gebhart/patrepeval huggingface dataset:
Metabolic and functional consequences of inhibiting adenosine deaminase during renal ischemia in rats. (1988)

The concentrations of renal ATP have been measured by 31P-nuclear magnetic resonance (NMR) before, during, and after bilateral renal artery occlusion. Using in vivo NMR, the initial postischemic recovery of ATP increased with the magnitude of the residual nucleotide pool at the end of ischemia. ATP levels after 120 min of reflow correlated with functional recovery at 24 h. In the present study the effect of blocking the degradation of ATP during ischemia upon the postischemic restoration of ATP was investigated. Inhibition of adenosine deaminase by 80% with the tight-binding inhibitor 2'-deoxycoformycin led to a 20% increase in the residual adenine nucleotide pool. This increased the ATP initial recovery after 45 min of ischemia from 52% (in controls) to 62% (in the treated animals), as compared to the basal levels. The inhibition also caused an accelerated postischemic restoration of cellular ATP so that at 120 min it was 83% in treated rats vs. 63% in untreated animals. There was a corresponding improvement in the functional recovery from the insult (increase of 33% in inulin clearance 24 h after the injury). Inhibition of adenosine deaminase during ischemia results in a injury similar to that seen after a shorter period of insult.
Inherited DNA repair and cell cycle gene defects in chronic lymphocytic leukemia. (2019)

1508 Background: Chronic lymphocytic leukemia (CLL) is among the most heritable cancers, with 60% of disease risk genetically determined. However, most of the genetic heritability of CLL remains unexplained. Previously, we identified ATM as the first CLL risk gene. Here, we leverage a deep-learning-based germline variant calling algorithm to explore germline mutational enrichment in DNA repair and cell cycle genes in CLL. Methods: A two-stage case-control analysis was conducted using gene-based mutational enrichment analysis of 50 established cancer predisposition DNA repair and cell cycle genes. In the discovery phase, a total of 285 Spanish patients and 5,608 ancestry-matched controls were evaluated. In the validation stage, an independent cohort of 514 European patients and 27,173 ancestry-matched controls were analyzed. An FDR correction was applied to both datasets and genes with a q-value &lt; 0.2 in both cohorts were considered significant. Results: Our joint analysis of 799 CLL patients from 2 genetically distinct cohorts and 32,781 ancestry-matched cancer-free controls identified ATM and CHEK2 as significantly enriched in both CLL datasets. First, our analysis recaptured the previously reported finding of ATM variant enrichment in CLL patients. Carriers of pathogenic ATM mutations in our cohorts (n = 9 patients, discovery: 1.05%, validation: 1.17%) were 2.8–3.7 times more likely to develop CLL compared to cancer-free individuals (discovery: OR = 2.8, 95%CI = 0.7–9.0, q-value = 0.181; validation: OR = 3.7, 95%CI = 1.6–8.3, q-value = 0.0454). In addition, our analysis identified 21 CLL patients carrying pathogenic CHEK2 alterations (discovery: 1.40%, validation: 3.31%), making CLL patients 4.4-8.0 times more likely to carry such alterations compared to controls (discovery: OR = 8.0, 95%CI = 2.3–27.0, q-value = 0.026; validation: OR = 4.4, 95%CI = 2.5–7.3, q-value &lt; 0.001). Conclusions: Our analysis of genetically distinct CLL cohorts, using a high-sensitivity variant calling algorithm, supports CHEK2 as a potentially novel CLL predisposition gene that may explain a portion of the missing monogenic heritability of CLL. In addition, this study highlights the DNA repair and cell cycle regulation pathways as potential drivers of CLL susceptibility.
Oxysterol formation in foods (1995)

This review focuses on the mechanisms of formation of oxysterols and factors that influence on their formation and content in foods. Aspects of growing interest because of the numerous biological effects reported for these compounds.
Lipid-dependence of target membrane stability during influenza viral fusion (2018)

Although influenza kills about a half million people each year, even after excluding pandemics, there is only one set of antiviral drugs: neuraminidase inhibitors. By using a new approach utilizing giant unilamellar vesicles and infectious X-31 influenza virus, and testing for the newly identified pore intermediate of membrane fusion, we observed ∼30-87% poration, depending upon lipid composition. Testing the hypothesis that spontaneous curvature (SC) of the lipid monolayer controls membrane poration, our Poisson model and Boltzmann energetic considerations suggest a transition from a leaky to a non-leaky fusion pathway depending on the SC of the target membrane. When the target membrane SC is below approximately -0.20 nm<sup>-1</sup> fusion between influenza virus and target membrane is predominantly non-leaky while above that fusion is predominantly leaky, suggesting that influenza hemagglutinin (HA)-catalyzed topological conversion of target membranes during fusion is associated with a loss of membrane integrity.
Operational analytics data management systems (2016)

Prior to mid-2000s, the space of data analytics was mainly confined within the area of decision support systems . It was a long era of isolated enterprise data ware houses curating information from live data sources and of business intelligence software used to query such information. Most data sets were small enough in volume and static enough invelocity to be segregated in warehouses for analysis. Data analysis was not ad-hoc; it required pre-requisite knowledge of underlying data access patterns for the creation of specialized access methods (e.g. covering indexes, materialized views) in order to efficiently execute a set of few focused queries.
An Automated Technique for Statistical Characterization of Brain Tissues in Magnetic Resonance Imaging (1997)

A procedure for estimating the joint probability density function (pdf) of T 1 , T 2 and proton spin density (P D ) for gray matter (GM), white matter (WM), and cerebrospinal fluid (CSF) in the brain is presented. The pdf's have numerous applications, including the study of tissue parameter variability in pathology and across populations. The procedure requires a multispectral, spin echo magnetic resonance imaging (MRI) data set of the brain. It consists of five automated steps: (i) preprocess the data to remove extracranial tissue using a sequence of image processing operators; (ii) estimate T 1 , T 2 and P D by fitting the preprocessed data to an imaging equation; (iii) perform a fuzzy c-means clustering on the same preprocessed data to obtain a spatial map representing the membership value of the three tissue classes at each pixel location; (iv) reject estimates which are not from pure tissue or have poor fits in the parameter estimation, and classify the remaining estimates as either GM, WM or CSF; (v) compute statistics on the classified estimates to obtain a probability mass function and a Gaussian joint pdf of the tissue parameters for each tissue class. Some preliminary results are shown comparing computed pdf's of young, elderly and Alzheimer's subjects. Two brief examples applying the joint pdf's to pulse sequence optimization and generation of computational phantoms are also provided.
Neuromorphic mixed-signal circuitry for Asynchronous Pulse Processing (2016)

We demonstrate a software reconfigurable mixed-signal Printed Circuit Board (PCB) prototype and a custom mixed-signal Application Specific Integrated Circuit (ASIC) prototype of a cognitive signal processor using neuromorphic methods to perform adaptive nonlinear filtering based real-time wideband signal processing algorithms. The cognitive processor effectively implements a trending computing paradigm called Reservoir Computer (RC). Hardware implementation of the RC is achieved by a novel analog signal processor architecture called the Asynchronous Pulse Processor (APP).
Medical Error Avoidance in Intraoperative Neurophysiological Monitoring: The Communication Imperative (2017)

Error avoidance in medicine follows similar rules that apply within the design and operation of other complex systems. The error-reduction concepts that best fit the conduct of testing during intraoperative neuromonitoring are forgiving design (reversibility of signal loss to avoid/prevent injury) and system redundancy (reduction of false reports by the multiplication of the error rate of tests independently assessing the same structure). However, error reduction in intraoperative neuromonitoring is complicated by the dichotomous roles (and biases) of the neurophysiologist (test recording and interpretation) and surgeon (intervention). This "interventional cascade" can be given as follows: test → interpretation → communication → intervention → outcome. Observational and controlled trials within operating rooms demonstrate that optimized communication, collaboration, and situational awareness result in fewer errors. Well-functioning operating room collaboration depends on familiarity and trust among colleagues. Checklists represent one method to initially enhance communication and avoid obvious errors. All intraoperative neuromonitoring supervisors should strive to use sufficient means to secure situational awareness and trusted communication/collaboration. Face-to-face audiovisual teleconnections may help repair deficiencies when a particular practice model disallows personal operating room availability. All supervising intraoperative neurophysiologists need to reject an insular or deferential or distant mindset.
Computational Principles of Mobile Robotics20013Computational Principles of Mobile Robotics. Cambridge University Press, 2000. 280 pp., ISBN: ISBN 0‐521‐56876‐5 £19.95 (paperback) (2001)

Mobile robotics is a multidisciplinary field involving both computer science and engineering. Addressing the design of automated systems, it lies at the intersection of artificial intelligence, computational vision, and robotics. This textbook for advanced undergraduates and graduate students emphasizes algorithms for a range of strategies for locomotion, sensing, and reasoning. It concentrates on wheeled and legged mobile robots but discusses a variety of other propulsion systems. The new edition includes advances in robotics and intelligent machines over the last ten years, including significant coverage of SLAM (simultaneous localization and mapping) and multi-robot systems. It includes additional mathematical background and an extensive list of sample problems. Various mathematical techniques that were assumed in the first edition are now briefly introduced in appendices at the end of the text to make the book more self-contained. Researchers as well as students in the field of mobile robotics will appreciate this comprehensive treatment of state-of-the-art methods and key technologies.
Minireview: Epigenetic Alterations in Human Prostate Cancers (2009)

Human prostate cancer cells carry a myriad of genome defects, including both genetic and epigenetic alterations. These changes, which can be maintained through mitosis, generate malignant phenotypes capable of selective growth, survival, invasion, and metastasis. During prostatic carcinogenesis, epigenetic changes arise earlier than genetic defects, linking the appearance of epigenetic alterations in some way to disease etiology. The most common genetic defect thus far described, leading to fusion transcripts between the androgen-regulated gene TMPRSS2 and genes from the ETS family of transcription factors, likely endows prostate cancer cells with the ability to co-opt androgen signaling, the major prostate differentiation pathway, to support the malignant phenotype. Whether epigenetic changes promote the appearance of TMPRSS2-ETS family fusion transcripts or collaborate with fusion transcript expression in the pathogenesis of prostate cancer has not been established. However, a growing list of epigenetic alterations has provided new opportunities for clinical tests that might aid in prostate cancer screening, detection, diagnosis, staging, and risk stratification. The epigenetic changes appear to be more attractive than genetic changes as prostate cancer biomarkers because epigenetic alterations are present in a greater fraction of prostate cancer cases than any of the known genetic defects. In addition, an emerging generation of assay strategies for detection of specific DNA sequences carrying 5-meC, the major epigenetic genome mark, has pushed somatic epigenetic alterations to the forefront of molecular biomarker assay development for cancer. Finally, a growing portfolio of epigenetic drugs, capable of reversing the phenotypic consequences of somatic epigenetic defects, has entered clinical trials for prostate cancer in the search for a new rational therapy for the disease.
Flow chemistry for process optimisation using design of experiments (2021)

Abstract Implementing statistical training into undergraduate or postgraduate chemistry courses can provide high-impact learning experiences for students. However, the opportunity to reinforce this training with a combined laboratory practical can significantly enhance learning outcomes by providing a practical bolstering of the concepts. This paper outlines a flow chemistry laboratory practical for integrating design of experiments optimisation techniques into an organic chemistry laboratory session in which students construct a simple flow reactor and perform a structured series of experiments followed by computational processing and analysis of the results.
A transformation approach to stochastic model reduction (1984)

A new and direct approach to stochastic model reduction is developed. The order reduction algorithm is obtained by establishing an equivalence between canonical correlation analysis and solutions to algebraic Riccati equations. Also the concept of balanced stochastic realization (BSR) plays a fundamental role. Asymptotic stability of the reduced-order realization is established, and spectral domain interpretations for the BSR are given.
ECG Signal as Robust and Reliable Biometric Marker: Datasets and Algorithms Comparison (2019)

In this paper, the possibility of using the ECG signal as an unequivocal biometric marker for authentication and identification purposes has been presented. Furthermore, since the ECG signal was acquired from 4 sources using different measurement equipment, electrodes positioning and number of patients as well as the duration of the ECG record acquisition, we have additionally provided an estimation of the extent of information available in the ECG record. To provide a more objective assessment of the credibility of the identification method, some selected machine learning algorithms were used in two combinations: with and without compression. The results that we have obtained confirm that the ECG signal can be acclaimed as a valid biometric marker that is very robust to hardware variations, noise and artifacts presence, that is stable over time and that is scalable across quite a solid (~100) number of users. Our experiments indicate that the most promising algorithms for ECG identification are LDA, KNN and MLP algorithms. Moreover, our results show that PCA compression, used as part of data preprocessing, does not only bring any noticeable benefits but in some cases might even reduce accuracy.
O1‐12‐01: PHASE II STUDY DATA ON SAFETY AND EFFICACY OF GM‐CSF/LEUKINE® IN MILD‐TO‐MODERATE ALZHEIMER'S DISEASE (2018)

Rheumatoid arthritis (RA) patients have a reduced risk of developing Alzheimer's disease (AD), which was originally hypothesized as attributable to their usage of non-steroidal anti-inflammatory drugs (NSAIDs). However, clinical trials with NSAIDs were unsuccessful in both AD and MCI subjects. We therefore pursued our hypothesis that intrinsic factors within RA pathogenesis itself may underlie the AD protective effect(s). We focused on the innate immune system, tested several protein cytokines upregulated in RA blood, and found that 20 daily injections of 5 mg GM-CSF reduced AD pathology by greater than 50% and completely reversed the cognitive impairment of transgenic AD mice. Additionally, we found that bone marrow transplant (BMT) patients treated with Leukine® (recombinant human GM-CSF) plus recombinant G-CSF to treat leukopenia showed significantly improved cognitive functioning at six months compared to BMT patients who received G-CSF alone or no treatment. We are conducting two double blind Phase II pilot safety and efficacy trials of Leukine® in mild-to-moderate AD subjects at 250 mg/m2/day SC for 5 days/week for either three weeks or 24 weeks with follow-up visits at 45 and 90 days. Neurological and neuropsychological assessments, and MRI and amyloid-PET scans are performed to assess the effects of treatment. Interim analyses of 15 subjects treated with Leukine® and 15 subjects treated with placebo in our three-week trial showed no drug-related adverse events, including no evidence of amyloid-related imaging abnormalities (ARIAs), which indicate micro-hemorrhage or vasogenic edema. When comparing measures at the end of treatment to baseline, the mean changes of the MMSE score showed improvement in the Leukine® group relative to baseline (p=0.0029) and to the placebo group (p=0.0175) by repeated measures mixed model analysis. Differences were not significant by the follow-up visits. Amyloid PET data are only available for the last 10 subjects and did not reach significance. These results, although preliminary and based on a small number of subjects, indicate that completing the three-week trial and continuing our Alzheimer's Association “Part the Cloud”-funded 24-week trial of GM-CSF/ Leukine® in subjects with mild-to-moderate AD are warranted. We will report on the progress of both trials.
Measurement of brain activity by near-infrared light (2005)

We review our most recent results on near-IR studies of human brain activity, which have been evolving in two directions: detection of neuronal signals and measurements of functional hemodynamics. We discuss results obtained so far, describing in detail the techniques we developed for detecting neuronal activity, and presenting results of a study that, as we believe, confirms the feasibility of neuronal signal detection. We review our results on near-IR measurements of cerebral hemodynamics, which are performed simultaneously with functional magnetic resonance imaging (MRI) These results confirm the cerebral origin of hemodynamic signals measured by optical techniques on the surface of the head. We also show how near-IR methods can be used to study the underlying physiology of functional MRI signals.
The Design of a Novel Prismatic Drive for a Three-DOF\n Parallel-Kinematics Machine (2007)

The design of a novel prismatic drive is reported in this paper. This\ntransmission is based on Slide-O-Cam, a cam mechanism with multiple rollers\nmounted on a common translating follower. The design of Slide-O-Cam was\nreported elsewhere. This drive thus provides pure-rolling motion, thereby\nreducing the friction of rack-and-pinions and linear drives. Such properties\ncan be used to design new transmissions for parallel-kinematics machines. In\nthis paper, this transmission is optimized to replace ball-screws in\nOrthoglide, a three-DOF parallel robot optimized for machining applications.\n
Direct Assessment of Platelet Adhesion to Glass: A Study of the Forces of Interaction and the Effects of Plasma and Serum Factors, Platelet Function, and Modification of the Glass Surface (1972)

Abstract Platelet adhesion to glass has been directly determined with a cover slip chamber. These studies have separated the functions of platelet adhesion to a foreign surface from platelet cohesion (aggregation). The forces of the platelet-glass interaction have been studied, and the qualitative variables affecting this interaction have been defined. Fibrinogen and calcium or magnesium are required for adhesion of either unwashed or washed platelets in plasma. Platelet adhesion in fresh serum requires thrombin and probably the fibrinogen of the platelet surface, since washed platelets are not adherent in fresh serum. Platelets incubated at 37°C for 48 hr can neither spread nor adhere to glass, a defect that may reflect decreased platelet surface area and membrane deformability. Platelets are equally as adherent to siliconized glass as to untreated glass surfaces. However, platelets cannot adhere to glass treated with the hydrogen-bonding polymer, poly(ethylene oxide). In contrast to silicone, poly(ethylene oxide)-treated glass surfaces do not impede blood coagulation. These surface properties further distinguish the two major factors involved in thrombogenesis: platelet adhesion and plasma coagulation.
Intrastriatal administration of human immunodeficiency virus‐1 glycoprotein 120 reduces glial cell‐line derived neurotrophic factor levels and causes apoptosis in the substantia nigra (2006)

Uninfected neurons of the substantia nigra (SN) degenerate in human immunodeficiency virus (HIV)-positive patients through an unknown etiology. The HIV envelope glycoprotein 120 (gp120) causes apoptotic neuronal cell death in the rodent striatum, but its primary neurotoxic mechanism is still under investigation. Previous studies have shown that gp120 causes neurotoxicity in the rat striatum by reducing brain-derived neurotrophic factor (BDNF). Because glial cell line-derived neurotrophic factor (GDNF) and BDNF are neurotrophic factors crucial for the survival of dopaminergic neurons of the SN, we investigated whether gp120 reduces GDNF and BDNF levels concomitantly to induce apoptosis. Rats received a microinjection of gp120 or vehicle into the striatum and were sacrificed at various time intervals. GDNF but not BDNF immunoreactivity was decreased in the SN by 4 days in gp120-treated rats. In these animals, a significant increase in the number of caspase-3- positive neurons, both tyrosine hydroxylase (TH)-positive and -negative, was observed. Analysis of TH immunoreactivity revealed fewer TH-positive neurons and fibers in a medial and lateral portion of cell group A9 of the SN, an area that projects to the striatum, suggesting that gp120 induces retrograde degeneration of nigrostriatal neurons. We propose that dysfunction of the nigrostriatal dopaminergic system associated with HIV may be caused by a reduction of neurotrophic factor expression by gp120.
Ambient ultraviolet radiation and skin cancer incidence. (1988)

Environmental ultraviolet radiation (UVR) was monitored for one year at Durham (latitude 55 degrees N) using a stationary, horizontal sensor, and a sensor rotating in a vertical plane designed to simulate the random motion of subjects outdoors. From these data it was possible to calculate the personal solar UVR representative of populations living at different geographical locations and experiencing varying patterns of cloud cover. The conclusion was that present monitoring programmes that record ambient solar UVR in a horizontal plane at different locations as input data to studies on the epidemiology of skin cancer are appropriate for obtaining a relative estimate of the population exposure in locations with different climatic conditions, providing, of course, that the outdoor exposure habits of different populations are comparable.