gebhart/patrepeval huggingface dataset:
Advantages and limitations of next‐generation sequencing technologies: A comparison of electrophoresis and non‐electrophoresis methods (2008)

The reference human genome provides an adequate basis for biological researchers to study the relationship between genotype and the associated phenotypes, but a large push is underway to sequence many more genomes to determine the role of various specificities among different individuals that control these relationships and to enable the use of human genome data for personalized and preventative healthcare. The current electrophoretic methodology for sequencing an entire mammalian genome, which includes standard molecular biology techniques for genomic sample preparation and the separation of DNA fragments using capillary array electrophoresis, remains far too expensive ($5 million) to make genome sequencing ubiquitous. The National Human Genome Research Institute has put forth goals to reduce the cost of human genome sequencing to $100,000 in the short term and $1000 in the long term to spur the innovative development of technologies that will permit the routine sequencing of human genomes for use as a diagnostic tool for disease. Since the announcement of these goals, several companies have developed and released new, non-electrophoresis-based sequencing instruments that enable massive throughput in the gathering of genomic information. In this review, we discuss the advantages and limitations of these new, massively parallel sequencers and compare them with the currently developing next generation of electrophoresis-based genetic analysis platforms, specifically microchip electrophoresis devices, in the context of three distinct types of genetic analysis.
Spectrogram approach to S^2 fiber mode analysis to distinguish between dispersion and distributed scattering (2012)

We report on the significant effect that intermodal dispersion can have on spatially and spectrally resolved interferometric (S(2)) fiber mode analysis. This dispersion can significantly broaden the measured intermodal group delay and could be misinterpreted as distributed scattering. In our new approach, the spectral interference data is analyzed over multiple wavelength windows staggered across the measurement bandwidth and assembled together to form a spectrogram that reveals the wavelength dependence of the intermodal group delay. Measurements on standard telecom single-mode and large-mode-area fibers are presented. This spectrogram analysis is a more accurate map of mode conversion along the fiber and is essential for evaluating fibers and fiber devices.
CGRP – a target for acute therapy in migraine: Clinical data (2018)

Exciting results have been obtained targeting the calcitonin gene-related peptide pathway to abort acute migraine attacks, thus reinforcing the relevance of mechanism-based treatments specific for migraine.
S&#x0C1;DI - Statistical Analysis for Data Type Identification (2008)

A key task in digital forensic analysis is the location of relevant information within the computer system. Identification of the relevancy of data is often dependent upon the identification of the type of data being examined. Typical file type identification is based upon file extension or magic keys. These typical techniques fail in many typical forensic analysis scenarios such as needing to deal with embedded data, such as with Microsoft Word files, or file fragments. The SADI (Statistical Analysis Data Identification) technique applies statistical analysis of the byte values of the data in such a way that the accuracy of the technique does not rely on the potentially misleading metadata information but rather the values of the data itself. The development of SADI provides the capability to identify what digitally stored data actually represents and will also allow for the selective extraction of portions of the data for additional investigation; i.e., in the case of embedded data. Thus, our research provides a more effective type identification technique that does not fail on file fragments, embedded data types, or with obfuscated data.
Overview of pediatric bone problems and related osteoporosis. (2012)

Osteoporosis is a well-established clinical problem in adults. Osteoporosis in pediatrics, on the other hand, is a new and evolving area, with certain unique diagnostic and clinical challenges. Recently, there has been an increased awareness of osteoporosis in children, both as a primary problem due to genetic mutations and enzyme deficiencies, and as secondary to various diseases, medications, and lifestyle issues. In this review we discuss the common forms of osteoporosis, including candidate genes, mutations of which can lead to primary osteoporosis, the mechanisms involved in the pathogenesis of secondary bone loss, and possible ways of diagnosing, preventing, or treating these conditions. The purpose of the article is to provide a summary of our current knowledge of pediatric bone problems and to provide a basis for discussion of the most appropriate ways to detect, treat, or prevent such problems.
Association of Dopamine Transporter Loss in the Orbitofrontal and Dorsolateral Prefrontal Cortices With Methamphetamine-Related Psychiatric Symptoms (2003)

Chronic methamphetamine use may cause dopamine transporter reduction in the orbitofrontal cortex, dorsolateral prefrontal cortex, and amygdala in the brain. Psychiatric symptoms in methamphetamine users may be attributable to the decrease in dopamine transporter density in the orbitofrontal cortex and the dorsolateral prefrontal cortex.
Abstract P6-07-01: Anti-tumor efficacy of PI3K-mTOR pathway inhibitors in combination with PARP inhibitor plus carboplatin in BRCA1-competent TNBC, beyond PTEN: A proof of concept study (2015)

Abstract Background: Recently we reported that PI3K-mTOR inhibition potentiated anti-tumor effects in BRCA-competent TNBC cells when combined with ABT888 (A) and carboplatin (C) (De et al., Neoplasia, 2014). Pro-proliferative and anti-apoptotic actions of this pathway constitute one of the main effector signals of RAS. Here, we tested the anti-tumor effect of either single or dual node blockade of PI3K-mTOR pathway when combined with A and C on BRCA-competent TNBC cells with WT-PTEN background and activated RAS-RAF pathway. Materials & Methods: Athymic mice bearing TNBC xenograft tumors were treated with pan PI3K inhibitor, GDC-0941 or PI3K-mTOR dual inhibitor, GDC-0980 alone or in combination with A and C. Mechanism-based in vitro studies were performed using a panel of BRCA-wt/mutants TNBC cells with varying genetic backgrounds. Results: Blocking a single nodal point of PI3K by GDC-0941 failed to significantly inhibit growth of pre-established tumors (&gt; 20%) even in combination with A and C in MDA-MB231 xenografts, while GDC-0980 potentiated an anti-tumor effect by inhibiting tumor growth by 90%. In vitro treatment (1) decreased proliferation signals (pAKT, pP70S6K, p4EBP1, pS6RP), cell cycle progression, vascular mimicry & 2D clonogenic growth, and (2) increased apoptosis markers (cl-caspase3, 9, BIM, cl-PARP, & annexinV positivity). GDC-0980 in combination with A plus C concomitantly decreased Ki67, cl-caspse3, pVEGFR, CD31, p4EBP1, and pS6RP in vivo (IHC). In contrast, combination of GDC-0941 with A plus C failed to affect the cell cycle, apoptosis or 2D clonogenic growth in MDA-MB231 cells. Alternatively, Treatment with RAD001 increased pAKT while it perturbed the activation of S6RP/4EBP1. Conclusion: Our data indicate that following dual inhibition of PI3K-mTOR, S6RP/4EBP1 de-phosphorylation tracks more consistently with the drug’s tumor-growth inhibitory response rather than the upstream state of AKT-activation. Unlike mTORC1 inhibitor RAD001, GDC-0980 potently eliminates (in vitro & in vivo) feed-back re-activation of the pathway as, (1) it targets PI3K, reactivation of AKTT308 is blocked and (2) inhibition of the mTORC2 complex blocks the reactivation of AKTS473. TNBC tumors with PTEN independent RAS/RAF mutation-mediated activation of PI3K-mTOR pathway can be controlled by dual node blockade of the pathway when combined with a PARP inhibitor and carboplatin. Citation Format: Nandini Dey, Yuliang Sun, Jennifer Carlson, Lori Friedman, Pradip De, Brian Leyland-Jones. Anti-tumor efficacy of PI3K-mTOR pathway inhibitors in combination with PARP inhibitor plus carboplatin in BRCA1-competent TNBC, beyond PTEN: A proof of concept study [abstract]. In: Proceedings of the Thirty-Seventh Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2015;75(9 Suppl):Abstract nr P6-07-01.
Research on An-Based Decode of Tail-Biting Convolutional Codes and Their Performance Analyses Used in LTE System (2009)

Tail-biting convolutional codes has been used in physical broadcast channel and physical downlink control channel of LTE, this paper introduces the architecture of the convolutional encoder and physical broadcast channel used in LTE, elaborating two common Viterbi algorithm, then a new CVA-based improved scheme is proposed, and in Physical broadcast channel system simulation is carried out. The conclusions indicate that the tail-biting convolutional codes can meet the requirements of LTE channel. Furthermore, the result proved that the double traceback Viterbi algorithm process improves the error performance.
The Art of Fermentation (2013)

Webcast sponsored by the Irving K. Barber Learning Centre and hosted by the UBC Reads Sustainability. The Art of Fermentation is the most comprehensive guide to do-it-yourself home fermentation ever published. Sandor Katz presents the concepts and processes behind fermentation in ways that are simple enough to guide a reader through their first experience making sauerkraut or yogurt, and in-depth enough to provide greater understanding and insight for experienced practitioners. While Katz expertly contextualizes fermentation in terms of biological and cultural evolution, health and nutrition, and even economics, this is primarily a compendium of practical information—how the processes work; parameters for safety; techniques for effective preservation; troubleshooting; and more. With full-color illustrations and extended resources, this book provides essential wisdom for cooks, homesteaders, farmers, gleaners, foragers, and food lovers of any kind who want to develop a deeper understanding and appreciation for arguably the oldest form of food preservation, and part of the roots of culture itself. Readers will find detailed information on fermenting vegetables; sugars into alcohol (meads, wines, and ciders); sour tonic beverages; milk; grains and starchy tubers; beers (and other grain-based alcoholic beverages); beans; seeds; nuts; fish; meat; and eggs, as well as growing mold cultures, using fermentation in agriculture, art, and energy production, and considerations for commercial enterprises. Sandor Katz has introduced what will undoubtedly remain a classic in food literature, and is the first—and only—of its kind.
Electrostatic imaging via conformal mapping (2002)

Summary: We present the solution of an inverse boundary value problem for harmonic functions arising in electrostatic imaging through conformal mapping techniques. The numerical method consists of two parts. In a first step, by successive approximations a nonlinear equation is solved to determine the boundary values of a holomorphic function on the outer boundary circle of an annulus. Then in a second step an ill-posed Cauchy problem is solved to determine the holomorphic function in the annulus. The method extends and modifies an earlier analysis of \textit{M. Idemen} and \textit{I. Akduman} [SIAM J. Appl. Math. 48, 703--718 (1988; Zbl 0659.35103)]. We establish a convergence result for the iteration procedure and through numerical examples we illustrate the feasibility of the method.
Gain of a gas photomultiplier with CsI photocathode (2007)

A Gas PMT with the CsI photocathode was fabricated as a phototube of a glass vessel identical to a conventional vacuum PMT. A GEM and a Micromegas were installed in the phototube of the Gas PMT. The Gas PMT was operated with two different gas mixtures, Ar (90%) + CH4 (10%) and Ne (90%) + CF4 (10%), at the gas pressure of 1 atm. The gain of 105 was obtained for both the gas mixtures. It was found that the gain of the Gas PMT can be described using the Townsend ionization coefficient for the Micromegas. The imaging capability of the Ne gas mixture was checked by an optical imaging capillary (CP) gas detector, using X-ray beams. The image of an X-ray resolution chart indicates that the imaging resolution is determined by the diameter of the capillary, here 100 μm. The Ne gas mixture appropriate to the Gas PMT is well suited for a fine imaging detector.
Performance and Reliability Analysis of Cross-Layer Optimizations of NAND Flash Controllers (2015)

NAND flash memories are becoming the predominant technology in the implementation of mass storage systems for both embedded and high-performance applications. However, when considering data and code storage in Non-Volatile Memories (NVMs), such as NAND flash memories, reliability and performance become a serious concern for systems designers. Designing NAND flash-based systems based on worst-case scenarios leads to waste of resources in terms of performance, power consumption, and storage capacity. This is clearly in contrast with the request for runtime reconfigurability, adaptivity, and resource optimization in modern computing systems. There is a clear trend toward supporting differentiated access modes in flash memory controllers, each one setting a differentiated tradeoff point in the performance-reliability optimization space. This is supported by the possibility of tuning the NAND flash memory performance, reliability, and power consumption through several tuning knobs such as the flash programming algorithm and the flash error correcting code. However, to successfully exploit these degrees of freedom, it is mandatory to clearly understand the effect that the combined tuning of these parameters has on the full NVM subsystem. This article performs a comprehensive quantitative analysis of the benefits provided by the runtime reconfigurability of an MLC NAND flash controller through the combined effect of an adaptable memory programming circuitry coupled with runtime adaptation of the ECC correction capability. The full NVM subsystem is taken into account, starting from a characterization of the low-level circuitry to the effect of the adaptation on a wide set of realistic benchmarks in order to provide readers a clear view of the benefit this combined adaptation may provide at the system level.
Evaluating Carrier Accumulation in Degraded Bulk Heterojunction Organic Solar Cells by a Thermally Stimulated Current Technique (2009)

Abstract Here, the initial photo‐degradation of encapsulated P3HT:PCBM bulk heterojunction organic solar cells is investigated. The degraded device is recovered by thermal annealing treatment. Thermally stimulated current measurements reveal that the cause of photo‐degradation is carrier accumulation and that the degraded organic solar cell has two broad trap levels, of 0.71 and 0.81 eV. These traps are independent of the thickness of the photoactive layers, the mixing ratio of the photoactive materials and the cathode materials. In addition, it is confirmed that there is a close relationship between the degree of degradation and the amount of accumulated charge carriers.
Discovering Logical Vulnerabilities in the Wi-Fi Handshake Using Model-Based Testing (2017)

We use model-based testing techniques to detect logical vulnerabilities in implementations of the Wi-Fi handshake. This reveals new fingerprinting techniques, multiple downgrade attacks, and Denial of Service (DoS) vulnerabilities. Stations use the Wi-Fi handshake to securely connect with wireless networks. In this handshake, mutually supported capabilities are determined, and fresh pairwise keys are negotiated. As a result, a proper implementation of the Wi-Fi handshake is essential in protecting all subsequent traffic. To detect the presence of erroneous behaviour, we propose a model-based technique that generates a set of representative test cases. These tests cover all states of the Wi-Fi handshake, and explore various edge cases in each state. We then treat the implementation under test as a black box, and execute all generated tests. Determining whether a failed test introduces a security weakness is done manually. We tested 12 implementations using this approach, and discovered irregularities in all of them. Our findings include fingerprinting mechanisms, DoS attacks, and downgrade attacks where an adversary can force usage of the insecure WPA-TKIP cipher. Finally, we explain how one of our downgrade attacks highlights incorrect claims made in the 802.11 standard.
Effects of Intensive Glucose Lowering in Type 2 Diabetes The Action to Control Cardiovascular Risk in Diabetes Study Group (2008)

Background Epidemiologic studies have shown a relationship between glycated hemoglobin levels and cardiovascular events in patients with type 2 diabetes. We investigated whether intensive therapy to target normal glycated hemoglobin levels would reduce cardiovascular events in patients with type 2 diabetes who had either established cardiovascular disease or additional cardiovascular risk factors. Methods In this randomized study, 10,251 patients (mean age, 62.2 years) with a median glycated hemoglobin level of 8.1% were assigned to receive intensive therapy (targeting a glycated hemoglobin level below 6.0%) or standard therapy (targeting a level from 7.0 to 7.9%). Of these patients, 38% were women, and 35% had had a previous cardiovascular event. The primary outcome was a composite of nonfatal myocardial infarction, nonfatal stroke, or death from cardiovascular causes. The finding of higher mortality in the intensive-therapy group led to a discontinuation of intensive therapy after a mean of 3.5 years of follow-up. Results At 1 year, stable median glycated hemoglobin levels of 6.4% and 7.5% were achieved in the intensive-therapy group and the standard-therapy group, respectively. During follow-up, the primary outcome occurred in 352 patients in the intensive-therapy group, as compared with 371 in the standard-therapy group (hazard ratio, 0.90; 95% confidence interval [CI], 0.78 to 1.04; P = 0.16). At the same time, 257 patients in the intensive-therapy group died, as compared with 203 patients in the standardtherapy group (hazard ratio, 1.22; 95% CI, 1.01 to 1.46; P = 0.04). Hypoglycemia requiring assistance and weight gain of more than 10 kg were more frequent in the intensive-therapy group (P<0.001). Conclusions As compared with standard therapy, the use of intensive therapy to target normal glycated hemoglobin levels for 3.5 years increased mortality and did not significantly reduce major cardiovascular events. These findings identify a previously unrecognized harm of intensive glucose lowering in high-risk patients with type 2 diabetes. (ClinicalTrials.gov number, NC0620.)
The Human-Robot Cloud: Situated collective intelligence on demand (2012)

The Human-Robot Cloud (HRC) is an innovative extension of Cloud Computing across two important directions: First, while traditional cloud computing enables transparent utilization of distributed computational as well as storage resources, the HRC enables, in addition to the above two, the utilization of (a) distributed sensing (sensor network technology) and (b) actuator networks (including robot networks). Thus, HRC extends the concept of cloud computing by connecting it to the “Physical World”, through sensing and action. Second, while traditional cloud computing involves the usage of only electronic components, such as computers and storage devices, the HRC's capability is extended by the support of human physical and cognitive “components” as part of the cloud, which are neither expected to be experts nor to be engaged with the cloud full-time. Such components are primarily expected to interact with the system for only short periods of time (seconds), essentially providing crowd-servicing for the Cloud. Human components provide any or a mixture of the following: a) input arising from a number of sources through the usage of their sensory faculties (auditory, visual etc.), - thus, acting as “intelligent sensors” attached to the cloud; b) input that results from the usage of their cognitive faculties (pattern recognition, prediction, identification, planning etc.) - thus, acting as “intelligent systems” attached to the cloud; and c) actuation services to the Cloud (by moving around their bodies or other objects) - thus acting as “actuators” attached to the cloud. Thus, the proposed HRC is aiming to achieve the best of both worlds, i.e., either humans or machines, being able to carry out tasks which are very difficult or impossible for either humans or machines alone to carry out. Furthermore, the HRC enables the construction of situated agents exhibiting collective intelligence on demand, and the transformation of situated agency from a “capital investment” to a service, components of which can be provided by multiple providers, in a transparent fashion to the end user.
Robust High Dynamic Range Imaging by Rank Minimization (2014)

This paper introduces a new high dynamic range (HDR) imaging algorithm which utilizes rank minimization. Assuming a camera responses linearly to scene radiance, the input low dynamic range (LDR) images captured with different exposure time exhibit a linear dependency and form a rank-1 matrix when stacking intensity of each corresponding pixel together. In practice, misalignments caused by camera motion, presences of moving objects, saturations and image noise break the rank-1 structure of the LDR images. To address these problems, we present a rank minimization algorithm which simultaneously aligns LDR images and detects outliers for robust HDR generation. We evaluate the performances of our algorithm systematically using synthetic examples and qualitatively compare our results with results from the state-of-the-art HDR algorithms using challenging real world examples.
Four-Corner Arthrodesis Using the Quad Memory Staple (2009)

Range of motion, pain, consolidation and complications were evaluated for nine patients who underwent four-corner arthrodesis using the Quad Memory Staple (QMS) at a mean follow-up of 44 months. The mean pre-operative range of motion was 50 degrees extension, 62 degrees flexion, 9 degrees radial deviation and 24 degrees ulnar deviation. The postoperative range of motion was similar to previous studies at 32 degrees extension, 31 degrees flexion, 15 degrees radial deviation and 20 degrees ulnar deviation. The grip strength was 28 kg pre-operatively and 26 kg postoperatively. The mean pain score improved from 41 to 23 and the Disabilities of Arm, Shoulder, and Hand (DASH) score from 24 to 20. Non-union, haematoma and wound infection were not seen and eventually all four-corner fusions were consolidated. The main advantages of the QMS are its compressive property and the simple fixation technique. It gives good stability, enables early rehabilitation and avoids the risks of pin fixation methods.