gebhart/patrepeval huggingface dataset:
Duplex DNA Capture (2000)

This article describes the sequence-specific isolation and purification of intact double-stranded DNA (dsDNA) by oligonucleotide/PNA-assisted affinity capture (OPAC). The OPAC assay is based on selective tagging of a DNA duplex by biotinylated oligodeoxyribonucleotide (ODN) through formation of a so-called PD-loop. The PD-loop is assembled with the aid of a pair of PNA "openers", which allow sequence-specific targeting with a Watson-Crick complementary ODN probe in the exposed region of the dsDNA. The protocol involves three steps. First, two cationic bis-PNAs locally pry the DNA duplex apart at a predetermined site. Then, the exposed DNA single strand is targeted by a complementary biotinylated ODN to selectively form a stable PD-loop complex. Finally, the capture of dsDNA is performed using streptavidin covered magnetic beads. The OPAC procedure has many advantages in the isolation of highly purified native DNA over other affinity capture and amplification techniques.
South Africa's electrical energy economy: environmental impacts, future developments and constraints (1998)

South Africa alone produces move than half of the electricity generated in the entire African continent. In spite of this about, half of South Africans are without electricity in their homes. South Africa&apos;s energy production and distribution patterns bear a striking resemblance to its overall economy-a heterogeneous intermingling of First and Third World characteristics. South Africa as a whole is responsible for about 2% of the world&apos;s greenhouse gas emissions although it has only 1% of the world&apos;s population. The normalisation and democratisation of the country will require enormous efforts to provide electricity, running water and education for the majority of the South Africans previously disadvantaged in the apartheid era. South Africa is trying to comply with the global demand for sustainable development by improving the technologies of its power plants, implementing renewable energy sources, improving efficiency of utilisation of electricity in industry and homes, adopting more efficient standards for electrical appliances, changing of the way of life etc. Although there are some constraints, the country is capable of overcoming these in the years ahead given the political will and proper international assistance.
Defective Human T-Cell Lymphotropic Virus Type I (HTLV-I) Provirus in 10 Chilean Seronegative Patients with Tropical Spastic Paraparesis or HTLV-I-Associated Myelopathy (1998)

We studied the presence of tax and ltr genes from human T-cell lymphotropic virus type I (HTLV-I) provirus in the peripheral blood mononuclear cells from 15 seronegative patients with tropical spastic paraparesis or HTLV-I-associated myelopathy by PCR. Only a region of the tax gene from 10 patients was amplified. The nucleotide homologies of six Chilean isolates to the ATK-1 clone ranged between 98.7 and 99.4%.
Breast cancer in women 65-74 years old: earlier detection by mammographic screening. (1997)

Screening mammography revealed significantly smaller and earlier stage tumors in 65- to 74-year-old women. This finding inferentially supports the efficacy of screening in this age population.
Natural Selection for Survival Improves Freezing Tolerance, Forage Yield, and Persistence of Festulolium (2002)

Festulolium [ Festulolium loliaceum (Hudson) P.V. Fournier] is a hybrid between meadow fescue ( Festuca pratensis Huds.) and Italian ryegrass ( Lolium multiflorum Lam.) or perennial ryegrass ( L. perenne L.). The ryegrass parentage gives festulolium cultivars marginal winterhardiness in regions with severely cold winters. The objective of this research was to determine if natural selection for field survival resulted in a genetic improvement in freezing tolerance, forage yield, or persistence in northcentral and northeastern USA environments. The component strains of ‘Spring Green’ festulolium were compared with their unselected parents in a controlled‐environment freezing test. The component strains of Spring Green had 186% greater plant survival and 34% greater tiller survival than their unselected parents. Spring Green was compared with its two commercially available parents in a 13‐location field test. Spring Green averaged 5.0% higher in 2‐yr forage yield than ‘Kemal’, but was similar in forage yield to ‘Tandem’ in a 13‐location test ranging from Minnesota to Virginia. Spring Green averaged 30% more ground cover than its unselected parents at the six locations within USDA hardiness zones 2 through 4, but was generally similar to its parents outside of these severe hardiness zones. The increased freezing tolerance of Spring Green, obtained by phenotypic selection for field survival at several locations, appears to have resulted in increased adaptation to northern USA forage production environments.
KDD Workshop on Machine Learning in Finance (2023)

The finance industry is constantly faced with an ever evolving set of challenges including credit card fraud, identity theft, network intrusion, money laundering, human trafficking, and illegal sales of firearms. There is also the newly emerging threat of fake news in financial media that can lead to distortions in trading strategies and investment decisions. In addition, traditional problems such as customer analytics, forecasting, and recommendations take on a unique flavor when applied to financial data. A number of new ideas are emerging to tackle all these problems including self-supervised learning methods, deep learning algorithms, network/graph based solutions as well as linguistic approaches. These methods must often be able to work in real-time and be able handle large volumes of data. The purpose of this workshop is to bring together researchers and practitioners to discuss both the problems faced by the financial industry and potential solutions. We plan to invite regular papers, positional papers and extended abstracts of work in progress. We will also encourage short papers from financial industry practitioners that introduce domain specific problems and challenges to academic researchers.
Abstracting access patterns of dynamic memory using regular expressions (2009)

Unless the speed gap between CPU and memory disappears, efficient memory usage remains a decisive factor for performance. To optimize data usage of programs in the presence of the memory hierarchy, we are particularly interested in two compiler techniques: pool allocation and field layout restructuring . Since foreseeing runtime behaviors of programs at compile time is difficult, most of the previous work relied on profiling. On the contrary, our goal is to develop a fully automatic compiler that statically transforms input codes to use memory efficiently. Noticing that regular expressions , which denote repetition explicitly, are sufficient for memory access patterns, we describe how to extract memory access patterns as regular expressions in detail. Based on static patterns presented in regular expressions, we apply pool allocation to repeatedly accessed structures and exploit field layout restructuring according to field affinity relations of chosen structures. To make a scalable framework, we devise and apply new abstraction techniques, which build and interpret access patterns for the whole programs in a bottom-up fashion. We implement our analyses and transformations with the CIL compiler. To verify the effect and scalability of our scheme, we examine 17 benchmarks including 2 SPECINT 2000 benchmarks whose source lines of code are larger than 10,000. Our experiments demonstrate that the static layout transformations for dynamic memory can reduce L1D cache misses by 16% and execution times by 14% on average.
Evidence for dietary regulation of microRNA expression in cancer cells (2008)

MicroRNAs (miRNAs) are an abundant class of short noncoding RNAs that are widely expressed in mammalian cells and are important in post-translational gene regulation, including regulation of cell proliferation, apoptosis, and differentiation processes. miRNAs are involved in cancer initiation and progression and their expression patterns serve as phenotypic signatures of different cancers. Recent evidence suggests that dietary components as diverse as folate, retinoids, and curcumin exert cancer-protective effects through modulation of miRNA expression. miRNAs may be useful as biomarkers of cancer prevention or nutritional status, as well as serve as potential molecular targets that are influenced by dietary interventions.
Retroperitoneal sarcomas: A review of disease spectrum, radiological features, characterisation and management (2013)

Retroperitoneal sarcomas are a rare disease. The overall 5-year survival rate for these lesions remains low, and surgical management offers the only option for effective treatment and potential for cure. Radiotherapy is increasingly being employed in addition to standard surgical treatment. Improvements in cross-sectional imaging have also facilitated better characterisation of lesions, preoperative planning and long-term follow-up. This article reviews the current literature and documents the various types of retroperitoneal sarcomas with a particular approach to their imaging features. We also highlight the pathology, diagnostic methods and most current management of these tumours.
Impact of Spectral Correction on Bifacial Silicon Heterojunction Module Energy Yield in High Latitude Locations (2021)

Bifacial photovoltaics present a clean and cheaper alternative to diesel generators for high-latitude remote communities; however, solar cells are tested at air mass 1.5, while average air mass increases with increasing latitude. For example, Cambridge Bay (69ºN) has an irradiance-weighted average air mass of 3.1. We demonstrate improved efficiency of bifacial silicon heterojunction modules under high air mass spectra due to reduced incident UV light. We implement air mass correction in our bifacial PV modelling software, and we quantify the impact of air mass on energy yield for fixed-tilt and tracked systems in high latitude locations.
Artificial Intelligence: The Future for Organic Chemistry? (2018)

On the basis of a recent article "<i>Predicting reaction performance in C-N cross-coupling using machine learning</i>" that appeared in <i>Science</i>, we had decided to highlight the way forward for artificial intelligence in chemistry. Synthesis of molecules remains one of the most important challenges in organic chemistry, and the standard approach involved by a chemist to solve a problem is based on experience and constitutes a repetitive, time-consuming task, often resulting in nonoptimized solutions. Thus, considering the recent phenomenal progresses that have been made in machine learning, there is little doubt that these systems, once fully operational in organic chemistry, will dramatically speed up development of new drugs and will constitute the future of chemistry.
A TCAD Tool of DOE Combining with Simulation forIC Optimization Design (2002)

A TCAD tool of DOE(Design of Experiment) combining with simulations for IC optimization design was implemented on a PC,some simulation software such as SUPREM,MINIMOS and PSPICE were utilized.The programs for fitting response surface,extracting SPICE model parameters and converting data files were completed.The application of DOE on IC optimization design was studied using the TCAD tool.
Challenges in ethics, safety, best practices, and oversight regarding HIT vendors, their customers, and patients: a report of an AMIA special task force (2010)

The current commercial health information technology (HIT) arena encompasses a number of competing firms that provide electronic health applications to hospitals, clinical practices, and other healthcare-related entities. Such applications collect, store, and analyze patient information. Some vendors incorporate contract language whereby purchasers of HIT systems, such as hospitals and clinics, must indemnify vendors for malpractice or personal injury claims, even if those events are not caused or fostered by the purchasers. Some vendors require contract clauses that force HIT system purchasers to adopt vendor-defined policies that prevent the disclosure of errors, bugs, design flaws, and other HIT-software-related hazards. To address this issue, the AMIA Board of Directors appointed a Task Force to provide an analysis and insights. Task Force findings and recommendations include: patient safety should trump all other values; corporate concerns about liability and intellectual property ownership may be valid but should not over-ride all other considerations; transparency and a commitment to patient safety should govern vendor contracts; institutions are duty-bound to provide ethics education to purchasers and users, and should commit publicly to standards of corporate conduct; and vendors, system purchasers, and users should encourage and assist in each others' efforts to adopt best practices. Finally, the HIT community should re-examine whether and how regulation of electronic health applications could foster improved care, public health, and patient safety.
Efficient operating system scheduling for performance-asymmetric multi-core architectures (2007)

Recent research advocates asymmetric multi-core architectures, where cores in the same processor can have different performance. These architectures support single-threaded performance and multithreaded throughput at lower costs (e.g., die size and power). However, they also pose unique challenges to operating systems, which traditionally assume homogeneous hardware. This paper presents AMPS, an operating system scheduler that efficiently supports both SMP-and NUMA-style performance-asymmetric architectures. AMPS contains three components: asymmetry-aware load balancing, faster-core-first scheduling, and NUMA-aware migration. We have implemented AMPS in Linux kernel 2.6.16 and used CPU clock modulation to emulate performance asymmetry on an SMP and NUMA system. For various workloads, we show that AMPS achieves a median speedup of 1.16 with a maximum of 1.44 over stock Linux on the SMP, and a median of 1.07 with a maximum of 2.61 on the NUMA system. Our results also show that AMPS improves fairness and repeatability of application performance measurements.
Automated and Continuous Redox Potential Measurements in Soil (2004)

Redox potential (Eh) describes the electrical state of a matrix. In soils, Eh is an important parameter controlling the persistence of many organic and inorganic compounds. A popular, but also criticized, manual measuring method makes use of a small tip of Pt placed on a copper wire that is placed in the soil; a reference electrode is placed in the same soil at a fixed distance. Fluctuations in redox potential values measured in the soil can be very large and depth-dependent. This will be overlooked when making single-point measurements. We developed the datalogger Hypnos 2.0 for continuous redox potential and temperature measurements at various depths in the soil and without disturbance of the site. Hypnos is field-deployable, relatively cheap, and runs on batteries. The datalogger can use a "sleep mode" between sampling events. In sleep mode, there is no constant voltage on the Pt wire or the reference electrode, but there is only a short pulse during sampling. We did not measure an effect of this short pulse on the measured redox potential. In sandy soils in mesocosms and in a salt marsh soil we measured changes in the Eh as large as from -400 to +100 mV within 4 d, and daily cycles of 200 mV. Both absolute redox potential values and their diurnal variations were depth-dependent. Because single redox measurements are insufficient in describing redox conditions in some soil systems, Hypnos can be a powerful tool when studying the effects of fluctuating redox conditions on metal availability and pollutant degradation.
Viral Reprogramming of the Daxx Histone H3.3 Chaperone during Early Epstein-Barr Virus Infection (2014)

Epstein-Barr Virus (EBV) is a human herpesvirus that efficiently establishes latent infection in primary B lymphocytes. Cellular chromatin assembly plays an important role in regulating the establishment of EBV latency. We show that the EBV tegument protein BNRF1 functions to regulate chromatin assembly on the viral genome during early infection. BNRF1 alters the host cellular chromatin assembly to prevent antiviral repressive chromatin and establish chromatin structure permissive for viral gene expression and the establishment of latent infection.
CD9-mediated activation of the p46 Shc isoform leads to apoptosis in cancer cells (2004)

CD9, a member of the tetraspanin family, has been shown to be involved in a range of cellular activities, including migration, proliferation and adhesion, but the molecular mechanisms by which it mediates such events is unclear. Here, we found that anti-CD9 monoclonal antibody ALB6 inhibited cell proliferation, reduced cell viability and induced not only morphological changes specific to apoptosis but also molecular changes, as evidenced by TUNEL and annexin-V staining. For the possible mechanism of ALB6-induced apoptosis, ALB6 activated the c-Jun NH2-terminal kinase/stress-activated protein kinase (JNK/SAPK) and p38 mitogen-activated-protein kinase (MAPK) within 5-15 minutes, as well as caspase-3 within 24-48 hours. It is noteworthy that ALB6 induced tyrosine phosphorylation of the p46 Shc isoform specifically and that the overexpression of its dominant-negative form completely suppressed the ALB6-induced activation of JNK/SAPK, p38 MAPK and caspase-3, resulting in the inhibition of apoptotic cell death. These results suggest that CD9 might regulate apoptosis through the specialized signals in human cancer cell lines.
Quantification of the surface- and bulk-order parameters of a homogeneously aligned nematic liquid crystal using fully leaky guided modes (1999)

An optical waveguide technique, involving the excitation of fully leaky guided modes, has been used to quantify the director distortions induced by the application of weak in-plane electric fields to a homogeneously aligned nematic liquid crystal, E7. The twist profile of the nematic is determined by fitting angle-dependent reflectivity and transmission data to multilayer optical theory. By considering the Frank–Oseen free energy in the bulk, with Rapini–Papoular-type anchoring at the surfaces, we have determined accurate values for both the azimuthal anchoring strength Wa and the twist elastic constant k22 as a function of temperature. Values for the temperature-dependent surface and bulk average-order parameters have also been deduced by allowing for a spatially varying nematic-order parameter.
High resolution laser spectroscopy of the ozone molecule at the dissociation threshold (2021)

International audience
Gitonic and Distonic Alkanonium Dications (Diprotonated Alkane Dications CnH2n+42+, n = 1−4)1 (2001)

The structures and stabilities of gitonic and distonic alkanonium dications, i.e., diprotonated alkane dications C(n)H(2n+4)(2+) (n = 1-4), were investigated at the MP4(SDTQ)/6-311G**//MP2/6-31G** level. The global minimum energy structures (2, 4, 7, and 10) of the C(n)H(2n+4)(2+) dications are double C--H protonated alkanes to give structures with two two electron three-center (2e-3c) bonds. Two different dissociation pathways for the dications, viz deprotonation and demethylation, were also computed. Demethylation was found to be the favorable mode of dissociation.
A fiber-based polarization-sensitive optical coherence tomography system with passive components (2014)

In this work we present a fiber-based polarization-sensitive optical coherence tomography (PS-OCT) system implemented with passive components. The proposed system features circularly-polarized light incident on the sample and a hybrid 50/50 fiber coupler – with single-mode fiber inputs and polarization maintaining (PM) fiber outputs – to combine reflections from the sample and reference arms. Images acquired ex-vivo from chicken breast are presented to verify the performance of the proposed system.
Graphene—A rather ordinary nonlinear optical material (2014)

An analytical expression for the nonlinear refractive index of graphene has been derived and used to obtain the performance metrics of third order nonlinear devices using graphene as a nonlinear medium. None of the metrics is found to be superior to the existing nonlinear optical materials.
Die kubischen Phasen Na16(ARb6)Sb7, Verbindungen mit den Anionen A = Rb−, Na−, Au−, I− (1996)

Abstract Die neuartigen Verbindungen Na 16 (ARb 6 )Sb 7 wurden aus den entsprechenden Elementen in verschweißten Nb‐Ampullen bei 873 K (A = Rb) bzw. 823 K (A = I, Na, Au) dargestellt. Sie bilden spröde silberfarbene Kuboktaeder (A = Rb) bzw. unregelmäßige Polyeder (silberglänzend: A = Na, I; metallisch golden glänzend: A = Au). Die Verbindungen zersetzen sich schnell an feuchter Luft zu grauen Produkten. Die Kristallstrukturen wurden an Einkristallen bestimmt (A = Rb: a = 1565,8(2) pm; A = I: a = 1563,3(2) pm; A = Na: a = 1562,6(2) pm; A = Au: a = 1560,7(2) pm). Sie kristallisieren in der Raumgruppe Fm 3 m (Nr. 225) mit Z = 4 Formeleinheiten und sind isotyp zu Sc 11 Ir 4 . Die Verbindungen sind Zintl‐Phasen, deren Strukturen als achtfache Defektvariante der Li 3 Bi‐Struktur ( cF 128‐8; a = 2a′ (Li 3 Bi)) beschrieben werden können. Die Sb‐Atome bilden ein Netz von Kuboktaedern, die abwechselnd durch SbNa 8 ‐Würfel bzw. durch ARb 6 ‐Oktaeder zentriert werden. Wesentliches Strukturmerkmal sind die A − ‐Anionen im Rb 6 ‐Oktaeder, deren Existenz durch die Darstellung der isotypen Verbindungen mit typischen Anionenbildnern (A = Au, I), durch elektrostatische Betrachtungen und Berechnungen der Volumeninkremente manifestiert wird. Im Einklang mit den nach dem Zintl ‐Konzept zu erwartenden elektronischen Eigenschaften ist Na 16 (RbRb 6 )Sb 7 ein diamagnetischer Halbleiter mit E g = 0,33 eV und χ mol = −508 × 10 −6 cm 3 mol −1 .
Peroxisomes as dynamic organelles: peroxisomal matrix protein import (2010)

The heterogeneity of peroxisomal matrix proteins which are imported in a folded, even oligomeric state, requires adaptive and dynamic properties of the translocation machinery. Dynamic multicompartmental subcellular distribution of peroxisomal proteins is governed by the accessibility of targeting signals. Conformational changes of peroxisomal targeting receptors upon cargo-binding might serve as a docking 'quality control'. Although the mechanisms are not understood in detail, recent work suggests the existence of a transient translocon within the peroxisomal membrane. Rapid formation and disassembly of the transient import pore ensures the integrity of the peroxisomal membrane barrier for small metabolites. In this review, we will focus on the regulatory aspects of peroxisomal matrix protein import.
Optics at the service of geoscience: high-precision fiber interferometer development for applications in geophysics and industry (2018)

International audience
A novel design of short-seeking control for hard disk drives (2006)

This paper discusses short seeking control for a hard disk drive with voice coil motor (VCM). A novel design method is proposed based on the track following control and initial value adjustment (IVA). Initial value adjustment, which adjusts the initial values of the track-following controllers for short seeking, makes the use of the feedforward controller and reference trajectory unnecessary. The proposed design also takes into consideration the compromise between speed and overshoot in short seeking when seeking distance becomes longer by using a two-stage IVA scheme: (1) In the first stage (when the read/write head is far away from the target track), the integral action of the track following controller is inactivated and IVA is designed to yield a high-speed seeking; (2) In the second stage (when the head approaches the target track), the integral action is switched on, and IVA is designed to produce a fast and smooth response without overshoot. A design example verifies the effectiveness of the proposed method.