gebhart/patrepeval huggingface dataset:
A Domain Responsible for the Transformation Suppressor Activity in K<i>rev</i>‐1 Protein (1990)

Krev-1 cDNA encodes a ras-related protein and exhibits an activity of inducing flat revertants at certain frequencies (2-5% of total transfectants) when introduced into a v-K-ras-transformed mouse NIH3T3 cell line, DT. To explore the functional organization of Krev-1 protein, we constructed a series of chimeric genes consisting of fragments of H-ras and Krev-1 cDNAs, and tested their biological activities in DT cells. The results indicated that the determinant for the transformation suppressor activity resides in the N-terminal one-third of the Krev-1 encoded polypeptide within which a highly conserved, putative effector-binding domain is present.
Get Your Head Out of the Clouds: The Illusion of Confidentiality &amp; Privacy (2018)

The cloud has been leveraged for many applications across different industries. Despite its popularity, the cloud technologies are still immature. The security implications of cloud computing also dominate the research space. Many confidentiality-and integrity-based (C-I) security controls concerning data-at-rest and data-in-transit are focused on encryption. In the world where social-media platforms transparently gather data about user behaviors and user interests, the need for user privacy and data protection is of the utmost importance. However, how can a user know that his data is safe, that her data is secure, that his data's integrity is upheld; to be confident that her communications only reach the intended recipients? We propose: they can't. Many threats have been hypothesized in the shared-service arena, with many solutions formulated to avert those threats; however, we illustrate that many technologies and standards supporting C-I controls may be ineffective, not just against the adversarial actors, but also against trusted entities. Service providers and malicious insiders can intercept and decrypt network-and host-based data without any guest or user knowledge.
4 Anti-retinoblastoma protein antibodies are negatively associated with lupus nephritis (2019)

<h3>Background</h3> Retinoblastoma protein (RB) regulates nucleosome/chromatin structures and is linked to tumor suppression. It regulates the cell cycle by repression of E2F transcription factor and stabilization of heterochromatin. Because SLE is the prototypic autoimmune disease with autoantibodies against the nucleosome and chromatin, the presence of anti-RB antibodies and the association with disease manifestations were examined. <h3>Methods</h3> 222 SLE patients from the Hopkins longitudinal cohort seen consecutively in clinic were studied (85% female, 94% Caucasian, mean age 51 years). Anti-RB antibodies were assayed by immunoprecipitation of 35S-methionine-labeled protein generated by <i>in vitro</i> transcription and translation from full length human cDNA. Odds ratios and p-values for univariate analyses were calculated using Fishers exact t-test. Exact logistic regression and odds ratios were calculated for the multi-variate model due to a cell frequency of zero for proteinuria ever and positive anti-RB antibody status. <h3>Results</h3> Anti-RB antibodies were present in 8.6% of these SLE patients, 6.3% with medium-high titer. Univariate associations with SLE manifestations for the medium-high titer positive patients are included in table 1. Of note, medium/high titer anti-RB antibodies were never found in patients with proteinuria (p=0.0028). In a multi-variate model for proteinuria, anti-RB antibodies remained negatively associated (OR 0.1112, p=0.016) after correction for female gender (OR 0.417, p=0.0498), ethnicity (Caucasian, OR 0.288, p=0.0833), low anti-dsDNA ever (OR 1.806, p=0.1192), anti-Sm positive ever (OR 1.273, p=0.7127) and low complement ever (OR 2.111, p=0.0377). <h3>Conclusions</h3> Anti-RB antibodies are a novel specificity not previously described in SLE. These antibodies are strongly negatively associated with lupus nephritis, even in multivariate models that include other variables (female gender, Caucasian ethnicity, anti-dsDNA, anti-Sm, and low complement). Intriguingly, anti-RB antibodies are positively associated with stroke in SLE. Additional studies are warranted to understand the mechanism of this finding. <h3>Funding Source(s):</h3> The Hopkins Lupus Cohort was funded by NIH Grant R01-AR069572.
Abstract 3717: Randomized phase II trial of cladribine with or without immediate rituximab for newly diagnosed or previously treated hairy cell leukemia to eliminate minimal residual disease: Interim report (2010)

Abstract Purine analogs including cladribine can induce complete remission (CR) in a high percentage of patients with previously untreated hairy cell leukemia (HCL), but late relapses are common and disease-free survival curves show no convincing evidence of cure. Many patients in CR after cladribine have minimal residual disease (MRD) which strongly expresses CD20, and the anti-CD20 Mab rituximab, particularly with a purine analog, can eliminate MRD to undetectable levels. To determine the potential benefit of adding rituximab to cladribine for initial or 2nd-line treatment of HCL, a randomized trial was begun in 150 HCL patients with 0-1 prior courses of cladribine requiring therapy. Patients receive cladribine 0.15 mg/Kg by 5 daily 2-hr i.v. infusions, and 8 weekly i.v. infusions of rituximab 375 mg/m2. Rituximab in half the patients is begun with the 1st dose of cladribine, and in the other half is delayed at least 6 months when MRD is detectable in blood. Endpoints include determining whether MRD rates are lower at 6 months with immediate rituximab, and whether blood MRD-free survival is longer when rituximab is delayed at least 6 months or begun with cladribine. HCL variant (HCLv) patients, known to respond poorly to initial cladribine alone, are not randomized and receive rituximab with cladribine. Bone marrow and blood are assessed for MRD by immunohistochemistry, PCR and flow cytometry at 1 and 6 months after cladribine. At this time 14 patients are enrolled, including 6 untreated and 8 with 1 prior course of cladribine, the latter group including 1 with HCLv. So far, the overall response rate is 100% with 10 (83%) CRs in 12 evaluable patients at 61-243 (median 202) days of follow-up. By 1 month, 0 of 5 patients after cladribine alone vs 5 (71%) of 7 after cladribine with immediate rituximab were MRD-free (p=0.028), including the patient with HCLv. Neutropenic fever was more frequent in patients receiving immediate rituximab, and was associated with both infusional reactions and reversible infections. We conclude that rituximab with cladribine can result in early clearing of MRD which is frequently present after cladribine alone. Additional accrual and follow-up is needed to determine whether simultaneous cladribine and rituximab can reduce MRD rates at 6 months, whether MRD-free survival might be longer or shorter with delayed rituximab, and whether rituximab added to cladribine for 1st or 2nd line treatment of HCL can prevent or delay clinical relapse. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 3717.
Distinct thalamocortical network dynamics are associated with the pathophysiology of chronic low back pain (2020)

Thalamocortical dysrhythmia is a key pathology of chronic neuropathic pain, but few studies have investigated thalamocortical networks in chronic low back pain (cLBP) given its non-specific etiology and complexity. Using fMRI, we propose an analytical pipeline to identify abnormal thalamocortical network dynamics in cLBP patients and validate the findings in two independent cohorts. We first identify two reoccurring dynamic connectivity states and their associations with chronic and temporary pain. Further analyses show that cLBP patients have abnormal connectivity between the ventral lateral/posterolateral nucleus (VL/VPL) and postcentral gyrus (PoCG) and between the dorsal/ventral medial nucleus and insula in the less frequent connectivity state, and temporary pain exacerbation alters connectivity between the VL/VPL and PoCG and the default mode network in the more frequent connectivity state. These results extend current findings on thalamocortical dysfunction and dysrhythmia in chronic pain and demonstrate that cLBP pathophysiology and clinical pain intensity are associated with distinct thalamocortical network dynamics.
Resolution of Enantiomers in Solution and Determination of the Chirality of Extended Metal Atom Chains (2007)

The resolution of enantiomers of extended metal atom chains of the type Ni3[(C5H5N)2N]4Cl2 has been accomplished by chromatographic methods in solution, and the chirality was determined using vibrational circular dichroism, electronic circular dichroism, optical rotatory dispersion, and density functional theory calculations.
Dose‐dependent mesothelioma induction by intraperitoneal administration of multi‐wall carbon nanotubes in p53 heterozygous mice (2012)

Among various types of multi-wall carbon nanotubes (MWCNT) are those containing fibrous particles longer than 5 μm with an aspect ratio of more than three (i.e. dimensions similar to mesotheliomagenic asbestos). A previous study showed that micrometer-sized MWCNT (μm-MWCNT) administered intraperitoneally at a dose of 3000 μg/mouse corresponding to 1 × 10(9) fibers per mouse induced mesotheliomas in p53 heterozygous mice. Here, we report a dose-response study; three groups of p53 heterozygous mice (n = 20) were given a single intraperitoneal injection of 300 μg/mouse of μm-MWCNT (corresponding to 1 × 10(8) fibers), 30 μg/mouse (1 × 10(7)) or 3 μg/mouse (1 × 10(6)), respectively, and observed for up to 1 year. The cumulative incidence of mesotheliomas was 19/20, 17/20 and 5/20, respectively. The severity of peritoneal adhesion and granuloma formation were dose-dependent and minimal in the lowest dose group. However, the time of tumor onset was apparently independent of the dose. All mice in the lowest dose group that survived until the terminal kill had microscopic atypical mesothelial hyperplasia considered as a precursor lesion of mesothelioma. Right beneath was a mononuclear cell accumulation consisting of CD45- or CD3-positive lymphocytes and CD45/CD3-negative F4/80 faintly positive macrophages; some of the macrophages contained singular MWCNT in their cytoplasm. The lesions were devoid of epithelioid cell granuloma and fibrosis. These findings were in favor of the widely proposed mode of action of fiber carcinogenesis, that is, frustrated phagocytosis where the mesotheliomagenic microenvironment on the peritoneal surface is neither qualitatively altered by the density of the fibers per area nor by the formation of granulomas against agglomerates.
Zero-Shot Audio Classification using Image Embeddings (2022)

Supervised learning methods can solve the given problem in the presence of a large set of labeled data. However, the acquisition of a dataset covering all the target classes typically requires manual labeling which is expensive and time-consuming. Zero-shot learning models are capable of classifying the unseen concepts by utilizing their semantic information. The present study introduces image embeddings as side information on zero-shot audio classification by using a nonlinear acoustic-semantic projection. We extract the semantic image representations from the Open Images dataset and evaluate the performance of the models on an audio subset of AudioSet using semantic information in different domains; image, audio, and textual. We demonstrate that the image embeddings can be used as semantic information to perform zero-shot audio classification. The experimental results show that the image and textual embeddings display similar performance both individually and together. We additionally calculate the semantic acoustic embeddings from the test samples to provide an upper limit to the performance. The results show that the classification performance is highly sensitive to the semantic relation between test and training classes and textual and image embeddings can reach up to the semantic acoustic embeddings when the seen and unseen classes are semantically similar.
Reflections of mentoring midshipmen and high school students at the United States Naval Academy—With student recollections (2019)

For 38 years, MSK has developed mentoring undergraduate students in the Physics Department. Mentorship is a unique dance, a growing tree—with kind branches embracing any challenge—a give and take enjoyed by both the mentor and mentee. It should be fun—filled with goals to achieve (often wrapped in a research challenge). “Acoustics” and “Underwater Acoustics and Sonar,” courses—inspire projects. Students have presented research at ASA meetings. Some become co-authors on published papers. For 35 years, MSK developed a high school mentorship program at USNA. Rising juniors and seniors may apply. HS mentees start their research on a project that evolves over one or two months working twice a week for 2.5–3 h sessions. Students often continue over the summer. Recently, MSK took HS mentorship students to the ASA Boston Meeting, the 17th ISNA Meeting (Santa Fe 2018), Louisville and Internoise 2019 in Madrid. Three HS seniors at the ISNA conference presented research (published in POMA) on (1) nonlinear acoustic landmine detection with wetted and dry beads [EVS], (2) acoustic levitation and nonlinear sound scattering by a bubble [KAH], and (3) the interaction of two crossed ultrasonic streaming jets [JMC]. Their dedication and insights are highly valued.
Supplementary Materials and Methods from A Central Role for RAF→MEK→ERK Signaling in the Genesis of Pancreatic Ductal Adenocarcinoma (2023)

&lt;p&gt;PDF file - 65K&lt;/p&gt;
Virtual Communities For Creating Shared Music Channels. (2007)

[TODO] Add abstract here.
CatFedAvg: Optimising Communication-efficiency and Classification Accuracy in Federated Learning (2020)

Federated learning has allowed the training of statistical models over remote devices without the transfer of raw client data. In practice, training in heterogeneous and large networks introduce novel challenges in various aspects like network load, quality of client data, security and privacy. Recent works in FL have worked on improving communication efficiency and addressing uneven client data distribution independently, but none have provided a unified solution for both challenges. We introduce a new family of Federated Learning algorithms called CatFedAvg which not only improves the communication efficiency but improves the quality of learning using a category coverage maximization strategy. We use the FedAvg framework and introduce a simple and efficient step every epoch to collect meta-data about the client's training data structure which the central server uses to request a subset of weight updates. We explore two distinct variations which allow us to further explore the tradeoffs between communication efficiency and model accuracy. Our experiments based on a vision classification task have shown that an increase of 10% absolute points in accuracy using the MNIST dataset with 70% absolute points lower network transfer over FedAvg. We also run similar experiments with Fashion MNIST, KMNIST-10, KMNIST-49 and EMNIST-47. Further, under extreme data imbalance experiments for both globally and individual clients, we see the model performing better than FedAvg. The ablation study further explores its behaviour under varying data and client parameter conditions showcasing the robustness of the proposed approach.
Time-domain optical mammography: initial clinical results on detection and characterization of breast tumors (2003)

Mammograms of 35 patients suspected of breast cancer were taken along craniocaudal and mediolateral projections with a dual-wavelength scanning laser pulse mammograph measuring time-resolved transmittance. Among 26 tumors known from routine clinical diagnostics, 17 tumors were detected retrospectively in optical mammograms. Effective tumor optical properties derived from a homogeneous model were used to deduce physiological information. All tumors exhibited increased total hemoglobin concentration and decreased or unchanged blood oxygen saturation compared with surrounding healthy tissue. Scatter plots based on a pixelwise analysis of individual mammograms were introduced and applied to represent corelations between characteristic quantities derived from measured distributions of times of flight of photons.
A new approach to text searching (1989)

We introduce a family of simple and fast algorithms for solving the classical string matching problem, string matching with don't care symbols and complement symbols, and multiple patterns. In addition we solve the same problems allowing up to k mismatches. Among the features of these algorithms are that they are real time algorithms, they don't need to buffer the input, and they are suitable to be implemented in hardware.
Receiver-less silicon-germanium avalanche p-i-n photodetectors (2021)

On-chip avalanche photodetectors (APDs) are attractive for a sensitive detection of high-speed data light signals with low intensities. Silicon-germanium (Si-Ge) APDs are leading candidates to build reliable short-reach optical links. Appeal for Si-Ge APDs stems from larger (lower) gain-bandwidth (excess noise) at reduced voltages, CMOS-compliant production, and monolithic integration compared to their III-V alternatives [1] - [5] . Typically, Si-Ge APDs are metal-semiconductor-metal (MSM) [3] , separate absorption charge multiplication (SACM) [4] , or p-i-n [5] devices - each of them having their own advantages and drawbacks [1] . Although many Si-Ge APDs have appealing performances on their own, they are usually operated with other electronic components such as amplification stages, impeding low power consumption and low-cost detection on Si chips.
Conductometric Microbiosensors for Environmental Monitoring (2008)

This review presents the principles of conductometric measurements in ionic media and the equivalent electrical circuits of different designs for conductometric measurements. These types of measurements were first applied for monitoring biocatalytic reactions. The use of conductometric microtransducers is then presented and detailed in the case of pollutant detection for environmental monitoring. Conductometric biosensors have advantages over other types of transducers: they can be produced through inexpensive thinfilm standard technology, no reference electrode is needed and differential mode measurements allow cancellation of a lot of interferences. The specifications obtained for the detection of different pesticides, herbicides and heavy metal ions, based on enzyme inhibition, are presented as well as those obtained for the detection of formaldehyde, 4- chlorophenol, nitrate and proteins as markers of dissolved organic carbon based on enzymatic microbiosensors.
Reaching out in anticipation: bacterial membrane extensions represent a permanent investment in polysaccharide sensing and utilization (2021)

Outer membrane extensions are common in many marine bacteria. However, the function of these surface enlargements or extracellular compartments is poorly understood. Using a combined approach of microscopy and subproteome analyses, we therefore examined Pseudoalteromonas distincta ANT/505, an Antarctic polysaccharide degrading gamma-proteobacterium. P. distincta produced outer membrane vesicles (MV) and vesicle chains (VC) on polysaccharide and non-polysaccharide carbon sources during the exponential and stationary growth phase. Surface structures of carbohydrate-grown cells were equipped with increased levels of highly substrate-specific proteins. At the same time, proteins encoded in all other polysaccharide degradation-related genomic regions were also detected in MV and VC samples under all growth conditions, indicating a basal expression. In addition, two alkaline phosphatases were highly abundant under non-limiting phosphate conditions. Surface structures may thus allow rapid sensing and fast responses in nutritionally deprived environments. It may also facilitate efficient carbohydrate processing and reduce loss of substrates and enzymes by diffusion as important adaptions to the aquatic ecosystem.
5G K-SimSys: Open/Modular/Flexible System Level Simulator for 5G System (2018)

Accurate and rapid performance evaluation using a system level simulator (SLS) is an indispensable element of research & development (R&D) on mobile communication system design and standard specification. Due to the various usage-scenarios, the 5G system requires development of the different simulators that deal with the individual evaluation scenarios and environments. To minimize the time and effort required for their implementation, we have designed and implemented 5G K-SimSys, which is a system-level simulator with a modular & flexible structure, facilitating its reuse thorough open source code sharing. Moreover, this simulator can be easily extended for testing and evaluating the various 5G specifications in the future.
Microstructure and Composition of Full Fat Cheddar Cheese Made with Ultrafiltered Milk Retentate (2013)

Milk protein is often standardised prior to cheese-making using low concentration factor ultrafiltration retentate (LCUFR) but the effect of LCUFR addition on the microstructure of full fat gel, curd and Cheddar cheese is not known. In this work, Cheddar cheeses were made from cheese-milk with or without LCUFR addition using a protein concentration of 3.7%-5.8% w/w. The fat lost to sweet whey was higher in cheese made from cheese-milk without LCUFR or from cheese-milk with 5.8% w/w protein. At 5.8% w/w protein concentration, the porosity of the gel increased significantly and the fat globules within the gel and curd tended to pool together, which possibly contributed to the higher fat loss in the sweet whey. The microstructure of cheese from cheese-milk with a higher protein concentration was more compact, consistent with the increased hardness, although the cohesiveness was lower. These results highlight the potential use of LCUFR for the standardization of protein concentration in cheese-milk to 4%-5% w/w (equivalent to a casein to total protein ratio of 77%-79% w/w) to increase yield. Beyond this concentration, significant changes in the gel microstructure, cheese texture and fat loss were observed.
Conductive electroactive polymers : intelligent materials systems (2003)

Preface Introduction. Assembly of Polypyrroles. Properties of Polypyrroles. Synthesis of Polyanilines. Properties of Polyanilines. Synthesis and Properties of Polythiophenes. Processing and Device Fabrication.
Experimentally Observed Anomalies from Inclining a Vapor Compression Cycle (2021)

Vapor compression cycles would have many applications in the space industry if it was not for the uncertainty imposed by microgravity environments on two-phase systems. A first step towards Zero-G for technologies involving fluid dynamics can be terrestrial testing at different orientations. For vapor compression cycles, there is very little literature describing this type of research. This paper describes the anomalies encountered during the pursuit of a continuous operation of a R134a vapor compression cycle while positioning it at fixed angles around one axis between 0 and 360°. Experimental data was collected on a dedicated test stand across two configurations, one using a flat-plate evaporator and the other configuration using a tube-in-tube evaporator. Liquid flooding of the suction line was observed for both configurations but also continuous operation throughout a complete loop for certain cycle conditions. Charge migration towards the evaporator when it was put at the bottom was calculated based on differing measurements of the two mass flow meters in the liquid and suction line.