gebhart/patrepeval huggingface dataset:
Proteasome inhibitors increase tubulin polymerization and stabilization in tissue culture cells. A possible mechanism contributing to peripheral neuropathy and cellular toxicity following proteasome inhibition. (2008)

3268 Bortezomib (Velcade®), a proteasome inhibitor, is approved by the FDA for the treatment of multiple myeloma (MM). While effective, its use has been hampered by peripheral neurotoxicity of unexplained etiology. Since proteasome inhibitors alter protein degradation, we speculated that proteins regulating microtubule (MT) stability may be affected after treatment and examined MT polymerization in cells by comparing the distribution of tubulin between polymerized (P) and soluble (S) fractions. We observed increased MT polymerization following treatment of SY5Y and KCNR [neuroblastoma], HCN2 [neural] and 8226 [multiple myeloma] cells, using five proteasome inhibitors; the baseline proportion of polymerized α-tubulin ranged from ~41-68%, and increased to ~55-99% after treatment. We also observed increased MT polymerization in 786-0 [renal carcinoma] cells following treatment with either MG-132 or bortezomib, further indicating the generality of these findings in a variety of cell types. Furthermore, increased acetylated α-tubulin, a post-translational marker of stabilized MTs, was observed in the neural cell lines HCN1A and HCN2 and this was sustained up to 144 hours after the proteasome inhibitor was removed. Cell cycle analysis of three cell lines after drug treatment, showed ~50-75% increases in the G 2 M phase. Immunofluorescent localization studies of proteasome inhibitor treated cells did not reveal microtubule bundles in contrast to paclitaxel treated cells, suggesting MT stabilization following a proteasome inhibitor is occurring via a different mechanism. One possibility is an increase in the levels of microtubule associated proteins. We observed a 1.4 - 3.7 fold increase for MAP2 in HCN2 cells following treatment with proteasome inhibitors. These data provide a plausible explanation for the neurotoxicity observed clinically and raise the possibility that microtubule stabilization mediated by a mechanism other than direct drug binding, contributes to cytotoxicity.
Evaluating deep learning methods in detecting and segmenting different sizes of brain metastases on 3D post-contrast T1-weighted images (2021)

<b>Purpose:</b> We investigate the impact of various deep-learning-based methods for detecting and segmenting metastases with different lesion volume sizes on 3D brain MR images. <b>Approach:</b> A 2.5D U-Net and a 3D U-Net were selected. We also evaluated weak learner fusion of the prediction features generated by the 2.5D and the 3D networks. A 3D fully convolutional one-stage (FCOS) detector was selected as a representative of bounding-box regression-based detection methods. A total of 422 3D post-contrast T1-weighted scans from patients with brain metastases were used. Performances were analyzed based on lesion volume, total metastatic volume per patient, and number of lesions per patient. <b>Results:</b> The performance of detection of the 2.5D and 3D U-Net methods had recall of <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:mo>></mml:mo> <mml:mn>0.83</mml:mn></mml:mrow> </mml:math> and precision of <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:mo>></mml:mo> <mml:mn>0.44</mml:mn></mml:mrow> </mml:math> for lesion volume <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:mo>></mml:mo> <mml:mn>0.3</mml:mn> <mml:mtext> </mml:mtext> <mml:msup><mml:mi>cm</mml:mi> <mml:mn>3</mml:mn></mml:msup> </mml:mrow> </mml:math> but deteriorated as metastasis size decreased below <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:mn>0.3</mml:mn> <mml:mtext> </mml:mtext> <mml:msup><mml:mrow><mml:mi>cm</mml:mi></mml:mrow> <mml:mrow><mml:mn>3</mml:mn></mml:mrow> </mml:msup> </mml:mrow> </mml:math> to 0.58 to 0.74 in recall and 0.16 to 0.25 in precision. Compared the two U-Nets for detection capability, high precision was achieved by the 2.5D network, but high recall was achieved by the 3D network for all lesion sizes. The weak learner fusion achieved a balanced performance between the 2.5D and 3D U-Nets; particularly, it increased precision to 0.83 for lesion volumes of 0.1 to <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:mn>0.3</mml:mn> <mml:mtext> </mml:mtext> <mml:msup><mml:mrow><mml:mi>cm</mml:mi></mml:mrow> <mml:mrow><mml:mn>3</mml:mn></mml:mrow> </mml:msup> </mml:mrow> </mml:math> but decreased recall to 0.59. The 3D FCOS detector did not outperform the U-Net methods in detecting either the small or large metastases presumably because of the limited data size. <b>Conclusions:</b> Our study provides the performances of four deep learning methods in relationship to lesion size, total metastasis volume, and number of lesions per patient, providing insight into further development of the deep learning networks.
The Challenge of Estimating Video Quality in Video Communication Applications [In the Spotlight] (2012)

Video communication over the Internet has gone from science fiction to reality. Not only is video streaming and two-way video conferencing becoming common, but, as recently reported by the Associated Press through ABC News [1], today even broadcast television programs such as eyewitness news often use live video from camera phones or Skype on a notebook or desktop computer to interview people and share information. A desired goal in these scenarios is to ensure the best video quality possible. This leads to the challenge of estimating video quality as a key step to achieving the above. This article's goal is to describe the need for video quality estimation and why it is challenging as well as highlight the different types of video quality estimators (VQEs) being developed. Signal processing is viewed as critical throughout this work.
Biologically Inspired Optimal Terminal Iterative Learning Control for the Swing Phase of Gait in a Hybrid Neuroprosthesis: A Modeling Study (2022)

(1) Background: An iterative learning control (ILC) strategy was developed for a "Muscle First" Motor-Assisted Hybrid Neuroprosthesis (MAHNP). The MAHNP combines a backdrivable exoskeletal brace with neural stimulation technology to enable persons with paraplegia due to spinal cord injury (SCI) to execute ambulatory motions and walk upright. (2) Methods: The ILC strategy was developed to swing the legs in a biologically inspired ballistic fashion. It maximizes muscular recruitment and activates the motorized exoskeletal bracing to assist the motion as needed. The control algorithm was tested using an anatomically realistic three-dimensional musculoskeletal model of the lower leg and pelvis suitably modified to account for exoskeletal inertia. The model was developed and tested with the OpenSim biomechanical modeling suite. (3) Results: Preliminary data demonstrate the efficacy of the controller in swing-leg simulations and its ability to learn to balance muscular and motor contributions to improve performance and accomplish consistent stepping. In particular, the controller took 15 iterations to achieve the desired outcome with 0.3% error.
Chondral defects of the glenohumeral joint (2017)

Even though microfracturing does not prevent radiographic progression, microfracture of the glenohumeral joint might be worth considering as part of a treatment regimen for younger patients who may not yet be treated with arthroplasty.
Corrosion‐fatigue behaviour of Cr–Mo steel under biaxial tension (2020)

Abstract Combined cyclic tension and internal pressure tests with various proportions of each loading were run on a 2.5%Cr–1%Mo steel in air and in 3.5% NaCl solution, with and without cathodic protection to investigate the effect of positive stress biaxiality on corrosion‐fatigue lives and damage mechanisms. At free potential, a strong reduction in fatigue resistance was observed for uniaxial as well as for equibiaxial cyclic tension and attributed to multiple crack initiation from corrosion pits. Cathodic protection completely cancelled the detrimental effect of the corrosive environment on fatigue lives whatever the load biaxiality was, in spite of an obvious enhancement of intergranular fracture attributed to hydrogen embrittlement.
Flicker Estimation Associated with PV Integrated Distribution Network (2018)

The interest for solar Photovoltaic (PV) systems installation has been recently increasing due to their reducing cost and high electricity price from the utilities. However, the PV power generation is sensitive to variable solar irradiation, which causes technical difficulties related to power quality and control. Severity of those problems directly depends on PV penetration level, grid design and geographic location. This paper explores the flicker indices of grid-tied PV power plant, one of the major power quality issues. The study has been carried out on a real grid-integrated PV system, situated at Engineering Center, Florida International University (FIU). The field measurements of various solar output power and flicker quantifying indices at the point of common coupling (PCC) have been recorded using data acquisition system and power quality meter respectively. The collected data has been categorized and analyzed for voltage fluctuations and flicker. Different approaches have been done to investigate the influence of PV power plant on the flicker indices. Results show that solar output power has a marginal effect towards flicker indices with existing penetration level. Load connection and variation are the key indicators of high flicker value during observation time.
Improving the Performance of Cooperative Platooning With Restricted Message Trigger Thresholds (2022)

Cooperative Vehicular Platooning (Co-VP) is one of the most prominent and challenging applications of Intelligent Traffic Systems. To support such vehicular communications, the ETSI ITS G5 standard specifies event-based communication profiles, triggered by kinematic parameters such as speed. The standard defines a set of threshold values for such triggers but no careful assessment in realistic platooning scenarios has been done to confirm the suitability of such values. In this work, we investigate the safety and performance limitations of such parameters in a realistic platooning co-simulation environment. We then propose more conservative threshold values, that we formalize as a new profile, and evaluate their impact in the longitudinal and lateral behaviour of a vehicular platoon as it carries out complex driving scenarios. Furthermore, we analyze the overhead introduced in the network by applying the new threshold values. We conclude that a pro-active message transmission scheme leads to improved platoon performance for highway scenarios, notably an increase greater than 40% in the longitudinal performance of the platoon, while not incurring in a significant network overhead. The obtained results also demonstrated an improved platoon performance for for semi-urban scenarios, including obstacles and curves, where the heading error decreases in 26%, with slight network overhead.
AirKeyLogger: Hardwareless Air-Gap Keylogging Attack (2023)

This paper presents AirKeyLogger - a novel radio frequency (RF) keylogging attack for air-gapped computers.Our keylogger exploits radio emissions from a computer’s power supply to exfiltrate real-time keystroke data to a remote attacker. Unlike hardware keylogging devices, our attack does not require physical hardware. Instead, it can be conducted via a software supply-chain attack and is solely based on software manipulations. Malware on a sensitive, air-gap computer can intercept keystroke logging by using global hooking techniques or injecting malicious code into a running process. To leak confidential data, the processor’s working frequencies are manipulated to generate a pattern of electromagnetic emissions from the power unit modulated by keystrokes. The keystroke information can be received at distances of several meters away via an RF receiver or a smartphone with a simple antenna. We provide related work, discuss keylogging methods and present multi-key modulation techniques. We evaluate our method at various typing speeds and on-screen keyboards as well. We show the design and implementation of transmitter and receiver components and present evaluation findings. Our tests show that malware can eavesdrop on keylogging data in real-time over radio signals several meters away and behind concrete walls from highly secure and air-gapped systems.
Imaging and analysis of axial heterostructured silicon nanowires (2010)

Silicon nanowires with axially varying n- and p-doping were grown by the vapor-liquid-solid approach using gold as the catalyst. The microstructures of the axial heterostructured silicon nanowires were studied using electron microscopy techniques. The nanowire sidewalls exhibit periodic nanofaceting, which is dopant-dependent. The nanofaceting occurs during the enhanced sidewall growth that arises when the diborane dopant gas is introduced. It is also found that the silicon nanowire can crystallize in a hexagonal phase, which is thermodynamically unstable in bulk silicon at ambient and may be due to the large surface stress present during the nucleation of SiNWs.
Injectable polyethylene glycol hydrogel for islet encapsulation: an <i>in vitro</i> and <i>in vivo</i> characterization (2017)

An injection of hydrogel-encapsulated islets that controls blood glucose levels over long term would provide a much needed alternative treatment for type 1 diabetes mellitus (T1DM). To this end, we tested the feasibility of using an injectable polyethylene glycol (PEG) hydrogel as a scaffold for islet encapsulation. Encapsulated islets cultured <i>in vitro</i> for 6 days showed excellent cell viability and released insulin with higher basal and stimulated insulin secretion than control islets. Host responses to PEG hydrogels were studied by injecting PEG hydrogels (no treatment and vehicle controls used) into the peritoneal cavities of B6D2F1 mice and monitoring alterations in body weight, food and water intake, and blood glucose levels. After 2 weeks, peritoneal cavity cells were harvested, followed by hydrogel retrieval, and extraction of spleens. Body weights, food and water intake, and blood glucose levels were unaltered in mice injected with hydrogels compared to no treatment and vehicle-injected control mice. Frozen sections of a hydrogel showed the presence of tissues and small number of immune cells surrounding the hydrogel but no cell infiltration into the hydrogel bulk. Spleen sizes were not significantly different under the experimental conditions. Peritoneal cavity cells were slightly higher in mice injected with hydrogels compared to control mice but no statistical difference between vehicle- and hydrogel-injected mice was noted. As an <i>in vivo</i> feasibility study, streptozotocin-induced diabetic mice were injected with vehicle or hydrogels containing 50 islets each into two sites, the peritoneal cavity and a subcutaneous site on the back. Transient control of blood glucose levels were observed in mice injected with hydrogels containing islets. In summary, we developed an injectable PEG hydrogel that supported islet function and survival <i>in vitro</i> and <i>in vivo</i> and elicited only a mild host response. Our work illustrates the feasibility of using injectable PEG hydrogels for islet encapsulation.
Defining the Pathophysiological Role of Tau in Experimental TBI (2016)

Abstract : After traumatic brain injury (TBI), the human brain sometimes develops tau pathology partly resembling the hallmark neuropathological features of the tauopathy of Alzheimer's disease (AD). Although tau has been strongly linked to the pathogenesis of AD, its involvement in the pathophysiology of TBI and its influence on brain structural and functional outcomes are unclear. Here we are critically evaluating three hypotheses: (i) tau exacerbates the neuronal damage and cognitive dysfunction after single and repetitive mild TBI in the acute and chronic post-injury periods; (ii) mild TBI promotes the severity and spread of tau pathology to contribute to development of a chronic neurodegenerative disorder; and (iii) novel biomarkers for neurodegeneration are non-invasive blood measures of brain damage and dysfunction valuable for the diagnosis, prognosis, and theragnosis of mild TBI-triggered brain damage and chronic neurodegenerative disease. At the completion of year 2 of the project, we conclude that in the acute post-injury time period there is no structural, functional, or biomarker evidence for interaction between hippocampal input-specific expression of pathological human tau and either single or repetitive mild TBI. This lack of acute interaction sets the stage for the second phase of the project, examining interactions between tau and mild TBI that may only develop chronically after brain injury, and may contribute to the development of a chronic neurodegenerative condition.
Metal Thio/Selenophosphates: A Novel Two-Dimensional Materials System (2019)

Ever since the discovery of graphene in 2004, interest in van der Waals materials have increased exponentially. This material system, which includes black phosphorus (BP), hexagonal boron nitride (h-BN), and the transition metal dichalcogenides (TMD) are found to possess many interesting properties when reduced to the 2D limit that can both complement and supplement that of graphene. For example, due to the extreme spatial confinement present in these structures, MoS2 undergoes an indirect to direct bandgap transition.
Supplementary Figure S2 from The Suppression of &lt;i&gt;Aurora-A/STK15/BTAK&lt;/i&gt; Expression Enhances Chemosensitivity to Docetaxel in Human Esophageal Squamous Cell Carcinoma (2023)

Supplementary Figure S2 from The Suppression of &lt;i&gt;Aurora-A/STK15/BTAK&lt;/i&gt; Expression Enhances Chemosensitivity to Docetaxel in Human Esophageal Squamous Cell Carcinoma
Long-Term Survival of De Novo Stage IV Human Epidermal Growth Receptor 2 (HER2) Positive Breast Cancers Treated with HER2-Targeted Therapy (2018)

In this retrospective review at two institutions, it was demonstrated that 13% of patients with de novo stage IV, human epidermal growth receptor 2 positive metastatic breast cancer achieved no evidence of disease (NED) status with trastuzumab-based therapy plus/minus local therapies, and these patients had a very high progression-free survival (100%) and overall survival (98%) at both the 5- and 10-year time points. Achieving NED status may be an important therapeutic goal. However, further randomized studies are required to fully understand the impact of systemic or locoregional therapy on achieving these excellent long-term outcomes.
Synergistic bactericidal effect of nisin and phytic acid against Escherichia coli O157:H7 (2022)

The food industry must prevent food contamination caused by pathogenic Escherichia coli strains as they pose a severe public health threat worldwide and lead to unimaginable economic losses. In this study, the synergistic antibacterial activity in vitro of nisin and phytic acid (PA), a natural metal chelate, against 5 foodborne isolates of E. coli were evaluated by a checkerboard assay. Checkerboard assay showed that nisin and PA showed a synergistic effect (FICI <0.375) on three O157 serogroup strains and an addictive effect (0.5<FICI <0.5625) on the remaining two non-O157 serogroup strains. Then the combined bactericidal effect of these compounds against E. coli O157:H7 was investigated. Results showed the number of planktonic and biofilm cells inactivated in groups treated with a combination of 0.512 mg/mL nisin plus 1 × MIC or 2 × MIC PA was significantly higher than the sum of groups treated alone (P < 0.05). Electron scanning microscopy studies revealed that the nisin plus PA treatment had a severe effect on E. coli O157:H7, which after treatment cell morphology appeared deflated with large invaginations. The effect of nisin plus PA against E. coli O157:H7 was furthermore assessed on cold-stored beef, where a similar synergistic bactericidal effect was observed. The studies demonstrate the great potential of the food-approved nisin to control the growth of undesired E. coli pathogens in foods. We used PA to overcome the permeability barrier of the outer membrane to nisin, but other food-grade metal ion chelators such as polyphosphate most likely could be used as well.
Association of physical activity with blood pressure and blood glucose among Malaysian adults: a population-based study (2015)

A significant negative association was observed between PA level and blood glucose only. Future studies should employ an objective measurement in estimating PA level in order to elucidate the actual relationship between PA, hypertension and diabetes for the development of effective interventions to combat the increasing burden of premature-mortality and cardiovascular disease-related morbidity in Malaysia.
R1441G but not G2019S mutation enhances LRRK2 mediated Rab10 phosphorylation in human peripheral blood neutrophils (2021)

Heterozygous gain-of-kinase function variants in LRRK2 (leucine-rich repeat kinase 2) cause 1-2% of all cases of Parkinson's disease (PD) albeit with incomplete and age-dependent penetrance. All pathogenic LRRK2 mutations reside within the two catalytic domains of LRRK2-either in its kinase domain (e.g. G2019S) with modest effect or its ROC-COR GTPase domain (e.g. R1441G/H) with large effect on LRRK2 kinase activity. We have previously reported assays to interrogate LRRK2 kinase pathway activity in human bio-samples measuring phosphorylation of its endogenous substrate Rab10, that mirrors LRRK2 kinase activation status. Here, we isolated neutrophils from fresh peripheral blood from 101 participants including 42 LRRK2 mutation carriers (21 with the G2019S and 21 with the R1441G mutations), 27 patients with idiopathic PD, and 32 controls. Using a dual approach, LRRK2 dependent Rab10 phosphorylation at Threonine 73 (pRab10<sup>Thr73</sup>) was measured by quantitative multiplexed immunoblotting for pRab10<sup>Thr73</sup>/total Rab10 as well as targeted mass-spectrometry for absolute pRab10<sup>Thr73</sup> occupancy. We found a significant over fourfold increase in pRab10<sup>Thr73</sup> phosphorylation in carriers of the LRRK2 R1441G mutation irrespective of clinical disease status. The effect of the LRRK2 G2019S mutation did not reach statistical significance. Furthermore, we show that LRRK2 phosphorylation at Serine 935 is not a marker for LRRK2 kinase activity in human neutrophils. When analysing pRab10<sup>Thr73</sup> phosphorylation in post-mortem brain samples, we observed overall high variability irrespective of clinical and LRRK2 mutation status and attributed this mainly to the adverse effect of the peri- and post-mortem period on the stability of posttranslational modifications such as protein phosphorylation. Overall, in vivo LRRK2 dependent pRab10<sup>Thr73</sup> phosphorylation in human peripheral blood neutrophils is a specific, robust and promising biomarker for significant LRRK2 kinase hyperactivation, as with the LRRK2 R1441G mutation. Additional readouts and/or assays may be needed to increase sensitivity to detect modest LRRK2 kinase activation, as with the LRRK2 G2019S mutation. Our assays could be useful for patient stratification and target engagement studies for LRRK2 kinase inhibitors.