gebhart/patrepeval huggingface dataset:
Liver Transplantation for Hepatocellular Carcinoma: Is there Evidence for Expanding the Selection Criteria? (2005)

A consequent application of the Milan criteria in patients undergoing liver transplantation for hepatocellular carcinoma (HCC) may lead to excellent long-term survival and a low incidence of recurrence. Expanding the selection criteria will result in more patients with hepatocellular carcinoma being potentially curative treated, but this approach is associated with at least a higher incidence of recurrence. Kaplan-Meier analysis of 110 patients, who underwent liver transplantation for HCC in our institution between 1987 and 2004, showed a significant improvement in patient survival with time. A change in criteria for patient selection may have contributed to the improved outcome. In 28 of 110 patients a recurrence of HCC was observed. In 82% of patients, who developed recurrence of carcinoma, the Milan criteria were not met. Dropout from the waiting list is common and several methods, including percutaneous ethanol injection, radiofrequency ablation, and chemoembolization, are used to prevent tumor progression and thus prevent dropout. As no randomized trials are available some uncertainty remains, whether these neoadjuvant procedures improve outcome. At present, there is no evidence that this approach enables expansion of the selection criteria. Hepatocellular carcinoma is a major indication for living related liver transplantation because the risk of dropout while waiting is negligible. Extension of the Milan criteria in the setting of living related liver transplantation may offer more patients a potentially curative treatment, without reducing the donor pool of organs for other patients on the waiting list with nonmalignant liver disease.
Interaction between macrophages, TGF‐β1, and the COX‐2 pathway during the inflammatory phase of skeletal muscle healing after injury (2007)

Inflammation, an important phase of skeletal muscle healing, largely involves macrophages, TGF-beta1, and the COX-2 pathway. To improve our understanding of how these molecules interact during all phases of muscle healing, we examined their roles in muscle cells in vitro and in vivo. Initially, we found that depletion of macrophages in muscle tissue led to reduced muscle regeneration. Macrophages may influence healing by inducing the production of TGF-beta1 and PGE2 in different muscle cell types. We then found that the addition of TGF-beta1 induced PGE2 production in muscle cells, an effect probably mediated by COX-2 enzyme. It was also found that TGF-beta1 enhanced macrophage infiltration in wild-type mice after muscle injury. However, this effect was not observed in COX-2(-/-) mice, suggesting that the effect of TGF-beta1 on macrophage infiltration is mediated by the COX-2 pathway. Furthermore, we found that PGE2 can inhibit the expression of TGF-beta1. PGE2 and TGF-beta1 may be involved in a negative feedback loop balancing the level of fibrosis formation during skeletal muscle healing. In conclusion, our results suggest a complex regulatory mechanism of skeletal muscle healing. Macrophages, TGF-beta1, and the COX-2 pathway products may regulate one another's levels and have profound influence on the whole muscle healing process.
Upregulation of RANTES in Psoriatic Keratinocytes: a Possible Pathogenic Mechanism for Psoriasis (1999)

Intraepidermal collections of neutrophils and lymphocytes are unique features of the inflammatory reaction of psoriasis. Migration of leukocytes from dermis to the epidermis suggests a role for chemotactic agent(s). In recent years, increased levels of chemokines such as IL-8 , GRO-a and MCP-1 have been reported in the keratinocytes of psoriatic tissue. IL-8 and GRO-alpha belong to a subfamily (C x C) class and MCP-1 is a beta chemokine. In this study, we investigated RANTES, which is a beta chemokine (C-C class); RANTES has been found to be associated with various cell-mediated hypersensitive disorders. We obtained eight skin biopsies from chronic psoriatic plaques, and five biopsies each from non-lesional psoriatic skin, lichen planus, eczematous dermatitis and skin from healthy controls. Snap-frozen samples were cut into 7 microm cryosections and stained with 6 mg/ml of monoclonal anti-RANTES mouse IgG (DNAX, Palo Alto, CA). Standard immunohistochemistry techniques were applied. RANTES was detected only in the keratinocytes. The number of keratinocytes in per mm2 of epidermis stained for RANTES were 116.79+/-98.42 in psoriatic tissues compared to 32.00+/-46.05 (p<0.05), 6.39+/-3.59 (p<0.01), 2.64 +/-1.15 (p<0.01) and 3.53+/-5.26 (p<0.01), respectively, in the non-lesional, lichen planus, eczematous lesions and normal skin. This is the first study to report that the keratinocytes of psoriatic tissue express high levels of RANTES compared to the controls. IL-8 and related molecules (C x C class) are predominantly chemotactic for neutrophils and MCP-1 is a strong chemotactic factor for monocytes. In contrast, RANTES is chemotactic for memory T cells and activated naive T cells. Increased amounts of RANTES as reported here provide an explanation for migration of the activated T cells to the epidermis of the psoriatic lesions. In addition, RANTES activates T cells. These results suggest that RANTES may have a significant role in the inflammatory process of psoriasis. Our findings further substantiate a regulatory role for keratinocytes in the inflammatory process of psoriasis.
Branch Metrics for Effective Long-Haul MLSE IMDD Receivers (2006)

Recent results indicate that high-complexity MLSE processors could recover large amounts of chromatic dispersion. We propose a new branch metric that minimizes complexity while preserving very good performance.
A WBAN System for Ambulatory Monitoring of Physical Activity and Health Status: Applications and Challenges (2005)

Recent technological advances in sensors, low-power integrated circuits, and wireless communications have enabled the design of low-cost, miniature, lightweight, intelligent physiological sensor platforms that can be seamlessly integrated into a body area network for health monitoring. Wireless body area networks (WBANs) promise unobtrusive ambulatory health monitoring for extended periods of time and near real-time updates of patients' medical records through the Internet. A number of innovative systems for health monitoring have recently been proposed. However, they typically rely on custom communication protocols and hardware designs, lacking generality and flexibility. The lack of standard platforms, system software support, and standards makes these systems expensive. Bulky sensors, high price, and frequent battery changes are all likely to limit user compliance. To address some of these challenges, we prototyped a WBAN utilizing a common off-the-shelf wireless sensor platform with a ZigBee-compliant radio interface and an ultra low-power microcontroller. The standard platform interfaces to custom sensor boards that are equipped with accelerometers for motion monitoring and a bioamplifier for electrocardiogram or electromyogram monitoring. Software modules for on-board processing, communication, and network synchronization have been developed using the TinyOS operating system. Although the initial WBAN prototype targets ambulatory monitoring of user activity, the developed sensors can easily be adapted to monitor other physiological parameters. In this paper, we discuss initial results, implementation challenges, and the need for standardization in this dynamic and promising research field.
Porous-wall hollow glass microspheres as carriers for biomolecules (2023)

The present invention includes compositions of porous-wall hollow glass microspheres and one or more biomolecules, wherein the one or more biomolecules are positioned within a void location within the hollow glass microsphere, and the use of such compositions for the diagnostic and/or therapeutic delivery of biomolecules.
Digital Tomosynthesis: A Viable Alternative to Noncontrast Computed Tomography for the Follow-Up of Nephrolithiasis? (2016)

We found DT to be a comparable imaging modality to NCCT for the detection of intrarenal stones, without a significant effect from stone size and BMI and adequate reproducibility between multiple readers. DT appears to be an ideal alternative for following patients with nephrolithiasis due to its acceptable stone detection rates, low radiation exposure, and decreased cost compared to NCCT.
Robust pose-graph loop-closures with expectation-maximization (2013)

In this paper, we model the robust loop-closure pose-graph SLAM problem as a Bayesian network and show that it can be solved with the Classification Expectation-Maximization (EM) algorithm. In particular, we express our robust pose-graph SLAM as a Bayesian network where the robot poses and constraints are latent and observed variables. An additional set of latent variables is introduced as weights for the loop-constraints. We show that the weights can be chosen as the Cauchy function, which are iteratively computed from the errors between the predicted robot poses and observed loop-closure constraints in the Expectation step, and used to weigh the cost functions from the pose-graph loop-closure constraints in the Maximization step. As a result, outlier loop-closure constraints are assigned low weights and exert less influences in the pose-graph optimization within the EM iterations. To prevent the EM algorithm from getting stuck at local minima, we perform the EM algorithm multiple times where the loop constraints with very low weights are removed after each EM process. This is repeated until there are no more changes to the weights. We show proofs of the conceptual similarity between our EM algorithm and the M-Estimator. Specifically, we show that the weight function in our EM algorithm is equivalent to the robust residual function in the M-Estimator. We verify our proposed algorithm with experimental results from multiple simulated and real-world datasets, and comparisons with other existing works.
ChemInform Abstract: INTERACTION OF COMPLEXES OF COMPOSITION MNLX2 (L = TERTIARY PHOSPHINE) WITH DIOXYGEN (1985)

Abstract Das Verhalten von auf IR‐Zellenfenstem als Filme aufgebrachten MnBrZL‐Komplexen (L: PMe3, PEt 3 , PPhMez) in einem Dioxygenierungs/ Evakuierungs‐Zyklus wird untersucht.
HNO Protects the Myocardium against Reperfusion Injury, Inhibiting the mPTP Opening via PKCε Activation (2022)

Donors of nitroxyl (HNO), the one electron-reduction product of nitric oxide (NO<sup>.</sup>), positively modulate cardiac contractility/relaxation while limiting ischemia-reperfusion (I/R) injury. The mechanisms underpinning HNO anti-ischemic effects remain poorly understood. Using isolated perfused rat hearts subjected to 30 min global ischemia/1 or 2 h reperfusion, here we tested whether, in analogy to NO<sup>.</sup>, HNO protection requires PKCε translocation to mitochondria and K<sub>ATP</sub> channels activation. To this end, we compared the benefits afforded by ischemic preconditioning (IPC; 3 cycles of I/R) with those eventually granted by the NO<sup>.</sup> donor, diethylamine/NO, DEA/NO, and two chemically unrelated HNO donors: Angeli's salt (AS, a prototypic donor) and isopropylamine/NO (IPA/NO, a new HNO releaser). All donors were given for 19 min before I/R injury. In control I/R hearts (1 h reperfusion), infarct size (IS) measured via tetrazolium salt staining was 66 ± 5.5% of the area at risk. Both AS and IPA/NO were as effective as IPC in reducing IS [30.7 ± 2.2 (AS), 31 ± 2.9 (IPA/NO), and 31 ± 0.8 (IPC), respectively)], whereas DEA/NO was significantly less so (36.2 ± 2.6%, <i>p</i> < 0.001 vs. AS, IPA/NO, or IPC). IPA/NO protection was still present after 120 min of reperfusion, and the co-infusion with the PKCε inhibitor (PKCV1-2500 nM) prevented it (IS = 30 ± 0.5 vs. 61 ± 1.8% with IPA/NO alone, <i>p</i> < 0.01). Irrespective of the donor, HNO anti-ischemic effects were insensitive to the K<sub>ATP</sub> channel inhibitor, 5-OH decanoate (5HD, 100 μM), that, in contrast, abrogated DEA/NO protection. Finally, both HNO donors markedly enhanced the mitochondrial permeability transition pore (mPTP) ROS threshold over control levels (≅35-40%), an action again insensitive to 5HD. Our study shows that HNO donors inhibit mPTP opening, thus limiting myocyte loss at reperfusion, a beneficial effect that requires PKCε translocation to the mitochondria but not mitochondrial K<sup>+</sup> channels activation.
Characterization of tau binding by gosuranemab (2020)

Deposition of tau aggregates in the brain is a pathological hallmark of several neurodegenerative diseases, termed tauopathies, such as Alzheimer's disease (AD), corticobasal degeneration, and progressive supranuclear palsy (PSP). As transcellular spread of pathological tau aggregates has been implicated in disease progression, immunotherapy is being considered as a treatment for tauopathies. Here we report a detailed biochemical and biophysical characterization of the tau-binding properties of gosuranemab, a humanized monoclonal antibody directed against N-terminal tau that is currently being investigated as a treatment for AD. Binding experiments showed that gosuranemab exhibited high affinity for tau monomer, tau fibrils, and insoluble tau from different tauopathies. Epitope mapping studies conducted using X-ray crystallography and mutagenesis showed that gosuranemab bound to human tau residues 15-22. Immunodepletion of pathological human brain homogenates and transgenic mouse interstitial fluid (ISF) with gosuranemab resulted in reduced tau aggregation in tau biosensor cells. Preincubation of seed-competent AD-tau with gosuranemab significantly inhibited tau aggregation in mouse primary cortical neurons. Gosuranemab also significantly reduced unbound N-terminal tau in cerebrospinal fluid (CSF) from individuals with PSP and AD, and in ISF and CSF of treated transgenic mice. These results are consistent with the >90% target engagement observed in the CSF of some clinical trial dosing cohorts and support the evaluation of gosuranemab as a potential treatment for AD.
Statistical Shape Models of Bone and Cartilage for Predicting Demographics: Data from the Osteoarthritis Initiative (2023)

Three-dimensional statistical shape models built from MRI data can predict future disease and distinguish between groups. However, these models do not leverage the major advantage of MRI &amp;ndash; the ability to visualize and quantify soft tissues such as cartilage. This study built three MRI-based statistical shape models, 1) bone shape, 2) cartilage thickness, 3) both bone shape and cartilage thickness. We showed that bone shape and bone shape + cartilage thickness models predicted sex with an R 2 of ~0.9, significantly outperforming cartilage thickness alone (0.8). However, cartilage thickness alone was significantly better at predicting radiographic knee osteoarthritis.
Investigation of Feel for 6DOF Inputs: Isometric and Elastic Rate Control for Manipulation in 3D Environments (1993)

An increasing need exists for both a theoretical basis and practical human factors guidelines for designing and selecting high degree-of-freedom (DOF) computer input devices for 3D interactive environments such as telerobotic and virtual reality systems. This study evaluates elastic versus isometric rate control devices, in a 3D object positioning task. An experiment was conducted with a stereoscopic virtual reality system. The results showed that the elastic rate controller facilitated faster task completion time in the first of four phases of the experiment. The results are discussed in light of psychomotor literature. While the richer proprioceptive feedback afforded by an elastic controller is necessary for achieving superior performance in the early stages of learning, subjects performed equally well with the isometric controller in later learning stages. The study provides evidence to support a theory of skill shift from closed-loop to open-loop behaviour as learning progresses.
ChemInform Abstract: An Efficient Approach to Asymmetric Synthesis of Dipeptide β‐Turn Mimetics: Indolizidinone Amino Acids. (2001)

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.
Mechanisms of Transcriptional Activation of bcl-2 Gene Expression by 17β-Estradiol in Breast Cancer Cells (1999)

bcl-2 gene expression is induced by 17beta-estradiol (E2) in T47D and MCF-7 human breast cancer cells, and the mechanism of E2 responsiveness was further investigated by analysis of the bcl-2 gene promoter. The -1602 to -1534 distal region (bcl-2j) of the promoter was E2-responsive; however, in gel mobility shift assays, the estrogen receptor alpha (ER(alpha)) did not bind [(32)P]bcl-2j, whereas Sp1 protein formed a retarded band complex. Further analysis demonstrated that the upstream region (-1603 to -1579) of the bcl-2 gene promoter contained two GC/GA-rich sites at -1601 (5'-GGGCTGG-3') and -1588 (3'-GGAGGG-5') that bound Sp1 protein. Subsequent studies confirmed that transactivation by E2 was dependent on ER(alpha)/Sp1 interactions with both GC-rich sites, and this was confirmed by in vitro footprinting. In contrast, a 21-base pair E2-responsive downstream region (-1578 to -1534) did not bind Sp1 or ER(alpha) protein; however, analysis of a complex binding pattern with nuclear extracts showed that ATF-1 and CREB-1 bound to this motif. These data coupled with results of transient transfection studies demonstrated that transcriptional activation by E2 of the -1578 to -1534 region of the bcl-2 gene promoter was dependent on induction of cAMP and subsequent activation through a cAMP response element. Thus, hormone regulation of bcl-2 gene expression in breast cancer cells involves multiple enhancer elements and E2-mediated transactivation does not require direct binding of the estrogen receptor with promoter DNA.
ChemInform Abstract: SYNTHESIS OF PROSTAGLANDIN E2 AND PROSTAGLANDIN C2 FROM 5‐ENDO,7‐ANTI‐DISUBSTITUTED BICYCLO(2.2.1)HEPTAN‐2‐ONES (1978)

Abstract Auf den im Formelschema skizzierten Wegen werden PG‐Ez (VI) und PG‐CQ (XII) dargestellt.
Sequential forward feature selection for facial expression recognition (2016)

Facial expression recognition is an important computer vision problem with various applications. In this study, we investigate the effectiveness of features derived from facial landmarks in facial expression recognition. Distances between two combinations of facial landmarks constitute a distance vector. Features we use are the changes in the distance vectors extracted from expressive and neutral states of the face. The obtained feature vector contains elements that are relatively useless in expression recognition. By applying forward sequential feature selection, a subset of the most effective elements is formed. The chosen features are classified using a multi-class support vector machine. The performance of the proposed method is measured using Extended Cohn-Kanade dataset with seven expressions (anger, contempt, disgust, fear, happy, sad and surprised) and resulted in 89.9% mean class recognition accuracy.
Protein signal pathway mapping of human breast cancer from I-SPY: Correlations with response and genomic subtyping. (2010)

10512 Background: Profiling signaling pathway activation in cancer is critical as these pathways represent targets for new molecular guided therapeutics. The I-SPY TRIAL (CALGB 150007/150012, ACRIN 6657) is a trial of neoadjuvant anthracycline- and taxane-based chemotherapy that provides a unique series of biopsy specimens that have been subjected to extensive and detailed molecular characterization, together with detailed clinical and radiographic information. Methods: Purified tumor epithelium from 149 frozen pre-treatment biopsy specimens were procured via laser capture microdissection. Reverse phase protein microarray (RPMA) technology was used to quantitatively measure the activation of 40 key signaling proteins including components of pathways of interest for targeted therapy in breast cancer (HER2, IGFR, EGFR, mTOR, AKT and PLK1). Association between pathway activation and genomic subtype, pCR, residual cancer burden (RCB), and other clinical measures including tumor size, and nodal involvement was examined. Results: Protein pathway activation measured in pretreatment samples divided patients into 5 groups by hierarchical clustering. Activation of HER2 and AKT pathways was associated with pCR and minimal residual disease following neoadjuvant chemotherapy (p < 0.05). Activation of HER2, AKT, PLK1 and EGFR were each associated with HER2 positivity as measured by IHC and/or FISH. Individual pathway activation levels were not observed to be associated with tumor molecular subtype as determined by transcriptome profiling. Patients with global signaling activation had higher rates of cancer recurrence. Conclusions: Using RPMA technology and minimal tissue from core biopsies, it is possible to measure functional pathway activation for which targeted therapies are available. The clinical significance of the five pathway activation subtypes and the activity of individual pathways will be prospectively tested in I-SPY 2, where agents targeted to these pathways will be introduced in the neoadjuvant setting. Author Disclosure Employment or Leadership Position Consultant or Advisory Role Stock Ownership Honoraria Research Funding Expert Testimony Other Remuneration Theranostics Health Theranostics Health Theranostics Health
Exploring the Unknown Nature of Data (2010)

To classify objects based on their features and characteristics is one of the most important and primitive activities of human beings. The task becomes even more challenging when there is no ground truth available. Cluster analysis allows new opportunities in exploring the unknown nature of data through its aim to separate a finite data set, with little or no prior information, into a finite and discrete set of “natural,” hidden data structures. Here, the authors introduce and discuss clustering algorithms that are related to machine learning and computational intelligence, particularly those based on neural networks. Neural networks are well known for their good learning capabilities, adaptation, ease of implementation, parallelization, speed, and flexibility, and they have demonstrated many successful applications in cluster analysis. The applications of cluster analysis in real world problems are also illustrated. Portions of the chapter are taken from Xu and Wunsch (2008).
Erratum (2001)

Due to a printing error, Figures 3 and 5 of “The stem-loop binding protein forms a highly stable and specific complex with the 3′ stem-loop of histone mRNAs” by Battle and Doudna in RNA 7-1 (pages 123–132) were reproduced incorrectly, without shaded grey areas. Herewith are the figures correctly pictured. The Editor and Publisher regret the mistake.
Tunable nanometer electrode gaps by MeV ion irradiation (2012)

We report the use of MeV ion-irradiation-induced plastic deformation of amorphous materials to fabricate electrodes with nanometer-sized gaps. Plastic deformation of the amorphous metal Pd(80)Si(20) is induced by 4.64 MeV O(2+) ion irradiation, allowing the complete closing of a sub-micrometer gap. We measure the evolving gap size in situ by monitoring the field emission current-voltage (I-V) characteristics between electrodes. The I-V behavior is consistent with Fowler-Nordheim tunneling. We show that using feedback control on this signal permits gap size fabrication with atomic-scale precision. We expect this approach to nanogap fabrication will enable the practical realization of single molecule controlled devices and sensors.