gebhart/patrepeval huggingface dataset:
Tailoring Multi-Dimensional Outcomes to Level of Functional Recovery after Traumatic Brain Injury (2022)

There is increasing emphasis on assessing multi-dimensional outcomes in traumatic brain injury (TBI), but achieving this aim is hampered by a plethora of overlapping assessment tools. There is a clear need for advice on the choice of outcomes and we examined level of functional recovery as a framework to guide selection of assessments. In this cohort study we analysed cross-sectional data from 2604 patients enrolled in the Collaborative European NeuroTrauma Effectiveness Research in Traumatic Brain Injury (CENTER-TBI) project. Patients were followed up 6 months after injury and assessed on the Glasgow Outcome Scale-Extended (GOSE), cognitive tests, and patient-reported outcomes. We describe assessment completeness and prevalence of impairment. Relationships between outcomes were visualized using UpSet plots and hierarchical cluster analysis. GOSE categories varied markedly for both completion rates, 34-91% for patient-reported outcomes and 9-81% for cognitive tests, and prevalence of impairment, 3-82% for patient-reported outcomes and 9-59% for cognitive tests. In complete case samples, the GOSE identified impairment in 59-61%, whereas the most impaired patient-reported outcome was the Short Form-12 version 2 (SF-12v2) Physical Component Summary (28% overall), and the most impaired cognitive test was Trail Making Test (TMT) Part A (19% overall). The findings show that degree of disability is a key context of use for cognitive tests and patient-reported outcomes. Level of functional recovery provides a guide to the feasibility of different types of assessment and the likelihood of impairment, and can help tailor suitable assessment approaches in clinical practice and research studies.
Modiolar Proximity of Slim Modiolar Electrodes and Cochlear Duct Length: Correlation for Potential Basis of Customized Cochlear Implantation With Perimodiolar Electrodes (2020)

A preponderance of less modiolar proximity of the electrode was observed exclusively among congenital deafness cases, demonstrated by a less tight spiral configuration even under the pull-back technique. Our data suggest that shorter CDL is associated with a less tight spiral configuration of slim modiolar electrodes postoperatively. Depending on the insertion technique, the differential degree of modiolar proximity of slim modiolar electrodes can be alleviated in cases with short CDL, which justifies cochlear duct length-based customized insertion of slim modiolar electrodes.
BBN VISER TRECVID 2011 Multimedia Event Detection System (2011)

We describe the Raytheon BBN (BBN) VISER system that is designed to detect events of interest in multimedia data. We also present a comprehensive analysis of the different modules of that system in the context of the MED 2011 task. The VISER system incorporates a large set of low-level features that capture appearance, color, motion, audio, and audio-visual co-occurrence patterns in videos. For the low-level features, we rigorously analyzed several coding and pooling strategies, and also used state-of-the-art spatio-temporal pooling strategies to model relationships between different features. The system also uses high-level (i.e., semantic) visual information obtained from detecting scene, object, and action concepts. Furthermore, the VISER system exploits multimodal information by analyzing available spoken and videotext content using BBN's state-of-the-art Byblos automatic speech recognition (ASR) and video text recognition systems. These diverse streams of information are combined into a single, fixed dimensional vector for each video. We explored two different combination strategies: early fusion and late fusion. Early fusion was implemented through a fast kernel-based fusion framework and late fusion was performed using both Bayesian model combination (BAYCOM) as well as an innovative a weighted-average framework. Consistent with the previous MED'10 evaluation, low-level visual features exhibit strong performance and form the basis of our system. However, high-level information from speech, video-text, and object detection provide consistent and significant performance improvements. Overall, BBN's VISER system exhibited the best performance among all the submitted systems with an average ANDC score of 0.46 across the 10 MED'11 test events when the threshold was optimized for the NDC score, and <30% missed detection rate when the threshold was optimized to minimize missed detections at 6% false alarm rate. Description of Submitted Runs BBNVISER-LLFeat: Uses a combination of 6 high-performing, multimodal, and complementary low-level features, namely, appearance, color, motion based, MFCC, and audio energy. We combine these low-level features using an early fusion strategy. The threshold is estimated to minimize the NDC score. BBNVISER-Fusion1: Combines several sub-systems, each based on some combination of low-level features, ASR, video text OCR, and other high-level concepts using a late-fusion, Bayesian model combination strategy. The threshold is estimated to minimize the NDC score. BBNVISER-Fusion2: Combines same set of subsystems as BBNVISER-Fusion1. Instead of BAYCOM, it uses a novel weighted average fusion strategy. The fusion weights (for each sub-system) are estimated for each video automatically at runtime. BBNVISER-Fusion3: Combines all the sub-systems used in BBNVISER-Fusion3 with separate end-to-end systems from Columbia and UCF. In all, 18 sub-systems were combined using weighted average fusion. The threshold is estimated to minimize the probability of missed detection in the neighborhood of ALADDIN's Year 1 false alarm rate ceiling.
Smartphone fluorescence spectroscopy (2015)

We demonstrate the first use of smartphone spectrophotometry for readout of fluorescence-based biological assays. We evaluated the smartphone fluorimeter in the context of a fluorescent molecular beacon (MB) assay for detection of a specific nucleic acid sequences in a liquid test sample. The capability of distinguishing a one-point mismatch is also demonstrated by detecting single-base mutation in target nucleic acids. Our approach offers a route towards portable biomolecular assays for viral/bacterial pathogens, disease biomarkers, and toxins.
Proteasome Inhibitors from Neoboutonia melleri (2011)

Thirty new cycloartane derivatives (1-3, 5-12, 14-32) have been isolated from the leaves of Neoboutonia melleri. Their novelty stems from the loss of one of the C-4 methyl groups (1-3, 5-12, 14-25, and 32) and from the presence of an "extra" carbon atom in the side chain (1-3, 5-12, 14-20, 26-29, and 30-32). Furthermore, compound 32 possesses a rare triterpene skeleton with the cyclopropane ring fused onto C-1 and C-10, instead of C-9 and C-10. The structures were determined by spectrometric means, chemical correlations, and X-ray crystallography of derivative 1c. The substitution pattern in ring A, with a cyclopropyl ring conjugated with an α,β-unsaturated carbonyl moiety, confers to the molecule a particular reactivity, giving rise to a formal inversion of the stereochemistry of the cyclopropane ring under UV irradiation. These compounds showed an interesting level of activity on the proteasome pathway, thus motivating their evaluation as possible anticancer agents. The large number of isolated compounds permitted a structure-activity relationship analysis, which showed that the presence of the two enone functions was a requirement for the activity.
Relations between continuous and discrete models of excitable media (2002)

The authors derived a general eikonal equation describing the evolution of a wavefront propagating in an excitable medium this equation implements the relation between the propagation speed and the wavefront curvature known from a more detailed theory. The authors used an approximate solution to obtain equations linking the excitation time scale /spl tau/ and diffusion constant D of a continuous reaction rate model with the excitation parameters of a discrete cellular automaton model on a randomized lattice.
Influence of spacer chains and percentage ring substitution on phase-transfer catalytic activity of phosphonium salts bonded to polystyrene matrix (1983)

In nucleophilic aliphatic substitutions carried out under liquid–liquid phase-transfer conditions, the catalytic activity of tributylphosphonium groups directly bonded to a polystyrene matrix through a methylene bridge decreases by about one order of magnitude on passing from 10 to 60% ring substitution; log kobs. is linearly related to the loading of the catalytic sites. When tributylphosphonium groups are bonded to the polymer matrix by a linear spacer chain of 13 atoms for 10–30% ring substitution, kobs. increases 1.7–3.1 times with respect to directly bonded catalysts. However, for spaced catalysts with 60% ring substitution, the observed rate increase is 4.1–10-fold. This behaviour is explained by the combination of two opposing effects: (i) a polarity increase at the catalytic site by increasing percentage ring substitution leading to a decrease of nucleophilic activity of the anions; (ii) a polarity decrease at the catalytic site by insertion of spacer chains, due to the intrinsic lipophilicity of the alkyl chains as well as the more even distribution of catalytic sites within the polymer matrix. The reactivities of the catalysts, all prepared from chloromethylated polystyrene (200–400 mesh), are independent of the size of particles separated by sieves.
Cardiac Function Modifies the Impact of Heart Base Dose on Survival: A Voxel-Wise Analysis of Patients With Lung Cancer From the PET-Plan Trial (2022)

This work validates previous image-based data mining studies by revealing a strong association between dose to the base of the heart and overall survival. For the first time, an interaction between baseline cardiac health and heart base dose was identified, potentially suggesting preexisting cardiac dysfunction exacerbates the impact of heart dose on survival.
Enabling Inference Privacy with Adaptive Noise Injection (2021)

User-facing software services are becoming increasingly reliant on remote servers to host Deep Neural Network (DNN) models, which perform inference tasks for the clients. Such services require the client to send input data to the service provider, who processes it using a DNN and returns the output predictions to the client. Due to the rich nature of the inputs such as images and speech, the input often contains more information than what is necessary to perform the primary inference task. Consequently, in addition to the primary inference task, a malicious service provider could infer secondary (sensitive) attributes from the input, compromising the client's privacy. The goal of our work is to improve inference privacy by injecting noise to the input to hide the irrelevant features that are not conducive to the primary classification task. To this end, we propose Adaptive Noise Injection (ANI), which uses a light-weight DNN on the client-side to inject noise to each input, before transmitting it to the service provider to perform inference. Our key insight is that by customizing the noise to each input, we can achieve state-of-the-art trade-off between utility and privacy (up to 48.5% degradation in sensitive-task accuracy with &lt;1% degradation in primary accuracy), significantly outperforming existing noise injection schemes. Our method does not require prior knowledge of the sensitive attributes and incurs minimal computational overheads.
Automated Workflow Synthesis (2013)

By coordinating efforts from humans and machines, human computation systems can solve problems that machines cannot tackle alone. A general challenge is to design efficient human computation algorithms or workflows with which to coordinate the work of the crowd. We introduce a method for automated workflow synthesis aimed at ideally harnessing human efforts by learning about the crowd's performance on tasks and synthesizing an optimal workflow for solving a problem. We present experimental results for human sorting tasks, which demonstrate both the benefit of understanding and optimizing the structure of workflows based on observations. Results also demonstrate the benefits of using value of information to guide experiments for identifying efficient workflows with fewer experiments.
Nondestructive spatial heterodyne imaging of cold atoms (2001)

We demonstrate a new method for nondestructive imaging of laser-cooled atoms. This spatial heterodyne technique forms a phase image by interfering a strong reference laser beam with a weak probe beam that passes through the cold atom cloud. The figure of merit equals or exceeds that of phase-contrast imaging, and the technique can be used over a wider range of spatial scales. We show images of a dark-spot magneto-optic trap taken with imaging fluences as low as 61 pJ/cm(2) at a detuning of 11? , resulting in 0.0004 photons scattered per atom.
Effect of Vasicinone against Paraquat-Induced MAPK/p53-Mediated Apoptosis via the IGF-1R/PI3K/AKT Pathway in a Parkinson’s Disease-Associated SH-SY5Y Cell Model (2019)

Vasicinone is a quinazoline alkaloid isolated from the <i>Adhatoda vasica</i> plant. In this study, we explored the neuroprotective effect and underlying molecular mechanism of vasicinone against paraquat-induced cellular apoptosis in SH-SY5Y cells. Vasicinone reduced the paraquat-induced loss of cell viability, rescued terminal deoxynucleotide transferase-mediated dUTP nick end-labeling (TUNEL)-positive apoptotic nuclei, and suppressed generation of reactive oxygen species (ROS) in a dose-dependent manner. Western blotting analysis revealed that vasicinone increased the phosphorylation of IGF1R/PI3K/AKT cell survival signaling molecules and downregulated the paraquat-induced, mitogen-activated protein kinase (MAPK)/c-Jun N-terminal kinase (JNK)-mediated apoptotic pathways compared to that observed in cells not treated with vasicinone. This protection depended critically on the activation of IGF1R, and the silencing of IGF1R by siRNA completely abrogated the protective effect of vasicinone in SH-SY5Y cells. Our findings indicated that vasicinone is a potential candidate for the treatment of Parkinson's disease and possibly other oxidative stress-related neurodegenerative disorders.
An Intrarenal Adrenocortical Carcinoma Arising in an Adrenal Rest (2018)

We describe a case of a 61-year-old Korean man who was diagnosed with renal cell carcinoma that was discovered on abdominopelvic computed tomography obtained after the patient complained of back pain. A radical nephrectomy was performed, and the surgical specimen showed a relatively well-circumscribed and yellowish lobulated hard mass. Microscopically, the tumor showed sheets and nests of hypercellular pleomorphic cells with thick fibrous septation, frequent mitoses, and areas of adrenal cortical-like tissue. Immunohistochemical staining revealed that the tumor cells were positive for inhibin-α, vimentin, synaptophysin, and melan A. It also revealed that the tumor cells were negative for pan-cytokeratin, epithelial membrane antigen, paired box 8, α-methylacyl-coenzyme A racemase, CD10, cytokeratin 7, carbonic anhydrase 9, c-Kit, renal cell carcinoma, transcription factor E3, human melanoma black 45, desmin, smooth muscle actin, S-100, chromogranin A, CD34, anaplastic lymphoma kinase, and integrase interactor 1. Based on these histopathological and immunohistochemical findings, we diagnosed the tumor as intrarenal adrenocortical carcinoma arising in an adrenal rest. Several cases of intrarenal adrenocortical carcinoma have been reported, although they are very rare. Due to its poor prognosis and common recurrence or metastasis, clinicians and pathologists must be aware of this entity.
Biomechanical Evaluation of a Novel Fenestrated Pedicle Screw Augmented With Bone Cement in Osteoporotic Spines (2011)

Significant increases in pullout strength can be accomplished by injecting a limited quantity of bone cement through a fenestrated screw while minimizing the risks associated with higher volume. The majority of implants were removed without damaging the vertebra as the bone cement sheared off at the fenestrations.
Advanced PMOS Device Architecture for Highly-Doped Ultra-Shallow Junctions (2004)

In this paper we study the integration of Boron ultra-shallow junctions (USJ) obtained by Germanium pre-amorphization, Fluorine co-implantation and fast ramp-up and ramp-down anneals into advanced p-channel metal-oxide-semiconductor (PMOS) devices. Several integration issues associated to these USJ are investigated: short-channel effects control, implantation tilt angle influence, junction de-activation, thermal budget, silicide process. We show that remarkable PMOS device performance enhancement ( I on =450 µA/µm at I off =250 nA/µm for devices with L g \cong50 nm) can be achieved when full potential of highly-active and abrupt USJ is exploited by combining it with a low thermal budget integration scheme and a low contact resistance NiSi.
Programming of neuroendocrine self in the thymus and its defect in the development of neuroendocrine autoimmunity (2013)

For centuries after its first description by Galen, the thymus was considered as only a vestigial endocrine organ until the discovery in 1961 by Jacques FAP Miller of its essential role in the development of T (thymo-dependent) lymphocytes. A unique thymus first appeared in cartilaginous fishes some 500 million years ago, at the same time or shortly after the emergence of the adaptive (acquired) immune system. The thymus may be compared to a small brain or a computer highly specialized in the orchestration of central immunological self-tolerance. This was a necessity for the survival of species, given the potent evolutionary pressure imposed by the high risk of autotoxicity inherent in the stochastic generation of the diversity of immune cell receptors that characterize the adaptive immune response. A new paradigm of "neuroendocrine self-peptides" has been proposed, together with the definition of "neuroendocrine self." Neuroendocrine self-peptides are secreted by thymic epithelial cells (TECs) not according to the classic model of neuroendocrine signaling, but are processed for presentation by, or in association with, the thymic major histocompatibility complex (MHC) proteins. The autoimmune regulator (AIRE) gene/protein controls the transcription of neuroendocrine genes in TECs. The presentation of self-peptides in the thymus is responsible for the clonal deletion of self-reactive T cells, which emerge during the random recombination of gene segments that encode variable parts of the T cell receptor for the antigen (TCR). At the same time, self-antigen presentation in the thymus generates regulatory T (Treg) cells that can inhibit, in the periphery, those self-reactive T cells that escaped negative selection in the thymus. Several arguments indicate that the origin of autoimmunity directed against neuroendocrine glands results primarily from a defect in the intrathymic programming of self-tolerance to neuroendocrine functions. This defect may be genetic or acquired, for example during an enteroviral infection. This novel knowledge of normal and pathologic functions of the thymus constitutes a solid basis for the development of a novel type of tolerogenic/negative self-vaccination against type 1 diabetes (T1D).
Molecular markers in cancer diagnosis. (1995)

Clonal genetic alterations are a hallmark of human cancer pathogenesis. These genetic alterations may include specific gene mutations that drive the cancer process or phenotypic changes such as microsatellite instability that may be caused by specific genetic events. Identification of clonal cell populations that share a specific genetic alteration is virtually synonymous with the detection of cancer. These clonal cells can be detected among a large population of normal cells from limited clinical samples by DNA amplification techniques. Because of their unprecedented sensitivity and specificity, these approaches offer new hope for the early diagnosis of human cancer.
Data from Novel Methylated DNA Markers in the Surveillance of Colorectal Cancer Recurrence (2023)

&lt;div&gt;AbstractPurpose:&lt;p&gt;We aimed to assess the concordance of colorectal cancer–associated methylated DNA markers (MDM) in primary and metastatic colorectal cancer for feasibility in detection of distantly recurrent/metastatic colorectal cancer in plasma.&lt;/p&gt;Experimental Design:&lt;p&gt;A panel of previously discovered colorectal cancer–associated MDMs was selected. MDMs from primary and paired metastatic colorectal cancer tissue were assayed with quantitative methylation-specific PCR. Plasma MDMs were measured blindly by target enrichment long-probe quantitative-amplified signal assays. Random forest modeling was used to derive a prediction algorithm of MDMs in archival plasma samples from primary colorectal cancer cases. This algorithm was validated in prospectively collected plasma samples from recurrent colorectal cancer cases. The accuracy of the algorithm was summarized as sensitivity, specificity, and area under the curve (AUC).&lt;/p&gt;Results:&lt;p&gt;Of the 14 selected MDMs, the concordance between primary and metastatic tissue was considered moderate or higher for 12 MDMs (86%). At a preset specificity of 95% (91%–98%), a panel of 13 MDMs, in plasma from 97 colorectal cancer cases and 200 controls, detected stage IV colorectal cancer with 100% (80%–100%) sensitivity and all stages of colorectal cancer with an AUC of 0.91 (0.87–0.95), significantly higher than carcinoembryonic antigen [AUC, 0.72 (0.65–0.79)]. This panel, in plasma from 40 cases and 60 healthy controls, detected recurrent/metastatic colorectal cancer with 90% (76%–97%) sensitivity, 90% (79%–96%) specificity, and an AUC of 0.96 (0.92–1.00). The panel was positive in 0.30 (0.19–0.43) of 60 patients with no evidence of disease in post-operative patients with colorectal cancer.&lt;/p&gt;Conclusions:&lt;p&gt;Plasma assay of novel colorectal cancer–associated MDMs can reliably detect both primary colorectal cancer and distantly recurrent colorectal cancer with promising accuracy.&lt;/p&gt;&lt;/div&gt;
Pressure generation in a 6-8-2 type multi-anvil system: a performance test for third-stage anvils with various diamonds (2008)

Abstract We developed a 6-8-2 cell for multi-anvil apparatus, where a pair of diamond rods are used as a pressure intensifier. We tested single crystal diamond (SCD), conventional sintered diamond (SD), and nano-polycrystalline diamond (NPD) as the third-stage anvils for the 6-8-2 system. In situ X-ray diffraction experiments were conducted to test the performance of the present cell, and pressure generation of ∼ 90 GPa was confirmed at a press load of 700 tons at room temperature, regardless of the difference in anvil material. Upon the heating of the sample, however, the pressure substantially dropped with increasing temperature>800 K when SCD and SD were used as third-stage anvils, and ultimately decreased to 20–30 GPa at 1400 K due to significant plastic deformation of the anvils. In contrast, pressures of 80–90 GPa were maintained at temperatures up to ∼ 1250 K when the NPD anvils were used. The pressure decreased significantly at still higher temperatures, but remained higher (∼ 55 GPa, at 1400 K) than those observed by using SCD and SD anvils. The plastic deformation of the NPD anvils was obviously smaller than that of the other anvils, suggesting that NPD is the most suitable anvil material for the 6-8-2 system. Keywords: high pressure generationnano-polycrystalline diamond6-8-2 type multi-anvil system Acknowledgements We are grateful to Yuji Higo, Akihiro Yamada, Toru Inoue, Ikumi Ohnishi and Ken-ichi Funakoshi for their technical assistance, comments and discussion. We also thank Takeo Ohnishi for supplying the NPD rods used in the present study. In situ X-ray experiments were carried out at SPring-8 (Proposal No. 2007A1756), supported by Grant-in-Aid for Creative Scientific Research from the Japanese Government.