gebhart/patrepeval huggingface dataset:
The use of vaccination as an option for the control of avian influenza (2003)

Recent epidemics of highly contagious animal diseases included in list A of the Office International des Epizooties, such as foot-and-mouth disease, classical swine fever and avian influenza (AI), have led to the implementation of stamping-out policies resulting in the depopulation of millions of animals. The enforcement of a control strategy based on culling animals that are infected, suspected of being infected or suspected of being contaminated, which is based only on the application of sanitary restrictions on farms, may not be sufficient to avoid the spread of infection, particularly in areas that have high animal densities, thus resulting in mass depopulation. In the European Union, the directive that imposes the enforcement of a stamping-out policy (92/ 40/EC) for AI was adopted in 1992 but was drafted in the 1980s. The poultry industry has undergone substantial changes in the past 20 years, mainly resulting in shorter production cycles and in higher animal densities per territorial unit. Due to these organizational changes, infectious diseases are significantly more difficult to control because of the greater number of susceptible animals reared per given unit of time and due to the difficulties in applying adequate biosecurity measures. The slaughter and destruction of great numbers of animals is also questionable from an ethical point of view. For this reason, mass depopulation has raised serious concerns for the general public and has recently led to very high costs and economic losses for national and federal governments, stakeholders and, ultimately, for consumers. In the past, the use of vaccines in such emergencies has been limited by the impossibility of differentiating vaccinated/infected from vaccinated/non-infected animals. The major concern was that through trade or movement of apparently uninfected animals or products, the disease could spread further or might be exported to other countries. For this reason, export bans have been imposed on countries enforcing a vaccination policy. This review considers the possible strategies for the control of avian influenza infections, bearing in mind the new proposed definition of AI, including the advantages and disadvantages of using conventional inactivated (homologous and heterologous) vaccines and recombinant vaccines. Reference is made to the different control strategies, including the restriction measures to be applied in case of the enforcement of a vaccination policy. In addition, the implications of a vaccination policy on trade are discussed. It is concluded that if vaccination is accepted as an option for the control of AI, vaccine banks, including companion diagnostic tests, must be established and made available for immediate use.
A computed tomography scan and anatomical cadaveric study of the pterygopalatine ganglion for use in Gamma Knife treatment of cluster headache (2007)

Object Gamma Knife surgery has recently been used to treat patients with cluster headaches. Both the trigeminal nerve root and the pterygopalatine ganglion (PPG) have been targeted. However, there are no clear-cut anatomical landmarks on computed tomography (CT) scans or magnetic resonance images that accurately identify the PPG. Therefore, the authors performed microsurgical dissections on latex-injected cadaver heads to expose the PPG and correlated the findings with thin-slice axial CT scans obtained in the same heads to determine how best to target the PPG. Methods Three cadaver heads (five sides) previously injected with colored latex were dissected using skull base approaches and microsurgical techniques to identify the PPG and surrounding structures. Measurements were then made to different osseous anatomical landmarks such as the foramen rotundum, vidian canal, and so on. The PPG was marked with a radiopaque marker and thin-slice CT scans were obtained in the cadaver heads to develop some correlates that could be used to identify where the PPG is located on CT scans. Results The PPG was clearly identified in all specimens and had a mean diameter of 3.58 ± 0.6 mm. The PPG was always located in the same plane (lateral and vertical) as the vidian canal and was located on average 2.7 ± 0.3 mm from the end of the canal. The vidian canal was clearly identified on coronal CT scans and had a diameter of 3.05 mm. Conclusions There was a clear and constant relationship between the PPG and vidian canal. The vidian canal is easily identified on coronal CT scans and can be used as a landmark to target the PPG with the Gamma Knife.
Guided wave based structural health monitoring: A review (2016)

The paper provides a state of the art review of guided wave based structural health monitoring (SHM). First, the fundamental concepts of guided wave propagation and its implementation for SHM is explained. Following sections present the different modeling schemes adopted, developments in the area of transducers for generation, and sensing of wave, signal processing and imaging technique, statistical and machine learning schemes for feature extraction. Next, a section is presented on the recent advancements in nonlinear guided wave for SHM. This is followed by section on Rayleigh and SH waves. Next is a section on real-life implementation of guided wave for industrial problems. The paper, though briefly talks about the early development for completeness,. is primarily focussed on the recent progress made in the last decade. The paper ends by discussing and highlighting the future directions and open areas of research in guided wave based SHM.
Contemporary outcomes of cardiac surgery patients supported by the intra-aortic balloon pump (2022)

The use of the perioperative IABP proved to be safe and demonstrated relatively low complication rates, particularly for leg ischaemia. As such, we believe that specialists should not be held back to use this widely available treatment in high-risk cardiac surgical patients when indicated.
Computational Chemistry (2010)

Enhancement of the capability of electroactive polymer (EAP) materials to induce large strain and stress can be accomplished by conventional enhancement techniques as well as through computational chemistry. Enhancing the load carrying capability of EAP materials can be obtained by increasing their stiffness with a minimum compromise of their displacement actuation. Such an enhancement requires taking into account the properties of the produced material and their compatibility with the operation conditions. Additional enhancement can be obtained by allowing for internal molecular realignment in response to Coulomb forces. Such improvement can be applicable to the electrostrictive polymers however obtaining improvement of other types of materials requires fundamental research at the molecular level as can be obtained by computational chemistry.
Microcystin-LR promotes migration and invasion of colorectal cancer through matrix metalloproteinase-13 up-regulation (2015)

Microcystin-LR (MC-LR) is an environmental toxin from blooms of cyanobacteria and it has been shown to be one of the environmental carcinogens for the progression of colorectal carcinoma. However, there is no direct evidence that MC-LR can induce colorectal cancer migration and invasion. In the present study, 0.04 or 40 µg/kg/d (human tolerable daily intake value of MC-LR) MC-LR treatment was observed to induce Matrix Metalloproteinase-13 (MMP-13) expression in tumor tissues and local invasion in DLD-1 xenograft model. The results are consistent with those of cell test showing that MC-LR treatment enhanced migration and invasion of DLD-1, HT-29, and SW480 cells and are also correlated with the increased mRNA and protein levels of MMP-13 by Quantitative real-time PCR, Luciferase assay, and Western blot assay respectively in DLD-1 cells and HT-29 cells after MC-LR exposure. In addition, MMP-13 siRNA inhibited MC-LR induced migration and invasion enhancement and MMP-13 over-expression in DLD-1 cells and HT-29 cells. This is the first paper confirming MC-LR-induced MMP-13 expression can promote colorectal cancer invasion and migration. Further investigation revealed that phosphorylation of AKT increased in MC-LR-treated cells, and the phosphatidylinositol 3-kinase/Akt. (PI3-K/AKT) inhibitor LY294002 effectively abolished MC-LR-enhanced migration and invasion and MMP-13 expression. Therefore, based on these observations, we concluded that the activation of PI3K/AKT by MC-LR results in MMP-13 expression, leading to the migration and invasion of DLD-1 cells and HT-29 cells. The study provides a mechanistic insight into the promoting colorectal cancer functions of MC-LR.
Carbon cycling in the Amazon River: Implications from the 13C compositions of particles and solutes (1992)

The 13C:12C of suspended particu-late organic C (POC), dissolved organic C (DOC), and dissolved inorganic C (DIC) were measured during 1982–1984 at 11 main-channel and 7 tributary stations over an 1,800 km reach of the Amazon River between Vargem Grande and Obidos, Brazil. The measured δ13C range vs. marine carbonate (PDB) was –32 to −26‰ for suspended POC, −30 to −28‰ for DOC, and −26 to −12% for DIC. The δ13C of the fine particulate organic C (FPOC) decreased downriver from Vargem Grande, with values lowest during the falling-water portion of the runoff cycle; these trends were the result primarily of input of 13C-depleted FPOC from tributaries draining the lowland regions of the Amazon basin and floodplain soils. The δ13C of the FPOC at Obidos implies that at least 35% of the POC exported by the Amazon River is derived from the lowland portion of the Amazon basin. The δ13C of DIC decreased downriver with the lowest values measured during falling water; these trends were due primarily to within-river respiration and tributary input. The δ13C of the DIC suggests that ∼40% of the organic matter being respired in the river is C4 plant material derived from floodplain grasses.
Structure Preserving CCA Secure Encryption and Its Application to Oblivious Third Parties. (2011)

Abstract. In this paper we present the first public key encryption scheme that is structure preserving, i.e., our encryption scheme uses only algebraic operations. In particular it does not use hash-functions or interpret group elements as bit-strings. This makes our scheme a perfect building block for cryptographic protocols where parties for instance want to prove, to each other, properties about ciphertexts or jointly compute ciphertexts. Our scheme is also very efficient and is secure against adaptive chosen ciphertext attacks. We also provide a few example protocols for our scheme. For instance, a joint computation of a ciphertext, generated from two secret plaintexts from each party respectively, where in the end, only one of the parties learns the ciphertext. This latter protocol serves as a building block for our second contribution which is a set of protocols that implement the concept of oblivious trusted third parties. This concept has been proposed before, but no concrete realization was known. 1
Antiferromagnetic spin fluctuations in CeRhSn probed bySn119NMR (2004)

We have carried out $^{119}\mathrm{Sn}$ nuclear magnetic resonance (NMR) measurements on the quasi-Kagom\'e compound CeRhSn. We found that $^{119}\mathrm{Sn}$ Knight shift $(^{119}K)$ is highly anisotropic and shows Curie-Weiss type temperature $(T)$ dependence above $25\phantom{\rule{0.3em}{0ex}}\mathrm{K}$. In this $T$ range, the NMR relaxation rate shows $^{119}(1∕{T}_{1})\ensuremath{\propto}\sqrt{T}$ and is enhanced by magnetic fluctuations. At low $T$'s, $^{119}K$ stays constant and the enhanced Korringa relation of $^{119}({T}_{1}T{K}^{2})=\mathrm{const}$ is observed, differently from the non-Fermi-liquid behavior observed for bulk measurements. The present NMR results suggest that antiferromagnetic spin fluctuations exist in CeRhSn.
Pediatric Glial Heterotopia in the Medial Canthus (2017)

Glial heterotopias are rare, benign, congenital, midline, and nonteratomatous extracranial glial tissue. They may be confused as encephalocele or dermoid cysts and are mostly present in the nose.An 8-month-old African female child presented with a slow growing paranasal mass. The mass had been present at the left upper medial canthus since birth and had slowly and progressively enlarged. There was no communication between the mass and the cranial cavity during the operational procedure. The mass was immunohistochemically positive for S-100 protein as well as for glial fibrillary acidic protein, but negative for proliferating cell nuclear antigen. This suggested that the mass was composed of benign glial tissues with many astrocytes.The purpose of this report is to demonstrate the first patient with pediatric glial heterotopic tissue in the medial canthus and to report the clinical importance of its immunohistochemical findings.
Color-center powder laser: the effect of pulverization on color-center characteristics (1997)

Stimulated emission is obtained and characterized in a powder of LiF crystal with color centers. Absorption, luminescent, and kinetics properties of color centers are studied in powder samples of LiF. They are found to be rather different from those in a bulk material. The difference is explained by dislocations mechanically created during the pulverization of the material. The characteristics of stimulated emission in LiF powder samples were found very different from those in scattering Nd-doped luminophosphors. This difference can be ascribed to a much higher emission cross section and a much smaller lifetime of emitting centers in LiF.
Clinical Performance of an In-Line Point-of-Care Monitor in Neonates (2000)

Repeated laboratory testing of critically ill neonates using an ex vivo in-line monitor designed for use in neonates provides reliable laboratory results. The blood loss and hemolysis data obtained suggests that this monitoring device offers potential for reducing neonatal blood loss-and possibly transfusion needs-during the first weeks of life. Before this promising technology can be routinely recommended for care of critically ill neonates, greater practical experience in a variety of clinical settings is needed.
Rethinking origin licensing (2017)

Human cells that lack a subunit in their origin recognition complex are viable, which suggests the existence of alternative mechanisms to initiate DNA replication.
THE RELATIVE RIGIDITY OF WELDED AND RIVETED CONNECTIONS (1934)

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Protein design on pyruvate decarboxylase (PDC) by site-directed mutagenesis. Application to mechanistical investigations, and tailoring PDC for the use in organic synthesis. (1997)

Pyruvate decarboxylases (E.C. 4.1.1.1) from various organisms have been studied for many years, mainly with respect to the mechanism of the non-oxidative decarboxylation reaction. Although the C-C-bond-forming properties of these enzymes are known and have been applied for many years in biotransformations for the synthesis of chiral alpha-hydroxy ketones, only little is known about the factors influencing the carboligase side-reaction. The present review surveys recent efforts in the study of site-directed mutagenesis on PDCs, which are discussed against a background of the structural and kinetical investigations. It also includes recent studies on tailoring the PDCs of Zymomonas mobilis for the syntheses of (R)-phenylacetyl carbinol (PAC), a pre-step in the synthesis of L-ephedrine, by protein design techniques.
Protocol for bulk RNA sequencing of enriched human neutrophils from whole blood and estimation of sample purity (2023)

Although neutrophils are the most abundant leukocyte in healthy individuals and impact outcomes of diseases ranging from sepsis to cancer, they remain understudied due to technical constraints of isolation, preservation, and sequencing. We present a modified Smart-Seq2 protocol for bulk RNA sequencing of neutrophils enriched from whole blood. We describe steps for neutrophil isolation, cDNA generation, library preparation, and sample purity estimation via a bioinformatic approach. Our approach permits the collection of large cohorts and enables detection of neutrophil transcriptomic subtypes. For complete details on the use and execution of this protocol, please refer to LaSalle et al. (2022)<sup>1</sup> and Boribong et al. (2022).<sup>2</sup>.
Mixed-valence compounds as polarizing agents for Overhauser dynamic\n nuclear polarization in solids (2021)

In this paper we investigate a novel set of polarizing agents --\nmixed-valence compounds -- by theoretical and experimental methods and\ndemonstrate their performance in high-field Dynamic Nuclear Polarization (DNP)\nexperiments in the solid state. Mixed-valence compounds constitute a group of\nmolecules, in which molecular mobility persists even in solids. Consequently,\nsuch polarizing agents can be used to perform Overhauser-DNP experiments in\nsolid-state, with favorable conditions for dynamic nuclear polarization\nformation at ultra-high magnetic fields.\n
Enhanced preservation of the auditory nerve following cochlear perfusion with nerve growth factors. (1995)

Survival of auditory neurons in the cochlea is thought to be an important factor in the success of cochlear implantations. Damage to the cochlear end-organ often produces loss of dendrites in the osseous spiral lamina. The authors have established a method that delivers water soluble pharmacologic agents to the cochlea using a mini osmotic pump with a polyethylene cannula that is inserted into the scala tympani via cochleostomy. The cannula is filled with an ototoxic agent, neomycin, that destroys the end-organ over the first 24 hours after insertion. Nerve growth factor (NGF), or a control substance, is placed in the pump reservoir and is pumped into the cochlea over a 2-week period. In this study, auditory nerve fibers in the osseous spiral lamina were counted in the apical, middle, and basal turns of the cochlea in 16 guinea pigs. At each location, fiber counts were significantly higher when neomycin was followed by perfusion with NGF, than when it was followed by infusion with control substances. The study demonstrates that NGF confers some protection against ototoxic induced degeneration of the auditory nerve in vivo.
Imaging issues for interferometric measurement of aspheric surfaces using CGH null correctors (2010)

Aspheric surfaces are measured using standard interferometers coupled with computer generated holograms (CGHs) that compensate the aspheric wavefronts. Such systems can measure complex aspheric shapes with accuracy of a few nanometers. However, the imaging properties of the interferometer-CGH combination can provide limitations for data mapping, resolution, and accuracy. These effects are explored, with an emphasis on the diffraction effects that are unique to interferometry.
Electrical, optical, and mechanical behavior of ferroelectric Gd2(MoO4)3 (1970)

Results of a number of electrical, optical and mechanical measurements on ferroelectric Gd2(MoO4)3, are presented Based on these results it is concluded that the symmetry in the paraelectric phase above 159°C is tetragonal 42m, and the symmetry below the transition is orthorhombic mm2. Twin walls are shown to be ferroelectric domain walls with the relationship between the polarity of the spontaneous polarization P, and the relative positions of the orthorhombic a and b axes being dictated by the piezoelectric effect in the paraelectric phase. A large mechanical dimension change and large optical effects accompanying ferroelectric switching are discussed and possible applications of these effects are considered briefly.
Decorin has an appetite for endothelial cell autophagy (2013)

DCN (decorin), an extracellular matrix constituent and archetypical small leucine-rich proteoglycan (SLRP), acts as a soluble tumor repressor. DCN exerts high-affinity binding interactions with receptor tyrosine kinases and evokes receptor internalization consequent with lysosomal degradation for tumorigenic and angiogenic suppression. In our recent study, we discovered that DCN evokes synthesis of PEG3 (paternally expressed 3), an imprinted gene often silenced in various forms of cancer. Upon DCN stimulation, PEG3 relocalizes to BECN1- and LC3-positive phagophores. Importantly, PEG3 physically associates with BECN1- and LC3-containing supramolecular complexes, in a DCN-inducible manner, and PEG3 is necessary to maintain homeostatic levels of BECN1. Furthermore, DCN evokes a protracted autophagic program via transactivation of the BECN1 and MAPLC3A loci that is critically dependent on PEG3 expression. Mechanistically, DCN directly binds to the Ig domains 3-5 of the KDR/VEGFR2 ectodomain, in a region that partially overlaps with the canonical binding site for VEGFA. Therefore, we have unveiled a novel mechanism for a secreted proteoglycan to induce endothelial cell autophagy in a PEG3-dependent manner. These findings are consistent with earlier preclinical studies focusing on DCN-mediated tumorigenic and angiogenic suppression and may represent the mechanism of action to achieve these effects. Therefore, DCN and perhaps other members of this class of matrix constituents may represent a novel control of autophagy from the outside of the cells.
Performance of the high-definition circulating tumor cells (HD-CTC) assay in patients with non-small cell lung cancer (NSCLC). (2012)

e21074 Background: Technologies to isolate and study circulating tumor cells (CTCs) became available in recent years. To date, the most widely employed techniques to detect CTCs use EpCAM based enrichment protocols. However, those assays are only able to find CTCs in a minority of patients with NSCLC, thus limiting its potential applicability. We are reporting performance of a new enrichment-free HD-CTC assay in patients with NSCLC. Methods: This multi-institutional study recruited patients with all stages of NSCLC. Blood was collected at the time of the study entry, 3 weeks, 3m, 6m, 9m, and 12 m. CTCs were identified with enrichment free fluorescent labeling followed by automated digital microscopy. CTCs were physically and morphologically characterized by cytokeratin (CK) intensity, nuclear size, apoptotic changes, and aggregate formation. Cells were classified as HD-CTCs if they met strict morphologic and immunofluorescence characteristics. This assay has been previously validated in 15 normal controls. Results: 106 patients were recruited (I-10, II-3, III-34, IV-59), 78 were chemotherapy naïve. 85%, 79%, and 53% of patients with stages, I+II, III, and IV had detectable HD-CTCs. The chemotherapy naïve cohort had median HD-CTCs of 4.4/mL (range 0–515.6) and a mean of 44.1 (±95.2)/mL. No significant differences were detected in median HD-CTC count between tumor stages (p = 0.32). CK intensity, nuclear size, frequency of apoptosis and aggregate formation was also similar across stages. 28 patients with stage IV disease were analyzed with multiple draws over time. Mean CTC counts were averaged over multiple draws. In each individual patient there was a trend for increased CTC prevalence with advancement of the disease. Median survival was 244 days for patients with ≥5 CTC/mL vs. 304 days for patients with &lt; 5 CTC/mL. HR 4.0, (p=0.0084). Conclusions: The HD-CTC assay can detect CTCs in a high percentage of patients with early and advanced NSCLC. Small subset analysis demonstrated the prognostic value for the enumeration of HD-CTCs. The high prevalence of HD-CTCs across stages could make this assay an ideal candidate for larger scale investigation into prognostic and predictive features of HD-CTCs.
Rhenium(VII) Oxo Complexes as Extremely Active Catalysts in the Dehydration of Primary Amides and Aldoximes to Nitriles (2002)

An economical and environmentally benign process for the preparation of nitriles by the dehydration of primary amides and aldoximes is catalyzed by rhenium(VII) oxo complexes such as perrhenic acid and trimethylsilylperrhenate (see scheme). The reaction proceeds at azeotropic reflux (with the removal of water) under essentially neutral conditions.