Tag: statistics

Proc Natl Acad Sci U S A. 2023 May 16;120(20):e2220789120. doi: 10.1073/pnas.2220789120. Epub 2023 May 8.

ABSTRACT

Machine learning (ML) is causing profound changes to chemical research through its powerful statistical and mathematical methodological capabilities. However, the nature of chemistry experiments often sets very high hurdles to collect high-quality data that are deficiency free, contradicting the need of ML to learn from big data. Even worse, the black-box nature of most ML methods requires more abundant data to ensure good transferability. Herein, we combine physics-based spectral descriptors with a symbolic regression method to establish interpretable spectra-property relationship. Using the machine-learned mathematical formulas, we have predicted the adsorption energy and charge transfer of the CO-adsorbed Cu-based MOF systems from their infrared and Raman spectra. The explicit prediction models are robust, allowing them to be transferrable to small and low-quality dataset containing partial errors. Surprisingly, they can be used to identify and clean error data, which are common data scenarios in real experiments. Such robust learning protocol will significantly enhance the applicability of machine-learned spectroscopy for chemical science.

PMID:37155896 | DOI:10.1073/pnas.2220789120

Proc Natl Acad Sci U S A. 2023 May 16;120(20):e2220552120. doi: 10.1073/pnas.2220552120. Epub 2023 May 8.

ABSTRACT

Reliable, noninvasive biomarkers that reveal the internal state of a subject are an invaluable tool for neurological diagnoses. Small fixational eye movements, called microsaccades, are a candidate biomarker thought to reflect a subject’s focus of attention [Z. M. Hafed, J. J. Clark, VisionRes. 42, 2533-2545 (2002); R. Engbert, R. Kliegl, VisionRes. 43, 1035-1045 (2003)]. The linkage between the direction of microsaccades and attention has mainly been demonstrated using explicit and unambiguous attentional cues. However, the natural world is seldom predictable and rarely provides unambiguous information. Thus, a useful biomarker must be robust to such changes in environmental statistics. To determine how well microsaccades reveal visual-spatial attention across behavioral contexts, we analyzed these fixational eye movements in monkeys performing a conventional change detection task. The task included two stimulus locations and variable cue validities across blocks of trials. Subjects were adept at the task, showing precise and graded modulations of visual attention for subtle target changes and performing better and faster when the cue was more reliable [J. P. Mayo, J. H. R. Maunsell, J. Neurosci. 36, 5353 (2016)]. However, over tens of thousands of microsaccades, we found no difference in microsaccade direction between cued locations when cue variability was high nor between hit and miss trials. Instead, microsaccades were made toward the midpoint of the two target locations, not toward individual targets. Our results suggest that the direction of microsaccades should be interpreted with caution and may not be a reliable measure of covert spatial attention in more complex viewing conditions.

PMID:37155892 | DOI:10.1073/pnas.2220552120

Swiss Med Wkly. 2023 Apr 22;153:40061. doi: 10.57187/smw.2023.40061.

ABSTRACT

AIMS OF THE STUDY: To analyse gender-specific differences in comorbidities, multisubstance abuse, in-hospital complications, intensive care unit transfers and referrals to psychiatric wards of emergency department patients with ethanol intoxication. Several lines of evidence suggest an influence of gender differences on diagnostic and therapeutic approaches to various diseases.

METHODS: Over a period of 7 years, all patients with signs or symptoms of ethanol intoxication and a positive blood ethanol test admitted for the first time to the emergency department of a Swiss regional tertiary referral hospital were prospectively enrolled. Patients were categorised into two subgroups: patients without additional drug use were considered ethanol-only cases, whereas patients who had also ingested other substances (as determined from bystanders, physicians and urine drug screening) were considered multisubstance cases. A retrospective analysis of this database evaluated gender-specific differences in comorbidities, multisubstance abuse, in-hospital complications, intensive care unit transfers and referrals to psychiatric wards within these two subgroups. Statistical analysis included Fisher’s exact test for categorical data and Wilcoxon rank sum test for continuous data.

RESULTS: Of 409 enrolled patients, 236 cases were ethanol-only and 173 were multisubstance cases. The three most common comorbidities in multisubstance patients showed significant gender differences: psychiatric disorders (43% males vs 61% females; p = 0.022), chronic ethanol abuse (55% males vs 32% females; p = 0.002) and drug addiction (44% males vs 17% females; p = 0.001). Gender differences were also found for the most frequently co-ingested substances: benzodiazepines (35% males vs 43% females; p = 0.014), cannabis (45% males vs 24% females; p = 0.006) and cocaine (24% males vs 6% females; p = 0.001). Male and female ethanol-only patients were transferred to the intensive care unit in 8% of cases. In multisubstance cases, 32% of male and 43% of female patients were transferred to the intensive care unit (no significant gender difference). The psychiatric ward referral rate in male (30%) and female (48%) patients with multisubstance abuse was significantly different (p = 0.028). No significant gender difference in psychiatric ward referral rates was observed for ethanol-only patients (12% males, 17% females).

CONCLUSION: Among emergency department patients admitted with ethanol intoxication, gender differences in comorbidities, substance use and psychiatric ward referrals were highly significant among patients who presented with multisubstance abuse. Rates of intensive care unit transfer for patients with ethanol intoxication are substantial for both genders, reflecting relevant disease burden and resource demand, as well as the need for further preventive efforts.

PMID:37155832 | DOI:10.57187/smw.2023.40061

ACS Synth Biol. 2023 May 8. doi: 10.1021/acssynbio.3c00074. Online ahead of print.

ABSTRACT

The reconstitution of basic cellular functions in micrometer-sized liposomes has led to a surge of interest in the construction of synthetic cells. Microscopy and flow cytometry are powerful tools for characterizing biological processes in liposomes with fluorescence readouts. However, applying each method separately leads to a compromise between information-rich imaging by microscopy and statistical population analysis by flow cytometry. To address this shortcoming, we here introduce imaging flow cytometry (IFC) for high-throughput, microscopy-based screening of gene-expressing liposomes in laminar flow. We developed a comprehensive pipeline and analysis toolset based on a commercial IFC instrument and software. About 60 thousands of liposome events were collected per run starting from one microliter of the stock liposome solution. Robust population statistics from individual liposome images was performed based on fluorescence and morphological parameters. This allowed us to quantify complex phenotypes covering a wide range of liposomal states that are relevant for building a synthetic cell. The general applicability, current workflow limitations, and future prospects of IFC in synthetic cell research are finally discussed.

PMID:37155828 | DOI:10.1021/acssynbio.3c00074

Opt Express. 2023 Mar 27;31(7):11649-11658. doi: 10.1364/OE.481126.

ABSTRACT

We develop a BiB₃O₆ (BiBO)-based optical parametric amplifier in the spectral region around 2 µm using a Yb:KGW amplifier operating at 100 kHz. The two-stage degenerate optical parametric amplification results in a typical output energy of 30 µJ after compression, spectrum covering 1.7-2.5 µm range, and a pulse duration fully compressible down to 16.4 fs, corresponding to 2.3 cycles. Due to the inline difference frequency generation of the seed pulses, the carrier envelope phase (CEP) is passively stabilized without feedback over 11 hours at the level below 100 mrad including a long-term drift. Short-term statistical analysis in the spectral domain further shows a behavior qualitatively different from that of parametric fluorescence, indicating high degree of suppression of optical parametric fluorescence. The high phase stability together with the few-cycle pulse duration is promising for the investigation of high-field phenomena such as subcycle spectroscopy in solids or high harmonics generation.

PMID:37155795 | DOI:10.1364/OE.481126

Opt Express. 2023 Mar 27;31(7):11308-11319. doi: 10.1364/OE.482733.

ABSTRACT

Speckle patterns observed in coherent optical imaging reflect important characteristic information of the scattering object. To capture speckle patterns, angular resolved or oblique illumination geometries are usually employed in combination with Rayleigh statistical models. We present a portable and handheld 2-channel polarization-sensitive imaging instrument to directly resolve terahertz (THz) speckle fields in a collocated telecentric back-scattering geometry. The polarization state of the THz light is measured using two orthogonal photoconductive antennas and can be presented in the form of the Stokes vectors of the THz beam upon interaction with the sample. We report on the validation of the method in surface scattering from gold-coated sandpapers, demonstrating a strong dependence of the polarization state on the surface roughness and the frequency of the broadband THz illumination. We also demonstrate non-Rayleigh first-order and second-order statistical parameters, such as degree of polarization uniformity (DOPU) and phase difference, for quantifying the randomness of polarization. This technique provides a fast method for broadband THz polarimetric measurement in the field and has the potential for detecting light depolarization in applications ranging from biomedical imaging to non-destructive testing.

PMID:37155769 | DOI:10.1364/OE.482733

Opt Express. 2023 Mar 27;31(7):11261-11273. doi: 10.1364/OE.481401.

ABSTRACT

To study nanostructures on substrates, surface-sensitive reflection-geometry scattering techniques such as grazing incident small angle X-ray scattering are commonly used to yield an averaged statistical structural information of the surface sample. Grazing incidence geometry can probe the absolute three-dimensional structural morphology of the sample if a highly coherent beam is used. Coherent surface scattering imaging (CSSI) is a powerful yet non-invasive technique similar to coherent X-ray diffractive imaging (CDI) but performed at small angles and grazing-incidence reflection geometry. A challenge with CSSI is that conventional CDI reconstruction techniques cannot be directly applied to CSSI because the Fourier-transform-based forward models cannot reproduce the dynamical scattering phenomenon near the critical angle of total external reflection of the substrate-supported samples. To overcome this challenge, we have developed a multislice forward model which can successfully simulate the dynamical or multi-beam scattering generated from surface structures and the underlying substrate. The forward model is also demonstrated to be able to reconstruct an elongated 3D pattern from a single shot scattering image in the CSSI geometry through fast-performing CUDA-assisted PyTorch optimization with automatic differentiation.

PMID:37155766 | DOI:10.1364/OE.481401

Bol Med Hosp Infant Mex. 2023;80(2):94-104. doi: 10.24875/BMHIM.22000119.

ABSTRACT

This essay questions mathematical truths as an explanatory principle of the medical scientific knowledge. It analyzes, in the first place, the current concept of normality based on a distribution of probabilistic values and its limitations and mistakes to capture the complexity of the human condition are highlighted. The closed systems (gambling) origin of the theory of probabilities and the binomial causality-chance are compared with open systems typical of the complexity of the vital process, and their extreme differences are argued. The nonsense of depositing in the causality-chance binomial the meaning of associations between events typical of the complexity of human life in health and disease is highlighted. The characteristics of mechanistic causality (punctual, homogeneous, linear, unidirectional and fixed), which equates the organism with a machine and is the only accepted scientific explanation of events of human life, are confronted with those of contextual causality (diffuse, heterogeneous, hierarchical, multidirectional and changing), which specifies various interacting causal orders that shape of human condition: the historical, the social, the political, the economical, the cultural or the biological that represents a scrutinizing and penetrating look at the complexity of human beings. It concludes the superiority of contextual causality over mechanistic causality that opens up explanatory possibilities of the vital events that are usually put away as “effects of chance”. This integrative approach to the human complexity can enrich and strengthen the clinical method that is now degraded and at risk of extinction.

PMID:37155718 | DOI:10.24875/BMHIM.22000119

Am J Health Syst Pharm. 2023 May 8:zxad100. doi: 10.1093/ajhp/zxad100. Online ahead of print.

ABSTRACT

DISCLAIMER: In an effort to expedite the publication of articles, AJHP is posting manuscripts online as soon as possible after acceptance. Accepted manuscripts have been peer-reviewed and copyedited, but are posted online before technical formatting and author proofing. These manuscripts are not the final version of record and will be replaced with the final article (formatted per AJHP style and proofed by the authors) at a later time.

PURPOSE: To compare rates of prescriber acceptance of interruptive and noninterruptive clinical decision support (CDS) alerts regarding potential diminished therapeutic effectiveness and safety risks associated with proton pump inhibitor (PPI) use in carriers of gene variants affecting cytochrome P450 (CYP) isozyme 2C19 metabolism.

METHODS: A retrospective study was conducted at a large rural health system to examine different approaches to improving CDS alert acceptance while minimizing alert fatigue. Manual reviews were conducted to identify alerts regarding CYP2C19 metabolizer status displayed at the time of PPI ordering over 30-day periods before and after the transition from interruptive to noninterruptive CDS alert functionality. A chi-square test was conducted to analyze prescriber acceptance CDS recommendations by alert modality and type of treatment modification.

RESULTS: Overall, interruptive alerts had an acceptance rate of 18.6% (64/344), compared to 8.4% acceptance (30/357 alerts) for noninterruptive alerts (P ≤ 0.0001). Analysis of acceptance criteria revealed the noninterruptive alert cohort had higher acceptance, as determined by documented medication dose adjustments, than the interruptive alert cohort (53.3% [16/30] and 4.7% [3/64], respectively). The difference in acceptance rates by CDS modality and treatment modification was statistically significant (P ≤ 0.00001). The predominant indication for PPI use was gastroesophageal reflux disease (GERD) in both cohorts.

CONCLUSION: Interruptive alerts that actively influenced workflow had higher acceptance rates than noninterruptive alerts that served an informational purpose without a direct disruption of workflow. The study results suggest the utilization of noninterruptive alerts may be a beneficial tool for prompting clinicians to alter dosing regimens rather than transition to an alternative agent.

PMID:37155711 | DOI:10.1093/ajhp/zxad100

PLoS One. 2023 May 8;18(5):e0285520. doi: 10.1371/journal.pone.0285520. eCollection 2023.

ABSTRACT

To examine the genetic diversity of Leishmania major, 100 Giemsa-stained positive slides were collected from endemic foci of Iran (Northeast, Central, and Southwest provinces) over two consecutive years during 2019-2021. The Leishmania ITS-rDNA gene was amplified and Leishmania sp. was recognized by PCR-RFLP and sequencing. In addition, 178 registered ITS-rDNA sequences from other geographical regions of Iran were retrieved from GenBank, including different host species (human, sandfly and rodent). A total of 40 new haplotypes were discovered using the ITS-rDNA sequence analysis. IR29 (20.6%) and IR34 (61%) were the two most common haplotypes, represented by a star-like feature in the overall population. Analysis of the molecular variance test revealed low genetic diversity of L. major in human cases (Haplotype diversity; 0.341), rodent (Hd; 0.387) and sandfly (Hd; 0.390) sequences. The lowest genetic diversity of L. major was observed in Southwest/Southeast Iran (Hd: 0.104-0.286). The statistically Fst value indicated that L. major is not genetically differentiated between geographic regions of Iran, except for the Northeast-Southwest (Fst: 0.29055) and Central-Southwest (Fst: 0.30294) population pairs. The current study as the first investigation discloses new perspectives for further evaluation in the identification local transmission paradigms and initiating effective prevention strategies.

PMID:37155684 | DOI:10.1371/journal.pone.0285520