gebhart/patrepeval huggingface dataset:
Sequence analysis of rat hypothalamic corticotropin-releasing factor with the o-phthalaldehyde strategy (1983)

Sequence analysis was performed on a 41-residue polypeptide that has been identified as the predominant form of high intrinsic corticotropin-releasing activity of rat hypothalamus. The sequence of residues 1-39 of this corticotropin-releasing factor (CRF) was determined by Edman degradation of a partially purified peptide in a highly sensitive spinning cup sequencer after selective blocking of CRF or its main contaminant with o-phthalaldehyde. This approach was validated by peptide mapping of CRF of a highly purified preparation. Peptide mapping was accomplished with reverse-phase high-pressure liquid chromatography of CRF fragments obtained by digestion with clostripain. The identities of the fragments cleaved from CRF were established by chromatographic comparison with synthetic peptides, amino acid analysis, and Edman degradation. On the basis of these experiments, the primary structure of rat hypothalamic CRF was established to be H-Ser-Glu-Glu-Pro-Pro-Ile-Ser-Leu-Asp-Leu-Thr-Phe-His-Leu- Leu-Arg-Glu-Val-Leu-Glu-Met-Ala-Arg-Ala-Glu-Gln-Leu-Ala-Gln-Gln-Ala-His-Ser-Asn - Arg-Lys-Leu-Met-Glu-Ile-Ile-NH2. It is expected that the o-phthalaldehyde strategy will facilitate the sequence analysis of partially purified peptides containing proline residues.
Performance of 18F-Florbetaben PET Image Reading Training in Japanese language. (2016)

1822 Objectives The efficacy of the visual assessment of 18F-Florbetaben (FBB) positron emission tomography (PET) scans against histopathology confirmation of presence or absence of β-amyloid neuritic plaque in the brain has been previously established [1]. The aim of this study was to assess the performance of the 18F-FBB PET image reading training in the Japanese language, as it is intended to be used as part of the future training for nuclear medicine physicians in Japan. Methods Five blinded Japanese readers without previous experience reading FBB images were trained in-person by an expert Japanese nuclear medicine physician using the 18F-FBB PET image reading training materials in the Japanese language. PET images of 50 subjects (mostly Japanese) from a number of studies were pooled (n=17 patients diagnosed with Alzheimer’s disease, n=17 Healthy Volunteers and n=16 subjects with Mild Cognitive Impairment), and randomly assigned for blinded visual assessment using the image assessment criteria defined by the sponsor company. These images were previously assessed with the same criteria by 5 independent non-Japanese, electronically trained blinded readers as 25 positive and 25 negative scans, which was used as reference. The final assessment was binary as positive (β-amyloid present) or negative (β-amyloid absent). Percent agreement between the results of each Japanese reader with the majority results of the non-Japanese readers was separately calculated. Percent agreement among majority reads from both groups was calculated. Inter-reader agreement was assessed by calculating Fleiss’s kappa across all five readers and Cohen’s kappa between each pair of readers. Intra-reader agreement was assessed by calculating Cohen’s kappa values per reader for a re-read of 10 randomly selected cases from the image data set. Results The percent agreement between the majority read of the non-Japanese readers and the majority read of the Japanese readers was 100.0% (95% CI: 92.9 - 100.0). A very high agreement between individual Japanese readers and the majority read of non-Japanese readers was observed (mean (range): 96.4 (86-100) %); (100% (n=3), 96% (n=1) and 86% (n=1)). Excellent inter-reader agreement was observed; kappa across 5 blinded readers was 0.87 (95% CI: 0.78 - 0.96). The average inter-reader agreement between reader pairs was 0.87 (range: 0.72 - 1.00). The mean percent of intra-reader agreement was 90% (range: 70-100%). Mean intra-reader variability for each of the five blinded readers was 0.78 (range: 0.34-1.00). Conclusions This study confirms that readers taught by the in-person training in the Japanese language perform similar to non-Japanese readers in the visual assessment of FBB scans. The visual assessment method and the in-person training in the Japanese language is appropriate for clinical use in Japan.
1.	Sabri, O., et al., Florbetaben PET imaging to detect amyloid beta plaques in Alzheimer disease: Phase 3 study. Alzheimer9s & Dementia, 2015. 11(8): p. 964-974.
A Residual Deficit for Global Motion Processing after Acuity Recovery in Deprivation Amblyopia (2005)

There was a selective deficit for global motion processing that was not due to the visibility of the stimuli and was nonselective for spatial scale. The eye with the more complete recovery (acuity 20/20) from pattern deprivation in childhood exhibited the more severe global motion deficit. discussion. The results suggest a primary extrastriate deficit in the dorsal pathway, possibly involving the middle temporal (MT) and the medial superior temporal (MST) cortical areas, that is unrelated to the acuity deficit thought to be in area V1. A similar deficit has recently been shown in strabismic amblyopia.
Towards experimentally realizable Hamiltonian gadgets (2013)

Application of the adiabatic model of quantum computation requires efficient encoding of the solution to computational problems into the lowest eigenstate of a Hamiltonian that supports universal adiabatic quantum computation. Experimental systems are typically limited to restricted forms of 2-body interactions. Therefore, universal adiabatic quantum computation requires a method for approximating quantum many-body Hamiltonians up to arbitrary spectral error using at most 2-body interactions. Hamiltonian gadgets, introduced around a decade ago, offer the only current means to address this requirement. Although the applications of Hamiltonian gadgets have steadily grown since their introduction, little progress has been made in overcoming the limitations of the gadgets themselves. In this experimentally motivated theoretical study, we introduce several gadgets which require significantly more realistic control parameters than similar gadgets in the literature. We employ analytical techniques which result in a reduction of the resource scaling as a function of spectral error for the commonly used subdivision, 3- to 2-body and $k$-body gadgets. Accordingly, our improvements reduce the resource requirements of all proofs and experimental proposals making use of these common gadgets. Next, we numerically optimize these new gadgets to illustrate the tightness of our analytical bounds. Finally, we introduce a new gadget that simulates a $YY$ interaction term using Hamiltonians containing only $\{X,Z,XX,ZZ\}$ terms. Apart from possible implications in a theoretical context, this work could also be useful for a first experimental implementation of these key building blocks by requiring less control precision without introducing extra ancillary qubits.
CAD: An Image Perception Perspective (2018)

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Classification de stades précancéreux et cancéreux précoces cutanés par spectroscopie bimodale /in vivo/ (2009)

National audience
Development of a unique laboratory standard indium gallium arsenide detector for the 500 to 1700 micron spectral region, phase 2. Final report (1990)

In the course of this work, 5 mm diameter InGaAs pin detectors were produced which met or exceeded all of the goals of the program. The best results achieved were: shunt resistance of over 300 K ohms; rise time of less than 300 ns; contact resistance of less than 20 ohms; quantum efficiency of over 50 percent in the 0.5 to 1.7 micron range; and devices were maintained and operated at 125 C without deterioration for over 100 hours. In order to achieve the goals of this program, several major technological advances were realized, among them: successful design, construction and operation of a hydride VPE reactor capable of growing epitaxial layers on 2 inch diameter InP substrates with a capacity of over 8 wafers per day; wafer processing was upgraded to handle 2 inch wafers; a double layer Si3N4/SiO2 antireflection coating which enhances response over the 0.5 to 1.7 micron range was developed; a method for anisotropic, precisely controlled CH4/H2 plasma etching for enhancement of response at short wavelengths was developed; and electronic and optical testing methods were developed to allow full characterization of detectors with size and spectral response characteristics. On the basis of the work and results achievedmore » in this program, it is concluded that large size, high shunt resistance, high quantum efficiency InGaAs pin detectors are not only feasible but also manufacturable on industrial scale. This device spans a significant portion of visible and near infrared spectral range and it will allow a single detector to be used for the 0.5 to 1.7 micron spectral region, rather than the presently used silicon (for 0.5 to 1.1 microns) and germanium (0.8 to 1.7 microns).« less
Entanglion (2018)

Educational games are a creative, enjoyable way for students to learn about technical concepts. We present Entanglion, a board game that aims to introduce the fundamental concepts of quantum computing -- a highly technical domain -- to students and enthusiasts of all ages. We describe our iterative design process and feedback from evaluations we conducted with students and professionals. Our playtesters gave positive feedback on our game, indicating it was engaging while simultaneously educational. We discuss a number of lessons we learned from our experience designing and evaluating a pedagogical game for a highly technical subject.
Dynamic propeller conformation for the unprecedentedly high degree of chiral amplification of supramolecular helices (2016)

An unprecedentedly high degree of chiral amplification of supramolecular helices in a sergeants and soldiers system was realized using a propeller-shaped molecule, triphenylamine (TPA), as the monomer. One sergeant controlled the handedness of 500 soldiers in supramolecular helices. We further demonstrated that a TPA derivative could switch its role from sergeant to soldier and <i>vice versa</i> depending on its partners. These achievements could be realized using the dynamic propeller conformation of TPA and provide new insights into supramolecular assemblies and the supramolecular chiral amplification of helices.
Processes and preliminary outputs for identification of actionable genes as incidental findings in genomic sequence data in the Clinical Sequencing Exploratory Research Consortium (2020)

As genomic and exomic testing expands in both the research and clinical arenas, determining whether, how, and which incidental findings to return to the ordering clinician and patient becomes increasingly important. Although opinion is varied on what should be returned to consenting patients or research participants, most experts agree that return of medically actionable results should be considered. There is insufficient evidence to fully inform evidence-based clinical practice guidelines regarding return of results from genome-scale sequencing, and thus generation of such evidence is imperative, given the rapidity with which genome-scale diagnostic tests are being incorporated into clinical care. We present an overview of the approaches to incidental findings by members of the Clinical Sequencing Exploratory Research network, funded by the National Human Genome Research Institute, to generate discussion of these approaches by the clinical genomics community. We also report specific lists of “medically actionable” genes that have been generated by a subset of investigators in order to explore what types of findings have been included or excluded in various contexts. A discussion of the general principles regarding reporting of novel variants, challenging cases (genes for which consensus was difficult to achieve across Clinical Sequencing Exploratory Research network sites), solicitation of preferences from participants regarding return of incidental findings, and the timing and context of return of incidental findings are provided.
AIMD algorithms and exponential functionals (2004)

The behavior of a connection transmitting packets into a network according to a general additive-increase multiplicative-decrease (AIMD) algorithm is investigated. It is assumed that loss of packets occurs in clumps. When a packet is lost, a certain number of subsequent packets are also lost (correlated losses). The stationary behavior of this algorithm is analyzed when the rate of occurrence of clumps becomes arbitrarily small. From a probabilistic point of view, it is shown that exponential functionals associated to compound Poisson processes play a key role. A formula for the fractional moments and some density functions are derived. Analytically, to get the explicit expression of the distributions involved, the natural framework of this study turns out to be the $q$-calculus. Different loss models are then compared using concave ordering. Quite surprisingly, it is shown that, for a fixed loss rate, the correlated loss model has a higher throughput than an uncorrelated loss model.
EFFICACY OFLOWER-ENERGYBIPHASICSHOCKS FORTRANSTHORACICDEFIBRILLATION: A FOLLOW-UPCLINICALSTUDY (2004)

Objective. This clinical study prospectively evaluated the first-shock defibrillation efficacy of 150-joule impedance-compensated, 200-µF biphasic truncated exponential (BTE) shocks in patients with electrically-induced ventricular fibrillation (VF), and compared it with a historical control group treated with 200-J monophasic damped sine (MDS) shocks. Methods. Ventricular tachyarrhythmias were induced in patients undergoing electrophysiologic (EP) testing for ventricular arrhythmias or testing of an implantable cardioverter-defibrillator (ICD). A 150-J shock was delivered as the primary therapy to terminate induced arrhythmias in the EP group, and as a “rescue” shock when a single ICD shock failed to terminate the arrhythmias in the ICD group. Results. Ninety-six patients received study shocks. The preshock rhythm was classified as VF in 77 patients and as ventricular tachycardia (VT) in 19 patients. First-shock success rates for VF and VT were 75 out of 77 (97.4%) and 19 out of 19 (100%) for the 150-J BTE compared with the historical control rates of 61 out of 68 (89.7%) and 29 out of 31 (94%) for 200-J MDS. The first-shock success rate for VF treated with 150-J BTE was technically equivalent to that of 200-J MDS (p = 0.001). The transthoracic impedance did not vary between groups, yet the peak current delivered by the 150-J BTE shock was about 50% lower. Conclusions. This study demonstrated that 150-J shocks of this impedance-compensated, 200-µF BTE waveform provided very high efficacy for defibrillation of short duration, electrically-induced VF. These lower-energy biphasic shocks had a success rate equivalent to that of 200-J MDS shocks, and they provided this efficacy while exposing patients to much less current than the monophasic shocks.
Findings of the WMT 2018 Biomedical Translation Shared Task: Evaluation on Medline test sets (2018)

Machine translation enables the automatic translation of textual documents between languages and can facilitate access to information only available in a given language for nonspeakers of this language, e.g. research results presented in scientific publications. In this paper, we provide an overview of the Biomedical Translation shared task in the Workshop on Machine Translation (WMT) 2018, which specifically examined the performance of machine translation systems for biomedical texts. This year, we provided test sets of scientific publications from two sources (EDP and Medline) and for six language pairs (English with each of Chinese, French, German, Portuguese, Romanian and Spanish). We describe the development of the various test sets, the submissions that we received and the evaluations that we carried out. We obtained a total of 39 runs from six teams and some of this year's BLEU scores were somewhat higher that last year's, especially for teams that made use of biomedical resources or state-of-the-art MT algorithms (e.g. Transformer). Finally, our manual evaluation scored automatic translations higher than the reference translations for German and Spanish.
Trehalose and Vitreous States: Desiccation Tolerance of Dormant Stages of the CrustaceansTriopsandDaphnia (2011)

Several aquatic organisms are able to withstand extreme desiccation in at least one of their life stages. This is commonly known as "anhydrobiosis." It was often thought that to tolerate such a desiccated state required high amounts of compatible solutes such as the nonreducing disaccharide trehalose, which protects cellular structures by water replacement and glass formation. Trehalose levels of dormant eggs and cysts of five freshwater crustaceans (Daphnia magna, Daphnia pulex, Triops longicaudatus, Triops cancriformis, and Triops australiensis) were observed in different states of hydration and dehydration. Although trehalose was detected in all species, the concentration was under 0.5% of the dry weight (0.05 μg/μg protein), and no change between the different states was observed. Differential scanning calorimetry (DSC) measurements indicated that dried cysts of all Triops species were in a glassy state, supporting the vitrification hypothesis. No indication for a vitreous state was found in dried resting eggs of Daphnia.
Use of Leuco-Dyes in the Quantitative Colorimetric Microdetermination of Hemoglobin and Other Heme Compounds (1975)

Sensitivity, stability, and specificity of the color-producing reaction of hydrogen peroxide with bezidine, leuco-malachite green, or o-dianisidine were tested in numerous systems containing hemoglobin and other hemoproteins. Use of urea or low temperature (to minus 12 degrees C), or both, was highly beneficial, especially with leuco-malachite green, for which the color reaction was stable, after about 15 min, for longer than 24 h, with a colorless bank. Absorbance was 0.3 at a final hemoglobin concentration of 0.27 mg/liter. Nonspecific color produced by substances such as FeCl-3 and ascorbic acid was completely eliminated. Of the three leuco-dyes studied, only benzidine yielded a completely linear calibration curve, but its relative instability and reported carcinogenicity are serious disadvantages. No system tested eliminated completely the known inhibition by plasma of the peroxidase activity of these leuco dyes.
Mutations in the GCH1 Gene Are Associated with Parkinson Disease (S17.001) (2014)

OBJECTIVE: To systematically explore the relationship between GCH1 mutations and Parkinson disease. BACKGROUND: GTP cyclohydrolase-1, encoded by the GCH1 gene, is an essential enzyme for dopamine production in nigrostriatal cells. Heterozygous loss-of-function mutations in GCH1 are the most common cause of dopa-responsive dystonia, a metabolic disease that classically presents in childhood with generalized dystonia and a dramatic long-lasting response to levodopa. DESIGN/METHODS: We describe clinical, genetic and nigrostriatal dopaminergic imaging findings ([123I]FP-CIT SPECT) of four unrelated pedigrees in which pathogenic GCH1 mutations were identified in patients with classic dopa-responsive dystonia and in family members with adult-onset parkinsonism. The frequency of GCH1 coding or splice-mutation mutations was evaluated in the exome-sequencing data of 1337 Parkinson disease cases without a family of history of dystonia and 5209 ethnicity-matched controls. RESULTS: Dopamine-transporter imaging was abnormal in all parkinsonian patients, indicating Parkinson disease-like nigrostriatal dopaminergic denervation. In the exome sequencing data we identified 11 different heterozygous GCH1 mutations, including four mutations known to cause dopa-responsive dystonia (Q110X, V204I, K224R, M230I), six novel mutations (L92I, T112A, A120S, D134G, R198Q, G217V) and one benign variant (P69L). The frequency of pathogenic and novel non-synonymous coding mutations in GCH1 was significantly higher in cases (7/1337=0.52%) than in controls (8/5209=0·15%; p=0·02; odds ratio 3·4, 95% confidence interval=1·2-9·4). All parkinsonian cases identified with GCH1 mutations fully met the UK Parkinson's Disease Society Brain Bank clinical diagnostic criteria for Parkinson’s disease. CONCLUSIONS: Our results show that GCH1 mutations should be considered as a novel risk factor for PD. GTP cyclohydrolase-1 deficiency not only leads to biochemical striatal dopamine depletion and dopa-responsive dystonia, but also predisposes to nigrostriatal cell loss. Further insight into GCH1-associated pathogenetic mechanisms will shed light on the role of dopamine metabolism in nigral degeneration and Parkinson disease.
Characterization of low-temperature wafer bonding by infrared spectroscopy (2000)

We present the results of an infrared (IR) spectroscopic investigation of interfaces between two hydrophilic Si wafers bonded at low temperature. Multiple internal transmission IR spectra were recorded of the bonds, with different chemical pretreatments of Si surfaces employed before bonding. The analysis of IR spectra shows that the number of O–H and H–Si–Ox species at the interface depends strongly on the chemical pretreatment type, which determines the bonding energy. The annealing procedure used in the bonding process leads to dissociation of water molecules, oxidation of silicon at the interfaces, and diffusion of hydrogen into silicon oxide layer formed at the interface. The difference in bonding processes is discussed.
Generalized Data Naming and Scalable State Announcements for Reliable Multicast (1997)

Abstract : Traditional ARQ-based reliable protocols for unicast (e.g., TCP) as well as multicast (e.g., Horus, RMTP etc.) use sequential numbering of data units and detect losses from discontinuities in the sequence of received packets. The Application Level Framing (ALF) model encourages application control over loss-detection and recovery. With sequence numbers, the application must express its reliability requirements using sub-sequences of the sequence space. This is both cumbersome and restrictive for applications that have no a priori knowledge of the data stream. Distributed whiteboard applications, webcast, and file system multicasting are some examples of applications where data is continuously generated and receivers cannot predict which sub-sequences must be received reliably. In this paper, we propose an alternative data naming scheme which enhances the expressibility of applications' reliability and ordering requirements. We apply the new data naming scheme to build a framework for light-weight Scalable, Reliable Multicast (SRM) sessions, and develop a State Announcement Protocol (SAP) for loss detection. Using simulations, we study the scaling behavior of SAP and show how the protocol scales well for large group sizes. We also suggest heuristics for certain classes of applications that improve the convergence times and message complexity of the protocol.
Low-density parity-check codes for multilevel modulation (2003)

The application of low-density parity-check (LDPC) codes to multilevel modulation systems is studied. A family of binary LDPC codes that offer good performance and do not suffer from error-floor effects at low bit-error rates is introduced. A number of properties render these codes attractive for practical applications: they are specified via a small number of parameters, are encodable in linear time, and the generation of their parity-check matrix is deterministic, involving a small number of preprocessing operations. In addition, the symbol-mapping technique based on "double Gray-code labeling" for obtaining coded multilevel transmit symbols is described. Finally, it is shown that the proposed LDPC coding technique is well suited for multicarrier digital-subscriber-line transmission applications as it permits a wide range of trade-offs between latency, complexity, and system performance.