gebhart/patrepeval huggingface dataset:
Targeted drug combination therapy design based on driver genes (2019)

Targeted therapies against cancer types with more than one driver gene hold bright but elusive promise, since approved drugs are not available for all driver mutations and monotherapies often result in resistance. Targeting multiple driver genes in different pathways at the same time may provide an impact extensive enough to fight resistance. Our goal was to find synergistic drug combinations based on the availability of targeted drugs and their biological activity profiles and created an associated compound library based on driver gene-related protein targets. In this study, we would like to show that driver gene pattern based customized combination therapies are more effective than monotherapies on six cell lines and patient-derived primary cell cultures. We tested 55-102 drug combinations targeting driver genes and driver pathways for each cell line and found 25-85% of these combinations highly synergistic. Blocking 2-5 cancer pathways using only 2-3 targeted drugs was sufficient to reach high rates of tumor cell eradication at remarkably low concentrations. Our results demonstrate that the efficiency of cancer treatment may be significantly improved by combining drugs against multiple tumor specific drivers.
Adaptive classification (2002)

We present an online learning system that is capable of analyzing an input-output data sequence to construct a sequence of binary classifications, without being provided correct class information as part of the training process. The system employs a combination of supervised and unsupervised learning techniques to form two or more behavior models. By examining these models for consistency with the sequence of observed data, an estimate of the class at each time step can be constructed.
Maternal obesity characterized by gestational diabetes increases the susceptibility of rat offspring to hepatic steatosis via a disrupted liver metabolome (2015)

Maternal obesity is associated with a high risk for gestational diabetes mellitus (GDM), which is a common complication of pregnancy. The influence of maternal obesity and GDM on the metabolic health of the offspring is poorly understood. We hypothesize that GDM associated with maternal obesity will cause obesity, insulin resistance and hepatic steatosis in the offspring. Female Sprague-Dawley rats were fed a high-fat (45%) and sucrose (HFS) diet to cause maternal obesity and GDM. Lean control pregnant rats received low-fat (LF; 10%) diets. To investigate the interaction between the prenatal environment and postnatal diets, rat offspring were assigned to LF or HFS diets for 12 weeks, and insulin sensitivity and hepatic steatosis were evaluated. Pregnant GDM dams exhibited excessive gestational weight gain, hyperinsulinaemia and hyperglycaemia. Offspring of GDM dams gained more weight than the offspring of lean dams due to excess adiposity. The offspring of GDM dams also developed hepatic steatosis and insulin resistance. The postnatal consumption of a LF diet did not protect offspring of GDM dams against these metabolic disorders. Analysis of the hepatic metabolome revealed increased diacylglycerol and reduced phosphatidylethanolamine in the offspring of GDM dams compared to offspring of lean dams. Consistent with altered lipid metabolism, the expression of CTP:phosphoethanolamine cytidylyltransferase, and peroxisomal proliferator activated receptor-α mRNA was reduced in the livers of GDM offspring. GDM exposure programs gene expression and hepatic metabolite levels and drives the development of hepatic steatosis and insulin resistance in young adult rat offspring.
Approaching Optimal Centralized Scheduling With CSMA-Based Random Access Over Fading Channels (2016)

Carrier sense multiple access (CSMA) based distributed algorithms can attain the largest capacity region as the centralized Max-Weight policy does. Despite their capability of achieving throughput optimality, these algorithms can either incur large delay and have large complexity or only operate over nonfading channels. In this letter, by assuming arbitrary backoff time, we first propose a fully distributed randomized algorithm whose performance can be pushed to the performance of the centralized Max-Weight policy not only in terms of throughput but also in terms of delay for completely connected interference networks with fading channels. Then, inspired by the proposed algorithm, we introduce an implementable distributed algorithm for practical networks with a reservation scheme. We show that the proposed practical algorithm can still achieve the performance of the centralized Max-Weight policy.
Extraction of the interfacial generation velocity in MOSFETs (2002)

A novel method based upon gate controlled diode static characteristics is proposed to determine the interfacial generation velocity S/sub o/ in MOSFETs. S/sub o/ is deduced from the measurement of the apparent generation velocity of two long transistors with different channel lengths. Results concerning natural or implanted transistors, with single or double diffused drains, are presented and discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Plow and Ridge Nanofabrication (2013)

Traditionally, scanning probe lithography tools are limited in resolution by the radius of curvature of the tip used. Herein, an approach is described for patterning the ridge of piled-up polymer that naturally occurs when a scanning probe is pressed against a soft surface. The use of this phenomenon to transfer patterns to hard materials with 20 nm resolution is demonstrated.
Plasticity after perceptual narrowing for voice perception: reinstating the ability to discriminate monkeys by their voices at 12 months of age (2013)

Differentiating individuals by their voice is an important social skill for infants to acquire. In a previous study, we demonstrated that the ability to discriminate individuals by voice follows a pattern of perceptual narrowing (Friendly et al., 2013). Specifically, we found that the ability to discriminate between two foreign-species (rhesus monkey) voices decreased significantly between 6 and 12 months of age. Also during this period, there was a trend for the ability to discriminate human voices to increase. Here we investigate the extent to which plasticity remains at 12 months, after perceptual narrowing has occurred. We found that 12-month-olds who received 2 weeks of monkey-voice training were significantly better at discriminating between rhesus monkey voices than untrained 12-month-olds. Furthermore, discrimination was reinstated to a level slightly better than that of untrained 6-month-olds, suggesting that voice-processing abilities remain considerably plastic at the end of the first year.
List of SCC SUVmax correlated genes from <i>GFPT2</i>-Expressing Cancer-Associated Fibroblasts Mediate Metabolic Reprogramming in Human Lung Adenocarcinoma (2023)

&lt;p&gt;This supplement file contains the identified SUVmax correlated genes in the lung squamous cell carcinoma patients in the RG cohort.&lt;/p&gt;
BALB/c mouse model of RSV clinical isolate A2001/2-20 pathogenesis (49.13) (2011)

Abstract Airway mucus is a hallmark of respiratory syncytial virus (RSV) lower respiratory tract illness. Laboratory RSV strains (A2, Long, and Line 19) differentially induce airway mucus production in mice. We tested whether RSV strains differ in pathogenesis by screening low passage RSV clinical isolates for mucogenicity and virulence in BALB/c mice. RSV clinical isolates induced variable disease severity. Infection of BALB/c mice with clinical isolate RSV A2001/2-20 (2-20) resulted in greater disease severity and higher lung IL-13 levels than infection with RSV laboratory strains and other clinical isolates. Like the line 19 strain, 2-20 induced airway mucin expression in BALB/c mice and resulted in higher viral antigen levels in the bronchiolar epithelium than A2. 2-20 caused epithelial desquamation, airway hyperresponsiveness, and increased breathing effort in BALB/c mice. We hypothesize that the fusion (F) protein of 2-20 contributes to this phenotype. We generated a chimeric RSV by replacing the F gene of A2 with the F gene of 2-20. A2-2-20F grew to similar levels as 2-20 in mouse and human cells in vitro. In BALB/c mice, the A2-2-20F exhibited viral loads similar to 2-20 over a time course and showed comparable mucin levels to 2-20. We established a mouse model of clinical isolate strain-dependent RSV pathogenesis that recapitulates key features of RSV disease. Identification of virulence factors of RSV 2-20 may contribute to our understanding of RSV disease mechanisms.
Cell-free Protein Expression Using the Rapidly Growing Bacterium <em>Vibrio natriegens</em> (2019)

The marine bacterium Vibrio natriegens has garnered considerable attention as an emerging microbial host for biotechnology due to its fast growth rate. A general protocol is described for the preparation of V. natriegens crude cell extracts using common laboratory equipment. This high yielding protocol has been specifically optimized for user accessibility and reduced cost. Cell-free protein synthesis (CFPS) can be carried out in small scale 10 μL batch reactions in either a 96- or 384-well format and reproducibly yields concentrations of > 260 μg/mL super folder GFP (sfGFP) within 3 h. Overall, crude cell extract preparation and CFPS can be achieved in 1-2 full days by a single user. This protocol can be easily integrated into existing protein synthesis pipelines to facilitate advances in bio-production and synthetic biology applications.
Aortic stenosis: Is it simply a degenerative process or an active atherosclerotic process? (2005)

Aortic stenosis remains the most common cause of cardiac valve replacement in developed countries. The prevalence of this condition increases with age, and many of the risk factors for coronary artery disease also appear related to the development and progression of aortic stenosis. Recent studies also suggest a relationship between calcium and lipid accumulation in both coronary artery disease and aortic stenosis. Most important, there is growing evidence that aggressive treatment of coronary artery disease risk factors, particularly hyperlipidemia, may influence the progression of aortic stenosis. In this article the current literature is reviewed as it relates to vascular biology, pathogenesis of aortic valve disease, and current and newly emerging management approaches in the care of the patient with aortic stenosis.
Enabling alternating phase shifted mask designs for a full logic gate level (2001)

The International Technology Roadmap for Semiconductors lists F2 (1 = 157 nm) optical lithography and extreme ultraviolet next generation lithography as the two most feasible lithography solutions for the 70 nm technology node. It is likely that both of these solutions will be late, forcing ArF (1 = 193 nm) lithography to operate at unprecedented resolution levels. Theoretically, alternating phase shifted masks (“altPSM”) can achieve the resolution required to manufacture 70 nm logic products with ArF lithography equipment, but technical and logistical challenges associated with the broad implementation of altPSM require novel and invasive EDA solutions which have caused the industry to shy away from altPSM in the past. One of the biggest such challenges is the creation of robust design rule checking (DRC) tools which can predict whether a given layout has a valid, manufacturable altPSM solution. This paper takes a detailed look at the technical and practical issues associated with altPSM design rules and DRC.
The CSI Framework for Compiler-Inserted Program Instrumentation (2018)

The CSI framework provides comprehensive static instrumentation that a compiler can insert into a program-under-test so that dynamic-analysis tools - memory checkers, race detectors, cache simulators, performance profilers, code-coverage analyzers, etc. - can observe and investigate runtime behavior. Heretofore, tools based on compiler instrumentation would each separately modify the compiler to insert their own instrumentation. In contrast, CSI inserts a standard collection of instrumentation hooks into the program-under-test. Each CSI-tool is implemented as a library that defines relevant hooks, and the remaining hooks are "nulled" out and elided during either compile-time or link-time optimization, resulting in instrumented runtimes on par with custom instrumentation. CSI allows many compiler-based tools to be written as simple libraries without modifying the compiler, lowering the bar for the development of dynamic-analysis tools. We have defined a standard API for CSI and modified LLVM to insert CSI hooks into the compiler's internal representation (IR) of the program. The API organizes IR objects - such as functions, basic blocks, and memory accesses - into flat and compact ID spaces, which not only simplifies the building of tools, but surprisingly enables faster maintenance of IR-object data than do traditional hash tables. CSI hooks contain a "property" parameter that allows tools to customize behavior based on static information without introducing overhead. CSI provides "forensic" tables that tools can use to associate IR objects with source-code locations and to relate IR objects to each other. To evaluate the efficacy of CSI, we implemented six demonstration CSI-tools. One of our studies shows that compiling with CSI and linking with the "null" CSI-tool produces a tool-instrumented executable that is as fast as the original uninstrumented code. Another study, using a CSI port of Google's ThreadSanitizer, shows that the CSI-tool rivals the performance of Google's custom compiler-based implementation. All other demonstration CSI tools slow down the execution of the program-under-test by less than 70%.
CCDC 115636: Experimental Crystal Structure Determination (1999)

An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
Electrodeposited magnetic nanoporous membrane for high-yield and high-throughput immunocapture of extracellular vesicles and lipoproteins (2022)

Superparamagnetic nanobeads offer several advantages over microbeads for immunocapture of nanocarriers (extracellular vesicles, lipoproteins, and viruses) in a bioassay: high-yield capture, reduction in incubation time, and higher capture capacity. However, nanobeads are difficult to "pull-down" because their superparamagnetic feature requires high nanoscale magnetic field gradients. Here, an electrodeposited track-etched membrane is shown to produce a unique superparamagnetic nano-edge ring with multiple edges around nanopores. With a uniform external magnetic field, the induced monopole and dipole of this nano edge junction combine to produce a 10× higher nanobead trapping force. A dense nanobead suspension can be filtered through the magnetic nanoporous membrane (MNM) at high throughput with a 99% bead capture rate. The yield of specific nanocarriers in heterogeneous media by nanobeads/MNM exceeds 80%. Reproducibility, low loss, and concentration-independent capture rates are also demonstrated. This MNM material hence expands the application of nanobead immunocapture to physiological samples.
Dynamic reactive compensation: Reactive power fundamentals (2011)

The panel presentation is a tutorial on the concept of reactive power and discusses its implications in power systems. The impact of reactive power on the system voltage as well as on component ratings and component size is discussed. The concept of reactive power and the so called `instantaneous' reactive power are presented. Finally, the mechanisms for generating reactive power using passive and active electrical apparatus are presented. The presentation is an introduction to more advanced dynamic compensation concepts to be covered by the other presenters.
New algorithms, data structures, and user interfaces for machine learning of large datasets with applications (2003)

This thesis comprises new algorithms, data structures, and user interfaces for learning analytic models from large datasets. The theoretical contributions have been validated experimentally in several domains using the Bayesian Networks framework. Two topics are studied in detail: learning good analytic models from data and providing an user friendly interface to visualizing and interacting with these large models. 
Learning from data is a hard problem. In particular learning Bayesian Network structure from data is NP-hard. Thus heuristic search is necessary to find good models. There are two approaches to improve heuristic search: Speeding up model evaluation in order to be able to search through a larger number of models in a given search time and using better heuristics to generate higher quality models early in the search. This research has addressed both issues through the development and experimental validation of the AD+Tree and Queue Learning. 
The AD+Tree is a data structure that caches counts from the dataset very efficiently, enabling fast evaluation of larger models. Under certain assumptions the AD+Tree allows one to process datasets one order of magnitude larger than those processed with other data structures of similar speed performance. These theoretical boundaries have been validated experimentally. The AD+Tree usefulness extends beyond Bayesian Networks to other analytic modeling paradigms based on discrete data. 
Queue Learning is an algorithm for learning Bayesian Network structure that I have shown experimentally produces better models early in the search than existing techniques when applied to large datasets. Queue learning is also an inherently parallel algorithm thus holding the potential for significant speed improvements when used in distributed systems. 
Existing using interfaces do not scale well with model size. New user interfaces have been developed to address the challenges of displaying and interacting with larger models. In particular the usage of coloring schemes has increased the number of attributes that can be manipulated comfortably from a few tens to a few hundreds. 
A chapter is devoted to presenting three case studies using real world datasets. They exemplify the usage of Bayesian Network automatic modeling and novel user interfaces in genomics, proteomics and financial arbitrage.
Parallel Counters for Low-Pass Phase Modulation–Demodulation ADCs (2018)

The signal-to-noise ratio (SNR) of a low-pass phase modulation-demodulation analog-to-digital converter (LP PMD ADC) depends on the number of channels in its demodulator (synchronizer or race arbiter). For 3, 7, and 15 channels, this gives 9.5, 16.9, and 23.5 dB theoretical SNR gain in comparison to a single channel. We have designed a family of parallel counters that sums the unweighted outputs of each synchronizer channel to produce a binary code. A 7-to-3 counter that can be truncated into 3-to-2 and extended into 15-to-4 adders was fabricated using 10 and 20 kA/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> MIT-LL processes and successfully tested. The completed designs of 1-, 3-, and 7-channel LP PMD ADC are also briefly discussed.
Operating mechanism of RF electromagnetic noise suppression sheets (2005)

Noise suppression sheets (NSS) are made of polymer-embedded magnetic flakes and widely used to suppress electromagnetic noise of electronic devices by means of shielding magnetic field and dissipating the noise power as ferromagnetic resonance losses that appear only at GHz frequency range. In spite of the good practical performance, it remains unclear how the NSS really act on the noise and inacts over signal. This paper discusses the mechanism of inter- and intra-decoupling noise suppression based on 3D FEM electromagnetic field simulation and experiments.
Near-field study of a turbulent freejet and velocity bias effects (1996)

A comparative study was conducted to measure turbulence parameters and to evaluate some of the velocitybias correction techniques in the near field of a turbulent freejet. The overall objective of this investigation was to develop a reliable technique for obtaining nonintrusive measurements of the mean flow velocity components and turbulence and to construct a complete set of data in the developing region of a turbulent freejet.
Antiatherogenic activity of fungal beauveriolides, inhibitors of lipid droplet accumulation in macrophages (2004)

Beauveriolides I and III, isolated from the culture broth of fungal Beauveria sp. FO-6979, showed potent inhibitory activity of lipid droplet accumulation in primary mouse peritoneal macrophages. The cellular molecular target of this inhibitory activity was studied in macrophages. Beauveriolides I and III strongly inhibited the cholesteryl ester (CE) synthesis with IC(50) values of 0.78 and 0.41 microM, respectively, without showing significant effects on the triacylglycerol and phospholipid synthesis. Furthermore, lysosomal cholesterol metabolism to CE in macrophages was inhibited by the compounds, indicating that the inhibition site lies within steps between cholesterol departure from the lysosome and CE synthesis in the endoplasmic reticulum. Therefore, acyl-CoA:cholesterol acyltransferase (ACAT) activity in the membrane fractions prepared from mouse macrophages was studied, resulting in a dose-dependent inhibition by beauveriolides I and III with IC(50) values of 6.0 and 5.5 microM, respectively. Thus, we showed that the beauveriolides inhibit macrophage ACAT activity specifically, resulting in blockage of the CE synthesis, leading to a reduction of lipid droplets in macrophages. ACAT activity in the membrane fractions prepared from mouse liver and Caco-2 cells was also inhibited, indicating that the beauveriolides block both ACAT-1 and -2. Moreover, beauveriolides I and III exert antiatherogenic activity in both low-density lipoprotein receptor- and apolipoprotein E-knockout mice without any side effects such as diarrhea or cytotoxicity to adrenal tissues as observed for many synthetic ACAT inhibitors. Beauveriolides I and III are the first microbial cyclodepsipeptides having an in vivo antiatherosclerotic effect and show promise as potential lead compounds for antiatherosclerotic agents.
Optical domain performance monitoring (2002)

The rapid evolution of terrestrial optical networks is driving the need for optical domain performance monitoring in order to provide the lowest transport cost per managed bit. This paper presents various techniques for monitoring optical signals between 3R interfaces in terms of their economic value to the network operator.
Learning to Reconstruct People in Clothing From a Single RGB Camera (2019)

We present Octopus, a learning-based model to infer the personalized 3D shape of people from a few frames (1-8) of a monocular video in which the person is moving with a reconstruction accuracy of 4 to 5mm, while being orders of magnitude faster than previous methods. From semantic segmentation images, our Octopus model reconstructs a 3D shape, including the parameters of SMPL plus clothing and hair in 10 seconds or less. The model achieves fast and accurate predictions based on two key design choices. First, by predicting shape in a canonical T-pose space, the network learns to encode the images of the person into pose-invariant latent codes, where the information is fused. Second, based on the observation that feed-forward predictions are fast but do not always align with the input images, we predict using both, bottom-up and top-down streams (one per view) allowing information to flow in both directions. Learning relies only on synthetic 3D data. Once learned, Octopus can take a variable number of frames as input, and is able to reconstruct shapes even from a single image with an accuracy of 5mm. Results on 3 different datasets demonstrate the efficacy and accuracy of our approach.