gebhart/patrepeval huggingface dataset:
Codeword Position Index Modulation Design for Sparse Code Multiple Access System (2020)

Codeword position index based sparse code multiple access (CPI-SCMA) is a novel variant of SCMA that employs the idea of index modulation (IM), which has been proposed recently as an effective alternative to the conventional SCMA system. In contrast to the conventional SCMA that directly maps the information bits of each user to a predefined M-point codebook, the data in CPI-SCMA is not only conveyed by the M-point codebook as in SCMA, but also by the indexes of the codeword positions. In this paper, we first propose a simplified detector termed as message passing algorithm aided index reliability detection (MPA-IRD) that is more suitable for practical implementation. Moreover, we investigate the spectral efficiency (SE) in CPI-SCMA, and two important features are identified to facilitate the design of the system. A tight approximation of the average block error probability (ABLEP) under the maximum likelihood detector (MLD) is also derived from studying the error rate performance of CPI-SCMA. Finally, to further improve the SE of CPI-SCMA, an enhanced version of CPI-SCMA termed as hybrid CPI-SCMA (HCPI-SCMA) is proposed. Itis shown via both simulation, and analytical results that the proposed scheme not only achieves better error rate performance in the high signal-to-noise ratio (SNR) region but also improves the SE, and the level of robustness under channel estimation error compares to SCMA.
Catalysis-associated Conformational Changes Revealed by Human CD38 Complexed with a Non-hydrolyzable Substrate Analog (2007)

Cyclic ADP-ribose (cADPR) is a calcium mobilization messenger important for mediating a wide range of physiological functions. The endogenous levels of cADPR in mammalian tissues are primarily controlled by CD38, a multifunctional enzyme capable of both synthesizing and hydrolyzing cADPR. In this study, a novel non-hydrolyzable analog of cADPR, N1-cIDPR (N1-cyclic inosine diphosphate ribose), was utilized to elucidate the structural determinants involved in the hydrolysis of cADPR. N1-cIDPR inhibits CD38-catalyzed cADPR hydrolysis with an IC(50) of 0.26 mM. N1-cIDPR forms a complex with CD38 or its inactive mutant in which the catalytic residue Glu-226 is mutated. Both complexes have been determined by x-ray crystallography at 1.7 and 1.76 A resolution, respectively. The results show that N1-cIDPR forms two hydrogen bonds (2.61 and 2.64 A) with Glu-226, confirming our previously proposed model for cADPR catalysis. Structural analyses reveal that both the enzyme and substrate cADPR undergo catalysis-associated conformational changes. From the enzyme side, residues Glu-146, Asp-147, and Trp-125 work collaboratively to facilitate the formation of the Michaelis complex. From the substrate side, cADPR is found to change its conformation to fit into the active site until it reaches the catalytic residue. The binary CD38-cADPR model described here represents the most detailed description of the CD38-catalyzed hydrolysis of cADPR at atomic resolution. Our structural model should provide insights into the design of effective cADPR analogs.
Centering mechanism for micro vessel robot using micropatterned shape memory polymers (2010)

Coronary artery disease refers to a variety of illnesses including angina pectoris, myocardial infarction, and other types of coronary artery disorders. Recently, there has been a significant increase in the incidence of these coronary artery diseases in part due to changes in eating habits, environmental pollution and mental stress. To address this issue, percutaneous coronary intervention (PCI) technology has been developed with remarkable advances in a range of surgery devices. However, some clinical operations, such as the treatment of chronic total occlusion (CTO), remain challenging because the fibro-calcific plaque of CTO hinders smooth navigation of a PCT catheter inside the coronary artery. This paper proposes a conceptual design of the centering mechanism of a micro-robot utilizing three-leg polymer arms and micropatterned polymer adhesives. In particular, shape memory polymer (SMP) actuators were used to exert a force on the vessel wall in the micro-robot arms. Micropatterned-thin suction pads were fabricated on the surface of micro-robot arms to increase the adhesion and friction force of micro-robot arms against the blood vessel. Our experimental findings demonstrate that the proposed centering mechanism is effective in maintaining the proper position of the micro-robot in the coronary artery and is potentially capable of providing a smart, self-navigating micro-robot for coronary artery diseases with sufficient traction force to maintain a precise centering location in the coronary artery.
Investigation of Lithium Sulfur Dioxide (Li/SO2) Battery Safety Hazards -- Chemical Studies. (1982)

Abstract : The chemistry associated with the discharge and forced overdischarge of the Li/SO2 cell was investigated in detail. A procedure for the quantitative determination of Li2S2O4 in discharged Li/SO2 cells is described. The amount of Li2S2O4 found in cells discharged to potentials down to zero volt was in very good agreement with the discharge stoichiometry, 2Li + 2SO2 yields Li2S2O4. The Li2S2O4 formed in the carbon cathode was also characterized by infrared, ESCA, and X-ray analyses. A number of organic compounds including CH4 and 3,5-diamino-2,4-hexenenitrile have been identified in forced overdischarged cells. Products identified in cells which vented during forced overdischarge include: CO2, CS2, COS, H2S, CH4, C2H4, C2H2, Li2S, and Li2SO3.
Dynamic reconfiguration of an optical interconnect (2003)

The advent of optical technology that can feasibly support extremely high bandwidth chip-to-chip communication raises a host of architectural questions in the design of digital systems. Terabit per second (and higher) bandwidths have not previously been available at the chip level. In this paper we examine the use of this optical technology in the design of a network router, a system for which previous designs have been I/O-limited at the chip level. Specifically, we examine the benefits of bandwidth reconfigurability, a capability of the proposed switch fabric, and illustrate the performance impact associated with different reconfiguration rates.
Localized cortical chronic traumatic encephalopathy pathology after single, severe axonal injury in human brain (2016)

Chronic traumatic encephalopathy (CTE) is a neurodegenerative disease associated with repetitive mild impact traumatic brain injury from contact sports. Recently, a consensus panel defined the pathognomonic lesion for CTE as accumulations of abnormally hyperphosphorylated tau (p-tau) in neurons (neurofibrillary tangles), astrocytes and cell processes distributed around small blood vessels at sulcal depths in irregular patterns within the cortex. The pathophysiological mechanism for this lesion is unknown. Moreover, a subset of CTE cases harbors cortical β-amyloid plaques. In this study, we analyzed postmortem brain tissues from five institutionalized patients with schizophrenia and history of surgical leucotomy with subsequent survival of at least another 40 years. Because leucotomy involves severing axons bilaterally in prefrontal cortex, this surgical procedure represents a human model of single traumatic brain injury with severe axonal damage and no external impact. We examined cortical tissues at the leucotomy site and at both prefrontal cortex rostral and frontal cortex caudal to the leucotomy site. For comparison, we analyzed brain tissues at equivalent neuroanatomical sites from non-leucotomized patients with schizophrenia, matched in age and gender. All five leucotomy cases revealed severe white matter damage with dense astrogliosis at the axotomy site and also neurofibrillary tangles and p-tau immunoreactive neurites in the overlying gray matter. Four cases displayed p-tau immunoreactivity in neurons, astrocytes and cell processes encompassing blood vessels at cortical sulcal depths in irregular patterns, similar to CTE. The three cases with apolipoprotein E ε4 haplotype showed scattered β-amyloid plaques in the overlying gray matter, but not the two cases with apolipoprotein E ε3/3 genotype. Brain tissue samples from prefrontal cortex rostral and frontal cortex caudal to the leucotomy site, and all cortical samples from the non-leucotomized patients, showed minimal p-tau and β-amyloid pathology. These findings suggest that chronic axonal damage contributes to the unique pathology of CTE over time.
A White Box Analysis of ColBERT (2020)

Transformer-based models are nowadays state-of-the-art in ad-hoc Information Retrieval, but their behavior is far from being understood. Recent work has claimed that BERT does not satisfy the classical IR axioms. However, we propose to dissect the matching process of ColBERT, through the analysis of term importance and exact/soft matching patterns. Even if the traditional axioms are not formally verified, our analysis reveals that ColBERT: (i) is able to capture a notion of term importance; (ii) relies on exact matches for important terms.
Beneficial Fatty Acid Ratio of Salvia hispanica L. (Chia Seed) Potentially Inhibits Adipocyte Hypertrophy, and Decreases Adipokines Expression and Inflammation in Macrophage (2020)

The present study aimed to determine the role of <i>Salvia hispanica</i> L., (chia seed) fatty acid content in adipocyte lipid accumulation and human macrophage immunoregulatory potential. Chia seed fatty acid was extracted using hexane by the cold percolation method. A gas chromatography-mass spectrometry (GC-MS) analysis showed a 3:1 ratio of omega 3 and omega 6 fatty acid composition and it was more beneficial for human health. We treated it with increasing concentrations (0-6.4 μg/mL) of chia seed fatty acid extract to determine the cytotoxicity on the preadipocytes and macrophage; no significant cytotoxicity was observed. Chia seed, in 0.2 and 0.4 μg/mL doses, significantly arrested adipocyte hypertrophy and macrophage foam cell development. The gene expression levels of adipocyte confirmed the increased expression of adipocyte mitochondrial thermogenesis related genes, such as uncoupling protein-1 (UCP-1), peroxisome proliferator activated receptor gamma coactivator 1 alpha (PPARγC1α) and PR domain containing 16 (PRDM16); and the down regulated expression of the lipid synthesis related gene sterol regulatory element binding of protein-1c (SREBP-1c). In addition, adipogenesis related genes, such as the proliferator activated receptor γ (PPARγ) and CCAAT/enhancer binding protein (C/EBPα) expressions, have been down regulated by chia seed treatment. Macrophage treated with chia seed-treated adipocyte condition media significantly inhibited the obesity associated inflammatory genes and protein expression levels, such as monocyte chemo attractant protein-1 (MCP-1), prostaglandins E2, interleukin-6, plasminogen activator inhibitor-1 (PAI-1) and tumor necrosis factor-α (TNF-α). In conclusion, a 3:1 ratio of omega 3 and omega 6 fatty acid composition of chia seed fatty acid content potentially inhibits lipid accumulation, and enhanced fatty acid oxidation, via UCP-1 and PRDM16 expression. Macrophage recruitment to adipocyte and the development of obesity associated inflammation was suppressed by chia seeds.
Supplementary Methods from Targeting Bromodomain and Extra-Terminal (BET) Family Proteins in Castration-Resistant Prostate Cancer (CRPC) (2023)

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Synthesis of a Potent hNK-1 Receptor Antagonist via an SN2 Reaction of an Enantiomerically Pure α-Alkoxy Sulfonate (2004)

The concise synthesis of a stereochemically rich hNK-1 receptor antagonist is described. The synthesis is highlighted by an S(N)2 reaction of an enantiomerically pure alpha-alkoxy sulfonate (orthogonally protected butane triol), which was prepared by utilizing salen-mediated hydrolytic kinetic resolution technology. A stereocontrolled acetalization was employed to connect two enantiomerically pure fragments with a high degree of diastereoselectivity.
Oligonucleotide and polynucleotide — drug complexes in the crystalline state (1981)

It has been known for many years that various molecules possessing a planar aromatic grouping as a common structural feature can interact with genetic material. Thus, acridine orange, in particular, has long been used as a vital stain in cytological procedures, as have various other acridine derivatives with antibacterial properties. It is now well established that numerous such molecules, many of which are of medicinal interest and use, exert their major in vivo effects by direct DNA interaction, thereby interfering with processes of nucleic acid expression and synthesis (see, for example, Gale et al., 1972). Interaction with ribonucleic acids, both single and double stranded has also been implicated in the action of these druges (see, for example, Finkelstein and Weinstein, 1967).
A Charge Pump With MPPT Circuit Employed in Batteryless Photovoltaic IoT Tags (2016)

A dc-dc regulator is proposed to attach to the battery-less solar tag applied in the Internet of Things (IoTs) market. Two main purposes in this design is to maximize the power transfer efficiency and to provide a high voltage supply to the back-end circuit. The overall circuit consists of the cross-coupled charge pump, optimal power point tracking and timing control circuit. It is expected to boost the input voltage from 0.55–0.65V to the output of 1–1.1V at 80–100μW condition. Gated PFM circuit is adopted in the optimal power point tracking system to modulate the input frequency of the charge pump to match the inner resistance of the solar cell. This system has been taped-out by TSMC 0.18UM 1P6M process twice and N-fab 0.35UM process once. The experimental results of this chip show that the voltage conversion efficiency (VCE) is 97% and the power conversion efficiency (PCE) is 11.7% at 30μW input power condition. The reason of the low efficiency has been found and improved by enhancing the pumping capacitance. The efficiency of the 3rd tape-out in N-fab has been improved to 81.2% according to the simulation results.
Anti-Inflammatory Peptide Attenuates Edema and Promotes BMP-2-Induced Bone Formation in Spine Fusion (2018)

Recombinant human bone morphogenic protein-2 (BMP-2)-loaded absorbable collagen sponges (ACS) have been successfully used to enhance bone formation and to induce spinal fusion in humans. However, side effects, such as soft tissue edema and inflammation, have been reported. NEMO binding domain peptide (NBD) inhibits activation of nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB), a central regulator of immune response. In this study, we investigated NBD's potential to reduce BMP-2-induced soft tissue inflammation without affecting BMP-2-mediated spinal fusion in rat. For evaluation of soft tissue inflammation, ACS containing BMP-2, BMP-2+NBD, NBD, or ACS only were implanted into intramuscular paraspinal sites of 32 rats. At day 2 postsurgery, edema formation at the implant sites was assessed using magnetic resonance imaging. T2-weighted relaxation time (T2-RT) values were increased in the BMP-2 group compared with BMP-2+NBD, NBD, and ACS groups. No difference in T2-RT values was detected between BMP-2+NBD versus NBD and ACS controls. Postsacrifice, histological analysis of the implant-surrounding zones showed increased mononuclear cell infiltration in the BMP-2 group compared with BMP-2+NBD and controls. The presence of BMP-2 increased relative NF-κB binding and gene expression of inflammatory markers, interleukin (IL)1β, IL6, IL18, and chemokine ligand (CCL)2 and CCL3 compared with controls. In the BMP-2+NBD group, cytokine expression was blocked. No differences were found between BMP-2+NBD and control groups. For evaluation of spinal fusion, posterolateral intertransverse lumbar fusion procedures were performed on 16 rats. ACS were loaded with BMP-2 or BMP-2+NBD. After sacrifice at week 12, microcomputed tomographic assessment of the fusion site detected a higher bone volume and reduced trabecular spacing in the BMP-2+NBD group compared with BMP-2. Histological analysis did not show any differences in newly formed bone microarchitecture. In summary, addition of NBD to BMP-2-loaded ACS reduces BMP-2-induced soft tissue edema formation and mononuclear cell infiltration, diminishes NF-κB binding, and thus blocks transcription of NF-κB-regulated cytokines in rat. Furthermore, NBD stimulates bone formation in BMP-2-mediated spinal fusion, possibly through crosstalk of the NF-κB pathway with other pathways. The results of this study might provide the basis to develop new therapeutic bone grafting approaches with combinatory administration of BMP-2 and NBD for spinal fusion.
Polymorphisms in the genes encoding interferon‐γ and interferon‐γ receptors in multiple sclerosis (2004)

Genome screens suggest that several genes, each contributing to a small extent, are involved in multiple sclerosis (MS) susceptibility. Simultaneous analysis of related genes may improve the power to detect such small effects. Interferon-gamma (IFN-gamma), mediating its effects through the IFN-gamma receptor, is a pleiotropic, pro-inflammatory cytokine for which a detrimental effect on the course of MS has been reported. The role of IFN-gamma receptor 1 (IFNGR1) and IFN-gamma receptor 2 (IFNGR2) gene polymorphisms has not been studied in MS, and, for the IFNG gene polymorphism there is only one previous study, which incorporates clinical, but not imaging, data. The aim of this study was to investigate whether polymorphisms in the IFNG and IFNGR1 and IFNGR2 genes are associated with susceptibility to MS, or disease characteristics, as defined by clinical and imaging criteria. Genotypes for IFNG, IFNGR1 and IFNGR2 were determined in 509 patients with MS and in 193 healthy controls. Patient files were reviewed for disease course, age at onset of disease, and rate of progression. Serial magnetic resonance imaging (MRI) data were available for 107 patients. No significant differences in the distribution of IFNG, IFNGR1 and IFNGR2 genotype and allele frequencies were found between patients and controls. A progressive, as opposed to a relapsing, onset was significantly more frequent in carriers of the IFNGR2 allele Arg64 (P = 0.028). Moreover, IFNGR2 allele Arg64 carriers had a lower black hole ratio than non-carriers (P = 0.016). No other associations with clinical parameters, such as age at onset or rate of progression, or with imaging parameters, were observed. The IFNG intron 1 gene polymorphism studied is unlikely to play a major role in MS susceptibility or disease course. The IFNGR1 and IFNGR2 gene polymorphisms studied do not exert an important influence on MS susceptibility, but allele IFNGR2*Arg64 may be associated with a progressive disease onset.
A Unique Set of the Burkholderia Collagen-Like Proteins Provides Insight into Pathogenesis, Genome Evolution and Niche Adaptation, and Infection Detection (2015)

Burkholderia pseudomallei and Burkholderia mallei, classified as category B priority pathogens, are significant human and animal pathogens that are highly infectious and broad-spectrum antibiotic resistant. Currently, the pathogenicity mechanisms utilized by Burkholderia are not fully understood, and correct diagnosis of B. pseudomallei and B. mallei infection remains a challenge due to limited detection methods. Here, we provide a comprehensive analysis of a set of 13 novel Burkholderia collagen-like proteins (Bucl) that were identified among B. pseudomallei and B. mallei select agents. We infer that several Bucl proteins participate in pathogenesis based on their noncollagenous domains that are associated with the components of a type III secretion apparatus and membrane transport systems. Homology modeling of the outer membrane efflux domain of Bucl8 points to a role in multi-drug resistance. We determined that bucl genes are widespread in B. pseudomallei and B. mallei; Fischer's exact test and Cramer's V2 values indicate that the majority of bucl genes are highly associated with these pathogenic species versus nonpathogenic B. thailandensis. We designed a bucl-based quantitative PCR assay which was able to detect B. pseudomallei infection in a mouse with a detection limit of 50 CFU. Finally, chromosomal mapping and phylogenetic analysis of bucl loci revealed considerable genomic plasticity and adaptation of Burkholderia spp. to host and environmental niches. In this study, we identified a large set of phylogenetically unrelated bucl genes commonly found in Burkholderia select agents, encoding predicted pathogenicity factors, detection targets, and vaccine candidates.
ParSets for parallelizing OODBMS traversals: implementation and performance (2002)

Describes the design and implementation of ParSets, a means of exploiting parallelism in the SHORE persistent object store. We used ParSets to create and parallelize the graph traversals of the OO7 OODBMS benchmark, and present speedup and scaleup results from parallel SHORE running these traversals on a cluster of commodity workstations connected by a standard Ethernet. For some OO7 traversals, SHORE achieved excellent speedup and scaleup; for other OO7 traversals, only marginal speedup and scaleup occurred. The characteristics of these traversals shed light on when the ParSet approach to parallelism can and cannot be applied to speed up an application.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Effect of Underhead Design Configuration on Bolt Behavior Under Shear Loads (2015)

This study uses nonlinear 3-D finite element simulation to investigate the effect of bolt underhead design on its mechanical behavior under cyclic transverse shear loads. The effect of bolt underhead fillet radius and / or under-cut on bolt deformation as well as bolted joint behavior is studied in order to optimize the bolted flange performance under externally applied loads. Two levels of bolt preload and two transverse shear load cycles are studied. Bolt tensile and bending stiffnesses for various underhead designs are also evaluated and discussed.
THE ULTRALUMINOUS GRB 110918A (2013)

GRB 110918A is the brightest long gamma-ray burst (GRB) detected by Konus-WIND during its almost 19 yr of continuous observations and the most luminous GRB ever observed since the beginning of the cosmological era in 1997. We report on the final Interplanetary Network localization of this event and its detailed multiwavelength study with a number of space-based instruments. The prompt emission is characterized by a typical duration, a moderate peak energy of the time-integrated spectrum, and strong hard-to-soft evolution. The high observed energy fluence yields, at z = 0.984, a huge isotropic-equivalent energy release E-iso = (2.1 +/- 0.1) x 10(54) erg. The record-breaking energy flux observed at the peak of the short, bright, hard initial pulse results in an unprecedented isotropic-equivalent luminosity L-iso = (4.7 +/- 0.2) x 10(54) erg s(-1). A tail of the soft gamma-ray emission was detected with temporal and spectral behavior typical of that predicted by the synchrotron forward-shock model. The Swift/X-Ray Telescope and the Swift/Ultraviolet Optical Telescope observed the bright afterglow from 1.2 to 48 days after the burst and revealed no evidence of a jet break. The post-break scenario for the afterglow is preferred from our analysis, with a hard underlying electron spectrum and interstellar-medium-like circumburst environment implied. We conclude that, among the multiple reasons investigated, the tight collimation of the jet must have been a key ingredient to produce this unusually bright burst. The inferred jet opening angle of 1.degrees 7-3.degrees 4 results in reasonable values of the collimation-corrected radiated energy and the peak luminosity, which, however, are still at the top of their distributions for such tightly collimated events. We estimate a detection horizon for a similar ultraluminous GRB of z similar to 7.5 for Konus-WIND and z similar to 12 for the Swift/Burst Alert Telescope, which stresses the importance of GRBs as probes of the early Universe.