gebhart/patrepeval huggingface dataset:
Renal cortical albumin gene induction and urinary albumin excretion in response to acute kidney injury (2010)

This study evaluated the potential utility of albuminuria as a "biomarker" of acute kidney injury (AKI) and tested whether AKI induces renal expression of the normally silent albumin gene. Urine albumin concentrations were measured in mice with five different AKI models (maleate, ischemia-reperfusion, rhabdomyolysis, endotoxemia, ureteral obstruction). Albumin gene induction in renal cortex, and in antimycin A-injured cultured proximal tubular cells, was assessed (mRNA levels; RNA polymerase II binding to the albumin gene). Albumin's clinical performance as an AKI biomarker was also tested (29 APACHE II-matched intensive care unit patients with and without AKI). Results were contrasted to those obtained for neutrophil gelatinase-associated lipocalin (NGAL), an established "AKI biomarker" gene. The experimental and clinical assessments indicated albumin's equivalence to NGAL as an AKI biomarker (greater specificity in experimental AKI; slightly better receiver-operating curve in humans). Furthermore, experimental AKI markedly induced the albumin gene (mRNA/RNA polymerase II binding increases; comparable to those seen for NGAL). Albumin gene activation in patients with AKI was suggested by fivefold increases in RNA polymerase II binding to urinary fragments of the albumin gene (vs. AKI controls). Experimental AKI also increased renal cortical mRNA levels for α-fetoprotein (albumin's embryonic equivalent). A correlate in patients was increased urinary α-fetoprotein excretion. We conclude that AKI can unmask, in the kidney, the normally silent renal albumin and α-fetoprotein genes. In addition, the urinary protein data independently indicate that albuminuria, and perhaps α-fetoprotein, have substantial utility as biomarkers of acute tubular injury.
Enzyme-Capped Relay-Functionalized Mesoporous Carbon Nanoparticles: Effective Bioelectrocatalytic Matrices for Sensing and Biofuel Cell Applications (2013)

The porous high surface area and conducting properties of mesoporous carbon nanoparticles, CNPs (<500 nm diameter of NPs, pore dimensions ∼6.3 nm), are implemented to design electrically contacted enzyme electrodes for biosensing and biofuel cell applications. The relay units ferrocene methanol, Fc-MeOH, methylene blue, MB(+), and 2,2'-azinobis(3-ethylbenzothiazoline-6-sulfonic acid), ABTS(2-), are loaded in the pores of the mesoporous CNPs, and the pores are capped with glucose oxidase, GOx, horseradish peroxidase, HRP, or bilirubin oxidase, BOD, respectively. The resulting relay/enzyme-functionalized CNPs are immobilized on glassy carbon electrodes, and the relays encapsulated in the pores are sufficiently free to electrically contact the different enzymes with the bulk electrode supports. The Fc-MeOH/GOx CNP-functionalized electrode is implemented for the bioelectrocatalyzed sensing of glucose, and the MB(+)/HRP-modified CNPs are applied for the electrochemical sensing of H2O2. The ABTS(2-)/BOD-modified CNPs provide an effective electrically contacted material for the bioelectrocatalyzed reduction of O2 (kcat = 94 electrons·s(-1)). Integration of the Fc-MeOH/GOx CNP electrode and of the electrically wired ABTS(2-)/BOD CNP electrode as anode and cathode, respectively, yields a biofuel cell revealing a power output of ∼95 μW·cm(-2).
Supplementary Methods from Serial ctDNA Monitoring to Predict Response to Systemic Therapy in Metastatic Gastrointestinal Cancers (2023)

&lt;p&gt;Supplementary Methods&lt;/p&gt;
Myositis Ossificans Circumscripta of the Sacrotuberous Ligament: A Case Report and Review of the Literature (2002)

Soft tissue ossification is a well-known phenomenon in various pathologic conditions. Myositis ossificans circumscripta refers to posttraumatic calcification of soft tissue, including various ligaments. However, posttraumatic calcification of ligaments in the pelvis is a rare complication described only anecdotally in the past. We present a rare case of posttraumatic calcification of the sacrotuberous ligament in a patient, several months after suffering a pelvic trauma. This is one of the differential diagnoses of soft tissue pain and tenderness after trauma.
A Phase I Study of CUDC-101, a Multitarget Inhibitor of HDACs, EGFR, and HER2, in Combination with Chemoradiation in Patients with Head and Neck Squamous Cell Carcinoma (2015)

CUDC-101, cisplatin, and radiation were feasible in intermediate-/high-risk patients with HNSCC, with no unexpected patterns of AE. Although the MTD was identified, a high rate of DLT-independent discontinuation of CUDC-101 suggests a need for alternate schedules or routes of administration.
Synthesis and Characterization of a Fullerene Bearing a Triazole Group (2007)

A soluble fullerene, TAZC60, bearing an electron transport moiety (triazole) is synthesized and characterized. TAZC60 possesses a band gap of 2.2 eV, and HOMO and LUMO energy levels of 5.9 and 3.7 eV, respectively. Thin films of TAZC60 exhibit an electron mobility of 2.2 × 10-8 m2/V s, as determined from the current−voltage characteristics that fit with a space-charge limited current (SCLC). These properties are similar to those of [6,6]-phenyl C61 butyric acid methyl ester, PCBM, a soluble fullerene widely used in organic photovoltaics. The strategy of modifying fullerenes with a solublizing electron transport moiety may open avenues for the design of more specific polymers for controlling the morphology and transport properties of polymer-fullerene blends for polymer solar cells.
Development of Built-In Type and Noninvasive Sensor Systems for Smart Artificial Heart (2003)

It is very important to grasp the artificial heart condition and the physiologic conditions for the implantable artificial heart. In our laboratory, a smart artificial heart (SAH) has been proposed and developed. An SAH is an artificial heart with a noninvasive sensor; it is a sensorized and intelligent artificial heart for safe and effective treatment. In this study, the following sensor systems for SAH are described: noninvasive blood temperature sensor system, noninvasive blood pressure sensor system, and noninvasive small blood flow sensor system. These noninvasive sensor systems are integrated and included around the artificial heart to evaluate these sensor systems for SAH by the mockup experiments and the animal experiments. The blood temperature could be measured stably by the temperature sensor system. Aortic pressure was estimated, and sucking condition was detected by the pressure sensor system. The blood flow was measured by the flow meter system within 10% error. As a result of these experiments, we confirmed the effectiveness of the sensor systems for SAH.
Low temperature radical initiated hydrosilylation of silicon quantum dots (2020)

The photophysics of silicon quantum dots (QDs) is not well understood despite their potential for many optoelectronic applications. One of the barriers to the study and widespread adoption of Si QDs is the difficulty in functionalizing their surface, to make, for example, a solution-processable electronically-active colloid. While thermal hydrosilylation of Si QDs is widely used, the high temperature typically needed may trigger undesirable side-effects, like uncontrolled polymerization of the terminal alkene. In this contribution, we show that this high-temperature method for installing aromatic and aliphatic ligands on non-thermal plasma-synthesized Si QDs can be replaced with a low-temperature, radical-initiated hydrosilylation method. Materials prepared via this low-temperature route perform similarly to those created via high-temperature thermal hydrosilylation when used in triplet fusion photon upconversion systems, suggesting the utility of low-temperature, radical-initiated methods for creating Si QDs with a range of functional behavior.
Addition reactions of pendant epoxide group in poly(glycidyl methacrylate) with various active esters (1986)

Abstract Addition reactions of pendant epoxide groups in poly(glycidyl methacrylate) (PGMA) with various active esters such as 1‐benzotriazolyl benzoate, S‐(2‐benzoxazolyl) thiobenzoate, S‐(2‐benzothiazolyl) thiobenzoate, 4‐nitrophenyl benzoate (4NPB), and S‐phenyl thiobenzoate (PTB) were carried out using quaternary salts as catalysts. The reactions of PGMA with those active esters proceeded in diglyme at 100°C for 24 h quantitatively without the formation of 2‐hydroxyl pendant groups in the polymer when 10 mol % of tetraethylammonium bromide was used as a catalyst. Furthermore, it was found that the respective quaternary salts have higher catalytic activity than tertiary amines in the reaction of PGMA with the active esters, and the reaction of PGMA with 4NPB gave the corresponding polymer with the highest conversion by addition of tetrabutylammonium bromide as a catalyst, while tetraethylammonium chloride showed the highest activity for the reaction of PGMA with PTB. In addition, the rate of reaction of PGMA with 4NPB was proportional to third order kinetics of the epoxide concentration, the ester concentration and the catalyst concentration as follows: − d [Epoxide]/ dt = −[Ester]/ dt = k 3 [Epoxide] [Ester] [Catalyst].
Antiparasitic Activity of Some Xanthones and Biflavonoids from the Root Bark of <i>Garcinia livingstonei</i> (2006)

A new biflavanoid, ent-naringeninyl-(I-3alpha,II-8)-4'-O-methylnaringenin (6), along with five known xanthones and two known biflavonoids, was isolated from the root bark of Garcinia livingstonei collected in Tanzania. The absolute configuration of 6 was established by CD spectroscopy. This compound showed moderate activity against P. falciparum (IC(50) 6.7 microM). Antitrypanosomal activity (IC(50) 0.87 microM) was observed for 1,4,5-trihydroxy-3-(3-methylbut-2-enyl)-9H-xanthen-9-one (3). The dimeric xanthone garcilivin A (4) showed a higher and nonselective antiparasitic activity and cytotoxicity (IC(50) 2.0 microM against MRC-5 cells) than its diastereoisomer garcilivin C (5) (IC(50) 52.3 microM).
Dissecting the contributions of tumor heterogeneity on metastasis at single-cell resolution (2022)

Metastasis is the leading cause of cancer-related deaths, but metastasis research is challenged by limited access to patient material and a lack of experimental models that appropriately recapitulate tumor heterogeneity. Here, we analyzed single-cell transcriptomes of matched primary tumor and metastasis from patient-derived xenograft models of breast cancer, demonstrating that primary tumor and metastatic cells show profound transcriptional differences across heterogeneous tumors. While primary tumor cells upregulated several metabolic genes, metastatic cells displayed a motility phenotype in micrometastatic lesions and increased stress response signaling during metastatic progression. Additionally, we identified gene signatures that are associated with the metastatic potential and correlated with patient outcomes. Poorly metastatic primary tumors showed increased immune-regulatory control that may prevent metastasis, whereas highly metastatic primary tumors upregulated markers of epithelial-mesenchymal transition (EMT). We found that intra-tumor heterogeneity is dominated by epithelial-mesenchymal plasticity (EMP) which presented as a dynamic continuum with intermediate cell states that were characterized by novel, specific markers. These intermediate EMP markers correlated with worse patient outcomes and could serve as potential new therapeutic targets to block metastatic development.
Fabrication and Ions Irradiation Study of AlN:Gd Thin Films (2022)

Thin films of Aluminum Nitride (AlN) doped with Gadolinium (Gd) are deposited on Si (111) substrates, in pure Nitrogen (N) atmosphere using reactive magnetron sputtering technique at room temperature. The as-deposited thin films are irradiated by protons carrying 335 keV energy with a fluence of 1 × 10 14 ions cm −2 . Rutherford Backscattering Spectroscopy (RBS) is carried out using a 2 MeV He ++ beam to understand the stoichiometric and dimensional features of the films. Modifications in the structural, electronic, optical, and electrical properties are investigated prior to and after the irradiation using X-ray diffraction (XRD), Fourier transforms, infrared spectroscopy (FTIR), diffuse reflectance spectroscopy (DRS), and four-probe point method. Stopping power and range of ions in matters (SRIM) is used to study the non-ionizing energy loss (NIEL) and Frenkel defect density/vacancies in AlN, caused by irradiation. Proton irradiation-induced changes in the structure and enhancement in the optical and electrical characteristics of the films make AlN:Gd a good candidate for advanced electronics and optical technology.
Local Bubble Dilation Functions: Hypersphere-bounded Landscape Deformations Simplify Global Optimization (2022)

Solving optimization problems is one of the most complex and widespread task in Computer Science. In many scenarios, finding the global optimum of a function is hampered by several features that characterize the fitness landscapes, such as noisiness, multi-modality, non-convexity, non-separability, and non-differentiability. In order to facilitate the optimization process, a variety of methods have been proposed to manipulate either the search space or the fitness landscape. Among these, Dilation Functions (DFs) were introduced to expand regions of the search space that are characterized by promising fitness values. In this work, we extend the family of DFs by introducing Local Bubble Dilation Functions (LBDFs), a novel approach that generates local distortions bounded by hyper-spheres. By performing an appropriate mapping of the search space, LBDFs can improve the optimization performance, since they expand and reveal the promising regions around the global optimum, while leaving the rest of the fitness landscape untouched. The additional advantage of LBDFs, with respect to DFs, is that different dilations can be applied to each dimension of the search space, which is useful in the case of asymmetric landscapes. In order to show the benefits of local dilations, we executed several tests on the Michalewicz benchmark function, with different settings for the LBDFs. Our results show that a properly designed LBDF can lead to statistically significant better results than using vanilla optimization. Finally, we investigated the use of LBDFs to facilitate the solution of the parameter estimation problem in Systems Biology by analyzing the landscape related to a stochastic model of enzyme kinetics.
Dual Subcellular Localization in the Endoplasmic Reticulum and Peroxisomes and a Vital Role in Protecting against Oxidative Stress of Fatty Aldehyde Dehydrogenase Are Achieved by Alternative Splicing (2007)

Fatty aldehyde dehydrogenase (FALDH, ALDH3A2) is thought to be involved in the degradation of phytanic acid, a saturated branched chain fatty acid derived from chlorophyll. However, the identity, subcellular distribution, and physiological roles of FALDH are unclear because several variants produced by alternative splicing are present in varying amounts at different subcellular locations. Subcellular fractionation experiments do not provide a clear-cut conclusion because of the incomplete separation of organelles. We established human cell lines heterologously expressing mouse FALDH from each cDNA without tagging under the control of an inducible promoter and detected the variant FALDH proteins using a mouse FALDH-specific antibody. One variant, FALDH-V, was exclusively detected in peroxisomal membranes. Human FALDH-V with an amino-terminal Myc sequence also localized to peroxisomes. The most dominant form, FALDH-N, and other variants examined, however, were distributed in the endoplasmic reticulum. A gas chromatography-mass spectrometry-based analysis of metabolites in FALDH-expressing cells incubated with phytol or phytanic acid showed that FALDH-V, not FALDH-N, is the key aldehyde dehydrogenase in the degradation pathway and that it protects peroxisomes from oxidative stress. In contrast, both FALDHs had a protective effect against oxidative stress induced by a model aldehyde for lipid peroxidation, dodecanal. These results suggest that FALDH variants are produced by alternative splicing and share an important role in protecting against oxidative stress in an organelle-specific manner.
Homing by parameterized scene matching (1997)

In visual homing tasks, animals as well as robots can compute their movements from the current view and a snapshot taken at a home position. Solving this problem exactly would require knowledge about the distances to visible landmarks, information, which is not directly available to passive vision systems. We propose a homing scheme that dispenses with accurate distance information by using parameterized disparity fields. These are obtained from an approximation that incorporates prior knowledge about perspective distortions of the visual environment. A mathematical analysis proves that the approximation does not prevent the scheme from approaching the goal with arbitrary accuracy. Mobile robot experiments are used to demonstrate the practical feasibility of the approach. 1 Introduction For many animal species it is vital to be able to find their way back to a shelter or to a rewarding food source. In particular, flying animals cannot rely on idiothetic information for this task, as ...
Current Perspectives on Circulating Tumor DNA, Precision Medicine, and Personalized Clinical Management of Cancer (2020)

Circulating tumor DNA (ctDNA) has recently emerged as a minimally invasive "liquid biopsy" tool in precision medicine. ctDNA-genomic DNA fragments that are released into the bloodstream after the active secretion of microvesicles or tumor cell lysis reflects tumor evolution and the genomic alterations present in primary and/or metastatic tumors. Notably, ctDNA analysis might allow the stratification of patients, the monitoring of the therapeutic response, and the establishment of an opportunity for early intervention independent of detection by imaging modalities or clinical symptoms. As oncology moves towards precision medicine, the information in ctDNA provides a means for the individual management of the patient based on their tumor's genetic profile. This review presents current evidence on the potential role for ctDNA in helping to guide individualized clinical treatment decisions for patients with melanoma, castration-resistant prostate cancer, breast cancer, metastatic colorectal cancer, and non-small cell lung cancer.
Automated Drive Analysis of Naturalistic Driving Studies with Looking-out Video (2014)

Presented at the Fourth International Symposium on Naturalistic Driving Research in Blacksburg, VA
Operator Awareness in Human–Robot Collaboration Through Wearable Vibrotactile Feedback (2018)

In industrial scenarios, requiring human-robot collaboration, the understanding between the human operator and his/her robot coworker is paramount. On the one side, the robot has to detect human intentions, and on the other side, the human needs to be aware of what is happening during the collaborative task. In this letter, we address the first issue by predicting human behavior through a new recursive Bayesian classifier, exploiting head, and hand tracking data. Human awareness is tackled by endowing the human with a vibrotactile ring that sends acknowledgments to the user during critical phases of the collaborative task. The proposed solution has been assessed in a human-robot collaboration scenario, and we found that adding haptic feedback is particularly helpful to improve the performance when the human-robot cooperation task is performed by nonskilled subjects. We believe that predicting operator's intention and equipping him/her with wearable interface, able to give information about the prediction reliability, are essential features to improve performance in a human-robot collaboration in industrial environments.
Hemorrhage, Disseminated Intravascular Coagulopathy, and Thrombosis Complications Among Critically Ill Patients with COVID-19: An International COVID-19 Critical Care Consortium Study* (2023)

HECTOR events are frequent complications of severe COVID-19 in ICU patients. Patients receiving ECMO are at particular risk of hemorrhagic complications. Hemorrhagic, but not thrombotic complications, are associated with increased ICU mortality.
Bortezomib prior to autologous transplant in multiple myeloma: Effects on mobilization, engraftment, and markers of immune function (2006)

To explore the potential role of bortezomib (VELCADE®) in the frontline treatment of multiple myeloma, we conducted a study of bortezomib administered prior to autologous transplant. The primary objective was to determine the effects of bortezomib on cytokine based mobilization and engraftment. Given the critical role NF-κB in lymphocyte development and survival, we also sought to determine the effects of bortezomib on markers of immune function. Following induction, two cycles of bortezomib 1.3 mg/m2 were administered on days 1, 4, 8, and 11 of a 21-day treatment cycle. Peripheral blood stem cells were mobilized with G-CSF 10 mcg/kg/day for 5 days and harvested by large volume apheresis (20 L/day) until a minimum of 2.5 × 106 CD34+ cells/kg were collected. High-dose melphalan 200 mg/m2 was administered followed by autologous stem cell transplant with GM-CSF 250 mcg/m2/day support until neutrophil engraftment. Peripheral blood was collected at baseline (cycle 1, day 1) and after treatment with bortezomib (cycle 2, day 18) for analysis of lymphocyte subsets and serum cytokines. Forty patients were enrolled with 37 continuing on to autologous transplant. Prior to receiving bortezomib, 20 patients had been previously treated with an anthracycline, 22 with thalidomide, and two patients had no induction therapy. Stem cell collection was successful in 37 of 38 patients (97%) with the median first collection of 4.24 × 106 CD34+cells/kg. Following transplant, all patients engrafted with a median time to neutrophil engraftment (ANC ⩾ 500/mm3) of 11 days (range 9-14 days) and platelet engraftment (platelet count ⩾ 20,000/mm3) of 11 days (range 9-31 days). In an intention-to-treat analysis at 100 days post-transplant, we observed a CR in 6 patients (15%), a near CR in 10 patients (25%) and a PR in an additional 19 patients (48%) for an overall response rate of 88%. Following treatment with bortezomib, we observed a 38% decrease in CD56+ NK cells (P = .02) and a 26% increase in CD4/CD8 ratio (P = .0006) with a 18% decrease in CD8+ cytotoxic T-cells (P = .054). No significant changes were detected in either Th1 or Th2 serum cytokine levels: IL-2 (P = .116), TNF-alpha (P = .854), IFN-γ (P = .070), IL-4 (P = .240), IL-6 (0.236), IL-10 (0.151). We conclude that pretransplant bortezomib does not adversely impair stem cell mobilization or engraftment. Bortezomib also decreases NK and cytotoxic T cell subsets without measurable change in serum Th1 and Th2 cytokines.
A Review of Epilepsy Diagnosis Using PET Parameters (2012)

Epilepsy is caused by abnormal excessive electric discharges from the neurons in the brain. Epileptic seizures are non- specific responses of the brain to many types of insults. The structural abnormalities causing epilepsy can be identified using various state of art imaging methods. Through a combination of brain activity monitoring, imaging and mapping techniques, physicians can locate the specific area in the brain causing epileptic discharges and identify its location in relation to those areas in the brain controlling vital functions. Positron Emission Tomography (PET) has emerged as a useful tool to identify abnormal metabolic activity of the epileptogenic foci. Parameters like asymmetric index, stan- dard uptake value (SUV) etc obtained by PET are processed and analyzed for identifying the origin of epileptic sei- zures. This paper discuss the techniques used to diagnose in general and to localize the epileptogenic regions using post-processing other features on PET imaging.