gebhart/patrepeval huggingface dataset:
Abstract P6-05-12: Comprehensive molecular analysis of estrogen receptor positive breast cancer to determine clinically actionable alterations (2013)

Abstract Introduction. Understanding the genetic landscape of estrogen receptor positive breast caner is critical for defining clinically actionable alleles that may be targeted using next generation biologics. PIK3CA mutations have previously been reported to be the most common mutation within estrogen receptor positive breast cancer, however the overlap and mutual exclusivity with other key driving alleles is poorly understood, especially how these biomarkers change following treatment failure. We custom designed a mutation, copy number variation and RNA expression panels to profile biomarkers from low quality formalin fixed paraffin embedded extracted material. Data relating to key pathways, such as PI3K and immune modulatory pathways, and overlap with other biomarkers will be presented. Methods. Formalin fixed paraffin embedded material was available from 195 primary cases and 95 paired metastatic estrogen receptor positive breast cancer patients. Samples were assayed for the expression of PTEN by IHC, hotspot mutations in 11 oncogenic driving genes using Q-PCR based technology, copy number alterations in 42 genes using Q-PCR based technology and RNA expression using a custom designed 400 breast cancer specific NanoString gene panel. Results. PTEN loss, as defined by H-score of 0, was found in 4.5% of primary samples and in 4.3% of metastatic samples. PIK3CA mutations were found in 43% of primary samples and in 38% of metastatic samples and were largely found to be mutually exclusive with PTEN loss. AKT1 mutations were found in 5.4% of primary samples and in 4.1% of metastatic samples. Less frequent mutations in KRAS (7.0%) and BRAF (1.7%) were found in the primary sample, and some were co-existing with PIK3CA mutations. Copy number gains were found in CCND1 (23.5%), ZNF703 (19.5%), FGFR1 (16.8%) and PAK1 (11.4%) and were largely concordant with the paired metastatic sample. Analysis with clinical outcome is ongoing. Conclusions. PIK3CA was the most frequently altered gene detected and was mutually exclusive with other key driving mutations within the PI3K pathway (AKT1 and PTEN). A strong concordance was observed between genetic alterations found in the primary sample and the paired metastatic sample. Mutations and expression gains within clinically actionable targets were found less frequently, but may provide alternative treatment strategies for these patients following failure of endocrine therapy. Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P6-05-12.
Reference advice for word sense disambiguation (2013)

Much of the world's knowledge is encoded in natural language. Accessing this information would be invaluable for applications such as agent systems, question answering, the semantic web, expert systems, and many more. However, language is very ambiguous – each word in a natural language utterance can have a variety of meanings. Word sense disambiguation is the task of determining the dictionary (or lexical) sense of each word in a context. Knowing which sense a word represents allows us to ascertain its meaning. 
In this work, we introduce a new resource for WSD processing: reference advice. Reference advice uses reference resolution methods to infer potential meanings of referring expressions, such as 'he', 'she,' 'this,' 'it' and many more. We present a method for creating reference advice, and incorporating that advice into WSD processing. We also develop several system configurations which act as points of comparison for evaluation. 
Lastly, we discuss the impact of the success of reference advice in supporting WSD processing. We explore a shift away from pipeline text processing architectures, wherein each processing component feeds its results downstream until a final processing component presents a solution. We discuss how our system represents a step toward text processing architectures where each processing component is able to provide input to many other processing components, not just those components that are rigidly positioned downstream.
Angiogenic marker associated with resistance to neoadjuvant chemoradiotherapy in rectal cancer. (2013)

11030 Background: The ability to achieve pathologic down staging after neoadjuvant chemoradiotherapy (CRT) is correlated with improved survival. However, there is no effective method of predicting which patients will response to neoadjuvant CRT. Neoadjuvant CRT can change the expression of angiogenic factors. However, little is known about its possible changes in response to preoperative CRT. We examined the expression of angiogenic factors in rectal cancer tissues before preoperative CRT and after surgery. Methods: Fifty five patients with locally advanced rectal cancer were studied. All patients were given preoperative CRT of 5040 cGy for 5-6 weeks with concurrent administration of 5-fluorouracil and leucovorin. Surgical resection was performed 6–8 weeks later in all patients. Immunohistochemical staining for angiogenenic markers (vascular endothelial growth factor [VEGF], placenta growth factor [PLGF], hypoxia inducible factor 1α [HIF 1α], stromal cell derived factor [SDF 1α]) were performed on specimens obtained before preoperative CRT and after surgery. A semiquantitative-immunohistochemical score established from the extension and intensity of the angiogenic factors was used for analysis. Results: The positive expression rate of VEGF, PLGF, SDF 1α, and HIF 1α was 56.4% (31/55), 65.5% (36/55), 70.9% (39/55), and 47.3% (26/55), respectively. The expression rate of VEGF, PLGF, SDF 1α, and HIF 1α was increased by 3.6% (2/55), 7.3% (4/55), 30.9% (17/55), and 1.8% (1/55) after neoadjuvant CRT, respectively. Expression of VEGF, PLGF, and HIF 1α protein was downregulated after neoadjuvant CRT in the rectal cancer tissues (P &lt; 0.001, P = 0.001, P = 0.044, respectively). However, SDF 1α was upregulated after neoadjuvant CRT (P &lt; 0.001). And also, upregulated expression of SDF 1α after neoadjuvant CRT was significantly associated with resistance to CRT (P = 0.035). However, SDF 1α showed no correlation with other clinical factors (age, sex, clinical stage). Conclusions: Expression of SDF-1α was increased in the rectal cancer tissue after neoadjuvant CRT, as well as has been associated with CRT resistance. Our data suggests that SDF 1α should be evaluated as new target for antiangiogenic therapy.
Urticaria, arthralgia, and nephropathy without amyloidosis: another variant of the Muckle‐Wells syndrome? (1996)

The term Muckle-Wells syndrome (MWS) describes an autosomal dominant disorder characterised by various combinations of urticaria, sensorineural deafness, amyloidosis, arthralgia and skeletal abnormalities. We describe a family with nephropathy and several symptoms of MWS, but no evidence of deafness or amyloidosis. Since nephropathy without amyloidosis has never been reported in MWS, but deafness is a feature of all reported pedigrees, we conclude that members of this family have a previously unreported inherited predisposition to urticaria, arthralgia and nephropathy which is distinct from the MWS phenotype.
Z-Axis Interconnection in Organic Packaging (2011)

Greater I/O density at the die level, more demanding performance requirements, and the continued desire to package more function into smaller devices is driving the need for improved wiring density and a concomitant reduction in feature sizes for electronic packages. Traditionally, greater wiring densities have been achieved by reducing the dimensions of vias, lines, and spaces, while also increasing the number of wiring layers. However, each of these methods possesses inherent limitations in today's most challenging multi-chip module (MCM) and system-in-package (SiP) applications that also demand reduction in size, weight and power (SWaP). These applications are forcing new methods to be developed for achieving greater wiring densities while also meeting the cost for performance challenges that exist within this industry. One method of extending wiring density beyond the limits imposed by today's traditional approaches is the strategy of making metal-to-metal z-axis interconnection of subcomposites during lamination to form a composite structure. Conductive joints can be formed during lamination using an electrically conductive paste. As a result, one is able to fabricate structures with vertically-terminated vias of arbitrary depth. Replacement of conventional plated through holes with vertically-terminated vias opens up additional wiring channels on layers above and below the terminated vias, enables die shrink, and eliminates via stubs which cause reflective signal loss. In addition, parallel lamination of individually testable subcomposites offers opportunity for yield improvement, shorter cycle times, and ease of incorporating embedded features conducive to SiP applications. This technique has also been shown to be viable across a multitude of dielectric material sets (including Teflon, PPE, LCP and Epoxies) as well as various conductive joining materials allowing it to be utilized in various applications as well as giving designers the flexibility to mix materials within the same package to incorporate various functionality.
P128 The role of small bowel capsule endoscopy as a diagnostic tool in isolated complex perianal disease (2023)

Abstract Background Isolated complicated perianal disease (cPD) might be the sole representation of Crohn’s disease (CD). We aimed to evaluate the impact of small bowel capsule endoscopy (SBCE) as a diagnostic tool for CD in this population. Methods A multicenter, retrospective cohort study from three tertiary centers. Patients with cPD who had a negative workup for CD (Ileocolonoscopy and cross-sectional imaging) and underwent evaluation with SBCE were included. Demographics, biomarkers, and the Lewis inflammatory score (LS) were recorded and analyzed. A LS≥135 was considered a positive SBCE. Results Ninety-one patients were included: 65 males (71.4%), mean age 40 (14) years, median duration of cPD 25.13 months (12.53-66.1). SBCE was positive in 24 patients (26.37%). Median LS was 675 (222-1518). Fecal calprotectin (FC) positively correlated with LS (r=0.81; p&amp;lt;0.0001): patients with a positive vs. negative SBCE had a significantly higher mean FC level (255 [389] vs 97[180], p=0.02), Figure 1. Correspondingly, a FC level ≥ 300 mg/kg had a specificity of 90% for a positive SBCE, while a cutoff of FC level &amp;lt;100 mg/kg or &amp;lt;50 mg/kg had a sensitivity of only 40% or 50% to rule out small bowel CD, respectively. Conclusion SBCE was positive in over a quarter of patients with cPD and a negative workup for CD. FC levels correlated with the degree of inflammation defined by the LS. However, the sensitivity of low FC to rule out CD was low. These results suggest that SBCE is an essential diagnostic tool for patients with cPD even after negative workup.
Sidewall Surface Roughness of Sputtered Silicon I: Surface Modelling (2003)

Mathematical models for the calculation of sidewall surface roughness have been developed for focused ion beam (FIB) sputtering. The surface roughness profile at the sidewall was different to the bottom surface profile for the same sputtering parameters and substrate material. The cumulative sputtering by the Gaussian beam creates a steady state surface profile at the sidewall which has been used to develop surface roughness models. The ion intensity distribution profile was considered to be Gaussian. The beam function includes ion type, ion acceleration voltage, beam radius, tailing and neighbouring of the successive beams. Knowing the beam radius and pixel spacing, sidewall surface roughness of FIB sputtered microfeatures can be calculated using these models. The substrate material function has no direct effect on the sidewall surface profile if the same material is used for the study of beam profile and fabrication of microfeatures.
Fractional Reserve Banking in Grain (1984)

FRACTIONAL RESERVE BANKS, namely, enterprises being legally liable to pay some substance on demand while regularly having too little on hand to satisfy all their obligations, are commonly associated exclusively with money. Conceivably, fractional reserve banks can deal in substances other than money. As it happens, Chicago's warehousemen of the 1860s practiced fractional reserve banking not in dollars or sterling but in grain. l These warehousemen operated in the style of a conventional financial intermediary, borrowing short through demand deposits in order to lend long. The natural evolution of fractional reserve banking in grain in nineteenth-century Chicago was interrupted, however. Ever more stringent laws, the result of repeated campaigns against fraudulent receipts, eventually forced Chicago's warehousemen to keep 100 percent reserves. Consequently, the organization of the grain trade past and present not only provides information about the development of fractional reserve banking in general but reveals the effects of a rare experiment in outlawing fractional reserve banking.
Sparse Bayesian DOA Estimation Using Hierarchical Synthesis Lasso Priors for Off-Grid Signals (2020)

Within the conventional sparse Bayesian learning (SBL) framework, only Gaussian scale mixtures have been adopted to model sparsity-inducing priors that guarantee the exact inverse recovery. In light of the relative scarcity of formal SBL tools in enforcing a proper sparsity profile of signal vectors, we explore the use of hierarchical synthesis lasso (HSL) priors for representing the same small subset of features among multiple responses. We outline a viable approximation to this particular choice of sparse prior, leading to tractable marginalization over all weights and hyperparameters. We then discuss how the statistical variables of the hierarchical Bayesian model can be estimated via an adaptive updating formula, and include a refined one dimensional searching procedure to extraordinarily improve the direction of arrival (DOA) estimation performance when take the off-grid DOAs into account. Using these modifications, we show that exploiting HSL priors are very helpful in encouraging sparseness. Numerical simulations also verify the superiority of the proposal in terms of convergence speed and root mean squared estimation error, as compared to the traditional and more recent sparse Bayesian algorithms.
Graphical language interpreter and meshing tool for electromagnetic computations (1992)

The authors present three software tools that were developed together with an electromagnetic field computation program within the framework of finite and boundary element (possibly coupled) methods. The first tool consists of a two-dimensional or three-dimensional structure generator whose results are transmitted to a second tool: an interactive meshing program or an automatic surface generator. These three programs, written in FORTRAN and associated with the submission of a dynamic memory allocation module, are very simple to use and have proved to be extremely useful by allowing the submission of complicated real cases in a short time. Two examples are considered: a stepping motor and a hairpin transformer.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A Simple G-Banding Technique Adaptable for Fluorescent in situ Hybridization (FISH) and Physical Ordering of Human Renin (REN) and Catepsin E (CTSE) Genes by Multi-Color FISH. (1993)

We developed a simple technique for delineation of refined replication G-band in combination with fluorescent in situ hybridization (FISH). By using this system we localized three genes of pepsinogen C (PGC), renin (REN), and cathepsin E (CTSE) on 6p21.1, 1q32, and 1q32, respectively. Further, we determined the physical order of REN and CTSE on chromosome band 1q32 as cen-(1q32)-REN-CTSE-tel by multi-color FISH.
Treated sewage effluent - an alternative water supply for irrigation in the Maltese Island (2005)

Water is a scarce substance in the Maltese islands because of geographic and climatic conditions.&#13;\nMalta has no surface waters that can be economically exploited; the islands depend on frail&#13;\ngroundwater resources that are subject to fierce competition and constant pressure resulting from&#13;\nintense human activity over a relatively small territory. As a result, the status of groundwater in Malta&#13;\nis today under constant threat of anthropogenic activity that is reflected through quality and quantity&#13;\ndepletion of the resource. Malta is among the first 10 top-ranking countries in global water scarcity&#13;\nwith the highest competition index (Table 1) of 24,800 inh/hm3.yr in 1995 (Margat and Vallee, 2000).
Quality of life of patients with total loss of teeth and psychometric properties of the OHIP-20 DG enquireR. Part 2. Monitoring stages of dental orthopedic treatment (2022)

BACKGROUND: The most affordable and economical types of prosthetics are modern designs of completely removable plate prostheses. However, in most cases, they do not meet the patients expectation. OHIP-20-DG, which is a specific quality-of-life (QOL) questionnaire, is a valid tool that allows diagnosis of patients response to treatment, assessment of the effectiveness of prosthetics, and better understanding of patients complaints and dissatisfaction. AIM: To create a sensitive specific questionnaire of dental QOL indicators for patients with total loss of teeth based on the well-known valid questionnaire Dental health impact profile OHIP-49 and to examine patients quality of life before and after prosthetic application. MATERIAL AND METHODS: The QOL of 50 patients with total loss of teeth (17 women and 33 men, aged 4287 years), who received removable dentures with an acrylic polymer base and set teeth, was examined. QOL monitoring was performed using the proposed specific questionnaire OHIP-20 DG. RESULTS: The integral QOL index increased to 47.42% after prosthetic application and to 78.43% following adaptation to the prosthesis after 6 months. Age and gender differences in the QOL level of patients were determined. According to the domains physical discomfort, psychological discomfort, and social maladjustment, men and women assessed their satisfaction with their physical, psychological, emotional, and social functioning differently. Gender differences in patients aged 55 years in the psychological discomfort and social maladjustment domains were significant (p=0.065) when compared with those of patients aged 55 years (p=0.115). CONCLUSION: Results of monitoring the QOL of patients with total loss of teeth before, during the stages, and after application of prosthetics with fully removable dentures, obtained using the OHIP-20 DG questionnaire, allow us to reliably assess the effectiveness of prosthetics.
A Simple and Efficient Interprocess Communication System for Actually Using a Laboratory Computer Network (1987)

An interprocess communication system (IPCS) is being developed at Lawrence Livermore National Laboratory to support a network of computers which do data acquisitioin and data processing for fusion experiments. The IPCS permits us to improve system performance by allowing us to move programs to different CPUs for increased efficiency or to add more CPUs for more parallel operation. We discuss motivations, architecture, implementation, usage and results of our experience with the IPCS.
Uptake and release of neurotransmitter candidates, [3H]serotonin, [3H]glutamate, and [3H]?-aminobutyric acid, in taste buds of the mudpuppy,Necturus maculosus (1998)

Neurotransmitters in vertebrate taste buds have not yet been identified with confidence. Serotonin, glutamate, and gamma-aminobutyric acid (GABA) have been postulated, but the evidence is incomplete. We undertook an autoradiographic study of [3H]serotonin, [3H]glutamate, and [3H]GABA uptake in lingual epithelium from the amphibian, Necturus maculosus, to determine whether taste bud cells would accumulate and release these substances. Lingual epithelium containing taste buds was incubated in low concentrations (0.4-6 microM) of these tritiated transmitter candidates and the tissue was processed for light microscopic autoradiography. Merkel-like basal taste cells accumulated [3H]serotonin. When the tissue was treated with 40 mM K+ after incubating the tissue in [3H]serotonin, cells released the radiolabelled transmitter. Furthermore, depolarization (KCl)-induced release of [3H]serotonin was Ca-dependent: if Ca2+ was reduced to 0.4 mM and 20 mM Mg2+ added to the high K+ bathing solution, Merkel-like basal cells did not release [3H]serotonin. In contrast, [3H]glutamate was taken up by several cell types, including non-sensory epithelial cells, Schwann cells, and some taste bud cells. [3H]glutamate was not released by depolarizing the tissue with 40 mM K+. [3H]GABA uptake was also widespread, but did not occur in taste bud cells. [3H]GABA accumulated in non-sensory epithelial cells and Schwann cells. These data support the hypothesis that serotonin is a neurotransmitter or neuromodulator released by Merkel-like basal cells in Necturus taste buds. The data do not support (nor rule out) a neurotransmitter role for glutamate or GABA in taste buds.
Improved Antifouling Properties of Polydimethylsiloxane Films via Formation of Polysiloxane/Polyzwitterion Interpenetrating Networks (2016)

Nonspecific adsorption of proteins is a challenging problem for the development of biocompatible materials, as well as for antifouling and fouling-release coatings, for instance for the marine industry. The concept of preparing amphiphilic systems based on low surface energy hydrophobic materials via their hydrophilic modification is being widely pursued. This work describes a novel two-step route for the preparation of interpenetrating polymer networks of otherwise incompatible poly(dimethylsiloxane) and zwitterionic polymers. Changes in surface hydrophilicity as well as surface charge at different pH values are investigated. Characterization using atomic force microscopy provides thorough insight into surface changes upon hydrophilic modification. Protein fouling of the materials is assessed using fibrinogen as a model protein.
Photoabsorption spectrum of Mg i in the range 226–170 Å (54–70 eV) (1979)

The photoabsorption spectrum of Mg i has been observed in the spectral region 226–170 Å (54–70 eV) using synchrotron radiation as a background source. The one-electron excitation levels associated with the series: 1s2 2s2 2p63s2 1So → 1s2 2s2 2p5 [2P3/2,1/2]3s2n s, n d were observed as well as 29 two- and three-electron excitation resonances. A critical analysis of the one-electron excitation spectrum was made and classifications for all the multiple electron excitations have been suggested on the basis of their quantum defects to known limits in Mg ii.
Analysis of the First NIF Neutron Images (u) (2011)

Abstract Not Provided
THE CAUSES OF LOW OESTROGEN EXCRETION IN PREGNANCY: THE DEVELOPMENT OF DIAGNOSTIC METHODS FOR THE ANTENATAL DETECTION OF FAMILIAL CONGENITAL ADRENOCORTICAL HYPOPLASIA (1980)

A pregnancy producing a boy with congeital adrenocortical hypoplasia is described. Consistently low oestrogen excretion, less than 10 umol/24 h, was not associated with any anatomical abnormality or diminished growth of the fetus as judged by ultrasound examination. Fetoplacental steroid sulphatase definciency was excluded by finding normal maternal excretion of oestrogen precursors, the 3Beta-hydroxy-5-ene steroid sulphates. Generalized adrenocortical hypoplasia was proven in the baby boy by analysis of steroid netabolites excreted in his urine. He suffered from salt loss and progressive jaundice. Both were responsive to gluco- and mineralo-corticoid replacement therapy. It is suggested that amniocentesis may be required for the antenatal diagnosis of congenital adrenocortical hypoplasia.