gebhart/patrepeval huggingface dataset:
Photo‐magnetic imaging: a new functional imaging modality for more accurate photothermal therapy planning (2022)

In photothermal therapy, heat generated from absorbed light energy is used to treat cancerous tissue. Thus, determining laser parameters that control temperature elevation prior to therapy is crucial for an effective outcome. These parameters can be defined by modeling the expected temperature increase via numerical simulations. The quality of these simulations highly depends on the accurate knowledge of optical properties of the treated tissue. Multi-wavelength Photo Magnetic Imaging (PMI) utilizes four laser wavelengths from the near infrared (NIR) window to induce a relatively low temperature increase, while measuring the laser-induced temperature increase using Magnetic Resonance Thermometry. These measured temperature maps are then used by the PMI image reconstruction algorithm to provide high spatial resolution absorption maps at these wavelengths. These absorption maps are then processed to recover the concentration of the main chromophores of the tissue, and consequently obtain its total optical absorption spectrum at any wavelength in the NIR region based on the Beer-Lambert law. In this paper, PMI was used to recover the absorption coefficient of a gelatin tissuesimulating phantom at four wavelengths. These spatially-resolved absorption values were used to successfully recover the concentration of the chromophores of the phantom and calculate its total absorption spectrum in the NIR spectral window with an error as low as ∼ 2.3%. Therefore, applications of photothermal therapy applied in NIR window can benefit from the absorption spectrum recovered by PMI to achieve accurate simulations and determine important laser parameters, which are key for accurate therapy planning.
Continuous Wavelet Transform: ECG Recognition Based on Phase and Modulus Representations and Hidden Markov Models (2017)

Biomedical signals are fundamental observations for analyzing the body function and for diagnosing a wide spectrum of diseases. One of the major areas where new insights can be expected is the cardiovascular domain. For diagnosis purpose, the noninvasive electrocardiogram (ECG) is of great value in clinical practice. Wavelet transforms have been applied to ECG signals for enhancing late potentials, reducing noise, QRS detection, normal and abnormal beat recognition. The chapter considers the use of local symmetry properties in automatic ECG recognition and identification by means of hidden Markov models (HMMs). The set of standard mathematical tools devoted to the use of HMMs constitutes a found theoretical basis. The chapter highlights how a suitable parameter vector, corresponding to the input observation sequence of the Markov chain, can be built and applied. It describes the local behavior of the phase of continuous wavelet transform of signals with particular points as local extrema or inflection points.
P394 Preoperative serum vedolizumab levels do not predict postoperative outcomes in inflammatory bowel disease (IBD) (2018)

It is unknown whether patients with IBD undergoing abdominal surgery after biologic drug exposure are at increased risk of postoperative complications. Prior studies on the association of preoperative vedolizumab (VEDO) therapy use and postoperative outcomes in IBD have been conflicting. Serum levels of anti-TNF drugs are a surrogate for biologic effect on inflammatory mechanisms and have been correlated with postoperative outcomes. In a similar fashion, we sought to clarify associations between serum VEDO levels and postoperative outcomes in IBD. IBD patients on VEDO, with serum drawn within 7 days before surgery, were identified. Serum VEDO levels were measured by investigators blinded to clinical outcomes using the homogenous mobility shift assay (Prometheus Laboratories Inc.). Patients were divided into 2 groups according to serum levels: Group 1 (undetectable VEDO levels; ≤1.8 μg/ml)) and Group 2 (detectable serum VEDO levels; >1.8 μg/ml). To assess whether a higher level of VEDO affected outcomes, Group 2 was further divided into high and low levels as determined by median detectable serum level. Postoperative outcomes, including the Comprehensive Complication index (CCI)), within 30 days of surgery were collected prospectively. The study cohort of 48 patients had a median age of 31 (range, 14–65) years and included 21 (44%) males. Indications for surgery were ulcerative colitis (n = 25;52%), Crohn’s disease (n = 20;42%) or indeterminate colitis (n = 3;6%). Index procedures included subtotal colectomy (n = 21;44%), small bowel/ileocolic resection (n = 11; 23%) and ileal pouch-anal anastomoses (n = 9;19%). Serum VEDO levels were detectable in 30 (63%) patients and not detectable in 18 (38%) patients. Median detectable serum VEDO level at the time of surgery was 8.6 μg/ml (range, 1.9–54.4). Groups 1 and 2 were similar in all preoperative characteristics. There were no significant differences between groups in regards to overall postoperative morbidity (39% vs. 30%; p = 0.54), infectious complications (17% vs. 7%; p = 0.35) or 30-day readmission rates after surgery (22% vs. 13%; p = 0.62), or CCI (p = 0.35). Fifteen (31%) patients had low detectable levels and 15 (31%) had high detectable levels. There was no association between level of VEDO (high vs. undetectable) and overall postoperative morbidity (39% vs. 20%; p = 0.28), infectious complications (17% vs. 7%; p = 0.61), 30-day readmission rates (22% vs. 13%; p = 0.66) or CCI (p = 0.11) after surgery. This study showed that the presence and magnitude of serum VEDO levels do not adversely influence postoperative outcomes in IBD patients. Contrary to other studies, there appears to be no deleterious effect of preoperative VEDO use in IBD patients requiring surgery.
Machine Learning, Human Factors and Security Analysis for the Remote Command of Driving: An MCity Pilot (2020)

Conducted under the U.S. DOT Office of the Assistant Secretary for Research and Technology’s (OST-R) University Transportation Centers (UTC) program.
Supplementary Table and Figures from Exposure–Response Relationships of the Efficacy and Safety of Ipilimumab in Patients with Advanced Melanoma (2023)

&lt;p&gt;Supplementary Table and Figures - PDF file 297K, Supporting data related to the covariates included in the exposure-response analyses&lt;/p&gt;
VCSEL with Multiple Transverse Coupled Cavities for Ultra-Wide Bandwidth (Conference Presentation) (2020)

We propose a vertical-cavity surface-emitting laser (VCSEL) laterally coupled to multiple transverse cavities (MTCCs) providing modulation bandwidth beyond the relaxation-oscillation-frequency. We show a 3dB modulation bandwidth of 45 GHz, five times greater than it’s conventional VCSEL fabricated on the same epi-wafer.
Sodium Spray Fire Simulations using CONTAIN-LMR. (2018)

Abstract not provided.
Interfacial Layer Engineering to Enhance Noise Immunity of FeFETs for IMC Applications (2022)

This article reports an improvement in the low- frequency noise characteristics in hafnium oxide-based (HfO <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> ) ferroelectric field-effect transistors (FeFET) by interfacial layer (IL) engineering. FeFET devices with silicon dioxide (SiO <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> ) and silicon oxynitride (SiON) as IL were fabricated and characterised. FeFETs with SiON interfaces demonstrated an excellent improvement in variation, and low-frequency noise characteristics. The wider memory window for operation in FeFETs with SiON IL also allows for a higher noise tolerance during the inference operation. Finally, the evaluation of system performance by neuromorphic simulation shows that FeFET with SiON IL are highly immune to noise degradation and endurance, without retention penalty.
Minimizing Replay under Way-Prediction (2019)

Way-predictors are effective at reducing dynamic cache energy by reducing the number of ways accessed, but introduce additional latency for incorrect way-predictions. While previous work has studied the impact of the increased latency for incorrect way-predictions, we show that the latency variability has a far greater effect as it forces replay of in-flight instructions on an incorrect way-prediction. To address the problem, we propose a solution that learns the confidence of the way-prediction and dynamically disables it when it is likely to mispredict. We further improve this approach by biasing the confidence to reduce latency variability further at the cost of reduced way-predictions. Our results show that instruction replay in a way-predictor reduces IPC by 6.9% due to 10% of the instructions being replayed. Our confidence-based way-predictor degrades IPC by only 2.9% by replaying just 3.4% of the instructions, reducing way-predictor cache energy overhead (compared to serial access cache) from 8.5% to 1.9%.
The measurement design of information security management system (2014)

Information is an asset, such as important business assets, has value to an organization and consequently must be well protected. In organizations, information becomes an important and must remain available, and its existence should be maintained from unauthorized access. The use of information by unauthorized parties could be used for negative purposes which would be detrimental to the organization. Therefore, information security must be implemented correctly in order to avoid the impact of loss to the organization. Information security must satisfy the elements of confidentiality, integrity and availability. The international standard ISO / IEC 27000: 2014, SNI ISO / IEC 27001: 2013 and SNI ISO / IEC 27002: 2013 are a standard for Information Security Management System that can be used for the organization. These standard are able to test the security of the information and to measure the effectiveness of an implemented Information Security Management System (ISMS) which has been adopted as SNI ISO / IEC 27004: 2013. The standardization of Information Security Management Systems need an adjustment, the version of ISO / IEC 27004. The latter has adopted the development of ISO / IEC 27000, ISO / IEC 27001 and ISO / IEC 27002 which is required the measurement design of Information Security Management System. This study results in the design of the size of the Information Security Management System in accordance with the rules of international standards and the latest ISO standards. So it can be a reference for various organizations. This study aims to make a measurement design of Information Security Management System by adopting the best practices based on information security standard defined by ISO / IEC.
Quantum Čerenkov radiation in weakly and strongly-coupled regimes (2018)

We present the time-dependent quantum electrodynamic theory of Čerenkov radiation, which reveals orders of magnitude corrections to the decay rate from the conventional theory, as well as significant modifications to the well-established Čerenkov dispersion relation.
Applications and case studies of laser hybrid welding in the automotive industry (2010)

In joining technology, the high welding speed on the one and the good gap bridging ability on the other hand play a significant part. It is no doubt that the laser beam welding and the GMA welding have been established in the welding technology for very long, and that both processes allow a wide field of application in the joining technology. New possibilities and synergetic effects, however, are based on the combination of both processes. The laser radiation causes a very narrow thermally affected zone with a high ratio between welding depth and seam width. In the case of the laser welding process, the gap bridging ability is very low due to the small focus diameter, however very high welding speeds can be achieved. The GMA or Tandem welding process features a significantly lower energy density has a larger focused spot on the material surface and is characterised by its good gap bridging ability.
Stochastic anomaly of methylome but persistent SRY hypermethylation in disorder of sex development in canine somatic cell nuclear transfer (2016)

Somatic cell nuclear transfer (SCNT) provides an excellent model for studying epigenomic reprogramming during mammalian development. We mapped the whole genome and whole methylome for potential anomalies of mutations or epimutations in SCNT-generated dogs with XY chromosomal sex but complete gonadal dysgenesis, which is classified as 78, XY disorder of sex development (DSD). Whole genome sequencing revealed no potential genomic variations that could explain the pathogenesis of DSD. However, extensive but stochastic anomalies of genome-wide DNA methylation were discovered in these SCNT DSD dogs. Persistent abnormal hypermethylation of the SRY gene was observed together with its down-regulated mRNA and protein expression. Failure of SRY expression due to hypermethylation was further correlated with silencing of a serial of testis determining genes, including SOX9, SF1, SOX8, AMH and DMRT1 in an early embryonic development stage at E34 in the XY(DSD) gonad, and high activation of the female specific genes, including FOXL2, RSPO1, CYP19A1, WNT4, ERα and ERβ, after one postnatal year in the ovotestis. Our results demonstrate that incomplete demethylation on the SRY gene is the driving cause of XY(DSD) in these XY DSD dogs, indicating a central role of epigenetic regulation in sex determination.
Enhanced Bug Prediction in JavaScript Programs with Hybrid Call-Graph Based Invocation Metrics (2020)

Bug prediction aims at finding source code elements in a software system that are likely to contain defects. Being aware of the most error-prone parts of the program, one can efficiently allocate the limited amount of testing and code review resources. Therefore, bug prediction can support software maintenance and evolution to a great extent. In this paper, we propose a function level JavaScript bug prediction model based on static source code metrics with the addition of a hybrid (static and dynamic) code analysis based metric of the number of incoming and outgoing function calls (HNII and HNOI). Our motivation for this is that JavaScript is a highly dynamic scripting language for which static code analysis might be very imprecise; therefore, using a purely static source code features for bug prediction might not be enough. Based on a study where we extracted 824 buggy and 1943 non-buggy functions from the publicly available BugsJS dataset for the ESLint JavaScript project, we can confirm the positive impact of hybrid code metrics on the prediction performance of the ML models. Depending on the ML algorithm, applied hyper-parameters, and target measures we consider, hybrid invocation metrics bring a 2–10% increase in model performances (i.e., precision, recall, F-measure). Interestingly, replacing static NOI and NII metrics with their hybrid counterparts HNOI and HNII in itself improves model performances; however, using them all together yields the best results.
ChemInform Abstract: Synthesis of Topostins B567 and D654 (WB-3559D, Flavolipin), DNA Topoisomerase I Inhibitors of Bacterial Origin. (2010)

ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Fundamentals of Membrane Lipid Replacement: A Natural Medicine Approach to Repairing Cellular Membranes and Reducing Fatigue, Pain, and Other Symptoms While Restoring Function in Chronic Illnesses and Aging (2021)

Membrane Lipid Replacement (MLR) uses natural membrane lipid supplements to safely replace damaged, oxidized lipids in membranes in order to restore membrane function, decrease symptoms and improve health. Oral MLR supplements contain mixtures of cell membrane glycerolphospholipids, fatty acids, and other lipids, and can be used to replace and remove damaged cellular and intracellular membrane lipids. Membrane injury, caused mainly by oxidative damage, occurs in essentially all chronic and acute medical conditions, including cancer and degenerative diseases, and in normal processes, such as aging and development. After ingestion, the protected MLR glycerolphospholipids and other lipids are dispersed, absorbed, and internalized in the small intestines, where they can be partitioned into circulating lipoproteins, globules, liposomes, micelles, membranes, and other carriers and transported in the lymphatics and blood circulation to tissues and cellular sites where they are taken in by cells and partitioned into various cellular membranes. Once inside cells, the glycerolphospholipids and other lipids are transferred to various intracellular membranes by lipid carriers, globules, liposomes, chylomicrons, or by direct membrane-membrane interactions. The entire process appears to be driven by 'bulk flow' or mass action principles, where surplus concentrations of replacement lipids can stimulate the natural exchange and removal of damaged membrane lipids while the replacement lipids undergo further enzymatic alterations. Clinical studies have demonstrated the advantages of MLR in restoring membrane and organelle function and reducing fatigue, pain, and other symptoms in chronic illness and aging patients.
Long-Period Gratings and Microcavity In-Line Mach Zehnder Interferometers as Highly Sensitive Optical Fiber Platforms for Bacteria Sensing (2020)

Selected optical fiber sensors offer extraordinary sensitivity to changes in external refractive (RI), which make them promising for label-free biosensing. In this work the most sensitive ones, namely long-period gratings working at (DTP-LPG) and micro-cavity in-line Mach-Zehnder interferometers (µIMZI) are discussed for application in bacteria sensing. We describe their working principles and RI sensitivity when operating in water environments, which is as high as 20,000 nm/RIU (Refractive index unit) for DTP-LPGs and 27,000 nm/RIU for µIMZIs. Special attention is paid to the methods to enhance the sensitivity by etching and nano-coatings. While the DTP-LPGs offer a greater interaction length and sensitivity to changes taking place at their surface, the µIMZIs are best suited for investigations of sub-nanoliter and picoliter volumes. The capabilities of both the platforms for bacteria sensing are presented and compared for strains of <i>Escherichia coli</i>, lipopolysaccharide <i>E. coli</i>, outer membrane proteins of <i>E. coli,</i> and <i>Staphylococcus aureus</i>. While DTP-LPGs have been more explored for bacteria detection in 10<sup>2</sup>-10<sup>6</sup> Colony Forming Unit (CFU)/mL for <i>S. aureus</i> and 10<sup>3</sup>-10<sup>9</sup> CFU/mL for <i>E. coli</i>, the µIMZIs reached 10<sup>2</sup>-10<sup>8</sup> CFU/mL for <i>E. coli</i> and have a potential for becoming picoliter bacteria sensors.
Supplementary Figure 1 from S-Nitrosylation of EGFR and Src Activates an Oncogenic Signaling Network in Human Basal-Like Breast Cancer (2023)

&lt;p&gt;PDF file - 2.5MB, LEF binding elements are prevalent in human breast cancer NOS2-associated gene expression&lt;/p&gt;
A Robust Shape-Aware Rib Fracture Detection and Segmentation Framework With Contrastive Learning (2023)

The rib fracture is a common type of thoracic skeletal trauma, and its inspections using computed tomography (CT) scans are critical for clinical evaluation and treatment planning. However, it is often challenging for radiologists to quickly and accurately detect rib fractures due to tiny objects and blurriness in large 3D CT images. Previous diagnoses for automatic rib fracture mostly relied on deep learning (DL)-based object detection, which highly depends on label quality and quantity. Moreover, general object detection methods did not take into consideration the typically elongated and oblique shapes of ribs in 3D volumes. To address these issues, we propose a shape-aware method based on DL called SA-FracNet for rib fracture detection and segmentation. First, we design a pixel-level pretext task founded on contrastive learning on massive unlabeled CT images. Second, we train the fine-tuned rib fracture detection model based on the pre-trained weights. Third, we develop a fracture shape-aware multi-task segmentation network to delineate the fracture based on the detection result. Experiments demonstrate that our proposed SA-FracNet achieves state-of-the-art rib fracture detection and segmentation performance on the public RibFrac dataset, with a detection sensitivity of 0.926 and segmentation Dice of 0.754. Test on a private dataset also validates the robustness and generalization of our SA-FracNet.
Performance analysis of jump-gliding locomotion for miniature robotics (2015)

Recent work suggests that jumping locomotion in combination with a gliding phase can be used as an effective mobility principle in robotics. Compared to pure jumping without a gliding phase, the potential benefits of hybrid jump-gliding locomotion includes the ability to extend the distance travelled and reduce the potentially damaging impact forces upon landing. This publication evaluates the performance of jump-gliding locomotion and provides models for the analysis of the relevant dynamics of flight. It also defines a jump-gliding envelope that encompasses the range that can be achieved with jump-gliding robots and that can be used to evaluate the performance and improvement potential of jump-gliding robots. We present first a planar dynamic model and then a simplified closed form model, which allow for quantification of the distance travelled and the impact energy on landing. In order to validate the prediction of these models, we validate the model with experiments using a novel jump-gliding robot, named the 'EPFL jump-glider'. It has a mass of 16.5 g and is able to perform jumps from elevated positions, perform steered gliding flight, land safely and traverse on the ground by repetitive jumping. The experiments indicate that the developed jump-gliding model fits very well with the measured flight data using the EPFL jump-glider, confirming the benefits of jump-gliding locomotion to mobile robotics. The jump-glide envelope considerations indicate that the EPFL jump-glider, when traversing from a 2 m height, reaches 74.3% of optimal jump-gliding distance compared to pure jumping without a gliding phase which only reaches 33.4% of the optimal jump-gliding distance. Methods of further improving flight performance based on the models and inspiration from biological systems are presented providing mechanical design pathways to future jump-gliding robot designs.
Pulse-induced crystallization in phase-change memories under set and disturb conditions (2015)

We introduce a new technique to study the crystallization process in phase-change memory. By this technique, crystallization is characterized in the ON-state at extremely low currents, allowing to extend the time scale of crystallization times to more than two decades. To describe the pulse-induced crystallization in the set regime, we develop a finite-element method model based on localized conduction in the amorphous phase and non-Arrhenius crystallization kinetics. The range of crystallization times is then extended to even lower currents in the subthreshold regime, where the model allows describing the crystallization kinetics thus providing the physics-based prediction of read disturb.