gebhart/patrepeval huggingface dataset:
O1–06–05: Monoclonal antibodies selective for Aβ protofibrils reduce plaque burden in transgenic mice models of Alzheimer's disease (2006)

In recent years there has been an increasing interest in soluble Aβ oligomers as the pathogenic species in Alzheimer's disease (AD). Different types of Aβ oligomers have been described: low molecular weight Aβ oligomers, Aβ derived diffusible ligands (ADDLs), amylospheroids and large soluble Aβ oligomers, so called protofibrils. We are focusing on the protofibrils, since the Arctic mutation (Aβ E22G) causes AD due to an enhanced propensity of Arctic Aβ peptides to form protofibrils. Enable measurement of Aβ protofibrils in biological tissues through novel antibody–based assays using protofibril selective monoclonal IgGs. In addition, to evaluate these antibodies for immunotherapy in cell culture and transgenic mice models. Protofibrils were generated of synthetic Aβ and analyzed by HPLC and non–denaturing gels. Monoclonal antibodies were raised against the protofibril preparations and characterized with ELISA and Biacore. Protofibril selective antibodies were used in immunoassays to measure protofibrils in APP transgenic mouse brain homogenates. Finally, the ability of the antbodies to inhibit protofibril–induced neurotoxicity was evaluated in vitro using PC12 cells, and the therapeutic efficacy was analyzed in vivo using our APP–ArcSwe transgenic mouse model, which display intraneuronal Aβ before deposition of senile plaques. The size of in vitro generated Aβ protofibrils was determined to be 250–500 kDa according to both Blue Native Gel electrophoresis and size exclusion chromatography. Using protofibrils as antigen, we developed protofibril selective monoclonal IgG2a antibodies. One of these, mAb8, had a hundred–fold higher affinity for protofibrils than for monomers. By using mAb8 in immunoassays, Aβ protofibrils could be detected at low pM levels, which enabled measurement in brain homogenates from transgenic mice. In immunotherapy experiments, mAb8 significantly reduced protofibril toxicity in PC12 cells and reduced Aβ plaque burden in transgenic mice brains. Protofibril selective monoclonal IgG antibodies have been developed and used to measure Aβ protofibrils in transgenic mouse brain homogenates. Measurements of protofibrils in human tissues are ongoing. The reduced protofibril toxicity in PC12 cells and diminished plaque burden in transgenic mice brain after administration of anti–protofibril antibodies indicate that these antibodies could be candidates for passive immunization in the treatment of AD.
A20 and ABIN-1 cooperate in balancing CBM complex-triggered NF-κB signaling in activated T cells (2022)

T cell activation initiates protective adaptive immunity, but counterbalancing mechanisms are critical to prevent overshooting responses and to maintain immune homeostasis. The CARD11-BCL10-MALT1 (CBM) complex bridges T cell receptor engagement to NF-κB signaling and MALT1 protease activation. Here, we show that ABIN-1 is modulating the suppressive function of A20 in T cells. Using quantitative mass spectrometry, we identified ABIN-1 as an interactor of the CBM signalosome in activated T cells. A20 and ABIN-1 counteract inducible activation of human primary CD4 and Jurkat T cells. While A20 overexpression is able to silence CBM complex-triggered NF-κB and MALT1 protease activation independent of ABIN-1, the negative regulatory function of ABIN-1 depends on A20. The suppressive function of A20 in T cells relies on ubiquitin binding through the C-terminal zinc finger (ZnF)4/7 motifs, but does not involve the deubiquitinating activity of the OTU domain. Our mechanistic studies reveal that the A20/ABIN-1 module is recruited to the CBM complex via A20 ZnF4/7 and that proteasomal degradation of A20 and ABIN-1 releases the CBM complex from the negative impact of both regulators. Ubiquitin binding to A20 ZnF4/7 promotes destructive K48-polyubiquitination to itself and to ABIN-1. Further, after prolonged T cell stimulation, ABIN-1 antagonizes MALT1-catalyzed cleavage of re-synthesized A20 and thereby diminishes sustained CBM complex signaling. Taken together, interdependent post-translational mechanisms are tightly controlling expression and activity of the A20/ABIN-1 silencing module and the cooperative action of both negative regulators is critical to balance CBM complex signaling and T cell activation.
Segmentation and Analysis of Early Reflections from a Binaural Room Impulse Response (2009)

In this paper, a novel method for analysis of binaural room impulse responses is presented. Individual reflections are localized in time and frequency from a measured binaural room impulse response based on the continuous cross-wavelet transform (XWT). The directions of the reflections are then analyzed based on KEMAR and CIPIC reference data lookup, and compared a previous approach. Analysis of the directions and arrival times of reflections allows detailed study of measured binaural room impulse responses. The reflections can also be resynthesized based on the continuous wavelet transform (CWT) and spread apart in time, resulting in a slow-motion room impulse response that can be useful for room acoustics design as well as in teaching room acoustics.
Analysis of <i>Haemophilus influenzae</i> type b lipooligosaccharide‐synthesis genes that assemble or expose a 2‐keto‐3‐deoxyoctulosonic acid epitope (1991)

We recently isolated a recombinant phage from a Haemophilus influenzae type b (Hib) library that assembles an oligosaccharide with an apparent molecular weight of 1400 (1.4 K) on a 4.1 K Escherichia coli lipopolysaccharide (LPS) structure, producing a 5.5 K LPS species that contains a KDO (2-keto-deoxyoctulosonic acid) epitope. Subcloning and deletional analysis of the 14 kb Haemophilus insert showed that three overlapping restriction fragments contained within a 7.2 kb Pstl-BamHl fragment sequentially modified an E. coli 4.1 K LPS structure, generating novel species of 4.5 K, 5.1 K and 5.5 K. Only the 5.5 K species contained the KDO epitope. We confirmed the relationship between the cloned genes and Hib lipooligosaccharide (LOS) biosynthesis by constructing a mutant that expressed an altered LOS. Thus, the Hib 7.2 kb Pstl-BamHl restriction fragment contained a cluster of at least three genetic loci whose products acted sequentially in LOS biosynthesis.
ICI Mitigation in MIMO OFDM Systems (2007)

It is proved that the intercarrier interference matrix in orthogonal frequency division multiplexing systems is unitary for an arbitrary value of frequency offset and any number of subcarriers. The benefit of a recently published precoding scheme in practical applications is thereby established.
A Fractional Model for IPMC Actuators (2008)

The paper proposes a new model for IPMC actuators, based on non-integer order models. IPMCs are very interesting because of their capability to transform electrical energy into mechanical energy and vice-versa, making them particularly attractive for possible applications in different fields, such as robotics, aerospace, biomedicine, etc. A great interest has been devoted to non-integer, or fractional, order systems because they well model a lot of physical systems. An experimental setup has been realized to study the IPMCs behavior and an algorithm has been developed in Matlab Environment to identify a fractional order model of IPMC actuators.
Decoding Motor Unit Activity From Forearm Muscles: Perspectives for Myoelectric Control (2017)

We prove the feasibility of decomposing high density surface EMG signals from forearm muscles in non-isometric wrist motor tasks of normally limbed and limb-deficient individuals with the perspective of using the decoded neural information for prosthesis control. For this purpose, we recorded surface EMG signals during motions of three degrees of freedom of the wrist in seven normally limbed subjects and two patients with limb deficiency. The signals were decomposed into individual motor unit activity with a convolutive blind source separation algorithm. On average, for each subject, 16 ± 7 motor units were identified per motor task. The discharge timings of these motor units were estimated with an accuracy > 85%. Moreover, the activity of 6 ± 5 motor units per motor task was consistently detected in all repetitions of the same task. The joint angle at which motor units were first identified was 62.5 ± 26.4% of the range of motion, indicating a prevalence in the identification of high threshold motor units. These findings prove the feasibility of accurate identification of the neural drive to muscles in contractions relevant for myoelectric control, allowing the development of a new generation of myocontrol methods based on motor unit spike trains.
Acute rheumatic carditis causing sudden death (1984)

An 18-year-old male died suddenly while running a confidence course in basic training. Past medical history was negative for acute rheumatic fever. At autopsy he had acute rheumatic mitral valvulitis with extensive myocarditis. Multiple Aschoff bodies were seen in perivascular regions in the right and left ventricle. Review of recent literature of the various causes of sudden cardiac death failed to reveal acute rheumatic valvulitis and myocarditis as reported causes of sudden death.
Alphafold prediction of the Plasmodium TRAP I domain for mutants design. (2023)

Plasmodium sporozoites have several surface proteins, including the single-pass transmembrane adhesin thrombospondin related anonymous protein (TRAP). TRAP harbors two extracellular domains, the I-domain and the thrombospondin type I repeat, TSR. TRAP I domain in the “closed” conformation is unbound and has low adhesion and no signaling activity. We use Alphafold to predict the Plasmodium TRAP I domain for mutants design. Here is the Alphafold predicted structures of the TRAP I domain.
Tracing the history of hepatitis B virus genotype D in western Japan (2005)

The major hepatitis B virus (HBV) genotypes in Japan are B and C. HBV genotype D (HBV/D), however, is widespread in a small area of Western Japan, where the Gianotti-Crosti syndrome caused by HBV subtype ayw, which is suspected to be HBV/D, was endemic in the 1970s. The aim of the study was to elucidate its origin, time of transmission, and spread in this area. Genotyping of HBV-DNA was done in 363 patients with HBV infection. The year of birth was checked in patients with HBV/D. The full genome sequences of 20 HBV/D strains, 2 of which were obtained from a single carrier with a 19-year-interval, were analyzed. An evolutionary rate, the date of the most recent common ancestor, and the effective number of HBV/D infections were calculated. Fifty-two of 363 patients were infected with HBV/D, and 39 were born in 1970s. In a phylogenetic tree, the 20 HBV/D strains produced a definite cluster, and the evolutionary rate was calculated to be 5.4 x 10(-5) nucleotide substitutions/site/year. The root of the tree was estimated to be in approximately 1,900 and began to spread from the 1940s, leading to a rapid increase of infected patients in the 1970s. From these results, it is suspected that HBV/D was likely transmitted to the area investigated approximately 100 years ago and then spread widely in the 1970s. From the history of the area and the genetic analysis, HBV/D in this area was speculated to be of Russian origin.
Implementation of the Nonbinary Encoder and Decoder for Systematic Low Density Parity Check Codes on Raspberry-pi boards (2020)

Since wireless communication systems supply a large amount of packet-sized (non-binary) data, a channel coding technique that can efficiently correct errors caused by channels is required. This paper focuses on systematic Low-Density Parity-Check (LDPC) code for non-binary codes with symbol size of at least 32 bits/symbol and investigates the transmission of non-binary data under different channel conditions through Message Passing Telemetry Transport (MQTT). Hard decision Message Passing-Vector Symbol Decoding (hMP-VSD) is used as a decoder of systematic LDPC. The encoder and decoder are implemented on the Raspberry Pi (R-pi) boards, and the wireless transmission is done by using the Wi-Fi module.
Identifying Autopalmitoylation Inhibitors Through Scaffold Ranking (2015)

Protein palmitoylation is a reversible posttranslational lipidation that plays an important role in cellular signaling, protein localization, stability, and aggregation. The dysregulation of palmitoylation has been implicated in a multitude of diseases including cancer, neurological disorders, and infectious diseases. A family of zinc‐finger “zDHHC” enzymes characterized by a conserved Asp‐His‐His‐Cys (DHHC) tetrapeptide sequence mediates palmitoylation. Having a unique inhibitor specific to the zDHHC enzyme(s) could lead to novel disease therapeutics. Despite advances in our understanding of the genetics and enzymology the current best inhibitor of palmitoylation, 2‐bromopalmitic acid, lacks specificity and affinity for zDHHC enzymes. Our lab has developed an assay amenable to high throughput screening, which measures the rate of the first step of the palmitoylation reaction, autopalmitoylation. During autopalmitoylation there is a release of CoASH, which is then coupled to an alpha‐ketoglutarate dehydrogenase reaction to produce fluorescent NADH. The production of NADH occurs at zero‐order kinetics and directly correlates to the reduction of CoA, and thus to the rate of autopalmitoylation. The introduction of an inhibitor of autopalmitoylation to this reaction would cause a reduction in the rate of NADH production. This coupled assay was used to screen for inhibitors of palmitoylation from a unique chemical scaffold library and resulted in the identification of a number of compounds. These results were supported through the use of orthogonal and bio orthogonal autopalmitoylation assays to further elucidate the type of inhibition.
Miniaturized electrostatic receiver with small-sized backing electrode (2013)

A miniaturized electrostatic receiver design, having a central cylindrical backing electrode of small radius surrounded by a flat annular cavity behind the circular membrane, can lead to both a higher sensitivity and a larger frequency bandwidth compared to the ones achieved with other designs, while bringing a geometrical simplicity which is advantageous from the point of view of microfabrication. An appropriate computational method, relying on a specific 2-D axisymmetrical simulation using an adaptive mesh and accounting for both viscous and thermal boundary layer effects, provides results against which analytical results can be tested. An analytical approach, which leads to solutions based on the eigenmode expansion of the membrane displacement, the acoustic pressure field depending on the radial coordinate in the central fluid gap but being assumed quasi-uniform in the annular cavity, is much faster in terms of running time and appears to be sufficiently accurate to achieve final optimization of this kind of devices.
Waveguide modulators with extended linear dynamic range-a theoretical prediction (1990)

A novel modification of the directional coupler modulator is described that reduces the nonlinear distortion and improves the linear dynamic range. The calculated results indicate that the ratio of optical signal power to the spurious signal power of this device is 30-40 dB larger than that of a Mach-Zehnder interferometric modulator.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Applications of speech quality measurement for 3G (2002)

The speech quality delivered by a 3G network is determined by many factors, including speech and channel coding, the design of the device, and signal processing algorithms and their interactions. This paper examines the key speech quality issues in 3G networks, describes the basics of objective speech quality measurement, and highlights its application in 3G planning, procurement, optimisation and network monitoring.
Limb salvage versus amputation in patients with osteosarcoma of the extremities: an update in the modern era using the National Cancer Database (2020)

Among patients in the NCDB, amputation for osteosarcoma is associated with advanced age, advanced stage, larger tumors, greater comorbidities, and lower income. Limb salvage is associated with a significant survival benefit, even when controlling for significant confounding variables and differences between cohorts.
Role of sensory afferents in the myoelectric response to acute enteric inflammation in the rabbit (1997)

The role of sensory afferents in inflammation-induced alterations in myoelectric activity in vivo was investigated in the rabbit small intestine. Isolated ileal loops were implanted with serosal electrodes and exposed to ricin or vehicle after pretreatment with 125 mg/kg of subcutaneous (125 mg over 3 days) or intraluminal (640 microM) capsaicin. After 5 h of myoelectric recording, the loops were prepared for histology and for ex vivo generation of eicosanoids. Capsaicin exacerbated mucosal damage after exposure to ricin but did not alter neutrophil infiltration. Subcutaneous capsaicin alone elevated slow-wave frequency and spike events and transiently suppressed the myoelectric response to ricin. In contrast, intraluminal capsaicin alone did not alter myoelectric activity but produced a sustained inhibition of the response to ricin. Eicosanoid production was unchanged by capsaicin alone. Intraluminal capsaicin blocked increases in leukotriene C4 and prostaglandin E2 during inflammation, an effect that paralleled its inhibition of myoelectric activity. Thus the contribution of sensory afferents to altered motility during acute ileitis involves the release of mucosal inflammatory mediators that influence neural control of smooth muscle.
Medizinische Chemie der Diuretika: Entwicklung einer erfolgreichen Wirkstoffgruppe (2006)

Abstract Diuretika sind nicht nur aus der Sicht des Klinikers, sondern auch aus der des medizinischen Chemikers eine interessante Arzneistoffklasse. Historisch gesehen sind sie ein Paradebeispiel für die erfolgreiche Entwicklung hochwirksamer Arzneistoffe – ausgehend von Leitstrukturen, deren diuretische Wirkung zufällig entdeckt worden war. Nach Jahrzehnten der Stagnation auf diesem Gebiet werden zur Zeit neue Diuretika mit verbesserten Eigenschaften und teilweise neuartigen Wirkungsmechanismen entwickelt.
Precise Placement and Variable Rate Fertilizer Application Technologies for Horticultural Crops (2010)

Fertilizer spreaders capable of variable rate application are increasingly important for enhancing nutrient management in horticultural crops because they improve placement and increase nutrient uptake efficiency. Matching applied fertilizer to fertilizer requirements represents a significant input cost saving for the grower and a reduction in potential pollutant loading to ground and surface water. Variable rate fertilization (VRF) is a precision agriculture technology made possible by embedded high-speed computers, accurate Global Positioning System (GPS) receivers, Geographic Information Systems (GIS), remote sensing, yield or soil maps, actuators, and electronic sensors capable of measuring and even forecasting crop properties in real time. For tree crops like Florida citrus ( Citrus spp.), the most important function of the VRF spreader is to detect and avoid fertilizing spaces of the orchard not occupied by trees. Treeless spaces are becoming more common in Florida as diseases such as citrus greening ( Candidatus Liberibacter asiaticus) and canker ( Xanthomonas axonopodis ) cause the removal of thousands of trees every year. VRF works best under those conditions. Because VRF exploits crop and soil variability, it has no value in a perfectly uniform field. VRF enables smaller trees including resets to be fertilized at lower, most appropriate rates, thus minimizing any excess application. This article examines the existing knowledge on using precision agriculture and variable rate technology to keep water and nutrients in the root zone of horticultural crops, thus facilitating maximum uptake efficiency.
Targeting the CDA1/CDA1BP1 Axis Retards Renal Fibrosis in Experimental Diabetic Nephropathy (2018)

Targeting cell division autoantigen 1 (CDA1) is postulated to attenuate the profibrotic actions of transforming growth factor-β in diabetic nephropathy. This study has identified a regulatory protein for CDA1 and has then used genetic and pharmacological approaches to test in vivo whether strategies to target this pathway would lead to reduced renal injury. A novel protein, named CDA1BP1 (CDA1 binding protein 1), was identified as critical in regulating the profibrotic activity of CDA1. Genetic deletion of CDA1BP1 attenuated key parameters of renal fibrosis in diabetic mice. Furthermore, a series of short synthetic CDA1BP1 peptides competitively inhibited CDA1-CDA1BP1 binding in vitro with a hybrid peptide, CHA-050, containing a 12mer CDA1BP1 peptide and a previously known "cell-penetrating peptide," dose-dependently reducing expression of collagens I and III in HK-2 cells. In vivo, a d-amino acid retro-inverso peptide, CHA-061, significantly attenuated diabetes-associated increases in the renal expression of genes involved in fibrotic and proinflammatory pathways. In a delayed intervention study, CHA-061 treatment reversed diabetes-associated molecular and pathological changes within the kidney. Specifically, CHA-061 significantly attenuated renal extracellular matrix accumulation and glomerular injury. Taken together, targeting the CDA1/CDA1BP1 axis is a safe, efficacious, and feasible approach to retard experimental diabetic nephropathy.
The crystal structure of ZSM-10, a powder X-ray and electron diffraction study (2006)

Abstract The crystal structure of the aluminosilicate, ZSM-10 (T 108 O 216 , where T = Si, Al), has been determined from electron diffraction and powder X-ray diffraction data. The material crystallizes in space group P 6/ mmm , where a = 31.390(2), c = 7.5147(8) Å. The framework [001] projection was determined independently with 300 kV precession electron diffraction amplitudes by direct methods. T-site positions in this projection were consistent with two models proposed in 1996 by Higgins and Schmitt. Subsequent Rietveld refinement favors their model A, comprising stacked cancrinite cages and hexagonal prisms. The framework density is 16.6 T sites/1000 Å 3 , similar to zeolite framework LTL . However, the refinement against synchrotron data from a dehydrated sample ( R wp = 0.1600, R ( F 2 ) = 0.1418) finds no extra-framework species, despite the detection of some K + in the material.