gebhart/patrepeval huggingface dataset:
Genome sequencing for detection of pathogenic deep intronic variation: A clinical case report illustrating opportunities and challenges (2021)

Variants in JAM3 have been reported in four families manifesting a severe autosomal recessive disorder characterized by hemorrhagic destruction of the brain, subependymal calcification, and cataracts. We describe a 7-year-old male with a similar presentation found by research-based quad genome sequencing to have two novel splicing variants in trans in JAM3, including one deep intronic variant (NM_032801.4: c.256+1260G>C) not detectable by standard exome sequencing. Targeted sequencing of RNA isolated from transformed lymphoblastoid cell lines confirmed that each of the two variants has a deleterious effect on JAM3 mRNA splicing. The role for genome sequencing as a clinical diagnostic test extends to those patients with phenotypes strongly suggestive of a specific Mendelian disorder, especially when the causal genetic variant(s) are not found by a more targeted approach. Barriers to diagnosis via identification of pathogenic deep intronic variation include lack of laboratory consensus regarding in silico splicing prediction tools and limited access to clinically validated confirmatory RNA experiments.
Preliminary results of botulinum toxin A switch after first detrusor injection failure as a treatment of neurogenic detrusor overactivity (2014)

In case of failure after a first detrusor injection of abobotulinum toxin, switching for onabotulinum toxin is efficient. Further investigations should be performed to assess whether the replacement of onabotulinum toxin by abobotulinum toxin provides the same results.
Camera-Based System for User Friendly Annotation of Documents (2016)

We propose a system for document annotation using a camera mounted on a smartphone. It works both on paper documents and electronic documents thanks to the functionality of document image retrieval. An important characteristic of this system is in the way of annotating documents. The system employs simple character stickers which represent user's opinions ("hard to understand", "interesting", "boring", "surprising", "doubtful") for friendly annotation on documents. We evaluated our system by changing the way of annotation and found that users most liked the proposed way of annotation with stickers though it sometimes caused a confusion about the interpretation of stickers. We discuss the possible way of solving this issue as a result of the analysis of experimental results.
ActionGSR: A Combination Galvanic Skin Response-Accelerometer for Physiological Measurements in Active Environments (2006)

The galvanic skin response (GSR), also known as elec- trodermal response, measures changes in electrical resistance across two regions of the skin. Galvanic skin response can measure arousal levels in children with autism; however, the GSR signal may be overwhelmed by the vigorous movements of the children. This paper introduces ActionGSR, a wireless sensor capable of measuring both GSR and acceleration simultaneously in an attempt to dis ambiguate valid GSR signals from motion artifacts.
A Kennedy Space Center Implementation of IEEE 1451 Networked Smart Sensors and Lessons Learned (2006)

To meet the need for more specific and reliable information from ground support instrumentation systems and future spacecraft sensors and to support intelligent health management systems (IHMS), NASA's Instrumentation Branch and ASRC's Advanced Electronics and Technology Development Laboratory at Kennedy Space Center (KSC) have consulted the IEEE 1451 family of smart-sensor standards to develop smart network elements (SNEs). SNEs provide reliable signal conditioning to raw sensors, complex data processing, and communication capabilities with a light implementation of the IEEE 1451 family of standards. They are capable of assessing the health of the raw sensors and the electronics and the reliability and tolerance of the measurement, and they relay this information to higher-level systems. The KSC SNEs employ a scaled-down version of the IEEE 1451.1 object model for smart sensors. The sensors are capable of publish-subscribe and client-server communication over an Ethernet network using a custom on-the-wire transmission format that is bandwidth-conservative. KSC, together with NASA Stennis Space Center, has also implemented a user-defined transducer electronic data sheet (TEDS) to store health information about the sensor, defined as the health electronic data sheet (HEDS). The KSC SNEs expand upon the IEEE 1451 family of standards to include a well-defined communication protocol for high-level sensor-to-sensor interaction and a HEDS structure for passing relevant health data over the network.
Statistical and functional convergence of common and rare genetic influences on autism at chromosome 16p (2022)

The canonical paradigm for converting genetic association to mechanism involves iteratively mapping individual associations to the proximal genes through which they act. In contrast, in the present study we demonstrate the feasibility of extracting biological insights from a very large region of the genome and leverage this strategy to study the genetic influences on autism. Using a new statistical approach, we identified the 33-Mb p-arm of chromosome 16 (16p) as harboring the greatest excess of autism's common polygenic influences. The region also includes the mechanistically cryptic and autism-associated 16p11.2 copy number variant. Analysis of RNA-sequencing data revealed that both the common polygenic influences within 16p and the 16p11.2 deletion were associated with decreased average gene expression across 16p. The transcriptional effects of the rare deletion and diffuse common variation were correlated at the level of individual genes and analysis of Hi-C data revealed patterns of chromatin contact that may explain this transcriptional convergence. These results reflect a new approach for extracting biological insight from genetic association data and suggest convergence of common and rare genetic influences on autism at 16p.
Spatial light modulators and their applications: introduction by the guest editors (1992)

The feature in this issue of Applied Optics includes a collection of papers originally presented at the 1990 Lake Tahoe topical meeting on Spatial Light modulators. These papers emphasize materials and devices for spatial light modulation, smart pixels, and applications.
Decreased levels of hepatic epidermal growth factor receptors in obese hyperglycemic rodents. (1987)

Stimulation of epidermal growth factor (EGF) receptor autophosphorylation by EGF and phosphorylation of a Mr 52,000 protein endogenous to the membrane extracts were decreased 6-12-fold in liver membrane extracts from mice homozygous for either the ob/ob or db/db mutation when compared to controls. Liver membranes from the mutant mice bound 4-5-fold less 125I-EGF/unit of protein than did their normal littermates, but exhibited normal EGF binding affinity. Similar decreases in EGF binding were noted in liver membranes from homozygous fa/fa Zucker rats, another obese, hyperinsulinemic animal model, when compared to values from control animals. We also immunoprecipitated hepatic EGF receptors from mice injected with [35S]methionine, and found that livers from db/db mice contained approximately 35% of the labeled EGF receptors found in control animals. Both ob/ob and db/db mice had serum immunoreactive EGF levels similar to or lower than those found in unaffected littermates, suggesting that ligand-mediated down-regulation of receptors was not the cause of the decreased EGF binding. In one mutant, db/db, the decreased binding was associated with a 6-fold decrease in the levels of liver EGF receptor mRNA transcripts; in the ob/ob mice, at most a 2-fold decrease in the level of liver EGF receptor transcripts was observed. EGF binding to cultured peritoneal fibroblasts derived from db/db mice was normal, suggesting that the abnormality in the mutant mice might result from altered environmental or tissue-specific factors rather than an abnormal receptor gene. This was supported by Southern blot analysis of DNA from these animals, which showed identical restriction fragment patterns for the EGF receptor gene in both control and mutant animals. These data indicate that three distinct strains of obese hyperglycemic rodents have decreased levels of hepatic EGF receptors, and suggest that this decrease may result from altered environmental stimuli or tissue-specific factors rather than a primary defect in the EGF receptor gene.
Branched Fatty Acids: The Potential of Zeolite Catalysis (2022)

Isostearic acid, a C18 saturated branched chain fatty acid containing one or more methyl or ethyl groups on the carbon chain, is of great interest for the oleochemical industry due to its interesting physicochemical properties. Its current industrial production, as a side product of the acid clay catalyzed dimerization of unsaturated fatty acids, lacks efficiency. Therefore, research focuses strongly on new catalytic systems based on zeolites. Significantly higher yields of branched fatty acids can be obtained using zeolites, demonstrating their superiority compared to acid clay catalysts. Despite previous efforts, there is insufficient insight in the product itself and the catalytic system to use it optimally. With this knowledge, it would, however, be possible to tune zeolite catalysts to meet predetermined product compositions and thus application characteristics. This perspective aims to provide the knowledge required to get a profound insight in the current state-of-the-art while pointing at remaining questions and challenges. Focus is on the reaction mechanisms taking place during reaction, the analysis of the reaction product and the zeolite catalysts themselves.
Testing Inhaled Drug Therapies for Treating Tuberculosis (2016)

This chapter reviews examples of inhaled therapies in current practice and animal studies that indicate the promise of this approach for treating tuberculosis. It also reviews how to perform inhaled drug efficacy studies using the guinea pig model of TB and aerosol dosing chambers. The chapter considers practical guide for researchers who want to test the efficacy of TB drugs delivered by inhalation and inspire others. Some of the drugs available for MDR and XDR TB are only available as injectables, making treatment even more onerous. With MDR and XDR TB, treatment fatigue and lack of adherence is an even bigger problem than is associated with the standard four-drug therapy for drug-sensitive TB. Inhaled drug therapies have proven stable, easy to deliver and effective. While the number of studies testing the efficacy of aerosol-delivered TB drugs remains small, experiments show this approach to be a promising alternative or addition to standard treatment with first-line drugs.
Direct bonding between poly(oxy‐2,6‐dimethyl‐1,4‐phenylene) and rubber with radicals (2004)

Abstract The solubility parameter value (SP value, δ) is one of the most important factors in bonding technology. It was found that various kinds of rubber, such as VMQ (δ ≒ 7.3 cal 1/2 /cm 3/2 ) compounds, EPDM (δ ≒ 7.9 cal 1/2 /cm 3/2 ) compounds, and X‐NBR (δ ≒ 9.3 cal 1/2 /cm 3/2 ), can bond to poly(oxy‐2,6‐dimethyl‐1,4‐phenylene) in their vulcanization process. This means that this bonding mechanism depends less on SP values. In this study, the bonding mechanism is hypothesized as an interfacial radical reaction, and the hypothesis is validated by molecular orbital (MO) calculations and experiments. All experimental results and MO calculation results are consistent with each other. © 2004 Wiley Periodicals, Inc. J Appl Polym Sci 95: 53–59, 2005
Anatomic considerations for C2 pedicle screw placement: the use of computerized tomography measurements (2009)

OBJECTIVE: more detailed anatomical knowledge of the C2 pedicle is required to optimize and minimize the risk of screw placement. The aim of this study was to evaluate the linear and angular dimensions of the true C2 pedicle using axial CT. METHODS: ninety three patients (47 males, 46 females mean age 48 years) who had cervical spinal CT imaging performed were evaluated for this study. Axial images of the C2 pedicle were selected and the following pedicle parameters were determined: pedicle width (PW, the mediolateral diameter of the pedicle isthmus, perpendicular to the pedicle axis) and pedicle transverse angle (PTA, that is, the angle between the pedicle axis and the midline of the vertebral body). RESULTS: the overall mean pedicle width was 5.8 1.2mm. The mean pedicle width in males (6.01.3mm) was greater than that in the female subjects (5.6 1.1mm). This difference was not found to be statistically significant (p=.6790). The overall mean pedicle transverse angle was 43.93.9 degrees. The mean PTA in males was 43.23.8 degrees, while that in females was 44.73.7 degrees. CONCLUSION: preoperative planning is absolutely mandatory, particularly in determining not only screw trajectory, but in analyzing individual patient anatomy and reception to a C2 pedicle screw.
Correction: HDAC6 inhibitor WT161 downregulates growth factor receptors in breast cancer (2021)

[This corrects the article DOI: 10.18632/oncotarget.19019.].
Convergence Analysis of Classes of Asymmetric Networks of Cucker-Smale Type with Deterministic Perturbations (2016)

We introduce and discuss two nonlinear perturbed extensions of the Cucker-Smale model with asymmetric coupling weights. The first model assumes a finite collection of autonomous agents aiming to perform a consensus process in the presence of identical internal dynamics. The second model describes a similar population of agents that perform velocity alignment with the restriction of collision-free orbits. Although qualitatively different, we explain how these two non-trivial types of perturbations are analyzed under a unified framework. Rigorous analysis is conducted towards establishing new sufficient conditions for asymptotic flocking to a synchronized motion. Applications of our results are compared with simulations to illustrate the effectiveness of our theoretical estimates.
The chemistry of polycyclic arene imines. III. N‐alkylation of phenanthrene 9,10‐imineN‐alkylation of phenanthrene 9,10‐imine (1984)

Abstract Phenanthrene 9,10‐imine ( 1 ) was shown to undergo N ‐alkylation without aziridine ring cleavage by (a) metallation with sodium methylsulfinylmethide followed by addition of an alkyl halide at −20° (b) reaction of 1 , sodium hydride and the halide in dimethylformamide at 40° (c) treatment of a dichloromethane solution of 1 , the halide and triethylbenzylammonium chloride with aqueous sodium hydroxide under phase transfer conditions. The syntheses of N ‐isopropyl‐, N ‐butyl‐, N ‐pentyl‐, N ‐allyl‐ and N ‐benzylphenanthrene 9,10‐imine ( 2–6 ) are described.
Whole-genome immunoinformatic analysis of Mycobacterium tuberculosis towards large scale identification of immunodominant CD8 epitopes (2010)

Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis, infects ~8 million annually culminating in ~2 million deaths. Moreover, about one third of the population is latently infected, 10% of which develop disease during lifetime. Current approved prophylactic TB vaccines (BCG and derivatives thereof) are of variable efficiency in adult protection against pulmonary tuberculosis (0%--80%), and directed essentially against early phase infection. It is well established that cellular immunity plays a pivotal role against intracellular bacterial infections, such as tuberculosis. The limited knowledge existing to date on Mtb antigens recognized by T-cells in general and CD8 in particular, motivates an in-depth, genome-scale identification and analysis of potential CTL epitopes, in order to map the immunodominant determinants responsible for shaping the cellular response elicited by Mtb. Such an analysis should allow the design of a synthetic peptide library enriched for genomic regions containing promiscuous HLA-I predicted epitopes. Accordingly, we have developed a comprehensive immunoinformatic analysis for mapping of clusters of CTL epitopes. The 3989 Mtb H37Rv ORF products were scanned for putative 9-11mers binders to 12 HLA-I supertypes, using the ANN-based NetMHC-3.0 program. In order to maximize the number of "promising" epitopes in the library, a comprehensive analysis tool was developed for mapping clusters of CTL binders and visualization of "hotspots" of epitopes. The ~30,000 mapped clusters, containing at least two consecutive, overlapping predicted binders, were subsequently prioritized by employing a ranking strategy based on measures such as epitope density, median binding affinity, allelic coverage and processing. Different scoring schemes were tested, assessing the sensitivity and relative impact of each of the measures employed on the composition of the final 15mer library generated. Finally, a total score was calculated for each cluster, and the top-ranking clusters were selected as the basis for compilation of a final synthetic library of 40,000 15mer peptides. Such a library contains actually a much larger number (~140,000) of putative, promiscuous HLA-I binders, demonstrating the power of the clustering approach in enrichment of potential immune-determinants per library. Validation of these in silico preselected epitopes and antigens awaits ex vivo examination of the peptides in the library for their response with Mtb-specific T cells.
Infrared Photodetection in the Picowatt Range Using Uncooled Micromechanical Sensors (1996)

Abstract Bi-material microcantilever beams have been used to photothermally detect infrared and visible radiation with 10 pW resolution for power and 3 fJ for energy, while operating at room temperature. The resolution was improved by an order of magnitude by optimizing the thickness ratio of the two beam materials, as well as by modulating the input radiation at sufficiently high frequency to be in the thermal white-noise limit of the cantilever. Noise-equivalent radiative power was detected with a noise-spectral density of 100 pW/Hz and a detectivity, D*, higher than 108cmHz/W.
CONTROLLABLE V-SHAPE MULTISCROLL BUTTERFLY ATTRACTOR: SYSTEM AND CIRCUIT IMPLEMENTATION (2012)

In this paper, a new controllable V-shape multiscroll attractor is presented, where a variety of symmetrical and unsymmetrical attractors with a variable number of scrolls can be controlled using new staircase nonlinear function and the parameters of the system. This attractor can be used to generate random signals with a variety of symbol distribution. Digital implementation of the proposed generator is also presented using a Xilinx Virtex ® 4 Field Programmable Gate Array and experimental results are provided. The digital realization easily fits into a small area (&lt;1.5% of the total area) and expresses a high throughput (4.3 Gbit/sec per state variable).
Caesar (2019)

Detecting activities from video taken with a single camera is an active research area for ML-based machine vision. In this paper, we examine the next research frontier: near real-time detection of complex activities spanning multiple (possibly wireless) cameras, a capability applicable to surveillance tasks. We argue that a system for such complex activity detection must employ a hybrid design: one in which rule-based activity detection must complement neural network based detection. Moreover, to be practical, such a system must scale well to multiple cameras and have low end-to-end latency. Caesar, our edge computing based system for complex activity detection, provides an extensible vocabulary of activities to allow users to specify complex actions in terms of spatial and temporal relationships between actors, objects, and activities. Caesar converts these specifications to graphs, efficiently monitors camera feeds, partitions processing between cameras and the edge cluster, retrieves minimal information from cameras, carefully schedules neural network invocation, and efficiently matches specification graphs to the underlying data in order to detect complex activities. Our evaluations show that Caesar can reduce wireless bandwidth, on-board camera memory, and detection latency by an order of magnitude while achieving good precision and recall for all complex activities on a public multi-camera dataset.
Effect of metformin on recurrence-free survival and overall survival in diabetic patients affected by advanced ovarian cancer. (2013)

5522^ Background: Metformin, has recently shown some anti-cancer activities in ovarian cancer, both in vitro and in vivo. Methods: Analysis of Recurrence Free Survival (RFS) and Overall Survival (OS) was performed in patients (pts) with diabetes (D) treated with metformin (DMet + ) or not (DMet - ) enrolled in the MIMOSA trial, a randomized double-blind placebo-controlled international trial of Abagovomab maintenance therapy in 888 pts with advanced ovarian cancer. In the MIMOSA trial, no differences in the RFS and OS were observed between Abagovomab (n = 593) and Placebo arm (n = 295); hence, the present RFS and OS analysis (DMet + vs DMet - ) was run regardless of treatment allocation. A Cox proportional hazards model was used for adjusting the analysis for the predefined prognostic factors: Figo stage (III, IV), tumor size after debulking (residual tumor &lt;1 cm, &gt;1cm); CA125 serum level after 3 th cycle (&lt;35U/ml, &gt;35U/ml). In addition, comparison of RFS and OS was done between DMet + and the overall MIMOSA population not exposed to metformin (ALLMet - ), and between the overall diabetic pts (ALLD + ) and non-diabetic pts (ALLD - ). Results: In the ALL population (n = 888), 42 pts were affected by diabetes (ALLD + ) divided to DMet + (n = 27) and DMet - (n = 15), without difference in the prognostic factors distribution. When analysis was done in ALLD + , RFS median time was not reached in the DMet + group whereas it was 328 days [CI: 30-660] in DMet - group with HR favoring DMet + =0.419 [CI:0.175-1.002]; p = 0.05. Median OS time was also not reached in the DMet + group whereas it was 786 days [CI:262-NE] in DMet - group with HR=0.295 [CI:0.109-0.803]; p = 0.02. Interestingly HR for RFS time was still in favour of DMet + group when compared to the ALLMet - (n=861) with HR=0.575 (CI=0.324-1.022); p = 0.06. When ALLD + were compared with ALLD - (n = 846), no significant differences was detected in RFS and OS time. Conclusions: The present results are the first prospectively analyzed data demonstrating a favourable impact of metformin treatment on RFS and OS in pts affected by advanced ovarian cancer. Clinical trial information: NCT00418574.
Quantitative phase imaging for tracing the motion of waveguide trapped bead particle (2023)

Motility of cells plays an important role to determine the cell growth, health and to monitor the gene transformation. The aim of the current study is to propose a combination of a high-contrast label-free imaging method and a computational approach (conventionally used for super-resolution) which can be used as a tool in tracing the motion of the cells and organelles. Here, we integrate quantitative phase microscopy (QPM) with waveguide-based trapping (WT) and applied multiple signal classification algorithm (MUSICAL) to analyze the motion of the trapped particle. We successfully trapped and displaced a 1 µm polystyrene bead particle on a strip waveguide using a 1064 nm laser beam. While propelling the polystyrene bead particle, we recorded time-lapsed interferometric images using a partially spatially coherent (PSC) light-based off-axis QPM system. The reconstruction of time-lapsed phase images of the trapped particle is accomplished using the Fourier transform and transport of intensity algorithm, which further used in MUSICAL for the motion trace analysis. Here, we traced the motion of a trapped bead particle with scale finer than the size of the object i.e., diffraction limit of the system. We show super-resolved motion trace even though the particle’s image is itself diffraction limited in each frame. The proposed study could be useful in different biological applications such as cell monitoring, cell tracking, manipulation, and classification between healthy and unhealthy cells.