gebhart/patrepeval huggingface dataset:
ASAC-Analysis/Synthesis Audio Codec for Very Low-Bit Rates (1996)

An Analysis/Synthesis Audio Codec (ASAC) is presented, which allows the coding of audio signals at very low bit rates for applications like mobile communication or multimedia database access via modem and analog telephone lines. Compression with bit rates between 6 kbit/s and 24 kbit/s is addressed. Furthermore the implementation of special effects like independent pitch change and speed change in the decoder is described. 1 Introduction Many applications for very low bit rate storage and transmission of digital audio signals mainly focus on speech signals. Therefore a lot of optimizations for speech codecs operating at bit rates between 6 and 16 kbit/s were carried out during the past years. However there is an increasing interest in extensions which also allow the transmission of music signals in areas like mobile communications or multimedia database access via modem and analog telephone lines [1]. The presented Analysis/Synthesis Audio Codec is therefore designed to represent musi...
Development of Coupling Controlled Polymerizations by Adapter-ligation in Mate-pair Sequencing for Detection of Various Genomic Variants in One Single Assay (2018)

Abstract The diversity of disease presentations warrants one single assay for detection and delineation of various genomic disorders. Herein, we describe a gel-free and biotin-capture-free mate-pair method through coupling Controlled Polymerizations by Adapter-Ligation (CP-AL). We first demonstrated the feasibility and ease-of-use in monitoring DNA nick-translation and primer extension by limiting the nucleotide input. By coupling these two controlled polymerizations by a reported non-conventional adapter ligation reaction 3’ branch ligation, we evidenced that CP-AL significantly increased DNA-circularization efficiency (by 4-fold) and was applicable for different sequencing methods but at a faction of current cost. Its advantages were further demonstrated by fully elimination of small-insert-contaminated (by 39.3-fold) with a ~50% increment of physical coverage, and producing uniform genome/exome coverage and the lowest chimeric rate. It achieved single-nucleotide variants detection with sensitivity and specificity up to 97.3 and 99.7%, respectively, compared with data from small-insert libraries. In addition, this method can provide a comprehensive delineation of structural rearrangements, evidenced by a potential diagnosis in a patient with oligo-atheno-terato-spermia. Moreover, it enables accurate mutation identification by integration of genomic variants from different aberration types. Overall, it provides a potential single-integrated solution for detecting various genomic variants, facilitating a genetic diagnosis in human diseases.
Statistical analysis of neural data: Addenda to Brown's point process notes (2007)

4: Two applications of the point process likelihood formula Two-alternative forced choice (2AFC) discrimination. Let’s assume we have some model that assigns some conditional intensity function λ~x(t) to any given stimulus ~x. We may use this model to perform discrimination tasks: given the observed spike train data D = {ti}, which of the two stimuli ~x1 or ~x2 are more likely to have produced this spike train? (The detection task is a special case: here we would like to know whether ~x0 or ~x = 0 produced the observed response.) According to Neyman-Pearson, we should simply compare loglikelihoods:
Supplementary Video S5 from Nonlinear Optics with Near-Infrared Excitation Enable Real-Time Quantitative Diagnosis of Human Cervical Cancers (2023)

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Development and Evaluation of an Avian Influenza, Neuraminidase Subtype 1, Indirect Enzyme-Linked Immunosorbent Assay for Poultry Using the Differentiation of Infected from Vaccinated Animals Control Strategy (2010)

An indirect enzyme-linked immunosorbent assay (ELISA) was developed using baculovirus, purified, recombinant N1 protein from A/chicken/Indonesia/PA7/2003 (H5N1) virus. The N1-ELISA showed high selectivity for detection of N1 antibodies, with no cross-reactivity with other neuraminidase subtypes, and broad reactivity with sera to N1 subtype isolates from North American and Eurasian lineages. Sensitivity of the N1-ELISA to detect N1 antibodies in turkey sera, collected 3 wk after H1N1 vaccination, was comparable to detection of avian influenza antibodies by the commercial, indirect ELISAs ProFLOK AIV Plus ELISA Kit (Synbiotics, Kansas City, MO) and Avian Influenza Virus Antibody Test Kit (IDEXX, Westbrook, ME). However, 6 wk after vaccination, the Synbiotics ELISA kit performed better than the N1-ELISA and the IDEXX ELISA kit. An evaluation was made of the ability of the N1-ELISA to discriminate vaccinated chickens from subsequently challenged chickens. Two experiments were conducted, chickens were vaccinated with inactivated H5N2 and H5N9 viruses and challenged with highly pathogenic H5N1 virus, and chickens were vaccinated with recombinant poxvirus vaccine encoding H7 and challenged with highly pathogenic H7N1 virus. Serum samples were collected at 14 days postchallenge and tested by hemagglutination inhibition (HI), quantitative neuraminidase inhibition (NI), and N1-ELISA. At 2 days postchallenge, oropharyngeal swabs were collected for virus isolation (VI) to confirm infection. The N1-ELISA was in fair agreement with VI and HI results. Although the N1-ELISA showed a lower sensitivity than the NI assay, it was demonstrated that detection of N1 antibodies by ELISA was an effective and rapid assay to identify exposure to the challenge virus in vaccinated chickens. Therefore, N1-ELISA can facilitate a vaccination strategy with differentiation of infected from vaccinated animals using a neuraminidase heterologous approach.
human NBD1 of CFTR in complex with nanobodies T2a and T4 (2018)

The leading cause of cystic fibrosis (CF) is the deletion of phenylalanine 508 (F508del) in the first nucleotide-binding domain (NBD1) of the cystic fibrosis transmembrane conductance regulator (CFTR). The mutation affects the thermodynamic stability of the domain and the integrity of the interface between NBD1 and the transmembrane domain leading to its clearance by the quality control system. Here, we develop nanobodies targeting NBD1 of human CFTR and demonstrate their ability to stabilize both isolated NBD1 and full-length protein. Crystal structures of NBD1-nanobody complexes provide an atomic description of the epitopes and reveal the molecular basis for stabilization. Furthermore, our data uncover a conformation of CFTR, involving detachment of NBD1 from the transmembrane domain, which contrast with the compact assembly observed in cryo-EM structures. This unexpected interface rearrangement is likely to have major relevance for CF pathogenesis but also for the normal function of CFTR and other ABC proteins.
Ignition of Cs-Ba Tacitron during breakdown and extinguishing modes (1992)

Single effect experiments are performed to determine the conditions for ignition of the Cs‐Ba tacitron in the breakdown mode as functions of the emitter temperature. Cs pressure, Ba pressure, and the grid and collector voltages; experimental data is used to determine the off‐time required for ignition. To determine the applicability of the ignition data in the breakdown mode to the extinguishing mode of operation, the off‐time values of the former are compared with those of the latter at different grid potentials. Results show that in both the breakdown and extinguishing mode of operation the off‐time required for ignition both is strongly dependence on the Cs pressure in the gap, but weakly dependent on the other operating parameters. For a given Cs pressure, the off‐time in the extinguishing mode increases as the grid potential decreases and/or the modulation time increases. Reducing the grid potential not only increases the off‐time for ignition in the extinguishing mode, hence decreasing the modulation frequency, but also can result in unstable current modulation. Results show that in order to maintain stable modulation at a frequency ≥4 kHz, a positive grid potential in excess of 24 V needs to be applied for ignition.
HLA ligandome analysis of primary chronic lymphocytic leukemia (CLL) cells under lenalidomide treatment confirms the suitability of lenalidomide for combination with T-cell-based immunotherapy (2017)

Recent studies suggest that CLL is an immunogenic disease, which might be effectively targeted by antigen-specific T-cell-based immunotherapy. However, CLL is associated with a profound immune defect, which might represent a critical limitation for mounting clinically effective antitumor immune responses. As several studies have demonstrated that lenalidomide can reinforce effector T-cell responses in CLL, the combination of T-cell-based immunotherapy with the immunomodulatory drug lenalidomide represents a promising approach to overcome the immunosuppressive state in CLL. Antigen-specific immunotherapy also requires the robust presentation of tumor-associated HLA-presented antigens on target cells. We thus performed a longitudinal study of the effect of lenalidomide on the HLA ligandome of primary CLL cells <i>in vitro</i>. We showed that lenalidomide exposure does not affect absolute HLA class I and II surface expression levels on primary CLL cells. Importantly, semi-quantitative mass spectrometric analyses of the HLA peptidome of three CLL patient samples found only minor qualitative and quantitative effects of lenalidomide on HLA class I- and II-restricted peptide presentation. Furthermore, we confirmed stable presentation of previously described CLL-associated antigens under lenalidomide treatment. Strikingly, among the few HLA ligands showing significant modulation under lenalidomide treatment, we identified upregulated IKZF-derived peptides, which may represent a direct reflection of the cereblon-mediated effect of lenalidomide on CLL cells. Since we could not observe any relevant influence of lenalidomide on the established CLL-associated antigen targets of anticancer T-cell responses, this study validates the suitability of lenalidomide for the combination with antigen-specific T-cell-based immunotherapies.
SOP and PMD monitoring with WDM polarimeter (2002)

A broadband WDM polarimeter is used in online determination of the state of polarisation (SOPs) of WDM channels. Wavelength resolved SOP measurements and the degree of polarisation of a single channel indicate signal distortions which are caused by PMD, and may be applied to multi channel PMD compensation.
Fundamentals of GSM Performance Evaluation (2010)

This chapter contains sections titled: Introduction On the GSM Radio System Performance Engineering Simulation Tools Key Performance Indicators EFL Methodology Further Reading References
PANCREATIC CYST FLUID CEA AND AMYLASE IN THE DIFFERENTIAL DIAGNOSIS OF PANCREATIC CYSTS (2007)

Background/Aims: Pancreatic mucinous cystic lesions (MCL) (mucinous cystic neoplasm [MCN] and intraductal papillary mucinous neoplasms [IPMN]) are often incidentally identified, but can present with pancreatitis. Non-mucinous pancreatic cystic lesions (NMCL) (e.g., pseudocysts [PC] and serous cystadenoma [SCA]) are the common differential diagnosis for MCLs, SCA for asymptomatic cysts and PC for those with pancreatitis. We evaluated the utility of cyst fluid CEA and amylase in the differential diagnosis of pancreatic cysts. Methods: We reviewed medical records of 116 patients with MCLs and 47 with NMCLs who underwent cyst fluid analyses and had a firm clinical diagnosis. The diagnosis was histologically confirmed in all 32 pseudocysts, 15 SCA, 25 MCN, and 55/91 IPMN; additionally, 36 asymptomatic cysts that clearly communicated with the pancreatic duct were classified as IPMN. Results: CEA and amylase did not distinguish MCN from IPMN and amylase did not distinguish PC from MCL. (Table 1)TABLE 1: Caption not available.Conclusions: Use of cyst fluid markers to distinguish among cystic pancreatic lesions is a complex exercise in pattern recognition. While high CEA (≥ 278 ng/ml) is virtually diagnostic of MCL, a very low CEA (<5 ng/ml) is a feature of SCA. However, at these cutoffs the sensitivity of CEA is not high. Cyst fluid amylase does not distinguish MCL from NMCL or between MCN and IPMN. PCs have high amylase, but so do many MCLs. Better markers of individual cystic lesions are clearly needed.
Regional-level injury risk sensitivity to pre-crash driver position within simplified real world motor vehicle crash reconstructions (2015)

Two full-frontal Crash Injury Research and Engineering Network (CIREN) motor vehicle crashes (MVCs) were reconstructed using finite element (FE) models. A FE simplified vehicle model (SVM) was tuned to mimic the frontal crash response of the CIREN case vehicle using frontal NCAP crash test data. The Total HUman Model for Safety (THUMS) was positioned in 120 pre-crash configurations per case within the tuned SVM. Seat track position, seat back angle, D-ring height, steering column angle, and steering column telescoping position variables were varied. An additional baseline simulation was performed that aimed to match the pre-crash occupant position documented in CIREN for each case. FE simulations were performed using the delta-V pulse from the vehicle’s event data recorder (EDR). HIC15, combined thoracic index (CTI), and femur forces were evaluated to predict regional-level injury risks. Tuning the SVM to specific vehicle models resulted in close matches between simulated and test injury metric data, allowing the tuned SVM to be used in each case reconstruction. Simulations with the most rearward seats and reclined seat backs had the greatest HIC15, head injury risk, CTI and chest injury risk. More than half of the Camry occupant positions tested indicated a risk of AIS 2+ chest injury such as the hemomediastinum seen in the real world case. The injury metrics evaluated for the Cobalt case occupant indicated a low risk of injury. The highest risk of injury was in the chest region. The baseline simulation estimated 33% risk of any AIS 2+ chest injury and only a 4% chance of AIS 3+ chest injury, while the Cobalt case occupant had an AIS 3 pulmonary contusion. The reconstruction process and analysis allows for quantification of the sensitivity of the injury risk predictions based on occupant position to further understand important factors leading to severe MVC injuries.
641 Spatially organized multicellular immune hubs in MMRd and MMRp colorectal cancer (2021)

<h3>Background</h3> Immune responses to cancer are highly variable, with DNA mismatch repair-deficient (MMRd) tumors exhibiting more anti-tumor immunity than mismatch repair-proficient (MMRp) tumors. Almost all tumors are infiltrated with immune cells, but the types of immune responses and their effects on tumor growth, metastasis and death, vary greatly between different cancers and individual tumors. Which of the numerous cell subsets in a tumor contribute to the response, how their interactions are regulated, and how they are spatially organized within tumors remains poorly understood. <h3>Methods</h3> To understand the rules governing these varied responses, we transcriptionally profiled 371,223 single cells from colorectal tumors and adjacent normal tissues of 28 MMRp and 34 MMRd treatment-naive patients. We developed a systematic approach to discover cell types, their underlying gene programs, and cellular communities based on single cell RNA-seq (scRNAseq) profiles and applied it to study the distinguishing features of human MMRd and MMRp colorectal cancer. Cellular communities discovered from this analysis were spatially mapped in tissue sections using multiplex RNA in situ hybridization microscopy. <h3>Results</h3> To understand the basis for differential immune responses in CRC, we first determined and compared the immune cell composition of MMRd and MMRp CRC and normal colon tissue, finding dramatic remodeling between tumor and normal tissue and between MMRd and MMRp tumors, particularly within the myeloid, T cell, and stromal compartments. Among the clusters enriched in MMRd tumors were activated CXCL13+ CD8 T cells. Importantly, gene program co-variation analysis revealed multicellular networks. We discovered a myeloid cell-attracting hub at the tumor-luminal interface associated with tissue damage, and an MMRd-enriched immune hub within the tumor, with activated IFNG+ and CXCL13+ T cells together with malignant and myeloid cells expressing T-cell-attracting chemokines (figure 1). <h3>Conclusions</h3> Our study provides a rich dataset of cellular states, gene programs and their transformations in tumors across a relatively large cohort of patients with colorectal cancer. Our predictions of several multicellular hubs based on co-variation of gene expression programs, and subsequent spatial localization of two major immune-malignant hubs, organizes a large set of cell states and programs into a smaller number of coordinated networks of cells and processes. Understanding the molecular mechanisms underlying these hubs, and studying their temporal and spatial regulation upon treatment will be critical for advancing cancer therapy. <h3>Ethics Approval</h3> This study was approved by the DF-HCC institutional review board (protocols 03-189 and 02-240).
Performance Tests of a Single Camera Micro 3D-PTV through Measurements of Micro Backward Facing Step Flows (2008)

Abstract A micro 3D-PTV system has been constructed using single camera system. The system has two viewing holes just behind the object lens of the microscopic system. The system consists of one high-definition camera (1028 x 1024 pixel, 500fps), an Ar-ion laser and a host computer. In order to find particles&amp;apos; pair between the particles &amp;apos; images viewed through the stereoscopic holes, a hybrid genetic algorithm (GA) has been adopted. An epipolar concept has been adopted to eliminate spurious candidates that can’t be regarded as the same particle pairs. The performances of the system have been tested using the actual camera parameters that have been obtained from the stereoscopic holes. The measurement errors for X, Y and Z coordinates were 0.083µm, 0.045µm and 0.083µm, respectively. A micro backward facing step channel (H x h x W: 36µm x 70µm x 3000µm) have been measured with the constructed measurement system. The results showed good agreements with other results.
LAAS Ground Facility Design Improvements to Meet Proposed Requirements for Category II/III Operations (2002)

Stanford University has developed a Local Area 
Augmentation System (LAAS) ground facility prototype 
known as the Integrity Monitor Testbed (IMT) to 
demonstrate the feasibility of LAAS precision approaches 
under Category I conditions. While the Category I IMT is 
essentially complete, research on IMT algorithms 
continues to improve its performance so that it can 
eventually meet Category II/III approach requirements. 
To the extent possible, it is desirable to satisfy Category 
II/III requirements with modifications to the existing 
single-frequency (L1) LAAS architecture in order to 
provide Category II/III initial operational capability (IOC) 
before the second civil frequency (L5) is present on a 
sufficient number of GPS satellites. This will also 
provide a backup operational mode in a future dual-
frequency LAAS if either L1 or L5 is interfered with. This paper addresses IMT improvements to detection of 
satellite signal deformation, code-carrier divergence 
monitoring of both potential satellite failures and 
ionosphere spatial anomalies, and position-error 
monitoring at a “remote” monitor receiver that is some 
distance away from the existing reference receiver 
antennas. With these relatively-limited modifications to 
the existing Category I LGF architecture, significant 
performance improvements are demonstrated. While the 
degree to which these improvements are sufficient 
depends on changes now being considered to the 
Category II/III requirements, we believe that, with further 
refinement, they will be sufficient to provide acceptable 
IOC and dual-frequency backup availability.
Development of a simple, rapid sandwich enzyme immunoassay for the measurement of serum rat LH. (1996)

The present study describes the development and validation of a rapid, sensitive, specific and precise enzyme immunoassay (EIA) sandwich suitable for measuring luteinizing hormone (LH) in rat serum. Ninety-six well polystyrene microtiter plates were coated with 100 microliters (250 ng/ml) of a well-characterized monoclonal antibody (518B7, Roser, UC Davis) generated against bovine LH. A polyclonal antiserum raised in rabbits against ovine FSH (G4-215B, Papkoff) was conjugated to sodium periodate-activated horseradish peroxidase (HRP), and used as the second antibody of the sandwich assay. This anti-ovine FSH antiserum cross-reacted more than 200% with rat LH. Standards (r-LH-RP-3, NIADDK, range 0 pg/well to 2.5 ng/well or 100 microliters) diluted in a 3(N-Morpholino) propane sulfonic acid (MOPS) buffer, or serum, were incubated with the solid phase antibody for 2 hours. Plates were washed and the anti-oFSH:HRP (100 microliters) in MOPS buffer was added and incubated a further 2 hours before a second wash and the addition of the substrate (TMB, 3,3',5,5'-tetramethylbenzidine dihydrochloride and H2O2). The least detectable concentration of LH was 16.1 +/- 1.42 pg/ml. The recovery of known concentrations of LH added to several samples was 93.5 +/- 1.70%. Mean intra-assay and inter-assay coefficients of variation (%) were less than 10% (n = 20). The anti-FSH:HRP showed less than 8.0% cross reactivity with rFSH in this LH EIA system. The correlation coefficient (r) of samples analyzed by EIA in parallel with RIA was r = 0.90 (p < 0.001, n = 26). Results showed levels between 105.21 and 633.87 pg/ml. This new LH EIA sandwich offers a stable, rapid, and improved EIA system for the measurement of serum LH concentrations of this species over previously reported methods.
Preparation of delayed release tablet dosage forms by compression coating: Effect of coating material on theophylline release (2010)

In this study, compression-coated tablets were prepared and examined by real-time swelling/erosion analysis and dissolution studies. Of the coating materials, PVP showed no swelling behavior and had no impact on theophylline release. Polyox(®) exhibited swelling behavior of an entangled polymer, which was reflected in its > 14-hour delayed-release profile. Hydroxypropyl methylcellulose (HPMC), which revealed the characteristics of a disentangled polymer, caused a 2-h delay in theophylline release. Based on preliminary texture analysis data, Polyox(®)/PVP blends were used as coating materials to manipulate the onset of drug release from the compression-coated tablets. Of the blends, at a 1:1 ratio, for example, resulted in a burst release after 10 h, which demonstrated the feasibility of preparing delayed release dosage forms by compression coating. Furthermore, it was feasible to predict the dissolution behavior of polymers from their swelling/erosion data, which were generated from texture analysis.
Modeling and Budgeting of Timing Jitter and Noise (2008)

This chapter contains sections titled: Eye Diagram Bit Error Rate Jitter Sources and Budgets Noise Sources and Budgets Peak Distortion Analysis Methods Summary References Problems