gebhart/patrepeval huggingface dataset:
Data-Adaptive Selection of the Propensity Score Truncation Level for Inverse-Probability–Weighted and Targeted Maximum Likelihood Estimators of Marginal Point Treatment Effects (2022)

Inverse probability weighting (IPW) and targeted maximum likelihood estimation (TMLE) are methodologies that can adjust for confounding and selection bias and are often used for causal inference. Both estimators rely on the positivity assumption that within strata of confounders there is a positive probability of receiving treatment at all levels under consideration. Practical applications of IPW require finite inverse probability (IP) weights. TMLE requires that propensity scores (PS) be bounded away from 0 and 1. Although truncation can improve variance and finite sample bias, this artificial distortion of the IP weights and PS distribution introduces asymptotic bias. As sample size grows, truncation-induced bias eventually swamps variance, rendering nominal confidence interval coverage and hypothesis tests invalid. We present a simple truncation strategy based on the sample size, n, that sets the upper bound on IP weights at $\sqrt{\textit{n}}$ ln n/5. For TMLE, the lower bound on the PS should be set to 5/($\sqrt{\textit{n}}$ ln n/5). Our strategy was designed to optimize the mean squared error of the parameter estimate. It naturally extends to data structures with missing outcomes. Simulation studies and a data analysis demonstrate our strategy's ability to minimize both bias and mean squared error in comparison with other common strategies, including the popular but flawed quantile-based heuristic.
Mimosine Targets Serine Hydroxymethyltransferase (1996)

The plant amino acid, mimosine, is an extremely effective inhibitor of DNA replication in mammalian cells (Mosca, P. J., Dijkwel, P. A., and Hamlin, J. L. (1992) Mol. Cell. Biol. 12, 4375-4383). Mimosine appears to prevent the formation of replication forks at early-firing origins when delivered to mammalian cells approaching the G1/S boundary, and blocks DNA replication when added to S phase cells after a lag of approximately 2.5 h. We have shown previously that [3H]mimosine can be specifically photocross-linked both in vivo and in vitro to a 50-kDa polypeptide (p50) in Chinese hamster ovary (CHO) cells. In the present study, six tryptic peptides (58 residues total) from p50 were sequenced by tandem mass spectrometry and their sequences were found to be at least 77.5% identical and 96.5% similar to sequences in rabbit mitochondrial serine hydroxymethyltransferase (mSHMT). This assignment was verified by precipitating the [3H]mimosine-p50 complex with a polyclonal antibody to rabbit cSHMT. The 50-kDa cross-linked product was almost undetectable in a mimosine-resistant CHO cell line and in a CHO gly- cell line that lacks mitochondrial, but not cytosolic, SHMT activity. The gly- cell line is still sensitive to mimosine, suggesting that the drug may inhibit both the mitochondrial and the cytosolic forms. SHMT is involved in the penultimate step of thymidylate biosynthesis in mammalian cells and, as such, is a potential target for chemotherapy in the treatment of cancer.
Safe Flexibility in Active Distribution Grids: A Practical Data-Driven Approach (2021)

Distributed energy resources (DERs), such as photovoltaic units, wind turbines and batteries, are able to increase operational flexibility in Distribution Networks (DNs) that can be used to resolve power quality issues. Furthermore, the advances in metering infrastructure, such as the roll-out of smart meters in many countries worldwide, provides better observability of DNs. However, DERs in DNs usually belong to different stakeholders with alternative objectives that might even be conflicting (e.g., grid constraints are not considered by all). This paper presents a practical approach, based on a data-driven scheme, to safely use the DER operational flexibility and, at the same time, respect the objectives of individual households, network operators, and aggregators. First, a grid health estimator is constructed using Support-Vector Machines (SVM). Then, a real-time modification signal is used to alleviate network constraints violations. The performance of the proposed algorithm is demonstrated using the MV and LV European benchmark grids.
Minimizing the Effects of On-Chip Hotspots Using Multi-Objective Optimization of Flow Distribution in Water-Cooled Parallel Microchannel Heatsinks (2020)

Abstract The industry shift to multicore microprocessor architecture will likely cause higher temperature nonuniformity on chip surfaces, exacerbating the problem of chip reliability and lifespan. While advanced cooling technologies like two phase embedded cooling exist, the technological risks of such solutions make conventional cooling technologies more desirable. One such solution is remote cooling with heatsinks with sequential conduction resistance from chip to module. The objective of this work is to numerically demonstrate a novel concept to remotely cool chips with hotspots and maximize chip temperature uniformity using an optimized flow distribution under constrained geometric parameters for the heatsink. The optimally distributed flow conditions presented here are intended to maximize the heat transfer from a nonuniform chip power map by actively directing flow to a hotspot region. The hotspot-targeted parallel microchannel liquid cooling design is evaluated against a baseline uniform flow conventional liquid cooling design for the industry pressure drop limit of approximately 20 kPa. For an average steady-state heat flux of 145 W/cm2 on core areas (hotspots) and 18 W/cm2 on the remaining chip area (background), the chip temperature uniformity is improved by 10%. Moreover, the heatsink design has improved chip temperature uniformity without a need for any additional system level complexity, which also reduces reliability risks.
[11C]Methionine Positron Emission Tomography and Survival in Patients with Bone and Soft Tissue Sarcomas Treated by Carbon Ion Radiotherapy (2004)

MET uptake as measured by either baseline or post-CIRT T/N ratio was an independent predictor of survival in patients with bone and soft tissue sarcomas treated by carbon ion radiotherapy, whereas post-therapeutic MET uptake change might have potential value for the same purpose.
Adsorption: Liquid Separation (2005)

Abstract Adsorbate–Adsorbent Interactions Practical Adsorbents Commercial Processes Continuous Countercurrent Processes Cyclic‐Batch Processes Liquid Chromatography Outlook
Netrin‐1 and its receptor DCC modulate survival and death of dopamine neurons and Parkinson’s disease features (2020)

The netrin-1/DCC ligand/receptor pair has key roles in central nervous system (CNS) development, mediating axonal, and neuronal navigation. Although expression of netrin-1 and DCC is maintained in the adult brain, little is known about their role in mature neurons. Notably, netrin-1 is highly expressed in the adult substantia nigra, leading us to investigate a role of the netrin-1/DCC pair in adult nigral neuron fate. Here, we show that silencing netrin-1 in the adult substantia nigra of mice induces DCC cleavage and a significant loss of dopamine neurons, resulting in motor deficits. Because loss of adult dopamine neurons and motor impairments are features of Parkinson's disease (PD), we studied the potential impact of netrin-1 in different animal models of PD. We demonstrate that both overexpression of netrin-1 and brain administration of recombinant netrin-1 are neuroprotective and neurorestorative in mouse and rat models of PD. Of interest, we observed that netrin-1 levels are significantly reduced in PD patient brain samples. These results highlight the key role of netrin-1 in adult dopamine neuron fate, and the therapeutic potential of targeting netrin-1 signaling in PD.
Comparison of Computational Algorithms for the Classification of Liver Cancer using SELDI Mass Spectrometry: A Case Study (2007)

Introduction As an alternative to DNA microarrays, mass spectrometry based analysis of proteomic patterns has shown great potential in cancer diagnosis. The ultimate application of this technique in clinical settings relies on the advancement of the technology itself and the maturity of the computational tools used to analyze the data. A number of computational algorithms constructed on different principles are available for the classification of disease status based on proteomic patterns. Nevertheless, few studies have addressed the difference in the performance of these approaches. In this report, we describe a comparative case study on the classification accuracy of hepatocellular carcinoma based on the serum proteomic pattern generated from a Surface Enhanced Laser Desorption/Ionization (SELDI) mass spectrometer. Methods Nine supervised classification algorithms are implemented in R software and compared for the classification accuracy. Results We found that the support vector machine with radial function is preferable as a tool for classification of hepatocellular carcinoma using features in SELDI mass spectra. Among the rest of the methods, random forest and prediction analysis of microarrays have better performance. A permutation-based technique reveals that the support vector machine with a radial function seems intrinsically superior in learning from the training data since it has a lower prediction error than others when there is essentially no differential signal. On the other hand, the performance of the random forest and prediction analysis of microarrays rely on their capability of capturing the signals with substantial differentiation between groups. Conclusions Our finding is similar to a previous study, where classification methods based on the Matrix Assisted Laser Desorption/Ionization (MALDI) mass spectrometry are compared for the prediction accuracy of ovarian cancer. The support vector machine, random forest and prediction analysis of microarrays provide better prediction accuracy for hepatocellular carcinoma using SELDI proteomic data than six other approaches.
In Vitro Antibody Affinity Maturation Targeting Germline Hotspots (2008)

Affinity-matured antibodies can exhibit increased biological efficacy. Regardless of whether an antibody is isolated from a hybridoma or a human Fv phage library, the antibody affinity for its target may need improvement for therapeutic applications. An increased affinity may allow for a reduced dosage of a therapeutic antibody; toxic side effects may also be reduced. In the immune system, affinity maturation is a process involving somatic hypermutations in B cells. Therefore, germline hotspot residues are most likely to have a major impact on antibody affinity. Here, we describe procedures for germline hotspot mutagenesis with an emphasis on strategies for randomizing hotspots with PCR and phage display, using as an example the anti-CD22 monoclonal antibody.
Navigating in Unfamiliar Geometric Terrain (Preliminary Version) (1991)

Consider a robot that has to travel from a start location s to a target t in an environment with opaque obstacles that lie in its way. The robot always knows its current absolute position and that of the target. It does not, however, know the positions and extents of the obsta-cles in advance; rather, it finds out about obstacles as it encounters them. We compare the distance walked by the robot in going from.s to t to the length of the shortest path between s and t in the scene. We describe and analyze robot strategies that minimize this ratio for different kinds of scenes. In particular, we consider the cases of rectangular obstacles aligned with the axes, rectangular obstacles in more general orientations, and wider classes of convex bodies both in two and three dimensions. We study scenes with non-convex obsta-cles, which are related to the study of maze-traversal. We also show scenes where randomized algorithms are provably better than deterministic algorithms. 1. Motivation
What bugs cause production cloud incidents? (2019)

Cloud services have become the backbone of today's computing world. Runtime incidents, which adversely affect the expected service operations, are extremely costly in terms of user impacts and engineering efforts required to resolve them. Hence, such incidents are the target of much research effort. Unfortunately, there is limited understanding about cloud service incidents that actually happen during production runs: what cause them and how they are resolved.
Listening through a Vibration Motor (2016)

This paper demonstrates the feasibility of using the vibration motor in mobile devices as a sound sensor, almost like a microphone. We show that the vibrating mass inside the motor -- designed to oscillate to changing magnetic fields -- also responds to air vibrations from nearby sounds. With appropriate processing, the responses become intelligible, to the extent that humans can understand the vibra-motor recorded words with greater than 80% average accuracy. Even off-the-shelf speech recognition softwares are able to decode at 60% accuracy, without any training or machine learning. We present our overall techniques and results through a system called VibraPhone, and discuss implications to both sensing and security.
Supplementary Table 4 from Identification of Epigenetically Silenced Genes in Tumor Endothelial Cells (2023)

Supplementary Table 4 from Identification of Epigenetically Silenced Genes in Tumor Endothelial Cells
Predictive comparison of anti-Stokes fluorescence cooling in oxide and non-oxide fiber hosts doped with Er3+ or Yb3+ (2019)

A comprehensive study was performed to quantify anti-Stokes-fluorescence (ASF) cooling in fibers of various host compositions (telluride, fluorozirconates, fluorophosphates, phosphates, and chalcogenides) doped with Yb<sup>3+</sup> or Er<sup>3+</sup>. Published expressions were used to calculate the maximum heat that can be extracted per unit length and time from a single-mode fiber in the limit of negligible absorptive loss, and the associated cooling efficiency. These expressions consider host- and ion-dependent parameters, namely the absorption and emission cross-section spectra, the radiative and nonradiative lifetimes, and the critical concentration for quenching. Using these expressions with published values for these parameters, the maximum extractable heat was calculated for a large-mode-area fiber (NA = 0.05) doped with either Yb<sup>3+</sup> or Er<sup>3+</sup> in a variety of hosts. The results show that for a given ion, the maximum heat that can be extracted depends strongly on the host due to the strong dependence of quenching on host composition. In contrast, the cooling efficiency (ratio of extracted heat to pump power absorbed) depends very weakly on the host. The cooling efficiency is also almost twice as high for Er<sup>3+</sup> (average of 3.8%) than for Yb<sup>3+</sup> (average of 2.2%) due to the larger gap between the pump and mean fluorescence energy in Er<sup>3+</sup>. Of the limited number of materials for which a full set of data was found in the literature, the highest extractable heat for Yb<sup>3+</sup> is in phosphate (-51.5 mW/m), and for Er<sup>3+</sup> is in chalcogenide (-10.3 mW/m). This work provides a simple methodology to evaluate the quantitative cooling performance of these and other rare-earth ions in any amorphous host, a procedure that should guide researchers in the selection of optimum materials for ASF cooling of fibers.
Key Elements on LiFePO4: Performance, Stability and Availability (2006)

Abstract not Available.
The Krüppel-associated box repressor domain induces reversible and irreversible regulation of endogenous mouse genes by mediating different chromatin states (2015)

The Krüppel-associated box (KRAB) domain is a transcription repression module from the largest family of transcriptional regulators encoded by higher vertebrates. We developed a drug-controllable regulation system based on an artificial KRAB-containing repressor (tTS) that targets the endogenous Hprt gene to explore the regulatory mechanism and molecular basis of KRAB-containing regulators within the context of an endogenous gene in vivo. We show that KRAB can mediate irreversible and reversible regulation of endogenous genes in mouse that is dependent on embryonic developmental stage. KRAB-induced stable DNA methylation within the KRAB binding region during the early embryonic stage, resulting in irreversible gene repression. In later stages, KRAB mainly induced de-acetylation and methylation of histone, resulting in reversible gene repression. Thus, we have characterized the KRAB-mediated regulation system within the context of an endogenous gene and multiple spatiotemporal ranges, thereby providing a basis for identifying the function of KRAB-containing regulators and aiding development of novel KRAB-based gene regulation tools in vivo.
Table S2 from Dopamine Receptor D5 is a Modulator of Tumor Response to Dopamine Receptor D2 Antagonism (2023)

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Novel reassortant H9N2 viruses in pigeons and evidence for antigenic diversity of H9N2 viruses isolated from quails in Egypt (2016)

The endemicity of avian influenza viruses (AIVs) among Egyptian poultry represents a public health risk. Co-circulation of low pathogenic AIV H9N2 subtype with highly pathogenic AIV H5N1 subtype in Egyptian farms provides a possibility to generate novel reassortant viruses. Here, the genetic characteristics of surface glycoproteins of 59 Egyptian H9N2 viruses, isolated between 2013 and 2015, were analysed. To elucidate the potential of genetic reassortment, 10 H9N2 isolates were selected based on different avian hosts (chickens, ducks, pigeons and quails) and phylogenetic analyses of their full genome sequences were conducted. Additionally, we performed antigenic analysis to further investigate the antigenic evolution of H9N2 viruses isolated during 2011-2015. Different viral characteristics including receptor-binding affinity and drug resistance of representative Egyptian H9N2 viruses were further investigated. The surface glycoproteins of current Egyptian H9N2 viruses were closely related to viruses of the G1-like lineage isolated from Egypt. Several genetic markers that enhance virulence in poultry and transmission to humans were detected. Analysis of the full genome of 10 H9N2 isolates indicated that two pigeon isolates inherited five internal genes from Eurasian AIVs circulating in wild birds. Antigenic conservation of different Egyptian H9N2 isolates from chickens, pigeons and ducks was observed, whereas quail isolates showed antigenic drift. The Egyptian H9N2 viruses preferentially bound to the human-like receptor rather than to the avian-like receptor. Our results suggest that the endemic H9N2 viruses in Egypt contain elements that may favour avian-to-human transmission and thus represent a public health risk.
Studies Directed toward the Synthesis of the Unusual Antileukemic Diterpene Jatrophatrione. 1. A Solution to the Problem of Chirality Merger during Elaboration of the Entire Carbotricyclic Framework (1999)

A practical route for elaboration of the [5.9.5] tricyclic nucleus of jatrophatrione (1) is reported. The two key steps involve an oxyanionic Cope rearrangement and a Grob fragmentation. The building blocks required to reach 44 are the bicyclo[3.3.0]octanone 29 and the cyclopentadienyl bromide 35. The former was obtained in 12 steps from methylcyclopentadiene. The route to the latter began with 4,4-dimethylcyclopentenone. The charge-accelerated [3,3]-sigmatropic isomerization within 44 proceeds via a chairlike transition state to deliver, after enolate methylation, a highly strained product carrying a trans double bond in a medium-sized ring, one consequence of which is rapid transannular ring closure via an ene pathway. Acid hydrolysis of this enol ether and conversion to hydroxy mesylate 51 was followed by exposure to base. This sequence resulted in ring opening to provide the strategic advanced intermediate 52. The synthetic pathway developed here is expected to open a route to 9-epijatrophatrione (8) for the ultimate purpose of examining its anticipated isomerization to 1 under mildly basic conditions.
Country Program Evaluation Guyana 2012-2016 (2017)

This document presents an evaluation by the Office of Evaluation and Oversight (OVE) of the Country Program of the Inter-American Development Bank with Guyana over the period 2012-2016. This Country Program Evaluation (CPE) is the fourth independent evaluation of the Bank's program with Guyana. The main function of a CPE is to provide information on Bank performance at the country level that is credible and useful, and that enables the incorporation of lessons and recommendations that can be used to improve the development effectiveness of the Bank's overall strategy and program of country assistance. Like other CPEs, this evaluation seeks to examine the Bank's relationship with Guyana from an independent and comprehensive perspective, and serves the dual purpose of strengthening accountability and sharing lessons learned for future Bank support and, in particular, for the next Country Strategy. The CPE looks in depth at the design, implementation, and results of operations approved or active between July 2012 and December 2016, taking into account the country context and the applicable strategic documents.
Evolution of quasi-epitaxial growth of a crystalline organic semiconductor on graphite (1992)

We have studied the evolution of the growth of a crystalline organic semiconductor thin film using reflection high energy electron diffraction (RHEED). Our results indicate that highly ordered crystalline films of an organic compound; namely 3, 4, 9, 10-perylenetetracarboxylic dianhydride (PTCDA), can be grown on graphite by the ultrahigh vacuum process of organic molecular beam deposition even though the crystal structures of the two materials are highly mismatched. The RHEED patterns show the evolution of planar crystal growth from 2 monolayer (∼6 Å) coverage until at least 50 Å as the films are deposited onto substrates cooled to 100 K. At larger film thicknesses, somewhat nonplanar but still crystalline growth occurs. Furthermore, crystalline thin films were obtained independent of growth rate, which was as high as 3.0 Å/s. To our knowledge, this is the first direct experimental evidence of the evolution of growth from monolayer to bulk film coverage into an ordered, quasi-epitaxial structure.
A comparative study of field emission from NanoBuds, nanographite and pure or N‐doped single‐wall carbon nanotubes (2010)

Abstract Field emission characteristics of multi‐emitter flat cathodes prepared from NanoBuds, few‐layer graphite flakes (nanographite, NG) and pure or N‐doped single‐wall carbon nanotubes (SWNTs) have been examined. The cathodes demonstrated a low‐voltage electron emission with the threshold field values of few Volts per micron, which were ascribed to the high‐aspect ratio of nanocarbons. The films of NanoBuds and NG possess excellent emission pattern homogeneity with an emission site density of more than 10 5 cm −2 . This is much higher than for cathodes made of conventional SWNT films. It was found that the achievable maximal current density depends on the type of carbon material and reaches 10 A/cm 2 for NanoBuds film, while for the NG film cathodes, it is about one order of magnitude less. Possible mechanisms responsible for the experimentally observed differences are discussed. The materials examined are of great interest due to their high‐emission characteristics and are promising for the development of new types of vacuum electronic devices.