemoprevention strategies stemmed from large trials (e.g. QUIREDEX and E3A06) is beginning to shift the paradigm toward early detection of SMM by implementing screening strategies (e.g., PROMIS study). Lack of specific ICD code for SMM has been a major problem in epidemiologic studies aiming at characterizing the demographics and temporal dynamics of SMM. Here, we used the National Cancer Data Base (NCDB), which covers more than 70% of cancer pts in the USA, for this purpose. Methods: NCDB data from year 2010 to 2014 was analyzed. We defined SMM as pts with ICD-O 9732 that were placed on active surveillance or did not receive any therapy in the first 3 months (m) after diagnosis (Ravindran et al. Blood Cancer J. 2016). Institution size was categorized as small, medium and large if they reported &lt; 10, 10-50, and &gt; 50 cases per year, respectively. Results: Out of a total of 68234 MM pts, we identified 11643 (17%) with SMM. Median follow up was 32 m (0 - 85). Median age was 65 years (26 - 90), 52% were males, 71% were white and 24% were black. Median survival was 77.7 and 49.8 m for pts with SMM and MM, respectively ( p= 0.001). Median age at diagnosis of SMM was 62 and 66 years in blacks and whites, respectively ( p= 0.01). Over 87% of pts were diagnosed in small and medium size institutions (38% and 49%, respectively). Medicare was the main insurance payer (57%), followed by private insurance (32%) and Medicaid (5%), and 3% were not insured. The majority of pts (59.5%) lived in areas where the median income is less than $46K/year. Median distance traveled to treatment facility was 8.5 miles. During the first two years from diagnosis 18% needed treatment which is compatible with known estimated 10% per year risk of progression from SMM to MM. Conclusions: This large study of over 11,000 SMM pts highlights the national demographics of SMM diagnosed between years 2010 and 2014. Our results indicate that targeting small and medium size facilities should be an essential part of SMM screening strategies.
Involvement of caspases in apoptotic cell death of murine macrophages infected with Actinobacillus actinomycetemcomitans (2001)

Infection of murine macrophages in vitro with periodontopathic bacterium Actinobacillus actinomycetemcomitans induces apoptotic cell death. In this study, we investigated the involvement of caspases in apoptotic cell death of A. actinomycetemcomitans-infected macrophages. Two peptide inhibitors of caspases, benzyloxycarbonyl-Val-Ala-Asp (OMe)-fluoromethyl ketone (Z-VAD-FMK) and benzyloxycarbonyl-Asp-Glu-Val-Asp (OMe)-fluoromethyl ketone (Z-DEVD-FMK), inhibited apoptotic cell death of murine macrophage cell line J774.1 infected with A. actinomycetemcomitans. During the process of apoptosis, interleukin-1beta (IL-1beta) was detected in the culture supernatants of J774.1 cells. IL-1beta secretion was blocked by the caspase-1 inhibitor, Z-VAD-FMK, indicating that caspase-1 is involved in not only the induction of apoptosis but also the IL-1beta secretion from A. actinomycetemcomitans-infected J774.1 cells. Immunoblot analysis revealed that the infection of A. actinomycetemcomitans to J774.1 cells induced the cleavage of retinoblastoma protein (Rb), suggesting that caspase-3 was activated by A. actinomycetemcomitans infection. The cytosol from A. actinomycetemcomitans-infected J774.1 cells induced Rb proteolysis in vitro, which was inhibited by the caspase-3 inhibitor, Z-DEVD-FMK. Furthermore, caspase-3-like activity was markedly increased in J774.1 cells infected with A.actinomycetemcomitans between 12 h and 24 h, which was subsequently inhibited by the addition of caspase-3 inhibitor, Z-DEVD-FMK. These findings indicate that caspase-3 induces apoptosis in J774.1 cells infected with A. actinomycetemcomitans. Taken together, these results suggest that caspase-1 and caspase-3 are involved in the induction of apoptosis in A. actinomycetemcomitans-infected macrophages.
<title>Shape memory alloys for damage-resistant composite structures</title> (1995)

Shape memory alloy (SMA) materials such as nitinol have unique properties associated with the shape recovery effect and the material's phase changes that have been used in a variety of actuator and sensing applications. By embedding SMA elements into host composite materials, control or modification of the SMA hybrid composite's structural properties can be accomplished in-service, thereby increasing the hybrid composite's structural functionality. Utilizing the SMA's substantial capacity to dissipate strain energy to increase the hybrid composite's static functionality is addressed herein. Specific applications of SMA hybrid composites for improving polymer matrix composite material's impact damage resistance is presented. Hybridizing composites with nitinol improves their impact resistance because of nitinol's tremendous capacity to dissipate impact strain energy through the stress-induced martensitic phase transformation. The amount of impact damage is reduced and the material's resistance to impact perforation at various velocities is improved. The experimental response of nitinol hybrid composites to low and high velocity impact perforation is presented. The unique toughness and resistance to permanent deformation that is a result of the stress-induced martensitic phase transformation enables the nitinol to dissipate on the order of 4 times the strain energy of high alloy steel and 16 times that of many graphite/epoxy composites.
Pain and dissociation (1993)

London Psychiatric Hospital, London, Ontario N6A 4H1 Canada ∗Corresponding author: H. Merskey, London Psychiatric Hospital, 850 Highbury Avenue, P.O. Box 2532, London, Ontario N6A 4H1, Canada. (Received and accepted 25 August 1993.)
Integration and expression of a truncated simian virus 40 early gene fragment in mammalian cells. (1982)

The recombinant plasmid p102 based on pBR322 carrying approximately equal to 50% of the replicator proximal early region of simian virus 40 (SV40) DNA, including the viral origin of replication, has been constructed. It lacks a major part of the large tumor (T) antigen 3'-coding region, the T-antigen termination codon, and the polyadenylylation site. The plasmid was transferred together with the herpes simplex virus thymidine kinase (TK) gene as a selectable marker to mouse LTK- cells. TK+ cell clones were isolated and their high molecular weight DNAs were shown by DNA blotting and hybridization experiments to contain the SV40 DNA fragment from the recombinant. In some of these clones, heterogeneous expression of the SV40 DNA fragment could be detected by immunofluorescence while, in control experiments in which a plasmid containing the complete SV40 early DNA region was used, this extensive heterogeneity of T-antigen expression was not observed. RNA . DNA hybridization experiments showed that the SV40-specific RNA of those clones is polyadenylylated. The molecular weight of the T-antigen-related protein coded by p102 corresponded well to the expected coding capacity of the SV40 DNA fragment. Small tumor antigen was not expressed.
Increased Corneal Thickness Simulating Elevated Intraocular Pressure (1978)

A 17-year-old girl had intraocular pressure readings of 30 to 40 mm Hg in both eyes, with normal visual fields and optic nerve heads. Medical treatment was unsuccessful in lowering the IOP measurements substantially. The central corneal thickness was 0.90 mm in each eye in the absence of corneal edema. Cannulation of the left anterior chamber revealed an IOP of 11 mm Hg, while the Perkins' and Schiŏtz' tonometers gave readings of 35 and 34 mm Hg, respectively. Previously, elevated tonometry readings had been obtained by Goldmann's, Perkins', Schiŏtz', MacKay and Marg's, pneumatic tonometer and air puff tonometer. This suggested that measurement of central corneal thickness be performed in cases in which IOP recordings do not correspond to other clinical findings.