gebhart/patrepeval huggingface dataset:
Application-level power and performance characterization and optimization on IBM Blue Gene/Q systems (2013)

In order to understand application-level power/performance tradeoffs on current computer systems, runtime monitoring capabilities are needed. Specifically, very fine-grained monitoring capabilities are needed to gain detailed insights on power and performance behavior. Performing fine-grained application-level characterizations not only helps fine-tune application code, but it also increases the chances to detect optimization opportunities for improving next-generation systems. In this paper, we describe a new experimental technique to perform automatic fine-grained power and performance characterization of applications on the IBM Blue Gene®/Q platform. We use it to perform high-resolution measurements and attendant characterizations of key benchmarks for high-performance computing systems: the Tier-1 Sequoia suite and Linpack. The characterization shows that these benchmarks exhibit large time periods in which the memory and network resources are underutilized. We quantify these periods to predict the performance gains of shifting power from the underutilized resources (the network and the memory) to the processor. We explore potential improvements in energy efficiency if power-saving and shifting mechanisms are implemented in future generation systems.
The coming decade of digital brain research - A vision for neuroscience at the intersection of technology and computing (2022)

Brain research has in recent years indisputably entered a new epoch, driven by substantial methodological advances and digitally enabled data integration and modeling at multiple scales – from molecules to the whole system. Major advances are emerging at the intersection of neuroscience with technology and computing. This new science of the brain integrates high-quality basic research, systematic data integration across multiple scales, a new culture of large-scale collaboration and translation into applications. A systematic approach, as pioneered in Europe’s Human Brain Project (HBP), will be essential in meeting the pressing medical and technological challenges of the coming decade. The aims of this paper are To develop a concept for the coming decade of digital brain research To discuss it with the research community at large, with the aim of identifying points of convergence and common goals To provide a scientific framework for current and future development of EBRAINS To inform and engage stakeholders, funding organizations and research institutions regarding future digital brain research To identify and address key ethical and societal issues While we do not claim that there is a ‘one size fits all’ approach to addressing these aspects, we are convinced that discussions around the theme of digital brain research will help drive progress in the broader field of neuroscience. You can submit your comments here and be considered for <strong>co-authorship</strong> Or become a <strong>supporter</strong> by clicking here More information below <strong>Comments on this manuscript are welcome</strong> This manuscript is a living document that is being further developed in a participatory process. The work has been initiated by the Science and Infrastructure Board of the Human Brain Project (HBP). Now, the entire research community is invited to contribute to shaping the vision by submitting comments. Comments can be submitted via an online commentary form here. All submitted comments will be considered and discussed. The final decision on whether edits or additions will be made to the next version of the manuscript based on an individual comment will be made by the Science and Infrastructure Board (SIB) of the Human Brain Project (HBP) at regular intervals. New versions of the manuscript will be published every few months on Zenodo. Comments may be submitted until the beginning of 2023. During the Human Brain Project Summit 2023, the manuscript will be adopted by HBP and non-HBP participants, and a final version will be published shortly after. <strong>Supporters of the paper</strong>: Pietro Avanzini, Marc Beyer, Maria Del Vecchio, Jitka Annen, Maurizio Mattia, Steven Laureys, Rosanne Edelenbosch, Rafael Yuste, Jean-Pierre Changeux, Linda Richards.
Approaches to Physical Mapping of the Human Genome (1986)

Macroscopic methods of examining the map of the human genome include cytogenetics, somatic cell genetics, and linkage analysis. Each of these methods is powerful, and all are quite complementary. In practice, however, each becomes progressively more tedious when structural data are required at finer resolution than 10,000 kb. It seems unlikely that any of these methods will be extended, in the near future, to provide routine analysis of the human genome at 1000-kb resolution.
Phylogenetic composition of enrichment cultures of thermophilic prokaryotes reducing poorly crystalline Fe(III) oxide with and without direct contact between the cells and mineral (2010)

Thirty enrichment cultures of thermophilic microorganisms were obtained from Kamchatka terrestrial hydrotherms that reduced insoluble poorly crystalline Fe(III) oxide (ferrihydrite) with and without direct contact between the cells and the mineral. Restricted access to the Fe(III) mineral was achieved by incorporation of ferrihydrite into alginate beads. According to phylogenetic analysis of 22 enrichment cultures by denaturing gradient gel electrophoresis of 16S rRNA gene fragments, Firmicutes were predominant among bacteria in all the variants. Microorganisms of the phylogenetic types Aquificae, Bacteroidetes, Nitrospirae, Planctomycetes, Spirochaetes, Synergistetes, and Thermotogae were also revealed. The archaea revealed belonged to the genera Desulfurococcus, Pyrobaculum, and Thermofilum. In the case of free access to ferrihydrite, most of the phylotypes belonged to genera known for Fe(III) reduction. In the absence of direct contact with the mineral, together with known iron reducers, organisms for which ability to reduce Fe(III) was unknown were detected. Members of the genera Carboxydothermus, Thermoanaerobacter, and Thermotoga were detected most often both in the presence and absence of contact with ferrihydrite. These organisms probably possess efficient mechanisms for Fe(III) reduction within the experimental temperature range. Microbial phylogenetic diversity was higher when acetate, rather than lactate, was used as a potential electron donor.
The Role of Neuronal Dynamics and Positional Cues in the Patterning of Nerve Connections (1990)

One of the most striking features of the nervous system is the topography of most of its interconnections. During development, neurons navigate over relatively long distances to connect in a predictable orientation and order. Understanding the genesis of these topographic connections is central not only to research on neural development, but also to efforts to regenerate a working set of connections following injury. Unfortunately, the events that are critical to the ordering of neuronal projections are difficult to observe directly; therefore, most attempts to study these processes in the vertebrate central nervous system rely upon a neuroanatomical examination of populations of axons in fixed tissue. Based upon such data, some of the principles important for neuronal patterning have been elucidated. Furthermore, the data has been used to infer the single cell behaviors that might be responsible for the formation of patterned nerve connections. The challenge now facing the field is to test experimentally the predictions made for the cellular dynamics and positional cues proposed to underlie the formation of neuronal maps.
Dopant-Free Tetrakis-Triphenylamine Hole Transporting Material for Efficient Tin-Based Perovskite Solar Cells (2017)

Developing dopant-free hole transporting layers (HTLs) is critical in achieving high-performance and robust state-of-the-art perovskite photovoltaics, especially for the air-sensitive tin-based perovskite systems. The commonly used HTLs require hygroscopic dopants and additives for optimal performance, which adds extra cost to manufacturing and limits long-term device stability. Here we demonstrate the use of a novel tetrakis-triphenylamine (TPE) small molecule prepared by a facile synthetic route as a superior dopant-free HTL for lead-free tin-based perovskite solar cells. The best-performing tin iodide perovskite cells employing the novel mixed-cation ethylenediammonium/formamidinium with the dopant-free TPE HTL achieve a power conversion efficiency as high as 7.23%, ascribed to the HTL's suitable band alignment and excellent hole extraction/collection properties. This efficiency is one of the highest reported so far for tin halide perovskite systems, highlighting potential application of TPE HTL material in low-cost high-performance tin-based perovskite solar cells.
A High-Throughput Photon Processing Technique for Range Extension of SPAD-Based LiDAR Receivers (2021)

There has recently been a keen interest in developing Light Detection and Ranging (LiDAR) systems using Single Photon Avalanche Diode (SPAD) sensors. This has led to a variety of implementations in pixel combining techniques and Time to Digital Converter (TDC) architectures for such sensors. This paper presents a comparison of these approaches and demonstrates a technique capable of extending the range of LiDAR systems with improved resilience to background conditions. A LiDAR system emulator using a reconfigurable SPAD array and FPGA interface is used to compare these different techniques. A Monte Carlo simulation model leveraging synthetic 3D data is presented to visualize the sensor performance on realistic automotive LiDAR scenes.
The first-round results of a population-based cohort study of HPV testing in Japanese cervical cancer screening: baseline characteristics, screening results, and referral rate (2021)

After first screening, introduction of HPV testing appears to contribute to significantly higher referral rates, suggesting that the number of colposcopies as a detailed examination may increase. These preliminary findings suggest that if HPV testing is introduced into screening, medical institutions need to be prepared for an increasing number of follow-up examinations.
Augmenting and Exploiting Auditory Perception for Complex Scene Analysis (2013)

I was invited to participate in this workshop that advises DARPA on scientific frontiers; the topic was ways to use technology to enhance individual senses. My talk covers some basics of auditory/acoustic scene analysis in humans and machines, and speculates about future "super sense" augmentations.
Oncolytic Measles Virotherapy and Opposition to Measles Vaccination (2019)

Recent measles epidemics in US and European cities where vaccination coverage has declined are providing a harsh reminder for the need to maintain protective levels of immunity across the entire population. Vaccine uptake rates have been declining in large part because of public misinformation regarding a possible association between measles vaccination and autism for which there is no scientific basis. The purpose of this article is to address a new misinformed antivaccination argument-that measles immunity is undesirable because measles virus is protective against cancer. Having worked for many years to develop engineered measles viruses as anticancer therapies, we have concluded (1) that measles is not protective against cancer and (2) that its potential utility as a cancer therapy will be enhanced, not diminished, by prior vaccination.
Sex differences in chronic obstructive pulmonary disease evaluated using optical coherence tomography (2014)

Although there are more women than men dying of chronic obstructive pulmonary disease (COPD) in the United States and elsewhere, we still do not have a clear understanding of the differences in the pathophysiology of airflow obstruction between the sexes. Optical coherence tomography (OCT) is an emerging imaging technology that has the capability of imaging small bronchioles with resolution approaching histology. Therefore, our objective was to compare OCT-derived airway wall measurements between males and females matched for lung size and in anatomically matched small airways. Subjects 50-80 yrs were enrolled in the British Columbia Lung Health Study and underwent OCT and spirometry. OCT was performed using a 1.5mm diameter probe/sheath in anatomically matched airways for males and females; the right lower lobe (RB8 or RB9) or left lower lobe (LB8 or LB9) during end-expiration. OCT airway wall area (Aaw) was obtained by manual segmentation. For males and females there was no significant difference in OCT Aaw (p=0.12). Spearman correlation coefficients indicated that the forced expiratory volume in 1 second (FEV1) and Aaw were significantly correlated for males (r=-0.78, p=0.004) but not for females (r=-0.20, p=0.49) matched for lung size. These novel OCT findings demonstrate that while there were no overall sex differences in airway wall thickness, the relationship between lung function and airway wall thickness was correlated only in men. Therefore, factors other than airway remodeling may be driving COPD pathogenesis in women and OCT may provide important information for investigating airway remodeling and its relationship with COPD progression.
Patterns and Advice for Managing Distributed Product Development Teams. (2005)

Canine mammary tumor (CMT) has always been an ideal animal model for human breast cancer (HBC) research, however, there is a lack of various established CMT cell lines corresponding to HBC cell lines. This study was designed to establish a new type of CMT cell line. The primary tumor, CMT-7364, was identified as the intraductal papillary carcinoma, and showed negative immunoreactivity to estrogen receptors (ER), progesterone receptors (PR), and human epidermal growth factor receptor-2 (HER-2) by immunohistochemistry (IHC) analysis. The CMT-7364 cell line from this primary tumor also shows a negative immunoreactivity to ER, PR, and HER-2, and was negative to epithelial cell markers and positive to mesenchymal cell markers by immunocytochemistry (ICC) analysis. This cell line, which has been stably cultured for more than 115 passages, and was characterized by epithelial origin with the expression of the epithelial antigen by ICC analysis and invasion ability by transwell analysis. In vivo, tumor mass and metastases in the lung were found after inoculating the CMT-7364 cells in the nude mice model, and the immune-complete mice model respectively. The tissues from the xenograft tumor were also negative to ER, PR, and HER-2 by IHC analysis. Thus, a novel triple negative canine mammary cancer cell line, CMT-7364, was successfully established, which could be used as a promising model for the research of immunotherapy and Epithelial-Mesenchymal Transition (EMT) mechanism of the triple-negative breast cancer both in canine and human.
Anti-Vascular Endothelial Growth Factor Treatment for Retinal Vein Occlusions (2012)

Retinal vein occlusion (RVO) encompasses two conditions: central RVO, in which the major outflow vessel of the retina is obstructed, and branch RVO, in which a proximal branch of the central retinal vein is obstructed. In both conditions, there is increased intraluminal and interstitial pressure throughout the retina drained by the obstructed vessels, resulting in reduced arterial perfusion, which is exacerbated by preexistent arterial insufficiency, and in variable amounts of retinal ischemia. Retinal ischemia causes increased production of vascular endothelial growth factor (VEGF), which causes vascular leakage and macular edema. High levels of VEGF also promote retinal hemorrhages and exacerbate capillary nonperfusion. Intraocular injections of a VEGF-binding protein reduce vascular leakage, resulting in improvement in macular edema, accelerate resorption of retinal hemorrhages, and prevent worsening of capillary nonperfusion. The ideal regimen has not been defined, but it appears that monthly injections early in the course control edema and may help to limit disease severity in a large percentage of patients. Over time, treatment should be individualized based upon timing and severity of recurrent edema and/or progression of nonperfusion. The role of adjunctive treatments is yet to be defined, but it is clear that VEGF antagonists provide excellent first-line treatment that has dramatically improved visual outcomes in patients with RVO.
New Techniques for Studying Some Effects of Suprathermal Alpha Particles (1977)

AbstractPhase-space grouping techniques have been applied to two distinct problems in fusion product physics: (a) slowing down drift motion of highly energetic alpha particles in a symmetric toroidal field, and (b) first wall loading by 3.52-MeV alpha particles resulting from magnetic ripple. In the former, a weighted energy-loss approximation method permits the evolving orbits to be determined for any representative phase-space group. This enables rapid computation of several important suprathermal effects in a tokamak plasma. For example, code SYMALF, which embodies this idea, is applied to plasma heating and alpha-particle thermalization source problems. In the ripple field case, a probabilistic density function is employed to determine drift losses associated with ripple-trapped, 3.52-MeV alpha particles. When used to determine 3.52-MeV alpha-particle wall loadings, code RIPALF, which is based on this probability function, predicts the position of local “hot spots” along the first wall.
Transcriptional survey of peripheral blood links lower oxygen saturation during sleep with reduced expressions of CD1D and RAB20 that is reversed by CPAP therapy (2019)

Abstract Sleep Disordered Breathing (SDB) is associated with a wide range of physiological changes due, in part, to the influence of hypoxemia during sleep. We studied gene expression in peripheral blood mononuclear cells in association with three measures of SDB: Apnea Hypopnea Index (AHI); average oxyhemoglobin saturation (avgO2) during sleep; and minimum oxyhemoglobin saturation (minO 2 ) during sleep. We performed discovery association analysis in two community-based studies, the Framingham Offspring Study (FOS; N=571) and the Multi-Ethnic Study of Atherosclerosis (MESA; N = 580). An association with false discovery rate (FDR) q &lt; 0.05 in one study was considered “replicated” if a p &lt; 0.05 was observed in the other study. Those genes that replicated across MESA and FOS, or with FDR q &lt; 0.05 in meta-analysis, were used for analysis of gene expression in the blood of 15 participants from the Heart Biomarkers In Apnea Treatment (HeartBEAT) trial. HeartBEAT participants had moderate or severe obstructive sleep apnea (OSA) and were studied pre- and post-treatment (three months) with continuous positive airway pressure (CPAP). We also performed Gene Set Enrichment Analysis (GSEA) on all traits and cohort analyses. Twenty-two genes were associated with SDB traits in both MESA and FOS. Of these, lower expression of CD1D and RAB20 was associated with lower avgO2 in MESA and FOS. CPAP treatment increased the expression of these genes in HeartBEAT participants. Immunity and inflammation pathways were up-regulated in subjects with lower avgO2; i.e ., in those with a more severe SDB phenotype (MESA), whereas immuno-inflammatory processes were down-regulated in response to CPAP treatment (HeartBEAT). One Sentence Summary We studied the association of gene expression in blood with obstructive sleep apnea traits, including oxygen saturation during sleep, and identified mechanisms that are reversed by treatment with Continuous Positive Airway Pressure.
Study on the anti-wear properties of metal-forming lubricants with TiO2 and CuO nanoparticle additives (2018)

The metal-mechanic industry is intensive in operations of transformation of materials that demand a high energy consumption to overcome the coefficient of friction (COF) generated in the manufacturing process. One of the most demanding processes is the deep drawing forming process of chassis for the automotive industry. Every day more resistant and lighter steels are developed with the aim of contributing to the efficiency in the use of fuel. The problem is generated by having a speed of development of structural steels greater than that of tool steels; these (tool steels) suffer the consequences: wear and fractures as well as increases in the COF. Currently, the aim is to reduce the coefficient of friction and the wear generated by several technologies: a) surface engineering with coatings, surface thermal treatments and laser texturing among others. b) In addition, work is being done to produce lubricants that are more efficient and to reduce the COF and wear to the maximum. It is well known that lubrication is essential for protecting moving surfaces against friction and wear in metalworking applications. Nanotechnology is a science that is improving the tribological performance of lubricants in big leaps through the addition of nanoparticles in concentrations ranging from 0.01 wt.% to 2 wt. %. In this work one metal-working polymeric lubricant with viscosity of 529 Cst, was treated with varying wt.% (0.01, 0.05 and 0.1) of CuO and TiO2 nanoparticle additives. Antiwear properties of wear scar diameter (WSD) and coefficient of friction (COF) were characterized with a four-ball T-02 tribotester according to ASTM D 5183 and with a ball-on-disk apparatus. The dispersion method used for combining nanoparticles and lubricant also is explained. Nanoparticle additives showed an overall improvement of the tribological properties of polymeric lubricant. An important improvement of anti-wear properties for CuO at 0.05 wt.% and TiO2 at 0.01 wt.% of 33% and 77%, respectively, (WSD improvement) were obtained demonstrating the potential of nanolubricants for improving the efficiency of mechanical components. This work in addition to showing the improvements found presents the possible tribological mechanisms that explain the anti-wear behavior obtained in the laboratory.
Fabrication of ternary and quaternary chalcogenide compounds based on Cu, Zn, Sn and Si for thin film photovoltaic applications (2017)

We investigated the use of ternary and quaternary chalcogenide compounds based on Cu, Zn, Sn and Si for use as high band gap absorber layers in thin film photovoltaics. We have investigated the fabrication of Cu 2 Zn(Sn,Si)Se 4 , Cu 2 Si(S,Se) 3 and Cu 8 Si(S,Se) 6 thin film layers. Whereas, Cu 2 Zn(Sn,Si)Se 4 and Cu 2 Si(S,Se) 3 appeared to be difficult to fabricate, because the Si did not intermix well with the rest of the elements at the typical process temperatures used for glass substrates, Cu 2 ZnSiSe 4 and Cu 8 Si(S,Se) 6 could be formed. The fabricated layers were polycrystalline with a typical thickness of about 1 μm. We also fabricated solar cells with the different absorber materials, using a standard Mo back contact and CdS/ZnO buffer layer combination, but despite very bright photoluminescence response of the Cu 8 SiS 6 and Cu 8 SiSe 6 layers at an energy of about 1.84 and 1.3 eV respectively, the measured efficiencies remained below 0.1% due to particularly low photocurrents.