gebhart/patrepeval huggingface dataset:
Forma (2007)

This article presents Forma , a practical, safe, and automatic data reshaping framework that reorganizes arrays to improve data locality. Forma splits large aggregated data-types into smaller ones to improve data locality. Arrays of these large data types are then replaced by multiple arrays of the smaller types. These new arrays form natural data streams that have smaller memory footprints, better locality, and are more suitable for hardware stream prefetching. Forma consists of a field-sensitive alias analyzer, a data type checker, a portable structure reshaping planner, and an array reshaper. An extensive experimental study compares different data reshaping strategies in two dimensions: (1) how the data structure is split into smaller ones ( maximal partition × frequency-based partition × affinity-based partition ); and (2) how partitioned arrays are linked to preserve program semantics ( address arithmetic-based reshaping × pointer-based reshaping ). This study exposes important characteristics of array reshaping. First, a practical data reshaper needs not only an inter-procedural analysis but also a data-type checker to make sure that array reshaping is safe. Second, the performance improvement due to array reshaping can be dramatic: standard benchmarks can run up to 2.1 times faster after array reshaping. Array reshaping may also result in some performance degradation for certain benchmarks. An extensive micro-architecture-level performance study identifies the causes for this degradation. Third, the seemingly naive maximal partition achieves best or close-to-best performance in the benchmarks studied. This article presents an analysis that explains this surprising result. Finally, address-arithmetic-based reshaping always performs better than its pointer-based counterpart.
Session 14 Overview: mm-Wave Transceivers for Communication and Radar (2021)

The session is focused on key advances in mm-wave wireless communication and radar systems. It features papers describing a state-of-the-art multi-user beamforming receiver, an early fusion radar-LiDAR system, self-interference cancellation techniques, FMCW radar MIMO transceivers, along with temperature-healing techniques and crystal-less transceivers.
Depression pathophysiology, risk prediction of recurrence and comorbid psychiatric disorders using genome-wide analyses (2023)

Depression is a common psychiatric disorder and a leading cause of disability worldwide. Here we conducted a genome-wide association study meta-analysis of six datasets, including >1.3 million individuals (371,184 with depression) and identified 243 risk loci. Overall, 64 loci were new, including genes encoding glutamate and GABA receptors, which are targets for antidepressant drugs. Intersection with functional genomics data prioritized likely causal genes and revealed new enrichment of prenatal GABAergic neurons, astrocytes and oligodendrocyte lineages. We found depression to be highly polygenic, with ~11,700 variants explaining 90% of the single-nucleotide polymorphism heritability, estimating that >95% of risk variants for other psychiatric disorders (anxiety, schizophrenia, bipolar disorder and attention deficit hyperactivity disorder) were influencing depression risk when both concordant and discordant variants were considered, and nearly all depression risk variants influenced educational attainment. Additionally, depression genetic risk was associated with impaired complex cognition domains. We dissected the genetic and clinical heterogeneity, revealing distinct polygenic architectures across subgroups of depression and demonstrating significantly increased absolute risks for recurrence and psychiatric comorbidity among cases of depression with the highest polygenic burden, with considerable sex differences. The risks were up to 5- and 32-fold higher than cases with the lowest polygenic burden and the background population, respectively. These results deepen the understanding of the biology underlying depression, its disease progression and inform precision medicine approaches to treatment.
Pulsed Stable Isotope Labeling of Amino Acids in Cell Culture Uncovers the Dynamic Interactions between HIV-1 and the Monocyte-Derived Macrophage (2011)

Dynamic interactions between human immunodeficiency virus-1 (HIV-1) and the macrophage govern the tempo of viral dissemination and replication in its human host. HIV-1 affects macrophage phenotype, and the macrophage, in turn, can modulate the viral life cycle. While these processes are linked to host-cell function and survival, the precise intracellular pathways involved are incompletely understood. To elucidate such dynamic virus-cell events, we employed pulsed stable isotope labeling of amino acids in cell culture. Alterations in de novo protein synthesis of HIV-1 infected human monocyte-derived macrophages (MDM) were examined after 3, 5, and 7 days of viral infection. Synthesis rates of cellular metabolic, regulatory, and DNA packaging activities were decreased, whereas, those affecting antigen presentation (major histocompatibility complex I and II) and interferon-induced antiviral activities were increased. Interestingly, enrichment of proteins linked to chromatin assembly or disassembly, DNA packaging, and nucleosome assembly were identified that paralleled virus-induced cytopathology and replication. We conclude that HIV-1 regulates a range of host MDM proteins that affect its survival and abilities to contain infection.
Rictor Overexpression and mTORC2 Signaling in Chronic Lymphocytic Leukemia (2012)

Abstract Abstract 3884 Signaling via the B-cell receptor (BCR) stimulates growth and survival of CLL leukemic cells and inhibits apoptosis by phosphorylating immunoreceptor tyrosine based activation motifs. This signaling subsequently activates PI3 Kinase/AKT, mTOR, ERK and other pathways. Activation of Akt in turn requires phosphorylation by mTOR kinase, which assembles in two complexes mTORC1 and mTORC2 and it is the mTORC2 complex that phosphorylates and activates Akt. This phosphorylation of Akt in CLL specimen's upregulates anti-apoptotic proteins such as Mcl-1, Bcl-xl and XIAP. We have identified that Rictor, a component of mTORC2 complex is over-expressed in CLL specimens as compared to normal peripheral mononuclear B cells. This over-expression was noted by real time PCR that showed 1.5 to 4 fold upregulation (n=12). Western blot analysis also showed Rictor overexpression in all the twelve CLL specimens tested. Rictor overexpression was also seen in Mantle cell lymphoma cell lines and to study its role in BCR signaling, stable Mantle cell lymphoma lines with SiRNA mediated Rictor knockdown were established. Rictor knockdown resulted in a significant decrease in Akt activation as phosphorylation (phospho S473) of Akt both in unstimulated cells and when the cells were stimulated with BCR crosslinking was decreased. To determine the effect of Rictor and mTORC2 inhibition on CLL specimens, we tested the activity of three compounds isolated via yeast two hybrid drug screen designed to identify molecules that inhibit Rictor/mTOR interaction. When tested on CLL specimens in the presence of BCR crosslinking, these mTORC2 inhibitor compounds inhibited the downstream phosphorylation of Akt S473. Functionally the inhibitors also induced apoptosis in CLL cells with 40–60% of CLL cells undergoing apoptosis (1.0mM, cells treated for 48 hours). In comparison, rapamycin (mTORC1 inhibitor) and ppp242 (mTORC1, 2 inhibitor) were comparatively less active in CLL specimens as they were less effective in the induction of apoptosis. Western blot analysis of mTORC2 inhibitor treated cells also showed PARP cleavage and an increase in the pro-apoptotic protein BAD. Our data indicates that Rictor overexpression in CLL specimens is required for Akt phosphorylation activation and downstream BCR signaling. Inhibition of this pathway by mTORC2 inhibitors in CLL will be an effective therapeutic strategy. Disclosures: No relevant conflicts of interest to declare.
Clinically Deployed Distributed Magnetic Resonance Imaging Reconstruction: Application to Pediatric Knee Imaging (2018)

Magnetic resonance imaging is capable of producing volumetric images without ionizing radiation. Nonetheless, long acquisitions lead to prohibitively long exams. Compressed sensing (CS) can enable faster scanning via sub-sampling with reduced artifacts. However, CS requires significantly higher reconstruction computation, limiting current clinical applications to 2D/3D or limited-resolution dynamic imaging. Here we analyze the practical limitations to T2 Shuffling, a four-dimensional CS-based acquisition, which provides sharp 3D-isotropic-resolution and multi-contrast images in a single scan. Our improvements to the pipeline on a single machine provide a 3x overall reconstruction speedup, which allowed us to add algorithmic changes improving image quality. Using four machines, we achieved additional 2.1x improvement through distributed parallelization. Our solution reduced the reconstruction time in the hospital to 90 seconds on a 4-node cluster, enabling its use clinically. To understand the implications of scaling this application, we simulated running our reconstructions with a multiple scanner setup typical in hospitals.
Helicobacter pylori Heat Shock Protein A: Serologic Responses and Genetic Diversity (1999)

Helicobacter pylori synthesizes an unusual GroES homolog, heat shock protein A (HspA). The present study was aimed at an assessment of the serological response to HspA in a group of Chinese patients with defined gastroduodenal pathologies and determination of whether diversity is present in the nucleotide sequences encoding HspA in isolates from these patients. Serum samples collected from 154 patients who had an upper gastrointestinal pathology and the presence of H. pylori defined by biopsy were tested for an immunoglobulin G (IgG) serologic response to H. pylori HspA by an enzyme linked immunosorbant assay. HspA-encoding nucleotide sequences in H. pylori isolates from 14 patients (7 seropositive and 7 seronegative for HspA) were analyzed by PCR and direct sequencing of the PCR products. The sequencing results were compared to those of 48 isolates from other parts of the world. Of the 154 known H. pylori-positive patients, 54 (35.1%) were seropositive for HspA. The A domain (GroES homology) of HspA was highly conserved in the 14 isolates tested. Although the B domain (metal-binding site unique to H. pylori) resembled that in the known major variant, particular amino acid substitutions allowed definition of an HspA variant associated with isolates from East Asia. There were no associations between patient characteristics and HspA seropositivity or amino acid sequences. We confirmed in this study that the clinical outcomes of H. pylori infection are not related to HspA antigenicity or to sequence variation. However, B-domain sequence variation may be a marker for the study of the genetic diversity of H. pylori strains of different geographic origins.
Spin-valve and pseudo-spin-valve device switching for giant magnetoresistive random access memory applications (2004)

In this paper we reports results of switching characteristics and resistance properties of current- in-plane spin-valve (SV) and PSV devices that in particular can be applied to GMRAM two-resistor/two-transistor (2R2T) latch memory architectures.
Resolvin D1 Attenuates Polyinosinic-Polycytidylic Acid–Induced Inflammatory Signaling in Human Airway Epithelial Cells via TAK1 (2014)

The respiratory epithelium consists of lung sentinel cells, which are the first to contact inhaled inflammatory insults, including air pollutants, smoke, and microorganisms. To avoid damaging exuberant or chronic inflammation, the inflammatory process must be tightly controlled and terminated once the insult is mitigated. Inflammation resolution is now known to be an active process involving a new genus of lipid mediators, called "specialized proresolving lipid mediators," that includes resolvin D1 (RvD1). We and others have reported that RvD1 counteracts proinflammatory signaling and promotes resolution. A knowledge gap is that the specific cellular targets and mechanisms of action for RvD1 remain largely unknown. In this article, we identified the mechanism whereby RvD1 disrupts inflammatory mediator production induced by the viral mimic polyinosinic-polycytidylic acid [poly(I:C)] in primary human lung epithelial cells. RvD1 strongly suppressed the viral mimic poly(I:C)-induced IL-6 and IL-8 production and proinflammatory signaling involving MAPKs and NF-κB. Most importantly, we found that RvD1 inhibited the phosphorylation of TAK1 (TGF-β-activated kinase 1), a key upstream regulatory kinase common to both the MAPK and NF-κB pathways, by inhibiting the formation of a poly(I:C)-induced signaling complex composed of TAK1, TAB1 (TAK1 binding protein), and TRAF6 (TNF receptor-associated factor 6). We confirmed that ALX/FPR2 and GPR32, two RvD1 receptors, were expressed on human small airway epithelial cells. Furthermore, blocking these receptors abrogated the inhibitory action of RvD1. In this article, we present the idea that RvD1 has the potential to be used as an anti-inflammatory and proresolving agent, possibly in the context of exuberant host responses to damaging respirable agents such as viruses.
<title>Conventional and fiber optics interferometry for vibration mode analysis</title> (2004)

The visualization and analysis methods for studying vibration modes of macro and micro scale objects with spectrally reflecting and scattering surfaces, developed at the Institute of Micromechanics and Photonics of the Warsaw University of Technology, are presented. Silicon technology prepared microspecimens (AFM cantilevers and active PZT micromembranes) are investigated using two-beam time-average interferometry. Vibration modes of flat and non-flat surface microelements are displayed using four and five-frame temporal phase stepping methods. The calculated contrast of vibrating object interferograms provides the information on the vibration amplitude. Scattering surface objects are studied by time-average fiber-optics digital speckle pattern interferometer (DSPI) with heterodyning. Sinusoidal phase modulation introduced at the object vibration frequency enables quantitative analysis of the amplitude and phase of sinusoidal type vibrations. Laser diode modulation and/or single mode fiber stretching is applied for that purpose. For low vibration amplitudes (a<sub>0</sub> &lt; l/20) the method using linear approximation of the zero order Bessel function provides an automatic analysis tool for quantitative estimation of the vibration modes.
Magnetization Reversal in Micron-Sized Magnetic Thin Films (1998)

We have measured and simulated the dynamics of magnetization reversal in 5 nm by 0.8 by 1.6 $\ensuremath{\mu}\mathrm{m}$ ${\mathrm{Ni}}_{60}{\mathrm{Fe}}_{40}$ thin films. The films measured form the upper electrode of a spin-polarized tunnel junction so that the magnetization direction of the film can be probed by measuring the tunneling resistance of the junction. When a magnetic field pulse is applied, the time to switch the film magnetization changes from greater than 10 ns to less than 500 ps as the pulse amplitude is increased from the coercive field to 10 mT and beyond. We have simulated these transitions using micromagnetic modeling of the exact experimental conditions. The simulations agree well with the experimental measurements.
Individual pulse monitoring and dose control system for pre-clinical implementation of FLASH-RT (2022)

<i>Objective.</i>Existing ultra-high dose rate (UHDR) electron sources lack dose rate independent dosimeters and a calibrated dose control system for accurate delivery. In this study, we aim to develop a custom single-pulse dose monitoring and a real-time dose-based control system for a FLASH enabled clinical linear accelerator (Linac).<i>Approach.</i>A commercially available point scintillator detector was coupled to a gated integrating amplifier and a real-time controller for dose monitoring and feedback control loop. The controller was programmed to integrate dose for each radiation pulse and stop the radiation beam when the prescribed dose was delivered. Additionally, the scintillator was mounted in a solid water phantom and placed underneath mice skin for<i>in vivo</i>dose monitoring. The scintillator was characterized in terms of its radiation stability, mean dose-rate (Ḋm), and dose per pulse (<i>D</i><sub>p</sub>) dependence.<i>Main results.</i>The<i>D</i><sub>p</sub>exhibited a consistent ramp-up period across ∼4-5 pulse. The plastic scintillator was shown to be linear withḊm(40-380 Gy s<sup>-1</sup>) and<i>D</i><sub>p</sub>(0.3-1.3 Gy Pulse<sup>-1</sup>) to within +/- 3%. However, the plastic scintillator was subject to significant radiation damage (16%/kGy) for the initial 1 kGy and would need to be calibrated frequently. Pulse-counting control was accurately implemented with one-to-one correspondence between the intended and the actual delivered pulses. The dose-based control was sufficient to gate on any pulse of the Linac.<i>In vivo</i>dosimetry monitoring with a 1 cm circular cut-out revealed that during the ramp-up period, the average<i>D</i><sub>p</sub>was ∼0.045 ± 0.004 Gy Pulse<sup>-1</sup>, whereas after the ramp-up it stabilized at 0.65 ± 0.01 Gy Pulse<sup>-1</sup>.<i>Significance.</i>The tools presented in this study can be used to determine the beam parameter space pertinent to the FLASH effect. Additionally, this study is the first instance of real-time dose-based control for a modified Linac at ultra-high dose rates, which provides insight into the tool required for future clinical translation of FLASH-RT.
Treatment of central sleep apnoea in congestive heart failure with nasal ventilation (1998)

Cheyne-Stokes respiration (CSR) is common in patients with congestive heart failure (CHF). These features may lead to complaints of daytime somnolence, fatigue, insomnia, and many of the symptoms typical of sleep disordered breathing.
Cooperation between somatic mutation and germline-encoded residues enables antibody recognition of HIV-1 envelope glycans (2019)

Viral glycoproteins are a primary target for host antibody responses. However, glycans on viral glycoproteins can hinder antibody recognition since they are self glycans derived from the host biosynthesis pathway. During natural HIV-1 infection, neutralizing antibodies are made against glycans on HIV-1 envelope glycoprotein (Env). However, such antibodies are rarely elicited with vaccination. Previously, the vaccine-induced, macaque antibody DH501 was isolated and shown to bind to high mannose glycans on HIV-1 Env. Understanding how DH501 underwent affinity maturation to recognize glycans could inform vaccine induction of HIV-1 glycan antibodies. Here, we show that DH501 Env glycan reactivity is mediated by both germline-encoded residues that contact glycans, and somatic mutations that increase antibody paratope flexibility. Only somatic mutations in the heavy chain were required for glycan reactivity. The paratope conformation was fragile as single mutations within the immunoglobulin fold or complementarity determining regions were sufficient for eliminating antibody function. Taken together, the initial germline VHDJH rearrangement generated contact residues capable of binding glycans, and somatic mutations were required to form a flexible paratope with a cavity conducive to HIV-1 envelope glycan binding. The requirement for the presence of most somatic mutations across the heavy chain variable region provides one explanation for the difficulty in inducing anti-Env glycan antibodies with HIV-1 Env vaccination.
Supplementary Movie Legend from Molecular Imaging of CXCR4 Receptor Expression in Human Cancer Xenografts with [<sup>64</sup>Cu]AMD3100 Positron Emission Tomography (2023)

Supplementary Movie Legend from Molecular Imaging of CXCR4 Receptor Expression in Human Cancer Xenografts with [&lt;sup&gt;64&lt;/sup&gt;Cu]AMD3100 Positron Emission Tomography
Data from: Non-monotonic kilohertz frequency neural block thresholds arise from amplitude- and frequency-dependent charge imbalance (2021)

Reversible block of nerve conduction using kilohertz frequency electrical signals has substantial potential for treatment of disease. However, the ability to block nerve fibers selectively is limited by poor understanding of the relationship between waveform parameters and the nerve fibers that are blocked. Previous in vivo studies reported non-monotonic relationships between block signal frequency and block threshold, suggesting the potential for fiber-selective block. However, the mechanisms of non-monotonic block thresholds were unclear, and these findings were not replicated in a subsequent in vivo study. We used high-fidelity computational models and in vivo experiments in anesthetized rats to show that non-monotonic threshold-frequency relationships do occur, that they result from amplitude- and frequency-dependent charge imbalances that cause a shift between kilohertz frequency and direct current block regimes, and that these relationships can differ across fiber diameters such that smaller fibers can be blocked at lower thresholds than larger fibers. These results reconcile previous contradictory studies, clarify the mechanisms of interaction between kilohertz frequency and direct current block, and demonstrate the potential for selective block of small fiber diameters.
Assessment of Patient Selection Criteria for Treatment of the Infected Hip Arthroplasty (2000)

In a group of 37 infected hip arthroplasties (36 patients) treated consecutively between January 1997 and October 1999, the feasibility of published patient selection criteria for direct exchange arthroplasty was tested. These criteria include the requirement of a healthy patient with good soft tissues, minimal femoral bone loss, and an organism identified preoperatively as an antibiotic sensitive gram-positive organism. After assignment of the selection criteria, only four patients (four hips) (11%) were deemed potential candidates for a direct exchange procedure. Infected arthroplasties excluded from a primary exchange included 14 patients (15 hips) with gram-negative or methicillin-resistant gram-positive organisms obtained from preoperative joint aspirations, 10 patients (10 hips) with moderate or severe femoral bone loss, four patients (four hips) who required a proximal femoral osteotomy for component removal, two patients (two hips) with poor health status, and two patients (two hips) with poor soft tissues. Because of the increasing emergence of antibiotic-resistant bacteria and an increased prevalence of revision arthroplasties with associated bone loss, the feasibility of published selection criteria for direct exchange are limited. A philosophy of delayed reconstruction for the treatment of the infected hip arthroplasty seems most appropriate in the current era of patient treatment.