gebhart/patrepeval huggingface dataset:
Adverse Events in Adults with Relapsed or Refractory Acute Lymphoblastic Leukemia (ALL): A Literature Review of Recent Clinical Trials (2016)

Background: With the introduction of new therapy options for adult patients with relapsed or refractory (R/R) acute lymphoblastic leukemia (ALL), a better understanding of existing toxicity profiles is needed. Methods: A systematic literature review was conducted to summarize the toxicity profiles in clinical trials using chemotherapeutic regimens, tyrosine kinase inhibitor (TKI)-based approaches in Philadelphia chromosome-positive (Ph+) and Philadelphia chromosome-negative (Ph-) R/R ALL, or other targeted therapies. Seventeen eligible articles were identified that reported toxicity profiles. We grouped adverse events into the following categories: hematological, infectious, gastrointestinal, cardiovascular/renal/hepatic, and neurological, stratified by treatment type. Treatment-related or early/induction mortality was also summarized. Results: With cytotoxic chemotherapy and its combinations, hematological adverse events were the most common, affecting virtually all patients, followed by infections, which were reported in most patients. Neurologic toxicity was the most common adverse event associated with liposomal vincristine. TKI-based treatments showed a distinct safety profile compared with the chemotherapies. Although hematological adverse events still represented the most common toxicity, infections were less common with TKI-based therapies (9-18%) than with chemotherapies (56-100%). Nausea, vomiting, and diarrhea were the predominant gastrointestinal adverse events after receipt of TKIs, whereas mucositis appeared to be more characteristic of cytotoxic chemotherapy. Conclusions: This paper provides a systematic review of the safety profile of current standard chemotherapy for adults with R/R Ph- or Ph+ ALL. Overall, documentation of adverse events was highly variable across the studies, precluding direct comparisons or pooling of results. However, this systematic literature review is the first to summarize and quantify the toxicity profiles of mainly chemotherapeutic and TKI-based regimens for adult patients with R/R ALL, providing a baseline for comparison with emerging therapies.
Ordering kinetics of a chemisorbed overlayer: O/W(110) (1989)

The ordering kinetics of an oxygen submonolayer on W(110) is investigated at several coverages and temperatures using low-energy electron diffraction. Coverages correspond to ordering in a single-phase region and two different two-phase coexistence regions. The growth follows a power law at early times at each coverage. Dynamic scaling of the growth is investigated at two coverages. It is shown that from the activation energy for the ordering process, an activation energy for non- equilibrium diffusion can be determined. The values are compared to those for equilibrium diffusion.
Data streaming algorithms for accurate and efficient measurement of traffic and flow matrices (2005)

The traffic volume between origin/destination (OD) pairs in a network, known as traffic matrix, is essential for efficient network provisioning and traffic engineering. Existing approaches of estimating the traffic matrix, based on statistical inference and/or packet sampling, usually cannot achieve very high estimation accuracy. In this work, we take a brand new approach in attacking this problem. We propose a novel data streaming algorithm that can process traffic stream at very high speed (e.g., 40 Gbps) and produce traffic digests that are orders of magnitude smaller than the traffic stream. By correlating the digests collected at any OD pair using Bayesian statistics, the volume of traffic flowing between the OD pair can be accurately determined. We also establish principles and techniques for optimally combining this streaming method with sampling, when sampling is necessary due to stringent resource constraints. In addition, we propose another data streaming algorithm that estimates flow matrix , a finer-grained characterization than traffic matrix. Flow matrix is concerned with not only the total traffic between an OD pair (traffic matrix), but also how it splits into flows of various sizes. Through rigorous theoretical analysis and extensive synthetic experiments on real Internet traffic, we demonstrate that these two algorithms can produce very accurate estimation of traffic matrix and flow matrix respectively.
Coating Carboxylic Acids on Amorphous Iron Nanoparticles (1999)

Nanophased amorphous iron particles were coated by various carboxylic acids and their physical properties (differential scanning calorimetry, thermogravimetric analysis, temperature-programmed desorption, Fourier transform infrared spectroscopy, X-ray photoelectron spectroscopy, and magnetism) were measured. The various properties were measured as a function of the alkyl chain length. The desorption pattern at 400 °C revealed a keto derivative.
Performance of Gadoxetic Acid–Enhanced Liver Magnetic Resonance Imaging for Predicting Patient Eligibility for Liver Transplantation Based on the Milan Criteria (2016)

Gd-EOB-MRI showed high specificity but poor sensitivity for assessing transplant eligibility based on MC when adopting the conventional radiological hallmarks of HCC. Our modified criteria showed significantly better sensitivity and accuracy than the conventional radiological hallmarks.
Abstract PR07: Calorie restriction normalizes global microRNA expression by preventing the loss of Dicer expression during mammary tumorigenesis (2015)

Abstract MicroRNA (miRNAs) are small, post-transcriptional regulators that play an integral role in maintenance of cellular functions and whose dyregulation has been shown to promote many types of cancer, including breast cancer. Global downregulation of miRNAs has emerged as a common theme in human breast tumors and has been shown to contribute to oncogenesis. One of the primary mechanisms through which miRNAs are globally dysregulated is downregulation of enzymes involved in miRNA biogenesis. We aim to establish how calorie restriction (CR), which potently inhibits breast cancer progression, regulates global miRNA expression and miRNA biogenesis enzyme functionality in mammary tumors. To address these questions, 100 female Sprague Dawley rats were administered either dimethylbenz(a)anthracene (DMBA) or vehicle control at 50 days of age, then randomized to receive either control (AIN-76A) diet ad-libitum (n=40) or a 30% CR diet regiment (n=60). Resultant mammary tumors were allowed to develop for 12 weeks. Calorie restriction significantly increased survival to study endpoint relative to control diet (75% vs 35%, respectively) (p=0.0047). Furthermore, of the animals that developed tumors, CR significantly decreased median tumor area by 56% compared to control diet (109.4 mm2 vs 250.9 mm2, respectively) (p=0.0286). Global miRNA expression was analyzed through miRNA-specific sequencing. Calorie restriction had a broad effect on miRNA expression, illustrated by the fact that of all the miRNAs with a greater than two-fold expression difference between CR and control, 80% are overexpressed in CR tumors compared to control tumors. These results can be explained by the additional finding that CR was able to prevent the loss of Dicer expression, a key miRNA biogenesis enzyme, observed in control-fed mammary tumor tissue compared to normal tissue. This important finding suggests that global miRNA normalization through the retention of Dicer expression during cancer progression could be a contributing mechanism to CR's anticancer effects. We plan to further these investigations by exogenously manipulating Dicer expression in Rama25 cells, which were originally derived from a DMBA-induced mammary tumor from a Sprague Dawley rat, and analyzing the resultant tumorigenic potential in vitro and in vivo. The results obtained will provide insights into the mechanisms of breast cancer progression and how CR inhibits progression through microRNA modulation. Citation Format: Kaylyn L. Devlin, Tiffany Sanford, Elizabeth Mambo, Stephen D. Hursting. Calorie restriction normalizes global microRNA expression by preventing the loss of Dicer expression during mammary tumorigenesis. [abstract]. In: Proceedings of the Thirteenth Annual AACR International Conference on Frontiers in Cancer Prevention Research; 2014 Sep 27-Oct 1; New Orleans, LA. Philadelphia (PA): AACR; Can Prev Res 2015;8(10 Suppl): Abstract nr PR07.
Inflammatory bowel disease and colon cancer (1992)

Patients who have had extensive colitis for more than 10 years are at increased risk for colorectal cancer. The risk may be greatest for those whose onset of illness is in childhood. Management options for patients at increased risk include prophylactic colectomy or endoscopic surveillance. The object of surveillance is prevention of cancer by detecting premalignant lesions that predispose to cancer. A less desirable objective is the diagnosis of cancer at an early curable stage. Patients must be well informed about their risk for cancer, the limitations of endoscopic surveillance, and the availability of surgical alternatives. Current endoscopic and pathologic techniques focus on the detection of dysplasia, but newer biomarkers may offer greater sensitivity and specificity in the future.
Constructing indices from citations in collections of research papers (1999)

We describe Rosetta, an indexing and retrieval system for collections of research papers. Rosetta indexes papers in a collection based on the way they have been described when referenced by other papers in the collection. With this technique, indices for papers describe information provided in the same way a query describes information needed. Using Rosetta, simple natural language queries retrieve high-precision results in which descriptions based on citations clearly summarize retrieved papers; allowing users to quickly determine which papers most closely meet their information needs. Introduction In the past few years the volume of on-line information has exploded. As a result, millions of people use information retrieval systems every day. Unfortunately, far too many either do not nd the information they are looking for or are forced to work too hard to nd it (Spink, Bateman, &amp;amp; Jansen 1998). The problem here is that users are unfamiliar with Information Retrieval (IR) technology...
Design Considerations and Fabrication Challenges of Surface Electrode Ion Trap with TSV Integration (2019)

Surface electrode ion trap with through-silicon-via (TSV) integration enables 3D stacking of ion trap chip on an interposer to eliminate the wire-bonds on the surface electrodes and also addresses the challenge of the ever increasing complexity of surface electrode design with low-parasitic and high-density interconnect requirements. In this work, we demonstrate the design and fabrication of TSV integrated surface electrode ion trap on a 300-mm Si wafer platform. By designing the TSV arrays directly underneath the surface electrodes, the surface electrode foot print is reduced and the TSV traps show better RF performance compared to the planar traps with wire-bonding pads.
915. Global 2018 Surveillance of Eravacycline Against Gram-positive Pathogens, Including Resistant Isolates (2020)

Abstract Background Eravacycline (ERV) is a fully-synthetic, fluorocycline antibacterial approved by the FDA and EMA for the treatment of complicated intra-abdominal infections (cIAI) in patients ≥18 years of age. The purpose of this study was to further monitor the in vitro activity of ERV against Gram-positive pathogens, such as Staphylococcus aureus (including methicillin-resistant S. aureus, MRSA), Enterococcus spp. (including vancomycin-resistant Enterococcus, VRE) and Streptococcus spp. Methods Isolates were collected globally during 2018 from various body sites. Minimum inhibitory concentrations (MICs) were determined by CLSI broth microdilution. Antibiotic susceptibility was determined using the most recent CLSI breakpoints (30th ed CLSI M100 document), except for ERV and tigecycline (TGC) where FDA breakpoints from 2018 and 2005, respectively, were applied. Results Summary MIC data for ERV and select comparators are shown in the Table. ERV MIC50/90 for Enterococcus spp were 0.06/0.12 μg/mL and were not affected by the presence of vancomycin resistant mechanisms. The MIC90 of ERV against VRE was 2-fold lower than TGC, at a value of 0.12 μg/mL. ERV MIC90 values for methicillin-susceptible S. aureus (MSSA) was 0.12 μg/mL and for MRSA was 0.25 μg/mL. Generally, for all pathogens, ERV MIC90 values were 2- to 4-fold lower than TGC. Table Conclusion ERV in vitro activity was demonstrated for clinically important Gram-positive pathogens, including resistant isolates. Overall, ERV demonstrated lower MIC90 values than comparators for all organisms. This 2018 global surveillance highlights ERV’s utility against Gram-positive organisms and further underscores its role in cIAI, where these pathogens play a causative role. Disclosures Steven Morgan, PharMD, Tetraphase Pharmaceuticals (Employee) Sara Hwang, PharMD, Tetraphase Pharmaceuticals (Employee) Ekaterina Efimova, PharMD, Tetraphase Pharmaceuticals (Employee) Stephen Hawser, PhD, Tetraphase Pharmaceuticals (Scientific Research Study Investigator) Virgil Lijfrock, PharMD, Tetraphase (Employee)
Histidine Production by Coiynebacterium glutamaicum Mutants, Multiresistant to Analogs of Histidine, Tryptophan, Purine and Pyrimidine (1974)

The histidine productivity of 1, 2, 4-triazole-3-alanine (TRA)-resistant histidine producer, Corynebacterium glutmnicum KY-10260 was improved by successive additions of such markers as purine, pyrimidine, histidine and tryptophan analog-resistance to the mutant. A selected mutant AT-83, multi-resistant to 6-mercaptoguanine, 8-azaguanine, 4-thiouracil, 6-methylpurine, TRA and 5-methyltryptophan, accumulated twice as much histidine as KY-10260 in the culture medium. The level of histidine production by this mutant reached 15mg/ml or 10% (w/w) of the initial suagr in the medium containing 6% (as glucose concentration) cane molasses and 9% sucrose as carbon sources. 2-Fluoroadenine-resistant mutants produced adenine in addition to histidine.
Conditional Targeting of the DNA Repair Enzyme hOGG1 into Mitochondria (2002)

Oxidative damage to mitochondrial DNA (mtDNA) has been suggested to be a key factor in the etiologies of many diseases and in the normal process of aging. Although the presence of a repair system to remove this damage has been demonstrated, the mechanisms involved in this repair have not been well defined. In an effort to better understand the physiological role of recombinant 8-oxoguanine DNA glycosylase/apurinic lyase (OGG1) in mtDNA repair, we constructed an expression vector containing the gene for OGG1 downstream of the mitochondrial localization sequence from manganese-superoxide dismutase. This gene construct was placed under the control of a tetracycline-regulated promoter. Transfected cells that conditionally expressed OGG1 in the absence of the tetracycline analogue doxycycline and targeted this recombinant protein to mitochondria were generated. Western blots of mitochondrial extracts from vector- and OGG1-transfected clones with and without doxycycline revealed that removal of doxycycline for 4 days caused an approximate 8-fold increase in the amount of OGG1 protein in mitochondria. Enzyme activity assays and DNA repair studies showed that the doxycycline-dependent recombinant OGG1 is functional. Functional studies revealed that cells containing recombinant OGG1 were more proficient at repairing oxidative damage in their mtDNA, and this increased repair led to increased cellular survival following oxidative stress.
Use of Phosphatidylcholine in the Treatment of Localized Fat Deposits. Results and expectations (2017)

Obesity represents a global health problem. According to the latest studies released by the World Health Organisation (WHO), 1.7 billion currently in excess of normal weight individuals, of which approx. 75% are overweight (body mass index - BMI 25 to 30). The common form of excess adipose tissue manifestation in overweight individuals is localized fat deposits with high (abdominal) or low (buttocks and thighs) disposition. Although the overweight can be corrected relatively easy by changing behavioral habits or food, a constant physical exercises program or following a diet food are not accessible to all through the efforts of will, financial and time involved. Several methods have been studied and tested over time to eliminate more or less invasive fat deposits with varying efficacy and adverse effects. Chemical lipolysis using phosphatidylcholine as the basic substance was initially used in hypercholesterolemia and its complications and was rapidly adopted in mesotherapy techniques for the treatment of fat deposits. This study reveals the results obtained using Dermastabilon on a sample of 16 patients, the time allocated to treatment and discomfort being minimal, and rapid and notable results. There were no side effects.
An enhanced WiFi indoor localization system based on machine learning (2016)

The Global Navigation Satellite Systems (GNSS) suffer from accuracy deterioration and outages in dense urban canyons and are almost unavailable for indoor environments. Nowadays, developing indoor positioning systems has become an attractive research topic due to the increasing demands on ubiquitous positioning. WiFi technology has been studied for many years to provide indoor positioning services. The WiFi indoor localization systems based on machine learning approach are widely used in the literature. These systems attempt to find the perfect match between the user fingerprint and pre-defined set of grid points on the radio map. However, Fingerprints are duplicated from available Access Points (APs) and interference, which increase number of matched patterns with the user's fingerprint. In this research, the Principle Component Analysis (PCA) is utilized to improve the performance and to reduce the computation cost of the WiFi indoor localization systems based on machine learning approach. All proposed methods were developed and physically realized on Android-based smart phone using the IEEE 802.11 WLANs. The experimental setup was conducted in a real indoor environment in both static and dynamic modes. The performance of the proposed method was tested using K-Nearest Neighbors, Decision Tree, Random Forest and Support Vector Machine classifiers. The results show that the performance of the proposed method outperforms other indoor localization reported in the literature. The computation time was reduced by 70% when using Random Forest classifier in the static mode and by 33% when using KNN in the dynamic mode.
Simulations of large enhancement of light out-coupling from periodically corrugated OLEDs (Conference Presentation) (2019)

Poor light extraction efficiency from OLEDs is among the leading problems facing the science and commercialization of OLEDs. The light outcoupling ~1/2n2, where n is the refractive index of the organic emitting layer, and is only 17-20% for planar OLEDs. The remaining light is waveguided in the organic +ITO layers (>30%), waveguided in the substrate, or lost to plasmonic excitation in the cathode that can be very severe (>40%) for thin ETLs. To enhance outcoupling we investigate the light emission from periodically corrugated OLEDs where the OLED stack is grown conformally on a periodic textured substrate [1]. The corrugation diffracts wave-guided modes to the air cone, thereby increasing outcoupling, but no simulations have predicted enhancements or optimal corrugations. We utilize rigorous scattering matrix simulations solving Maxwell’s equations in Fourier space, for all polarizations. We find the corrugated OLEDS display a remarkable light outcoupling of 60-70%, approaching the targeted value of 70% in the solid-state lighting road-map. We find optimal corrugation pitch of 0.75-3 microns with only a small roll off for larger pitch. The optimal corrugation heights exceed 150 nm. There is a marked decrease in plasmonic losses. Corrugations induce strong diffraction of light into the air cone. We also find that adding a microlens on the air-substrate interface can increase by a further ~5-10%. We compare simulations with experimental results [1].Supported by DOE-EERE [1] C. Hippola et al, Adv. Optical Materials 6, 1701244 (2018).
Recent Progress in Voltage-Sensitive Dye Imaging for Neuroscience (2014)

Voltage-sensitive dye imaging (VSDi) enables visualization of information processing in different areas of the brain with reasonable spatial and temporal resolution. VSDi employs different chemical compounds to transduce neural activity directly into the changes in intrinsic optical signal. Physically, voltage-sensitive dyes (VSDs) are chemical probes that reside in the neural membrane and change their fluorescence or absorbance in response to membrane potential changes. Based on these features, VSDs can be divided into two groups-absorbance and fluorescence. The spatial and temporal resolution of the VSDi is limited mainly by the technical characteristics of the optical imaging setup (e.g., computer and light-sensitive device-charge-coupled device (CCD) camera or photodiode array). In this article, we briefly review the development of the VSD, technique of VSDi and applications in functional brain imaging.
Conductive Hydrogels: Mechanically Robust Hybrids for Use as Biomaterials (2012)

A hybrid system for producing conducting polymers within a doping hydrogel mesh is presented. These conductive hydrogels demonstrate comparable electroactivity to conventional conducting polymers without requiring the need for mobile doping ions which are typically used in literature. These hybrids have superior mechanical stability and a modulus significantly closer to neural tissue than materials which are commonly used for medical electrodes. Additionally they are shown to support the attachment and differentiation of neural like cells, with improved interaction when compared to homogeneous hydrogels. The system provides flexibility such that biologic incorporation can be tailored for application.