gebhart/patrepeval huggingface dataset:
Prediction of risk of osteoporosis after gastrectomy for gastric cancer (2021)

Gastrectomy was a risk factor for osteoporosis, and its incidence in the first 10 years after surgery was high. This nomogram can help clinicians to identify patients with gastric cancer most at risk of developing osteoporosis after surgery.
De Novo Assembly of the Complete Genome of an Enhanced Electricity-Producing Variant of Geobacter sulfurreducens Using Only Short Reads (2010)

State-of-the-art DNA sequencing technologies are transforming the life sciences due to their ability to generate nucleotide sequence information with a speed and quantity that is unapproachable with traditional Sanger sequencing. Genome sequencing is a principal application of this technology, where the ultimate goal is the full and complete sequence of the organism of interest. Due to the nature of the raw data produced by these technologies, a full genomic sequence attained without the aid of Sanger sequencing has yet to be demonstrated.We have successfully developed a four-phase strategy for using only next-generation sequencing technologies (Illumina and 454) to assemble a complete microbial genome de novo. We applied this approach to completely assemble the 3.7 Mb genome of a rare Geobacter variant (KN400) that is capable of unprecedented current production at an electrode. Two key components of our strategy enabled us to achieve this result. First, we integrated the two data types early in the process to maximally leverage their complementary characteristics. And second, we used the output of different short read assembly programs in such a way so as to leverage the complementary nature of their different underlying algorithms or of their different implementations of the same underlying algorithm.The significance of our result is that it demonstrates a general approach for maximizing the efficiency and success of genome assembly projects as new sequencing technologies and new assembly algorithms are introduced. The general approach is a meta strategy, wherein sequencing data are integrated as early as possible and in particular ways and wherein multiple assembly algorithms are judiciously applied such that the deficiencies in one are complemented by another.
Expression of Keratin 12 and Maturation of Corneal Epithelium during Development and Postnatal Growth (2006)

In the mouse, the corneal epithelium does not become fully mature until 3 to 6 months after birth, in that a significant number of corneal basal epithelial cells of young mice (<P30), which derive from embryonic surface ectoderm remain undifferentiated and serve as corneal epithelial progenitor cells. These progenitor cells may have some stem cell characteristics.
Mode synchronization in adaptive coding and interleaving systems (2002)

Communication systems employing variable rate adaptive error correction codes and adaptive interleaving have been proposed previously. These systems require the receiver to feedback the channel state information to the transmitter so that the most efficient mode of operation can be selected. A problem behind these systems is to ensure that both the transmitter and receiver are operating at the same modes. This refers to mode synchronization. We propose and compare two general schemes, namely the closed-loop and quasi-closed loop schemes. The closed loop method, which embeds the mode sequence of the current frame in the control header of the forward channel, achieves mode synchronization at the expense of huge overhead. Thus, we proposed the quasi-closed loop method to achieve tradeoff between performance and overhead. Simulation results show that low lost sync rate is achieved with minimal overhead with the proposed scheme.
Muscle Enzyme Release in the Acute Psychoses (1969)

ACOMMON expression of the disease process in an organ is the spilling of large amounts of normally intracellular enzymes into the circulation. For example, increased serum activity of creatine kinase (CPK) and aldolase, two soluble cytoplasmic enzymes of muscle and brain, has diagnostic and prognostic significance in skeletal or cardiac muscle disease, particularly myopathies and myocardial infarction, or both.<sup>1,2</sup>Recent reports indicate that increases of the activity of these enzymes can also occur in the serum of some patients with such neurologic and psychiatric disorders as brain trauma, cerebral vascular disease, encephalitis, meningitis, and acute psychosis.<sup>3-10</sup> Three of the latter studies particularly relevant to the investigations reported here. Schiavone and Kaldor found elevated serum CPK activity in 60% of 109 patients with cerebral dysfunction, including nine of 24 cases of schizophrenia.<sup>4</sup>Bengzon et al, after finding an elevation of serum alkaline
Analysis of brevetoxins by micellar electrokinetic capillary chromatography and laser‐induced fluorescence detection (1997)

Micellar electrokinetic capillary chromatography (MEKC) with laser-induced fluorescence (LIF) detection was used to measure four red tide brevetoxins at sub-attomole levels. The separation of four brevetoxins by MEKC was achieved with a sodium borate/sodium dodecyl sulfate buffer at pH 9.3 Brevetoxins with a terminal alcohol group were derivatized with an acyl azide coumarin to form stable, highly fluorescent products. Brevetoxins with a terminal aldehyde group were reduced to the alcohol with sodium borohydride prior to derivatization with the coumarin. Three derivatized brevetoxins (PbTx-3, PbTx- 5, and PbTx-9) were separated by MEKC and detected using He/Cd laser excitation at 354 nm and fluorescence emission at 410 nm. A fourth brevetoxin (PbTx-2) was converted to PbTx-3 prior to derivatization and was then determined by subtraction. Instrumental detection limits for all four toxins were approximately 0.10 fg or about 10(6)-fold more sensitive than existing liquid chromatographic methods. Brevetoxins were isolated from cell cultures and fish tissue using an alumina column/gel-permeation chromatography procedure. Method detection limits for the brevetoxins in fish tissue were approximately 4 pg/g. These method detection limits are at least 100-fold better than previous chromatographic and/or electrophoretic methods. The MEKC-LIF method reported here allows measurement of brevetoxins at the trace levels considered critical for understanding toxin metabolism and mode of action.
Coherent reflectometer with a two-fibre scattered-light interferometer (2011)

We have designed and implemented a new fibre-optic phase-sensitive coherent reflectometer configuration, which allows one to avoid signal fading owing to the use of a two-fibre scattered-light interferometer.
Dry powder inhaled compound delivery for early pre-clinical in vivo efficacy studies (2013)

Inhaled dry powders are the preferred route of delivery for many respiratory medicines. Toxicology studies are routinely carried out on inhaled dry powders whereas early pre-clinical in vivo efficacy studies often use aqueous formulations. Ideally evaluation of in- vivo efficacy, duration of action and DMPK of novel compounds, delivered as dry powders, should be carried out at an earlier stage in the drug development process. This would allow direct comparisons to be made with toxicology data to establish a therapeutic index and enable a more relevant prediction of clinical efficacy.
A bridge to lower overhead quantum computation (2012)

Two primary challenges stand in the way of practical large-scale quantum computation, namely achieving sufficiently low error rate quantum gates and implementing interesting quantum algorithms with a physically reasonable number of qubits. In this work we address the second challenge, presenting a new technique, bridge compression, which enables remarkably low volume structures to be found that implement complex computations in the surface code. The surface code has a number of highly desirable properties, including the ability to achieve arbitrarily reliable computation given sufficient qubits and quantum gate error rates below approximately 1%, and the use of only a 2-D array of qubits with nearest neighbor interactions. As such, our compression technique is of great practical relevance.
Region segmentation of CT images using mathematical morphology (2002)

A automatic region segmentation method based on mathematical morphology is presented. This method is composed of morphological filtering, multiresolution morphological decomposition, morphological gradient transform, hit/miss transform etc. In applications to CT image region segmentation, it is shown that this approach bears higher level of segmentation accuracy, consistency and robustness to various cases compared to most other existing approaches.
G-NEST: a gene neighborhood scoring tool to identify co-conserved, co-expressed genes (2012)

In previous studies, gene neighborhoods—spatial clusters of co-expressed genes in the genome—have been defined using arbitrary rules such as requiring adjacency, a minimum number of genes, a fixed window size, or a minimum expression level. In the current study, we developed a Gene Neighborhood Scoring Tool (G-NEST) which combines genomic location, gene expression, and evolutionary sequence conservation data to score putative gene neighborhoods across all possible window sizes simultaneously. Using G-NEST on atlases of mouse and human tissue expression data, we found that large neighborhoods of ten or more genes are extremely rare in mammalian genomes. When they do occur, neighborhoods are typically composed of families of related genes. Both the highest scoring and the largest neighborhoods in mammalian genomes are formed by tandem gene duplication. Mammalian gene neighborhoods contain highly and variably expressed genes. Co-localized noisy gene pairs exhibit lower evolutionary conservation of their adjacent genome locations, suggesting that their shared transcriptional background may be disadvantageous. Genes that are essential to mammalian survival and reproduction are less likely to occur in neighborhoods, although neighborhoods are enriched with genes that function in mitosis. We also found that gene orientation and protein-protein interactions are partially responsible for maintenance of gene neighborhoods. Our experiments using G-NEST confirm that tandem gene duplication is the primary driver of non-random gene order in mammalian genomes. Non-essentiality, co-functionality, gene orientation, and protein-protein interactions are additional forces that maintain gene neighborhoods, especially those formed by tandem duplicates. We expect G-NEST to be useful for other applications such as the identification of core regulatory modules, common transcriptional backgrounds, and chromatin domains. The software is available at http://docpollard.org/software.html
TheTrans‐6 fatty acids ofPicramnia sellowii seed oil (1970)

The C18 monoenoic acids inPicramnia sellowii Planch. seed oil include bothcis-andtrans-6-octadecenoic acids, as well as oleic acid. The hexadecenoic acids are also thecis- andtrans-Δ6-isomers, and the eicosenoic acids have Δ6-unsaturation of undetermined geometric configuration. The C18 polyenoic acids detected are 9,12- and 6,9-octadecadienoic and 9,12,15- and 6,9,12-octadecatrienoic acids. Partial investigation of another species,P. pentandra Sw., revealed its oil to have a similar fatty acid composition.
Epidemiological trends of head and neck Cancer survivors in Alberta: Towards improved understanding of the burden of disease (2020)

There is a significant population of head and neck survivors who are younger, male, and more than 10 years post-treatment. While oral cavity cancers have shown stable disease prevalence in recent decades, the number of OPSCC survivors have increased. With an improved understanding of the distribution and characteristics of HNC survivors, a more guided healthcare support network can be fostered for these patients.
Atmospheric Pressure Chemical Vapor Deposition and characterization of TiO<inf>2</inf> antireflection coatings for monocrystalline silicon solar cells (2011)

This paper presents an efficient and less expensive method to fabricate high quality titanium dioxide (TiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> ) thin films by APCVD technique using TiCl <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</sub> as precursor for application as antireflection coatings on monocrystalline silicon solar cells. The structural, electrical and optical properties of the produced coatings were successfully characterized by Atomic Force Microscopy (AFM), Four Point Probe (FPP) and Spectroscopic Ellipsometry (SE) combined with Transmission Spectroscopy, respectively. A perfect agreement between the AFM results and ellipsometric results was confirmed. For ellipsometry modelling process, the TiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> optical constants were successfully modelled by means of the “Multilayer Structure Model” which offers the best results. The refractive index of our TiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> thin films was found to be n = 2.25 at the wavelength λ = 550 nm, with a thickness of 56.2 nm. The obtained results demonstrate the real opportunity of the APCVD technique to prepare high quality antireflection coatings for high efficiency silicon solar cells.
Imaging Across Scale: the Promise of Multi-modal Imaging (2006)

Comprehending neural function requires techniques that permit measurement of large-scale activity over complex networks even as we gain greater understanding of the foundations of this activity at the level of single or small populations of neurons. The measurement techniques currently available, while having yielded important and relevant information on the complexity of global neural networks, still provide only snapshots of the full picture. At present, recording and analysis remain linked to the spatial or temporal resolution inherent to each technique. Thus, the ability to integrate electrophysiological and functional imaging techniques to gain access to the spatio-temporal dynamics of neural activity is an important frontier in modern imaging science
Continuous-wave operation of a YAG laser by off-centered LD side pumping (1989)

Recent advances in high power laser diodes (IDs) provide an ideal optical source for pumping solid state lasers. Many researchers have started to study these types of laser, and most of the work has concentrated on end pumped devices, which have the advantage of low thresholds and high slope efficiencies. Although these devices are compact and efficient, they are not suitable for high power devices.
Structural and biophysical correlation of anti-NANP antibodies with in vivo protection against P. falciparum (2021)

The most advanced P. falciparum circumsporozoite protein-based malaria vaccine, RTS,S/AS01 (RTS,S), confers partial protection but with antibody titers that wane relatively rapidly, highlighting the need to elicit more potent and durable antibody responses. Here, we elucidate crystal structures, binding affinities and kinetics, and in vivo protection of eight anti-NANP antibodies derived from an RTS,S phase 2a trial and encoded by three different heavy-chain germline genes. The structures reinforce the importance of homotypic Fab-Fab interactions in protective antibodies and the overwhelmingly dominant preference for a germline-encoded aromatic residue for recognition of the NANP motif. In this study, antibody apparent affinity correlates best with protection in an in vivo mouse model, with the more potent antibodies also recognizing epitopes with repeating secondary structural motifs of type I β- and Asn pseudo 3<sub>10</sub> turns; such insights can be incorporated into design of more effective immunogens and antibodies for passive immunization.
Formation of Three-Dimensional Ordered Hierarchically Porous Metal Oxides via a Hybridized Epoxide Assisted/Colloidal Crystal Templating Approach (2013)

Three-dimensionally ordered hierarchically porous alumina, iron(III) oxide, yttria, and nickel oxide have been prepared through the hybridization of colloidal crystal-templating and a modified sol-gel method. Simply, highly ordered arrays of poly(methyl methacrylate) (PMMA) were infiltrated with a precursor solution of metal salt and epoxide. Calcination after solidification of the material removed the polymer template while forming the inverse replicas, simultaneously. These hierarchical structures possessing macropore windows and mesopore walls were characterized by powder X-ray diffraction (PXRD), thermogravimetric analysis (TGA), scanning electron microscopy (SEM), and N2 adsorption/desorption techniques to probe the structural integrity. It was revealed by PXRD that the prepared 3D frameworks were single-phase polycrystalline structures with grain sizes between 5 and 27 nm. The thermal stability as studied by TGA illustrates expected weight losses and full decomposition of the PMMA template. SEM reveals the bimodal, hierarchical macroporous frameworks with well-defined macropore windows and mesoporous walls. Gas sorption measurements of the ordered materials display surface areas as high as 93 m(2) g(-1), and average mesopore diameter up to 33 nm. Due to the versatility of this method, we expect these materials will be ideal candidates for applications in catalysis, adsorption, and separations. Furthermore, the implementation of this technology for production of three-dimensionally ordered macroporous materials can improve the cost and efficiency of metal oxide frameworks (MOFs) due to its high versatility and amenability to numerous systems.
Prolonged, Contemporaneous Administration of Pilocarpine and Timolol Increases the Aqueous Humor Pilocarpine Levels in Rabbits (1999)

The purpose of this study was to gather information on the mechanism by which timolol/pilocarpine (TI/PI) combination eyedrops provide additive ocular hypotensive effects. An hypothesis, according to which the combination eyedrops prolong the intraocular permanence of PI as a consequence of decreased aqueous humor secretion induced by TI, was not supported by clear-cut literature evidence. It was thus sought to verify if repeated instillations in albino rabbits of combination TI/PI eyedrops do effectively prolong the turnover of PI. Commercial eyedrops containing 0.68% w/v TI maleate and 2.0% w/v PI hydrochloride, buffered at pH 6.8, and two reference solutions containing PI hydrochloride alone (2% w/v), buffered at pH 5.5 and 6.8, were instilled b.i.d. in albino rabbits for five days. Aqueous humor samples, analyzed after the last treatment, showed that the aqueous humor PI levels observed after administration of the combination eyedrops were significantly higher than those resulting from administration of the reference formulations. When compared with the pH 6.8 reference solution, the pH 5.5 one produced slightly higher and more sustained drug levels in the aqueous humor. The present results appear to confirm the assumption that an increased retention of PI in the aqueous humor is responsible for the additive effects on intraocular pressure reported by several authors for the combination TI/PI eyedrops.
Differential Control of Alveolar and Ductal Development in Grafts of Monodispersed Rat Mammary Epithelium (1991)

Multicellular secretory alveolar units (AU) develop in grafts of monodispersed mammary cells in intact recipient rats co-grafted with mammotropic hormone-secreting pituitary tumor (MtT). The cumulative evidence is consistent with a postulated clonal origin of these structures. Small numbers of multicellular structures of a second type, mammary ductal units (DU), were found in mammary cell grafts in intact Wistar/Furth recipients co-grafted with MtT W10 but not in intact F344 recipients co-grafted with MtT F4. Studies in (Wistar/Furth x F344) F1 hybrid recipients grafted with mammary cells from either parent strain demonstrated that this difference in DU formation is dependent on the strain of grafted MtT, and is not a genetic characteristic of the rat strain. DU formation is stimulated and AU formation is inhibited by elevation of mammotropic hormones from MtT coupled with glucocorticoid deficiency induced by adrenalectomy. cortisol treatment reverses this effect. Finally, in mammary glands in situ in intact rats, the total numbers of AU-forming clonogens decrease during 6 weeks after MtT transplantation. In contrast, during the same period, elevated mammotropins from grafted MtT coupled with glucocorticoid deficiency from adrenalectomy cause an increase in the total number of cells that are capable of AU formation when transplanted to intact recipients co-grafted with MtT. Thus, the same hormonal combination that stimulates DU formation in mammary cell grafts and has previously been shown to promote cancer in mammary glands in situ also stimulates an increase in the glandular content of assayable AU-forming cells in situ.
Predictive Value of Delayed Graft Function Definitions Following Donation After Circulatory Death Renal Transplantation in the United Kingdom (2022)

Purpose: A variety of definitions for delayed graft function (DGF) have been proposed, but none has consistently been shown to be superior for predicting long-term graft outcomes for kidney donation after circulatory death (DCD) transplantation. In this study, real-world clinical outcome data following DCD transplantation were explored to determine the value of various DGF definitions for predicting graft survival. Patients and Methods: Data from 4 centers registered in the UK-based National Health Service Blood and Transplant registry (2010 to mid-2015) were used to assess 4 definitions of DGF in this retrospective chart review study. Results: Depending on the definition used, the frequency of DGF ranged from 119/362 (32.9%) when DGF was determined with available registry data and based on a requirement for dialysis within 7 days post-transplantation, to 224/315 (71.1%) when based on failure to achieve a 10% fall in serum creatinine (SCr) versus baseline per 24 hours averaged over the first 72 hours. Patients without clinical DGF as determined by a physician upon chart review, or when defined as < 30% reduction in baseline SCr within 7 days post-transplantation with or without dialysis, had significantly better graft survival probability 1 year (hazard ratio 2.08 and 4.48, respectively) and 5 years post-transplant, whereas serum creatinine level over the first 72 hours post-transplant was not predictive of graft survival at 1 year. Patients with clinical DGF upon physician chart review also had higher SCr, lower estimated glomerular filtration rate levels, and were dialyzed more (2.3 days) versus patients without (0.2 days). Conclusion: Delayed graft function, determined clinically or using a functional definition, is associated with poorer renal function and remains a useful predictor of graft survival at 1 year after DCD kidney transplantation. Keywords: delayed graft function, DGF, donation after circulatory death, DCD, serum creatinine, SCr
Front Matter: Volume 9100 (2014)

This PDF file contains the front matter associated with SPIE Proceedings Volume 9100, including the Title Page, Copyright information, Table of Contents, Invited Panel Discussion, and Conference Committee listing.