gebhart/patrepeval huggingface dataset:
Serum insulin-like growth factor-I and breast cancer (2000)

Insulin-like growth factor I (IGF-I) is a systemic hormone with potent mitogenic and anti-apoptotic properties, which could influence the proliferative behavior of normal breast cells. Limited epidemiological observations suggest that the hormone may play a role in the etiology of breast cancer, especially at pre-menopausal ages. In a prospective case-control study nested within a cohort of New York City women, IGF-I, IGF-binding protein 3 (IGFBP-3) and C peptide were measured in frozen serum samples from 172 pre-menopausal and 115 post-menopausal subjects who were subsequently diagnosed with breast cancer. Subjects were eligible if diagnosed 6 months or more after recruitment into the study (7 to 120 months). Cohort members who matched the cases on age, menopausal status, date of blood sampling and day of menstrual cycle at blood collection served as controls. Post-menopausal breast cancer was not associated with serum IGF-I, IGFBP-3 or C-peptide levels. However, the risk of breast cancer increased with increasing serum concentrations of IGF-I in pre-menopausal women. The odds ratio (OR) for the highest quartile of IGF-I (>256 ng/ml) compared to the lowest (<168 ng/ml) was 1.60 [95% confidence interval (CI) 0.91-2. 81]. The OR decreased to 1.49 (95% CI 0.80-2.79) after adjustment for IGFBP-3. In analyses restricted to subjects who were pre-menopausal at the time of blood sampling and whose cancer was diagnosed before age 50, the top vs. bottom quartile OR increased appreciably to 2.30 (95% CI 1.07-4.94). Adjustment for IGFBP-3 reduced the OR to 1.90 (95% CI 0.82-4.42). There was no association between pre-menopausal breast cancer and IGFBP-3, IGF-I:IGFBP-3 ratio or non-fasting levels of C peptide. Elevated circulating levels of IGF-I may be an indicator of increased risk of breast cancer occurring before age 50.
Single-Wall Carbon Nanotubes Growing Radially from Ni Fine Particles Formed by Arc Evaporation (1994)

DC arc evaporation of nickel-graphite composite in helium atmosphere produces single-wall (SW) nanotubes. Electron microscopy examination of carbonaceous soot synthesized by this method revealed that the SW tubes grew radially from ultrafine nickel particles, and that they were found exclusively in soot material formed on the surface of a sluglike deposit grown on the end of a cathode.
A central axis algorithm for 3D bronchial tree structures (2002)

Accurate measurements of the physiological parameters like branching angles, branch lengths and diameters of bronchial tree structures help in addressing the diagnostic questions related to obstructive lung disease. To facilitate these measurements, 3D bronchial trees are reduced to a straight line central axis tree. We designed a two pass algorithm to compute the central axis tree of bronchial tree structures. In the first pass, the topological branching tree structure T is obtained by using a top-down region growing algorithm on the tree volume. In the second pass, T is used to region grow bottom-up from the leaves, in order to obtain accurate centroid points that lie along the axes of the branches. Using these centroid points at each bifurcation, the branch point and the three direction vectors along the branches are computed, by solving a non-linear optimization problem. By connecting the computed branch points at each bifurcation with straight lines, we obtain the central axis tree on which we make the measurements. We also ran our algorithm on 3D tree model (cylindrical branches) that simulate bronchial trees and the computed central axis compared favorably with the ground truth central axis in terms of the measured physiological parameters.
Fragment-Based Screening of the Bromodomain of ATAD2 (2014)

Cellular and genetic evidence suggest that inhibition of ATAD2 could be a useful strategy to treat several types of cancer. To discover small-molecule inhibitors of the bromodomain of ATAD2, we used a fragment-based approach. Fragment hits were identified using NMR spectroscopy, and ATAD2 was crystallized with three of the hits identified in the fragment screen.
How common is non‐alcoholic fatty liver disease in the Asia–Pacific region and are there local differences? (2007)

Risk factors for development of non-alcoholic steatohepatitis include obesity, especially central adiposity, glucose intolerance or type 2 diabetes mellitus (T2DM), and dyslipidemia. Non-alcoholic fatty liver disease (NAFLD) is now considered a manifestation of metabolic syndrome. During the last two decades, NAFLD has become the most common chronic liver disease in North America and Europe, but until recently was thought to be uncommon (perhaps due to the lack of study) in Asia. Fatty liver can be identified on imaging modalities (ultrasonography, computed tomography scans, and magnetic resonance imaging) with high sensitivity, but steatohepatitis and fibrosis cannot be distinguished. Thus, an inherent drawback in studying the epidemiology of NAFLD is the lack of definitive laboratory tests, no uniform definition-with different studies using cut-off values of alcohol consumption from <20 g/week to 210 g/week, and case selections where biopsy was used for definition. In studies outside the region, the prevalence of NAFLD varies from 16% to 42% by imaging, and 15-39% of liver biopsies. The major risk factors for NAFLD, central obesity, T2DM, dyslipidemia, and metabolic syndrome, are now widely prevalent and are increasing geometrically in the Asia-Pacific region. It is therefore not surprising that NAFLD is common in this region. Estimates of current prevalence range from 5% to 30%, depending on the population studied. Central obesity, diabetes, and metabolic syndrome are the major risk factors. To date, however, data on the natural history and impact of NAFLD causing serious significant chronic liver disease are lacking and there is a need for prospective, cooperative studies.
SPA에 의한 신체활동 에너지소비량 평가를 위한 컴퓨터 프로그램 개발 (2010)

규칙적인 신체활동은 심혈관계 질환 및 비만을 예방하는 등 건강증진에 긍정적인 영향을 미치는 것으로 알려져 있다. 따라서 신체활동 에너지소비량을 추정하기 위한 다양한 방법들에 대한 연구가 최근 들어 증가하고 있는 추세이며, 자기보고법에 의한 신체활동 측정이 현장에서 가장 많이 사용되고 있는 방법 중에 하나이다. 자기보고법이 현장에서 가장 많이 활용되고 있는 이유는 Ainsworth 등(2000)에 의해 신체활동목록 (compendium of physical activity)이 개발되면서 에너지소비량 계산이 용이해졌기 때문이다. 그러나 이 신체활동목록은 605개의 방대한 활동내용에 대한 MET 값이 제시되어 있지만 정확하게 에너지소비량을 평가하기 위해서는 신체활동내용을 단위별(앉아있기, 노래하기, 걷기)로 기억해야하기 때문에 피험자의 인지적인 문제를 반영하지 못한다는 단점이 있다. 김혜진(2008)은 기억에 대한 인지적인 문제를 최소화하기 위해 기존의 신체활동목록을 수정하여 장소와 목적별로 에너지소비량을 추정하는 신체활동목록(SPA)을 개발하였다. 따라서 본 연구는 김혜진(2008)에 의해 개발된 신체활동내용 조합(SPA) 목록을 기초로 컴퓨터에 의한 자료입력과 출력(에너지소비량 계산)을 자동화한 컴퓨터 소프트웨어를 개발하는 것이 목적이다. 장소별 신체활동 목록(SPA)은 중학생의 평상시 활동에서 일어날 수 있는 장소와 장소에 노출된 목적으로 구분되어 있다. 신체활동장소는 집, 학교, 학원, 밖, 기타로 구분되어 있으며, 각 장소에 노출되는 목적이 전체 32개로 구분되어 있다. 따라서 신체활동목록은 자기보고법에 의한 신체활동 측정시 현장에서뿐만 아니라 신체활동 연구, 운동처방 등 다양한 영역에서 효과적으로 활용할 수 있을 것이다. 컴퓨터를 기반으로 자동화된 프로그램은 다양한 측면에서 장점을 가지고 있으며, 신체활동 내용 입력의 오류를 줄일 수 있을뿐만 아니라 비용 측면에서도 효율성이 높다. 또한 컴퓨터에 입력된 자료는 에너지소비량을 비롯해 다양한 분석을 언제든지 빠르게 가능하게 한다는 장점이 있다. ADSPA 프로그램은 기본정보와 신체활동 장소를 입력하는 입력창 2개와 신장, 체중을 활용한 BMI 판정결과와 장소별 에너지소비량을 나타낸 기본결과와 장소별, 목적별로 에너지소비량을 나타낸 결과보기 창, 그리고 지난 일주일간의 에너지소비량을 보여주는 요일별 결과보기 창 3개로 구성되어 있다. 따라서 본 연구에서 개발된 컴퓨터 프로그램은 현장에서 신체활동 에너지소비량을 평가하기 위한 유용한 도구로 활용이 가능할 것이며, 후속연구를 통해 인터넷이나 GPS, GIS 등을 활용한 컴퓨터나 스마트폰의 어플리케이션으로도 활용이 가능할 것으로 생각된다.
Ideal ratio mask estimation using deep neural networks for robust speech recognition (2013)

We propose a feature enhancement algorithm to improve robust automatic speech recognition (ASR). The algorithm estimates a smoothed ideal ratio mask (IRM) in the Mel frequency domain using deep neural networks and a set of time-frequency unit level features that has previously been used to estimate the ideal binary mask. The estimated IRM is used to filter out noise from a noisy Mel spectrogram before performing cepstral feature extraction for ASR. On the noisy subset of the Aurora-4 robust ASR corpus, the proposed enhancement obtains a relative improvement of over 38% in terms of word error rates using ASR models trained in clean conditions, and an improvement of over 14% when the models are trained using the multi-condition training data. In terms of instantaneous SNR estimation performance, the proposed system obtains a mean absolute error of less than 4 dB in most frequency channels.
Long noncoding RNAs: functional surprises from the RNA world (2009)

Most of the eukaryotic genome is transcribed, yielding a complex network of transcripts that includes tens of thousands of long noncoding RNAs with little or no protein-coding capacity. Although the vast majority of long noncoding RNAs have yet to be characterized thoroughly, many of these transcripts are unlikely to represent transcriptional "noise" as a significant number have been shown to exhibit cell type-specific expression, localization to subcellular compartments, and association with human diseases. Here, we highlight recent efforts that have identified a myriad of molecular functions for long noncoding RNAs. In some cases, it appears that simply the act of noncoding RNA transcription is sufficient to positively or negatively affect the expression of nearby genes. However, in many cases, the long noncoding RNAs themselves serve key regulatory roles that were assumed previously to be reserved for proteins, such as regulating the activity or localization of proteins and serving as organizational frameworks of subcellular structures. In addition, many long noncoding RNAs are processed to yield small RNAs or, conversely, modulate how other RNAs are processed. It is thus becoming increasingly clear that long noncoding RNAs can function via numerous paradigms and are key regulatory molecules in the cell.
Evaluation of T-Cell Responses Against Shared Melanoma Associated Antigens and Predicted Neoantigens in Cutaneous Melanoma Patients Treated With the CSF-470 Allogeneic Cell Vaccine Plus BCG and GM-CSF (2020)

The CSF-470 vaccine consists of lethally-irradiated allogeneic cells derived from four cutaneous melanoma cell lines administered plus BCG and GM-CSF as adjuvants. In an adjuvant phase II study vs. IFN-α2b, the vaccine significantly prolonged the distant metastasis-free survival (DMFS) of stages IIB-IIC-III melanoma patients with evidence of the induction of immune responses against vaccine cells. <b>Purpose:</b> The aim of this study was to analyze the antigens against which the immune response was induced, as well as the T-helper profile and lytic ability of immune cells after CSF-470 treatment. <b>Methods:</b> HLA-restricted peptides from tumor-associated antigens (TAAs) were selected from TANTIGEN database for 13 evaluable vaccinated patients. In addition, for patient #006 (pt#006), tumor somatic variants were identified by NGS and candidate neoAgs were selected by predicted HLA binding affinity and similarity between wild type (wt) and mutant peptides. The patient's PBMC reactivity against selected peptides was detected by IFNγ-ELISPOT. T-helper transcriptional profile was determined by quantifying GATA-3, T-bet, and FOXP3 mRNA by RT-PCR, and intracellular cytokines were analyzed by flow cytometry. Autologous tumor cell lysis by PBMC was assessed in an <i>in vitro</i> calcein release assay. <b>Results:</b> Vaccinated patient's PBMC reactivity against selected TAAs derived peptides showed a progressive increase in the number of IFNγ-producing cells throughout the 2-yr vaccination protocol. ELISPOT response correlated with delayed type hypersensitivity (DTH) reaction to CSF-470 vaccine cells. Early upregulation of GATA-3 and Foxp3 mRNA, as well as an increase in CD4+IL4+cells, was associated with a low DMFS. Also, IFNγ response against 9/73 predicted neoAgs was evidenced in the case of pt#006; 7/9 emerged after vaccination. We verified in pt# 006 that post-vaccination PBMC boosted <i>in vitro</i> with the vaccine lysate were able to lyse autologous tumor cells. <b>Conclusions:</b> A progressive increase in the immune response against TAAs expressed in the vaccine and in the patient's tumor was induced by CSF-470 vaccination. In pt#006, we demonstrated immune recognition of patient's specific neoAgs, which emerged after vaccination. These results suggest that an initial response against shared TAAs could further stimulate an immune response against autologous tumor neoAgs.
Masked left ventricular restriction in elderly patients with atrial septal defects: A contraindication for closure? (2001)

The impact of an atrial septal defect in the elderly with reduced diastolic elasticity of the left ventricle is unclear. We studied the hemodynamic changes during balloon occlusion of atrial septal defects in patients over 60 years of age. In 18 patients (61–78 years old; median, 70), the left atrial pressure and the mitral valve inflow was measured during complete balloon occlusion of the defect and after deflation of the balloon. In seven patients, the left atrial pressure and the E/A ratio of the mitral valve inflow increased markedly (P = 0.02). Mean atrial pressures reached values of 27 mm Hg and the v-wave peak values of 55 mm Hg. Two patients received a transcatheter device closure and developed congestive heart failure. In the elderly, an atrial septal defect can have a decompressive impact on the left ventricle. Therefore, caution appears to be warranted if atrial septal closure is planned. Cathet Cardiovasc Intervent 2001;52:177–180. © 2001 Wiley-Liss, Inc.
[Monoclonal antibodies against inflammatory mediators for the treatment of patients with sepsis]. (2002)

Sepsis is a common cause of morbidity and mortality, particularly in immunocompromised and critically ill patients. Recently, a new designation, systemic inflammatory response syndrome(SIRS), has been studied. When an abnormal generalized inflammatory reaction is due to an infection, the terms sepsis and SIRS are synonymous. The systemic response to infection is mediated via the macrophage-derived cytokines that target end organ receptors in response to injury or infection. One strategy used to perturb the septic cascade is to block a particular inflammatory molecule. Results have been published on clinical trials in sepsis patients treated with several monoclonal antibodies, such as antiendotoxin antibodies, anti-tumor necrosis factor antibodies, and anti CD14 antibodies. In this chapter, the results of clinical trials in patients and in vivo data from animal models of sepsis are summarized.
Transferrin-polycation-DNA complexes: the effect of polycations on the structure of the complex and DNA delivery to cells. (1991)

We have previously described a gene delivery system based upon the receptor-mediated endocytosis of DNA complexed with transferrin-polycation conjugates. This delivery system has been found to be very effective for both the internalization and the expression of genetic material in cells that have many transferrin receptors. Upon scrutinization of the parameters involved in this method, which we have termed transferrinfection, we note two important features of the process: the polycation in polycation-transferrin conjugates, as expected, serves to attach the transferrin moiety to the DNA and, in addition, the polycation functions to condense the DNA into a doughnut structure. Electron microscopic analysis of a range of poorly active to highly active transferrinfection samples reveals a strong correlation between DNA condensation and cellular DNA uptake. Furthermore, we demonstrate that the transfection activity of the DNA complex can be increased by addition of free polycation as long as a sufficient quantity of polycation-transferrin conjugates remains in the complex to ensure its binding to the cellular receptor.
Synthesis and characterization of a new photocrosslinking CTP analog and its use in photoaffinity labelingE.coliand T7 RNA polymerases (1993)

A new photocrosslinking CTP analog that functioned as a substrate during transcription was synthesized and used to photoaffinity label E. coli and bacteriophage T7 RNA polymerases. This analog, 5-((4-azidophenacyl)thio) cytidine-5'-triphosphate (5-APAS-CTP) contains an aryl azide group approximately 10 A from the nucleotide base and specifically replaced CTP during synthesis of RNA by both polymerases. Analog was placed at the 3' end or internally within RNA. Both polymerases inefficiently incorporated two 5-APAS-CMP molecules sequentially, as was found for the related 5-APAS-UMP. Analog was placed at the 3' end of RNA in transcription complexes paused at the site of Q-modification of E. coli RNA polymerase, downstream of the lambda PR' promoter (+16), a pause that requires specific DNA sequences but no apparent RNA hairpin. Crosslinking was examined in the presence and absence of the NusA protein, which enhances the transcriptional pause at this site and is required for Q modification of the polymerase. Crosslinking of the 3' end of the RNA to NusA was not observed, consistent with our earlier results involving a NusA-enhanced pause site downstream from an RNA hairpin.
Extremely high-accuracy correction of air refractive index using two-colour optical frequency combs (2013)

Optical frequency combs have become an essential tool for distance metrology, showing great advantages compared with traditional laser interferometry. However, there is not yet an appropriate method for air refractive index correction to ensure the high performance of such techniques when they are applied in air. In this study, we developed a novel heterodyne interferometry technique based on two-colour frequency combs for air refractive index correction. In continuous 500-second tests, a stability of 1.0 × 10(-11) was achieved in the measurement of the difference in the optical distance between two wavelengths. Furthermore, the measurement results and the calculations are in nearly perfect agreement, with a standard deviation of 3.8 × 10(-11) throughout the 10-hour period. The final two-colour correction of the refractive index of air over a path length of 61 m was demonstrated to exhibit an uncertainty better than 1.4 × 10(-8), which is the best result ever reported without precise knowledge of environmental parameters.
Recurrent Models of Visual Attention (2014)

Applying convolutional neural networks to large images is computationally expensive because the amount of computation scales linearly with the number of image pixels. We present a novel recurrent neural network model that is capable of extracting information from an image or video by adaptively selecting a sequence of regions or locations and only processing the selected regions at high resolution. Like convolutional neural networks, the proposed model has a degree of translation invariance built-in, but the amount of computation it performs can be controlled independently of the input image size. While the model is non-differentiable, it can be trained using reinforcement learning methods to learn task-specific policies. We evaluate our model on several image classification tasks, where it significantly outperforms a convolutional neural network baseline on cluttered images, and on a dynamic visual control problem, where it learns to track a simple object without an explicit training signal for doing so.
Chitinase 3-Like-1 (CHI3L1): A Putative Disease Marker at the Interface of Proteomics and Glycomics (2008)

Chitinase 3-Like-1 (CHI3L1) is a secreted 40 kDa glycoprotein that is upregulated in a number of human cancers and in non-neoplastic disease states characterized by chronic inflammation and tissue remodeling. Increased serum levels of CHI3L1 parallel disease severity, poorer prognosis, and shorter survival in many human neoplasias, including cancers of the breast, colon, prostate, ovaries, brain, thyroid, lung, and liver. Increased serum CHI3L1 also correlates with disease severity in rheumatoid arthritis, osteoarthritis, liver fibrosis, inflammatory bowel disease, and bacterial septicemia. CHI3L1 is a rheumatoid arthritis (RA) autoantigen, and MHC complexes containing specific CHI3L1 peptides have been found in RA patients; however, intranasal introduction of these same CHI3L1 peptides can induce tolerance towards them. CHI3L1 is a nonhydrolytic member of the human chitinase family that binds chitin tightly and heparin at lower affinity. Interactions with type I collagen, CHI3L1's only known protein-binding partner, helps regulate collagen fibril formation. The principal sources of CHI3L1 are activated macrophages and chondrocytes, neutrophils, and some tissue and tumor cells. CHI3L1 can act as a fibroblast mitogen and can activate several signaling pathways, however, no cell surface-binding partner for CHI3L1 has been identified. The ability of CHI3L1 to bind both proteins and carbohydrates allows potential interactions with a variety of cell-surface and extracellular-matrix proteins, proteoglycans, and polysaccharides, and thus CHI3L1 can interface between proteomics and glycomics.
XGFR*, a novel affinity-matured bispecific antibody targeting IGF-1R and EGFR with combined signaling inhibition and enhanced immune activation for the treatment of pancreatic cancer (2016)

The epidermal growth factor receptor (EGFR) and the insulin-like growth factor-1 receptor (IGF-1R) play critical roles in tumor growth, providing a strong rationale for the combined inhibition of IGF-1R and EGFR signaling in cancer therapy. We describe the design, affinity maturation, in vitro and in vivo characterization of the bispecific anti-IGF-1R/EGFR antibody XGFR*. XGFR* is based on the bispecific IgG antibody XGFR, which enabled heterodimerization of an IGF-1R binding scFab heavy chain with an EGFR-binding light and heavy chain by the "knobs-into-holes" technology. XGFR* is optimized for monovalent binding of human EGFR and IGF-1R with increased binding affinity for IGF-1R due to affinity maturation and highly improved protein stability to oxidative and thermal stress. It bears an afucosylated Fc-portion for optimal induction of antibody-dependent cell-mediated cytotoxicity (ADCC). Stable Chinese hamster ovary cell clones with production yields of 2-3 g/L were generated, allowing for large scale production of the bispecific antibody. XGFR* potently inhibits EGFR- and IGF-1R-dependent receptor phosphorylation, reduces tumor cell proliferation in cells with heterogeneous levels of IGF-1R and EGFR receptor expression and induces strong ADCC in vitro. A comparison of pancreatic and colorectal cancer lines demonstrated superior responsiveness to XGFR*-mediated signaling and tumor growth inhibition in pancreatic cancers that frequently show a high degree of IGF-1R/EGFR co-expression. XGFR* showed potent anti-tumoral efficacy in the orthotopic MiaPaCa-2 pancreatic xenograft model, resulting in nearly complete tumor growth inhibition with significant number of tumor remissions. In summary, the bispecific anti-IGF-1R/EGFR antibody XGFR* combines potent signaling and tumor growth inhibition with enhanced ADCC induction and represents a clinical development candidate for the treatment of pancreatic cancer.