gebhart/patrepeval huggingface dataset:
Joint Model for Mortality and Hospitalization (2016)

Abstract: Modeling hospitalization is complicated because the follow-up time can be censored due to death. In this paper, we propose a shared frailty joint model for survival time and hospitalization. A random effect semi-parametric proportional hazard model is assumed for the survival time and conditional on the follow-up time, hospital admissions or total length of stay is modeled by a generalized linear model with a nonparametric offset function of the follow-up time. We assume that the hospitalization and the survival time are correlated through a latent subject-specific random frailty. The proposed model can be implemented using existing software such as SAS Proc NLMIXED. We demonstrate the feasibility through simulations. We apply our methods to study hospital admissions and total length of stay in a cohort of patients on hemodialysis. We identify age, albumin, neutrophil to lymphocyte ratio (NLR) and vintage as significant risk factors for mortality, and age, gender, race, albumin, NLR, pre-dialysis systolic blood pressure (preSBP), interdialytic weight gain (IDWG) and equilibrated Kt/V (eKt/V) as significant risk factors for both hospital admissions and total length of stay. In addition, hospitalization admissions is positively associated with vintage.
Distinct nonrandom patterns of chromosomal aberrations in the progression of squamous cell carcinomas of the head and neck. (1995)

Fifty-one randomly selected primary squamous cell carcinomas of the head and neck, derived from the larynx (n = 18) and pharynx (oropharynx, n = 18, and hypopharynx, n = 15) were analyzed with centromeric probes for chromosomes 1, 7, 9, 11, 17, and 18 to study numerical aberrations, chromosome imbalances, and aneuploidy by fluorescence in situ hybridization. The tumors were grouped into nonmetastasizing (N0) tumors (from patients clinically free of lymph node metastases for at least 18 months after surgery, n = 25) and metastasizing (N1-3) tumors (n = 26). We found a significant association between the tumor ploidy and the nodal status; in the N0 group, diploidy prevailed, and the most common aberration was loss to monosomy for chromosome 9 (44%), whereas in the N1-3 group, aneuploidy predominated (P = 0.002). Specifically, these genomic changes associated with progression to metastasis were: (a) tetrasomic or polysomic chromosomes were detected in 17 of 26 N1-3 tumors but in none of the 25 N0 tumors (P < 0.0001); (b) heterogeneous chromosomal copy numbers (i.e., extensive chromosomal imbalances) were also much more frequent in the N1-3 tumors (69.2% versus 24.0% in the N0 group; P = 0.018); and (c) loss of chromosome 9 (73%) and gains of chromosomes 7 (35%) and 17 (31%) persisted, but in addition, loss of chromosome 18 occurred in 31%. Overexpression of the p53 protein correlated with an increased incidence of chromosomal imbalances and aneuploidy (P < 0.001) and, hence, constituted an additional risk factor. The lower metastatic potential of larynx tumors as compared with tumors from the pharynx was reflected by a lower incidence of these genomic changes. These specific patterns of chromosomal aberrations can characterize and distinguish different stages of tumor progression of squamous cell carcinomas of the head and neck and should be valuable diagnostic and prognostic markers.
Applicability of the critical chromatography concept to proteomics problems: Experimental study of the dependence of peptide retention time on the sequence of amino acids in the chain (2008)

Experimental data on the separation of synthetic and natural peptides are presented as treated in terms of the separation model proposed by the authors, which allows for the chain connectivity of amino acid residues and the cooperative character of their interaction with the surface. It was shown that the model accurately predicts the separation of peptides with identical amino acid contents and different sequences of units in the chain. The differences in the sequence may be permutation of amino acid residues and the presence of terminal groups, amino acid isomers, or mirror sequences in the chain. The separation model was used to predict the retention times of peptides prepared via the enzymatic hydrolysis of E. coli proteins and bovine serum albumin with trypsin. It was shown that in general the model accurately explains the array of experimental data on the separation of such peptides, thus being the first successful attempt to relate the chain sequence to the retention volume.
Assigning the phenotype of a natural regulatory T-cell to the human T-cell line, KARPAS-299 (2006)

The human CD30-positive anaplastic large (T-) cell lymphoma cell line, KARPAS-299 (DSM ACC31), was established from blast cells in the peripheral blood from a case of non-Hodgkin lymphoma in 1988. We describe the mRNA and surface expression in KARPAS-299 cells of a panel of markers highly restricted to human natural regulatory T-cells and associated with their suppressive activity, including FOXP3, CD25, IL-10, TGF-beta1, CD62L, and Lag-3. Results obtained from co-culturing human peripheral blood leukocytes with KARPAS-299 cells assigned a suppressive phenotype to the latter ones. In conclusion, KARPAS-299 cells show characteristics typical of natural regulatory T-cells and, thus, represent a valuable model for studying regulatory T-cell function, which may also facilitate drug development aimed at the modulation of regulatory T-cell activity for the pharmacological therapy of, for example, autoimmune diseases.
Ultra-compact highly-selective dual-mode pseudoelliptic filters (2010)

An innovative ultra-compact dual-mode waveguide filter is presented. The basic idea consists of using a pair of TMmn0 degenerate cavity modes, while non-resonant modes provide a direct input-to-output coupling. In this manner, the single cavity provides two reflection and two transmission zeros, and is at the same time very compact in the longitudinal direction. Theoretical and experimental results of a two-cavity filter with four transmission zeros demonstrate the feasibility of the approach.
Affordable and personalized lighting using inverse modeling and virtual sensors (2014)

Wireless sensor networks (WSN) have great potential to enable personalized intelligent lighting systems while reducing building energy use by 50%-70%. As a result WSN systems are being increasingly integrated in state-ofart intelligent lighting systems. In the future these systems will enable participation of lighting loads as ancillary services. However, such systems can be expensive to install and lack the plug-and-play quality necessary for user-friendly commissioning. In this paper we present an integrated system of wireless sensor platforms and modeling software to enable a↵ordable and user-friendly intelligent lighting. It requires ⇠ 60% fewer sensor deployments compared to current commercial systems. Reduction in sensor deployments has been achieved by optimally replacing the actual photo-sensors with real-time discrete predictive inverse models. Spatially sparse and clustered sub-hourly photo-sensor data captured by the WSN platforms are used to develop and validate a piece-wise linear regression of indoor light distribution. This deterministic data-driven model accounts for sky conditions and solar position. The optimal placement of photo-sensors is performed iteratively to achieve the best predictability of the light field desired for indoor lighting control. Using two weeks of daylight and artificial light training data acquired at the Sustainability Base at NASA Ames, the model was able to predict the light level at seven monitored workstations with 80%-95% accuracy. We estimate that 10% adoption of this intelligent wireless sensor system in commercial buildings could save 0.2-0.25 quads BTU of energy nationwide.
Is Deadline Oblivious Scheduling Efficient for Controlling Real-Time Traffic in Cellular Downlink Systems? (2020)

The emergence of bandwidth-intensive latency-critical traffic in 5G Networks, such as Virtual Reality and Cloud Gaming, has motivated interest in wireless resource allocation problems for flows with hard-deadlines. Attempting to solve this problem brings about the following two key challenges: (i) The flow arrival and the wireless channel state information are not known to the Base Station (BS) apriori, thus, the allocation decisions need to be made in an online manner. (ii) Resource allocation algorithms that attempt to maximize a reward in the wireless setting will likely be unfair, causing unacceptable service for some users. In the first part of this paper, we model the problem of allocating resources to deadline-sensitive traffic as an online convex optimization problem, where the BS acquires a per-request reward that depends on the amount of traffic transmitted within the required deadline. We address the question of whether we can efficiently solve that problem with low complexity. In particular, whether we can design a constant-competitive scheduling algorithm that is oblivious to requests' deadlines. To this end, we propose a primal-dual Deadline-Oblivious (DO) algorithm, and show it is approximately 3.6-competitive. Furthermore, we show via simulations that our algorithm tracks the prescient offline solution very closely, significantly outperforming several algorithms that were previously proposed. Our results demonstrate that even though a scheduler may not know the deadlines of each flow, it can still achieve good theoretical and empirical performance. In the second part, we impose a stochastic constraint on the allocation, requiring a guarantee that each user achieves a certain timely throughput (amount of traffic delivered within the deadline over a period of time). We propose a modified version of our algorithm, called the Long-term Fair Deadline Oblivious (LFDO) algorithm for that setup. We combine the Lyapunov framework for stochastic optimization with the Primal-Dual analysis of online algorithms, to show that LFDO retains the high-performance of DO, while satisfying the long-term stochastic constraints.
Supplementary Table S1-9 from Across-Site Differences in the Mechanism of Alcohol-Induced Digestive Tract Carcinogenesis: An Evaluation by Mediation Analysis (2023)

&lt;p&gt;Supplementary Table S1 shows the first-visit hospital unit among controls in each study. Supplementary Table S2 shows the baseline characteristics of case and control subjects. Supplementary Table S3 contains the frequencies of never/ever drinkers and median (IQR) values of alcohol intake (g/day) among ever drinkers across ALDH2 genotypes in control subjects. Supplementary Table S4 presents the sample size (n cases/n controls) for each group for both the exposure and mediator association, and the mediator and outcome association. Supplementary Table S5 shows the total-effect odds ratios (ORs) of ALDH2 Lys allele in each cancer risk. Supplementary Table S6 shows the direct- and indirect-effect odds ratios (ORs) in stomach cancer for ALDH2 Lys allele with further adjustment for Helicobacter pylori [H.pylori] infection and atrophic gastritis statuses. Supplementary Table S7 shows the direct- and indirect-effect odds ratios (ORs) on each cancer for ALDH2 Glu/Lys and Lys/Lys. Supplementary Table S8 presents the results for smoking-drinking interaction analyses on each cancer risk. Supplementary Table S9 shows the direct- and indirect-effect odds ratios (ORs) on each cancer for ALDH2 Lys allele in strata of cumulative smoking exposure (pack-years).&lt;/p&gt;
Conservation of a room: A treatment proposal for Mark Rothko's Harvard Murals (2015)

A treatment with projected light for Mark Rothko's Harvard Murals (1962) is proposed. The group of five paintings on canvas has changed color due to the presence of a fugitive red pigment and excessive exposure to natural light in a room with large windows. For the conservation of Rothko's Harvard room, it is brought into context within his other commissions and environments. The original color of the works is determined by the digital restoration of contemporary photographs. With a camera projector system a compensation image is calculated that is projected onto the original canvas resulting in a restored color appearance. This approach of inpainting with light is compared with considerations of cleaning and inpainting in conventional conservation treatments. Overall lighting and architecture including the unusual wall color carefully chosen by Rothko play a key role in the treatment of the Mural cycle as an environment.
Distinguishability dynamics and quantum speed limits in the Bloch ball (2015)

We derive a necessary and sufficient condition on a time-independent Hamiltonian and arbitrary initial state of a two-level quantum system which guarantees that the initial state will time evolve to another state from which it can be distinguished with an a priori established minimal error probability $\delta \in [0,1/2]$. The time required for the initial state to evolve to such a probabilistically distinguishable state is compared to previously established quantum speed limits giving lower bounds on the time required for evolution between nonorthogonal states. We use the explicit distinguishability time to provide a succinct derivation of the quantum brachistochrone, i.e., the Hamiltonian generating shortest time evolution between two states having equal magnitude Bloch vectors. As a consequence of the distinguishability condition, we find that if a given unitary does not evolve a given pure state to an orthogonal state, then there exist mixed states in the Bloch ball that time evolve faster than the given pure state and that reach a greater level of distinguishability under the given unitary. We show that such mixed states exist even in the case of nonunitary evolution by considering a two-level system resonantly coupled to a single mode electromagnetic field.
Tokamak ripple transport at arbitrary collision frequency (1988)

The bounce averaged Fokker-Planck equation for the distribution function of ripple trapped particles in a tokamak has been solved, for arbitrary collision frequencies, in the 'tokamak' limit in which ripple wells are localized close to the midplane. The equation includes the main terms contributing to collisionless (de)trapping. The solution employs power series expansions for the distribution function in the pitch angle variable k2 and the poloidal angle θ; the series in k2 and θ both terminate. The boundary conditions applied at the trapping/detrapping boundary, that f and ∂f/∂k2 be continuous, become the requirement that in the collisionless limit the derivative with respect to k2 reflect the scale length set by the motion in toroidally blocked orbits. The resulting series solutions reduce to the usual expressions in the high collision frequency limit, but they are considerably lower than the results of previous calculations (which neglect the collisionless detrapping effects), in the low collision frequency limit. Comparison with Monte Carlo calculations for INTOR parameters shows that, in all cases, the analytic results lie somewhat below the numerical results, which is to be expected since banana drift diffusion is also present in the Monte Carlo calculation. However, previous analytic calculations give diffusion coefficients which are much larger than the Monte Carlo results.
Urocortin II mediates pro-inflammatory effects in human colonocytes via corticotropin-releasing hormone receptor 2α (2007)

Background/Aims: Urocortin II (UcnII) is a neuropeptide that binds with high affinity to the corticotropin-releasing hormone receptor 2 (CRHR2) in peripheral tissues. UcnII is synthesised in the intestine, but its role in human intestinal inflammation is largely unknown. Methods: Responses of human colonic epithelial cells expressing CRHR2 to stimulation by UcnII were measured using ELISA, western blot analysis, real-time reverse transcription-PCR (RT-PCR) and interleukin (IL)8 promoter activity. Expression levels of CRHR2 and UcnII in human colitis were determined by immunofluorescence and real-time RT-PCR in mucosal biopsies from patients with Crohn’s and ulcerative colitis, and in human intestinal xenografts after exposure to Clostridium difficile toxin A. Results: It is reported here that expression of CRHR2 mRNA and protein in human colonic epithelial cells (HT-29) are increased by exposure to C difficile toxin A or tumour necrosis factor (TNF)α. Stimulation of non-transformed NCM460 colonocytes overexpressing CRHR2α receptor with UcnII resulted in a time- and concentration-dependent increase in IL8 production. UcnII stimulation also led to activation of nuclear factor-κB (NF-κB) and mitogen-acivated protein (MAP) kinase in these cells, as evidenced by degradation of IκBα and phosphorylation of the p65 subunit of NF-κB and extracellularly regulated kinase (ERK) 1/2. Furthermore, expression of UcnII and CRHR2 mRNA was increased in mucosal samples of patients with inflammatory bowel disease, and after exposure of human intestinal xenografts to C difficile toxin A. Conclusions: These results suggest that UcnII has pro-inflammatory effects in human intestinal cells via the CRHR2α receptor and may play an important role in the pathophysiology of colitis in humans.
Study on Model-Based Control of the Cable-Conduit Drive System (1993)

The cable-conduit system, one of the remote drive system, is advantageous for integrating multiple-degrees of freedom. However, from the perspective of accurate motion control, a difference is caused between the actuator motion and the joint motion because a considerable friction between the cable and the conduit which varies according to the change in cable route. Therefore, the behaviors of cable must be clarified in order to realize highly accurate motion control. The objective of this study is to clarify the relationship between the actuator motion and the joint motion and to establish the motion control technique of the cable-conduit system. The present paper discusses the model-based control of the cable system. First, we modelled the cable-conduit system using the bend angles and the number of roots and crests of cable. Next, for precisely expressing the behaviors during start-up, we formulated the relationship between the actuator torque and the joint motion in consideration of the static friction and the kinetic friction. In addition, we verified the effectiveness of this formula through an experiment. As a result of the verification experiment, the motion computed from the formula strictly coincided with the actual behavior, thus displaying the effectiveness of the model.
Myopathy phenotype in transgenic mice expressing mutated PABPN1 as a model of oculopharyngeal muscular dystrophy (2003)

Autosomal dominant oculopharyngeal muscular dystrophy (OPMD) is a late-onset disorder characterized clinically by progressive ptosis, dysphagia and limb weakness, and by unique intranuclear inclusions in the skeletal muscle fibers. The disease is caused by the expansion of a 10-alanine stretch to 12-17 alanine residues in the poly(A)-binding protein, nuclear 1 (PABPN1; PABP2). While PABPN1 is a major component of the inclusions in OPMD, the exact cause of the disease is unknown. To elucidate the molecular mechanism and to construct a useful model for therapeutic trials, we have generated transgenic mice expressing the hPABPN1. Transgenic mice lines expressing a normal hPABPN1 with 10-alanine stretch did not reveal myopathic changes, whereas lines expressing high levels of expanded hPABPN1 with a 13-alanine stretch showed an apparent myopathy phenotype, especially in old age. Pathological studies in the latter mice disclosed intranuclear inclusions consisting of aggregated mutant hPABPN1 product. Furthermore, some TUNEL positive nuclei were shown around degenerating fibers and a cluster of it in the lesion in necrotic muscle fibers. Interestingly, the degree of myopathic changes was more prominent in the eyelid and pharyngeal muscles. Further, muscle weakness in the limbs was apparent as shown by the fatigability test. Nuclear inclusions seemed to develop gradually with aging, at least after 1 week of age, in model mouse muscles. We established the first transgenic mouse model of OPMD by expressing mutated PABPN1, and our model mice appear to have more dramatic alternations in myofiber viability.
Function-level power estimation methodology for microprocessors (2000)

We have developed a function-level power estimation methodology for predicting the power dissipation of embedded software. For a given microprocessor core, we empirically build the “power data bank”, which stores the power information of the built-in library functions and basic instructions. To estimate the average power of an embedded software on this core, we first get the execution information of the target software from program profiling/tracing tools. Then we evaluate the total energy consumption and execution time based on the “power data bank”, and take their ratio as the average power. High efficiency is achieved because no power simulator is used once the “power data bank” is built. We apply this method to a commercial microprocessor core and get power estimates with an average error of 3%. With this method, microprocessor vendors can provide users the “power data bank” without releasing details of the core to help users get early power estimates and eventually guide power optimization.
A family of mitogen-activated protein kinase-related proteins interacts in vivo with activator protein-1 transcription factor (1994)

The activator protein-1 (AP-1) transcription factor modulates expression of genes involved in growth regulation, differentiation, and neoplastic transformation. Several mitogen-activated protein kinases (MAP kinases) as well as other kinases phosphorylate c-Jun and c-Fos in vitro and are postulated to control AP-1 activity. However, since many protein kinases phosphorylate substrates in vitro with which they have no association in vivo, we sought evidence for interaction in vivo between AP-1 and MAP kinase proteins. We now report detection of an association in vivo of MAP kinase-related proteins with c-Jun and AP-1 dimers by peptide mapping and two-dimensional electrophoretic analyses of proteins co-immunoprecipitated with AP-1 antigens. Extracellular signal-regulated kinase-2 and several apparently novel MAP kinase-related proteins are among the species that bind to AP-1. The large number of MAP kinase-related proteins associated with AP-1 implicates them on an important gene regulation pathway. Combinatorial association between MAP kinase-related proteins and AP-1 dimers could potentially create numerous distinct complexes that could regulate diverse genes.