gebhart/patrepeval huggingface dataset:
A PROSPECTIVE RANDOMIZED CONTROLLED TRIAL DEMONSTRATING THE EFFECTIVENESS OF AN EDUCATIONAL INTERVENTION IN IMPROVING PROTON PUMP INHIBITOR DOSING HABITS (2004)

Purpose: Proton pump inhibitors (PPIs) achieve maximal acid suppression when dosed up to an hour before a meal. PPIs are incorrectly dosed in over 50% of patients (Gastroenterology 2001:120: A2205). Interventions to improve PPI dosing may improve GERD symptoms and decrease drug utilization. We aim to assess the effect of a focused educational intervention on PPI dosing. Methods: 638 patients from a local HMO newly prescribed a PPI for GERD were identified and invited to participate in a prospective randomized, double blind controlled study assessing the effect of an educational intervention on PPI dosing behavior. Participants were considered optimal dosers if they took their PPI 15–30 minutes prior to their first meal of the day, correct dosers if they took their PPI up to 60 minutes prior to any meal and incorrect dosers if they took their PPI at any other time. Dosing behavior was assessed at baseline and patients were randomly selected into a control or intervention group and sent letters at 2 weeks. The control group received lifestyle modification suggestions to reduce GERD. The intervention group received a letter which highlighted the importance of pre-meal PPI dosing in addition to a label reminding them to dose their PPI 15–30 minutes before a meal which they affixed to their pill bottle. Both groups were resurveyed 2 weeks later regarding their dosing habits. Results: 625 subjects were contacted, 173 subjects participated in the study and 139 patients completed the study. No differences were identified between participants and non-participants based on age, gender, or formulation of PPI prescribed. At followup, slightly more control group patients took their PPI optimally than at baseline (12% vs. 8%) but the change was not statistically significant (p = .41, McNemars). Greater improvement was seen in the intervention group, 23% taking optimally at follow up vs. 8% at baseline (p = .01, McNemars). Conclusions: This prospective, randomized controlled trial demonstrated that a focused educational intervention improved dosing behavior in new PPI users. This simple cost-effective intervention could be instituted for a larger group of PPI users, and may lead to improved GERD symptoms and decreased resource utilization.
Probing the functions of microglial cyclin-dependent kinase 5 under physiological and pathological conditions (2020)

Abstract Cyclin dependent kinase 5 (Cdk5) regulates various developmental and physiological processes in the central nervous system. Deregulation of Cdk5 activity in neurons induces severe neurodegeneration and has been implicated in Alzheimer’s disease (AD) and other neurodegenerative conditions. A large fraction of AD risk genes are highly expressed in microglia, highlighting an important role for these cells in AD pathogenesis. While Cdk5 function in neurons is well characterized, our understanding of its roles in microglial function under physiological and neurodegenerative conditions remain rudimentary. Here, we investigate the roles of Cdk5 in microglia using myeloid-specific Cdk5 conditional knockout mice. Using microglia-specific transcriptome profiling, histological analyses, and behavioral assessments, we found that knockout of Cdk5 in microglia for 1 month induced transcriptional changes characterized by upregulation of cell cycle processes and type I interferon signaling genes in both physiological conditions and AD-related amyloidogenesis. In contrast to the robust transcriptional changes, conditional loss of microglial Cdk5 produced minimal effects on the density and morphology of microglia and their phagocytic activity toward myelin debris. Moreover, Cdk5cKO mice exhibited little change in synaptic density and tasks associated with locomotor, anxiety-like, and memory-related behaviors. Our findings indicate that the conditional loss of Cdk5 in microglia induces rapid alterations of microglial transcriptome with minimal or delayed effects on histological and behavioral responses.
Anefficient Alternative to Network Pruning Through Ensemble Learning (2020)

Convolutional Neural Networks (CNNs) currently represent the best tool for classification of image content. CNNs are trained in order to develop generalized expressions in form of unique features to distinguish different classes. During this process, one or more filter weights might develop the same or similar values. In this case, the redundant filters can be pruned without damaging accuracy.Unlike normal pruning methods, we investigate the possibility of replacing a full-sized convolutional neural network with an ensemble of its narrow versions. Empirically, we show that the combination two narrow networks, which has only half of the original parameter count in total, is able to contest and even outperform the full-sized original network. In other words, a pruning rate of 50% can be achieved without any compromise on accuracy. Furthermore, we introduce a novel approach on ensemble learning called ComboNet, which increases the accuracy of the ensemble even further.
Analysis of Nitrogen Accumulation and Use in Bread and Durum Wheat (1989)

Since a significant portion of applied soil N is lost by leaching and denitrification, it is desirable to breed crop cultivars with improved N use efficiency. This study was undertaken to determine the influence of soil N supply on genotypic variation for preanthesis and postanthesis shoot N accumulation, the effect of preanthesis N and grain N yield on postanthesis N accumulation, and N use efficiency. A set of 12 bread ( Triticum aestivum L.) and two durum ( T. turgidum L. var durum Desf.) wheat genotypes was studied over three planting dates in 2 yr with three N levels within each planting date on a Ramona type A sandy loam (coarse fine‐loamy, mixed thermic Typic Haploxeralf). Differences among genotypes for shoot N accumulation before and after anthesis became obvious at the highest soil N level. At this level, some genotypes either stopped accumulating or showed a net loss of shoot N between anthesis and maturity, which appeared to be associated with superior preanthesis N accumulation capacity and reduced grain N yield of such genotypes. Uptake efficiency (total shoot N/soil N supply) became slightly more important than utilization efficiency (grain yield/total shoot N) in determining N use efficiency (grain yield/soil N supply) with increasing soil N supply. Nitrogen harvest index (grain N yield/total shoot N) fully explained the reduced contribution of utilization efficiency at higher soil N levels. We suggest that bread wheat genotypes G4843 and ‘Anza’ should be crossed in an attempt to recombine the superior N accumulation capacity of the former with the superior grain yield of the latter to develop a cultivar with improved N use efficiency.
Blinded Ultrasound Examination of the Subscapularis Following Anatomic Shoulder Arthroplasty (2019)

The utility of ultrasound examination of the subscapularis tendon following shoulder arthroplasty is limited by timing and may be most useful when used by the physician within clinical context. Significant improvement was noted in disease-specific quality-of-life scores regardless of the status of the subscapularis tendon as read on ultrasound.
Solar Electric Propulsion Gravity-Assist Tours For Jupiter Missions (2012)

Several Hall thrusters (e.g. BPT-4000, BHT-600, SPT-100, etc.) are able that operate with useful thrust at the sub-kilowatt power levels that would be available from solar arrays at Jupiter distance. We have found that a combination of a multi-kilowatt thruster (e.g. the BPT-4000) for the interplanetary trajectory with a sub-kilowatt thruster (e.g. the BHT-600) is sufficient for a Europa flyby mission. A roughly 1200 kg spacecraft using this propulsion approach would be able to launch on a Falcon 9 and reach Jupiter in 4.9 years. We demonstrate the feasibility of a Solar Electric Propulsion (SEP) Jovian tour with an example tour that reaches Europa 1.6 years after Jupiter arrival with a remaining capability of 400 m/s of ΔV for additional flybys.
Phosphorylation patterns of tumour antigens in cells lytically infected or transformed by simian virus 40 (1981)

The phosphorylation sites of simian virus 40 (SV40) large tumor (T) antigens have been analyzed by partial proteolysis peptide mapping and phosphoamino acid analysis of the resulting products. At least four sites were found to be phosphorylated. An amino-terminal part of the molecule contained both phosphoserine and phosphothreonine. One phosphothreonine residue was located in the proline-rich carboxy-terminal end of the molecule, either at position 701 or at position 708. The mutant dl 1265, which is defective in adenovirus helper function, lacked this phosphorylation site. In addition, the carboxy-terminal part of the molecule contained phosphoserine at a more central position. T-antigen-associated proteins of SV40-transformed cell (nonviral T; 51,000 to 55,000 daltons) also contained multiple phosphorylation sites involving at least two serine residues in mouse antigens and an additional threonine residue in rat, human, and monkey antigens. The latter residue and at least one phosphoserine residue were located near one terminus of the human NVT molecule. We did not find any evidence for phosphorylation of tyrosine residues in any of the multiple species of either large T or nonviral T molecules. Several forms of large T antigens were extracted from both SV40-transformed and SV40-infected permissive and nonpermissive cells, and their phosphorylation patterns were compared. No evidence was found for a different phosphorylation pattern of T antigen in transformed cells.
Learning to Score Figure Skating Sport Videos (2019)

This paper aims at learning to score the figure skating sports videos. To address this task, we propose a deep architecture that includes two complementary components, i.e., Self-Attentive LSTM and Multi-scale Convolutional Skip LSTM. These two components can efficiently learn the local and global sequential information in each video. Furthermore, we present a large-scale figure skating sports video dataset - FisV dataset. This dataset includes 500 figure skating videos with the average length of 2 minutes and 50 seconds. Each video is annotated by two scores of nine different referees, i.e., Total Element Score(TES) and Total Program Component Score (PCS). Our proposed model is validated on FisV and MIT-skate datasets. The experimental results show the effectiveness of our models in learning to score the figure skating videos. The codes and datasets would be downloaded from https://github.com/loadder/MS_LSTM.git.
Long-Term Results of Patellar Bone-Grafting for Severe Patellar Bone Loss During Revision Total Knee Arthroplasty (2019)

Background: There is no consensus on managing severe patellar bone loss after total knee arthroplasty. We previously described an initial series involving a novel technique of patellar bone-grafting with a short follow-up. The purpose of this study was to determine long-term survivorship and the radiographic and clinical results of patellar bone-grafting during revision total knee arthroplasty in a larger series with an extended follow-up. Methods: We identified 90 patients from a single institution who underwent 93 patellar bone-grafting procedures for severe patellar bone loss from 1997 to 2014. The mean age of the patients was 70 years, and 46% of patients were female. Forty-five knees (48%) underwent first-time revisions, and 19 knees (20%) had undergone a failed attempt at patellar resurfacings. Intraoperative patellar caliper thickness increased from a mean of 7 to 25 mm after patellar bone-grafting (p &lt; 0.01). Radiographic review determined changes in patellar height, tracking, and remodeling. Knee Society scores (KSSs) were calculated. The mean follow-up was 8 years (range, 2 to 18 years). Kaplan-Meier methods determined survivorship free of any revision and any reoperation. Cox proportional hazards analysis determined predictive factors for failure. Results: Survivorship free of patellar revision was 96% at 10 years. Survivorship free of any revision was 84% at 10 years. Survivorship free of any reoperation was 78% at 10 years. Increasing patient age was the only protective factor against further patellar revision (hazard ratio, 0.95; p &lt; 0.01). When comparing initial radiographs with final radiographs, patellar height decreased from 22 to 19 mm (p &lt; 0.01), 80% compared with 59% of patellae articulated centrally in the trochlea (p = 0.01), and 32% compared with 77% had remodeling over the lateral femoral condyle (p &lt; 0.01). Anterior knee pain decreased from 51% to 27% postoperatively (p = 0.01). The mean knee flexion improved from 101° to 108° (p = 0.03). The mean KSS improved from 50 to 85 points (p &lt; 0.01). Conclusions: Reliable long-term clinical results can be expected with patellar bone-grafting for severe patellar bone loss during revision total knee arthroplasty. Pain, range of motion, and other reported outcomes improve despite radiographic changes to patellar height, tracking, and remodeling. This technique is a durable and reliable option when standard patellar resurfacing is not possible. Level of Evidence: Therapeutic Level IV . See Instructions for Authors for a complete description of levels of evidence.
White Box AES Using Intel's New AES Instructions (2013)

White box cryptography deals with content protection scenarios where software decrypts some contents, using a secret key (embedded in the code in some obfuscated way), while the adversary has access to the code and its execution. Obviously, performance is slowed down by the obfuscation overheads. This paper demonstrates a method for using Intel's New AES Instructions to write decryption code without directly using the cipher key or any of the round keys in a register (or in memory). Such implementation can enjoy some of the performance benefits that the AES instructions offer. We show an example where it is more than 2.5 times faster than a lookup table based alternative.
ChemInform Abstract: Synthesis of an Eight‐Carbon Homologue of α‐Homomannojirimycin via a Bicyclic Aminolactone. (1999)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Search for the rare decaysB0→J/ψγandBs0→J/ψγ (2015)

A search for the rare decay of a ${B}^{0}$ or ${B}_{s}^{0}$ meson into the final state $J/\ensuremath{\psi}\ensuremath{\gamma}$ is performed, using data collected by the LHCb experiment in $pp$ collisions at $\sqrt{s}=7$ and 8 TeV, corresponding to an integrated luminosity of $3\text{ }\text{ }{\mathrm{fb}}^{\ensuremath{-}1}$. The observed number of signal candidates is consistent with a background-only hypothesis. Branching fraction values larger than $1.5\ifmmode\times\else\texttimes\fi{}1{0}^{\ensuremath{-}6}$ for the ${B}^{0}\ensuremath{\rightarrow}J/\ensuremath{\psi}\ensuremath{\gamma}$ decay mode are excluded at 90% confidence level. For the ${B}_{s}^{0}\ensuremath{\rightarrow}J/\ensuremath{\psi}\ensuremath{\gamma}$ decay mode, branching fraction values larger than $7.3\ifmmode\times\else\texttimes\fi{}1{0}^{\ensuremath{-}6}$ are excluded at 90% confidence level; this is the first branching fraction limit for this decay.
A Digital LDO in 22nm CMOS with a 4b Self-triggered Binary Search Windowed Flash ADC Featuring Automatic Analog Layout Generator Framework (2022)

Complex compute and communication SoCs in scaled CMOS process integrate synthesizable digital logic along with many analog/mixed-signal circuits such as PLLs and LDOs. While the digital logic blocks can be ported easily across process nodes, the analog/mixed-signal circuits demand custom manual re-design for physical layout, verification and optimization. Furthermore, fine-grain power management and noise isolation necessitate implementation of a large number (>50) of independent voltage domains on die. The manual layout effort and time for such a large variety of critical analog/mixed-signal circuit blocks becomes increasingly unaffordable in practice. Also, physical layout requirements like common-centroid and inter-digitization, and routing requirements such as matching differential nets, minimizing interconnect parasitics of critical leaf cells like differential pairs, current mirrors, resistors and capacitor arrays, necessitate multiple iterations with post-layout verifications, thus significantly impacting overall design time and time-to-market. Furthermore, availability of high-quality mask-design engineers can pose a major bottleneck to timely completion of the design, especially for the increasingly complex layout design rules in scaled process nodes. Multiple EDA frameworks, such as ALIGN [1], BAG [2] and MAGICAL [3] were reported to generate analog layouts for improving design productivity of analog circuits in scaled CMOS. However, there is still a need for a methodology that can accommodate the varying needs of analog circuits and generate high quality layout while leveraging automated placement and/or routing. In this paper, we present an analog layout generator (ALG) methodology based digital LDO (DLDO) with a self-triggered binary search windowed flash ADC in 22nm CMOS (Fig. 1) to maximize the productivity of implementing analog circuit blocks in scaled CMOS process, thus significantly improving the overall design time & effort, as well as time-to-market for complex SoCs. A self-triggered binary search mechanism with a delay-based architecture is proposed to reduce the exponentially growing kickback noise and energy consumption of a traditional flash ADC down to the level of a SAR ADC while maintaining its high speed feature.
Modelling Spatial Intensity for Replicated Inhomogeneous Point Patterns in Brain Imaging (2004)

Summary Pharmacological experiments in brain microscopy study patterns of cellular activ- ation in response to psychotropic drugs for connected neuroanatomic regions. A typical ex- perimental design produces replicated point patterns having highly complex spatial variability. Modelling this variability hierarchically can enhance the inference for comparing treatments. We propose a semiparametric formulation that combines the robustness of a nonparametric kernel method with the efficiency of likelihood-based parameter estimation. In the convenient framework of a generalized linear mixed model, we decompose pattern variation by kriging the intensities of a hierarchically heterogeneous spatial point process. This approximation entails discretizing the inhomogeneous Poisson likelihood by Voronoi tiling of augmented point patterns. The resulting intensity-weighted log-linear model accommodates spatial smoothing through a reduced rank penalized linear spline. To correct for anatomic distortion between subjects, we interpolate point locations via an isomorphic mapping so that smoothing occurs relative to common neuroanatomical atlas co-ordinates. We propose a criterion for choosing the degree and spatial locale of smoothing based on truncating the ordered set of smoothing covariates to minimize residual extra-dispersion. Additional spatial covariates, experimental design factors, hierarchical random effects and intensity functions are readily accommodated in the linear predictor, enabling comprehensive analyses of the salient properties underlying replicated point patterns. We illustrate our method through application to data from a novel study of drug effects on neuronal activation patterns in the brain of rats.
Fast algorithms for joint power control and scheduling in wireless networks (2010)

This paper studies the problem of finding a minimum-length schedule of a power-controlled wireless network subject to traffic demands and SINR (signal-to-interference-plus-noise ratio) constraints. We propose a column generation based algorithm that finds the optimal schedules and transmit powers. The column generation method decomposes a complex linear optimization problem into a restricted master problem and a pricing problem. We develop a new formulation of the pricing problem using the Perron-Frobenius eigenvalue condition, which enables us to integrate link scheduling with power control in a single framework. This new formulation reduces the complexity of the pricing problem, and thus improves the overall efficiency of the column generation method significantly - for example, the average runtime is reduced by 99.86% in 18-link networks compared with the traditional column generation method. Furthermore, we propose a branch-and-price method that combines column generation with the branch-and-bound technique to tackle the integer constraints on time slot allocation. We develop a new branching rule in the branch-and-price method that maintains the size of the pricing problem after each branching. Our branch-and-price method can obtain optimal integer solutions efficiently for example, the average runtime is reduced by 99.72% in 18-link networks compared with the traditional branch-and-price method. We further suggest efficient heuristic algorithms based on the structure of the optimal algorithms. Simulation results show that the heuristic algorithms can reach solutions within 10% of optimality for networks with less than 30 links.
Systematic, multiparametric analysis of Mycobacterium tuberculosis intracellular infection offers insight into coordinated virulence (2017)

A key to the pathogenic success of Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis, is the capacity to survive within host macrophages. Although several factors required for this survival have been identified, a comprehensive knowledge of such factors and how they work together to manipulate the host environment to benefit bacterial survival are not well understood. To systematically identify Mtb factors required for intracellular growth, we screened an arrayed, non-redundant Mtb transposon mutant library by high-content imaging to characterize the mutant-macrophage interaction. Based on a combination of imaging features, we identified mutants impaired for intracellular survival. We then characterized the phenotype of infection with each mutant by profiling the induced macrophage cytokine response. Taking a systems-level approach to understanding the biology of identified mutants, we performed a multiparametric analysis combining pathogen and host phenotypes to predict functional relationships between mutants based on clustering. Strikingly, mutants defective in two well-known virulence factors, the ESX-1 protein secretion system and the virulence lipid phthiocerol dimycocerosate (PDIM), clustered together. Building upon the shared phenotype of loss of the macrophage type I interferon (IFN) response to infection, we found that PDIM production and export are required for coordinated secretion of ESX-1-substrates, for phagosomal permeabilization, and for downstream induction of the type I IFN response. Multiparametric clustering also identified two novel genes that are required for PDIM production and induction of the type I IFN response. Thus, multiparametric analysis combining host and pathogen infection phenotypes can be used to identify novel functional relationships between genes that play a role in infection.
Positron-annihilation-induced ion desorption fromTiO2(110) (2014)

We have investigated the positron-stimulated desorption of ions from a ${\text{TiO}}_{2}(110)$ surface. Desorbed O${}^{+}$ ions were detected in coincidence with the emission of annihilation $\ensuremath{\gamma}$ rays. The energy dependence of the ion yields shows that the O${}^{+}$ ions were detected at energies much lower than the previously reported threshold for electron impact desorption corresponding to the excitation energy of Ti($3p$) core electrons. These results provide evidence that core-hole creation by positron annihilation with electrons in the core levels leads to ion desorption.