gebhart/patrepeval huggingface dataset:
Multispectral lensless imaging in the mid-infrared for label-free identification of Staphylococcus species (2021)

Identifying the microbial species present in a sample is critical in healthcare, industry, ecology and even national security. The traditional diagnosis process involves the growth of colonies of microorganisms on a solid-state medium in a Petri dish. This step provides great amounts of biological material, allows spatial separation of the different microorganisms and can help to visually discriminate potentially harmful species. However, it does not allow a precise identification and thereby requires further sample preparation and analysis to offer a proper diagnosis. Here, a new optical-based Petri dish analysis technology is discussed. This technique, called lensless multispectral mid-infrared imaging, relies on the acquisition of images at nine wavelengths corresponding to relevant chemical functions. It provides both morphological and discrete spectral data, which allows to discriminate even closely related species. The instrument is simply made of a laser source (four quantum cascade lasers) and a microbolometer array as the imager. A total of 1050 colonies belonging to three Staphylococcus species and two strains of Staphylococcus epidermidis have been acquired. After feature extraction and classification by Support Vector Machine, the tenfold cross-validation test yields a correct identification rate between 93 % and 96 %, with only a 5 % confusion between the two strains of S. epidermidis. Further work on the data analysis algorithms could dramatically improve these already promising results. Therefore, considering its label-free and non-destructive aspects, as well as its absence of secondary sample preparation, this technology has a great potential to offer precise Petri-dish based diagnosis.
High-Throughput Microfluidics Platform for Intracellular Delivery and Sampling of Biomolecules from Live Cells (2022)

Nondestructive cell membrane permeabilization systems enable the intracellular delivery of exogenous biomolecules for cell engineering tasks as well as the temporal sampling of cytosolic contents from live cells for the analysis of dynamic processes. Here, we report a <i>microwell array</i> format live-cell analysis device (LCAD) that can perform localized-electroporation induced membrane permeabilization, for cellular delivery or sampling, and directly interfaces with surface-based biosensors for analyzing the extracted contents. We demonstrate the capabilities of the LCAD via an automated high-throughput workflow for multimodal analysis of live-cell dynamics, consisting of quantitative measurements of enzyme activity using self-assembled monolayers for MALDI mass spectrometry (SAMDI) and deep-learning enhanced imaging and analysis. By combining a fabrication protocol that enables robust assembly and operation of multilayer devices with embedded gold electrodes and an automated imaging workflow, we successfully deliver functional molecules (plasmid and siRNA) into live cells at multiple time-points and track their effect on gene expression and cell morphology <i>temporally</i>. Furthermore, we report sampling performance enhancements, achieving saturation levels of protein tyrosine phosphatase activity measured from as few as 60 cells, and demonstrate control over the amount of sampled contents by optimization of electroporation parameters using a lumped model. Lastly, we investigate the implications of cell morphology on electroporation-induced sampling of fluorescent molecules using a deep-learning enhanced image analysis workflow.
Eine Methode zur Entwicklung modularer Produktfamilien (2011)

Im Rahmen der Arbeit wird eine Methode vorgestellt, die eine durchgehende Unterstützung bei der Entwicklung modularer Produktfamilien bietet. Unter Anwendung der Methode entwickelte Produktfamilien sollen nicht nur eine einfache Konfiguration von Produktvarianten erlauben, sondern auch den vielfältigen Anforderungen aus allen Produktlebensphasen gerecht werden. Dazu werden zuerst unabhängig Produktstrukturen aus Sicht der unterschiedlichen Produktlebensphasen entwickelt. Im Anschluss werden die Produktstrukturen in einem Prozess über das Produktleben zusammengefasst.
Reasoning, Metareasoning, and Mathematical Truth: Studies of Theorem Proving under Limited Resources (2013)

In earlier work, we introduced flexible inference and decision-theoretic metareasoning to address the intractability of normative inference. Here, rather than pursuing the task of computing beliefs and actions with decision models composed of distinctions about uncertain events, we examine methods for inferring beliefs about mathematical truth before an automated theorem prover completes a proof. We employ a Bayesian analysis to update belief in truth, given theorem-proving progress, and show how decision-theoretic methods can be used to determine the value of continuing to deliberate versus taking immediate action in time-critical situations.
Hypofractionated robotic radiosurgery for the treatment of clinically localized prostate cancer: Early biochemical results and acute toxicity. (2010)

e15134 Background: Clinical data suggest that fewer large fractions are radio-biologically superior to smaller fraction sizes in prostate cancer radiotherapy. The CyberKnife is the ideal delivery system for hypofractionated radiosurgery due to its ability to deliver highly conformal radiation and to track and adjust for prostate motion in real-time. We report our early experience using the CyberKnife system to deliver hypofractionated radiotherapy to localized prostate cancer. Methods: Thirty nine patients were treated with hypofractionated robotic radiosurgery with or without supplemental external radiation therapy and/or androgen deprivation therapy (26%). Four gold fiducials were placed within the prostate for X-ray guided prostate localization and beam adjustment. Fused CT and MRI scans were used for treatment planning. Sixteen patients were treated with radiosurgery alone (3625 cGy in five fractions). Twenty three patients were treated with radiosurgery (1950 cGy in three fractions) followed by IMRT (5040 cGy in 28 fractions). Quality of life data, including EPIC and IPSS questionnaires, was collected before and after treatment. The early PSA responses and acute urinary and rectal toxicities are reported here. Results: All 39 patients completed the proposed course of treatment without unplanned breaks. The mean pretreatment PSA was 9.63 ng/ml. PSA levels steadily decreased in all patients. The mean 6 month post-treatment PSA was 1.24 ng/ml. Acute side effects associated with treatment included grade 2 urinary and gastrointestinal toxicity. No patient experienced acute grade 3 or greater toxicity. IPSS scores returned to baseline by six months after treatment. Conclusions: Hypofractionated robotic radiosurgery using the CyberKnife system appears to be a well tolerated treatment alternative for older men with clinically localized prostate cancer. Early PSA results suggest an encouraging biochemical response. Author Disclosure Employment or Leadership Position Consultant or Advisory Role Stock Ownership Honoraria Research Funding Expert Testimony Other Remuneration Accuray, Inc. Accuray, Inc. Accuray, Inc.
The Detection of Bile Acids in the Lungs of Paediatric Cystic Fibrosis Patients Is Associated with Altered Inflammatory Patterns (2020)

<i>Background</i>: Cystic fibrosis (CF) is a hereditary disorder in which persistent unresolved inflammation and recurrent airway infections play major roles in the initiation and progression of the disease. Little is known about triggering factors modulating the transition to chronic microbial infection and inflammation particularly in young children. Cystic fibrosis respiratory disease starts early in life, with the detection of inflammatory markers and infection evident even before respiratory symptoms arise. Thus, identifying factors that dysregulate immune responsiveness at the earliest stages of the disease will provide novel targets for early therapeutic intervention. <i>Methods</i>: We evaluated the clinical significance of bile acid detection in the bronchoalveolar lavage fluid of clinically stable preschool-aged children diagnosed with CF. <i>Results</i>: We applied an unbiased classification strategy to categorize these specimens based on bile acid profiles. We provide clear associations linking the presence of bile acids in the lungs with alterations in the expression of inflammatory markers. Using multiple regression analysis, we also demonstrate that clustering based on bile acid profiles is a meaningful predictor of the progression of structural lung disease. <i>Conclusions</i>: Altogether, our work has identified a clinically relevant host-derived factor that may participate in shaping early events in the aetiology of CF respiratory disease.
Contraction of matchgate tensor networks on non-planar graphs (2009)

A tensor network is a product of tensors associated with vertices of some graph $G$ such that every edge of $G$ represents a summation (contraction) over a matching pair of indexes. It was shown recently by Valiant, Cai, and Choudhary that tensor networks can be efficiently contracted on planar graphs if components of every tensor obey a system of quadratic equations known as matchgate identities. Such tensors are referred to as matchgate tensors. The present paper provides an alternative approach to contraction of matchgate tensor networks that easily extends to non-planar graphs. Specifically, it is shown that a matchgate tensor network on a graph $G$ of genus $g$ with $n$ vertices can be contracted in time $T=poly(n) + 2^{2g} O(m^3)$ where $m$ is the minimum number of edges one has to remove from $G$ in order to make it planar. Our approach makes use of anticommuting (Grassmann) variables and Gaussian integrals.
Generation of two‐dimensional electron gas to normally depleted AlGaN/GaN hetero‐interface by SiO 2 deposition and subsequent high‐temperature annealing (2021)

Abstract SiO 2 film deposition and subsequent high‐temperature annealing resulted in the generation of a two‐dimensional electron gas (2DEG) at Al(Ga)N/GaN hetero‐interfaces, of which the 2DEG was originally fully depleted. The obtained mobilities and sheet carrier concentrations were over 1100 cm 2 /Vs and 3.0 × 10 12 cm –2 , respectively. Surface energy lowering, which is proof of the generated 2DEG, was observed by electron state analysis using hard X‐ray photoelectron spectroscopy. This damage‐less method that selectively generates a 2DEG can contribute not only toward improving some characteristics in existing devices but also toward creating entirely novel devices.
Proteome Half-Life Dynamics in Living Human Cells (2011)

Cells remove proteins by two processes: degradation and dilution due to cell growth. The balance between these basic processes is poorly understood. We addressed this by developing an accurate and noninvasive method for measuring protein half-lives, called "bleach-chase," that is applicable to fluorescently tagged proteins. Assaying 100 proteins in living human cancer cells showed half-lives that ranged between 45 minutes and 22.5 hours. A variety of stresses that stop cell division showed the same general effect: Long-lived proteins became longer-lived, whereas short-lived proteins remained largely unaffected. This effect is due to the relative strengths of degradation and dilution and suggests a mechanism for differential killing of rapidly growing cells by growth-arresting drugs. This approach opens a way to understand proteome half-life dynamics in living cells.
Columnar Liquid Crystal with a Spontaneous Polarization along the Columnar Axis (2010)

A fan-shaped molecule (2), carrying hydrogen-bonding amide groups in proximity to its polar aromatic core, self-assembles into a columnar liquid crystalline mesophase, which unprecedentedly possesses a spontaneous macroscopic polarization along the columnar axis. Due to its polar nature, the mesophase displays a signal of second harmonic generation (SHG), which disappears on phase transition to an isotropic melt and then retrieves its original intensity on subsequent cooling.
Uses of alpha particles, especially in nuclear reaction studies and medical radionuclide production (2016)

Abstract Alpha particles exhibit three important characteristics: scattering, ionisation and activation. This article briefly discusses those properties and outlines their major applications. Among others, α -particles are used in elemental analysis, investigation and improvement of materials properties, nuclear reaction studies and medical radionuclide production. The latter two topics, dealing with activation of target materials, are treated in some detail in this paper. Measurements of excitation functions of α -particle induced reactions shed some light on their reaction mechanisms, and studies of isomeric cross sections reveal the probability of population of high-spin nuclear levels. Regarding medical radionuclides, an overview is presented of the isotopes commonly produced using α -particle beams. Consideration is also given to some routes which could be potentially useful for production of a few other radionuclides. The significance of α -particle induced reactions to produce a few high-spin isomeric states, decaying by emission of low-energy conversion or Auger electrons, which are of interest in localized internal radiotherapy, is outlined. The α -particle beam, thus broadens the scope of nuclear chemistry research related to development of non-standard positron emitters and therapeutic radionuclides.
Fundamental Escherichia coli biochemical pathways for biomass and energy production: Identification of reactions (2003)

Abstract Cells grow by oxidizing nutrients using a complex network of biochemical reactions. During this process new biological material is produced along with energy used for maintaining cellular organization. Because the metabolic network is highly branched, these tasks can be accomplished using a wide variety of unique reaction sequences. However, evolutionary pressures under carbon‐limited growth conditions likely select organisms that utilize highly efficient pathways. Using elementary‐mode analysis, we demonstrate that the metabolism of the bacterium Escherichia coli contains four unique pathways that most efficiently convert glucose and oxygen into new cells and maintenance energy under any level of oxygen limitation. Observed regulatory patterns and experimental findings suggest growing cells use these highly efficient pathways. It is predicted that five knockout mutations generate a strain that supports growth using only the most efficient reaction sequence. The analysis approach should be generally useful for predicting metabolic capabilities and efficient network designs based on only genomic information. © 2003 Wiley Periodicals, Inc.
Long-Term Effects of Repeated Blast Exposure in United States Special Operations Forces Personnel: A Pilot Study Protocol (2022)

Emerging evidence suggests that repeated blast exposure (RBE) is associated with brain injury in military personnel. United States (U.S.) Special Operations Forces (SOF) personnel experience high rates of blast exposure during training and combat, but the effects of low-level RBE on brain structure and function in SOF have not been comprehensively characterized. Further, the pathophysiological link between RBE-related brain injuries and cognitive, behavioral, and physical symptoms has not been fully elucidated. We present a protocol for an observational pilot study, Long-Term Effects of Repeated Blast Exposure in U.S. SOF Personnel (ReBlast). In this exploratory study, 30 active-duty SOF personnel with RBE will participate in a comprehensive evaluation of: 1) brain network structure and function using Connectome magnetic resonance imaging (MRI) and 7 Tesla MRI; 2) neuroinflammation and tau deposition using positron emission tomography; 3) blood proteomics and metabolomics; 4) behavioral and physical symptoms using self-report measures; and 5) cognition using a battery of conventional and digitized assessments designed to detect subtle deficits in otherwise high-performing individuals. We will identify clinical, neuroimaging, and blood-based phenotypes that are associated with level of RBE, as measured by the Generalized Blast Exposure Value. Candidate biomarkers of RBE-related brain injury will inform the design of a subsequent study that will test a diagnostic assessment battery for detecting RBE-related brain injury. Ultimately, we anticipate that the ReBlast study will facilitate the development of interventions to optimize the brain health, quality of life, and battle readiness of U.S. SOF personnel.
The BITMAP exercise: a multi-laboratory performance assessment campaign of diffuse optical instrumentation (2019)

Performance assessment of instruments is a growing demand in the diffuse optics community and there is a definite need to get together to address this issue. Within the EU Network BITMAP1, we initiated a campaign for the performance evaluation of 10 diffuse optical instrumentation from 7 partner institutions adopting a set of 3 well accepted, standardized protocols. A preliminary analysis of the outcome along with future perspectives will be presented.
Abstract 1398: RNA DIRECT: A novel strategy for targeted RNA enrichment of transcripts associated with solid tumors (2016)

Abstract RNA sequencing (RNA-seq) has become a powerful platform for profiling transcriptomes that enables gene expression analysis and identification of nucleotide or structural variations. RNA-seq, however, can be cost prohibitive due to the size and complexity of most transcriptomes, which require deep sequencing coverage to achieve the necessary sensitivity for a reliable analysis. By combining targeted enrichment strategies with next-generation sequencing (NGS), a subset of transcript regions or sequences can be enriched for and analyzed with the resolution required for both research and clinical applications. The RNA DIRECT targeted enrichment method utilizes probe-based hybridization to capture only relevant cDNA sequences. Targeted sequences are then ligated to NGS platform specific adaptors and amplified by PCR. The RNA DIRECT strategy provides a robust and cost effective method for the enrichment of transcript sequences for the purpose of identification and detection of known or novel variants and gene fusions. To demonstrate the high specificity, sensitivity and uniformity of this method, we have applied it to the capture of targets commonly associated with solid tumors. Citation Format: Kruti M. Patel, Sarah K. Bowman, Theodore B. Davis, Salvatore Russello, Daniel C. Kraushaar, Amy B. Emerman, Noa Henig, Cynthia L. Hendrickson. RNA DIRECT: A novel strategy for targeted RNA enrichment of transcripts associated with solid tumors. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1398.
Patient-reported outcomes from the phase II FAST trial of zolbetuximab plus EOX compared to EOX alone as first-line treatment of patients with metastatic CLDN18.2+ gastroesophageal adenocarcinoma (2021)

ZOL/EOX allowed patients to maintain good QoL and low symptom burden for longer than EOX alone.
The role of an electronic alert system to detect acute kidney injury in hospitalized patients: DETECT-H Project (2018)

CKD and in-hospital AKI are under-recognized entities. Mortality and LOS are increased in-hospital patients with renal dysfunction. AKI severity was associated with higher mortality and LOS. An automated electronic detection system for identifying renal dysfunction would be a useful tool to improve renal outcomes.
Selective Remanent Ambipolar Charge Transport in Polymeric Field‐Effect Transistors For High‐Performance Logic Circuits Fabricated in Ambient (2014)

Ambipolar polymeric field-effect transistors can be programmed into a p- or n-type mode by using the remanent polarization of a ferroelectric gate insulator. Due to the remanent polarity, the device architecture is suited as a building block in complementary logic circuits and in CMOS-compatible memory cells for non-destructive read-out operations.
Optofluidics (2005)

"Optofluidics" is the marriage of optics, optoelectronics and nanophotonics with fluidics. Such integration represents a new approach for dynamic manipulation of optical properties at length scales both greater than and smaller than the wavelength of light with applications ranging from reconfigurable photonic circuits to fluidically adaptable optics to high sensitivity bio-detection currently under development. The capabilities in terms of fluidic control, mixing, miniaturization and optical property tuning afforded by micro-, nano- and electro-fluidics combined with soft lithography based fabrication provides an ideal platform upon which to build such devices. In this paper we provide a general overview of some of the important issues related to the fabrication, integration and operation of optofluidic devices and present three comprehensive application examples: nanofluidically tunable photonic crystals, optofluidic microscopy and DFB dye lasers.
Salt-inducible kinase 1 maintains HDAC7 stability to promote pathologic cardiac remodeling (2020)

Salt-inducible kinases (SIKs) are key regulators of cellular metabolism and growth, but their role in cardiomyocyte plasticity and heart failure pathogenesis remains unknown. Here, we showed that loss of SIK1 kinase activity protected against adverse cardiac remodeling and heart failure pathogenesis in rodent models and cardiomyocytes derived from human induced pluripotent stem cells. We found that SIK1 phosphorylated and stabilized histone deacetylase 7 (HDAC7) protein during cardiac stress, an event that is required for pathologic cardiomyocyte remodeling. Gain- and loss-of-function studies of HDAC7 in cultured cardiomyocytes implicated HDAC7 as a prohypertrophic signaling effector that can induce c-Myc expression, indicating a functional departure from the canonical MEF2 corepressor function of class IIa HDACs. Taken together, our findings reveal what we believe to be a previously unrecognized role for a SIK1/HDAC7 axis in regulating cardiac stress responses and implicate this pathway as a potential target in human heart failure.
Manipulating Spectral Width and Emission Wavelength towards Highly Efficient Blue Asymmetric Carbazole Fused Multi-Resonance Emitters (2022)

The novel carbazole-based multiresonance types of thermally activated delayed fluorescence (MR-TADF) emitters of mICz-DABNA and BFCz-DABNA are reported, and their spectroscopic properties are investigated with the inductive effect on the central nitrogen atom for pure and deep blue emission. With the introduction of electron-donating/-withdrawing properties of substituents, emitters exhibited the bathochromic/hypsochromic shifted emission, respectively, compared to simple carbazole-based MR-TADF. Moreover, their spectral bandwidths became narrower. Theoretical calculation indicated that the meta-positioned bulky moiety restricts the molecular geometry discrepancy and reduces the Huang–Rhys factors. Particularly, the organic light-emitting diode (OLED) with 3% BFCz-DABNA exhibited the maximum external quantum efficiency of 28.0% with the Commission International de l’Éclairage (CIE) of (0.13, 0.09), which is the best record value among single-boron MR-TADF devices of CIE y < 0.10.