ShOpt.jl: A Julia Package for Empirical Point Spread Function Characterization of JWST NIRCam Data

As astronomical data grows in volume and complexity, the scalability of analysis software becomes increasingly important. At the same time, astrophysics analysis software relies heavily on open-source contributions, so languages and tools that prioritize both performance and readability are especially valuable. Julia, with its just-in-time compiler and high level syntax, offers a compelling alternative to traditional languages like Python or C. In this paper, we outline ShOpt.jl, a new software package for point spread function (PSF) characterization written in Julia. ShOpt.jl features a number of performance optimizations, such as multithreading, the use of preconditioners, and the implementation of the memory-limited Broyden-Fletcher-Goldfarb-Shanno algorithm, as well as the flexibility to choose between principal component analysis, an autoencoder, and analytic profiles for PSF characterization. As observatories like the James Webb Space Telescope bring astrophysics into a new era of wide-field, high-resolution imaging, the challenges of PSF modeling become more pronounced. Tools like ShOpt.jl provide the community with a scalable, efficient, and accurate solution to these challenges, while also demonstrating the potential of Julia as a language that meets the demands of modern astrophysical research.Comment: 10 pages, 3 figures; submitted to the Journal of Open Source Softwar

The medical science DMZ: a network design pattern for data-intensive medical science

Abstract: Objective We describe a detailed solution for maintaining high-capacity, data-intensive network flows (eg, 10, 40, 100 Gbps+) in a scientific, medical context while still adhering to security and privacy laws and regulations. Materials and Methods High-end networking, packet-filter firewalls, network intrusion-detection systems. Results We describe a “Medical Science DMZ” concept as an option for secure, high-volume transport of large, sensitive datasets between research institutions over national research networks, and give 3 detailed descriptions of implemented Medical Science DMZs. Discussion The exponentially increasing amounts of “omics” data, high-quality imaging, and other rapidly growing clinical datasets have resulted in the rise of biomedical research “Big Data.” The storage, analysis, and network resources required to process these data and integrate them into patient diagnoses and treatments have grown to scales that strain the capabilities of academic health centers. Some data are not generated locally and cannot be sustained locally, and shared data repositories such as those provided by the National Library of Medicine, the National Cancer Institute, and international partners such as the European Bioinformatics Institute are rapidly growing. The ability to store and compute using these data must therefore be addressed by a combination of local, national, and industry resources that exchange large datasets. Maintaining data-intensive flows that comply with the Health Insurance Portability and Accountability Act (HIPAA) and other regulations presents a new challenge for biomedical research. We describe a strategy that marries performance and security by borrowing from and redefining the concept of a Science DMZ, a framework that is used in physical sciences and engineering research to manage high-capacity data flows. Conclusion By implementing a Medical Science DMZ architecture, biomedical researchers can leverage the scale provided by high-performance computer and cloud storage facilities and national high-speed research networks while preserving privacy and meeting regulatory requirements

Radiation-induced Acoustic Loss in Quartz Crystals

Physic

Reflexion: Language Agents with Verbal Reinforcement Learning

Large language models (LLMs) have been increasingly used to interact with external environments (e.g., games, compilers, APIs) as goal-driven agents. However, it remains challenging for these language agents to quickly and efficiently learn from trial-and-error as traditional reinforcement learning methods require extensive training samples and expensive model fine-tuning. We propose Reflexion, a novel framework to reinforce language agents not by updating weights, but instead through linguistic feedback. Concretely, Reflexion agents verbally reflect on task feedback signals, then maintain their own reflective text in an episodic memory buffer to induce better decision-making in subsequent trials. Reflexion is flexible enough to incorporate various types (scalar values or free-form language) and sources (external or internally simulated) of feedback signals, and obtains significant improvements over a baseline agent across diverse tasks (sequential decision-making, coding, language reasoning). For example, Reflexion achieves a 91% pass@1 accuracy on the HumanEval coding benchmark, surpassing the previous state-of-the-art GPT-4 that achieves 80%. We also conduct ablation and analysis studies using different feedback signals, feedback incorporation methods, and agent types, and provide insights into how they affect performance.Comment: v4 contains a few additional experiment

Comparison of FEV6 and FVC for detection of airway obstruction in a community hospital pulmonary function laboratory

SummaryThe National Lung Health Education Program recommends that primary care providers perform spirometry tests on cigarette smoking patients 45 years or older in order to detect airways obstruction and aid smoking cessation efforts [Ferguson GT, Enright Pl, Buist AS, et al. Office spirometry for lung health assessment in adults: a consensus statement from the national lung education program. Chest 2000; 117: 1146–61]. An abbreviated forced expiratory maneuver that requires exhalation for 6s (FEV6) has recently been proposed as a substitute for forced vital capacity (FVC) to facilitate performance of such spirometry. We set out to assess the accuracy of diagnosis of obstruction and abnormal pulmonary function using FEV6 in comparison to FVC in a community hospital population. One hundred pulmonary function tests performed at a community hospital were randomly selected and retrospectively analyzed. Sixty-three of the 100 tests had satisfactory 6-s expiration and were subject to further analysis. We compared the spirometric interpretation using Morris predictive equations for FEV1/FVC and Hankison predictive equations for FEV1/FVC and FEV1/FEV6. The Hankison set of equations is the only published reference formulas for prediction of FEV6. We found that versus our Morris gold standard, Hankison based FEV1/FVC interpretation was 100% sensitive and 67% specific for the diagnosis of obstruction and 100% sensitive and 65% specific for the diagnosis of any abnormality. The Hankison based FEV1/FEV6 interpretation was 97% sensitive and 47% specific for diagnosing obstruction and 100% sensitive and 50% specific for identifying any abnormality versus the Morris FVC based gold standard. In conclusion, in our hospital based pulmonary function laboratory, FEV6 based interpretation has excellent sensitivity for detection of spirometric abnormalities. However, its moderate specificity may hinder its utility as a screening test. Further testing is necessary to determine its reliability in different patient populations with less highly trained operators

Lymphocyte-Tropic Simian Immunodeficiency Virus Causes Persistent Infection in the Brains of Rhesus Monkeys

AbstractMolecularly cloned SIVmac239 is the prototypical SIVmaclymphocyte-tropic virus that replicates productively in lymphocytes but poorly in macrophages. In macaques, the virus causes activation and productive infection of T lymphocytes which invade the central nervous system (CNS) early after infection in the animal. However, infected animals develop immunosuppression and AIDS but rarely overt neurological disease. In this study, we examined multiple regions of the brain and spinal cord for the presence of SIVenvsequences and histological lesions in five macaques that had been infected with SIVmac239 for 1.7 to 2.25 years. Histopathological examination of the brain revealed no lesions consistent with encephalitis; however, viral DNA was found in all five brains. In one animal the virus caused infection in a widely disseminated pattern from the frontal cortex to the distal end of the spinal cord, whereas in the other four animals infection in the CNS occurred in a nonspecific, focal pattern. Sequence analyses were performed on gp120 sequences isolated from selected regions of the CNS and compared to gp120 sequences isolated from corresponding lymph nodes, a tissue known to support productive replication of SIVmac239. Examination of the viral sequences from the CNS tissue from two animals (macaques 10F and 14F) revealed a low mutation rate when compared to the sequences isolated from the lymph node tissues. The percentage change in the amino acid sequence was approximately 1% for CNS clones versus ≥3% for clones isolated from the lymph node. The majority of the CNS viral sequences of macaques 10F and 14F had none of the genetic markers shown in a previous study to be associated with macrophage-tropic variants and indeed retained a nucleotide sequence of similar to the original lymphocyte-tropic virus used for inoculation despite almost 2 years of persistent infection in the animals. Construction of chimeric viruses with V1–V5 regions of selected macaque 10F and macaque 14F CNS-gp120 clones confirmed the predicted lymphocyte-tropic nature of theseenvgenes. In contrast, the gp120 sequences isolated from the CNS tissue of one of the other three animals (macaque 13F) had a mutation rate comparable to that observed for the lymph node clones. The CNS clones from this animal had amino acid substitutions that were previously shown to be associated with macrophage tropism. Compared to the chimeric viruses constructed with V1–V5 sequences from macaques 10F and 14F, viruses constructed with the V1–V5 sequences of several macaque 13F brain clones did not yield infectious virus. These data suggest that following entry into the CSF early during infection in the animals, SIVmac239 caused infection in the CNS. In some animals, the viralenvsequences recovered by the PCR suggested that minimal replication had occurred, whereas in another macaque virus replication had progressed with gradual selection of a more macrophage-tropic genotype

Long Term Suboxone™ Emotional Reactivity As Measured by Automatic Detection in Speech

Addictions to illicit drugs are among the nation’s most critical public health and societal problems. The current opioid prescription epidemic and the need for buprenorphine/naloxone (Suboxone®; SUBX) as an opioid maintenance substance, and its growing street diversion provided impetus to determine affective states (“true ground emotionality”) in long-term SUBX patients. Toward the goal of effective monitoring, we utilized emotion-detection in speech as a measure of “true” emotionality in 36 SUBX patients compared to 44 individuals from the general population (GP) and 33 members of Alcoholics Anonymous (AA). Other less objective studies have investigated emotional reactivity of heroin, methadone and opioid abstinent patients. These studies indicate that current opioid users have abnormal emotional experience, characterized by heightened response to unpleasant stimuli and blunted response to pleasant stimuli. However, this is the first study to our knowledge to evaluate “true ground” emotionality in long-term buprenorphine/naloxone combination (Suboxone™). We found in long-term SUBX patients a significantly flat affect (p<0.01), and they had less self-awareness of being happy, sad, and anxious compared to both the GP and AA groups. We caution definitive interpretation of these seemingly important results until we compare the emotional reactivity of an opioid abstinent control using automatic detection in speech. These findings encourage continued research strategies in SUBX patients to target the specific brain regions responsible for relapse prevention of opioid addiction.United States. Dept. of Defense. Assistant Secretary of Defense for Research & Engineering (Air Force Contract FA8721-05-C-0002