gebhart/patrepeval huggingface dataset:
Cholate-dependent killing of Giardia lamblia by human milk (1985)

We showed previously that nonimmune human milk (NHM) kills Giardia lamblia trophozoites in vitro and presented evidence that killing requires the bile salt-stimulated lipase of milk. Since this enzyme is activated by bile salts, killing should be dependent on the presence of bile salts. We now show that killing by fresh NHM or NHM stored at -70 degrees C is totally dependent on sodium cholate (a bile salt). With less than 0.4 mM cholate, no parasites were killed, whereas with 1 mM cholate, greater than 99.7% were killed by 5% NHM in 30 min. Moreover, killing activity was completely heat labile. The G. lamblia-killing activity of human milk was greatly altered by storage at -10 or -20 degrees C. In less than 23 days, the 50% lethal dose decreased, cholate dependence was lost, and killing activity became heat stable. In contrast, the activity of milk stored at -70 degrees C remained unchanged. Milk lipase activity, like killing activity, became cholate independent during storage at -10 or -20 degrees C. On the basis of these results, we hypothesize that killing of G. lamblia by fresh NHM or NHM stored at -70 degrees C depends on bile salt-stimulated lipase, which must be activated by bile salts. In contrast, NHM stored at -20 degrees C accumulated free fatty acids which kill G. lamblia. In support of this thesis, milk stored at -10 degrees C had a concentration of 18.7 mM free fatty acids compared with only 1.1 mM in an identical sample stored at -70 degrees C.
Evaluation of the effects of systemic treatment with a sclerostin neutralizing antibody on bone repair in a rat femoral defect model (2013)

Systemic administration of a sclerostin neutralizing antibody (Scl-Ab) has been shown to enhance fracture callus density and strength in several animal models. In order to further evaluate the potential of Scl-Ab to improve healing in a bone defect model,we evaluated Scl-Ab in a 3mm femoral defect in young male outbred rats. Scl-Ab was given either continuously for 6 or 12 weeks after surgery or with 2 weeks of delay for 10 weeks. Bone formation was assessed by radiographs, µ-CT, and histology. Complete bony union was achieved in only a few defects after 12 weeks of healing (Scl-Ab treated 5/30, vehicle treated 1/15). µ-CT evaluation demonstrated a significant increase in the BV/TV in the defect in the delayed treatment group (65%, p<0.05), but a non-significant increase in the continuous group (35%, p = 0.11) compared to control. However, both regimens induced an anabolic response in the bone proximal and distal to the defect and in the un-operated femurs. We demonstrate that treatment with Scl-Ab can enhance bone repair in a bone defect and in the surrounding host bone, but lacks the osteoinductive activity to heal it. This agent seems to be most effective in bone repair scenarios where there is cortical integrity.
Gene finding for the helical cytokines (2005)

All data used and the results obtained in the cross-validation analysis are available at http://www.soi.city.ac.uk/~conklin/papers/GT/
Polarization state interference: a general investigation (1997)

On exprime de façon simple les paramètres de Stokes des lumières émergentes de chaque voie d'un interféromètre quelconque isolément, et de la lumière émergente dans le champ d'interférences; ils sont donnés en fonction de la polarisation incidente, à l'aide de ses coordonnées dans l'espace de la sphère de Poincaré sur quatre axes déterminés par l'interféromètre. Si les deux voies ne sont pas dichroïques, ces expressions se simplifient encore. On examine les effets d'une variation du déphasage entre les voies, et on compare avec le cas scalaire. Enfin, on étudie des cas d'interférences de polarisation pures (i.e. sans interférences au sens de l'amplitude): on indique des idées d'expériences où les `franges' d'interférences se traduisent seulement par des gradients des trois caractéristiques de la polarisation successivement (degré de polarisation, ellipticité, et orientation).
<title>Theoretically limited temperature sensitivity of thermal detectors with restricted spectral range</title> (1994)

Spectral characteristics of specific detectivity D<SUP>*</SUP>((lambda) <SUB>m</SUB>) and noise equivalent temperature difference NETD<SUP>*</SUP>((lambda) <SUB>m</SUB>) were calculated for background noise limited thermal detectors with restricted spectral range ((lambda) <SUB>m</SUB> - cut-off wavelength). In the actual spectral range ((lambda) <SUB>m</SUB>&lt;15 micrometers ) thermal detectors are able to ensure the same values of D<SUP>*</SUP>((lambda) <SUB>m</SUB>) and NETD<SUP>*</SUP>((lambda) <SUB>m</SUB>) as for quantum detectors. NETD<SUP>*</SUP>((lambda) <SUB>m</SUB>) and D<SUP>*</SUP>((lambda) <SUB>m</SUB>) values are shown to be connected by `kT<SUP>2</SUP>-rule': NETD<SUP>*</SUP>((lambda) <SUB>m</SUB>) - (root)2kT<SUP>2</SUP>D<SUP>*</SUP>((lambda) <SUB>m</SUB>). It was accentuated that this rule may be applied to quantum photodetectors but with some definitions. The approximations were offered permitting to calculate values of D<SUP>*</SUP>((lambda) <SUB>m</SUB>) and NETD<SUP>*</SUP>((lambda) <SUB>m</SUB>) in all spectral ranges with the accuracy of not worse than 2%. It was shown that as D<SUP>*</SUP>((lambda) <SUB>m</SUB>) of an ideal thermal detector with a cold filter increases the cooling temperature necessary for achievement of theoretical limited values of D<SUP>*</SUP>((lambda) <SUB>m</SUB>) and NETD<SUP>*</SUP>((lambda) <SUB>m</SUB>) also increases. Such a behavior is opposite to that known for quantum photodetectors.
Distribution of ceftazidime in ascitic fluid (1984)

The pharmacokinetics of ceftazidime were investigated in eight normal subjects and eight patients with ascites after intravenous administration of 1 g of the drug. Samples of blood and ascitic fluid were collected for 6 h after dosage, and urine samples were collected for 24 h. Pharmacokinetic data were calculated by using a one-compartment model. The apparent volume of distribution and half-life of elimination (t1/2 beta) in patients with ascites were approximately three times those in normal subjects. In contrast, renal clearance was greater in the normal subjects. With respect to ascites, the mean area under the concentration-time curve was 95.3 +/- 38.3 micrograms X h/ml. The mean ratio of the area under the concentration-time curve for ascitic fluid to that for plasma was 69.9% (+/- 38.2). These data show that ceftazidime rapidly diffuses into the peritoneal space, in which concentrations greater than 10 micrograms/ml were present for at least 6 h.
RNA from the 5′ end of the R2 retrotransposon controls R2 protein binding to and cleavage of its DNA target site (2006)

Non-LTR retrotransposons insert into eukaryotic genomes by target-primed reverse transcription (TPRT), a process in which cleaved DNA targets are used to prime reverse transcription of the element's RNA transcript. Many of the steps in the integration pathway of these elements can be characterized in vitro for the R2 element because of the rigid sequence specificity of R2 for both its DNA target and its RNA template. R2 retrotransposition involves identical subunits of the R2 protein bound to different DNA sequences upstream and downstream of the insertion site. The key determinant regulating which DNA-binding conformation the protein adopts was found to be a 320-nt RNA sequence from near the 5' end of the R2 element. In the absence of this 5' RNA the R2 protein binds DNA sequences upstream of the insertion site, cleaves the first DNA strand, and conducts TPRT when RNA containing the 3' untranslated region of the R2 transcript is present. In the presence of the 320-nt 5' RNA, the R2 protein binds DNA sequences downstream of the insertion site. Cleavage of the second DNA strand by the downstream subunit does not appear to occur until after the 5' RNA is removed from this subunit. We postulate that the removal of the 5' RNA normally occurs during reverse transcription, and thus provides a critical temporal link to first- and second-strand DNA cleavage in the R2 retrotransposition reaction.
Identification and characterization of a novel yeast ω3‐fatty acid desaturase acting on long‐chain n‐6 fatty acid substrates from Pichia pastoris (2007)

A cDNA sequence putatively encoding a omega(3)-fatty acid desaturase gene was isolated from methylotrophic yeast Pichia pastoris GS115. The deduced amino acid sequence of this cloned cDNA showed high identity to known fungal omega(3)-fatty acid desaturases. Functional identification of this gene heterologously in Saccharomyces cerevisiae strain INVScl indicated that the deduced amino acid sequence exhibited omega(3)-fatty acid desaturase activity. The newly identified omega(3)-fatty acid desaturase, named Pp-FAD3, is novel because it showed broad n-6 fatty acid substrate specificity by its ability to convert all the 18-carbon and 20-carbon n-6 substrates examined to the corresponding n-3 fatty acids, with an approximately equivalent high conversion rate. Pp-FAD3 is the first known yeast omega(3)-fatty acid desaturase to act on long-chain n-6 fatty acid substrates. Heterologous expression of the newly identified omega(3) desaturase in different hosts will be an alternative method to increase the flow of n-6 fatty acid intermediates into their n-3 derivatives.
Fibrinogen Prepared from Small Blood Samples for Autologous Use in a Tissue Adhesive System (1988)

The two-component tissue adhesive system where the one component is a concentrated human fibrinogen solution and the other component is a thrombin solution containing Ca2+ is becoming increasingly important in surgery. In the commercially available tissue adhesive, the fibrinogen is separated from pooled plasma. The risk of transmitting foreign immunogens and viruses, always present when foreign biological materials are used, will be eliminated if the fibrinogen is separated from the patient's own blood. A method using ethanol precipitation is described for preparing a concentrated fibrinogen solution from plasma separated from small amounts of blood. The method is fast, the final product can be obtained within 30-60 min after collection of the blood. The recovery is compared with the recovery obtained by separating the fibrinogen with ammonium sulfate precipitation and with cryoprecipitation. The method using ethanol is by far the most profitable, and the product is evaluated by experimental liver surgery in pigs.
Noninvasive detection of coronary artery wall thickening with age in healthy subjects using high resolution MRI with beat‐to‐beat respiratory motion correction (2011)

Despite the small size of our healthy cohort, using high-resolution MR imaging and B2B-RMC, we have demonstrated increasing coronary vessel wall thickness and W/OW with age. The results obtained are consistent with outward vessel wall remodeling.
A Topic-Based Approach to Multiple Corpus Comparison. (2019)

The 27th AIAI Irish Conference on Artificial Intelligence and Cognitive Science (AICS 2019), Galway, Ireland, 5-6 December 2019
Self-assembled polystyrene nanospheres for the evaluation of atomic force microscopy tip curvature radius (2009)

In this paper, self-assembled polystyrene nanospheres are proposed as a shape characterizer sample for SPM tips. Ordered arrays or 2D islands of polystyrene spheres may be prepared either by sedimentation or by crystallization of the colloidal spheres' suspension. The self-assembling mechanism guarantees high reproducibility; thus the characterizer sample can be 'freshly' prepared at each use, avoiding the problem of time and use deterioration and reducing the problem of sample structure fidelity that occurs when lithographic structures are employed. The spheres could also be deposited on the sample itself in order to speed up the characterization process in applications requiring frequent tip characterizations. We present numerical calculations of geometrical convoluted profiles on the proposed structures showing that, for a variety of different tip shapes, at the border between a couple of touching spheres the tip flanks do not come into contact with the spheres. Due to this behaviour, touching spheres are an optimum characterizer sample for SPM tip curvature radius characterization, enabling a straightforward procedure for calculating the curvature radius from the amplitude of tip oscillation along profiles connecting spheres' centres. The new procedure for the characterization of SPM probes was assessed exploiting different kinds of self-assembled structures and comparing results to those obtained by spiked structures and SEM observations.
Intravitreal bevacizumab for myopic choroidal neovascularization: short-term and 1-year results. (2009)

Short-term and twelve-month results indicate that IVB is a safe and effective method to improve visual, reduce CMT and inhibit progression of mCNV.
Effect of Varus/Valgus Malalignment on Bone Strains in the Proximal Tibia After TKR: An Explicit Finite Element Study (2006)

Malalignment is the main cause of tibial component loosening. Implants that migrate rapidly in the first two post-operative years are likely to present aseptic loosening. It has been suggested that cancellous bone stresses can be correlated with tibial component migration. A recent study has shown that patient-specific finite element (FE) models have the power to predict the short-term behavior of tibial trays. The stresses generated within the implanted tibia are dependent on the kinematics of the joint; however, previous studies have ignored the kinematics and only applied static loads. Using explicit FE, it is possible to simultaneously predict the kinematics and stresses during a gait cycle. The aim of this study was to examine the cancellous bone strains during the stance phase of the gait cycle, for varying degrees of varus/valgus eccentric loading using explicit FE. A patient-specific model of a proximal tibia was created from CT scan images, including heterogeneous bone properties. The proximal tibia was implanted with a commercial total knee replacement (TKR) model. The stance phase of gait was simulated and the applied loads and boundary conditions were based on those used for the Stanmore knee simulator. Eccentric loading was simulated. As well as examining the tibial bone strains (minimum and maximum principal strain), the kinematics of the bone-implant construct are also reported. The maximum anterior-posterior displacements and internal-external rotations were produced by the model with 20 mm offset. The peak minimum and maximum principal strain values increased as the load was shifted laterally, reaching a maximum magnitude for -20 mm offset. This suggests that when in varus, the load transferred to the bone is shifted medially, and as the bone supporting this load is stiffer, the resulting peak bone strains are lower than when the load is shifted laterally (valgus). For this particular patient, the TKR design analyzed produced the highest cancellous bone strains when in valgus. This study has provided an insight in the variations produced in bone strain distribution when the axial load is applied eccentrically. To the authors' knowledge, this is the first time that the bone strain distribution of a proximal implanted tibia has been examined, also accounting for the kinematics of the tibio-femoral joint as part of the simulation. This approach gives greater insight into the overall performance of TKR.
Use of Skin Surface Sampling and Ion Mobility Spectrometry as a Preliminary Screening Method for Drug Detection in an Emergency Room (1987)

We have evaluated the use of a novel method for detecting drug residues on the hands of emergency patients suspected of drug overdose. The residues are collected by means of a suction probe and subsequently analyzed by thermal desorption directly into an ion mobility spectrometer. All patients admitted to the Emergency Room had their palms, fingers and nostrils sampled. Of the 101 drug related ingestions, 50 were related to tablets, 47 to film or sugar-coated tablets and 4 to cocaine powder. Positive identification was possible in 42% of tablet related ingestions, 29% of coated tablet or capsule ingestions and in all patients using cocaine. In 53% of the cases where positive drug identification was made, sampling had been carried out within 30 minutes of the patient's arrival at the Emergency Room.
Design of 7 and 19 cells core air-guiding photonic crystal fibers for low-loss, wide bandwidth and dispersion controlled operation (2007)

We study the modal properties of feasible hollow-core photonic bandgap fibers (HC-PBGFs) with cores formed by omitting either 7 or 19 central unit-cells. Firstly, we analyze fibers with thin core surrounds and demonstrate that even for large cores the proposed structures are optimum for broad-band transmission. We compare these optimized structures with fibers which incorporate antiresonant core surrounds which are known to have low-loss. Trade-offs between loss and useful bandwidth are presented. Finally, we study the effects that small modifications to the core surround have on the fiber's group velocity dispersion, showing the possibility of engineering the dispersion in hollow-core photonic bandgap fibers.
Pro-inflammatory cytokines and the pathogenesis of Gaucher's disease: increased release of interleukin-6 and interleukin-10 (1997)

Gaucher's disease is characterized by hepatosplenomegaly, bone-marrow infiltration, osteonecrosis and bone thinning, associated with the presence of pathological macrophages that contain undegraded glycosphingolipids. To investigate the possible role of cytokines in the systemic and local manifestations of established Gaucher's disease, interleukin-1 beta (IL-1 beta), interleukin-6 (IL-6), tumour necrosis factor-alpha (TNF alpha) and interleukin-10 (IL-10) were measured in freshly-separated serum. Samples from eight male and 14 female patients with type 1 Gaucher's disease were compared with sera from 22 healthy age- and sex-matched controls. Concentrations of IL-6 and IL-10 were significantly elevated in sera from patients with Gaucher's disease (11.9 +/- 1.8 (SEM) pg/ml and 5.4 +/- 0.5 (SEM) pg/ml, respectively) compared with those of controls (4.1 +/- 0.9 (SEM) and 0.8 +/- 0.3 (SEM) pg/ml, p < 0.0001). No significant differences in concentrations of TNF alpha or IL-1 beta were identified. IL-6 has been implicated in the development of localized osteolysis in multiple myeloma and in the development of post-menopausal osteoporosis. High concentrations of IL-6 in the serum of patients with Gaucher's disease may thus reflect the development of the bone lesions commonly associated with this disorder. Since IL-6 and IL-10 are important regulators of lymphocyte growth and differentiation, and IL-6 concentrations were significantly raised in patients with oligo- or polyclonal increases in serum immunoglobulins, enhanced release of these cytokines from pathological macrophages provides a pathological link between Gaucher's disease and associated lympho-proliferative disorders.
Analysis of Events Associated With Cell Cycle Arrest at G2 Phase and Cell Death Induced by Cisplatin (1990)

DNA is the accepted target for cisplatin, but recent evidence has shed doubt on DNA synthesis as the critical process. L1210/0 cells incubated for 2 hours with cisplatin progress to the G2 phase of the cell cycle and are arrested there for several days. They then either progress in the cell cycle or die. In cells that eventually die, total transcription, polyadenylated [poly(A)+] RNA synthesis, and protein synthesis were markedly inhibited only after 48 hours. Nicotinamide adenine dinucleotide (NAD) and adenosine triphosphate (ATP) levels decreased after 3 days. Cell membrane integrity was lost after 4 days. These results demonstrate that cells can be lethally damaged, yet continue to undergo apparently normal metabolic activities for several days. In a previous study, DNA double-strand breaks were detected after 1 day. We now show that by 2 days, breaks are visible as fragmentation in the nucleosome spacer regions of chromatin. This type of damage is consistent with cell death occurring by the process of apoptosis. Cell shrinkage and morphology were also consistent with this type of cell death. The slow cell death reported here appears to occur at the G2/M transition and may involve events that normally occur at this stage of the cell cycle. These results demonstrate the importance of DNA degradation as an early and possibly essential step in cell death.
Highly Sensitive In Vitro Methods for Detection of Residual Undifferentiated Cells in Retinal Pigment Epithelial Cells Derived from Human iPS Cells (2012)

Human induced pluripotent stem cells (hiPSCs) possess the capabilities of self-renewal and differentiation into multiple cell types, and they are free of the ethical problems associated with human embryonic stem cells (hESCs). These characteristics make hiPSCs a promising choice for future regenerative medicine research. There are significant obstacles, however, preventing the clinical use of hiPSCs. One of the most obvious safety issues is the presence of residual undifferentiated cells that have tumorigenic potential. To locate residual undifferentiated cells, in vivo teratoma formation assays have been performed with immunodeficient animals, which is both costly and time-consuming. Here, we examined three in vitro assay methods to detect undifferentiated cells (designated an in vitro tumorigenicity assay): soft agar colony formation assay, flow cytometry assay and quantitative real-time polymerase chain reaction assay (qRT-PCR). Although the soft agar colony formation assay was unable to detect hiPSCs even in the presence of a ROCK inhibitor that permits survival of dissociated hiPSCs/hESCs, the flow cytometry assay using anti-TRA-1-60 antibody detected 0.1% undifferentiated hiPSCs that were spiked in primary retinal pigment epithelial (RPE) cells. Moreover, qRT-PCR with a specific probe and primers was found to detect a trace amount of Lin28 mRNA, which is equivalent to that present in a mixture of a single hiPSC and 5.0×10⁴ RPE cells. Our findings provide highly sensitive and quantitative in vitro assays essential for facilitating safety profiling of hiPSC-derived products for future regenerative medicine research.
Semantic Compositionality through Recursive Matrix-Vector Spaces (2012)

Single-word vector space models have been very successful at learning lexical information. However, they cannot capture the compositional meaning of longer phrases, preventing them from a deeper understanding of language. We introduce a recursive neural network (RNN) model that learns compositional vector representations for phrases and sentences of arbitrary syntactic type and length. Our model assigns a vector and a matrix to every node in a parse tree: the vector captures the inherent meaning of the constituent, while the matrix captures how it changes the meaning of neighboring words or phrases. This matrix-vector RNN can learn the meaning of operators in propositional logic and natural language. The model obtains state of the art performance on three different experiments: predicting fine-grained sentiment distributions of adverb-adjective pairs; classifying sentiment labels of movie reviews and classifying semantic relationships such as cause-effect or topic-message between nouns using the syntactic path between them. 1