gebhart/patrepeval huggingface dataset:
Evaluation on Reading Ability for Developmental Dyslexia Using Measurement of the Voice Onset Time for Single Hiragana Character (2007)

Many reports indicated that children with developmental dyslexia have distinctive disorder in reading ability, however, there are no studies to investigate such ability based upon the characteristics of quantitative measurement in reading single character. Purpose of this study is to develop an effective method to evaluate the reading ability quantitatively. Specifically, we built a system to precisely measure the voice onset time (VOT) for hiragana characters. Here we report the results of VOT measurements in both normal and dyslexic populations. A total of eight children with dyslexia, eight healthy children and 15 healthy adults participated in the study on informed consent basis. Characters independently composed of syllabic sounds (non-contracted and contracted sounds, 106 characters in total) were chosen as the target data sets. The system automatically detected each pause and VOT and determined the time length of pronunciation in milliseconds. As a result, the time to pronounce a single character by the children with dyslexia was significantly longer than that by the healthy children and adults. The difference in VOT between non-contracted and contracted sounds suggested that the phonetic difference may affect the VOT. In conclusion, our proposed system can evaluate the reading ability for dyslexic children and it also demonstrated the effectiveness to organize the optimal strategy for improving their reading ability.
2q23 de novo microdeletion involving the MBD5 gene in a patient with developmental delay, postnatal microcephaly and distinct facial features (2011)

We report on a female patient with a de novo interstitial deletion of chromosome region 2q23.1-23.3 identified by array-CGH. She had significant global delay with developmental regression at age 6 years. She developed seizures at age 3 years with progressive difficulties with balance, loss of fine motor skills and aggressive behavior. She had short stature, microcephaly, and distinct facial features. Her speech was dysarthric, and she demonstrated repetitive hand movements. In this article, we compare the clinical features of our patient with previously reported cases with a 2q23.1 deletion.
The effect of image quality on the appearance of lesions on breast ultrasound: implications for CADx (2007)

With the emergence of recent technology in breast ultrasound, sonographic image quality has changed profoundly. Most notably, the technique of real-time spatial compounding impacts the appearance of lesions and parenchyma. During image acquisition, spatial compounding can be turned on or off at the discretion of the radiologist, but this information is not stored along with the image data. The ability to distinguishing between lesions imaged with and without spatial compounding, using either single image features or a Bayesian neural net (BNN), was assessed using ROC analysis. Our database consisted of consecutively collected HDI5000 images of 129 lesions imaged without spatial compounding (357 images, cancer prevalence of 18%) and 370 lesions imaged with spatial compounding (965 images, cancer prevalence 15%). These were used in automated feature selection and BNN training. An additional 33 lesions were imaged for which identical views with and without spatial compounding were available (70 images, cancer prevalence 15%). These served as an independent test dataset. Lesions were outlined by a radiologist and image features, mathematically describing lesion characteristics, were calculated. In feature selection, the 4 best performing features were related to gradient strength and entropy. The average gradient strength within a lesion obtained an area under the ROC curve (AUC) of 0.78 in the task of distinguishing lesions imaged with and without spatial compounding. The BNN, using 4 features, achieved an AUC on the independent test dataset of 0.98 in this task. The sonographic appearance of breast lesions is affected by spatial compound imaging and lesion features may be used to automatically separate images as obtained with or without this technique. In computer-aided diagnosis (CADx), it will likely be beneficial to separate images as such before using separate classifiers for assessment of malignancy.
Pneumococcal meningitis post‐cochlear implantation: Potential routes of infection and pathophysiology (2010)

Objective This review describes the current concept of pneumococcal meningitis in cochlear implant recipients based on recent laboratory studies. It examines possible routes of Streptococcus pneumoniae infection to the meninges in cochlear implant recipients. It also provides insights into fundamental questions concerning the pathophysiology of pneumococcal meningitis in implant recipients. Data Sources Medline/PubMed database; English articles after 1960. Search terms: cochlear implants, meningitis, pneumococcus, streptococcus pneumonia. Review Methods Narrative review. All articles relating to post‐implant meningitis without any restriction in study designs were assessed and information extracted. Results The incidence of pneumococcal meningitis in cochlear implant recipients is greater than that of an age‐matched cohort in the general population. Based on the current clinical literature, it is difficult to determine whether cochlear implantation per se increases the risk of meningitis in subjects with no existing risk factors for acquiring the disease. As this question cannot be answered in humans, the study of implant‐related infection must involve the use of laboratory animals in order for the research findings to be applicable to a clinical situation. The laboratory research demonstrated the routes of infection and the effects of the cochlear implant in lowering the threshold for pneumococcal meningitis. Conclusion The laboratory data complement the existing clinical data on the risk of pneumococcal meningitis post‐cochlear implantation.
Photoaffinity Labeling with 8-Azidoadenosine and Its Derivatives:  Chemistry of Closed and Opened Adenosine Diazaquinodimethanes (2005)

The reactive intermediate produced upon photolysis of 8-azidoadenosine was studied by chemical trapping studies, laser flash photolysis with UV-vis and IR detection, and modern computational chemistry. It is concluded that photolysis of 8-azidoadenosine in aqueous solution releases the corresponding singlet nitrene which rapidly tautomerizes to form a closed adenosine diazaquinodimethane in less than 400 fs. A perbenzoylated derivative of 8-azidoadenosine cannot undergo this tautomerization, and instead, it fragments upon photolysis to form an opened adenosine diazaquinodimethane. The singlet nitrene is too short-lived to be observed and, thus, to relax to the lowest triplet state or to become covalently attached to targeted biological macromolecules. The pivotal closed adenosine diazaquinodimethane, the product of nitrene tautomerization, has a lifetime of ca. 1 min or longer in water and in HEPES buffer at ambient temperature. However, this intermediate reacts rapidly with good nucleophiles such as amines, thiols, and phenolates, and significantly more slowly with weak nucleophiles such as alcohols and water. On the basis of these studies, it is clear that the closed adenosine diazaquinodimethane, and not the singlet or triplet nitrene, is the pivotal reactive intermediate involved in photolabeling and cross-linking studies using the 8-azidoadenosine family of photoaffinity labeling reagents.
Impact and Epidemiological Investigations into the Incursion and Spread of Peste des Petits Ruminants in the Comoros Archipelago: An Increased Threat to Surrounding Islands (2014)

Late October 2012, a great number of deaths of unknown origin occurred in goat herds in the suburbs of Ngazidja, located in the Comoros archipelago. Few weeks later, laboratory testing requested by the animal health authorities resulted in the identification of peste des petits ruminants (PPR) infection. Notably, the Index case could be attributed to a sick goat imported from Tanzania. Viral isolation was successful from the lungs leading to the whole N nucleoprotein gene sequencing. Phylogenetic analysis revealed that the strain belongs to the lineage III which includes strains of eastern African origin. In addition, to evaluate the impact of PPR on the Comorian indigenous domesticated ruminant population, a cross-sectional PPR serological survey was conducted between April and July 2013. A low overall PPRV antibody prevalence 2.24% (95% CI [1.38; 3.08]) was detected with a Grande Comore prevalence of 3.34% (IC = [2.09; 4.63]) with a limited spread of the disease mainly due to farm practices such as limited contacts between farm animals and rapid slaughtering of sick animals.
Engineering human microbiota for disease prevention and therapy (2017)

Introduction: Bacteria living with us in commensalism at mucosal districts constitute a whole living kingdom, namely the human microbiota.Commensal bacteria have several beneficial effects and several strains have been identified to possess direct proactive interaction with the human immune system and metabolism, and more complex effects on behavior and the central nervous system.The overall protective effect exerted by the microbiota could therefore be potentiated by genetically engineering specific bacterial species for the delivery of prophylactic or therapeutic recombinant proteins.Among the diverse applications of this strategy, the engineering of anti-HIV live microbicides based on the genetic modification of lactic acid bacteria to express recombinant HIV protein blockers has been extensively investigated.Reported in detail here is the production of lactobacilli secreting recombinant human CCL5 variants acting as extremely potent HIV entry inhibitors.Methods: Following rational design of CCL5 mutants, recombinant lactobacilli were generated to secrete CCL5 mutants that, after semi-purification from supernatant, were tested for anti-HIV activity.Successful mutations were integrated in CCL5 via iterative cycles of engineering, semi-purification and activity testing, leading to the production of the most potent HIV inhibitors to date.Results: The dual use of engineered lactobacilli (as CCL5 mutants screening platform and as lead microbicides) led to the selection and initial development of potent anti-HIV live microbicides based on the expression and secretion of CCL5 variants with potentiated CCR5 binding affinity.Aside HIV, these CCL5 variants (either as lactobacilli-secreted live therapeutics or as purified proteins) could be used against a wealth of inflammation-related pathologies where the CCL5:CCR5 axis is of major relevance, including cancer, atherosclerosis and inflammatory bowel disease. Conclusion:The successful generation of potent CCR5 antagonists based on CCL5 engineering via the use of recombinant commensal bacteria constitutes a paradigmatic example of how microbiota engineering could enhance human health protection.
Low-latency pipelined crossbar arbitration (2005)

Heuristic, parallel, iterative matching algorithms for input-queued cell switches with virtual output queuing require O(log N) iterations to achieve good performance. If the hardware implementation of the number of iterations required is not feasible within the cell duration, the matching process can be pipelined to obtain a matching in every cell time slot. However, existing approaches incur a substantial latency penalty due to the way the pipelining is performed, which renders them unattractive in latency-sensitive applications such as parallel computer interconnects. We introduce a new class of pipelined matching algorithms that can be based on any existing iterative matching algorithm, makes the minimum latency independent of the pipeline depth, and is highly amenable to distributed implementation. Our simulation results confirm that specific instances of this class achieve significantly lower average latency throughout the load range than existing schemes do. We also propose an instantiation of the scheme that, in addition, significantly improves the performance with nonuniform traffic.
Tetrodecamycin and Dihydrotetrodecamycin, New Antimicrobial Antibiotics against Pasteurella piscicida Produced by Streptomyces nashvillensis MJ885-mF8. II. Structure Determination. (1995)

Novel antimicrobial antibiotics against Pasteurella piscicida, tetrodecamycin (1) and weakly active dihydrotetrodecamycin (2) were isolated from a culture broth of Streptomyces nashvillensis MJ885-mF8. The planar structure of 1 was determined to be 2-acyl-4-ylidene tetronic acid alkyl ether containing decaline ring by various NMR spectral data of 1 and its acetyl derivative (3). The structure of 2 was elucidated by comparison with the spectral data of 1 and confirmed by catalytic reduction of 1 into 2. The X-ray crystallography of 2 showed the relative stereochemistry. Their absolute configurations were determined by using modified Mosher's method.
Analysis of two gene regions involved in the expression of the imipenem-specific, outer membrane porin protein OprD ofPseudomonas aeruginosa (1992)

A Tn501 mutant of Pseudomonas aeruginosa resistant to imipenem and lacking the imipenemspecific outer membrane porin protein OprD was isolated. The mutation could be complemented to imipenem susceptibility and OprD-sufficiency by a cloned 6-kb EcoRI-PstI fragment of DNA from the region of chromosome of the wild-type strain surrounding the site of Tn501 insertion. However, this fragment did not contain the oprD structural gene as judged by its inability to hybridize with an oligonucleotide corresponding to the N-terminal amino acid sequence of OprD. DNA sequencing of 3.9 kb of the region surrounding the Tn501 insertion site revealed three large open reading frames, one of which would be interrupted by the Tn501 insertion in the mutant. This latter open reading frame, named opdE (for putative regulator of oprD), predicted a hydrophobic protein of MT 41 592. Using the above-mentioned oligonucleotide, the oprD structural gene was cloned and expressed in Escherichia coli on a 2.1-kb BamHI-KpnI fragment. DNA sequencing predicted a 420 amino acid mature OprD protein with a 23 amino acid signal sequence.
Analysis by plaque reduction neutralization assay of intertypic rotaviruses suggests that gene reassortment occurs in vivo (1987)

The SB-1A rotavirus recovered from a diarrheic piglet in the United States is a naturally occurring intertypic rotavirus. When studied by reciprocal neutralization tests, the SB-1A virus was similar, if not identical, to the porcine Gottfried virus (serotype 4) and the porcine OSU virus (serotype 5). Analysis of reassortant viruses prepared from the SB-1A virus and the serotype 2 human DS-1 virus revealed that the antigenic specificity of the outer capsid protein VP3 of SB-1A was shared with the OSU virus, while the antigenic specificity of another outer capsid protein, VP7, of SB-1A appeared to be shared with the Gottfried virus. This suggests that SB-1A is a naturally occurring reassortant rotavirus between OSU-like and Gottfried-like porcine rotaviruses. In addition, using a genetic approach, we found evidence that the fourth gene was responsible for the predominantly one-way cross-neutralizing reactivity between canine rotavirus strain CU-1 (serotype 3) and porcine rotavirus strains SB-1A (serotypes 4 and 5) and OSU (serotype 5). Assignment of hemagglutination function to the fourth genome segment of porcine rotaviruses SB-1A and OSU and canine rotavirus CU-1 confirmed a similar previous gene assignment established for certain rotaviruses. Analysis of single gene 4 substitution reassortants confirmed our previous finding that VP3 was as potent in stimulating neutralizing antibodies as VP7. The observations confirm the need for a binary system of rotavirus classification and nomenclature similar to that used for the influenza A viruses; in such a system the neutralization specificity of both VP3 and VP7 would be indicated.
Structure-Based Discovery of 1H-Indazole-3-carboxamides as a Novel Structural Class of Human GSK-3 Inhibitors (2015)

An in silico screening procedure was performed to select new inhibitors of glycogen synthase kinase 3β (GSK-3β), a serine/threonine protein kinase that in the last two decades has emerged as a key target in drug discovery, having been implicated in multiple cellular processes and linked with the pathogenesis of several diseases. GSK-3β inhibitors might prove useful as therapeutic compounds in the treatment of conditions associated with elevated levels of enzyme activity, such as type-2 diabetes and neurological disorders, for example, Alzheimer's disease, bipolar disorder, neuronal cell death, stroke, and depression. In this work, virtual screening studies were applied to proprietary compound libraries, and the functional activities of selected compounds were assayed on human GSK-3β. The in silico screening procedure enabled the identification of eight hit compounds showing pIC50 values ranging from 4.9 to 5.5. X-ray crystallographic studies resulted in a 2.50 Å three-dimensional structure of GSK-3β complexed with one of the selected compounds, confirming that the inhibitor interacts with the enzyme according to the docking hypothesis. Importantly, molecular docking was able to find a new chemical scaffold for GSK-3β inhibition, providing grounds for rational structure-based design aimed at further optimization of the initial hits.
A primary method for the complex calibration of a hydrophone from 1 Hz to 2 kHz (2017)

A primary calibration method is demonstrated to obtain the magnitude and phase of the complex sensitivity for a hydrophone at frequencies between 1 Hz and 2 kHz. The measurement is performed in a coupler reciprocity chamber ('coupler'); a closed test chamber where time harmonic oscillations in pressure can be achieved and the reciprocity conditions required for a primary calibration can be realized. Relevant theory is reviewed and the reciprocity parameter updated for the complex measurement. Systematic errors and corrections for magnitude are reviewed and more added for phase. The combined expanded uncertainties of the magnitude and phase of the complex sensitivity at 1 Hz were 0.1 dB re 1 V and ±, respectively. Complex sensitivity, sensitivity magnitude, and phase measurements are presented on an example primary reference hydrophone.
Novel approaches to thrombolysis based on modulation of endogenous fibrinolysis (1998)

Stefansson, Steingrimur; Lawrence, Daniel A.; Herren, Thomas; Plow, Edward F. Author Information
Supplementary Video S5 from Unexpected Activities in Regulating Ciliation Contribute to Off-target Effects of Targeted Drugs (2023)

&lt;p&gt;Supplementary Video S5. Time-lapse images of hTERT-RPE1-Arl13b-GFP cells starved in serum-free Opti-MEM for 48 hours, then incubated for 3 hours in 2.5 µM sunitinib.&lt;/p&gt;
Aerobic Denitration of 2,4,6-Trinitrotoluene in the Presence of Phenazine Compounds and Reduced Pyridine Nucleotides (2012)

Phenazine-containing spent culture supernatants of Pseudomonas aeruginosa concentrated with a C18 solid-phase extraction cartridge initiate NAD(P)H-dependent denitration of 2,4,6-trinitrotoluene (TNT). In this study, TNT denitration was investigated under aerobic conditions using two phenazine secondary metabolites excreted by P. aeruginosa, pyocyanin (Py) and its precursor phenazine-1- carboxylic acid (PCA), and two chemically synthesized pyocyanin analogs, phenazine methosulfate (PMS+) and phenazine ethosulfate (PES+). The biomimetic Py/NAD(P)H/O2 system was characterized and found to extensively denitrate TNT in unbuffered aqueous solution with minor production of toxic amino aromatic derivatives. To a much lesser extent, TNT denitration was also observed with PMS+ and PES+ in the presence of NAD(P)H. No TNT denitration was detected with the biomimetic PCA/NAD(P)H/O2 system. Electron paramagnetic resonance (EPR) spectroscopy analysis of the biomimetic Py/NAD(P)H/O2 system revealed the generation of superoxide radical anions (O2 •−). In vitro TNT degradation experiments in the presence of specific inhibitors of reactive oxygen species suggest a nucleophilic attack of superoxide radical anion followed by TNT denitration through an as yet unknown mechanism. The results of this research confirm the high functional versatility of the redox-active metabolite pyocyanin and the susceptibility of aromatic compounds bearing electron withdrawing substituents, such as nitro groups, to superoxide-driven nucleophilic attack.
Impact of high energy electron irradiation on high voltage Ni/4H-SiC Schottky diodes (2017)

We report the results of the high energy (0.9 MeV) electron irradiation impact on the electrical properties of high voltage Ni/4H-SiC Schottky diodes. Within the range of the irradiation dose from 0.2 × 1016 cm−2 to 7 × 1016 cm−2, electron irradiation led to 6 orders of magnitude increase in the base resistance, appearance of slow relaxation processes at pico-ampere current range, and increase in the ideality factor.
Intelligence-Based Spine Care Model: A New Era of Research and Clinical Decision-Making (2020)

Author(s): Mallow, G Michael; Siyaji, Zakariah K; Galbusera, Fabio; Espinoza-Orías, Alejandro A; Giers, Morgan; Lundberg, Hannah; Ames, Christopher; Karppinen, Jaro; Louie, Philip K; Phillips, Frank M; Pourzal, Robin; Schwab, Joseph; Sciubba, Daniel M; Wang, Jeffrey C; Wilke, Hans-Joachim; Williams, Frances MK; Mohiuddin, Shoeb A; Makhni, Melvin C; Shepard, Nicholas A; An, Howard S; Samartzis, Dino
Key Challenges and Opportunities for Recycling Electric Vehicle Battery Materials (2020)

The development and deployment of cost-effective and energy-efficient solutions for recycling end-of-life electric vehicle batteries is becoming increasingly urgent. Based on the existing literature, as well as original data from research and ongoing pilot projects in Canada, this paper discusses the following: (i) key economic and environmental drivers for recycling electric vehicle (EV) batteries; (ii) technical and financial challenges to large-scale deployment of recycling initiatives; and (iii) the main recycling process options currently under consideration. A number of policies and strategies are suggested to overcome these challenges, such as increasing the funding for both incremental innovation and breakthroughs on recycling technology, funding for pilot projects (particularly those contributing to fostering collaboration along the entire recycling value chain), and market-pull measures to support the creation of a favorable economic and regulatory environment for large-scale EV battery recycling.
Cooling Section Solenoid for the 5 MeV Fermilab Electron Cooling Project (2015)

The proposed electron cooling section solenoid will consist of ten 2-m long modules with a common ferromagnetic shield. Each module is a solenoid with a maximum longitudinal field of 150 G, flanked by 8-cm gaps for diagnostics, pump-out ports and correction coils. This paper discusses requirements on each module as well as the design criteria that would allow to keep transverse electron angles in the cooling section below 70 µrad. 1
Photolithographic fabrication of diffraction and interference slit patterns for the undergraduate laboratory (2004)

Measuring the interference and diffraction patterns produced by light passing through single and double narrow slits is a classic undergraduate physics experiment that dramatically confirms the wave nature of light. Despite this critical educational role, the experiment often is problematic because of the failings of commercially available slit patterns which produce faint unconvincing projected patterns. We discuss a low cost photolithographic process that produces diffraction slits in a chromium film deposited on a glass substrate. Slit dimensions as small as 4 μm are attainable with this method with complete control over the spacing of double slits. The method also can be used to expand the variety of slit patterns to two-dimensional arrays and circular patterns.