gebhart/patrepeval huggingface dataset:
Elevated pre-treatment levels of plasma C-reactive protein are associated with poor prognosis after breast cancer: a cohort study (2011)

We examined whether plasma C-reactive protein (CRP) levels at the time of diagnosis of breast cancer are associated with overall survival, disease-free survival, death from breast cancer, and recurrence of breast cancer. We observed 2,910 women for up to seven years after they were diagnosed with invasive breast cancer (median follow-up time was three years). Plasma levels of high-sensitivity CRP were measured at the time of diagnosis and we assessed the association between CRP levels and risk of reduced overall and disease-free survival, death from breast cancer, and recurrence of breast cancer by using the Kaplan-Meier method and Cox proportional hazards regression. During follow-up, 383 women died (225 of whom died from breast cancer) and 118 women experienced recurrence of breast cancer. Elevated CRP levels across tertiles at the time of diagnosis were associated with reduced overall and disease-free survival and with increased risk of death from breast cancer (log-rank trend for all, P < 0.001), but not with recurrence. The multifactor-adjusted hazard ratios (HR) of reduced overall survival among women in the middle and highest versus the lowest tertile of CRP were 1.30 (95% CI, 0.97 to 1.73) and 1.94 (1.48 to 2.55), respectively. Corresponding HRs of reduced disease-free survival were 1.16 (0.89 to 1.50) and 1.76 (1.38 to 2.25) and of death from breast cancer 1.22 (0.84 to 1.78) and 1.66 (1.15 to 2.41). Dividing CRP levels into octiles resulted in a stepwise increased risk of reduced overall survival (P for trend <0.001) and the multifactor-adjusted HR among women in the highest versus the lowest octile of CRP was 2.51 (1.53 to 4.12). Compared to women with CRP levels in the 0 to 25% percentile (<0.78 mg/L), the multifactor-adjusted HR of reduced overall survival among women with CRP levels ≥95% percentile (≥16.4 mg/L) was 3.58 (2.36 to 5.42). Among women with HER2-positive tumours, the multifactor-adjusted HR of reduced overall survival for the highest versus the lowest tertile of CRP was 8.63 (2.04 to 36.4). Elevated CRP levels at the time of diagnosis of breast cancer are associated with reduced overall and disease-free survival and with increased risk of death from breast cancer.
Computer-Aided Process Planning for Turned Parts Using Fundamental and Heuristic Principles (1992)

Research on generative computer-aided process planning (CAPP) for turned parts using combined fundamental and heuristic principles is presented. The rationale for the process planning approach is that many preconditions of machining processes can be expressed as a small number of domain principles. The domain is defined by processes and the part description as features for simple turned parts. The motivation is to detect faulty designs early on in the design process. Preliminary designs defined by features are first evaluated using manufacturability rules in a rule-based expert system, developed in LISP. Manufacturability rules are based on feature properties such as accessibility, stability, and critical material thickness. The rules were acquired from design and manufacturing personnel from industry through interviews. Parts that satisfy the manufacturability checks are used to generate all feasible process plans. A search algorithm selects the “best” process plan from the feasible set. Process plans are generated and subsequently optimized using two distinct sets of feasibility and optimality criteria which may be either fundamental or heuristic in nature. The presently incorporated criteria successfully restrict the set of plans to a small number without missing any apparently feasible process plans. Manufacturability evaluation, feasible process plans, and optimal process plans for actual industrial parts have been obtained and compared.
A new approach for extracting and summarizing abnormal activities in surveillance videos (2014)

In this paper, we propose a new approach to detect abnormal activities in surveillance videos and create suitable summary videos accordingly. The proposed approach first introduces a blob sequence optimization process which integrates spatial, temporal, size, and motion correlation among objects to extract suitable abnormal blob sequences. With this process, blob extraction errors due to occlusion or background interferences can be effectively avoided. Then, we also propose an abnormality-type-based method which creates short-period summary videos for long-period input surveillance videos by properly arranging abnormal blob sequences according to their activity types. Experimental results show that our proposed approach can effectively create satisfying summary videos from input surveillance videos.
Paired Electrosynthesis of Diacid and Diol Precursors Using Dienes and CO2 as the Carbon Source (2014)

Abstract A new electrochemical methodology was devised and optimized, allowing a net incorporation of carbon dioxide in conjugated dienes in a one‐compartment cell using a non‐sacrificial anode. This divergent paired electrosynthesis of diacid and diol precursors was achieved through simultaneous cathodic carboxylation and anodic acetoxylation of conjugated dienes. After optimization of the reaction conditions, 1,3‐cyclohexadiene was converted to its corresponding 1,4‐dicarboxylate salt and 1,4‐diacetate ester with high yields and current efficiencies. A large effect of alkyl substitution and molecular configuration on the reactivity of conjugated double bonds towards carboxylation and acetoxylation was observed.
Genetic Association and Brain Morphology Studies and the Chromosome 8p22 Pericentriolar Material 1 (PCM1) Gene in Susceptibility to Schizophrenia (2006)

The PCM1 gene is implicated in susceptibility to schizophrenia and is associated with orbitofrontal gray matter volumetric deficits.
Machine Learning Robustness, Fairness, and their Convergence (2021)

Responsible AI becomes critical where robustness and fairness must be satisfied together. Traditionally, the two topics have been studied by different communities for different applications. Robust training is designed for noisy or poisoned data where image data is typically considered. In comparison, fair training primarily deals with biased data where structured data is typically considered. Nevertheless, robust training and fair training are fundamentally similar in considering that both of them aim at fixing the inherent flaws of real-world data. In this tutorial, we first cover state-of-the-art robust training techniques where most of the research is on combating various label noises. In particular, we cover label noise modeling, robust training approaches, and real-world noisy data sets. Then, proceeding to the related fairness literature, we discuss pre-processing, in-processing, and post-processing unfairness mitigation techniques, depending on whether the mitigation occurs before, during, or after the model training. Finally, we cover the recent trend emerged to combine robust and fair training in two flavors: the former is to make the fair training more robust (i.e., robust fair training), and the latter is to consider robustness and fairness as two equals to incorporate them into a holistic framework. This tutorial is indeed timely and novel because the convergence of the two topics is increasingly common, but yet to be addressed in tutorials. The tutors have extensive experience publishing papers in top-tier machine learning and data mining venues and developing machine learning platforms.
Delineating the transcriptional landscape and clonal diversity of virus-specific CD4+ T cells during chronic viral infection (2022)

Although recent evidence indicates that CD4<sup>+</sup> T cells responding to chronic viral infection are functionally heterogenous, our understanding of the developmental relationships between these subsets, and a determination of how their transcriptional landscape compares to their acute infection counterparts remains unclear. Additionally, whether cell-intrinsic factors such as TCR usage influence CD4<sup>+</sup> T cell fate commitment during persistent infection has not previously been studied. Herein, we perform single-cell RNA sequencing (scRNA-seq) combined with single-cell T cell receptor sequencing (scTCR-seq) on virus-specific CD4<sup>+</sup> T cells isolated from mice infected with chronic lymphocytic choriomeningitis virus (LCMV) infection. We identify several transcriptionally distinct states among the Th1, Tfh, and memory-like T cell subsets that form at the peak of infection, including the presence of a previously unrecognized Slamf7<sup>+</sup> subset with cytolytic features. We further show that the relative distribution of these populations differs substantially between acute and persistent LCMV infection. Moreover, while the progeny of most T cell clones displays membership within each of these transcriptionally unique populations, overall supporting a one cell-multiple fate model, a small fraction of clones display a biased cell fate decision, suggesting that TCR usage may impact CD4<sup>+</sup> T cell development during chronic infection. Importantly, comparative analyses further reveal both subset-specific and core gene expression programs that are differentially regulated between CD4<sup>+</sup> T cells responding to acute and chronic LCMV infection. Together, these data may serve as a useful framework and allow for a detailed interrogation into the clonal distribution and transcriptional circuits underlying CD4<sup>+</sup> T cell differentiation during chronic viral infection.
Caffeinated FPGAs: FPGA framework For Convolutional Neural Networks (2016)

Convolutional Neural Networks (CNNs) have gained significant traction in the field of machine learning, particularly due to their high accuracy in visual recognition. Recent works have pushed the performance of GPU implementations of CNNs showing significant improvements in their classification and training times. With these improvements, many frameworks have become available for implementing CNNs on both CPUs and GPUs, with no support for FPGA implementations. In this work we present a modified version of the popular CNN framework Caffe, with FPGA support. This allows for classification using CNN models and specialized FPGA implementations with the flexibility of reprogramming the device when necessary, seamless memory transactions between host and device, simple-to-use test benches, and the ability to create pipelined layer implementations. To validate the framework, we use the Xilinx SDAccel environment to implement an FPGA-based Winograd convolution engine and show that it can be used alongside other layers running on a host processor to run several popular CNNs (AlexNet, GoogleNet, VGG A, Overfeat). The results show that our framework achieves 50 GFLOPS across 3×3 convolutions in the benchmarks. This is achieved within a practical framework, which will aid in future development of FPGA-based CNNs.
Optofluidics for Mobile Health, Bioenergy, and Nanoparticle Analysis (2014)

In this talk I will review recent progress on Optofluidics at Cornell in three application spaces: mobile and global health, bioenergy, and nanoparticle analysis. Fundamental science will be described as well as routes to commercialization and deployment.
Analysis of HIV Diversity Using a High-Resolution Melting Assay (2010)

HIV viruses are usually genetically homogeneous shortly after infection, and become more heterogeneous over time. We developed a high-resolution melting (HRM) assay to analyze HIV diversity without sequencing. Plasma samples from the HIVNET 012 trial were obtained from nine Ugandan mother-infant pairs. DNA amplified from the HIV gag region was analyzed to determine the number of degrees over which the DNA melted (HRM score). HRM gag DNA was also cloned and sequenced (50 clones/mother; 20 clones/infant). The median HRM score for infants (4.3, range 4.2-5.3) was higher than that for control plasmids (3.4, range 3.2-3.8, p < 0.001) and lower than that for mothers (5.7, range 4.4-7.7, p = 0.005, exact Wilcoxon rank sum test). The intraclass correlation coefficient reflecting assay reproducibility was 94% (95% CI: 89-98%). HRM scores were also compared to sequenced-based measures of HIV diversity; higher HRM scores were associated with higher genetic diversity (p < 0.001), complexity (p = 0.009), and Shannon entropy (p = 0.022), but not with length variation (p = 0.111). The HRM assay provides a novel, rapid method for assessing HIV diversity without sequencing. This assay could be applied to any region of the HIV genome or to other genetic systems that exhibit DNA diversity.
Subvastus and Medial Parapatellar Approaches in Total Knee Arthroplasty (2000)

This retrospective study compared the outcome of two consecutive groups of patients having primary total knee arthroplasty. The arthroplasties were performed in the first group (169 arthroplasties in 143 patients) from 1988 to 1992 using a medial parapatellar approach, and in the second group (167 arthroplasties in 148 patients) from 1992 to 1996 using a subvastus approach. The patient outcomes were evaluated at 6 months, and were based on clinical and radiographic measures, occurrence of intraoperative lateral retinacular release, and incidence of postoperative patellar subluxation. There were no significant differences between the two groups for range of motion, Knee Society knee and function scores, and stair climbing ability. The patella tracked centrally in significantly more knees with the subvastus approach (139 of 167 knees, 83%) than with the parapatellar approach (107 of 169 knees, 63%). There were significantly fewer knees in the subvastus group requiring a lateral retinacular release (62 of 167 knees, 37%), compared with the parapatellar group (113 of 169 knees, 67%). The authors concluded that the subvastus approach led to improved patellar tracking and stability. Although the surgical and rehabilitative protocols were identical for both groups, the results may have been affected by changing circumstances during the 9-year period of the study.
A Wnt- and β-catenin-dependent pathway for mammalian cardiac myogenesis (2003)

Acquisition of a cardiac fate by embryonic mesodermal cells is a fundamental step in heart formation. Heart development in frogs and avians requires positive signals from adjacent endoderm, including bone morphogenic proteins, and is antagonized by a second secreted signal, Wnt proteins, from neural tube. By contrast, mechanisms of mesodermal commitment to create heart muscle in mammals are largely unknown. In addition, Wnt-dependent signals can involve either a canonical beta-catenin pathway or other, alternative mediators. Here, we tested the involvement of Wnts and beta-catenin in mammalian cardiac myogenesis by using a pluripotent mouse cell line (P19CL6) that recapitulates early steps for cardiac specification. In this system, early and late cardiac genes are up-regulated by 1% DMSO, and spontaneous beating occurs. Notably, Wnt3A and Wnt8A were induced days before even the earliest cardiogenic transcription factors. DMSO induced biochemical mediators of Wnt signaling (decreased phosphorylation and increased levels of beta-catenin), which were suppressed by Frizzled-8Fc, a soluble Wnt antagonist. DMSO provoked T cell factor-dependent transcriptional activity; thus, induction of Wnt proteins by DMSO was functionally coupled. Frizzled-8Fc inhibited the induction of cardiogenic transcription factors, cardiogenic growth factors, and sarcomeric myosin heavy chains. Likewise, differentiation was blocked by constitutively active glycogen synthase kinase 3beta, an intracellular inhibitor of the Wntbeta-catenin pathway. Conversely, lithium chloride, which inhibits glycogen synthase kinase 3beta, and Wnt3A-conditioned medium up-regulated early cardiac markers and the proportion of differentiated cells. Thus, Wntbeta-catenin signaling is activated at the inception of mammalian cardiac myogenesis and is indispensable for cardiac differentiation, at least in this pluripotent model system.
The Data Encryption Standard (DES) and its strength against attacks (1994)

The Data Encryption Standard (DES) was developed by an IBM team around 1974 and adopted as a national standard in 1977. Since that time, many cryptanalysts have attempted to find shortcuts for breaking the system. In this paper, we examine one such attempt, the method of differential cryptanalysis, published by Biham and Shamir. We show some of the safeguards against differential cryptanalysis that were built into the system from the beginning, with the result that more than 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">15</sup> bytes of chosen plaintext are required for this attack to succeed.
Effects of Temperature, Strain Rate, and Specimen Orientation on Localized Plastic Deformation of Irradiated Zircaloy-2 (1980)

Abstract Both transverse and longitudinal Zircaloy-2 specimens irradiated up to 1.2 × 1020 n/cm2 (E> 1 MeV) were tested in tension with strain rates ranging 1.1 × 10-4~1.1 × 10-2 s-1 in the temperature range 200~400°C. Detailed observations of the specimen wall surface and microstructure were also made on samples deformed to various amounts of plastic strain, with a projector and an optical microscope. It was found that localized plastic deformation bands occurred in the temperature range approximately 280~330°C during straining to the ultimate tensile stress. Results also showed that the strain rate dependence of tensile properties, particularly the strain to the ultimate tensile stress, was associated with changes in the number and width of the localized deformation band with strain rates at a temperature of 300°C at which localized bands occurred. From a break of the straight line tracing the true stress-true plastic strain relationship, it was established that the onset stress and strain of the localized deformation band could be estimated. The effect of specimen orientation on localized deformation band was also discussed on the basis of differences in the onset stress and strain between the transverse and longitudinal specimens. KEYWORDS: Zircaloy 2neutron beamsirradiationplastic deformation bandtemperature dependencestrain ratetransverse specimenlongitudinal specimenspecimen wall surface appearancemicrostructureradiation hardeningincipient localized deformation bandyield stresstensile propertiesanisotropy
The Role of Surgery in the Management of Recurrent Adrenocortical Carcinoma (2012)

The best predictors of prolonged survival after first recurrence are TTFR over 12 months and R0-resection. Our data suggest that patients with longer TTFR and tumors amenable to radical resection should be operated, whereas individualized treatment decisions are needed for patients with short TTFR or with not completely resectable tumors.
A Novel Procedure for the Preparation of Zinc Reagents: A Practical Synthesis of (+)‐Biotin. (2004)

Abstract For Abstract see ChemInform Abstract in Full Text.
Modeling of natural sit-to-stand movement based on minimum jerk criterion for natural-like assistance and rehabilitation (2017)

Designing a sit-to-stand (STS) assistive system that mimics the normal transfer is important for improving the quality of life for elderly and mobility impaired people while reducing the burden on the caregivers. This paper presents a robotic-based STS assisting system that can provide assistance at the shoulder and the buttock. The minimum jerk criterion is used to model the natural STS motion. Anthropometry and characteristics of the natural STS motion are used to increase the simplicity and applicability of the STS motion model. This model can generate the shoulder and hip trajectories during STS. This enables the system to provide assistance either at the upper trunk or at the upper trunk and the hip simultaneously without inducing abnormal motion kinematics. The assisting system is used to assist subjects with different heights using the trajectories generated by the proposed motion model. In addition, the proposed trajectory is compared to the one that is resulted from a commercial lifter. The results show that the proposed method can accurately replicate the natural STS motion and results in a lower interaction force. Moreover, the subjects are more satisfied when they are assisted using the proposed method as indicated by the results of the post-experiment questionnaire.
Fragmentation inside proton-transfer-reaction-based mass spectrometers limits the detection of ROOR and ROOH peroxides (2022)

Abstract. Proton transfer reaction (PTR) is a commonly applied ionization technique for mass spectrometers, in which hydronium ions (H3O+) transfer a proton to analytes with higher proton affinities than the water molecule. This method has most commonly been used to quantify volatile hydrocarbons, but later-generation PTR instruments have been designed for better throughput of less volatile species, allowing detection of more functionalized molecules as well. For example, the recently developed Vocus PTR time-of-flight mass spectrometer (PTR-TOF) has been shown to agree well with an iodide-adduct-based chemical ionization mass spectrometer (CIMS) for products with 3–5 O atoms from oxidation of monoterpenes (C10H16). However, while several different types of CIMS instruments (including those using iodide) detect abundant signals also at “dimeric” species, believed to be primarily ROOR peroxides, no such signals have been observed in the Vocus PTR even though these compounds fulfil the condition of having higher proton affinity than water. More traditional PTR instruments have been limited to volatile molecules as the inlets have not been designed for transmission of easily condensable species. Some newer instruments, like the Vocus PTR, have overcome this limitation but are still not able to detect the full range of functionalized products, suggesting that other limitations need to be considered. One such limitation, well-documented in PTR literature, is the tendency of protonation to lead to fragmentation of some analytes. In this work, we evaluate the potential for PTR to detect dimers and the most oxygenated compounds as these have been shown to be crucial for forming atmospheric aerosol particles. We studied the detection of dimers using a Vocus PTR-TOF in laboratory experiments, as well as through quantum chemical calculations. Only noisy signals of potential dimers were observed during experiments on the ozonolysis of the monoterpene α-pinene, while a few small signals of dimeric compounds were detected during the ozonolysis of cyclohexene. During the latter experiments, we also tested varying the pressures and electric fields in the ionization region of the Vocus PTR-TOF, finding that only small improvements were possible in the relative dimer contributions. Calculations for model ROOR and ROOH systems showed that most of these peroxides should fragment partially following protonation. With the inclusion of additional energy from the ion–molecule collisions driven by the electric fields in the ionization source, computational results suggest substantial or nearly complete fragmentation of dimers. Our study thus suggests that while the improved versions of PTR-based mass spectrometers are very powerful tools for measuring hydrocarbons and their moderately oxidized products, other types of CIMS are likely more suitable for the detection of ROOR and ROOH species.